From 4b2e6de82f5b31d40e519d8ec3644fe8747862fa Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 25 Aug 2023 09:09:22 +0300 Subject: gn-auth: New package --- gn/packages/gn-auth.scm | 67 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 gn/packages/gn-auth.scm diff --git a/gn/packages/gn-auth.scm b/gn/packages/gn-auth.scm new file mode 100644 index 0000000..eb272e0 --- /dev/null +++ b/gn/packages/gn-auth.scm @@ -0,0 +1,67 @@ +(define-module (gn packages gn-auth) + #:use-module (guix) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix build-system python) + #:use-module ((guix licenses) #:prefix license:) + + ;; Packages from guix + #:use-module (gnu packages check) + + #:use-module (gnu packages django) + + #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) + #:use-module (gnu packages python-check) + #:use-module (gnu packages python-crypto) + + #:use-module (gnu packages databases) + + ;; Packages from guix-bioinformatics + #:use-module (gn packages python-web)) + +(define-public gn-auth + (package + (name "gn-auth") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/gn-auth.git") + (commit "a183445c6ecf7e99aee82a2d729378b79bed58e7"))) + (hash + (content-hash + (base32 + "053h4w705v8dai3xj3qhj54d8am39w8x504y4gvbrdyczkl2fxci"))))) + (build-system python-build-system) + (arguments + `(#:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) + (native-inputs + (list python-mypy + python-pytest + python-pylint + python-hypothesis + python-pytest-mock + python-mypy-extensions)) + (propagated-inputs + (list gunicorn + python-flask + python-redis + python-authlib + python-pymonad + yoyo-migrations + python-bcrypt ;; remove after removing all references + python-mysqlclient + python-argon2-cffi + python-email-validator)) + (home-page "https://github.com/genenetwork/gn-auth") + (synopsis "Authentication and Authorisation server for GeneNetwork services") + (description "Authentication and Authorisation server for GeneNetwork services.") + (license license:agpl3+))) -- cgit v1.2.3 From 23eadc951e924a049551d7b0e8763ccd2c2f3816 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 30 Aug 2023 13:09:09 +0300 Subject: Add missing `(guix gexp) module. Update package commit. --- gn/packages/gn-auth.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gn/packages/gn-auth.scm b/gn/packages/gn-auth.scm index eb272e0..05accfb 100644 --- a/gn/packages/gn-auth.scm +++ b/gn/packages/gn-auth.scm @@ -1,5 +1,6 @@ (define-module (gn packages gn-auth) #:use-module (guix) + #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -30,11 +31,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "a183445c6ecf7e99aee82a2d729378b79bed58e7"))) + (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd"))) (hash (content-hash (base32 - "053h4w705v8dai3xj3qhj54d8am39w8x504y4gvbrdyczkl2fxci"))))) + "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From 39da338e6dc84c4b79a9a924d36e96d165c17877 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 30 Aug 2023 13:21:26 +0300 Subject: Replace `(...) with (list ...): Fixes "undefined gexp" failure. Replace the backquoted expression in the (arguments ...) section of the package definition to fix the error where the build could not find the variable gexp --- gn/packages/gn-auth.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gn/packages/gn-auth.scm b/gn/packages/gn-auth.scm index 05accfb..a87b22c 100644 --- a/gn/packages/gn-auth.scm +++ b/gn/packages/gn-auth.scm @@ -38,12 +38,13 @@ "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) (build-system python-build-system) (arguments - `(#:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-k" "unit_test"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) (native-inputs (list python-mypy python-pytest -- cgit v1.2.3 From 0d743eb249bbdb67009d23ee53b2ee0ae881f725 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 31 Aug 2023 06:03:59 +0300 Subject: Pin guix-bioinformatics to commit with Python-3.9 A number of GeneNetwork services/applications will not run with Python-3.10. This commit pins guix-bioinformatics to a specific commit to allow use of the older Python-3.10 before we are able to update everything needed to get them running on Python-3.10 --- .guix-channel | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.guix-channel b/.guix-channel index e42b9ad..ea119e1 100644 --- a/.guix-channel +++ b/.guix-channel @@ -1,6 +1,11 @@ (channel (version 0) (dependencies + (channel + (name guix-bioinformatics) + (url "https://gitlab.com/genenetwork/guix-bioinformatics.git") + (branch "master") + (commit "fb1e8dbcf7cc46fa9a09a431f6842d9290f6e819")) (channel (name guix-past) (url "https://gitlab.inria.fr/guix-hpc/guix-past") -- cgit v1.2.3 From d003af7434689bb7f88aa963f5affa718f4cf605 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 31 Aug 2023 08:15:05 +0100 Subject: Revert "Pin guix-bioinformatics to commit with Python-3.9" This reverts commit 0d743eb249bbdb67009d23ee53b2ee0ae881f725. --- .guix-channel | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.guix-channel b/.guix-channel index ea119e1..e42b9ad 100644 --- a/.guix-channel +++ b/.guix-channel @@ -1,11 +1,6 @@ (channel (version 0) (dependencies - (channel - (name guix-bioinformatics) - (url "https://gitlab.com/genenetwork/guix-bioinformatics.git") - (branch "master") - (commit "fb1e8dbcf7cc46fa9a09a431f6842d9290f6e819")) (channel (name guix-past) (url "https://gitlab.inria.fr/guix-hpc/guix-past") -- cgit v1.2.3 From 2398844e27a3f80884ed2a008a30a9e6295e9133 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 31 Aug 2023 12:25:58 +0100 Subject: Downgrade guix to a4e9842. --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index e42b9ad..05e0512 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "d4e9ad2d42dddf06a8f1b01c9f49fee16c592d75") + (commit "a4e9842a70775a54bbe1369881b739e7ea9a6432") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 9a653d2d9aa566f6273bd2ceb3be7ac533fb372c Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 31 Aug 2023 12:37:30 +0100 Subject: Move gn-auth to (gn packages genenetwork). --- gn/packages/genenetwork.scm | 102 ++++++++++++++++++++++++++++++++------------ gn/packages/gn-auth.scm | 69 ------------------------------ 2 files changed, 74 insertions(+), 97 deletions(-) delete mode 100644 gn/packages/gn-auth.scm diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 36d3ae6..6e5bbce 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -463,47 +463,93 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public gn-auth + (package + (name "gn-auth") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/gn-auth.git") + (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd"))) + (hash + (content-hash + (base32 + "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) + (native-inputs + (list python-mypy + python-pytest + python-pylint + python-hypothesis + python-pytest-mock + python-mypy-extensions)) + (propagated-inputs + (list gunicorn + python-flask + python-redis + python-authlib + python-pymonad + yoyo-migrations + python-bcrypt ;; remove after removing all references + python-mysqlclient + python-argon2-cffi + python-email-validator)) + (home-page "https://github.com/genenetwork/gn-auth") + (synopsis "Authentication and Authorisation server for GeneNetwork services") + (description "Authentication and Authorisation server for GeneNetwork services.") + (license license:agpl3+))) + ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x (define-public genenetwork2-files-small (let ((pfff "xx")) (package - (name "genenetwork2-files-small") - (version "1.0") - (source - (origin - (method url-fetch) - (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") - (file-name (string-append name "-" pfff)) - (sha256 - (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) - (build-system trivial-build-system) - (native-inputs `(("lz4" ,lz4) - ("tar" ,tar) - ("source" ,source))) + (name "genenetwork2-files-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") + (file-name (string-append name "-" pfff)) + (sha256 + (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) + (build-system trivial-build-system) + (native-inputs `(("lz4" ,lz4) + ("tar" ,tar) + ("source" ,source))) - (arguments - `(#:modules ((guix build utils)) - #:builder - (let* ((out (assoc-ref %outputs "out")) - (name "gn2_data_s") - (tarfn (string-append name ".tar")) - (targetdir (string-append out "/share/genenetwork2/"))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (name "gn2_data_s") + (tarfn (string-append name ".tar")) + (targetdir (string-append out "/share/genenetwork2/"))) (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))) (and - (zero? (system* lz4unpack source "-d" tarfn)) - (zero? (system* tar "xf" tarfn)) - (mkdir-p targetdir) - (copy-recursively name targetdir))))))) - (home-page "http://genenetwork.org/") - (synopsis "Small file archive to run on genenetwork") - (description "Genenetwork genotype and mapping files.") - (license license:agpl3+)))) + (zero? (system* lz4unpack source "-d" tarfn)) + (zero? (system* tar "xf" tarfn)) + (mkdir-p targetdir) + (copy-recursively name targetdir))))))) + (home-page "http://genenetwork.org/") + (synopsis "Small file archive to run on genenetwork") + (description "Genenetwork genotype and mapping files.") + (license license:agpl3+)))) (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) diff --git a/gn/packages/gn-auth.scm b/gn/packages/gn-auth.scm deleted file mode 100644 index a87b22c..0000000 --- a/gn/packages/gn-auth.scm +++ /dev/null @@ -1,69 +0,0 @@ -(define-module (gn packages gn-auth) - #:use-module (guix) - #:use-module (guix gexp) - #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix build-system python) - #:use-module ((guix licenses) #:prefix license:) - - ;; Packages from guix - #:use-module (gnu packages check) - - #:use-module (gnu packages django) - - #:use-module (gnu packages python-web) - #:use-module (gnu packages python-xyz) - #:use-module (gnu packages python-check) - #:use-module (gnu packages python-crypto) - - #:use-module (gnu packages databases) - - ;; Packages from guix-bioinformatics - #:use-module (gn packages python-web)) - -(define-public gn-auth - (package - (name "gn-auth") - (version "1.0.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/genenetwork/gn-auth.git") - (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd"))) - (hash - (content-hash - (base32 - "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-k" "unit_test"))))))) - (native-inputs - (list python-mypy - python-pytest - python-pylint - python-hypothesis - python-pytest-mock - python-mypy-extensions)) - (propagated-inputs - (list gunicorn - python-flask - python-redis - python-authlib - python-pymonad - yoyo-migrations - python-bcrypt ;; remove after removing all references - python-mysqlclient - python-argon2-cffi - python-email-validator)) - (home-page "https://github.com/genenetwork/gn-auth") - (synopsis "Authentication and Authorisation server for GeneNetwork services") - (description "Authentication and Authorisation server for GeneNetwork services.") - (license license:agpl3+))) -- cgit v1.2.3 From aaa6e53e7b623105d05e67e95186aba5b4671010 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:05:11 +0300 Subject: Pin python to python@3.8.5 * gn/packages/genenetwork.scm: (genenetwork3, genenetwork2): Using python@3.8.5 Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 6e5bbce..7d8cb43 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -135,7 +135,7 @@ python-pytest-mock)) (propagated-inputs (list gemma-wrapper - python-wrapper + `("python" (specification->package "python@3.8.5")) csvdiff gn-rust-correlation python-bcrypt ;; Replace use of bcrypt with argon below @@ -218,7 +218,7 @@ ("gn-rust-correlation" ,gn-rust-correlation) ("glibc-utf8-locales" ,glibc-utf8-locales) ("nginx" ,nginx) - ("python" ,python-wrapper) + ("python" ,(specification->package "python@3.8.5")) ("python-pillow" ,python-pillow) ("python-coverage" ,python-coverage) ("python-configparser" ,python-configparser) ;; maintenance/scripts -- cgit v1.2.3 From 6e642662a1cbfff21b8e8d4e5aa30c53c142b165 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:26:48 +0300 Subject: Add guix-forge as an extra channel dependency * .guix-channel: Add guix-forge. Signed-off-by: Munyoki Kilyungi --- .guix-channel | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.guix-channel b/.guix-channel index 05e0512..f1b6e45 100644 --- a/.guix-channel +++ b/.guix-channel @@ -1,6 +1,15 @@ (channel (version 0) (dependencies + (channel + (name 'guix-forge) + (url "https://git.systemreboot.net/guix-forge/") + (branch "main") + (introduction + (make-channel-introduction + "0432e37b20dd678a02efee21adf0b9525a670310" + (openpgp-fingerprint + "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) (channel (name guix-past) (url "https://gitlab.inria.fr/guix-hpc/guix-past") -- cgit v1.2.3 From 7dee6d24dd9118d86e935320e6c75f78d9aff53d Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:41:35 +0300 Subject: Fix channel introduction in guix-forge Signed-off-by: Munyoki Kilyungi --- .guix-channel | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.guix-channel b/.guix-channel index f1b6e45..4e13dde 100644 --- a/.guix-channel +++ b/.guix-channel @@ -1,15 +1,15 @@ (channel (version 0) (dependencies - (channel - (name 'guix-forge) - (url "https://git.systemreboot.net/guix-forge/") - (branch "main") - (introduction - (make-channel-introduction - "0432e37b20dd678a02efee21adf0b9525a670310" - (openpgp-fingerprint - "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) + (channel + (name 'guix-forge) + (url "https://git.systemreboot.net/guix-forge/") + (branch "main") + (introduction + (make-channel-introduction + "0432e37b20dd678a02efee21adf0b9525a670310" + (openpgp-fingerprint + "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) (channel (name guix-past) (url "https://gitlab.inria.fr/guix-hpc/guix-past") -- cgit v1.2.3 From 963af9289ba9cd75fa7230867015842e82575740 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:44:42 +0300 Subject: Fix channel introduction Signed-off-by: Munyoki Kilyungi --- .guix-channel | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.guix-channel b/.guix-channel index 4e13dde..cc73e52 100644 --- a/.guix-channel +++ b/.guix-channel @@ -6,9 +6,10 @@ (url "https://git.systemreboot.net/guix-forge/") (branch "main") (introduction - (make-channel-introduction - "0432e37b20dd678a02efee21adf0b9525a670310" - (openpgp-fingerprint + (channel-introduction + (version 0) + (commit "0432e37b20dd678a02efee21adf0b9525a670310") + (signer "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) (channel (name guix-past) -- cgit v1.2.3 From 47b25529b7c04337458c18b7c0c283d8789682ed Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:49:59 +0300 Subject: Fix channel introduction Signed-off-by: Munyoki Kilyungi --- .guix-channel | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.guix-channel b/.guix-channel index cc73e52..961445a 100644 --- a/.guix-channel +++ b/.guix-channel @@ -2,9 +2,8 @@ (version 0) (dependencies (channel - (name 'guix-forge) - (url "https://git.systemreboot.net/guix-forge/") - (branch "main") + (name guix-forge) + (url "https://git.systemreboot.net/guix-forge") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 464fae24065332747a87fe8d92866494118bf3ae Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:51:21 +0300 Subject: Add trailing slash to forge url Signed-off-by: Munyoki Kilyungi --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index 961445a..abf2efe 100644 --- a/.guix-channel +++ b/.guix-channel @@ -3,7 +3,7 @@ (dependencies (channel (name guix-forge) - (url "https://git.systemreboot.net/guix-forge") + (url "https://git.systemreboot.net/guix-forge/") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 8fa81520252a33408e8b8a56cb995d1a602cdabc Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 13:53:18 +0300 Subject: Specify default branch for forge channel Signed-off-by: Munyoki Kilyungi --- .guix-channel | 1 + 1 file changed, 1 insertion(+) diff --git a/.guix-channel b/.guix-channel index abf2efe..a04aca4 100644 --- a/.guix-channel +++ b/.guix-channel @@ -4,6 +4,7 @@ (channel (name guix-forge) (url "https://git.systemreboot.net/guix-forge/") + (branch "main") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 1c8afbb56d57892a310552fb120b18a6f7a5a819 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 14:11:12 +0300 Subject: Remove guix-forge channel Signed-off-by: Munyoki Kilyungi --- .guix-channel | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/.guix-channel b/.guix-channel index a04aca4..05e0512 100644 --- a/.guix-channel +++ b/.guix-channel @@ -1,16 +1,6 @@ (channel (version 0) (dependencies - (channel - (name guix-forge) - (url "https://git.systemreboot.net/guix-forge/") - (branch "main") - (introduction - (channel-introduction - (version 0) - (commit "0432e37b20dd678a02efee21adf0b9525a670310") - (signer - "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) (channel (name guix-past) (url "https://gitlab.inria.fr/guix-hpc/guix-past") -- cgit v1.2.3 From 6f4a72968e473a52ac1a58971e7150823e96ba16 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 19:18:24 +0300 Subject: Revert "Pin python to python@3.8.5" This reverts commit aaa6e53e7b623105d05e67e95186aba5b4671010. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 7d8cb43..6e5bbce 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -135,7 +135,7 @@ python-pytest-mock)) (propagated-inputs (list gemma-wrapper - `("python" (specification->package "python@3.8.5")) + python-wrapper csvdiff gn-rust-correlation python-bcrypt ;; Replace use of bcrypt with argon below @@ -218,7 +218,7 @@ ("gn-rust-correlation" ,gn-rust-correlation) ("glibc-utf8-locales" ,glibc-utf8-locales) ("nginx" ,nginx) - ("python" ,(specification->package "python@3.8.5")) + ("python" ,python-wrapper) ("python-pillow" ,python-pillow) ("python-coverage" ,python-coverage) ("python-configparser" ,python-configparser) ;; maintenance/scripts -- cgit v1.2.3 From 01e8768aef5279c31b051266dcd7316c3843fcc9 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 4 Sep 2023 19:18:31 +0300 Subject: Update pinned guix version .guix-channel: Use guix at commit 8d70ff3a49f7cdf0eab93b3a1c54ec2f016afc4a. Signed-off-by: Munyoki Kilyungi --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index 05e0512..48fa53b 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "a4e9842a70775a54bbe1369881b739e7ea9a6432") + (commit "8d70ff3a49f7cdf0eab93b3a1c54ec2f016afc4a") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 543a0d0afd5205c839c79c27d57b4b43c9742387 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 5 Sep 2023 14:15:28 +0300 Subject: Adjust how native/propagated inputs are defined for GN3 Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 83 +++++++++++++++++++++++---------------------- 1 file changed, 42 insertions(+), 41 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 6e5bbce..c7dba3b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -127,48 +127,49 @@ (inputs (list python-click)) (native-inputs - (list python-hypothesis - python-mypy - python-mypy-extensions - python-pylint - python-pytest - python-pytest-mock)) + `(("python-hypothesis" ,python-hypothesis) + ("python-mypy" ,python-mypy) + ("python-mypy-extensions" ,python-mypy-extensions) + ("python-pylint" ,python-pylint) + ("python-pytest" ,python-pytest) + ("python-pytest-mock" ,python-pytest-mock))) (propagated-inputs - (list gemma-wrapper - python-wrapper - csvdiff - gn-rust-correlation - python-bcrypt ;; Replace use of bcrypt with argon below - python-argon2-cffi - python-flask - python-flask-cors - ;; Not working in Python > 3.8 - ;; python-ipfshttpclient - python-lmdb - python-mysqlclient - python-numpy - python-pandas - ;; python-pingouin << build failing - python-pingouin-without-tests - python-plotly - python-scikit-learn - python-pymonad - python-redis - python-requests - python-scipy - python-authlib - python-sparqlwrapper - python-email-validator - python-xapian-bindings - r-optparse - r-qtl - r-rjson - r-stringi - r-wgcna - r-ctl - rust-qtlreaper - diffutils - yoyo-migrations)) + `(("gemma-wrapper" ,gemma-wrapper) + ("python-wrapper" ,python-wrapper) + ("csvdiff" ,csvdiff) + ("gn-rust-correlation" ,gn-rust-correlation) + ;; Replace use of bcrypt with argon below + ("python-bcrypt" ,python-bcrypt) + ("python-argon2-cffi" ,python-argon2-cffi) + ("python-flask" ,python-flask) + ("python-flask-cors" ,python-flask-cors) + ;; Not working in Python > 3.8 + ;; python-ipfshttpclient + ("python-lmdb" ,python-lmdb) + ("python-mysqlclient" ,python-mysqlclient) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ;; python-pingouin << build failing + ("python-pingouin-without-tests" ,python-pingouin-without-tests) + ("python-plotly" ,python-plotly) + ("python-scikit-learn" ,python-scikit-learn) + ("python-pymonad" ,python-pymonad) + ("python-redis" ,python-redis) + ("python-requests" ,python-requests) + ("python-scipy" ,python-scipy) + ("python-authlib" ,python-authlib) + ("python-sparqlwrapper" ,python-sparqlwrapper) + ("python-email-validator" ,python-email-validator) + ("python-xapian-bindings" ,python-xapian-bindings) + ("r-optparse" ,r-optparse) + ("r-qtl" ,r-qtl) + ("r-rjson" ,r-rjson) + ("r-stringi" ,r-stringi) + ("r-wgcna" ,r-wgcna) + ("r-ctl" ,r-ctl) + ("rust-qtlreaper" ,rust-qtlreaper) + ("diffutils" ,diffutils) + ("yoyo-migrations" ,yoyo-migrations))) (build-system python-build-system) (arguments (list #:phases -- cgit v1.2.3 From 538b15b254c123e37c91a7fcd32fc41adeb3c611 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 5 Sep 2023 14:21:46 +0300 Subject: gn: python: Add yoyo-migrations-8.2.0 * gn/packages/python.scm: Import (gnu packages databases) and (guix hg-download). (yoyo-migrations-8.2.0): New package. Signed-off-by: Munyoki Kilyungi --- gn/packages/python.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 510546d..adfc2f4 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -3,6 +3,7 @@ #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages ghostscript) #:use-module (gnu packages icu4c) @@ -32,6 +33,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix hg-download) #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix build-system python) @@ -1878,3 +1880,23 @@ complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.") (license license:bsd-3))) + +(define-public yoyo-migrations-8.2.0 + (package + (inherit yoyo-migrations) + (name "yoyo-migrations") + (version "8.2.0") + (source + (origin + ;; We use the upstream repository, as the tests are not included in the + ;; PyPI releases. + (method hg-fetch) + (uri (hg-reference + (url "https://hg.sr.ht/~olly/yoyo") + (changeset (string-append "v" version "-release")))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 "1al030ix0w63hr4s3mqry6s0mlqdj8p242pdqks06br7c25nx3yj")))) + (propagated-inputs + (modify-inputs (package-propagated-inputs yoyo-migrations) + (append python-importlib-metadata))))) -- cgit v1.2.3 From 563c842a760c60c5e4f3f46e282f7994903a64df Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 5 Sep 2023 14:23:26 +0300 Subject: gn: python: Add python-mypy-0.981 * gn/packages/python.scm (python-mypy-0.981): New package. Signed-off-by: Munyoki Kilyungi --- gn/packages/python.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index adfc2f4..d728ef3 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1900,3 +1900,26 @@ concepts.") (propagated-inputs (modify-inputs (package-propagated-inputs yoyo-migrations) (append python-importlib-metadata))))) + +(define-public python-mypy-0.981 + (package + (inherit python-mypy) + (name "python-mypy") + (version "0.981") + (source + (origin + ;; Because of https://github.com/python/mypy/issues/9584, the + ;; mypyc/analysis directory is missing in the PyPI archive, leading to + ;; test failures. + (method git-fetch) + (uri (git-reference + (url "https://github.com/python/mypy") + (commit (string-append "v" version)) + ;; Fetch git submodules otherwise typeshed is not fetched. + ;; Typeshed is a collection of Python sources type annotation + ;; (data) files. + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0awigl51an7466yk236f9vsbqpz2jzd6dsg9v5a4cia37vz4li0a")))))) -- cgit v1.2.3 From ebd0a22dd7388379a530b4171e4bd47602d07ebc Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 5 Sep 2023 14:24:48 +0300 Subject: gn: genenetwork: Update mypy and yoyo * gn/packages/genenetwork.scm: Import (guix packages). (genenetwork3): Use yoyo-migrations v8.2.0 and python-mypy v0.981. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index c7dba3b..b2c6611 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -14,6 +14,7 @@ #:use-module (guix scripts graph) #:use-module (guix store) #:use-module (guix gexp) + #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioconductor) @@ -128,7 +129,7 @@ (list python-click)) (native-inputs `(("python-hypothesis" ,python-hypothesis) - ("python-mypy" ,python-mypy) + ("python-mypy" ,python-mypy-0.981) ("python-mypy-extensions" ,python-mypy-extensions) ("python-pylint" ,python-pylint) ("python-pytest" ,python-pytest) @@ -169,7 +170,7 @@ ("r-ctl" ,r-ctl) ("rust-qtlreaper" ,rust-qtlreaper) ("diffutils" ,diffutils) - ("yoyo-migrations" ,yoyo-migrations))) + ("yoyo-migrations" ,yoyo-migrations-8.2.0))) (build-system python-build-system) (arguments (list #:phases -- cgit v1.2.3 From 2a1cbd69761a2a32e1df525307b1aabc9b0fcb8e Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 6 Sep 2023 13:10:20 +0300 Subject: gn: gn-auth: Update yoyo and mypy Update yoyo and mypy to allow the use of Python-3.10 --- gn/packages/genenetwork.scm | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b2c6611..ab8f8bd 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -489,23 +489,23 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - (list python-mypy - python-pytest - python-pylint - python-hypothesis - python-pytest-mock - python-mypy-extensions)) + `(("python-mypy" ,python-mypy-0.981) + ("python-pytest" ,python-pytest) + ("python-pylint" ,python-pylint) + ("python-hypothesis" ,python-hypothesis) + ("python-pytest-mock" ,python-pytest-mock) + ("python-mypy-extensions" ,python-mypy-extensions))) (propagated-inputs - (list gunicorn - python-flask - python-redis - python-authlib - python-pymonad - yoyo-migrations - python-bcrypt ;; remove after removing all references - python-mysqlclient - python-argon2-cffi - python-email-validator)) + `(("gunicorn" ,gunicorn) + ("python-flask" ,python-flask) + ("python-redis" ,python-redis) + ("python-authlib" ,python-authlib) + ("python-pymonad" ,python-pymonad) + ("yoyo-migrations" ,yoyo-migrations-8.2.0) + ("python-bcrypt" ,python-bcrypt) ;; remove after removing all references + ("python-mysqlclient" ,python-mysqlclient) + ("python-argon2-cffi" ,python-argon2-cffi) + ("python-email-validator" ,python-email-validator))) (home-page "https://github.com/genenetwork/gn-auth") (synopsis "Authentication and Authorisation server for GeneNetwork services") (description "Authentication and Authorisation server for GeneNetwork services.") -- cgit v1.2.3 From ea986e95f6b2f66268a53a34945d858130bff018 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 19 Sep 2023 11:01:36 +0300 Subject: Remove `rust-clap-4` There is a `rust-clap-4` package upstream. --- gn/packages/crates-io.scm | 44 -------------------------------------------- 1 file changed, 44 deletions(-) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index e500d86..7e74b60 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -475,50 +475,6 @@ or any combination.") (description "Rust CLI tools for manipulation of Jupyter Notebooks.") (license #f)))) ; There is no license. -(define-public rust-clap-4 - (package - (name "rust-clap") - (version "4.0.9") - (source (origin - (method url-fetch) - (uri (crate-uri "clap" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1w0dxqzrh449s9l2k8g66pdsff02599bwi5mh0gny3227kcpsq1h")))) - (build-system cargo-build-system) - (arguments - `(#:skip-build? #t ; Not all inputs packaged. - #:cargo-inputs - (("rust-atty" ,rust-atty-0.2) - ("rust-backtrace" ,rust-backtrace-0.3) - ("rust-bitflags" ,rust-bitflags-1) - ("rust-clap-derive" ,rust-clap-derive-4) - ("rust-clap-lex" ,rust-clap-lex-0.3) - ("rust-once-cell" ,rust-once-cell-1) - ("rust-strsim" ,rust-strsim-0.10) - ("rust-termcolor" ,rust-termcolor-1) - ("rust-terminal-size" ,rust-terminal-size-0.1) - ("rust-unicase" ,rust-unicase-2) - ("rust-unicode-width" ,rust-unicode-width-0.1)) - ;#:cargo-development-inputs - ;(("rust-humantime" ,rust-humantime-2) - ; ("rust-rustversion" ,rust-rustversion-1) - ; ("rust-shlex" ,rust-shlex-1) - ; ("rust-snapbox" ,rust-snapbox-0.4) - ; ("rust-static-assertions" ,rust-static-assertions-1) - ; ("rust-trybuild" ,rust-trybuild-1) - ; ("rust-trycmd" ,rust-trycmd-0.13) - ; ("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9)) - )) - (home-page "https://github.com/clap-rs/clap") - (synopsis - "A simple to use, efficient, and full-featured Command Line Argument Parser") - (description - "This package provides a simple to use, efficient, and full-featured Command Line - Argument Parser") - (license (list license:expat license:asl2.0)))) - (define-public rust-clap-derive-4 (package (name "rust-clap-derive") -- cgit v1.2.3 From 382df9849ed64d6ef2ea6ecafbfb090ad49928eb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 6 Sep 2023 14:48:43 +0300 Subject: update julia-visuals --- gn/packages/julia.scm | 676 ++- julia-visuals-remove-manifests.diff | 10151 ++++++++++++++++++++++++++++++++++ 2 files changed, 10775 insertions(+), 52 deletions(-) create mode 100644 julia-visuals-remove-manifests.diff diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm index 31cc29c..aa163bf 100644 --- a/gn/packages/julia.scm +++ b/gn/packages/julia.scm @@ -17,6 +17,7 @@ #:use-module (gnu packages julia-xyz) #:use-module (gnu packages python) #:use-module (gnu packages statistics) + #:use-module (gnu packages version-control) #:use-module (gnu packages video) #:use-module (ice-9 match)) @@ -24,7 +25,7 @@ (define-public julia-visuals (let ((commit "e8e2b601f40a76c8f20f0ddfe80c56257dd9a294") - (revision "2")) + (revision "3")) (package (name "julia-visuals") (version (git-version "0.0.0" revision commit)) @@ -35,7 +36,8 @@ (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0lm9yhk0mq5cvvkcbsgcjc1y7fzhr8qz2nxn38cy1zdxd8vfknsx")))) + (base32 "0lm9yhk0mq5cvvkcbsgcjc1y7fzhr8qz2nxn38cy1zdxd8vfknsx")) + (patches (search-patches "julia-visuals-remove-manifests.diff")))) (build-system julia-build-system) (arguments `(#:tests? #f ; no test suite @@ -59,8 +61,15 @@ "environment.yml" "setup.py" "runpluto.sh" + "runsliderserver.sh" "notebooks" "Project.toml"))))) + (add-after 'install 'skip-julia-cairomakie + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion + (string-append (assoc-ref outputs "out") "/notebooks") + (delete-file "bayes.jl") + (delete-file "disease-testing.jl")))) (add-after 'install 'wrap-program (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -69,7 +78,7 @@ `("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin") ,(string-append (assoc-ref inputs "coreutils") "/bin"))) `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH"))))))) - (add-after 'install 'create-run-program + (add-after 'install 'create-runpluto (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (with-output-to-file (string-append out "/runpluto") @@ -94,6 +103,29 @@ (dirname (search-input-file inputs "/bin/yes")) (search-input-file inputs "/bin/julia")))) (chmod (string-append out "/runpluto") #o555)))) + (add-after 'install 'create-runsliderserver + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (with-output-to-file (string-append out "/runsliderserver") + (lambda () + (format #t "#!~a --no-auto-compile +!# +(setenv \"JULIA_LOAD_PATH\" \"~a\") +(setenv \"PATH\" \"~a\") +(zero? (system* + \"~a\" + \"--optimize=0\" + \"-e\" \"import PlutoSliderServer; + PlutoSliderServer.run_directory( + \\\"~a/notebooks/\\\", + SliderServer_port=4343, + SliderServer_host=\\\"0.0.0.0\\\")\"))\n" + (search-input-file inputs "/bin/guile") + (getenv "JULIA_LOAD_PATH") + (dirname (search-input-file inputs "/bin/yes")) + (search-input-file inputs "/bin/julia") + out))) + (chmod (string-append out "/runsliderserver") #o555)))) (replace 'precompile (lambda _ (invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\"")))))) @@ -104,14 +136,19 @@ ,(@ (gn packages python) python-jupyter-server-proxy-1)))) (inputs - (list julia-distributions + (list ;julia-cairomakie ; 0.8.13 + julia-distributions ; 0.25.76 ;julia-interactiveutils ; stdlib - julia-latexstrings + julia-latexstrings ; 1.3.0 ;julia-markdown ; stdlib - julia-optim - julia-plots - julia-pluto - julia-plutoui + julia-optim ; 1.7.2 + julia-plots ; 1.35.3 + julia-pluto ; 0.19.11 + julia-plutosliderserver ; * + julia-plutoui ; 0.7.46 + julia-prettytables ; 2.1.0 + julia-quadgk ; 2.5.0 + julia-roots ; 2.0.3 (@ (gnu packages guile) guile-3.0))) ; for wrap-script (home-page "https://github.com/sens/visuals") (synopsis "Visualizations using Pluto.jl notebooks") @@ -335,6 +372,282 @@ properties @end enumerate") (license license:expat))) +(define-public julia-fromfile + (package + (name "julia-fromfile") + (version "0.1.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Roger-luo/FromFile.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jn394294d4s1fqsfiwpiy6dzlca4ciy54l2xviwyzhvixmlfrwn")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f)) ; Tests require network access + (propagated-inputs + (list julia-requires)) + (home-page "https://github.com/Roger-luo/FromFile.jl") + (synopsis "Julia enhancement proposal for implicit per file module in Julia") + (description "This package exports a macro @code{@@from}, which can be used +to import objects from files.") + (license license:expat))) + +(define-public julia-git + (package + (name "julia-git") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaVersionControl/Git.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bznzg360cbvbzzpsdkin4dm2v980sb5pv58gy1bp3j9j8bj38h6")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-network-tests + (lambda _ + (substitute* "test/runtests.jl" + (("testset.*Git.jl.*" all) + (string-append all " return\n")))))))) + (propagated-inputs + (list julia-git-jll)) + (home-page "https://github.com/JuliaVersionControl/Git.jl") + (synopsis "Use command-line Git in your Julia packages") + (description "Git.jl allows you to use command-line Git in your Julia +packages. You do not need to have Git installed on your computer, and neither +do the users of your packages!") + (license license:expat))) + +(define-public julia-git-jll + (package + (name "julia-git-jll") + (version "2.36.1+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Git_jll.jl") + (commit (string-append "Git-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1n8k363q2mw5qfkagbbqpn4djx181qbn05l7brp3spspvf5aslgm")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'link-depot 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Git\", \"" + (assoc-ref inputs "git-minimal") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + (list git-minimal)) + (propagated-inputs + (list julia-jllwrappers + julia-expat-jll + julia-openssl-jll + ;julia-libcurl-jll + julia-libiconv-jll + ;julia-pcre2-jll + julia-zlib-jll)) + (home-page "https://github.com/JuliaBinaryWrappers/Git_jll.jl") + (synopsis "Git library wrappers") + (description "This package provides a wrapper for the git library.") + (license license:expat))) + +(define-public julia-terminalloggers + (package + (name "julia-terminalloggers") + (version "0.1.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLogging/TerminalLoggers.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01l9qsjljwa9pkpvf1pafmbrncjddwdw3737pf44y9q5hrp4hbr7")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-leftchildrightsiblingtrees + julia-progresslogging)) + (home-page "https://github.com/JuliaLogging/TerminalLoggers.jl") + (synopsis "Logging sinks and utilites for interactive terminals") + (description "TerminalLoggers provides a logger type @code{TerminalLogger} +which can format your log messages in a richer way than the default +@code{ConsoleLogger} which comes with the julia standard @code{Logging} +library.") + (license license:expat))) + +(define-public julia-roots + (package + (name "julia-roots") + (version "2.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/Roots.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17d62r8pib3cp73az00iz8nbnd5j0y3dl1mrmcssnj4ln8043056")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-expensive-tests + (lambda _ + (substitute* "test/runtests.jl" + ((".*test_composable.*") ""))))))) + (propagated-inputs + (list julia-commonsolve + julia-setfield)) + (native-inputs + (list julia-benchmarktools + julia-forwarddiff + julia-json + julia-specialfunctions)) + (home-page "http://juliamath.github.io/Roots.jl/") + (synopsis "Root finding functions for Julia") + (description "This package contains simple routines for finding roots, or +zeros, of scalar functions of a single real variable using floating-point +math.") + (license license:expat))) + +(define-public julia-commonsolve + (package + (name "julia-commonsolve") + (version "0.2.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SciML/CommonSolve.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w05fp02g5cmqzqp96hcpriwjpqx61sl481rj92gf4y4xpinmdf5")))) + (build-system julia-build-system) + (home-page "https://docs.sciml.ai/CommonSolve/stable") + (synopsis "Common solve function for scientific machine learning") + (description "This holds the common @code{solve}, @code{init}, +@code{step!}, and @code{solve!} commands. By using the same definition, solver +libraries from other completely different ecosystems can extend the functions +and thus not clash with SciML if both ecosystems export the @code{solve} +command. The rules are that you must dispatch on one of your own types.") + (license license:expat))) + +(define-public julia-setfield + (package + (name "julia-setfield") + (version "1.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jw3126/Setfield.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vdn9s639f120560599m4lhqkk0nsx7qa87fv2mixs1faaihsf6l")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Skip tests, not all dependencies packaged. + (propagated-inputs + (list julia-constructionbase + julia-macrotools + julia-staticarrayscore)) + (home-page "https://github.com/jw3126/Setfield.jl") + (synopsis "Update deeply nested immutable structs") + (description "Update deeply nested immutable structs.") + (license license:expat))) + +(define-public julia-staticarrayscore + (package + (name "julia-staticarrayscore") + (version "1.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/StaticArraysCore.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0m573mxvf0y9h7y8rxrk35haphhqisplx159r77g30qvw7zwpgar")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaArrays/StaticArraysCore.jl") + (synopsis "Interface package for StaticArrays.jl") + (description + "This package provides an interface package for @code{StaticArrays.jl}.") + (license license:expat))) + +(define-public julia-progresslogging + (package + (name "julia-progresslogging") + (version "0.1.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLogging/ProgressLogging.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ysixnl7wjdykaka892jrhsay2aivpch83h8dnfs43z2xynf9sqn")))) + (build-system julia-build-system) + (native-inputs + (list julia-offsetarrays)) + (home-page "https://github.com/JuliaLogging/ProgressLogging.jl") + (synopsis "Define progress logs") + (description "ProgressLogging.jl is a package for defining progress logs. +It can be used to report progress of a loop/loops with time-consuming body.") + (license license:expat))) + +(define-public julia-leftchildrightsiblingtrees + (package + (name "julia-leftchildrightsiblingtrees") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaCollections/LeftChildRightSiblingTrees.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1rijr0yqmbzhlk668v4rqw5xmxxzqvgziasyqrd6z837376mfyy6")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-abstracttrees)) + (home-page "https://github.com/JuliaCollections/LeftChildRightSiblingTrees.jl") + (synopsis "Representation of a tree with arbitrary number of children/node") + (description "A left child, right sibling tree (frequently abbreviated as +\"LCRS\") is a rooted tree data structure that allows a parent node to have +multiple child nodes. Rather than maintain a list of children (which requires +one array per node), instead it is represented as a binary tree, where the +\"left\" branch is the first child, whose \"right\" branch points to its first +sibling.") + (license license:expat))) + ;; ready to upstream (define-public julia-densityinterface (package @@ -363,7 +676,7 @@ densities and objects associated with a density in Julia.") (define-public julia-plots (package (name "julia-plots") - (version "1.16.6") + (version "1.35.6") (source (origin (method git-fetch) @@ -372,57 +685,258 @@ densities and objects associated with a density in Julia.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ipv9408r4czsx1j01sv2f7ww52b329jc0v79npn4x2mf827nsik")))) + (base32 "005za8a8al822xr0cz4yi1rm23qj1lzy9iw93vvhwq76x3n8bfpy")))) (build-system julia-build-system) (arguments `(#:tests? #f ; for now )) (propagated-inputs - `( - ;("julia-contour" ,julia-contour) - ("julia-ffmpeg" ,julia-ffmpeg) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-gr" ,julia-gr) - ("julia-geometrybasics" ,julia-geometrybasics) - ("julia-json" ,julia-json) - ;("julia-latexify" ,julia-latexify) - ("julia-measures" ,julia-measures) - ("julia-nanmath" ,julia-nanmath) - ("julia-plotthemes" ,julia-plotthemes) - ("julia-plotutils" ,julia-plotutils) - ("julia-recipesbase" ,julia-recipesbase) - ("julia-recipespipeline" ,julia-recipespipeline) - ("julia-reexport" ,julia-reexport) - ("julia-requires" ,julia-requires) - ("julia-scratch" ,julia-scratch) - ("julia-showoff" ,julia-showoff) - ("julia-statsbase" ,julia-statsbase) - )) + (list + ;julia-contour + julia-ffmpeg + julia-fixedpointnumbers + julia-gr + julia-geometrybasics + julia-jlfzf + julia-json + ;julia-latexify + julia-measures + julia-nanmath + julia-plotthemes + julia-plotutils + julia-recipesbase + julia-recipespipeline + julia-reexport + julia-relocatablefolders + julia-requires + julia-scratch + julia-showoff + julia-snoopprecompile + julia-statsbase + julia-unicodefun + julia-unzip)) (native-inputs - `( - ;("julia-distributions" ,julia-distributions) - ("julia-fileio" ,julia-fileio) - ;("julia-gtk" ,julia-gtk) - ;("julia-hdf5" ,julia-hdf5) - ("julia-imagemagick" ,julia-imagemagick) - ;("julia-images" ,julia-images) - ("julia-offsetarrays" ,julia-offsetarrays) - ;("julia-pgfplotsx" ,julia-pgfplotsx) - ;("julia-plotlyjs" ,julia-plotlyjs) - ;("julia-rdatasets" ,julia-rdatasets) - ("julia-stablerngs" ,julia-stablerngs) - ("julia-staticarrays" ,julia-staticarrays) - ;("julia-statsplots" ,julia-statsplots) - ("julia-testimages" ,julia-testimages) - ;("julia-unicodeplots" ,julia-unicodeplots) - ;("julia-visualregressiontests" ,julia-visualregressiontests) + (list + ;julia-distributions + julia-fileio + ;julia-gtk + ;julia-hdf5 + julia-imagemagick + ;julia-images + julia-offsetarrays + ;julia-pgfplotsx + ;julia-plotlyjs + ;julia-rdatasets + julia-stablerngs + julia-staticarrays + ;julia-statsplots + julia-testimages + ;julia-unicodeplots + ;julia-visualregressiontests )) (home-page "http://docs.juliaplots.org/") (synopsis "Powerful convenience for Julia visualizations and data analysis") (description "Plots is a plotting API and toolset.") (license license:expat))) +(define-public julia-snoopprecompile + (package + (name "julia-snoopprecompile") + (version "1.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timholy/SnoopCompile.jl") + (commit "v2.10.0"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14nnqknswjzlk786x4r7xc7898nmfk7ijfchrc09i81qi2d0mmcn")))) + (build-system julia-build-system) + (arguments + (list + #:tests? #f ; Most tests fail in the build environment. + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopPrecompile")))))) + (propagated-inputs + (list julia-preferences)) + (home-page "https://timholy.github.io/SnoopCompile.jl/dev/") + (synopsis "Effectively precompile code needed by your package") + (description "SnoopPrecompile is a small dependency used to effectively +precompile code needed by your package, particularly on Julia 1.8 and higher.") + (license license:expat))) + +(define-public julia-jlfzf + (package + (name "julia-jlfzf") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Moelf/JLFzf.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0fvcx80lzj0xc4imb9h0iybj8s0cazjc1wn9h8xncih9aln25is4")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f)) ; no tests + (propagated-inputs + (list julia-fzf-jll + julia-pipe)) + (home-page "https://github.com/Moelf/JLFzf.jl") + (synopsis "Julia bind to fzf fuzzy finder") + (description "Julia bind to fzf fuzzy finder.") + (license license:expat))) + +(define-public julia-pipe + (package + (name "julia-pipe") + (version "1.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/oxinabox/Pipe.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01anm76nfmcajcbr2piji0rknisf5wwhimfndwaadkqkcjv7k4xn")))) + (build-system julia-build-system) + (home-page "https://github.com/oxinabox/Pipe.jl") + (synopsis "Enhancement to Julia piping syntax") + (description "This package provides an enhancement to Julia piping syntax.") + (license license:expat))) + +(define-public julia-fzf-jll + (package + (name "julia-fzf-jll") + (version "0.35.1+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/juliabinarywrappers/fzf_jll.jl") + (commit (string-append "fzf-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0psl1lsvl6sza69g7qh8ha2ir89fibzid4ka3wzmjgh0r4yjfnw0")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'link-depot 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"fzf\", \"" + (assoc-ref inputs "fzf") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + (list (@ (gnu packages terminals) fzf))) + (propagated-inputs + (list julia-jllwrappers)) + (home-page "https://github.com/JuliaBinaryWrappers/fzf_jll.jl") + (synopsis "Fzf library wrappers") + (description "This package provides a wrapper for fzf.") + (license license:expat))) + +(define-public julia-unicodefun + (package + (name "julia-unicodefun") + (version "0.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SimonDanisch/UnicodeFun.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11hch4zpi8qby8pcqfvxnx88y45lxan4ind9kj2d0pgw614zkpg0")))) + (build-system julia-build-system) + (home-page "https://github.com/SimonDanisch/UnicodeFun.jl") + (synopsis "Transform text into unicode symbols") + (description "This package offers a unicode transformation library.") + (license license:expat))) + +(define-public julia-unzip + (package + (name "julia-unzip") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bramtayl/Unzip.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i4rkvyd8br024s0sgs3crpi6za2f51m42whkx0jd22wiwg675vb")))) + (build-system julia-build-system) + (native-inputs + (list julia-documenter)) + (home-page "https://github.com/bramtayl/Unzip.jl") + (synopsis "") + (description "") + (license license:expat))) + +;; Versions after 0.3.11 need a newer version of julia-http +(define-public julia-plutosliderserver + (package + (name "julia-plutosliderserver") + (version "0.3.11") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPluto/PlutoSliderServer.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1aqc836glwqqs1pd9173sbjwjns3zv197xqdqlkp2xgrkjiw2yzg")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f ; Tests require network access + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-source + (lambda _ + (setenv "GITHUB_ACTIONS" "false") + ;; Rip out betterfilewatching, it depends on a rust package. + (substitute* "src/PlutoSliderServer.jl" + ((".*watch_folder.*") "")) + ;; Remove GitHubActions + (substitute* "src/PlutoSliderServer.jl" + ((".*GitHubActions.*") ""))))))) + (propagated-inputs + (list julia-abstractplutodingetjes + ;julia-betterfilewatching ; should be disabled? + julia-configurations + julia-fromfile + julia-git + ;julia-githubactions ; can be disabled + julia-http + julia-json + julia-pluto + julia-terminalloggers)) + (home-page "https://github.com/JuliaPluto/PlutoSliderServer.jl") + (synopsis "Web server to run parts of a Pluto.jl notebook") + (description "This package provides a web server to run just the +@code{@@bind} parts of a @code{Pluto.jl} notebook.") + (license license:unlicense))) + ;; TODO: unbundle javascript calls to cdn.jsdelivr.net +;; The '-src' commit needs some nodejs packages to build the frontend. (define-public julia-pluto (package (name "julia-pluto") @@ -432,15 +946,20 @@ densities and objects associated with a density in Julia.") (method git-fetch) (uri (git-reference (url "https://github.com/fonsp/Pluto.jl") - (commit (string-append "v" version "-src")))) + ;(commit (string-append "v" version "-src")))) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0h9sz4mpf3a4k0f5fblbb6j07wdhrnarxajrn0wz6zsq6w30x6yj")))) + ;(base32 "0h9sz4mpf3a4k0f5fblbb6j07wdhrnarxajrn0wz6zsq6w30x6yj")))) + (base32 "1qml5id3fi4r6n7hrqvfjwdvp3zp8xfckir3mw7vwswmkc56jzpq")))) (build-system julia-build-system) (arguments `(#:tests? #f ; Test suite tries to download the package registry. - #:phases - (modify-phases %standard-phases + ;#:phases + #;(modify-phases %standard-phases + #;(add-before 'check 'pre-check + (lambda _ + (setenv "PLUTO_TEST_ONLY_COMPILETIMES" "true"))) (add-after 'link-depot 'dont-check-for-upgrades (lambda _ (substitute* "frontend/components/welcome/Welcome.js" @@ -561,6 +1080,59 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (list julia-bufferedstreams julia-json)))) +(define-public julia-http-1.0 + (package + (inherit julia-http) + (name "julia-http") + (version "1.0.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaWeb/HTTP.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "15bqf0gv4qz3990cv1s2nj9mjqaka1pkhzymgwc19wxqvacwvwqr")))) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'disable-network-tests + (lambda _ + (substitute* "test/runtests.jl" + (("\"async.jl") "# \"async.jl") + (("\"client.jl") "# \"client.jl") + (("\"websockets") "# \"websockets") + (("\"server") "# \"server")) + (substitute* "test/multipart.jl" + (("@testset \"Setting of Content-Type.*" all) + (string-append all "return\n")) + (("@testset \"Deprecation of .*" all) + (string-append all "return\n"))) + (substitute* "test/messages.jl" + (("@testset.*Read methods.*" all) + (string-append all "return\n")) + (("@testset.*Body - .*" all) + (string-append all "return\n")) + (("@testset.*Write to file.*" all) + (string-append all "return\n"))) + (substitute* "test/cookies.jl" + (("@testset.*Set-Cookie casing.*" all) + (string-append all "return\n"))) +))))) + (propagated-inputs + (list julia-codeczlib + julia-inifile + julia-loggingextras + julia-mbedtls + julia-simplebufferstream + julia-uris)) + ;; required for tests + (native-inputs + (list julia-bufferedstreams + julia-json)))) + (define-public julia-simplebufferstream (package (name "julia-simplebufferstream") diff --git a/julia-visuals-remove-manifests.diff b/julia-visuals-remove-manifests.diff new file mode 100644 index 0000000..358c42f --- /dev/null +++ b/julia-visuals-remove-manifests.diff @@ -0,0 +1,10151 @@ +diff --git a/notebooks/L1-penalty.jl b/notebooks/L1-penalty.jl +index 9f3d64b..7f1c4ee 100644 +--- a/notebooks/L1-penalty.jl ++++ b/notebooks/L1-penalty.jl +@@ -140,1106 +140,6 @@ Plots = "~1.25.4" + PlutoUI = "~0.7.29" + """ + +-# ╔═╡ 00000000-0000-0000-0000-000000000002 +-PLUTO_MANIFEST_TOML_CONTENTS = """ +-# This file is machine-generated - editing it directly is not advised +- +-julia_version = "1.8.1" +-manifest_format = "2.0" +-project_hash = "7e66a529aecc117666fc78bb2f204d6081a02e1c" +- +-[[deps.AbstractPlutoDingetjes]] +-deps = ["Pkg"] +-git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" +-uuid = "6e696c72-6542-2067-7265-42206c756150" +-version = "1.1.4" +- +-[[deps.Adapt]] +-deps = ["LinearAlgebra"] +-git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" +-uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +-version = "3.4.0" +- +-[[deps.ArgTools]] +-uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +-version = "1.1.1" +- +-[[deps.ArrayInterfaceCore]] +-deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +-git-tree-sha1 = "14c3f84a763848906ac681f94cf469a851601d92" +-uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" +-version = "0.1.28" +- +-[[deps.Artifacts]] +-uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +- +-[[deps.Base64]] +-uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +- +-[[deps.Bzip2_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" +-uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" +-version = "1.0.8+0" +- +-[[deps.Cairo_jll]] +-deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +-git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" +-uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" +-version = "1.16.1+1" +- +-[[deps.ChainRulesCore]] +-deps = ["Compat", "LinearAlgebra", "SparseArrays"] +-git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" +-uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" +-version = "1.15.6" +- +-[[deps.ChangesOfVariables]] +-deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +-git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" +-uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +-version = "0.1.4" +- +-[[deps.ColorSchemes]] +-deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] +-git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +-uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" +-version = "3.20.0" +- +-[[deps.ColorTypes]] +-deps = ["FixedPointNumbers", "Random"] +-git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +-uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" +-version = "0.11.4" +- +-[[deps.ColorVectorSpace]] +-deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] +-git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" +-uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" +-version = "0.9.10" +- +-[[deps.Colors]] +-deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] +-git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +-uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" +-version = "0.12.10" +- +-[[deps.CommonSubexpressions]] +-deps = ["MacroTools", "Test"] +-git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +-uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" +-version = "0.3.0" +- +-[[deps.Compat]] +-deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] +-git-tree-sha1 = "78bee250c6826e1cf805a88b7f1e86025275d208" +-uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" +-version = "3.46.0" +- +-[[deps.CompilerSupportLibraries_jll]] +-deps = ["Artifacts", "Libdl"] +-uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +-version = "0.5.2+0" +- +-[[deps.ConstructionBase]] +-deps = ["LinearAlgebra"] +-git-tree-sha1 = 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"Libdl", "Pkg"] +-git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" +-uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" +-version = "2.2.4+0" +- +-[[deps.Expat_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" +-uuid = "2e619515-83b5-522b-bb60-26c02a35a201" +-version = "2.4.8+0" +- +-[[deps.Extents]] +-git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" +-uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" +-version = "0.1.1" +- +-[[deps.FFMPEG]] +-deps = ["FFMPEG_jll"] +-git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" +-uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" +-version = "0.4.1" +- +-[[deps.FFMPEG_jll]] +-deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +-git-tree-sha1 = 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"1.6.38+0" +- +-[[deps.libvorbis_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] +-git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +-uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" +-version = "1.3.7+1" +- +-[[deps.nghttp2_jll]] +-deps = ["Artifacts", "Libdl"] +-uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +-version = "1.48.0+0" +- +-[[deps.p7zip_jll]] +-deps = ["Artifacts", "Libdl"] +-uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +-version = "17.4.0+0" +- +-[[deps.x264_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +-uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +-version = "2021.5.5+0" +- +-[[deps.x265_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +-uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +-version = "3.5.0+0" +- +-[[deps.xkbcommon_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +-git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" +-uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +-version = "1.4.1+0" +-""" +- + # ╔═╡ Cell order: + # ╟─ef2627bc-30a7-11ed-29fb-395b23c794b4 + # ╟─b9eb712a-0329-49ba-9409-d5c5a155c112 +diff --git a/notebooks/disease-testing.jl b/notebooks/disease-testing.jl +index b5fd722..4aa5c4a 100644 +--- a/notebooks/disease-testing.jl ++++ b/notebooks/disease-testing.jl +@@ -154,1257 +154,6 @@ Distributions = "~0.25.75" + PlutoUI = "~0.7.43" + """ + +-# ╔═╡ 00000000-0000-0000-0000-000000000002 +-PLUTO_MANIFEST_TOML_CONTENTS = """ +-# This file is machine-generated - editing it directly is not advised +- +-julia_version = "1.8.1" +-manifest_format = "2.0" +-project_hash = "fcf69300a3d26809fba645c97b613b229d740f40" +- +-[[deps.AbstractFFTs]] +-deps = ["ChainRulesCore", "LinearAlgebra"] +-git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +-uuid 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PrettyTables = "~2.1.0" + """ + +-# ╔═╡ 00000000-0000-0000-0000-000000000002 +-PLUTO_MANIFEST_TOML_CONTENTS = """ +-# This file is machine-generated - editing it directly is not advised +- +-julia_version = "1.8.1" +-manifest_format = "2.0" +-project_hash = "f8f2952378978d7572c9df3a8a9013b9291d03b8" +- +-[[deps.AbstractPlutoDingetjes]] +-deps = ["Pkg"] +-git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" +-uuid = "6e696c72-6542-2067-7265-42206c756150" +-version = "1.1.4" +- +-[[deps.ArgTools]] +-uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +-version = "1.1.1" +- +-[[deps.Artifacts]] +-uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +- +-[[deps.Base64]] +-uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +- +-[[deps.BitFlags]] +-git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +-uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +-version = "0.1.7" +- +-[[deps.Bzip2_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = 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a/notebooks/power.jl b/notebooks/power.jl +index b0071a3..7af3786 100644 +--- a/notebooks/power.jl ++++ b/notebooks/power.jl +@@ -113,1042 +113,6 @@ Plots = "~1.35.2" + PlutoUI = "~0.7.43" + """ + +-# ╔═╡ 00000000-0000-0000-0000-000000000002 +-PLUTO_MANIFEST_TOML_CONTENTS = """ +-# This file is machine-generated - editing it directly is not advised +- +-julia_version = "1.8.1" +-manifest_format = "2.0" +-project_hash = "d0db1733794fa43ca17555e440a1f90b9300a02c" +- +-[[deps.AbstractPlutoDingetjes]] +-deps = ["Pkg"] +-git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" +-uuid = "6e696c72-6542-2067-7265-42206c756150" +-version = "1.1.4" +- +-[[deps.ArgTools]] +-uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +-version = "1.1.1" +- +-[[deps.Artifacts]] +-uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +- +-[[deps.Base64]] +-uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +- +-[[deps.BitFlags]] +-git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +-uuid = 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a/notebooks/roc.jl b/notebooks/roc.jl +index f68bc58..597617a 100644 +--- a/notebooks/roc.jl ++++ b/notebooks/roc.jl +@@ -110,1042 +110,6 @@ PlutoUI = "~0.7.43" + QuadGK = "~2.5.0" + """ + +-# ╔═╡ 00000000-0000-0000-0000-000000000002 +-PLUTO_MANIFEST_TOML_CONTENTS = """ +-# This file is machine-generated - editing it directly is not advised +- +-julia_version = "1.8.1" +-manifest_format = "2.0" +-project_hash = "1db4060f32e52842c4aea9a25ec7e67e23aa69ed" +- +-[[deps.AbstractPlutoDingetjes]] +-deps = ["Pkg"] +-git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" +-uuid = "6e696c72-6542-2067-7265-42206c756150" +-version = "1.1.4" +- +-[[deps.ArgTools]] +-uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +-version = "1.1.1" +- +-[[deps.Artifacts]] +-uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +- +-[[deps.Base64]] +-uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +- +-[[deps.BitFlags]] +-git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +-uuid = 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"53915e50200959667e78a92a418594b428dffddf" +-uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" +-version = "0.4.1" +- +-[[deps.Unzip]] +-git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" +-uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +-version = "0.2.0" +- +-[[deps.Wayland_jll]] +-deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] +-git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" +-uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" +-version = "1.21.0+0" +- +-[[deps.Wayland_protocols_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" +-uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" +-version = "1.25.0+0" +- +-[[deps.XML2_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] +-git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +-uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" +-version = "2.10.3+0" +- +-[[deps.XSLT_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] +-git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +-uuid = "aed1982a-8fda-507f-9586-7b0439959a61" +-version = "1.1.34+0" +- +-[[deps.Xorg_libX11_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] +-git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" +-uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" +-version = "1.6.9+4" +- +-[[deps.Xorg_libXau_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" +-uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" +-version = "1.0.9+4" +- +-[[deps.Xorg_libXcursor_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] +-git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" +-uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" +-version = "1.2.0+4" +- +-[[deps.Xorg_libXdmcp_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" +-uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" +-version = "1.1.3+4" +- +-[[deps.Xorg_libXext_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +-git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +-uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" +-version = "1.3.4+4" +- +-[[deps.Xorg_libXfixes_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +-git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" +-uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" +-version = "5.0.3+4" +- +-[[deps.Xorg_libXi_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] +-git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" +-uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" +-version = "1.7.10+4" +- +-[[deps.Xorg_libXinerama_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] +-git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" +-uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" +-version = "1.1.4+4" +- +-[[deps.Xorg_libXrandr_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] +-git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" +-uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" +-version = "1.5.2+4" +- +-[[deps.Xorg_libXrender_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +-git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +-uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" +-version = "0.9.10+4" +- +-[[deps.Xorg_libpthread_stubs_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" +-uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" +-version = "0.1.0+3" +- +-[[deps.Xorg_libxcb_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +-git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +-uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" +-version = "1.13.0+3" +- +-[[deps.Xorg_libxkbfile_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] +-git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" +-uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" +-version = "1.1.0+4" +- +-[[deps.Xorg_xcb_util_image_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +-git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" +-uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" +-version = "0.4.0+1" +- +-[[deps.Xorg_xcb_util_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] +-git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" +-uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" +-version = "0.4.0+1" +- +-[[deps.Xorg_xcb_util_keysyms_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +-git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" +-uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" +-version = "0.4.0+1" +- +-[[deps.Xorg_xcb_util_renderutil_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +-git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" +-uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" +-version = "0.3.9+1" +- +-[[deps.Xorg_xcb_util_wm_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +-git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" +-uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" +-version = "0.4.1+1" +- +-[[deps.Xorg_xkbcomp_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] +-git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" +-uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" +-version = "1.4.2+4" +- +-[[deps.Xorg_xkeyboard_config_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] +-git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" +-uuid = "33bec58e-1273-512f-9401-5d533626f822" +-version = "2.27.0+4" +- +-[[deps.Xorg_xtrans_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" +-uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" +-version = "1.4.0+3" +- +-[[deps.Zlib_jll]] +-deps = ["Libdl"] +-uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +-version = "1.2.12+3" +- +-[[deps.Zstd_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" +-uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +-version = "1.5.2+0" +- +-[[deps.fzf_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +-uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +-version = "0.29.0+0" +- +-[[deps.libaom_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +-uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +-version = "3.4.0+0" +- +-[[deps.libass_jll]] +-deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +-git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" +-uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" +-version = "0.15.1+0" +- +-[[deps.libblastrampoline_jll]] +-deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +-uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +-version = "5.1.1+0" +- +-[[deps.libfdk_aac_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +-uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" +-version = "2.0.2+0" +- +-[[deps.libpng_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +-git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +-uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +-version = "1.6.38+0" +- +-[[deps.libvorbis_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] +-git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +-uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" +-version = "1.3.7+1" +- +-[[deps.nghttp2_jll]] +-deps = ["Artifacts", "Libdl"] +-uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +-version = "1.48.0+0" +- +-[[deps.p7zip_jll]] +-deps = ["Artifacts", "Libdl"] +-uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +-version = "17.4.0+0" +- +-[[deps.x264_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +-uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +-version = "2021.5.5+0" +- +-[[deps.x265_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +-git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +-uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +-version = "3.5.0+0" +- +-[[deps.xkbcommon_jll]] +-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +-git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" +-uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +-version = "1.4.1+0" +-""" +- + # ╔═╡ Cell order: + # ╟─33afb7f3-e52a-4f49-8be2-8634c66db010 + # ╟─70919378-b4d7-11eb-2d76-db01c83f87b8 -- cgit v1.2.3 From 3a54f09147e56d8f0cc8f9c1ff94712de78137a9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 6 Sep 2023 14:49:41 +0300 Subject: Update pluto server --- gn/services/pluto.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm index 720b769..64e82ac 100644 --- a/gn/services/pluto.scm +++ b/gn/services/pluto.scm @@ -43,9 +43,11 @@ (requirement '(networking)) (modules '((gnu build shepherd) (gnu system file-systems))) + #; (start #~(make-forkexec-constructor/container ;(list #$(file-append package "/runpluto.sh") #$port) - (list #$(file-append package "/runpluto")) + ;(list #$(file-append package "/runpluto")) + (list #$(file-append package "/runsliderservice")) #:log-file "/var/log/pluto.log" #:user "julia" #:group "julia" @@ -58,6 +60,16 @@ (file-system-mapping (source "/etc/ssl") (target source))))) + (start #~(make-forkexec-constructor + ;(list #$(file-append package "/runpluto.sh") #$port) + ;(list #$(file-append package "/runpluto")) + '(#$(file-append package "/runsliderservice")) + #:log-file "/var/log/pluto.log" + #:user "julia" + #:group "julia" + ;; This prevents the service from using /root as $HOME. + ;#:environment-variables '() + )) (stop #~(make-kill-destructor)))))))) (define pluto-service-type -- cgit v1.2.3 From 1e16fe6c90c88cb0a22716a2f9fe04b9a67981d1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 12:31:06 +0300 Subject: remove unneeded module import --- gn/packages/riscv.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gn/packages/riscv.scm b/gn/packages/riscv.scm index ae4a72e..e87f8a9 100644 --- a/gn/packages/riscv.scm +++ b/gn/packages/riscv.scm @@ -13,7 +13,6 @@ #:use-module (gn packages fpga) #:use-module (gnu packages cpp) #:use-module (gnu packages virtualization) - #:use-module (guix build utils) #:use-module (guix build-system gnu) #:use-module (guix gexp) #:use-module (guix git-download) -- cgit v1.2.3 From f1b32a21b7c45e3b974ecb543d845c2246339367 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 12:55:31 +0300 Subject: Update pluto notebook service and julia packages --- gn/packages/julia.scm | 755 ++- gn/services/pluto.scm | 27 +- julia-visuals-remove-manifests.diff | 10151 ---------------------------------- 3 files changed, 670 insertions(+), 10263 deletions(-) delete mode 100644 julia-visuals-remove-manifests.diff diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm index aa163bf..a00244f 100644 --- a/gn/packages/julia.scm +++ b/gn/packages/julia.scm @@ -36,8 +36,7 @@ (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0lm9yhk0mq5cvvkcbsgcjc1y7fzhr8qz2nxn38cy1zdxd8vfknsx")) - (patches (search-patches "julia-visuals-remove-manifests.diff")))) + (base32 "0lm9yhk0mq5cvvkcbsgcjc1y7fzhr8qz2nxn38cy1zdxd8vfknsx")))) (build-system julia-build-system) (arguments `(#:tests? #f ; no test suite @@ -53,6 +52,7 @@ (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/bin")) ;; Copied from the Dockerfile. (for-each (lambda (file) @@ -64,24 +64,22 @@ "runsliderserver.sh" "notebooks" "Project.toml"))))) - (add-after 'install 'skip-julia-cairomakie - (lambda* (#:key outputs #:allow-other-keys) - (with-directory-excursion - (string-append (assoc-ref outputs "out") "/notebooks") - (delete-file "bayes.jl") - (delete-file "disease-testing.jl")))) (add-after 'install 'wrap-program (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) ;; Do we need to wrap this with PYTHONPATH too? (wrap-script (string-append out "/runpluto.sh") + `("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin") + ,(string-append (assoc-ref inputs "coreutils") "/bin"))) + `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH")))) + (wrap-script (string-append out "/runsliderserver.sh") `("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin") ,(string-append (assoc-ref inputs "coreutils") "/bin"))) `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH"))))))) (add-after 'install 'create-runpluto (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) - (with-output-to-file (string-append out "/runpluto") + (with-output-to-file (string-append out "/bin/runpluto") (lambda () (format #t "#!~a --no-auto-compile !# @@ -102,53 +100,64 @@ (getenv "JULIA_LOAD_PATH") (dirname (search-input-file inputs "/bin/yes")) (search-input-file inputs "/bin/julia")))) - (chmod (string-append out "/runpluto") #o555)))) + (chmod (string-append out "/bin/runpluto") #o555)))) (add-after 'install 'create-runsliderserver (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) - (with-output-to-file (string-append out "/runsliderserver") + (with-output-to-file (string-append out "/bin/runsliderserver") (lambda () (format #t "#!~a --no-auto-compile !# (setenv \"JULIA_LOAD_PATH\" \"~a\") (setenv \"PATH\" \"~a\") -(zero? (system* - \"~a\" - \"--optimize=0\" - \"-e\" \"import PlutoSliderServer; - PlutoSliderServer.run_directory( - \\\"~a/notebooks/\\\", - SliderServer_port=4343, - SliderServer_host=\\\"0.0.0.0\\\")\"))\n" +;; First initialise or update the julia registry: +(zero? (system* \"~a\" + \"--optimize=0\" + ;; Used by L1-penalty.jl: + ;; \"-e\" \"import Pkg; Pkg.add(\\\"PlotlyBase\\\")\" + \"-e\" \"import Pkg; Pkg.update()\")) +(zero? (system* \"~a\" + \"--optimize=0\" + \"-e\" \"import PlutoSliderServer; + PlutoSliderServer.run_directory( + \\\"~a/notebooks/\\\", + SliderServer_port=4343, + SliderServer_host=\\\"0.0.0.0\\\")\"))\n" (search-input-file inputs "/bin/guile") (getenv "JULIA_LOAD_PATH") (dirname (search-input-file inputs "/bin/yes")) (search-input-file inputs "/bin/julia") + (search-input-file inputs "/bin/julia") out))) - (chmod (string-append out "/runsliderserver") #o555)))) + (chmod (string-append out "/bin/runsliderserver") #o555)))) (replace 'precompile (lambda _ (invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\"")))))) + #; (propagated-inputs + ;; This doesn't seem to actually be used anywhere `(;; from setup.py ("python-jupyter-server-proxy" ,(@ (gn packages python) python-jupyter-server-proxy-1)))) (inputs + ;; Ideally we'd use more of these packages, but we end up downloading + ;; most of them anyway when the service starts, so we've commented them + ;; out for now. (list ;julia-cairomakie ; 0.8.13 - julia-distributions ; 0.25.76 + ;julia-distributions ; 0.25.76 ;julia-interactiveutils ; stdlib - julia-latexstrings ; 1.3.0 + ;julia-latexstrings ; 1.3.0 ;julia-markdown ; stdlib - julia-optim ; 1.7.2 - julia-plots ; 1.35.3 - julia-pluto ; 0.19.11 + ;julia-optim ; 1.7.2 + ;julia-plots ; 1.35.3 + ;julia-pluto ; 0.19.11 julia-plutosliderserver ; * - julia-plutoui ; 0.7.46 - julia-prettytables ; 2.1.0 - julia-quadgk ; 2.5.0 - julia-roots ; 2.0.3 + ;julia-plutoui ; 0.7.46 + ;julia-prettytables ; 2.1.0 + ;julia-quadgk ; 2.5.0 + ;julia-roots ; 2.0.3 (@ (gnu packages guile) guile-3.0))) ; for wrap-script (home-page "https://github.com/sens/visuals") (synopsis "Visualizations using Pluto.jl notebooks") @@ -339,25 +348,35 @@ distributed computing.") (base32 "0nqlnkh8grxfm8d1mivi7dnrvb31bznj9s540a10d2v396ikfggn")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Some failed tests + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; Something about logpdf fails in both of these test sets. + (substitute* "test/multivariate/dirichlet.jl" + (("\\@testset \"_logpdf\" begin") + "@testset \"_logpdf\" begin return;")) + (substitute* "test/univariate/discrete/negativebinomial.jl" + ;; The negative numbers something something wrong in logpdf. + (("0, 10, 42, -1, -5, -13") "0, 10, 42"))))))) (propagated-inputs - `(("julia-chainrulescore" ,julia-chainrulescore) - ("julia-densityinterface" ,julia-densityinterface) - ("julia-fillarrays" ,julia-fillarrays) - ("julia-pdmats" ,julia-pdmats) - ("julia-quadgk" ,julia-quadgk) - ("julia-specialfunctions" ,julia-specialfunctions) - ("julia-statsbase" ,julia-statsbase) - ("julia-statsfuns" ,julia-statsfuns))) + (list julia-chainrulescore ; 1 + julia-densityinterface ; 0.4 + julia-fillarrays ; 0.9 .. 0.13 + julia-pdmats ; 0.10, 0.11 + julia-quadgk ; 2 + julia-specialfunctions ; 1.2, 2 + julia-statsbase ; 0.32, 0.33 + julia-statsfuns)) ; 0.9.15, 1 (native-inputs - `(("julia-calculus" ,julia-calculus) - ("julia-chainrulestestutils" ,julia-chainrulestestutils) - ("julia-finitedifferences" ,julia-finitedifferences) - ("julia-forwarddiff" ,julia-forwarddiff) - ("julia-json" ,julia-json) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-stablerngs" ,julia-stablerngs) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-calculus + julia-chainrulestestutils + julia-finitedifferences + julia-forwarddiff + julia-json + julia-offsetarrays + julia-stablerngs + julia-staticarrays)) (home-page "https://github.com/JuliaStats/Distributions.jl") (synopsis "Probability distributions and associated functions") (description "Julia package for probability distributions and associated @@ -471,6 +490,26 @@ do the users of your packages!") (description "This package provides a wrapper for the git library.") (license license:expat))) +(define-public julia-glob + (package + (name "julia-glob") + (version "1.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vtjnash/Glob.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05yp7ba3y3pfibs0hy2sp61phb5b6x7aacsjc93i3lz6wmlpj0jx")))) + (build-system julia-build-system) + (home-page "https://github.com/vtjnash/Glob.jl") + (synopsis "Posix-compliant file name pattern matching") + (description "This implementation of Glob is based on the IEEE Std 1003.1, +2004 Edition (Open Group Base Specifications Issue 6) for fnmatch and glob.") + (license license:expat))) + (define-public julia-terminalloggers (package (name "julia-terminalloggers") @@ -689,56 +728,227 @@ densities and objects associated with a density in Julia.") (build-system julia-build-system) (arguments `(#:tests? #f ; for now + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; Decrease the number of tests we're running. + (substitute* "test/runtests.jl" + ((".*VisualRegressionTests.*") "") + ((".*pgfplotsx.*") "") + ((".*plotlyjs.*") "") + )))) )) (propagated-inputs - (list - ;julia-contour - julia-ffmpeg - julia-fixedpointnumbers - julia-gr - julia-geometrybasics - julia-jlfzf - julia-json - ;julia-latexify - julia-measures - julia-nanmath - julia-plotthemes - julia-plotutils - julia-recipesbase - julia-recipespipeline - julia-reexport - julia-relocatablefolders - julia-requires - julia-scratch - julia-showoff - julia-snoopprecompile - julia-statsbase - julia-unicodefun - julia-unzip)) + (list julia-contour + julia-ffmpeg + julia-fixedpointnumbers + julia-gr + julia-geometrybasics + julia-jlfzf + julia-json + ;julia-latexify + julia-measures + julia-nanmath + julia-plotthemes + julia-plotutils + julia-recipesbase + julia-recipespipeline + julia-reexport + julia-relocatablefolders + julia-requires + julia-scratch + julia-showoff + julia-snoopprecompile + julia-statsbase + julia-unicodefun + julia-unzip)) (native-inputs - (list - ;julia-distributions - julia-fileio - ;julia-gtk - ;julia-hdf5 - julia-imagemagick - ;julia-images - julia-offsetarrays - ;julia-pgfplotsx - ;julia-plotlyjs - ;julia-rdatasets - julia-stablerngs - julia-staticarrays - ;julia-statsplots - julia-testimages - ;julia-unicodeplots - ;julia-visualregressiontests - )) + (list julia-aqua + julia-colors + ;julia-conda + julia-distributions + julia-fileio + julia-filepathsbase + ;julia-gaston + julia-geometrybasics + ;julia-gtk + ;julia-hdf5 + julia-imagemagick + ;julia-images + ;julia-inspectdr + julia-offsetarrays + ;julia-pgfplotsx + ;julia-plotlybase + ;julia-plotlyjs + ;julia-plotlykaleido + julia-pycall + julia-pyplot + ;julia-rdatasets + julia-sentinelarrays + julia-stablerngs + julia-staticarrays + ;julia-statsplots + julia-testimages + julia-unicodeplots + julia-unitful + ;julia-visualregressiontests + )) (home-page "http://docs.juliaplots.org/") (synopsis "Powerful convenience for Julia visualizations and data analysis") (description "Plots is a plotting API and toolset.") (license license:expat))) +(define-public julia-contour + (package + (name "julia-contour") + (version "0.5.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGeometry/Contour.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ai6lh5ap9qxhqm2k1pnkfbpm4b95d3v7izhyvrr9cxwbxfjv3vn")))) + (build-system julia-build-system) + (arguments `(#:tests? #f)) ;; FIX ME + (propagated-inputs + (list julia-staticarrays)) + (native-inputs + (list julia-offsetarrays + julia-statsbase)) + (home-page "https://github.com/JuliaGeometry/Contour.jl") + (synopsis "Calculating contour curves for 2D scalar fields in Julia") + (description "This package provides a generic implementation of the +@url{https://en.wikipedia.org/wiki/Marching_squares, marching squares} +algorithm for tracing contour curves on a scalar 2D field.") + (license license:expat))) + +(define-public julia-unicodeplots + (package + (name "julia-unicodeplots") + (version "2.12.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPlots/UnicodePlots.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0plkczznx1297m1lviczkm4873yl29anr5csgyhh9vnvyf1606y2")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; It is unclear why these tests fail and why some + ;; have a suprise dependency on AstroIO (from FileIO) + (substitute* "test/runtests.jl" + ((".*tst_world_age.*") "") + ((".*tst_io.*") "") + ((".*tst_densityplot.*") "")) + (substitute* "test/tst_canvas.jl" + ((".*HeatmapCanvas, \"heatmap\".*") "")) + (substitute* "test/tst_histogram.jl" + (("testset.*keyword.*" all) + (string-append all " return;\n")) + (("testset.*vertical\".*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_barplot.jl" + (("testset.*maximum.*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_spy.jl" + (("testset.*parameters.*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_boxplot.jl" + (("testset.*default.*" all) + (string-append all " return;\n")) + (("testset.*scaling.*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_volume.jl" + (("testset.*cube.*" all) + (string-append all " return;\n")))))))) + (propagated-inputs + (list julia-colortypes + julia-contour + julia-crayons + julia-fileio + julia-freetypeabstraction + julia-lazymodules + julia-marchingcubes + julia-nanmath + julia-staticarrays + julia-statsbase + julia-unitful)) + (native-inputs + (list julia-colortypes + julia-imagemagick + julia-referencetests + julia-stablerngs)) + (home-page "https://github.com/JuliaPlots/UnicodePlots.jl") + (synopsis "Unicode-based scientific plotting for working in the terminal") + (description "Advanced Unicode plotting library designed for use in Julia's REPL.") + (license license:expat))) + +(define-public julia-lazymodules + (package + (name "julia-lazymodules") + (version "0.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/johnnychen94/LazyModules.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11xz0aw5w338pka9jf3r7mfhgm98fnqzsky5ig9z7b996z0m7lpk")))) + (build-system julia-build-system) + (native-inputs + (list julia-colors + julia-offsetarrays)) + (home-page "https://github.com/johnnychen94/LazyModules.jl") + (synopsis "Lazily load Julia modules") + (description "This package provides package developers an alternative +option to delay package loading until used. If some dependency is not used, +then users don't need to pay for its latency.") + (license license:expat))) + +(define-public julia-marchingcubes + (package + (name "julia-marchingcubes") + (version "0.1.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGeometry/MarchingCubes.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14k47lz33j0fiashykf2a8ayiv482k5jkgw0iircw55mdkdrnxc3")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Maybe later + (propagated-inputs + (list julia-precompiletools + julia-staticarrays)) + #; + (native-inputs + (list julia-benchmarktools + julia-geometrybasics + julia-meshes + julia-plyio)) + (home-page "https://github.com/JuliaGeometry/MarchingCubes.jl") + (synopsis "Efficient Implementation of Marching Cubes' Cases with Topological Guarantees") + (description "Julia port of Efficient Implementation of Marching Cubes' Cases with Topological Guarantees.") + (license license:expat))) + (define-public julia-snoopprecompile (package (name "julia-snoopprecompile") @@ -769,6 +979,187 @@ densities and objects associated with a density in Julia.") precompile code needed by your package, particularly on Julia 1.8 and higher.") (license license:expat))) +(define-public julia-snoopcompile + (package + (name "julia-snoopcompile") + (version "1.7.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timholy/SnoopCompile.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xy0y5s7q980fl0kygvjbmn74i3sjpzbizsgvis70gd2fibz80h7")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-test-suite + (lambda _ + ;; This module fails to load its dependencies in the 'check phase. + (substitute* "test/runtests.jl" + ((".*snoopi\\.jl.*") "")) + (substitute* "test/snoopi.jl" + (("testset \"snoopi\" begin") + "testset \"snoopi\" begin return"))))))) + (propagated-inputs + (list julia-snoopcompileanalysis + julia-snoopcompilebot + julia-snoopcompilecore)) + (native-inputs + (list + ;julia-jld + ;julia-matlang + )) + (home-page "https://timholy.github.io/SnoopCompile.jl/dev/") + (synopsis "Making packages work faster with more extensive precompilation") + (description "SnoopCompile observes the Julia compiler, causing it to +record the functions and argument types it's compiling. From these lists of +methods, you can generate lists of @code{precompile} directives that may reduce +the latency between loading packages.") + (license license:expat))) + +(define-public julia-snoopcompileanalysis + (package/inherit julia-snoopcompile + (name "julia-snoopcompileanalysis") + (arguments + (list + #:tests? #f ; No test folder + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopCompileAnalysis")))))) + (propagated-inputs + (list julia-cthulhu + julia-orderedcollections)) + (native-inputs '()) + )) + +(define-public julia-snoopcompilebot + (package/inherit julia-snoopcompile + (name "julia-snoopcompilebot") + (arguments + (list + #:tests? #f ; Tests to be run in SnoopCompile.jl + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopCompileBot")))))) + (propagated-inputs + (list julia-filepathsbase + julia-snoopcompileanalysis + julia-snoopcompilecore + julia-yaml)) + (native-inputs '()) + )) + +(define-public julia-snoopcompilecore + (package/inherit julia-snoopcompile + (name "julia-snoopcompilecore") + (arguments + (list + #:tests? #f ; No test folder + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopCompileCore")))))) + (propagated-inputs '()) + (native-inputs '()) + )) + +(define-public julia-cthulhu + (package + (name "julia-cthulhu") + (version "1.6.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDebug/Cthulhu.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ziax1378kvyzikm4cigg4mq44r085zczqa0mkcbw5g36gcma6qi")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Skip for now + (propagated-inputs + (list julia-codetracking + julia-foldingtrees)) + (native-inputs + (list julia-staticarrays)) + (home-page "https://github.com/JuliaDebug/Cthulhu.jl") + (synopsis "Slow descent into madness") + (description "Cthulhu can help you debug type inference issues by +recursively showing the @code{code_typed} output until you find the exact point +where inference gave up, messed up, or did something unexpected. Using the +Cthulhu interface you can debug type inference problems faster.") + (license license:expat))) + +(define-public julia-codetracking + (package + (name "julia-codetracking") + (version "1.3.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timholy/CodeTracking.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0j6mclc7y1vpib5chj3hkabz9zbmdl76jgcr7314f5kbrdqjybbi")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-test-suite + (lambda _ + (substitute* "test/runtests.jl" + (("test pkgfiles\\(\"Color") + "test_skip pkgfiles\(\"Color"))))))) + (home-page "https://github.com/timholy/CodeTracking.jl") + (synopsis "It's editing-time, do you know where your methods are?") + (description "CodeTracking can be thought of as an extension of Julia's +InteractiveUtils library. It provides an interface for obtaining: +@enumerate +@item the strings and expressions of method definitions +@item the method signatures at a specific file & line number +@item location information for \"dynamic\" code that might have moved since it +was first loaded +@item a list of files that comprise a particular package.@end enumerate") + (license license:expat))) + +(define-public julia-foldingtrees + (package + (name "julia-foldingtrees") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaCollections/FoldingTrees.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1q3w44z1h9j22ykdwwgl8qdm9621m0qqwz4wd2rs2aj0921pdmm4")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-abstracttrees)) + (home-page "https://github.com/JuliaCollections/FoldingTrees.jl") + (synopsis "Dynamic tree structure with control over the accessibility of node children") + (description "FoldingTrees implements a dynamic tree structure in which +some nodes may be \"folded,\" i.e., marked to avoid descent among that node's +children. It also supports interactive text menus based on folding trees.") + (license license:expat))) + (define-public julia-jlfzf (package (name "julia-jlfzf") @@ -1133,6 +1524,192 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (list julia-bufferedstreams julia-json)))) +;; TODO: Unbundle fonts, more? +(define-public julia-makie + (package + (name "julia-makie") + (version "0.17.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/MakieOrg/Makie.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0s9rkfmshl3nz82zkgia6fxmfhz4v26ixam6ybqw8swlshdfijrd")))) + (build-system julia-build-system) + (propagated-inputs + (list ;julia-animations + ;julia-colorbrewer + julia-colorschemes + julia-colortypes + julia-colors + julia-contour + julia-distributions + julia-docstringextensions + julia-ffmpeg + julia-fileio + julia-fixedpointnumbers + julia-formatting + julia-freetype + julia-freetypeabstraction + julia-geometrybasics + ;julia-gridlayout + ;julia-imageio + julia-intervalsets + ;julia-isoband + ;julia-kerneldensity + julia-latexstrings + julia-makiecore + ;julia-match + ;julia-mathtexengine + julia-observables + julia-offsetarrays + ;julia-packing + julia-plotutils + ;julia-polygonops + julia-relocatablefolders + julia-showoff + ;julia-signeddistancefields + julia-statsbase + julia-statsfuns + julia-structarrays + julia-unicodefun)) + (home-page "https://docs.makie.org/stable") + (synopsis "Interactive data visualizations and plotting in Julia") + (description "Makie is a data visualization ecosystem for the Julia +programming language.") + (license license:expat))) + +(define-public julia-makiecore + (package/inherit julia-makie + (name "julia-makiecore") + (version "0.4.0") ; Same source, different version + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "MakieCore")))))) + (propagated-inputs + (list julia-observables)) + (synopsis "Backend core for Makie"))) + +(define-public julia-cairomakie + (package/inherit julia-makie + (name "julia-cairomakie") + (version "0.8.13") ; Same source, different version + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "CairoMakie")))))) + (propagated-inputs + (list ;julia-cairo + julia-colors + ;julia-fftw + julia-fileio + julia-freetype + julia-geometrybasics + julia-makie)) + (synopsis "Cairo Backend for Makie"))) + +(define-public julia-freetype + (package + (name "julia-freetype") + (version "4.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/FreeType.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08kf1x1c7gvllds1ryv6zwy9ai85p50a509ndlcjrkiw31i612m8")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-cenum + julia-freetype2-jll)) + (home-page "https://github.com/JuliaGraphics/FreeType.jl") + (synopsis "FreeType 2 bindings for Julia") + (description "This package provides FreeType bindings for Julia.") + (license license:zlib))) + +(define-public julia-freetypeabstraction + (package + (name "julia-freetypeabstraction") + (version "0.9.9") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/FreeTypeAbstraction.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zqpwysvxjqh5lmsz7lysgyid7xnis23rr0xzn3fwxlncka7dbyl")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Also find fonts in Guix environments. + (substitute* "src/findfonts.jl" + (("\"/usr/share/fonts\"," all) + (string-append all "\n " + "\"/run/current-system/profile/share/fonts\"," + "\n " + "joinpath(get(ENV, \"GUIX_ENVIRONMENT\", homedir())," + "\"share/fonts\")," + "\n " + "joinpath(get(ENV, \"GUIX_PROFILE\", homedir())," + "\"share/fonts\"),") )))))) + (build-system julia-build-system) + (arguments + (list + #:tests? #f ; Can't skip the one test as needed + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'skip-findfont-test + (lambda _ + (substitute* "test/runtests.jl" + ;; Can't make this find font-dejavu + (("@test findfont\\(font") "@test_skip findfont(font"))))))) + (propagated-inputs + (list julia-colorvectorspace + julia-colors + julia-freetype + julia-geometrybasics)) + (home-page "https://github.com/JuliaGraphics/FreeTypeAbstraction.jl") + (synopsis "Julian abstraction layer over FreeType.jl") + (description + "This package provides an abstraction layer over the FreeType Julia module.") + (license license:expat))) + +;; ready to upstream +(define-public julia-observables + (package + (name "julia-observables") + (version "0.5.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGizmos/Observables.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1l0rk60nrwwgcifqs72x76z9dv1kq6rvcbhy63kp27yqfsx6c20s")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaGizmos/Observables.jl") + (synopsis "Observable ref") + (description "This package provides the @code{Observable}s type in Julia, +which are like @code{Ref}s but you can listen to changes.") + (license license:expat))) + (define-public julia-simplebufferstream (package (name "julia-simplebufferstream") @@ -2066,7 +2643,7 @@ that still support Julia versions older than 1.6.") ("julia-fileio" ,julia-fileio) ;("julia-imagefiltering" ,julia-imagefiltering) ("julia-imagemagick" ,julia-imagemagick) - ;("julia-quartzimageio" ,julia-quartzimageio) + ;("julia-quartzimageio" ,julia-quartzimageio) ; for macOS ("julia-requires" ,julia-requires))) ;(native-inputs ; `(;("julia-gtk" ,julia-gtk) diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm index 64e82ac..420e2cf 100644 --- a/gn/services/pluto.scm +++ b/gn/services/pluto.scm @@ -43,33 +43,14 @@ (requirement '(networking)) (modules '((gnu build shepherd) (gnu system file-systems))) - #; - (start #~(make-forkexec-constructor/container - ;(list #$(file-append package "/runpluto.sh") #$port) - ;(list #$(file-append package "/runpluto")) - (list #$(file-append package "/runsliderservice")) - #:log-file "/var/log/pluto.log" - #:user "julia" - #:group "julia" - ;; This prevents the service from using /root as $HOME. - #:environment-variables '() - #:mappings (list (file-system-mapping - (source "/home/jovyan") - (target source) - (writable? #t)) - (file-system-mapping - (source "/etc/ssl") - (target source))))) (start #~(make-forkexec-constructor - ;(list #$(file-append package "/runpluto.sh") #$port) - ;(list #$(file-append package "/runpluto")) - '(#$(file-append package "/runsliderservice")) + '(#$(file-append package "/bin/runsliderserver")) #:log-file "/var/log/pluto.log" #:user "julia" #:group "julia" - ;; This prevents the service from using /root as $HOME. - ;#:environment-variables '() - )) + #:environment-variables + (list "SSL_CERT_DIR=/etc/ssl/certs" + "SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt"))) (stop #~(make-kill-destructor)))))))) (define pluto-service-type diff --git a/julia-visuals-remove-manifests.diff b/julia-visuals-remove-manifests.diff deleted file mode 100644 index 358c42f..0000000 --- a/julia-visuals-remove-manifests.diff +++ /dev/null @@ -1,10151 +0,0 @@ -diff --git a/notebooks/L1-penalty.jl b/notebooks/L1-penalty.jl -index 9f3d64b..7f1c4ee 100644 ---- a/notebooks/L1-penalty.jl -+++ b/notebooks/L1-penalty.jl -@@ -140,1106 +140,6 @@ Plots = "~1.25.4" - PlutoUI = "~0.7.29" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "7e66a529aecc117666fc78bb2f204d6081a02e1c" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.Adapt]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" --uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" --version = "3.4.0" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.ArrayInterfaceCore]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "14c3f84a763848906ac681f94cf469a851601d92" --uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" --version = "0.1.28" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.6" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.CommonSubexpressions]] --deps = ["MacroTools", "Test"] --git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" --uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" --version = "0.3.0" -- --[[deps.Compat]] --deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] --git-tree-sha1 = "78bee250c6826e1cf805a88b7f1e86025275d208" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "3.46.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.ConstructionBase]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" --uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" --version = "1.4.1" -- --[[deps.Contour]] --deps = ["StaticArrays"] --git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.5.7" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.DataValueInterfaces]] --git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" --uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" --version = "1.0.0" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DelimitedFiles]] --deps = ["Mmap"] --uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -- --[[deps.DiffResults]] --deps = ["StaticArraysCore"] --git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" --uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" --version = "1.1.0" -- --[[deps.DiffRules]] --deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] --git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" --uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" --version = "1.12.2" -- --[[deps.Distributed]] --deps = ["Random", "Serialization", "Sockets"] --uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.EarCut_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" --uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" --version = "2.2.4+0" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.Extents]] --git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" --uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" --version = "0.1.1" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FiniteDiff]] --deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] --git-tree-sha1 = "04ed1f0029b6b3af88343e439b995141cb0d0b8d" --uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" --version = "2.17.0" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.ForwardDiff]] --deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] --git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180" --uuid = "f6369f11-7733-5829-9624-2563aa707210" --version = "0.10.34" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.Future]] --deps = ["Random"] --uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -- --[[deps.GLFW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] --git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" --uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" --version = "3.3.8+0" -- --[[deps.GPUArraysCore]] --deps = ["Adapt"] --git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" --uuid = "46192b85-c4d5-4398-a991-12ede77f4527" --version = "0.1.2" -- --[[deps.GR]] --deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] --git-tree-sha1 = "c98aea696662d09e215ef7cda5296024a9646c75" --uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" --version = "0.64.4" -- --[[deps.GR_jll]] --deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" --uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" --version = "0.69.1+0" -- --[[deps.GeoInterface]] --deps = ["Extents"] --git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" --uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" --version = "1.0.1" -- --[[deps.GeometryBasics]] --deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] --git-tree-sha1 = "fe9aea4ed3ec6afdfbeb5a4f39a2208909b162a6" --uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" --version = "0.4.5" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] --git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "0.9.17" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.IterTools]] --git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" --uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" --version = "1.4.0" -- --[[deps.IteratorInterfaceExtensions]] --git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" --uuid = "82899510-4779-5014-852e-03e436cf321d" --version = "1.0.0" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LERC_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" --uuid = "88015f11-f218-50d7-93a8-a6af411a945d" --version = "3.0.0+1" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.Latexify]] --deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] --git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" --uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" --version = "0.15.18" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libglvnd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] --git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" --uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" --version = "1.6.0+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libtiff_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] --git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" --uuid = "89763e89-9b03-5906-acba-b20f662cd828" --version = "4.4.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LineSearches]] --deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] --git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" --uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" --version = "7.2.0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.7" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Measures]] --git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" --uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" --version = "0.3.2" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NLSolversBase]] --deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] --git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" --uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" --version = "7.8.3" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Optim]] --deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] --git-tree-sha1 = "bc0a748740e8bc5eeb9ea6031e6f050de1fc0ba2" --uuid = "429524aa-4258-5aef-a3af-852621145aeb" --version = "1.6.2" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.Parameters]] --deps = ["OrderedCollections", "UnPack"] --git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" --uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" --version = "0.12.3" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.2" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PlotThemes]] --deps = ["PlotUtils", "Requires", "Statistics"] --git-tree-sha1 = "a3a964ce9dc7898193536002a6dd892b1b5a6f1d" --uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" --version = "2.0.1" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.Plots]] --deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] --git-tree-sha1 = "d16070abde61120e01b4f30f6f398496582301d6" --uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" --version = "1.25.12" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.PositiveFactorizations]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" --uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" --version = "0.2.4" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.Qt5Base_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] --git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" --uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" --version = "5.15.3+2" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RecipesBase]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" --uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" --version = "1.3.3" -- --[[deps.RecipesPipeline]] --deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] --git-tree-sha1 = "dc1e451e15d90347a7decc4221842a022b011714" --uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" --version = "0.5.2" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "cdbd3b1338c72ce29d9584fdbe9e9b70eeb5adca" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "0.1.3" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Setfield]] --deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] --git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" --uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" --version = "1.1.1" -- --[[deps.SharedArrays]] --deps = ["Distributed", "Mmap", "Random", "Serialization"] --uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.StaticArrays]] --deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] --git-tree-sha1 = "6954a456979f23d05085727adb17c4551c19ecd1" --uuid = "90137ffa-7385-5640-81b9-e52037218182" --version = "1.5.12" -- --[[deps.StaticArraysCore]] --git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" --uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" --version = "1.4.0" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StructArrays]] --deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] --git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" --uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" --version = "0.6.14" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.TableTraits]] --deps = ["IteratorInterfaceExtensions"] --git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" --uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" --version = "1.0.1" -- --[[deps.Tables]] --deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] --git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" --uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" --version = "1.10.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.UnPack]] --git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" --uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" --version = "1.0.2" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.Unzip]] --git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" --uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" --version = "0.1.2" -- --[[deps.Wayland_jll]] --deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" --uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" --version = "1.21.0+0" -- --[[deps.Wayland_protocols_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" --uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" --version = "1.25.0+0" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXcursor_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" --uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" --version = "1.2.0+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXfixes_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" --uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" --version = "5.0.3+4" -- --[[deps.Xorg_libXi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] --git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" --uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" --version = "1.7.10+4" -- --[[deps.Xorg_libXinerama_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] --git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" --uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" --version = "1.1.4+4" -- --[[deps.Xorg_libXrandr_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" --uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" --version = "1.5.2+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_libxkbfile_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" --uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" --version = "1.1.0+4" -- --[[deps.Xorg_xcb_util_image_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" --uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] --git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" --uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_keysyms_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" --uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_renderutil_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" --uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" --version = "0.3.9+1" -- --[[deps.Xorg_xcb_util_wm_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" --uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" --version = "0.4.1+1" -- --[[deps.Xorg_xkbcomp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] --git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" --uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" --version = "1.4.2+4" -- --[[deps.Xorg_xkeyboard_config_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] --git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" --uuid = "33bec58e-1273-512f-9401-5d533626f822" --version = "2.27.0+4" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.Zstd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" --uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" --version = "1.5.2+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" -- --[[deps.xkbcommon_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] --git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" --uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" --version = "1.4.1+0" --""" -- - # ╔═╡ Cell order: - # ╟─e52889b0-9d46-11eb-33f1-cf0665f314a7 - # ╟─7a97d5bb-9871-454c-a0be-ed54a54aab12 -diff --git a/notebooks/bayes.jl b/notebooks/bayes.jl -index 6a8f571..00c366b 100644 ---- a/notebooks/bayes.jl -+++ b/notebooks/bayes.jl -@@ -234,1315 +234,6 @@ PlutoUI = "~0.7.40" - Roots = "~2.0.3" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "a550497986d35346ecad5959b6be1dacedb1cc51" -- --[[deps.AbstractFFTs]] --deps = ["ChainRulesCore", "LinearAlgebra"] --git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" --uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" --version = "1.2.1" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.AbstractTrees]] --git-tree-sha1 = "5c0b629df8a5566a06f5fef5100b53ea56e465a0" --uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" --version = "0.4.2" -- --[[deps.Adapt]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" --uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" --version = "3.4.0" -- --[[deps.Animations]] --deps = ["Colors"] --git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" --uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" --version = "0.4.1" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Automa]] --deps = ["Printf", "ScanByte", "TranscodingStreams"] --git-tree-sha1 = "d50976f217489ce799e366d9561d56a98a30d7fe" --uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" --version = "0.8.2" -- --[[deps.AxisAlgorithms]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] --git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" --uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" --version = "1.0.1" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.CEnum]] --git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" --uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" --version = "0.4.2" -- --[[deps.Cairo]] --deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] --git-tree-sha1 = "d0b3f8b4ad16cb0a2988c6788646a5e6a17b6b1b" --uuid = "159f3aea-2a34-519c-b102-8c37f9878175" --version = "1.0.5" -- --[[deps.CairoMakie]] --deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "SHA"] --git-tree-sha1 = "387e0102f240244102814cf73fe9fbbad82b9e9e" --uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" --version = "0.8.13" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.Calculus]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" --uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" --version = "0.5.1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "dc4405cee4b2fe9e1108caec2d760b7ea758eca2" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.5" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.CodecZlib]] --deps = ["TranscodingStreams", "Zlib_jll"] --git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" --uuid = "944b1d66-785c-5afd-91f1-9de20f533193" --version = "0.7.0" -- --[[deps.ColorBrewer]] --deps = ["Colors", "JSON", "Test"] --git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4" --uuid = "a2cac450-b92f-5266-8821-25eda20663c8" --version = "0.4.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] --git-tree-sha1 = "1fd869cc3875b57347f7027521f561cf46d1fcd8" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.19.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.9" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.8" -- --[[deps.CommonSolve]] --git-tree-sha1 = "332a332c97c7071600984b3c31d9067e1a4e6e25" --uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" --version = "0.2.1" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "5856d3031cdb1f3b2b6340dfdc66b6d9a149a374" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.2.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.Configurations]] --deps = ["ExproniconLite", "OrderedCollections", "TOML"] --git-tree-sha1 = "62a7c76dbad02fdfdaa53608104edf760938c4ca" --uuid = "5218b696-f38b-4ac9-8b61-a12ec717816d" --version = "0.17.4" -- --[[deps.ConstructionBase]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" --uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" --version = "1.4.1" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.DataAPI]] --git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.10.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.DataValueInterfaces]] --git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" --uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" --version = "1.0.0" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DensityInterface]] --deps = ["InverseFunctions", "Test"] --git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" --uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" --version = "0.4.0" -- --[[deps.Distributed]] --deps = ["Random", "Serialization", "Sockets"] --uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -- --[[deps.Distributions]] --deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] --git-tree-sha1 = "ee407ce31ab2f1bacadc3bd987e96de17e00aed3" --uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" --version = "0.25.71" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "5158c2b41018c5f7eb1470d558127ac274eca0c9" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.1" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.DualNumbers]] --deps = ["Calculus", "NaNMath", "SpecialFunctions"] --git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" --uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" --version = "0.6.8" -- --[[deps.EarCut_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" --uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" --version = "2.2.3+0" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.ExproniconLite]] --git-tree-sha1 = "07b85b02d910f90dde6b383484c5ee6c0f169fa3" --uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" --version = "0.7.0" -- --[[deps.Extents]] --git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" --uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" --version = "0.1.1" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FFTW]] --deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] --git-tree-sha1 = "90630efff0894f8142308e334473eba54c433549" --uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" --version = "1.5.0" -- --[[deps.FFTW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" --uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" --version = "3.3.10+0" -- --[[deps.FileIO]] --deps = ["Pkg", "Requires", "UUIDs"] --git-tree-sha1 = "94f5101b96d2d968ace56f7f2db19d0a5f592e28" --uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" --version = "1.15.0" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "87519eb762f85534445f5cda35be12e32759ee14" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.4" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.FreeType]] --deps = ["CEnum", "FreeType2_jll"] --git-tree-sha1 = "cabd77ab6a6fdff49bfd24af2ebe76e6e018a2b4" --uuid = "b38be410-82b0-50bf-ab77-7b57e271db43" --version = "4.0.0" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FreeTypeAbstraction]] --deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] --git-tree-sha1 = "b5c7fe9cea653443736d264b85466bad8c574f4a" --uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" --version = "0.9.9" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.Future]] --deps = ["Random"] --uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -- --[[deps.FuzzyCompletions]] --deps = ["REPL"] --git-tree-sha1 = "e16dd964b4dfaebcded16b2af32f05e235b354be" --uuid = "fb4132e2-a121-4a70-b8a1-d5b831dcdcc2" --version = "0.5.1" -- --[[deps.GeoInterface]] --deps = ["Extents"] --git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" --uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" --version = "1.0.1" -- --[[deps.GeometryBasics]] --deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] --git-tree-sha1 = "a7a97895780dab1085a97769316aa348830dc991" --uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" --version = "0.4.3" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.68.3+2" -- --[[deps.Graphics]] --deps = ["Colors", "LinearAlgebra", "NaNMath"] --git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" --uuid = "a2bd30eb-e257-5431-a919-1863eab51364" --version = "1.1.2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.GridLayoutBase]] --deps = ["GeometryBasics", "InteractiveUtils", "Observables"] --git-tree-sha1 = "53c7e69a6ffeb26bd594f5a1421b889e7219eeaa" --uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" --version = "0.9.0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] --git-tree-sha1 = "59ba44e0aa49b87a8c7a8920ec76f8afe87ed502" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "1.3.3" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.HypergeometricFunctions]] --deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] --git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" --uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" --version = "0.3.11" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.ImageCore]] --deps = ["AbstractFFTs", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Graphics", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "Reexport"] --git-tree-sha1 = "acf614720ef026d38400b3817614c45882d75500" --uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" --version = "0.9.4" -- --[[deps.ImageIO]] --deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] --git-tree-sha1 = "342f789fd041a55166764c351da1710db97ce0e0" --uuid = "82e4d734-157c-48bb-816b-45c225c6df19" --version = "0.6.6" -- --[[deps.Imath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "87f7662e03a649cffa2e05bf19c303e168732d3e" --uuid = "905a6f67-0a94-5f89-b386-d35d92009cd1" --version = "3.1.2+0" -- --[[deps.IndirectArrays]] --git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f" --uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" --version = "1.0.0" -- --[[deps.Inflate]] --git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" --uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" --version = "0.1.3" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.IntelOpenMP_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "d979e54b71da82f3a65b62553da4fc3d18c9004c" --uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" --version = "2018.0.3+2" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.Interpolations]] --deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] --git-tree-sha1 = "f67b55b6447d36733596aea445a9f119e83498b6" --uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" --version = "0.14.5" -- --[[deps.IntervalSets]] --deps = ["Dates", "Random", "Statistics"] --git-tree-sha1 = "076bb0da51a8c8d1229936a1af7bdfacd65037e1" --uuid = "8197267c-284f-5f27-9208-e0e47529a953" --version = "0.7.2" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.7" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.Isoband]] --deps = ["isoband_jll"] --git-tree-sha1 = "f9b6d97355599074dc867318950adaa6f9946137" --uuid = "f1662d9f-8043-43de-a69a-05efc1cc6ff4" --version = "0.1.1" -- --[[deps.IterTools]] --git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" --uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" --version = "1.4.0" -- --[[deps.IteratorInterfaceExtensions]] --git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" --uuid = "82899510-4779-5014-852e-03e436cf321d" --version = "1.0.0" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo]] --deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] --git-tree-sha1 = "a77b273f1ddec645d1b7c4fd5fb98c8f90ad10a5" --uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0" --version = "0.1.1" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.KernelDensity]] --deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] --git-tree-sha1 = "9816b296736292a80b9a3200eb7fbb57aaa3917a" --uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" --version = "0.6.5" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.LazyArtifacts]] --deps = ["Artifacts", "Pkg"] --uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" -- --[[deps.LazyModules]] --git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e" --uuid = "8cdb02fc-e678-4876-92c5-9defec4f444e" --version = "0.3.1" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "94d9c52ca447e23eac0c0f074effbcd38830deb5" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.18" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.LoggingExtras]] --deps = ["Dates", "Logging"] --git-tree-sha1 = "5d4d2d9904227b8bd66386c1138cf4d5ffa826bf" --uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" --version = "0.4.9" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MKL_jll]] --deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] --git-tree-sha1 = "41d162ae9c868218b1f3fe78cba878aa348c2d26" --uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" --version = "2022.1.0+0" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.9" -- --[[deps.Makie]] --deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "Printf", "Random", "RelocatableFolders", "Serialization", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "UnicodeFun"] --git-tree-sha1 = "b0323393a7190c9bf5b03af442fc115756df8e59" --uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" --version = "0.17.13" -- --[[deps.MakieCore]] --deps = ["Observables"] --git-tree-sha1 = "fbf705d2bdea8fc93f1ae8ca2965d8e03d4ca98c" --uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" --version = "0.4.0" -- --[[deps.MappedArrays]] --git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" --uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" --version = "0.4.1" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.Match]] --git-tree-sha1 = "1d9bc5c1a6e7ee24effb93f175c9342f9154d97f" --uuid = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf" --version = "1.2.0" -- --[[deps.MathTeXEngine]] --deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test"] --git-tree-sha1 = "114ef48a73aea632b8aebcb84f796afcc510ac7c" --uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" --version = "0.4.3" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "ae6676d5f576ccd21b6789c2cbe2ba24fcc8075d" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.5" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.0.2" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MosaicViews]] --deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"] --git-tree-sha1 = "b34e3bc3ca7c94914418637cb10cc4d1d80d877d" --uuid = "e94cdb99-869f-56ef-bcf0-1ae2bcbe0389" --version = "0.3.3" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.MsgPack]] --deps = ["Serialization"] --git-tree-sha1 = "a8cbf066b54d793b9a48c5daa5d586cf2b5bd43d" --uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671" --version = "1.1.0" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.Netpbm]] --deps = ["FileIO", "ImageCore"] --git-tree-sha1 = "18efc06f6ec36a8b801b23f076e3c6ac7c3bf153" --uuid = "f09324ee-3d7c-5217-9330-fc30815ba969" --version = "1.0.2" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Observables]] --git-tree-sha1 = "dfd8d34871bc3ad08cd16026c1828e271d554db9" --uuid = "510215fc-4207-5dde-b226-833fc4488ee2" --version = "0.5.1" -- --[[deps.OffsetArrays]] --deps = ["Adapt"] --git-tree-sha1 = "1ea784113a6aa054c5ebd95945fa5e52c2f378e7" --uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" --version = "1.12.7" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenEXR]] --deps = ["Colors", "FileIO", "OpenEXR_jll"] --git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633" --uuid = "52e1d378-f018-4a11-a4be-720524705ac7" --version = "0.3.2" -- --[[deps.OpenEXR_jll]] --deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "923319661e9a22712f24596ce81c54fc0366f304" --uuid = "18a262bb-aa17-5467-a713-aee519bc75cb" --version = "3.1.1+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.17+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.PCRE_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" --uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" --version = "8.44.0+0" -- --[[deps.PDMats]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" --uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" --version = "0.11.16" -- --[[deps.PNGFiles]] --deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] --git-tree-sha1 = "e925a64b8585aa9f4e3047b8d2cdc3f0e79fd4e4" --uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" --version = "0.3.16" -- --[[deps.Packing]] --deps = ["GeometryBasics"] --git-tree-sha1 = "1155f6f937fa2b94104162f01fa400e192e4272f" --uuid = "19eb6ba3-879d-56ad-ad62-d5c202156566" --version = "0.4.2" -- --[[deps.PaddedViews]] --deps = ["OffsetArrays"] --git-tree-sha1 = "03a7a85b76381a3d04c7a1656039197e70eda03d" --uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" --version = "0.5.11" -- --[[deps.Pango_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a121dfbba67c94a5bec9dde613c3d0cbcf3a12b" --uuid = "36c8627f-9965-5494-a995-c6b170f724f3" --version = "1.50.3+0" -- --[[deps.Parsers]] --deps = ["Dates"] --git-tree-sha1 = "3d5bf43e3e8b412656404ed9466f1dcbf7c50269" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.4.0" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PkgVersion]] --deps = ["Pkg"] --git-tree-sha1 = "f6cf8e7944e50901594838951729a1861e668cb8" --uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" --version = "0.3.2" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "21303256d239f6b484977314674aef4bb1fe4420" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.1" -- --[[deps.Pluto]] --deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "MIMEs", "Markdown", "MsgPack", "Pkg", "PrecompileSignatures", "REPL", "RelocatableFolders", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] --git-tree-sha1 = "c189ae928e2cfc3495b13e85d9e90ddedeac0a4d" --uuid = "c3e4b0f8-55cb-11ea-2926-15256bba5781" --version = "0.19.11" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "Markdown", "Random", "Reexport", "UUIDs"] --git-tree-sha1 = "a602d7b0babfca89005da04d89223b867b55319f" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.40" -- --[[deps.PolygonOps]] --git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" --uuid = "647866c9-e3ac-4575-94e7-e3d426903924" --version = "0.1.2" -- --[[deps.PrecompileSignatures]] --git-tree-sha1 = "18ef344185f25ee9d51d80e179f8dad33dc48eb1" --uuid = "91cefc8d-f054-46dc-8f8c-26e11d7c5411" --version = "3.0.3" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.ProgressMeter]] --deps = ["Distributed", "Printf"] --git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" --uuid = "92933f4c-e287-5a05-a399-4b506db050ca" --version = "1.7.2" -- --[[deps.QOI]] --deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] --git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" --uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65" --version = "1.0.0" -- --[[deps.QuadGK]] --deps = ["DataStructures", "LinearAlgebra"] --git-tree-sha1 = "3c009334f45dfd546a16a57960a821a1a023d241" --uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" --version = "2.5.0" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.Ratios]] --deps = ["Requires"] --git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" --uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" --version = "0.4.3" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "0.3.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.Rmath]] --deps = ["Random", "Rmath_jll"] --git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" --uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" --version = "0.7.0" -- --[[deps.Rmath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" --uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" --version = "0.3.0+0" -- --[[deps.Roots]] --deps = ["CommonSolve", "Printf", "Setfield"] --git-tree-sha1 = "90a03cebb786c568d3c1f0fb2f71dcb26115e13e" --uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" --version = "2.0.3" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.SIMD]] --git-tree-sha1 = "7dbc15af7ed5f751a82bf3ed37757adf76c32402" --uuid = "fdea26ae-647d-5447-a871-4b548cad5224" --version = "3.4.1" -- --[[deps.ScanByte]] --deps = ["Libdl", "SIMD"] --git-tree-sha1 = "2436b15f376005e8790e318329560dcc67188e84" --uuid = "7b38b023-a4d7-4c5e-8d43-3f3097f304eb" --version = "0.3.3" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Setfield]] --deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] --git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" --uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" --version = "1.1.1" -- --[[deps.SharedArrays]] --deps = ["Distributed", "Mmap", "Random", "Serialization"] --uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SignedDistanceFields]] --deps = ["Random", "Statistics", "Test"] --git-tree-sha1 = "d263a08ec505853a5ff1c1ebde2070419e3f28e9" --uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96" --version = "0.4.0" -- --[[deps.SimpleBufferStream]] --git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" --uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" --version = "1.1.0" -- --[[deps.Sixel]] --deps = ["Dates", "FileIO", "ImageCore", "IndirectArrays", "OffsetArrays", "REPL", "libsixel_jll"] --git-tree-sha1 = "8fb59825be681d451c246a795117f317ecbcaa28" --uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47" --version = "0.1.2" -- --[[deps.SnoopPrecompile]] --git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.1" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.0.1" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.StackViews]] --deps = ["OffsetArrays"] --git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c" --uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" --version = "0.1.1" -- --[[deps.StaticArrays]] --deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] --git-tree-sha1 = "efa8acd030667776248eabb054b1836ac81d92f0" --uuid = "90137ffa-7385-5640-81b9-e52037218182" --version = "1.5.7" -- --[[deps.StaticArraysCore]] --git-tree-sha1 = "ec2bd695e905a3c755b33026954b119ea17f2d22" --uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" --version = "1.3.0" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StatsFuns]] --deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] --git-tree-sha1 = "5783b877201a82fc0014cbf381e7e6eb130473a4" --uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" --version = "1.0.1" -- --[[deps.StructArrays]] --deps = ["Adapt", "DataAPI", "StaticArraysCore", "Tables"] --git-tree-sha1 = "8c6ac65ec9ab781af05b08ff305ddc727c25f680" --uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" --version = "0.6.12" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.TableTraits]] --deps = ["IteratorInterfaceExtensions"] --git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" --uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" --version = "1.0.1" -- --[[deps.Tables]] --deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] --git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" --uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" --version = "1.7.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TiffImages]] --deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] --git-tree-sha1 = "70e6d2da9210371c927176cb7a56d41ef1260db7" --uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" --version = "0.6.1" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "8a75929dcd3c38611db2f8d08546decb514fcadf" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.9" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "e59ecc5a41b000fa94423a578d29290c7266fc10" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.0" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.WoodburyMatrices]] --deps = ["LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" --uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" --version = "0.5.5" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.9.14+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.isoband_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" --uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4" --version = "0.2.3+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libsixel_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] --git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" --uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" --version = "1.10.3+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" --""" -- - # ╔═╡ Cell order: - # ╟─c3344b73-51bd-4c59-a987-e0adfcc282ea - # ╟─5bccbb9b-e69f-4c30-93b8-57e2d153c772 -diff --git a/notebooks/clt.jl b/notebooks/clt.jl -index 7082094..a935494 100644 ---- a/notebooks/clt.jl -+++ b/notebooks/clt.jl -@@ -99,1104 +99,6 @@ Plots = "~1.32.1" - PlutoUI = "~0.7.40" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "f7f1b85a50853c5738685f74eb0551bae2ee7108" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.Adapt]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" --uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" --version = "3.4.0" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.BitFlags]] --git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" --uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" --version = "0.1.7" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.Calculus]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" --uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" --version = "0.5.1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.6" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.CodecZlib]] --deps = ["TranscodingStreams", "Zlib_jll"] --git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" --uuid = "944b1d66-785c-5afd-91f1-9de20f533193" --version = "0.7.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.5.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.DataValueInterfaces]] --git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" --uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" --version = "1.0.0" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DelimitedFiles]] --deps = ["Mmap"] --uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -- --[[deps.DensityInterface]] --deps = ["InverseFunctions", "Test"] --git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" --uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" --version = "0.4.0" -- --[[deps.Distributions]] --deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] --git-tree-sha1 = "a7756d098cbabec6b3ac44f369f74915e8cfd70a" --uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" --version = "0.25.79" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.DualNumbers]] --deps = ["Calculus", "NaNMath", "SpecialFunctions"] --git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" --uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" --version = "0.6.8" -- --[[deps.EarCut_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" --uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" --version = "2.2.4+0" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.Extents]] --git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" --uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" --version = "0.1.1" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.GLFW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] --git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" --uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" --version = "3.3.8+0" -- --[[deps.GPUArraysCore]] --deps = ["Adapt"] --git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" --uuid = "46192b85-c4d5-4398-a991-12ede77f4527" --version = "0.1.2" -- --[[deps.GR]] --deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] --git-tree-sha1 = "cf0a9940f250dc3cb6cc6c6821b4bf8a4286cf9c" --uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" --version = "0.66.2" -- --[[deps.GR_jll]] --deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" --uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" --version = "0.69.1+0" -- --[[deps.GeoInterface]] --deps = ["Extents"] --git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" --uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" --version = "1.0.1" -- --[[deps.GeometryBasics]] --deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] --git-tree-sha1 = "fe9aea4ed3ec6afdfbeb5a4f39a2208909b162a6" --uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" --version = "0.4.5" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] --git-tree-sha1 = "fd9861adba6b9ae4b42582032d0936d456c8602d" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "1.6.3" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.HypergeometricFunctions]] --deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] --git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" --uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" --version = "0.3.11" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.IterTools]] --git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" --uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" --version = "1.4.0" -- --[[deps.IteratorInterfaceExtensions]] --git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" --uuid = "82899510-4779-5014-852e-03e436cf321d" --version = "1.0.0" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LERC_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" --uuid = "88015f11-f218-50d7-93a8-a6af411a945d" --version = "3.0.0+1" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.Latexify]] --deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] --git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" --uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" --version = "0.15.18" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libglvnd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] --git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" --uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" --version = "1.6.0+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libtiff_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] --git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" --uuid = "89763e89-9b03-5906-acba-b20f662cd828" --version = "4.4.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.LoggingExtras]] --deps = ["Dates", "Logging"] --git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" --uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" --version = "1.0.0" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.7" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Measures]] --git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" --uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" --version = "0.3.2" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL]] --deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] --git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" --uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" --version = "1.3.2" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.PDMats]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" --uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" --version = "0.11.16" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.2" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PlotThemes]] --deps = ["PlotUtils", "Statistics"] --git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" --uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" --version = "3.1.0" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.Plots]] --deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] --git-tree-sha1 = "e9cab2c5e3b7be152ad6241d2011718838a99a27" --uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" --version = "1.32.1" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.Qt5Base_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] --git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" --uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" --version = "5.15.3+2" -- --[[deps.QuadGK]] --deps = ["DataStructures", "LinearAlgebra"] --git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" --uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" --version = "2.6.0" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RecipesBase]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" --uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" --version = "1.3.3" -- --[[deps.RecipesPipeline]] --deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] --git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" --uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" --version = "0.6.11" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "0.3.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.Rmath]] --deps = ["Random", "Rmath_jll"] --git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" --uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" --version = "0.7.0" -- --[[deps.Rmath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" --uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" --version = "0.3.0+0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SimpleBufferStream]] --git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" --uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" --version = "1.1.0" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.StaticArrays]] --deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] --git-tree-sha1 = "6954a456979f23d05085727adb17c4551c19ecd1" --uuid = "90137ffa-7385-5640-81b9-e52037218182" --version = "1.5.12" -- --[[deps.StaticArraysCore]] --git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" --uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" --version = "1.4.0" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StatsFuns]] --deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] --git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" --uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" --version = "1.1.1" -- --[[deps.StructArrays]] --deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] --git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" --uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" --version = "0.6.14" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.TableTraits]] --deps = ["IteratorInterfaceExtensions"] --git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" --uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" --version = "1.0.1" -- --[[deps.Tables]] --deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] --git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" --uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" --version = "1.10.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.11" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.Unzip]] --git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" --uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" --version = "0.2.0" -- --[[deps.Wayland_jll]] --deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" --uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" --version = "1.21.0+0" -- --[[deps.Wayland_protocols_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" --uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" --version = "1.25.0+0" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXcursor_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" --uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" --version = "1.2.0+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXfixes_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" --uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" --version = "5.0.3+4" -- --[[deps.Xorg_libXi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] --git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" --uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" --version = "1.7.10+4" -- --[[deps.Xorg_libXinerama_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] --git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" --uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" --version = "1.1.4+4" -- --[[deps.Xorg_libXrandr_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" --uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" --version = "1.5.2+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_libxkbfile_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" --uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" --version = "1.1.0+4" -- --[[deps.Xorg_xcb_util_image_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" --uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] --git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" --uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_keysyms_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" --uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_renderutil_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" --uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" --version = "0.3.9+1" -- --[[deps.Xorg_xcb_util_wm_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" --uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" --version = "0.4.1+1" -- --[[deps.Xorg_xkbcomp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] --git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" --uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" --version = "1.4.2+4" -- --[[deps.Xorg_xkeyboard_config_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] --git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" --uuid = "33bec58e-1273-512f-9401-5d533626f822" --version = "2.27.0+4" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.Zstd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" --uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" --version = "1.5.2+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" -- --[[deps.xkbcommon_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] --git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" --uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" --version = "1.4.1+0" --""" -- - # ╔═╡ Cell order: - # ╟─ef2627bc-30a7-11ed-29fb-395b23c794b4 - # ╟─b9eb712a-0329-49ba-9409-d5c5a155c112 -diff --git a/notebooks/disease-testing.jl b/notebooks/disease-testing.jl -index b5fd722..4aa5c4a 100644 ---- a/notebooks/disease-testing.jl -+++ b/notebooks/disease-testing.jl -@@ -154,1257 +154,6 @@ Distributions = "~0.25.75" - PlutoUI = "~0.7.43" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "fcf69300a3d26809fba645c97b613b229d740f40" -- --[[deps.AbstractFFTs]] --deps = ["ChainRulesCore", "LinearAlgebra"] --git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" --uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" --version = "1.2.1" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.AbstractTrees]] --git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" --uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" --version = "0.4.4" -- --[[deps.Adapt]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "0310e08cb19f5da31d08341c6120c047598f5b9c" --uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" --version = "3.5.0" -- --[[deps.Animations]] --deps = ["Colors"] --git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" --uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" --version = "0.4.1" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Automa]] --deps = ["Printf", "ScanByte", "TranscodingStreams"] --git-tree-sha1 = "d50976f217489ce799e366d9561d56a98a30d7fe" --uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" --version = "0.8.2" -- --[[deps.AxisAlgorithms]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] --git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" --uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" --version = "1.0.1" -- --[[deps.AxisArrays]] --deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] --git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" --uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" --version = "0.4.6" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.CEnum]] --git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" --uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" --version = "0.4.2" -- --[[deps.Cairo]] --deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] --git-tree-sha1 = "d0b3f8b4ad16cb0a2988c6788646a5e6a17b6b1b" --uuid = "159f3aea-2a34-519c-b102-8c37f9878175" --version = "1.0.5" -- --[[deps.CairoMakie]] --deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "SHA"] --git-tree-sha1 = "387e0102f240244102814cf73fe9fbbad82b9e9e" --uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" --version = "0.8.13" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.Calculus]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" --uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" --version = "0.5.1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.7" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.ColorBrewer]] --deps = ["Colors", "JSON", "Test"] --git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4" --uuid = "a2cac450-b92f-5266-8821-25eda20663c8" --version = "0.4.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.5.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.DataValueInterfaces]] --git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" --uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" --version = "1.0.0" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DensityInterface]] --deps = ["InverseFunctions", "Test"] --git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" --uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" --version = "0.4.0" -- --[[deps.Distributed]] --deps = ["Random", "Serialization", "Sockets"] --uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -- --[[deps.Distributions]] --deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] --git-tree-sha1 = "74911ad88921455c6afcad1eefa12bd7b1724631" --uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" --version = "0.25.80" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.DualNumbers]] --deps = ["Calculus", "NaNMath", "SpecialFunctions"] --git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" --uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" --version = "0.6.8" -- --[[deps.EarCut_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" --uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" --version = "2.2.4+0" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.Extents]] --git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" --uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" --version = "0.1.1" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FFTW]] --deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] --git-tree-sha1 = "90630efff0894f8142308e334473eba54c433549" --uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" --version = "1.5.0" -- --[[deps.FFTW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" --uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" --version = "3.3.10+0" -- --[[deps.FileIO]] --deps = ["Pkg", "Requires", "UUIDs"] --git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" --uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" --version = "1.16.0" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.FreeType]] --deps = ["CEnum", "FreeType2_jll"] --git-tree-sha1 = "cabd77ab6a6fdff49bfd24af2ebe76e6e018a2b4" --uuid = "b38be410-82b0-50bf-ab77-7b57e271db43" --version = "4.0.0" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FreeTypeAbstraction]] --deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] --git-tree-sha1 = "b5c7fe9cea653443736d264b85466bad8c574f4a" --uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" --version = "0.9.9" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.GPUArraysCore]] --deps = ["Adapt"] --git-tree-sha1 = "57f7cde02d7a53c9d1d28443b9f11ac5fbe7ebc9" --uuid = "46192b85-c4d5-4398-a991-12ede77f4527" --version = "0.1.3" -- --[[deps.GeoInterface]] --deps = ["Extents"] --git-tree-sha1 = "e07a1b98ed72e3cdd02c6ceaab94b8a606faca40" --uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" --version = "1.2.1" -- --[[deps.GeometryBasics]] --deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] --git-tree-sha1 = "fe9aea4ed3ec6afdfbeb5a4f39a2208909b162a6" --uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" --version = "0.4.5" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphics]] --deps = ["Colors", "LinearAlgebra", "NaNMath"] --git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" --uuid = "a2bd30eb-e257-5431-a919-1863eab51364" --version = "1.1.2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.GridLayoutBase]] --deps = ["GeometryBasics", "InteractiveUtils", "Observables"] --git-tree-sha1 = "678d136003ed5bceaab05cf64519e3f956ffa4ba" --uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" --version = "0.9.1" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.HypergeometricFunctions]] --deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] --git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" --uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" --version = "0.3.11" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.ImageAxes]] --deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] --git-tree-sha1 = "c54b581a83008dc7f292e205f4c409ab5caa0f04" --uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac" --version = "0.6.10" -- --[[deps.ImageBase]] --deps = ["ImageCore", "Reexport"] --git-tree-sha1 = "b51bb8cae22c66d0f6357e3bcb6363145ef20835" --uuid = "c817782e-172a-44cc-b673-b171935fbb9e" --version = "0.1.5" -- --[[deps.ImageCore]] --deps = ["AbstractFFTs", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Graphics", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "Reexport"] --git-tree-sha1 = "acf614720ef026d38400b3817614c45882d75500" --uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" --version = "0.9.4" -- --[[deps.ImageIO]] --deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] --git-tree-sha1 = "342f789fd041a55166764c351da1710db97ce0e0" --uuid = "82e4d734-157c-48bb-816b-45c225c6df19" --version = "0.6.6" -- --[[deps.ImageMetadata]] --deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"] --git-tree-sha1 = "36cbaebed194b292590cba2593da27b34763804a" --uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49" --version = "0.9.8" -- --[[deps.Imath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "87f7662e03a649cffa2e05bf19c303e168732d3e" --uuid = "905a6f67-0a94-5f89-b386-d35d92009cd1" --version = "3.1.2+0" -- --[[deps.IndirectArrays]] --git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f" --uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" --version = "1.0.0" -- --[[deps.Inflate]] --git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" --uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" --version = "0.1.3" -- --[[deps.IntelOpenMP_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "d979e54b71da82f3a65b62553da4fc3d18c9004c" --uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" --version = "2018.0.3+2" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.Interpolations]] --deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] --git-tree-sha1 = "721ec2cf720536ad005cb38f50dbba7b02419a15" --uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" --version = "0.14.7" -- --[[deps.IntervalSets]] --deps = ["Dates", "Random", "Statistics"] --git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" --uuid = "8197267c-284f-5f27-9208-e0e47529a953" --version = "0.7.4" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.Isoband]] --deps = ["isoband_jll"] --git-tree-sha1 = "f9b6d97355599074dc867318950adaa6f9946137" --uuid = "f1662d9f-8043-43de-a69a-05efc1cc6ff4" --version = "0.1.1" -- --[[deps.IterTools]] --git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" --uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" --version = "1.4.0" -- --[[deps.IteratorInterfaceExtensions]] --git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" --uuid = "82899510-4779-5014-852e-03e436cf321d" --version = "1.0.0" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo]] --deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] --git-tree-sha1 = "a77b273f1ddec645d1b7c4fd5fb98c8f90ad10a5" --uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0" --version = "0.1.1" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.KernelDensity]] --deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] --git-tree-sha1 = "9816b296736292a80b9a3200eb7fbb57aaa3917a" --uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" --version = "0.6.5" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.LazyArtifacts]] --deps = ["Artifacts", "Pkg"] --uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" -- --[[deps.LazyModules]] --git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e" --uuid = "8cdb02fc-e678-4876-92c5-9defec4f444e" --version = "0.3.1" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MKL_jll]] --deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] --git-tree-sha1 = "2ce8695e1e699b68702c03402672a69f54b8aca9" --uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" --version = "2022.2.0+0" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Makie]] --deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "Printf", "Random", "RelocatableFolders", "Serialization", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "UnicodeFun"] --git-tree-sha1 = "b0323393a7190c9bf5b03af442fc115756df8e59" --uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" --version = "0.17.13" -- --[[deps.MakieCore]] --deps = ["Observables"] --git-tree-sha1 = "fbf705d2bdea8fc93f1ae8ca2965d8e03d4ca98c" --uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" --version = "0.4.0" -- --[[deps.MappedArrays]] --git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" --uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" --version = "0.4.1" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.Match]] --git-tree-sha1 = "1d9bc5c1a6e7ee24effb93f175c9342f9154d97f" --uuid = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf" --version = "1.2.0" -- --[[deps.MathTeXEngine]] --deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test"] --git-tree-sha1 = "114ef48a73aea632b8aebcb84f796afcc510ac7c" --uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" --version = "0.4.3" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MosaicViews]] --deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"] --git-tree-sha1 = "7b86a5d4d70a9f5cdf2dacb3cbe6d251d1a61dbe" --uuid = "e94cdb99-869f-56ef-bcf0-1ae2bcbe0389" --version = "0.3.4" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.Netpbm]] --deps = ["FileIO", "ImageCore", "ImageMetadata"] --git-tree-sha1 = "5ae7ca23e13855b3aba94550f26146c01d259267" --uuid = "f09324ee-3d7c-5217-9330-fc30815ba969" --version = "1.1.0" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Observables]] --git-tree-sha1 = "6862738f9796b3edc1c09d0890afce4eca9e7e93" --uuid = "510215fc-4207-5dde-b226-833fc4488ee2" --version = "0.5.4" -- --[[deps.OffsetArrays]] --deps = ["Adapt"] --git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64" --uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" --version = "1.12.8" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenEXR]] --deps = ["Colors", "FileIO", "OpenEXR_jll"] --git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633" --uuid = "52e1d378-f018-4a11-a4be-720524705ac7" --version = "0.3.2" -- --[[deps.OpenEXR_jll]] --deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "923319661e9a22712f24596ce81c54fc0366f304" --uuid = "18a262bb-aa17-5467-a713-aee519bc75cb" --version = "3.1.1+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.PDMats]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" --uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" --version = "0.11.16" -- --[[deps.PNGFiles]] --deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] --git-tree-sha1 = "f809158b27eba0c18c269cf2a2be6ed751d3e81d" --uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" --version = "0.3.17" -- --[[deps.Packing]] --deps = ["GeometryBasics"] --git-tree-sha1 = "1155f6f937fa2b94104162f01fa400e192e4272f" --uuid = "19eb6ba3-879d-56ad-ad62-d5c202156566" --version = "0.4.2" -- --[[deps.PaddedViews]] --deps = ["OffsetArrays"] --git-tree-sha1 = "03a7a85b76381a3d04c7a1656039197e70eda03d" --uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" --version = "0.5.11" -- --[[deps.Pango_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "84a314e3926ba9ec66ac097e3635e270986b0f10" --uuid = "36c8627f-9965-5494-a995-c6b170f724f3" --version = "1.50.9+0" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "8175fc2b118a3755113c8e68084dc1a9e63c61ee" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.3" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PkgVersion]] --deps = ["Pkg"] --git-tree-sha1 = "f6cf8e7944e50901594838951729a1861e668cb8" --uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" --version = "0.3.2" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.PolygonOps]] --git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" --uuid = "647866c9-e3ac-4575-94e7-e3d426903924" --version = "0.1.2" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.ProgressMeter]] --deps = ["Distributed", "Printf"] --git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" --uuid = "92933f4c-e287-5a05-a399-4b506db050ca" --version = "1.7.2" -- --[[deps.QOI]] --deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] --git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" --uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65" --version = "1.0.0" -- --[[deps.QuadGK]] --deps = ["DataStructures", "LinearAlgebra"] --git-tree-sha1 = "de191bc385072cc6c7ed3ffdc1caeed3f22c74d4" --uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" --version = "2.7.0" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RangeArrays]] --git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" --uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d" --version = "0.3.2" -- --[[deps.Ratios]] --deps = ["Requires"] --git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" --uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" --version = "0.4.3" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "0.3.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.Rmath]] --deps = ["Random", "Rmath_jll"] --git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" --uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" --version = "0.7.0" -- --[[deps.Rmath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" --uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" --version = "0.3.0+0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.SIMD]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "8b20084a97b004588125caebf418d8cab9e393d1" --uuid = "fdea26ae-647d-5447-a871-4b548cad5224" --version = "3.4.4" -- --[[deps.ScanByte]] --deps = ["Libdl", "SIMD"] --git-tree-sha1 = "2436b15f376005e8790e318329560dcc67188e84" --uuid = "7b38b023-a4d7-4c5e-8d43-3f3097f304eb" --version = "0.3.3" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.SharedArrays]] --deps = ["Distributed", "Mmap", "Random", "Serialization"] --uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SignedDistanceFields]] --deps = ["Random", "Statistics", "Test"] --git-tree-sha1 = "d263a08ec505853a5ff1c1ebde2070419e3f28e9" --uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96" --version = "0.4.0" -- --[[deps.SimpleTraits]] --deps = ["InteractiveUtils", "MacroTools"] --git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" --uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" --version = "0.9.4" -- --[[deps.Sixel]] --deps = ["Dates", "FileIO", "ImageCore", "IndirectArrays", "OffsetArrays", "REPL", "libsixel_jll"] --git-tree-sha1 = "8fb59825be681d451c246a795117f317ecbcaa28" --uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47" --version = "0.1.2" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.StackViews]] --deps = ["OffsetArrays"] --git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c" --uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" --version = "0.1.1" -- --[[deps.StaticArrays]] --deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] --git-tree-sha1 = "6954a456979f23d05085727adb17c4551c19ecd1" --uuid = "90137ffa-7385-5640-81b9-e52037218182" --version = "1.5.12" -- --[[deps.StaticArraysCore]] --git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" --uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" --version = "1.4.0" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StatsFuns]] --deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] --git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" --uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" --version = "1.1.1" -- --[[deps.StructArrays]] --deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] --git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" --uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" --version = "0.6.14" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.TableTraits]] --deps = ["IteratorInterfaceExtensions"] --git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" --uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" --version = "1.0.1" -- --[[deps.Tables]] --deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] --git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" --uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" --version = "1.10.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TiffImages]] --deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] --git-tree-sha1 = "7e6b0e3e571be0b4dd4d2a9a3a83b65c04351ccc" --uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" --version = "0.6.3" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.11" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.WoodburyMatrices]] --deps = ["LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" --uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" --version = "0.5.5" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.isoband_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" --uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4" --version = "0.2.3+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libsixel_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] --git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" --uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" --version = "1.10.3+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" --""" -- - # ╔═╡ Cell order: - # ╟─c3344b73-51bd-4c59-a987-e0adfcc282ea - # ╟─1b945a07-252b-429f-bc29-437bb05ed1e8 -diff --git a/notebooks/distributions.jl b/notebooks/distributions.jl -index 7d5cdf3..825217b 100644 ---- a/notebooks/distributions.jl -+++ b/notebooks/distributions.jl -@@ -184,1042 +184,6 @@ Plots = "~1.35.3" - PlutoUI = "~0.7.46" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "1e5fc33b5ad2e4f9ca4a46023babec60a0a73f0a" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.BitFlags]] --git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" --uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" --version = "0.1.7" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.Calculus]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" --uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" --version = "0.5.1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.6" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.CodecZlib]] --deps = ["TranscodingStreams", "Zlib_jll"] --git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" --uuid = "944b1d66-785c-5afd-91f1-9de20f533193" --version = "0.7.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.5.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DelimitedFiles]] --deps = ["Mmap"] --uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -- --[[deps.DensityInterface]] --deps = ["InverseFunctions", "Test"] --git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" --uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" --version = "0.4.0" -- --[[deps.Distributions]] --deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] --git-tree-sha1 = "a7756d098cbabec6b3ac44f369f74915e8cfd70a" --uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" --version = "0.25.79" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.DualNumbers]] --deps = ["Calculus", "NaNMath", "SpecialFunctions"] --git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" --uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" --version = "0.6.8" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.GLFW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] --git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" --uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" --version = "3.3.8+0" -- --[[deps.GR]] --deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] --git-tree-sha1 = "00a9d4abadc05b9476e937a5557fcce476b9e547" --uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" --version = "0.69.5" -- --[[deps.GR_jll]] --deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" --uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" --version = "0.69.1+0" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] --git-tree-sha1 = "fd9861adba6b9ae4b42582032d0936d456c8602d" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "1.6.3" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.HypergeometricFunctions]] --deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] --git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" --uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" --version = "0.3.11" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.JLFzf]] --deps = ["Pipe", "REPL", "Random", "fzf_jll"] --git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" --uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" --version = "0.1.5" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LERC_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" --uuid = "88015f11-f218-50d7-93a8-a6af411a945d" --version = "3.0.0+1" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.Latexify]] --deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] --git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" --uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" --version = "0.15.18" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libglvnd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] --git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" --uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" --version = "1.6.0+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libtiff_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] --git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" --uuid = "89763e89-9b03-5906-acba-b20f662cd828" --version = "4.4.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.LoggingExtras]] --deps = ["Dates", "Logging"] --git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" --uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" --version = "1.0.0" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.7" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Measures]] --git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" --uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" --version = "0.3.2" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL]] --deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] --git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" --uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" --version = "1.3.2" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.PDMats]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" --uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" --version = "0.11.16" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.2" -- --[[deps.Pipe]] --git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" --uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" --version = "1.3.0" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PlotThemes]] --deps = ["PlotUtils", "Statistics"] --git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" --uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" --version = "3.1.0" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.Plots]] --deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] --git-tree-sha1 = "b434dce10c0290ab22cb941a9d72c470f304c71d" --uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" --version = "1.35.8" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.Qt5Base_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] --git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" --uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" --version = "5.15.3+2" -- --[[deps.QuadGK]] --deps = ["DataStructures", "LinearAlgebra"] --git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" --uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" --version = "2.6.0" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RecipesBase]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" --uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" --version = "1.3.3" -- --[[deps.RecipesPipeline]] --deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] --git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" --uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" --version = "0.6.11" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "1.0.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.Rmath]] --deps = ["Random", "Rmath_jll"] --git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" --uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" --version = "0.7.0" -- --[[deps.Rmath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" --uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" --version = "0.3.0+0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SimpleBufferStream]] --git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" --uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" --version = "1.1.0" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StatsFuns]] --deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] --git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" --uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" --version = "1.1.1" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.11" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.Unzip]] --git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" --uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" --version = "0.2.0" -- --[[deps.Wayland_jll]] --deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" --uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" --version = "1.21.0+0" -- --[[deps.Wayland_protocols_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" --uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" --version = "1.25.0+0" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXcursor_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" --uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" --version = "1.2.0+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXfixes_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" --uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" --version = "5.0.3+4" -- --[[deps.Xorg_libXi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] --git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" --uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" --version = "1.7.10+4" -- --[[deps.Xorg_libXinerama_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] --git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" --uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" --version = "1.1.4+4" -- --[[deps.Xorg_libXrandr_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" --uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" --version = "1.5.2+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_libxkbfile_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" --uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" --version = "1.1.0+4" -- --[[deps.Xorg_xcb_util_image_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" --uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] --git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" --uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_keysyms_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" --uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_renderutil_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" --uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" --version = "0.3.9+1" -- --[[deps.Xorg_xcb_util_wm_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" --uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" --version = "0.4.1+1" -- --[[deps.Xorg_xkbcomp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] --git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" --uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" --version = "1.4.2+4" -- --[[deps.Xorg_xkeyboard_config_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] --git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" --uuid = "33bec58e-1273-512f-9401-5d533626f822" --version = "2.27.0+4" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.Zstd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" --uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" --version = "1.5.2+0" -- --[[deps.fzf_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" --uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" --version = "0.29.0+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" -- --[[deps.xkbcommon_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] --git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" --uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" --version = "1.4.1+0" --""" -- - # ╔═╡ Cell order: - # ╟─5e5914fa-c9e7-4dec-a9a8-d6ba15d0a90c - # ╟─8229f9da-4f0f-11ed-1349-ef269c9c2704 -diff --git a/notebooks/flips.jl b/notebooks/flips.jl -index 7a7bc4c..27a9581 100644 ---- a/notebooks/flips.jl -+++ b/notebooks/flips.jl -@@ -126,1063 +126,6 @@ PlutoUI = "~0.7.40" - PrettyTables = "~2.1.0" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "f8f2952378978d7572c9df3a8a9013b9291d03b8" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.BitFlags]] --git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" --uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" --version = "0.1.7" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.Calculus]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" --uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" --version = "0.5.1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.6" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.CodecZlib]] --deps = ["TranscodingStreams", "Zlib_jll"] --git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" --uuid = "944b1d66-785c-5afd-91f1-9de20f533193" --version = "0.7.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.5.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.Crayons]] --git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" --uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" --version = "4.1.1" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.DataValueInterfaces]] --git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" --uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" --version = "1.0.0" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DelimitedFiles]] --deps = ["Mmap"] --uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -- --[[deps.DensityInterface]] --deps = ["InverseFunctions", "Test"] --git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" --uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" --version = "0.4.0" -- --[[deps.Distributions]] --deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] --git-tree-sha1 = "a7756d098cbabec6b3ac44f369f74915e8cfd70a" --uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" --version = "0.25.79" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.DualNumbers]] --deps = ["Calculus", "NaNMath", "SpecialFunctions"] --git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" --uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" --version = "0.6.8" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.GLFW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] --git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" --uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" --version = "3.3.8+0" -- --[[deps.GR]] --deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] --git-tree-sha1 = "cf0a9940f250dc3cb6cc6c6821b4bf8a4286cf9c" --uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" --version = "0.66.2" -- --[[deps.GR_jll]] --deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" --uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" --version = "0.69.1+0" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] --git-tree-sha1 = "fd9861adba6b9ae4b42582032d0936d456c8602d" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "1.6.3" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.HypergeometricFunctions]] --deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] --git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" --uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" --version = "0.3.11" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.IteratorInterfaceExtensions]] --git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" --uuid = "82899510-4779-5014-852e-03e436cf321d" --version = "1.0.0" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LERC_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" --uuid = "88015f11-f218-50d7-93a8-a6af411a945d" --version = "3.0.0+1" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.Latexify]] --deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] --git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" --uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" --version = "0.15.18" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libglvnd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] --git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" --uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" --version = "1.6.0+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libtiff_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] --git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" --uuid = "89763e89-9b03-5906-acba-b20f662cd828" --version = "4.4.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.LoggingExtras]] --deps = ["Dates", "Logging"] --git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" --uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" --version = "1.0.0" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.7" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Measures]] --git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" --uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" --version = "0.3.2" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL]] --deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] --git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" --uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" --version = "1.3.2" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.PDMats]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" --uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" --version = "0.11.16" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.2" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PlotThemes]] --deps = ["PlotUtils", "Statistics"] --git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" --uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" --version = "3.1.0" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.Plots]] --deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] --git-tree-sha1 = "6062b3b25ad3c58e817df0747fc51518b9110e5f" --uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" --version = "1.33.0" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.PrettyTables]] --deps = ["Crayons", "Formatting", "Markdown", "Reexport", "StringManipulation", "Tables"] --git-tree-sha1 = "460d9e154365e058c4d886f6f7d6df5ffa1ea80e" --uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" --version = "2.1.2" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.Qt5Base_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] --git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" --uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" --version = "5.15.3+2" -- --[[deps.QuadGK]] --deps = ["DataStructures", "LinearAlgebra"] --git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" --uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" --version = "2.6.0" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RecipesBase]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" --uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" --version = "1.3.3" -- --[[deps.RecipesPipeline]] --deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] --git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" --uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" --version = "0.6.11" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "0.3.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.Rmath]] --deps = ["Random", "Rmath_jll"] --git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" --uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" --version = "0.7.0" -- --[[deps.Rmath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" --uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" --version = "0.3.0+0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SimpleBufferStream]] --git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" --uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" --version = "1.1.0" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StatsFuns]] --deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] --git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" --uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" --version = "1.1.1" -- --[[deps.StringManipulation]] --git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" --uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" --version = "0.3.0" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.TableTraits]] --deps = ["IteratorInterfaceExtensions"] --git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" --uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" --version = "1.0.1" -- --[[deps.Tables]] --deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] --git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" --uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" --version = "1.10.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.11" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.Unzip]] --git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" --uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" --version = "0.2.0" -- --[[deps.Wayland_jll]] --deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" --uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" --version = "1.21.0+0" -- --[[deps.Wayland_protocols_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" --uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" --version = "1.25.0+0" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXcursor_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" --uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" --version = "1.2.0+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXfixes_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" --uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" --version = "5.0.3+4" -- --[[deps.Xorg_libXi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] --git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" --uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" --version = "1.7.10+4" -- --[[deps.Xorg_libXinerama_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] --git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" --uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" --version = "1.1.4+4" -- --[[deps.Xorg_libXrandr_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" --uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" --version = "1.5.2+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_libxkbfile_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" --uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" --version = "1.1.0+4" -- --[[deps.Xorg_xcb_util_image_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" --uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] --git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" --uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_keysyms_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" --uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_renderutil_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" --uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" --version = "0.3.9+1" -- --[[deps.Xorg_xcb_util_wm_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" --uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" --version = "0.4.1+1" -- --[[deps.Xorg_xkbcomp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] --git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" --uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" --version = "1.4.2+4" -- --[[deps.Xorg_xkeyboard_config_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] --git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" --uuid = "33bec58e-1273-512f-9401-5d533626f822" --version = "2.27.0+4" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.Zstd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" --uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" --version = "1.5.2+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" -- --[[deps.xkbcommon_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] --git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" --uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" --version = "1.4.1+0" --""" -- - # ╔═╡ Cell order: - # ╟─7bb5a5cf-e386-440a-9310-f72d95a38c43 - # ╟─8c45a6ca-80c4-4066-8b5f-6fb28182e768 -diff --git a/notebooks/power.jl b/notebooks/power.jl -index b0071a3..7af3786 100644 ---- a/notebooks/power.jl -+++ b/notebooks/power.jl -@@ -113,1042 +113,6 @@ Plots = "~1.35.2" - PlutoUI = "~0.7.43" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "d0db1733794fa43ca17555e440a1f90b9300a02c" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.BitFlags]] --git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" --uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" --version = "0.1.7" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.Calculus]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" --uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" --version = "0.5.1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.6" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.CodecZlib]] --deps = ["TranscodingStreams", "Zlib_jll"] --git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" --uuid = "944b1d66-785c-5afd-91f1-9de20f533193" --version = "0.7.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.5.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DelimitedFiles]] --deps = ["Mmap"] --uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -- --[[deps.DensityInterface]] --deps = ["InverseFunctions", "Test"] --git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" --uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" --version = "0.4.0" -- --[[deps.Distributions]] --deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] --git-tree-sha1 = "a7756d098cbabec6b3ac44f369f74915e8cfd70a" --uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" --version = "0.25.79" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.DualNumbers]] --deps = ["Calculus", "NaNMath", "SpecialFunctions"] --git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" --uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" --version = "0.6.8" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.GLFW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] --git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" --uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" --version = "3.3.8+0" -- --[[deps.GR]] --deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] --git-tree-sha1 = "00a9d4abadc05b9476e937a5557fcce476b9e547" --uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" --version = "0.69.5" -- --[[deps.GR_jll]] --deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" --uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" --version = "0.69.1+0" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] --git-tree-sha1 = "fd9861adba6b9ae4b42582032d0936d456c8602d" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "1.6.3" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.HypergeometricFunctions]] --deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] --git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" --uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" --version = "0.3.11" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.JLFzf]] --deps = ["Pipe", "REPL", "Random", "fzf_jll"] --git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" --uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" --version = "0.1.5" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LERC_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" --uuid = "88015f11-f218-50d7-93a8-a6af411a945d" --version = "3.0.0+1" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.Latexify]] --deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] --git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" --uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" --version = "0.15.18" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libglvnd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] --git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" --uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" --version = "1.6.0+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libtiff_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] --git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" --uuid = "89763e89-9b03-5906-acba-b20f662cd828" --version = "4.4.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.LoggingExtras]] --deps = ["Dates", "Logging"] --git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" --uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" --version = "1.0.0" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.7" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Measures]] --git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" --uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" --version = "0.3.2" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL]] --deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] --git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" --uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" --version = "1.3.2" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.PDMats]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" --uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" --version = "0.11.16" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.2" -- --[[deps.Pipe]] --git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" --uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" --version = "1.3.0" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PlotThemes]] --deps = ["PlotUtils", "Statistics"] --git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" --uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" --version = "3.1.0" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.Plots]] --deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] --git-tree-sha1 = "b434dce10c0290ab22cb941a9d72c470f304c71d" --uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" --version = "1.35.8" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.Qt5Base_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] --git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" --uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" --version = "5.15.3+2" -- --[[deps.QuadGK]] --deps = ["DataStructures", "LinearAlgebra"] --git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" --uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" --version = "2.6.0" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RecipesBase]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" --uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" --version = "1.3.3" -- --[[deps.RecipesPipeline]] --deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] --git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" --uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" --version = "0.6.11" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "1.0.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.Rmath]] --deps = ["Random", "Rmath_jll"] --git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" --uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" --version = "0.7.0" -- --[[deps.Rmath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" --uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" --version = "0.3.0+0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SimpleBufferStream]] --git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" --uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" --version = "1.1.0" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StatsFuns]] --deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] --git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" --uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" --version = "1.1.1" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.11" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.Unzip]] --git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" --uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" --version = "0.2.0" -- --[[deps.Wayland_jll]] --deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" --uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" --version = "1.21.0+0" -- --[[deps.Wayland_protocols_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" --uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" --version = "1.25.0+0" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXcursor_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" --uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" --version = "1.2.0+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXfixes_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" --uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" --version = "5.0.3+4" -- --[[deps.Xorg_libXi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] --git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" --uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" --version = "1.7.10+4" -- --[[deps.Xorg_libXinerama_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] --git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" --uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" --version = "1.1.4+4" -- --[[deps.Xorg_libXrandr_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" --uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" --version = "1.5.2+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_libxkbfile_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" --uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" --version = "1.1.0+4" -- --[[deps.Xorg_xcb_util_image_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" --uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] --git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" --uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_keysyms_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" --uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_renderutil_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" --uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" --version = "0.3.9+1" -- --[[deps.Xorg_xcb_util_wm_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" --uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" --version = "0.4.1+1" -- --[[deps.Xorg_xkbcomp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] --git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" --uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" --version = "1.4.2+4" -- --[[deps.Xorg_xkeyboard_config_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] --git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" --uuid = "33bec58e-1273-512f-9401-5d533626f822" --version = "2.27.0+4" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.Zstd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" --uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" --version = "1.5.2+0" -- --[[deps.fzf_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" --uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" --version = "0.29.0+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" -- --[[deps.xkbcommon_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] --git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" --uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" --version = "1.4.1+0" --""" -- - # ╔═╡ Cell order: - # ╟─33afb7f3-e52a-4f49-8be2-8634c66db010 - # ╟─1d5602ee-5f7b-42ec-b8e0-c9f2bd2c5b94 -diff --git a/notebooks/prox.jl b/notebooks/prox.jl -index 22de773..4ad70ae 100644 ---- a/notebooks/prox.jl -+++ b/notebooks/prox.jl -@@ -184,1135 +184,6 @@ Plots = "~1.32.1" - PlutoUI = "~0.7.40" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "b18bb334f7da6eec2d52e8fadc201d8c164e838d" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.Adapt]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" --uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" --version = "3.4.0" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.ArrayInterfaceCore]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "14c3f84a763848906ac681f94cf469a851601d92" --uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" --version = "0.1.28" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.BitFlags]] --git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" --uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" --version = "0.1.7" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.6" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.CodecZlib]] --deps = ["TranscodingStreams", "Zlib_jll"] --git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" --uuid = "944b1d66-785c-5afd-91f1-9de20f533193" --version = "0.7.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.CommonSubexpressions]] --deps = ["MacroTools", "Test"] --git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" --uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" --version = "0.3.0" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.5.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.ConstructionBase]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" --uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" --version = "1.4.1" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.DataValueInterfaces]] --git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" --uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" --version = "1.0.0" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DelimitedFiles]] --deps = ["Mmap"] --uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -- --[[deps.DiffResults]] --deps = ["StaticArraysCore"] --git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" --uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" --version = "1.1.0" -- --[[deps.DiffRules]] --deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] --git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" --uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" --version = "1.12.2" -- --[[deps.Distributed]] --deps = ["Random", "Serialization", "Sockets"] --uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.EarCut_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" --uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" --version = "2.2.4+0" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.Extents]] --git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" --uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" --version = "0.1.1" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FiniteDiff]] --deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] --git-tree-sha1 = "04ed1f0029b6b3af88343e439b995141cb0d0b8d" --uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" --version = "2.17.0" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.ForwardDiff]] --deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] --git-tree-sha1 = "a69dd6db8a809f78846ff259298678f0d6212180" --uuid = "f6369f11-7733-5829-9624-2563aa707210" --version = "0.10.34" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.Future]] --deps = ["Random"] --uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -- --[[deps.GLFW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] --git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" --uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" --version = "3.3.8+0" -- --[[deps.GPUArraysCore]] --deps = ["Adapt"] --git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" --uuid = "46192b85-c4d5-4398-a991-12ede77f4527" --version = "0.1.2" -- --[[deps.GR]] --deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] --git-tree-sha1 = "cf0a9940f250dc3cb6cc6c6821b4bf8a4286cf9c" --uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" --version = "0.66.2" -- --[[deps.GR_jll]] --deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" --uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" --version = "0.69.1+0" -- --[[deps.GeoInterface]] --deps = ["Extents"] --git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" --uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" --version = "1.0.1" -- --[[deps.GeometryBasics]] --deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] --git-tree-sha1 = "fe9aea4ed3ec6afdfbeb5a4f39a2208909b162a6" --uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" --version = "0.4.5" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] --git-tree-sha1 = "fd9861adba6b9ae4b42582032d0936d456c8602d" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "1.6.3" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.IterTools]] --git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" --uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" --version = "1.4.0" -- --[[deps.IteratorInterfaceExtensions]] --git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" --uuid = "82899510-4779-5014-852e-03e436cf321d" --version = "1.0.0" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LERC_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" --uuid = "88015f11-f218-50d7-93a8-a6af411a945d" --version = "3.0.0+1" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.Latexify]] --deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] --git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" --uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" --version = "0.15.18" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libglvnd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] --git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" --uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" --version = "1.6.0+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libtiff_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] --git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" --uuid = "89763e89-9b03-5906-acba-b20f662cd828" --version = "4.4.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LineSearches]] --deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] --git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" --uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" --version = "7.2.0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.LoggingExtras]] --deps = ["Dates", "Logging"] --git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" --uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" --version = "1.0.0" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.7" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Measures]] --git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" --uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" --version = "0.3.2" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NLSolversBase]] --deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] --git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" --uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" --version = "7.8.3" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL]] --deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] --git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" --uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" --version = "1.3.2" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Optim]] --deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] --git-tree-sha1 = "1903afc76b7d01719d9c30d3c7d501b61db96721" --uuid = "429524aa-4258-5aef-a3af-852621145aeb" --version = "1.7.4" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.Parameters]] --deps = ["OrderedCollections", "UnPack"] --git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" --uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" --version = "0.12.3" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.2" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PlotThemes]] --deps = ["PlotUtils", "Statistics"] --git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" --uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" --version = "3.1.0" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.Plots]] --deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] --git-tree-sha1 = "e9cab2c5e3b7be152ad6241d2011718838a99a27" --uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" --version = "1.32.1" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.PositiveFactorizations]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" --uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" --version = "0.2.4" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.Qt5Base_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] --git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" --uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" --version = "5.15.3+2" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RecipesBase]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" --uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" --version = "1.3.3" -- --[[deps.RecipesPipeline]] --deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] --git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" --uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" --version = "0.6.11" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "0.3.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Setfield]] --deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] --git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" --uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" --version = "1.1.1" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SimpleBufferStream]] --git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" --uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" --version = "1.1.0" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.StaticArrays]] --deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] --git-tree-sha1 = "6954a456979f23d05085727adb17c4551c19ecd1" --uuid = "90137ffa-7385-5640-81b9-e52037218182" --version = "1.5.12" -- --[[deps.StaticArraysCore]] --git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" --uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" --version = "1.4.0" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StructArrays]] --deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] --git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" --uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" --version = "0.6.14" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.TableTraits]] --deps = ["IteratorInterfaceExtensions"] --git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" --uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" --version = "1.0.1" -- --[[deps.Tables]] --deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] --git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" --uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" --version = "1.10.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.11" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.UnPack]] --git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" --uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" --version = "1.0.2" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.Unzip]] --git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" --uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" --version = "0.2.0" -- --[[deps.Wayland_jll]] --deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" --uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" --version = "1.21.0+0" -- --[[deps.Wayland_protocols_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" --uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" --version = "1.25.0+0" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXcursor_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" --uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" --version = "1.2.0+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXfixes_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" --uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" --version = "5.0.3+4" -- --[[deps.Xorg_libXi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] --git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" --uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" --version = "1.7.10+4" -- --[[deps.Xorg_libXinerama_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] --git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" --uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" --version = "1.1.4+4" -- --[[deps.Xorg_libXrandr_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" --uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" --version = "1.5.2+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_libxkbfile_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" --uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" --version = "1.1.0+4" -- --[[deps.Xorg_xcb_util_image_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" --uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] --git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" --uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_keysyms_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" --uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_renderutil_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" --uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" --version = "0.3.9+1" -- --[[deps.Xorg_xcb_util_wm_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" --uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" --version = "0.4.1+1" -- --[[deps.Xorg_xkbcomp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] --git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" --uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" --version = "1.4.2+4" -- --[[deps.Xorg_xkeyboard_config_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] --git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" --uuid = "33bec58e-1273-512f-9401-5d533626f822" --version = "2.27.0+4" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.Zstd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" --uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" --version = "1.5.2+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" -- --[[deps.xkbcommon_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] --git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" --uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" --version = "1.4.1+0" --""" -- - # ╔═╡ Cell order: - # ╟─b216d222-3405-4f51-94f5-d5079c77fe9f - # ╟─0633f88f-e899-4170-badd-396c4cea3080 -diff --git a/notebooks/roc.jl b/notebooks/roc.jl -index f68bc58..597617a 100644 ---- a/notebooks/roc.jl -+++ b/notebooks/roc.jl -@@ -110,1042 +110,6 @@ PlutoUI = "~0.7.43" - QuadGK = "~2.5.0" - """ - --# ╔═╡ 00000000-0000-0000-0000-000000000002 --PLUTO_MANIFEST_TOML_CONTENTS = """ --# This file is machine-generated - editing it directly is not advised -- --julia_version = "1.8.1" --manifest_format = "2.0" --project_hash = "1db4060f32e52842c4aea9a25ec7e67e23aa69ed" -- --[[deps.AbstractPlutoDingetjes]] --deps = ["Pkg"] --git-tree-sha1 = "8eaf9f1b4921132a4cff3f36a1d9ba923b14a481" --uuid = "6e696c72-6542-2067-7265-42206c756150" --version = "1.1.4" -- --[[deps.ArgTools]] --uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" --version = "1.1.1" -- --[[deps.Artifacts]] --uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -- --[[deps.Base64]] --uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -- --[[deps.BitFlags]] --git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" --uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" --version = "0.1.7" -- --[[deps.Bzip2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" --uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" --version = "1.0.8+0" -- --[[deps.Cairo_jll]] --deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" --uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" --version = "1.16.1+1" -- --[[deps.Calculus]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" --uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" --version = "0.5.1" -- --[[deps.ChainRulesCore]] --deps = ["Compat", "LinearAlgebra", "SparseArrays"] --git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" --uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" --version = "1.15.6" -- --[[deps.ChangesOfVariables]] --deps = ["ChainRulesCore", "LinearAlgebra", "Test"] --git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" --uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" --version = "0.1.4" -- --[[deps.CodecZlib]] --deps = ["TranscodingStreams", "Zlib_jll"] --git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" --uuid = "944b1d66-785c-5afd-91f1-9de20f533193" --version = "0.7.0" -- --[[deps.ColorSchemes]] --deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] --git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" --uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" --version = "3.20.0" -- --[[deps.ColorTypes]] --deps = ["FixedPointNumbers", "Random"] --git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" --uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" --version = "0.11.4" -- --[[deps.ColorVectorSpace]] --deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] --git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" --uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" --version = "0.9.10" -- --[[deps.Colors]] --deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] --git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" --uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" --version = "0.12.10" -- --[[deps.Compat]] --deps = ["Dates", "LinearAlgebra", "UUIDs"] --git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" --uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" --version = "4.5.0" -- --[[deps.CompilerSupportLibraries_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" --version = "0.5.2+0" -- --[[deps.Contour]] --git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" --uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" --version = "0.6.2" -- --[[deps.DataAPI]] --git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" --uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" --version = "1.14.0" -- --[[deps.DataStructures]] --deps = ["Compat", "InteractiveUtils", "OrderedCollections"] --git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" --uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" --version = "0.18.13" -- --[[deps.Dates]] --deps = ["Printf"] --uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -- --[[deps.DelimitedFiles]] --deps = ["Mmap"] --uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -- --[[deps.DensityInterface]] --deps = ["InverseFunctions", "Test"] --git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" --uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" --version = "0.4.0" -- --[[deps.Distributions]] --deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] --git-tree-sha1 = "a7756d098cbabec6b3ac44f369f74915e8cfd70a" --uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" --version = "0.25.79" -- --[[deps.DocStringExtensions]] --deps = ["LibGit2"] --git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" --uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" --version = "0.9.3" -- --[[deps.Downloads]] --deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] --uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" --version = "1.6.0" -- --[[deps.DualNumbers]] --deps = ["Calculus", "NaNMath", "SpecialFunctions"] --git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" --uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" --version = "0.6.8" -- --[[deps.Expat_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" --uuid = "2e619515-83b5-522b-bb60-26c02a35a201" --version = "2.4.8+0" -- --[[deps.FFMPEG]] --deps = ["FFMPEG_jll"] --git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" --uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" --version = "0.4.1" -- --[[deps.FFMPEG_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] --git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" --uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" --version = "4.4.2+2" -- --[[deps.FileWatching]] --uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -- --[[deps.FillArrays]] --deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] --git-tree-sha1 = "9a0472ec2f5409db243160a8b030f94c380167a3" --uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" --version = "0.13.6" -- --[[deps.FixedPointNumbers]] --deps = ["Statistics"] --git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" --uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" --version = "0.8.4" -- --[[deps.Fontconfig_jll]] --deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" --uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" --version = "2.13.93+0" -- --[[deps.Formatting]] --deps = ["Printf"] --git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" --uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" --version = "0.4.2" -- --[[deps.FreeType2_jll]] --deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" --uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" --version = "2.10.4+0" -- --[[deps.FriBidi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" --uuid = "559328eb-81f9-559d-9380-de523a88c83c" --version = "1.0.10+0" -- --[[deps.GLFW_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] --git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" --uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" --version = "3.3.8+0" -- --[[deps.GR]] --deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] --git-tree-sha1 = "00a9d4abadc05b9476e937a5557fcce476b9e547" --uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" --version = "0.69.5" -- --[[deps.GR_jll]] --deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] --git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" --uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" --version = "0.69.1+0" -- --[[deps.Gettext_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" --uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" --version = "0.21.0+0" -- --[[deps.Glib_jll]] --deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" --uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" --version = "2.74.0+2" -- --[[deps.Graphite2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" --uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" --version = "1.3.14+0" -- --[[deps.Grisu]] --git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" --uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" --version = "1.0.2" -- --[[deps.HTTP]] --deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] --git-tree-sha1 = "fd9861adba6b9ae4b42582032d0936d456c8602d" --uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" --version = "1.6.3" -- --[[deps.HarfBuzz_jll]] --deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] --git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" --uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" --version = "2.8.1+1" -- --[[deps.HypergeometricFunctions]] --deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] --git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" --uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" --version = "0.3.11" -- --[[deps.Hyperscript]] --deps = ["Test"] --git-tree-sha1 = "8d511d5b81240fc8e6802386302675bdf47737b9" --uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" --version = "0.0.4" -- --[[deps.HypertextLiteral]] --deps = ["Tricks"] --git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" --uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" --version = "0.9.4" -- --[[deps.IOCapture]] --deps = ["Logging", "Random"] --git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" --uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" --version = "0.2.2" -- --[[deps.IniFile]] --git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" --uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" --version = "0.5.1" -- --[[deps.InteractiveUtils]] --deps = ["Markdown"] --uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -- --[[deps.InverseFunctions]] --deps = ["Test"] --git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" --uuid = "3587e190-3f89-42d0-90ee-14403ec27112" --version = "0.1.8" -- --[[deps.IrrationalConstants]] --git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" --uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" --version = "0.1.1" -- --[[deps.JLFzf]] --deps = ["Pipe", "REPL", "Random", "fzf_jll"] --git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" --uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" --version = "0.1.5" -- --[[deps.JLLWrappers]] --deps = ["Preferences"] --git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" --uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" --version = "1.4.1" -- --[[deps.JSON]] --deps = ["Dates", "Mmap", "Parsers", "Unicode"] --git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" --uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" --version = "0.21.3" -- --[[deps.JpegTurbo_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" --uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" --version = "2.1.2+0" -- --[[deps.LAME_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" --uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" --version = "3.100.1+0" -- --[[deps.LERC_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" --uuid = "88015f11-f218-50d7-93a8-a6af411a945d" --version = "3.0.0+1" -- --[[deps.LZO_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" --uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" --version = "2.10.1+0" -- --[[deps.LaTeXStrings]] --git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" --uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" --version = "1.3.0" -- --[[deps.Latexify]] --deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] --git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" --uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" --version = "0.15.18" -- --[[deps.LibCURL]] --deps = ["LibCURL_jll", "MozillaCACerts_jll"] --uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" --version = "0.6.3" -- --[[deps.LibCURL_jll]] --deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] --uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" --version = "7.84.0+0" -- --[[deps.LibGit2]] --deps = ["Base64", "NetworkOptions", "Printf", "SHA"] --uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -- --[[deps.LibSSH2_jll]] --deps = ["Artifacts", "Libdl", "MbedTLS_jll"] --uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" --version = "1.10.2+0" -- --[[deps.Libdl]] --uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -- --[[deps.Libffi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" --uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" --version = "3.2.2+1" -- --[[deps.Libgcrypt_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] --git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" --uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" --version = "1.8.7+0" -- --[[deps.Libglvnd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] --git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" --uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" --version = "1.6.0+0" -- --[[deps.Libgpg_error_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" --uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" --version = "1.42.0+0" -- --[[deps.Libiconv_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" --uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" --version = "1.16.1+2" -- --[[deps.Libmount_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" --uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" --version = "2.35.0+0" -- --[[deps.Libtiff_jll]] --deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] --git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" --uuid = "89763e89-9b03-5906-acba-b20f662cd828" --version = "4.4.0+0" -- --[[deps.Libuuid_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" --uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" --version = "2.36.0+0" -- --[[deps.LinearAlgebra]] --deps = ["Libdl", "libblastrampoline_jll"] --uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -- --[[deps.LogExpFunctions]] --deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] --git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239" --uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" --version = "0.3.19" -- --[[deps.Logging]] --uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -- --[[deps.LoggingExtras]] --deps = ["Dates", "Logging"] --git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" --uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" --version = "1.0.0" -- --[[deps.MIMEs]] --git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" --uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" --version = "0.1.4" -- --[[deps.MacroTools]] --deps = ["Markdown", "Random"] --git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" --uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" --version = "0.5.10" -- --[[deps.Markdown]] --deps = ["Base64"] --uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -- --[[deps.MbedTLS]] --deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] --git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" --uuid = "739be429-bea8-5141-9913-cc70e7f3736d" --version = "1.1.7" -- --[[deps.MbedTLS_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" --version = "2.28.0+0" -- --[[deps.Measures]] --git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" --uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" --version = "0.3.2" -- --[[deps.Missings]] --deps = ["DataAPI"] --git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" --uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" --version = "1.1.0" -- --[[deps.Mmap]] --uuid = "a63ad114-7e13-5084-954f-fe012c677804" -- --[[deps.MozillaCACerts_jll]] --uuid = "14a3606d-f60d-562e-9121-12d972cd8159" --version = "2022.2.1" -- --[[deps.NaNMath]] --deps = ["OpenLibm_jll"] --git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" --uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" --version = "1.0.1" -- --[[deps.NetworkOptions]] --uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" --version = "1.2.0" -- --[[deps.Ogg_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" --uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" --version = "1.3.5+1" -- --[[deps.OpenBLAS_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] --uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" --version = "0.3.20+0" -- --[[deps.OpenLibm_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "05823500-19ac-5b8b-9628-191a04bc5112" --version = "0.8.1+0" -- --[[deps.OpenSSL]] --deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] --git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" --uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" --version = "1.3.2" -- --[[deps.OpenSSL_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" --uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" --version = "1.1.19+0" -- --[[deps.OpenSpecFun_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" --uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" --version = "0.5.5+0" -- --[[deps.Opus_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" --uuid = "91d4177d-7536-5919-b921-800302f37372" --version = "1.3.2+0" -- --[[deps.OrderedCollections]] --git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" --uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" --version = "1.4.1" -- --[[deps.PCRE2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" --version = "10.40.0+0" -- --[[deps.PDMats]] --deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] --git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" --uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" --version = "0.11.16" -- --[[deps.Parsers]] --deps = ["Dates", "SnoopPrecompile"] --git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" --uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" --version = "2.5.2" -- --[[deps.Pipe]] --git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" --uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" --version = "1.3.0" -- --[[deps.Pixman_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" --uuid = "30392449-352a-5448-841d-b1acce4e97dc" --version = "0.40.1+0" -- --[[deps.Pkg]] --deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] --uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" --version = "1.8.0" -- --[[deps.PlotThemes]] --deps = ["PlotUtils", "Statistics"] --git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" --uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" --version = "3.1.0" -- --[[deps.PlotUtils]] --deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] --git-tree-sha1 = "5b7690dd212e026bbab1860016a6601cb077ab66" --uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" --version = "1.3.2" -- --[[deps.Plots]] --deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] --git-tree-sha1 = "b434dce10c0290ab22cb941a9d72c470f304c71d" --uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" --version = "1.35.8" -- --[[deps.PlutoUI]] --deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] --git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6" --uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" --version = "0.7.49" -- --[[deps.Preferences]] --deps = ["TOML"] --git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" --uuid = "21216c6a-2e73-6563-6e65-726566657250" --version = "1.3.0" -- --[[deps.Printf]] --deps = ["Unicode"] --uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -- --[[deps.Qt5Base_jll]] --deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] --git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" --uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" --version = "5.15.3+2" -- --[[deps.QuadGK]] --deps = ["DataStructures", "LinearAlgebra"] --git-tree-sha1 = "3c009334f45dfd546a16a57960a821a1a023d241" --uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" --version = "2.5.0" -- --[[deps.REPL]] --deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] --uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -- --[[deps.Random]] --deps = ["SHA", "Serialization"] --uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -- --[[deps.RecipesBase]] --deps = ["SnoopPrecompile"] --git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" --uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" --version = "1.3.3" -- --[[deps.RecipesPipeline]] --deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] --git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" --uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" --version = "0.6.11" -- --[[deps.Reexport]] --git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" --uuid = "189a3867-3050-52da-a836-e630ba90ab69" --version = "1.2.2" -- --[[deps.RelocatableFolders]] --deps = ["SHA", "Scratch"] --git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" --uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" --version = "1.0.0" -- --[[deps.Requires]] --deps = ["UUIDs"] --git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" --uuid = "ae029012-a4dd-5104-9daa-d747884805df" --version = "1.3.0" -- --[[deps.Rmath]] --deps = ["Random", "Rmath_jll"] --git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" --uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" --version = "0.7.0" -- --[[deps.Rmath_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" --uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" --version = "0.3.0+0" -- --[[deps.SHA]] --uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" --version = "0.7.0" -- --[[deps.Scratch]] --deps = ["Dates"] --git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd" --uuid = "6c6a2e73-6563-6170-7368-637461726353" --version = "1.1.1" -- --[[deps.Serialization]] --uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -- --[[deps.Showoff]] --deps = ["Dates", "Grisu"] --git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" --uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" --version = "1.0.3" -- --[[deps.SimpleBufferStream]] --git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" --uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" --version = "1.1.0" -- --[[deps.SnoopPrecompile]] --deps = ["Preferences"] --git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" --uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" --version = "1.0.3" -- --[[deps.Sockets]] --uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -- --[[deps.SortingAlgorithms]] --deps = ["DataStructures"] --git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" --uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" --version = "1.1.0" -- --[[deps.SparseArrays]] --deps = ["LinearAlgebra", "Random"] --uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -- --[[deps.SpecialFunctions]] --deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] --git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" --uuid = "276daf66-3868-5448-9aa4-cd146d93841b" --version = "2.1.7" -- --[[deps.Statistics]] --deps = ["LinearAlgebra", "SparseArrays"] --uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -- --[[deps.StatsAPI]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" --uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" --version = "1.5.0" -- --[[deps.StatsBase]] --deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] --git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" --uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" --version = "0.33.21" -- --[[deps.StatsFuns]] --deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] --git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932" --uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" --version = "1.1.1" -- --[[deps.SuiteSparse]] --deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] --uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -- --[[deps.TOML]] --deps = ["Dates"] --uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" --version = "1.0.0" -- --[[deps.Tar]] --deps = ["ArgTools", "SHA"] --uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" --version = "1.10.0" -- --[[deps.TensorCore]] --deps = ["LinearAlgebra"] --git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" --uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" --version = "0.1.1" -- --[[deps.Test]] --deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] --uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -- --[[deps.TranscodingStreams]] --deps = ["Random", "Test"] --git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" --uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" --version = "0.9.11" -- --[[deps.Tricks]] --git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" --uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" --version = "0.1.6" -- --[[deps.URIs]] --git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348" --uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" --version = "1.4.1" -- --[[deps.UUIDs]] --deps = ["Random", "SHA"] --uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -- --[[deps.Unicode]] --uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -- --[[deps.UnicodeFun]] --deps = ["REPL"] --git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" --uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" --version = "0.4.1" -- --[[deps.Unzip]] --git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" --uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" --version = "0.2.0" -- --[[deps.Wayland_jll]] --deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] --git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" --uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" --version = "1.21.0+0" -- --[[deps.Wayland_protocols_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da" --uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" --version = "1.25.0+0" -- --[[deps.XML2_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] --git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" --uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" --version = "2.10.3+0" -- --[[deps.XSLT_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] --git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" --uuid = "aed1982a-8fda-507f-9586-7b0439959a61" --version = "1.1.34+0" -- --[[deps.Xorg_libX11_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] --git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" --uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" --version = "1.6.9+4" -- --[[deps.Xorg_libXau_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" --uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" --version = "1.0.9+4" -- --[[deps.Xorg_libXcursor_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" --uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" --version = "1.2.0+4" -- --[[deps.Xorg_libXdmcp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" --uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" --version = "1.1.3+4" -- --[[deps.Xorg_libXext_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" --uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" --version = "1.3.4+4" -- --[[deps.Xorg_libXfixes_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" --uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" --version = "5.0.3+4" -- --[[deps.Xorg_libXi_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] --git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" --uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" --version = "1.7.10+4" -- --[[deps.Xorg_libXinerama_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] --git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" --uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" --version = "1.1.4+4" -- --[[deps.Xorg_libXrandr_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] --git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" --uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" --version = "1.5.2+4" -- --[[deps.Xorg_libXrender_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" --uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" --version = "0.9.10+4" -- --[[deps.Xorg_libpthread_stubs_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" --uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" --version = "0.1.0+3" -- --[[deps.Xorg_libxcb_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] --git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" --uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" --version = "1.13.0+3" -- --[[deps.Xorg_libxkbfile_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] --git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" --uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" --version = "1.1.0+4" -- --[[deps.Xorg_xcb_util_image_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" --uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] --git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" --uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_keysyms_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" --uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" --version = "0.4.0+1" -- --[[deps.Xorg_xcb_util_renderutil_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" --uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" --version = "0.3.9+1" -- --[[deps.Xorg_xcb_util_wm_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] --git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" --uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" --version = "0.4.1+1" -- --[[deps.Xorg_xkbcomp_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] --git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" --uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" --version = "1.4.2+4" -- --[[deps.Xorg_xkeyboard_config_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] --git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" --uuid = "33bec58e-1273-512f-9401-5d533626f822" --version = "2.27.0+4" -- --[[deps.Xorg_xtrans_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" --uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" --version = "1.4.0+3" -- --[[deps.Zlib_jll]] --deps = ["Libdl"] --uuid = "83775a58-1f1d-513f-b197-d71354ab007a" --version = "1.2.12+3" -- --[[deps.Zstd_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" --uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" --version = "1.5.2+0" -- --[[deps.fzf_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" --uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" --version = "0.29.0+0" -- --[[deps.libaom_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" --uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" --version = "3.4.0+0" -- --[[deps.libass_jll]] --deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" --uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" --version = "0.15.1+0" -- --[[deps.libblastrampoline_jll]] --deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] --uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" --version = "5.1.1+0" -- --[[deps.libfdk_aac_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" --uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" --version = "2.0.2+0" -- --[[deps.libpng_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] --git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" --uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" --version = "1.6.38+0" -- --[[deps.libvorbis_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] --git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" --uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" --version = "1.3.7+1" -- --[[deps.nghttp2_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" --version = "1.48.0+0" -- --[[deps.p7zip_jll]] --deps = ["Artifacts", "Libdl"] --uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" --version = "17.4.0+0" -- --[[deps.x264_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" --uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" --version = "2021.5.5+0" -- --[[deps.x265_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] --git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" --uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" --version = "3.5.0+0" -- --[[deps.xkbcommon_jll]] --deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] --git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" --uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" --version = "1.4.1+0" --""" -- - # ╔═╡ Cell order: - # ╟─33afb7f3-e52a-4f49-8be2-8634c66db010 - # ╟─70919378-b4d7-11eb-2d76-db01c83f87b8 -- cgit v1.2.3 From 7daf6ae8cb057bc1fec076c8fb73d1e0dc2864b9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 12:56:12 +0300 Subject: Update gem5 --- gn/packages/virtualization.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gn/packages/virtualization.scm b/gn/packages/virtualization.scm index 9e7efd7..e0eb016 100644 --- a/gn/packages/virtualization.scm +++ b/gn/packages/virtualization.scm @@ -21,7 +21,7 @@ (define-public gem5 (package (name "gem5") - (version "21.2.1.0") + (version "22.1.0.0") (source (origin (method git-fetch) @@ -30,7 +30,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0wyns8cfkigzw3m21331m8ydc7akm8l2lp0kci4pq8jyzsanmjm3")) + (base32 "1kcdn8rawzhf88lcb2app8m1r1px4ba041kyl7xigslix7qs05k3")) (snippet #~(begin (use-modules (guix build utils)) @@ -38,6 +38,7 @@ (substitute* "src/base/date.cc" (("__DATE__") "\"1970-01-01\"") (("__TIME__") "\"00:00:00\"")) + ;; Remove vendored pybind11. (substitute* "ext/sst/Makefile" (("-I../../ext/pybind11/include/") "${shell pybind11-config --includes}")) -- cgit v1.2.3 From 8885768936858286babae788a5dcfb01c2cad0a8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 19:00:45 +0300 Subject: gfaffix: Update to 0.1.5. --- gn/packages/bioinformatics.scm | 22 +++++----------------- gn/packages/crates-io.scm | 4 ++-- 2 files changed, 7 insertions(+), 19 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index db420b7..63934fc 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -469,7 +469,7 @@ reads.") (define-public gfaffix (package (name "gfaffix") - (version "0.1.3") + (version "0.1.5") (source (origin (method git-fetch) @@ -478,12 +478,7 @@ reads.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1biss5qv6ag1dfkn1nspwd528hpzgn8i4jydvbv2z7yv7sc685rh")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "Cargo.toml" - (("^handlegraph.*") "handlegraph = \"0.7\"\n")))))) + (base32 "181jxl8ldj39jgscyqzhz4l4k5kxj1j9hvzi8dxj59h2zzznb0kb")))) (build-system cargo-build-system) (arguments `(#:install-source? #f @@ -491,19 +486,12 @@ reads.") (("rust-clap" ,rust-clap-3) ("rust-rustc-hash" ,rust-rustc-hash-1) ("rust-regex" ,rust-regex-1) - ("rust-handlegraph" ,rust-handlegraph-0.7) + ("rust-handlegraph" ,rust-handlegraph-0.7.0-alpha.9) ("rust-gfa" ,rust-gfa-0.10) ("rust-quick-csv", rust-quick-csv-0.1) + ("rust-rayon" ,rust-rayon-1) ("rust-log" ,rust-log-0.4) - ("rust-env-logger" ,rust-env-logger-0.7)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'adjust-dependency-version - (lambda* (#:key inputs #:allow-other-keys) - (let ((handlebar-version ,(package-version rust-handlegraph-0.7))) - (substitute* "Cargo.toml" - (("\"0.7\"") - (string-append "{ version = \"" handlebar-version "\" }"))))))))) + ("rust-env-logger" ,rust-env-logger-0.7)))) (home-page "https://github.com/marschall-lab/GFAffix") (synopsis "Identify walk-preserving shared affixes in variation graphs") (description diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 7e74b60..a0e31ce 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -144,7 +144,7 @@ functions} for a collection of hashable objects.") "Library for working with graphs in the GFA (Graphical Fragment Assembly) format") (license license:expat))) -(define-public rust-handlegraph-0.7 +(define-public rust-handlegraph-0.7.0-alpha.9 (package (name "rust-handlegraph") (version "0.7.0-alpha.9") @@ -180,7 +180,7 @@ functions} for a collection of hashable objects.") (define-public rust-handlegraph-0.3 (package - (inherit rust-handlegraph-0.7) + (inherit rust-handlegraph-0.7.0-alpha.9) (name "rust-handlegraph") (version "0.3.0") (source (origin -- cgit v1.2.3 From 90d0c931a585ec862151a11b6a88fce678670b9d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 19:16:01 +0300 Subject: Add vcfbub --- gn/packages/bioinformatics.scm | 49 ++++++++++++++++++++++++++++++++++++++++++ gn/packages/crates-io.scm | 26 ++++++++++++++++++++++ 2 files changed, 75 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 63934fc..2b1d514 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -499,6 +499,55 @@ reads.") collapses them into a non-redundant graph structure.") (license license:expat))) +(define-public vcfbub + (package + (name "vcfbub") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pangenome/vcfbub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0sk2ab22z6qa00j1w8a8f5kbb7q2xb10fhd32zy4lh351v3mqmyg")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2) + ("rust-flate2" ,rust-flate2-1) + ("rust-vcf" ,rust-vcf-0.6)))) + (home-page "https://github.com/pangenome/vcfbub") + (synopsis "Popping bubbles in vg deconstruct VCFs") + (description + "The VCF output produced by a command like @command{vg deconstruct -e -a +-H '#' ...} includes information about the nesting of variants. With @code{-a}, +@code{--all-snarls}, we obtain not just the top level bubbles, but all nested +ones. This exposed snarl tree information can be used to filter the VCF to +obtain a set of non-overlapping sites (n.b. \"snarl\" is a generic model of +graph bubbles including tips and loops). +@code{vcfbub} lets us do two common operations on these VCFs: +@enumerate +@item We can filter sites by maximum level in the snarl tree. For instance, +@code{--max-level 0} would keep only sites with @code{LV=0}. In practice, vg's +snarl finder ensures that these are sites rooted on the main linear axis of the +pangenome graph. Those at higher levels occur within larger variants. +@item We can filter sites by maximum allele size, either for the reference +allele or any allele. In this case, @code{--max-ref-length 10000} would keep +only sites where the reference allele is less than 10kb long. Setting +@code{--max-ref-length} or @code{--max-allele-length} additionally ensures that +the output contains the bubbles nested inside of any popped bubble, even if +they are at greater than @code{--max-level}. +@end enumerate +@code{vcfbub} accomplishes a simple task: we keep sites that are the children +of those which we \"pop\" due to their size. These occur around complex large +SVs, such as multi-Mbp inversions and segmental duplications. We often need to +remove these, as they provide little information for many downstream +applications, such as haplotype panels or other imputation references.") + (license license:expat))) + (define-public gafpack (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022 (revision "1")) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index a0e31ce..79832bc 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -575,6 +575,32 @@ or any combination.") (description "Yet another format-preserving TOML parser.") (license (list license:expat license:asl2.0)))) +(define-public rust-vcf-0.6 + (package + (name "rust-vcf") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (crate-uri "vcf" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0dc0p00a19rpmhrqcshrn2qg5l716b5s1fy8vpd3p32bw77vpbs0")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Not all files included + #:cargo-inputs + (("rust-nom" ,rust-nom-7) + ("rust-once-cell" ,rust-once-cell-1) + ("rust-thiserror" ,rust-thiserror-1)) + #:cargo-development-inputs + (("rust-clap" ,rust-clap-2) + ("rust-flate2" ,rust-flate2-1)))) + (home-page "https://github.com/informationsea/vcf-rs") + (synopsis "Rust implmentation of VCF parser") + (description "This package provides a rust implmentation of a VCF parser.") + (license license:asl2.0))) + (define-public rust-gsl-sys (package (name "rust-gsl-sys") -- cgit v1.2.3 From c2415bfa014892a56be9b621089a0a2ffab234f7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 19:24:04 +0300 Subject: Add fastix --- gn/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ gn/packages/crates-io.scm | 25 +++++++++++++++++++++++++ 2 files changed, 51 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 2b1d514..4b37c8f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -548,6 +548,32 @@ remove these, as they provide little information for many downstream applications, such as haplotype panels or other imputation references.") (license license:expat))) +(define-public fastix + (package + (name "fastix") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (crate-uri "fastix" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1mzk65mg8vx0hz39xis6zqdmq56abhmza656gn9pgmlsn151gpx2")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2)) + #:cargo-development-inputs + (("rust-assert-cmd" ,rust-assert-cmd-0.12) + ("rust-predicates" ,rust-predicates-1)))) + (home-page "https://github.com/ekg/fastix") + (synopsis "Prefix-renaming FASTA records") + (description "A command line tool to add prefixes to FASTA headers. The +idea is to support pangenomic applications, following the +@url{https://github.com/pangenome/PanSN-spec, PanSN} hierarchical naming +specification.") + (license license:expat))) + (define-public gafpack (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022 (revision "1")) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 79832bc..557c980 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -10,6 +10,31 @@ #:use-module (gnu packages maths) #:use-module (gnu packages python)) +(define-public rust-assert-cmd-0.12 + (package + (name "rust-assert-cmd") + (version "0.12.2") + (source (origin + (method url-fetch) + (uri (crate-uri "assert-cmd" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1xfn2spazxk3ljj9q3250a24gndja9vwa0h0rnbccdrbd4ncyvwk")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-doc-comment" ,rust-doc-comment-0.3) + ("rust-escargot" ,rust-escargot-0.5) + ("rust-predicates" ,rust-predicates-1) + ("rust-predicates-core" ,rust-predicates-core-1) + ("rust-predicates-tree" ,rust-predicates-tree-1) + ("rust-wait-timeout" ,rust-wait-timeout-0.2)))) + (home-page "https://github.com/assert-rs/assert_cmd") + (synopsis "Test CLI Applications.") + (description "Test CLI Applications.") + (license (list license:expat license:asl2.0)))) + (define-public rust-bgzip-0.2 (package (name "rust-bgzip") -- cgit v1.2.3 From 29839033efcc894718b1596e66bcea811da19d7a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 19:38:52 +0300 Subject: Add pafplot --- gn/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++ gn/packages/crates-io.scm | 58 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 95 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 4b37c8f..75449f3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages cpp) #:use-module (gnu packages cran) #:use-module (gnu packages crates-io) + #:use-module (gnu packages crates-graphics) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) @@ -574,6 +575,42 @@ idea is to support pangenomic applications, following the specification.") (license license:expat))) +(define-public pafplot + (let ((commit "7dda24c0aeba8556b600d53d748ae3103ec85501") + (revision "1")) + (package + (name "pafplot") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/pafplot.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04ffz0zfj4mvfxmrwgisv213fypgl02f7sim950a067pm7375g1l")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2) + ("rust-boomphf" ,rust-boomphf-0.5) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-fnv" ,rust-fnv-1) + ("rust-lodepng" ,rust-lodepng-3) + ("rust-rgb" ,rust-rgb-0.8) + ("rust-line-drawing" ,rust-line-drawing-0.8)))) + (home-page "https://github.com/ekg/pafplot.git") + (synopsis "Base-level dotplots from PAF alignments") + (description "In the process of generating alignments between whole +genomes, we often need to understand the base-level alignment between +particular sequences. @command{pafplot} allows us to do so by rasterizing the +matches alignment set. It draws a line on a raster image to represent each +match found in a set of alignments. The resulting image provides a high-level +view of the structure of the alignments, and in consequence the homology +relationships between the sequences in consideration.") + (license license:expat)))) + (define-public gafpack (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022 (revision "1")) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 557c980..6db2716 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -246,6 +246,64 @@ functions} for a collection of hashable objects.") (description "Key String provides a Rust package optimized for map keys.") (license (list license:expat license:asl2.0)))) +(define-public rust-line-drawing-0.8 + (package + (name "rust-line-drawing") + (version "0.8.1") + (source (origin + (method url-fetch) + (uri (crate-uri "line-drawing" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "18a940s3mv8w5prpb99sdxykzhrvzrnymw3hvd7wisnkgbr11jqm")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-num-traits" ,rust-num-traits-0.2)) + #:cargo-development-inputs + (("rust-bresenham" ,rust-bresenham-0.1) + ("rust-image" ,rust-image-0.23) + ("rust-rand" ,rust-rand-0.8)))) + (home-page "https://github.com/expenses/line_drawing") + (synopsis + "A collection of line-drawing algorithms for use in graphics and video games.") + (description + "This package provides a collection of line-drawing algorithms for use in +graphics and video games.") + (license license:expat))) + +(define-public rust-lodepng-3 + (package + (name "rust-lodepng") + (version "3.8.0") + (source (origin + (method url-fetch) + (uri (crate-uri "lodepng" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1f5d9bva17sq7npw9qh7h6sh02k0ycrjx5hr147q0jv4m0qd2970")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-test-flags + (list "--release" "--" + ;; Not all files included. + "--skip=test::read_icc") + #:cargo-inputs + (("rust-crc32fast" ,rust-crc32fast-1) + ("rust-fallible-collections" ,rust-fallible-collections-0.4) + ("rust-flate2" ,rust-flate2-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-rgb" ,rust-rgb-0.8)))) + (home-page "https://lib.rs/crates/lodepng") + (synopsis + "Reading and writing PNG files without system dependencies. Pure Rust port of LodePNG.") + (description + "Reading and writing PNG files without system dependencies. Pure Rust port of +@code{LodePNG}.") + (license license:zlib))) + (define-public rust-pyo3-0.14 (package (name "rust-pyo3") -- cgit v1.2.3 From 9fd1f19078f055144f1192534d6f32eb26eb32f1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 20 Sep 2023 10:18:06 +0300 Subject: Add wfmash with glibc-hwcap libraries. --- gn/packages/bioinformatics.scm | 93 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 75449f3..a303baf 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -195,6 +195,99 @@ accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.") (license license:gpl3))) +(define-public wfmash-x86-64-v2 + (package/inherit wfmash + (name "wfmash-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public wfmash-x86-64-v3 + (package/inherit wfmash + (name "wfmash-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + #;(properties `((hidden? . #t))))) + +(define-public wfmash-x86-64-v4 + (package/inherit wfmash + (name "wfmash-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +;; This copy of wfmash will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public wfmash-hwcaps + (package/inherit wfmash + (name "wfmash-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs wfmash) + (append wfmash-x86-64-v2 + wfmash-x86-64-v3 + wfmash-x86-64-v4))))) + (define-public freec (package (name "control-freec") -- cgit v1.2.3 From 658464c22150e62c731ee1bfe1efb7253876f53a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 20 Sep 2023 10:24:10 +0300 Subject: remove crates existing upstream --- gn/packages/crates-io.scm | 45 --------------------------------------------- 1 file changed, 45 deletions(-) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 6db2716..331a179 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -91,25 +91,6 @@ for massive key sets}. It generates an @acronym{MPHF, minimal perfect hash functions} for a collection of hashable objects.") (license license:expat))) -(define-public rust-clap-lex-0.3 - (package - (name "rust-clap-lex") - (version "0.3.0") - (source (origin - (method url-fetch) - (uri (crate-uri "clap-lex" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1a4dzbnlxiamfsn0pnkhn7n9bdfjh66j9fxm6mmr7d227vvrhh8d")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs (("rust-os-str-bytes" ,rust-os-str-bytes-6)))) - (home-page "https://github.com/clap-rs/clap/tree/master/clap_lex") - (synopsis "Minimal, flexible command line parser") - (description "Minimal, flexible command line parser") - (license (list license:expat license:asl2.0)))) - (define-public rust-cuckoofilter-0.5 (package (name "rust-cuckoofilter") @@ -558,32 +539,6 @@ or any combination.") (description "Rust CLI tools for manipulation of Jupyter Notebooks.") (license #f)))) ; There is no license. -(define-public rust-clap-derive-4 - (package - (name "rust-clap-derive") - (version "4.0.9") - (source (origin - (method url-fetch) - (uri (crate-uri "clap-derive" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "02zhbbmyz3dpy9ml6xfp7i8p3ffj1djvkdnkg6gr6d0s5r4hg8x4")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-heck" ,rust-heck-0.4) - ("rust-proc-macro-error" ,rust-proc-macro-error-1) - ("rust-proc-macro2" ,rust-proc-macro2-1) - ("rust-quote" ,rust-quote-1) - ("rust-syn" ,rust-syn-1)))) - (home-page "https://github.com/clap-rs/clap/tree/master/clap_derive") - (synopsis - "Parse command line argument by defining a struct, derive crate.") - (description - "Parse command line argument by defining a struct, derive crate.") - (license (list license:expat license:asl2.0)))) - (define-public rust-trycmd-0.12 (package (name "rust-trycmd") -- cgit v1.2.3 From 7635e5c9277f353834ca2e92507de477c9af2667 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 20 Sep 2023 10:40:10 +0300 Subject: gn: javascript: Add htmx. * gn/packages/javascript.scm (javascript-htmx): Add htmx. --- gn/packages/javascript.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 7be9db4..a2db29b 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1881,3 +1881,27 @@ Popper will automatically put the tooltip in the right place near the button.") (description "Font Awesome is a full suite of pictographic icons for easy scalable vector graphics.") (license license:silofl1.1))) + + +(define-public javascript-htmx + (package + (name "javascript-htmx") + (version "1.9.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bigskysoftware/htmx") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14m9wan8sp5lzblfzbi1hln621p7ld3npajxrhq1a19zm5bcrz3y")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("dist/htmx.min.js"))) + (home-page "https://htmx.org/") + (synopsis "High Power Tools for HTML") + (description + "htmx allows you to access AJAX, CSS Transitions, WebSockets and Server Sent Events directly in HTML, using attributes, so you can build modern user interfaces with the simplicity and power of hypertext") + (license license:expat))) -- cgit v1.2.3 From bfd4ccbbe6ad79ff9a02ca6c8656914f1fc4c414 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 20 Sep 2023 10:40:41 +0300 Subject: gn: genenetwork2: Add htmx. * gn/packages/genenetwork.scm (genenetwork2) [propagated-inputs]: Add htmx. --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ab8f8bd..5cd663e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -287,6 +287,7 @@ ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) ("javascript-underscore-string" ,javascript-underscore-string) + ("javascript-htmx" ,javascript-htmx) ("javascript-qtip2" ,javascript-qtip2) ("javascript-d3js" ,javascript-d3js) ("javascript-nvd3" ,javascript-nvd3) -- cgit v1.2.3 From a599c69673da59fc129ceefffb73f8958f3d82f0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 20 Sep 2023 16:03:50 +0300 Subject: seqwish: Update to 0.7.9. --- gn/packages/bioinformatics.scm | 208 ++++++++--------------------------------- seqwish-paryfor-riscv.diff | 20 ++++ 2 files changed, 59 insertions(+), 169 deletions(-) create mode 100644 seqwish-paryfor-riscv.diff diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a303baf..b0865f3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1592,120 +1592,60 @@ runApp(launch.browser=0, port=4208)~%\n" (scRNA-seq) data analysis.") (license license:agpl3)))) -(define-public seqwish-0.1 +(define-public seqwish (package (name "seqwish") - (version "0.1") + (version "0.7.9") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/ekg/seqwish.git") - (commit (string-append "v" version)))) + (commit (string-append "v" version)) + (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 - "1gp72cmi13hbkmwwhgckmxkbx8w644jc5l6dvvvxdbl6sk8xsi5r")))) - (build-system gnu-build-system) + (base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x")) + (patches (search-patches "seqwish-paryfor-riscv.diff")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* '("deps/atomic_queue/Makefile" + "deps/mmmulti/deps/DYNAMIC/CMakeLists.txt" + "deps/mmmulti/deps/atomic_queue/Makefile" + "deps/mmmulti/deps/ips4o/CMakeLists.txt") + (("-march=native") "") + (("-mcx16") "")) + (substitute* '("deps/mmmulti/deps/sdsl-lite/CMakeLists.txt" + "deps/sdsl-lite/CMakeLists.txt") + (("-msse4.2 -march=native") "")))))) + (build-system cmake-build-system) (arguments - `(#:phases + `(#:configure-flags + '(,@(cond ((target-x86-64?) + ;; This seems to be about the minimum + '("-DEXTRA_FLAGS=-march=x86-64-v2")) + ((target-aarch64?) + '("-DEXTRA_FLAGS=-march=armv8-a")) + ((target-riscv64?) + '("-DEXTRA_FLAGS=-march=rv64imafdc")) + ((target-ppc64le?) + '("-DEXTRA_FLAGS=-mcpu=power8")) + ;; The default case is '-march=native' + (else '()))) + #:phases (modify-phases %standard-phases - (delete 'configure) - (replace 'build - (lambda* (#:key inputs #:allow-other-keys) - (let ((sdsl-lite (assoc-ref inputs "sdsl-lite")) - (sufsort (assoc-ref inputs "sufsort")) - (bsort (assoc-ref inputs "bsort")) - (mmap_allocator (assoc-ref inputs "mmap-allocator")) - (tayweeargs (assoc-ref inputs "tayweeargs-source")) - (gzipreader (assoc-ref inputs "gzipreader-source")) - (mmmultimap (assoc-ref inputs "mmmultimap-source")) - (iitii (assoc-ref inputs "iitii-source")) - (ips4o (assoc-ref inputs "ips4o-source"))) - (apply invoke "g++" "-o" "seqwish" - "-O3" "-g" "-std=c++14" "-fopenmp" - "-latomic" "-lz" - (string-append "-I" sdsl-lite "/include") - (string-append "-I" sdsl-lite "/include/sdsl") - (string-append "-I" bsort "/include") - (string-append "-I" tayweeargs) - (string-append "-I" gzipreader) - (string-append "-I" mmmultimap "/src") - (string-append "-I" iitii "/src") - (string-append "-I" mmap_allocator "/include") - (string-append "-I" ips4o) - (append - (find-files "src" ".") - (list - (string-append sdsl-lite "/lib/libsdsl.so") - (string-append sufsort "/lib/libdivsufsort.so") - (string-append sufsort "/lib/libdivsufsort64.so") - (string-append mmap_allocator "/lib/libmmap_allocator.a") - (string-append bsort "/lib/libbsort.a"))))))) (replace 'check - (lambda _ + (lambda* (#:key tests? #:allow-other-keys) ;; Add seqwish to the PATH for the tests. (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) - (with-directory-excursion "test" - (invoke "make")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (install-file "seqwish" (string-append out "/bin"))) - #t))))) + (when tests? + (with-directory-excursion "../source/test" + (invoke "make")))))))) (inputs - `(("bsort" ,ekg-bsort) - ("mmap-allocator" ,ekg-mmap-allocator) - ("openmpi" ,openmpi) - ("sdsl-lite" ,sdsl-lite) - ("sufsort" ,libdivsufsort) - ("zlib" ,zlib))) + (list jemalloc + zlib)) (native-inputs - `(("prove" ,perl) - ("tayweeargs-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/Taywee/args.git") - (commit "3de44ec671db452cc0c4ef86399b108939768abb"))) - (file-name "tayweeargs-source-for-seqwish") - (sha256 - (base32 - "1v8kq1gvl5waysrfp0s58881rx39mnf3ifdsl6pb3y3c4zaki2xh")))) - ("gzipreader-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/gatoravi/gzip_reader.git") - (commit "0ef26c0399e926087f9d6c4a56067a7bf1fc4f5e"))) - (file-name "gzipreader-source-for-seqwish") - (sha256 - (base32 - "1wy84ksx900840c06w0f1mgzvr7zsfsgxq1b0jdjh8qka26z1r17")))) - ("mmmultimap-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/mmmultimap.git") - (commit "88c734c36563048b0f3acc04dd8856f19e02b75f"))) - (file-name "mmmultimap-source-for-seqwish") - (sha256 - (base32 - "06mnf3bd32s3ngxkl573ylg2qsvlw80r1ksdwamx3fzxa1a5yls0")))) - ("iitii-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/iitii.git") - (commit "85209e07a3ee403fb6557387a7f897cd76be4406"))) - (file-name "iitii-source-for-seqwish") - (sha256 - (base32 - "0sszvffkswf89nkbjmjg3wjwqvy2w0d3wgy3ngy33ma4sy4s025s")))) - ("ips4o-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/SaschaWitt/ips4o.git") - (commit "bff3ccf0bf349497f2bb10f825d160b792236367"))) - (file-name "ips4o-source-for-seqwish") - (sha256 - (base32 - "0yjfvrkiwgmy5cn0a7b9j8jwc3zp0l8j4dl5n0jgz68pdnhlp96h")))))) + (list perl)) (home-page "https://github.com/ekg/seqwish") (synopsis "Alignment to variation graph inducer") (description "Seqwish implements a lossless conversion from pairwise @@ -1720,76 +1660,6 @@ limited by the use of sorted disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.") (license license:expat))) -(define ekg-bsort - (let ((commit "c3ab0d3308424030e0a000645a26d2c10a59a124") - (revision "1")) - (package - (name "bsort") - (version (git-version "0.0.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/bsort.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0dgpflzcp3vdhbjwbjw347czi86gyk73hxcwjdqnaqh5vg61bdb6")))) - (build-system cmake-build-system) - (arguments - '(#:tests? #f ; no test target - #:out-of-source? #f - #:phases - (modify-phases %standard-phases - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (install-file "bin/bsort" (string-append out "/bin")) - (install-file "src/bsort.hpp" (string-append out "/include")) - (install-file "lib/libbsort.a" (string-append out "/lib"))) - #t))))) - (home-page "") - (synopsis "") - (description "") - (license license:gpl2)))) - -(define ekg-mmap-allocator - (let ((commit "ed61daf094de1c2e1adbe8306287ad52da5f0264") - (revision "1")) - (package - (name "mmap-allocator") - (version (git-version "0.10.1" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/mmap_allocator.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1f30b2kpwwzh6333s0qi5samk458ghbnvyycf6rwx6n6j7xswhbw")))) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) ; no configure script - (add-before 'install 'pre-install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* "Makefile" - (("HEADERS=") "HEADERS=mmappable_vector.h ") - (("/usr") out)) - (mkdir-p (string-append out "/lib")) - (mkdir (string-append out "/include")) - #t)))) - #:test-target "test")) - (home-page "") - (synopsis "") - (description "") - (license license:lgpl2.0+)))) ; README just says "lpgl". - ;; TODO: Unbundle BBHash, parallel-hashmap, zstr (define-public graphaligner (package diff --git a/seqwish-paryfor-riscv.diff b/seqwish-paryfor-riscv.diff new file mode 100644 index 0000000..cecf806 --- /dev/null +++ b/seqwish-paryfor-riscv.diff @@ -0,0 +1,20 @@ +diff --git a/deps/paryfor/paryfor.hpp b/deps/paryfor/paryfor.hpp +index b8ced09..0536580 100644 +--- a/deps/paryfor/paryfor.hpp ++++ b/deps/paryfor/paryfor.hpp +@@ -51,6 +51,15 @@ static inline void spin_loop_pause() noexcept { + } + } // namespace atomic_queue + } // namespace paryfor ++#elif defined(__riscv) && (__riscv_xlen == 64) ++namespace paryfor { ++namespace atomic_queue { ++constexpr int CACHE_LINE_SIZE = 64; ++static inline void spin_loop_pause() noexcept { ++ asm volatile ("nop" ::: "memory"); ++} ++} ++} + #else + #error "Unknown CPU architecture." + #endif -- cgit v1.2.3 From fa03e6f84c0ff8e1c168568fd33316c170014251 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 21 Sep 2023 09:07:37 +0300 Subject: Add smoothxg --- gn/packages/bioinformatics.scm | 67 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b0865f3..8a4b278 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1660,6 +1660,73 @@ limited by the use of sorted disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.") (license license:expat))) +(define-public smoothxg + (package + (name "smoothxg") + (version "0.7.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pangenome/smoothxg" + "/releases/download/v" version + "/smoothxg-v" version ".tar.gz")) + (sha256 + (base32 "1px8b5aaa23z85i7ximdamk2jj7wk5hb7bpbrgxsvkxc69zlwy38")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* (find-files "." "CMakeLists.txt") + (("spoa_optimize_for_native ON") + "spoa_optimize_for_native OFF") + (("-msse4\\.2") "") + (("-march=native") "")))))) + (build-system cmake-build-system) + (arguments + (list + #:make-flags + #~(list (string-append "CC = " #$(cc-for-target))) + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'build-abPOA + (lambda* (#:key make-flags #:allow-other-keys) + ;; This helps with portability to other architectures. + (with-directory-excursion + (string-append "../smoothxg-v" #$version "/deps/abPOA") + (substitute* "Makefile" + (("-march=native") "")) + (apply invoke "make" "libabpoa" make-flags))))))) + (inputs + (list jemalloc + openmpi + pybind11 + python + zlib + (list zstd "lib"))) + (native-inputs + (list pkg-config)) + (home-page "https://github.com/ekg/smoothxg") + (synopsis + "Linearize and simplify variation graphs using blocked partial order alignment") + (description "Pangenome graphs built from raw sets of alignments may have +complex local structures generated by common patterns of genome variation. +These local nonlinearities can introduce difficulty in downstream analyses, +visualization, and interpretation of variation graphs. + +@command{smoothxg} finds blocks of paths that are collinear within a variation +graph. It applies partial order alignment to each block, yielding an acyclic +variation graph. Then, to yield a smoothed graph, it walks the original paths +to lace these subgraphs together. The resulting graph only contains cyclic or +inverting structures larger than the chosen block size, and is otherwise +manifold linear. In addition to providing a linear structure to the graph, +smoothxg can be used to extract the consensus pangenome graph by applying the +heaviest bundle algorithm to each chain. + +To find blocks, smoothxg applies a greedy algorithm that assumes that the graph +nodes are sorted according to their occurence in the graph's embedded paths. +The path-guided stochastic gradient descent based 1D sort implemented in +@command{odgi sort -Y} is designed to provide this kind of sort.") + (properties `((tunable? . #t))) + (license license:expat))) + ;; TODO: Unbundle BBHash, parallel-hashmap, zstr (define-public graphaligner (package -- cgit v1.2.3 From 88f74e4ae05a562c4a4373b9e3b86bac4ea132b2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 21 Sep 2023 10:31:05 +0300 Subject: odgi: Update to 0.8.3. --- gn/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 8a4b278..dba5f6f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2033,32 +2033,48 @@ available to other researchers.") (delete-file "scanpy/tests/test_pca.py") #t))))))))) -;; TODO: Unbundle everything +;; TODO: Unbundle everything before upstreaming (define-public odgi (package (name "odgi") - (version "0.8.1") + (version "0.8.3") + (outputs '("out" "static")) (source (origin (method url-fetch) (uri (string-append "https://github.com/pangenome/odgi/releases" "/download/v" version "/odgi-v" version ".tar.gz")) (sha256 - (base32 "175083pb9hp0vn9a00hbxlayyk5a5j8p52yq5qfmbnfvndisbmbv")) + (base32 "1gw1xdb945z25rar6pba6kq5xdx8l7fkhxjyrvc1z1brva53p9hk")) (snippet #~(begin (use-modules (guix build utils)) (substitute* "CMakeLists.txt" (("-march=native") "") - (("-msse4\\.2") "")) - (delete-file-recursively "deps/pybind11") - (delete-file-recursively "deps/sdsl-lite"))))) + (("-msse4\\.2") "")))))) (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'link-to-libodgi + (lambda _ + ;; This lets us provide libraries for different psABI levels. + (substitute* "CMakeLists.txt" + (("^ \\$.*") "") + (("target_link_libraries\\(odgi " all) + (string-append all "libodgi_shared "))))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append #$output:static "/lib")) + (rename-file (string-append #$output "/lib/libodgi.a") + (string-append #$output:static "/lib/libodgi.a"))))))) (native-inputs (list pkg-config)) (inputs (list jemalloc libdivsufsort + openmpi pybind11 python sdsl-lite)) -- cgit v1.2.3 From 91d55ae18950e470e32fbdbebd867196e691a82a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 21 Sep 2023 11:30:21 +0300 Subject: wfmash: Fix typos. --- gn/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index dba5f6f..71ea9c0 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -200,7 +200,7 @@ variants can be visualized using Delly-maze and Delly-suave.") (name "wfmash-x86-64-v2") (arguments (substitute-keyword-arguments (package-arguments wfmash) - ((#:configure-flags flags #~()) + ((#:configure-flags flags #~'()) #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" (string-append "-DCMAKE_INSTALL_RPATH=" #$output @@ -221,7 +221,7 @@ variants can be visualized using Delly-maze and Delly-suave.") (name "wfmash-x86-64-v3") (arguments (substitute-keyword-arguments (package-arguments wfmash) - ((#:configure-flags flags #~()) + ((#:configure-flags flags #~'()) #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" (string-append "-DCMAKE_INSTALL_RPATH=" #$output @@ -235,14 +235,14 @@ variants can be visualized using Delly-maze and Delly-suave.") (lambda _ (delete-file-recursively (string-append #$output "/bin")))))))) (supported-systems '("x86_64-linux")) - #;(properties `((hidden? . #t))))) + (properties `((hidden? . #t))))) (define-public wfmash-x86-64-v4 (package/inherit wfmash (name "wfmash-x86-64-v4") (arguments (substitute-keyword-arguments (package-arguments wfmash) - ((#:configure-flags flags #~()) + ((#:configure-flags flags #~'()) #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" (string-append "-DCMAKE_INSTALL_RPATH=" #$output @@ -286,7 +286,8 @@ variants can be visualized using Delly-maze and Delly-suave.") (modify-inputs (package-native-inputs wfmash) (append wfmash-x86-64-v2 wfmash-x86-64-v3 - wfmash-x86-64-v4))))) + wfmash-x86-64-v4))) + (properties `((tunable? . #f))))) (define-public freec (package -- cgit v1.2.3 From 283304f54edbac26a62368e76460528ec478dc61 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 21 Sep 2023 11:31:51 +0300 Subject: odgi: Add variant with glibc-hwcaps. --- gn/packages/bioinformatics.scm | 127 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 127 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 71ea9c0..7a20200 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2058,6 +2058,18 @@ available to other researchers.") (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'use-gnuinstalldirs-macros + (lambda _ + (substitute* "CMakeLists.txt" + (("project\\(odgi\\)" all) + (string-append all "\ninclude(GNUInstallDirs)")) + ;; This is different than the default. + ;(("PUBLIC_HEADER DESTINATION include/odgi") + ; "PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}") + (("LIBRARY DESTINATION lib") + "LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}") + (("ARCHIVE DESTINATION lib") + "ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}")))) (add-after 'unpack 'link-to-libodgi (lambda _ ;; This lets us provide libraries for different psABI levels. @@ -2100,6 +2112,121 @@ in-memory footprint at the cost of packing and unpacking.") (properties '((tunable? . #t))) (license license:expat))) +(define-public odgi-x86-64-v2 + (package/inherit odgi + (name "odgi-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public odgi-x86-64-v3 + (package/inherit odgi + (name "odgi-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public odgi-x86-64-v4 + (package/inherit odgi + (name "odgi-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +;; This copy of odgi will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public odgi-hwcaps + (package/inherit odgi + (name "odgi-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs odgi) + (append odgi-x86-64-v2 + odgi-x86-64-v3 + odgi-x86-64-v4))) + (properties `((tunable? . #f))))) + (define-public vg (package (name "vg") -- cgit v1.2.3 From 86583628060872edc5adb08cc73425087b153825 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 21 Sep 2023 12:32:27 +0300 Subject: mummer: Update to 4.0.0rc1. --- gn/packages/bioinformatics.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 7a20200..78cbcb7 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1796,19 +1796,30 @@ here}.") (define-public mummer (package (name "mummer") - (version "4.0.0beta2") + (version "4.0.0rc1") (source (origin (method url-fetch) (uri (string-append "https://github.com/mummer4/mummer/releases/" "download/v" version "/mummer-" version ".tar.gz")) (sha256 - (base32 - "14qvrmf0gkl4alnh8zgxlzmvwc027arfawl96i7jk75z33j7dknf")))) + (base32 "07bxw1vax1sai3g5xjn6sqngddlbnlabpqy373vw4fb55pdnl045")))) (build-system gnu-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'configure 'skip-test_md5-tests + (lambda _ + ;; There seems to be a bug with how these tests are called. + (substitute* "Makefile" + (("tests/mummer.sh") "") + (("tests/nucmer.sh") "") + (("tests/genome.sh") "") + (("tests/sam.sh") ""))))))) (inputs - `(("gnuplot" ,gnuplot) - ("perl" ,perl))) + (list gnuplot + perl)) (home-page "http://mummer.sourceforge.net/") (synopsis "Efficient sequence alignment of full genomes") (description "MUMmer is a versatil alignment tool for DNA and protein sequences.") -- cgit v1.2.3 From c944663d2d64824d7f947dc3f65bd5489fa1f8df Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 21 Sep 2023 15:31:42 +0300 Subject: rtg: Update package definition. --- gn/packages/java.scm | 85 ++++++++++++++++++++++++++++------------------------ 1 file changed, 46 insertions(+), 39 deletions(-) diff --git a/gn/packages/java.scm b/gn/packages/java.scm index cdd9d00..c8e1e9b 100644 --- a/gn/packages/java.scm +++ b/gn/packages/java.scm @@ -19,6 +19,7 @@ (define-module (gn packages java) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) @@ -27,11 +28,11 @@ #:use-module (guix build-system ant) #:use-module (gnu packages) #:use-module (gnu packages autotools) + #:use-module (gnu packages bash) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages certs) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) - #:use-module (gnu packages icu4c) #:use-module (gnu packages java) #:use-module (gnu packages java-compression) #:use-module (gnu packages perl) @@ -325,8 +326,7 @@ piece of information.") (("\"git\"") "\"echo\"") (("\\$\\{vcs\\.cmd\\.out\\}") "${product.version}") (("\\$\\{build\\.time\\}") "1970-01-01") - (("-\\$\\{rtg\\.vcs\\.commit\\.revision\\}") "")) - #t)) + (("-\\$\\{rtg\\.vcs\\.commit\\.revision\\}") "")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -337,52 +337,59 @@ piece of information.") (invoke "unzip" (string-append pkg "-nojre.zip")) (copy-recursively (string-append pkg "/") ".") (delete-file-recursively pkg) - (delete-file (string-append pkg "-nojre.zip"))) - #t))) + (delete-file (string-append pkg "-nojre.zip")))))) (add-after 'install 'create-rtg.cfg - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (with-output-to-file (string-append out "/rtg.cfg") (lambda _ (format #t "RTG_JAVA=\"~a\"~@ RTG_TALKBACK=false~@ RTG_USAGE=false~%" - (which "java")))) - #t))) - (add-after 'install 'install-completions - (lambda* (#:key outputs #:allow-other-keys) - (install-file "installer/resources/common/scripts/rtg-bash-completion" - (string-append (assoc-ref outputs "out") - "/share/bash-completion/completions")) - #t)) + (search-input-file inputs "/bin/java"))))))) + (add-after 'install 'create-wrapper-script + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (wrapper (string-append out "/bin/rtg"))) + ;; We want an executable in the bin directory without rewriting + ;; the existing wrapper script. + (mkdir-p (dirname wrapper)) + (with-output-to-file wrapper + (lambda _ + (format #t "#!~a~@ + exec -a \"$0\" \"~a/rtg\" \"$@\"~%" + (search-input-file inputs "/bin/bash") + out))) + (chmod wrapper #o555)))) + (add-after 'install 'install-completions + (lambda* (#:key outputs #:allow-other-keys) + (install-file "installer/resources/common/scripts/rtg-bash-completion" + (string-append (assoc-ref outputs "out") + "/share/bash-completion/completions")))) (delete 'generate-jar-indices)))) ; manually installed (inputs - `(("java-commons-collections" ,java-commons-collections) - ("java-commons-compress" ,java-commons-compress) - ("java-commons-lang" ,java-commons-lang) - ;("java-graal-sdk" ,java-graal-sdk) - ;("java-gzipfix" ,java-gzipfix) - ;("java-htsjdk" ,java-sam-rtg) - ("java-icu4j" ,java-icu4j) - ;("java-js" ,java-js) - ;("java-js-scriptengine" ,java-js-scriptengine) - ;("java-json-simple" ,java-json-simple) - ;("java-regex" ,java-regex) - ;("java-rplot" ,java-rplot) - ("java-snappy" ,java-snappy) - ;("java-truffle-api" ,java-truffle-api) - ;("java-velocity" ,java-velocity) - ;("java-velocity-tools-generic" ,java-velocity-tools-generic) - )) + (list bash-minimal ; for the wrapper script + java-commons-collections + java-commons-compress + java-commons-lang + ;java-gzipfix + ;java-sam-rtg + ;java-json-simple + ;java-rplot + java-snappy + ;java-velocity + ;java-velocity-tools-generic + )) (native-inputs - `(;("java-findbugs-annotations" ,java-findbugs-annotations) - ;("java-findbugs-jsr305" ,java-findbugs-jsr305) - ;("java-jumble-annotations" ,java-jumble-annotations) - ;; for tests - ("java-hamcrest-core" ,java-hamcrest-core) - ("java-junit" ,java-junit) - ;("java-spelling" ,java-spelling) - ("unzip" ,unzip))) + (list ;java-findbugs-annotations + ;java-findbugs-jsr305 + ;java-jumble-annotations + ;; for tests + java-hamcrest-core + java-junit + ;java-spelling + ;; For the 'install phase. + unzip)) (home-page "https://github.com/RealTimeGenomics/rtg-tools/") (synopsis "Utilities for accurate VCF comparison and manipulation") (description "RTG Tools is a subset of RTG Core that includes several useful -- cgit v1.2.3 From 10823be9475e16396365c04212d175b2dce31f3e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 22 Sep 2023 08:41:24 +0300 Subject: vg: Update to 1.50.0. --- gn/packages/bioinformatics.scm | 208 ++++++++++++++--------------------------- 1 file changed, 71 insertions(+), 137 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 78cbcb7..4f802f7 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2241,104 +2241,34 @@ in-memory footprint at the cost of packing and unpacking.") (define-public vg (package (name "vg") - (version "1.39.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/vgteam/vg/releases/download/v" version "/vg-v" version ".tar.gz")) (sha256 - (base32 "0cj575qr2jkingrm6r4ki7f89s7glrf18d4pvaa69smxh2vbajv3")) - (modules '((guix build utils))) + (base32 "1n06fh6qvffhbxy7m096r8cy16wi0nm6gfgi3rsjy9zrb7g1jzhs")) (snippet - '(begin - ;; List all the options, makes it easier to try to remove them. - ;(delete-file-recursively "deps/BBHash") - ;(delete-file-recursively "deps/DYNAMIC") - ;(delete-file-recursively "deps/FlameGraph") - ;(delete-file-recursively "deps/atomic_queue") - ;(delete-file-recursively "deps/backward-cpp") - (delete-file-recursively "deps/bash-tap") - ;(delete-file-recursively "deps/dozeu") - (delete-file-recursively "deps/elfutils") - (delete-file-recursively "deps/fastahack") - ;(delete-file-recursively "deps/fermi-lite") - ;(delete-file-recursively "deps/gbwt") - ;(delete-file-recursively "deps/gbwtgraph") - ;(delete-file-recursively "deps/gcsa2") - ;(delete-file-recursively "deps/gfakluge") - ;(delete-file-recursively "deps/gssw") - (delete-file-recursively "deps/htslib") - ;(delete-file-recursively "deps/ips4o") - (delete-file-recursively "deps/jemalloc") - ;(delete-file-recursively "deps/libVCFH") - ;(delete-file-recursively "deps/libbdsg") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps") - (delete-file-recursively "deps/libbdsg/bdsg/deps/BBHash") - (delete-file-recursively "deps/libbdsg/bdsg/deps/DYNAMIC") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps/DYNAMIC/deps/hopscotch-map") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps/hopscotch-map") - (delete-file-recursively "deps/libbdsg/bdsg/deps/libhandlegraph") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps/mio") - (delete-file-recursively "deps/libbdsg/bdsg/deps/pybind11") - (delete-file-recursively "deps/libbdsg/bdsg/deps/sdsl-lite") - (delete-file-recursively "deps/libbdsg/bdsg/deps/sparsepp") - ;(delete-file-recursively "deps/libdeflate") - ;(delete-file-recursively "deps/libhandlegraph") - ;(delete-file-recursively "deps/libVCFH") - ;(delete-file-recursively "deps/libvgio") - ;(delete-file-recursively "deps/libvgio/deps") ; libhandlegraph - ;(delete-file-recursively "deps/lru_cache") - ;(delete-file-recursively "deps/mio") - ;(delete-file-recursively "deps/mmmultimap") - (delete-file-recursively "deps/mmmultimap/deps/DYNAMIC") - (delete-file-recursively "deps/mmmultimap/deps/args") - (delete-file-recursively "deps/mmmultimap/deps/atomic_queue") - ;(delete-file-recursively "deps/mmmultimap/deps/hopscotch-map") - (delete-file-recursively "deps/mmmultimap/deps/ips4o") - (delete-file-recursively "deps/mmmultimap/deps/mio") - ;(delete-file-recursively "deps/mmmultimap/deps/paryfor") - (delete-file-recursively "deps/mmmultimap/deps/sdsl-lite") - ;(delete-file-recursively "deps/pinchesAndCacti") - ;(delete-file-recursively "deps/progress_bar") - (delete-file-recursively "deps/raptor") - ;(delete-file-recursively "deps/sdsl-lite") - ;(delete-file-recursively "deps/sha1") - (delete-file-recursively "deps/snappy") - ;(delete-file-recursively "deps/sonLib") - (delete-file-recursively "deps/sparsehash") - ;(delete-file-recursively "deps/sparsepp") - ;(delete-file-recursively "deps/ssw") - ;(delete-file-recursively "deps/structures") - ;(delete-file-recursively "deps/sublinear-Li-Stephens") - (delete-file-recursively "deps/sublinear-Li-Stephens/deps") - (delete-file-recursively "deps/tabixpp") - (delete-file-recursively "deps/vcflib") - ;(delete-file-recursively "deps/xg") - (delete-file-recursively "deps/xg/deps") - ;; libvgio doesn't search the correct include directory. - (copy-recursively "deps/libhandlegraph/src/include/handlegraph" - "deps/libvgio/include/handlegraph"))))) + #~(begin + (use-modules (guix build utils)) + (substitute* (find-files "." "(CMakeLists\\.txt|Makefile)") + (("-march=native") "") + (("-mtune=native") "") + (("-msse4.2") "") + (("-mcx16") "")))))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) ; no configure script - ,@(if (target-riscv64?) - ;; riscv64 doesn't take '-march=native. This needs to be removed - ;; for all architectures if/when vg is upstreamed. - `((add-after 'unpack 'dont-build-native - (lambda _ - (substitute* (append (find-files "." "CMakeLists\\.txt") - (find-files "." "Makefile")) - (("-march=native") ""))))) - '()) (add-after 'unpack 'patch-source (lambda* (#:key inputs #:allow-other-keys) + ;; Most of these are so that we can skip bootstrapping some of the sources. (substitute* "Makefile" ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything. - (("cairo jansson") - "cairo htslib jansson libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib") + (("cairo libzstd") + "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack") ;; Skip the part where we link static libraries special. It doesn't like the changes we make (("-Wl,-B.*") "\n") @@ -2359,13 +2289,9 @@ in-memory footprint at the cost of packing and unpacking.") (string-append " " (assoc-ref inputs "vcflib") "/lib/libvcflib.so")) ((" \\$\\(BIN_DIR\\)/vcf2tsv") (string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv")) - ((" \\$\\(VCFLIB_DIR\\)/bin/vcf2tsv") - (string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv")) ((" \\$\\(FASTAHACK_DIR\\)/fastahack") (string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) - ((" \\$\\(FASTAHACK_DIR\\)/bin/fastahack") - (string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o") (string-append "+= " (assoc-ref inputs "fastahack") "/lib/libfastahack.so")) @@ -2403,24 +2329,21 @@ in-memory footprint at the cost of packing and unpacking.") ;; vcf2tsv shows up in a couple of other places (substitute* "test/t/02_vg_construct.t" (("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv"))))) - (add-after 'unpack 'fix-fastahack-dependency + (add-after 'unpack 'dont-build-shared-vgio (lambda _ - (substitute* "src/aligner.hpp" - (("Fasta.h") "fastahack/Fasta.h")))) - (add-after 'unpack 'fix-hopscotch-dependency + ;; vg will link with libvgio and fail the 'validate-runpath phase. + (substitute* "deps/libvgio/CMakeLists.txt" + (("TARGETS vgio vgio_static") "TARGETS vgio_static")))) + (add-after 'unpack 'fix-fastahack-dependency (lambda _ - (substitute* "Makefile" - ;; The build directory for hopscotch_map-prefix. - (("rm -Rf build && ") "")) - ;; Don't try to download hopscotch_map from the internet. - (substitute* "deps/DYNAMIC/CMakeLists.txt" - ((".*GIT_REPOSITORY.*") - "SOURCE_DIR \"../../libbdsg/bdsg/deps/hopscotch-map\"\n") - ((".*BUILD_IN_SOURCE.*") "")) - ;; We still need to copy it to the expected location. - (copy-recursively - "deps/libbdsg/bdsg/deps/hopscotch-map" - "deps/DYNAMIC/build/hopscotch_map-prefix/src/hopscotch_map"))) + (substitute* (append (list "src/aligner.hpp" + "src/vg.hpp") + (find-files "deps/vcflib/src" "\\.cpp$")) + (("Fasta.h") "fastahack/Fasta.h")) + (substitute* '("deps/vcflib/src/Variant.h" + "src/constructor.hpp" + "src/index_registry.cpp") + (("") "\"fastahack/Fasta.h\"")))) (add-after 'unpack 'adjust-tests (lambda* (#:key inputs #:allow-other-keys) (let ((bash-tap (assoc-ref inputs "bash-tap"))) @@ -2429,13 +2352,21 @@ in-memory footprint at the cost of packing and unpacking.") (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n")) ((".*bash-tap-bootstrap") (string-append ". " bash-tap "/bin/bash-tap-bootstrap"))) - ;; Lets skip the 4 failing tests for now. They fail with our + (substitute* "test/t/02_vg_construct.t" + (("../deps/fastahack/fastahack") (which "fastahack")) + (("../bin/vcf2tsv") (which "vcf2tsv"))) + ;; Lets skip the 7 failing tests for now. They fail with our ;; bash-tap and the bundled one. (substitute* "test/t/02_vg_construct.t" + ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n") ((".*the graph contains.*") "is $(true) \"\" \"\"\n")) (substitute* '("test/t/07_vg_map.t" "test/t/33_vg_mpmap.t") ((".*node id.*") "is $(true) \"\" \"\"\n")) + (substitute* "test/t/50_vg_giraffe.t" + ((".*A long read can.*") "is $(true) \"\" \"\"\n") + ((".*A long read has.*") "is $(true) \"\" \"\"\n") + ((".*Long read minimizer.*") "is $(true) \"\" \"\"\n")) ;; Don't test the docs, we're not providing npm (substitute* "Makefile" ((".*test-docs.*") ""))))) @@ -2454,40 +2385,42 @@ in-memory footprint at the cost of packing and unpacking.") (find-files "doc/man" "\\.1$")))))) #:test-target "test")) (native-inputs - `(,@(if (member (%current-system) - (package-transitive-supported-systems ruby-asciidoctor)) - `(("asciidoctor" ,ruby-asciidoctor)) - '()) - ("bash-tap" ,bash-tap) - ("bc" ,bc) - ("cmake" ,cmake-minimal) - ("jq" ,jq) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("samtools" ,samtools) - ("util-linux" ,util-linux) - ("which" ,which) - ("xxd" ,xxd))) + (append + (if (supported-package? ruby-asciidoctor) + (list ruby-asciidoctor) + '()) + (list bash-tap + bc + cmake-minimal + jq + perl + pkg-config + samtools + util-linux + which + xxd))) (inputs - `(("boost" ,boost) - ("cairo" ,cairo) - ("curl" ,curl) - ("elfutils" ,elfutils) - ("fastahack" ,fastahack) - ("htslib" ,htslib) - ("jansson" ,jansson) - ("jemalloc" ,jemalloc) - ("libdivsufsort" ,libdivsufsort) - ("ncurses" ,ncurses) - ("protobuf" ,protobuf) - ("raptor2" ,raptor2) - ("sdsl-lite" ,sdsl-lite) - ("smithwaterman" ,smithwaterman) - ("snappy" ,snappy) - ("sparsehash" ,sparsehash) - ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib) - ("zlib" ,zlib))) + (list boost + cairo + curl + elfutils + fastahack + htslib + jansson + jemalloc + libdivsufsort + ncurses + openmpi + protobuf + raptor2 + sdsl-lite + smithwaterman + snappy + sparsehash + tabixpp + vcflib + zlib + (list zstd "lib"))) (home-page "https://www.biostars.org/t/vg/") (synopsis "Tools for working with genome variation graphs") (description "Variation graphs provide a succinct encoding of the sequences @@ -2501,7 +2434,8 @@ gene models and transcripts) as walks through nodes connected by edges @end enumerate This model is similar to sequence graphs that have been used in assembly and multiple sequence alignment.") - (properties `((release-monitoring-url . "https://github.com/vgteam/vg/releases"))) + (properties `((release-monitoring-url . "https://github.com/vgteam/vg/releases") + (tunable? . #t))) (license (list license:expat ; main program -- cgit v1.2.3 From 5b36e14b798dbebd0c1aeec818d4b7991dc29839 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 22 Sep 2023 16:00:58 +0300 Subject: vg: Prepare for using a shared library. --- gn/packages/bioinformatics.scm | 49 ++++++++++++++++++++++++++++++++++++------ 1 file changed, 43 insertions(+), 6 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 4f802f7..700dec4 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2268,7 +2268,7 @@ in-memory footprint at the cost of packing and unpacking.") (substitute* "Makefile" ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything. (("cairo libzstd") - "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack") + "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack libdeflate") ;; Skip the part where we link static libraries special. It doesn't like the changes we make (("-Wl,-B.*") "\n") @@ -2285,6 +2285,10 @@ in-memory footprint at the cost of packing and unpacking.") (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") (string-append " " (assoc-ref inputs "htslib") "/lib/pkgconfig/htslib.pc")) + (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a") + ((" \\$\\(LIB_DIR\\)/libdeflate\\.a") + (string-append " " (assoc-ref inputs "libdeflate") "/lib/libdeflate.so")) + ((" \\$\\(LIB_DIR\\)/libvcflib.a") (string-append " " (assoc-ref inputs "vcflib") "/lib/libvcflib.so")) ((" \\$\\(BIN_DIR\\)/vcf2tsv") @@ -2309,8 +2313,12 @@ in-memory footprint at the cost of packing and unpacking.") ;((" \\$\\(LIB_DIR\\)/libsdsl.a") ; (string-append " " (assoc-ref inputs "sdsl-lite") "/lib/libsdsl.so")) + ((" \\$\\(LIB_DIR\\)/%divsufsort.a") + (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/%divsufsort.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort.a") (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort.so")) + ((" \\$\\(LIB_DIR\\)/%divsufsort64.a") + (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/%divsufsort64.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a") (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort64.so")) @@ -2325,10 +2333,38 @@ in-memory footprint at the cost of packing and unpacking.") ((" \\$\\(LIB_DIR\\)/libraptor2.a") (string-append " " (assoc-ref inputs "raptor2") "/lib/libraptor2.so")) ((" \\$\\(BIN_DIR\\)/rapper") - (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))) - ;; vcf2tsv shows up in a couple of other places - (substitute* "test/t/02_vg_construct.t" - (("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv"))))) + (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))))) + #; + (add-before 'patch-source 'use-shared-libvg + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "Makefile" + (("libvg\\.a") "libvg.so") + ;; Have the linker find the shared library. + (("\\$\\(LIB_DIR\\)/libvg.\\$\\(SHARED_SUFFIX\\) \\$\\(LDFLAGS\\)") + "-lvg $(LDFLAGS)") + (("\\$\\(LDFLAGS\\) \\$\\(LIB_DIR\\)/libvg.so") + "$(LDFLAGS) -lvg")) + (setenv "LDFLAGS" (string-append "-Wl,-rpath=" + (assoc-ref outputs "out") "/lib")) + + ;; We need to tell a number of dependencies to build with -fPIC. + (substitute* "Makefile" + (("^CXXFLAGS := -O3") + (string-append "CFLAGS := -fPIC\n" + "CXXFLAGS := -O3 -fPIC")) + (("^export CXXFLAGS") + (string-append "export CFLAGS\n" + "$(info CFLAGS are $(CFLAGS))\n" + "export CXXFLAGS")) + ((" \\$\\(LIB_DIR\\)/libjemalloc.a") + (string-append " " (assoc-ref inputs "jemalloc") + "/lib/libjemalloc_pic.a"))) + ;; We don't want to pull in all the global CXXFLAGS here. + (substitute* "deps/sublinear-Li-Stephens/makefile" + (("^CXXFLAGS:=") "CXXFLAGS:= -fPIC ")) + ;; CMAKE_CXX_FLAGS aren't set globally. + (substitute* "deps/kff-cpp-api/CMakeLists.txt" + (("CMAKE_CXX_FLAGS \"") "CMAKE_CXX_FLAGS \" -fPIC ")))) (add-after 'unpack 'dont-build-shared-vgio (lambda _ ;; vg will link with libvgio and fail the 'validate-runpath phase. @@ -2378,7 +2414,7 @@ in-memory footprint at the cost of packing and unpacking.") (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (install-file "bin/vg" (string-append out "/bin")) - (install-file "lib/libvg.a" (string-append out "/lib")) + ;(install-file "lib/libvg.so" (string-append out "/lib")) (for-each (lambda (file) (install-file file (string-append out "/share/man/man1"))) @@ -2408,6 +2444,7 @@ in-memory footprint at the cost of packing and unpacking.") htslib jansson jemalloc + libdeflate libdivsufsort ncurses openmpi -- cgit v1.2.3 From 2ceeed2d0a9938327784b26a68f21ff533e9c634 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 22 Sep 2023 17:33:21 +0300 Subject: Add pggb. --- gn/packages/bioinformatics.scm | 129 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 129 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 700dec4..0a131f5 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages image) @@ -61,6 +62,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages ocaml) + #:use-module (gnu packages parallel) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) @@ -2483,6 +2485,133 @@ multiple sequence alignment.") license:zlib ; deps/sonLib/externalTools/cutest license:boost1.0)))) ; catch.hpp +(define-public pggb + (let ((commit "9ebff27320382e470ed38a85b4448402e1e7c353") + (revision "1")) + (package + (name "pggb") + (version (git-version "0.5.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pangenome/pggb") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rgpj52q3ai7f1saqbilgx5gz4f403x3427wq649qwv84ivmi1sf")))) + (build-system copy-build-system) + (arguments + (list + #:install-plan + #~'(("pggb" "bin/") + ("partition-before-pggb" "bin/") + ("scripts/" "bin/") + ("scripts" "bin/scripts")) + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'patch-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "scripts/vcf_preprocess.sh" + (("bcftools ") + (string-append (search-input-file inputs "/bin/bcftools") " "))) + (wrap-script "scripts/net2communities.py" + `("GUIX_PYTHONPATH" ":" prefix + (,(getenv "GUIX_PYTHONPATH")))))) + (add-after 'install 'wrap-scripts + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each + (lambda (file) + (wrap-script file + `("PATH" ":" prefix + ,(map (lambda (input) (string-append input "/bin")) + '#$(map (lambda (label) (this-package-input label)) + (list "bcftools" + "bedtools" + "gfaffix" + "fastix" + "multiqc" + "mummer" + "odgi-hwcaps" + "pafplot" + "parallel" + "pigz" + "r-data-table" + "rtg-tools" + "samtools" + "seqwish" + "smoothxg" + ;"tabix" + "vcfbub" + "vcflib" + "vg" + "wfmash-hwcaps")))))) + (list (string-append out "/bin/pggb") + (string-append out "/bin/partition-before-pggb") + (string-append out "/bin/gfa2evaluation.sh") + (string-append out "/bin/scripts/gfa2evaluation.sh")))))) + (add-after 'install 'substitute-file-paths + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* (string-append out "/bin/gfa2evaluation.sh") + (("/usr/local/bin/vcf_preprocess.sh") + (string-append out "/bin/vcf_preprocess.sh")) + (("/usr/local/bin/nucmer2vcf.R") + (string-append out "/bin/nucmer2vcf.R"))))))))) + (inputs + (list bcftools + bedtools + gfaffix + guile-3.0 ; for wrap-script + fastix + multiqc + mummer + odgi-hwcaps + pafplot + parallel + pigz + python-igraph + python-pycairo + python-wrapper + r-data-table + rtg-tools + samtools + seqwish + smoothxg + ;tabix + vcfbub + vcflib + vg + wfmash-hwcaps)) + (home-page "https://doi.org/10.1101/2023.04.05.535718") + (synopsis "PanGenome Graph Builder") + (description "@command{pggb} builds +@url{https://doi.org/10.1146%2Fannurev-genom-120219-080406, pangenome} +@url{https://doi.org/10.1038/nbt.4227, variation graphs} from a set of input +sequences. +A pangenome variation graph is a kind of generic multiple sequence alignment. +It lets us understand any kind of sequence variation between a collection of +genomes. It shows us similarity where genomes walk through the same parts of +the graph, and differences where they do not. +@command{pggb} generates this kind of graph using an all-to-all alignment of +input sequences (@url{https://github.com/waveygang/wfmash, wfmash}), graph +induction (@url{https://doi.org/10.1101/2022.02.14.480413, seqwish}), and +progressive normalization (@url{https://github.com/pangenome/smoothxg, +smoothxg}, @url{https://github.com/marschall-lab/GFAffix, gfaffix}). After +construction, @command{pggb} generates diagnostic visualizations of the graph +(@url{https://doi.org/10.1093/bioinformatics/btac308, odgi}). A variant call +report (in VCF) representing both small and large variants can be generated +based on any reference genome included in the graph +(@url{https://github.com/vgteam/vg, vg}). @command{pggb} writes its output in +@url{https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md, GFAv1} format, +which can be used as input by numerous \"genome graph\" and pangenome tools, +such as the @url{https://github.com/vgteam/vg, vg} and +@url{https://doi.org/10.1093/bioinformatics/btac308, odgi} toolkits. +@command{pggb} has been tested at scale in the @acronym{Human Pangenome +Reference Consortium, HPRC} as a method to build a graph from the +@url{https://doi.org/10.1101/2022.07.09.499321, draft human pangenome}.") + (license license:expat)))) + (define-public ucsc-genome-browser (package (name "ucsc-genome-browser") -- cgit v1.2.3 From b50a05b1b907d8eb0728e7b21ddff3b645aaf53e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 08:46:51 +0300 Subject: pggb: Add htslib for tabix dependency. --- gn/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 0a131f5..969f11c 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2529,6 +2529,7 @@ multiple sequence alignment.") (list "bcftools" "bedtools" "gfaffix" + "htslib" "fastix" "multiqc" "mummer" @@ -2541,7 +2542,6 @@ multiple sequence alignment.") "samtools" "seqwish" "smoothxg" - ;"tabix" "vcfbub" "vcflib" "vg" @@ -2563,6 +2563,7 @@ multiple sequence alignment.") bedtools gfaffix guile-3.0 ; for wrap-script + htslib ; tabix fastix multiqc mummer @@ -2578,7 +2579,6 @@ multiple sequence alignment.") samtools seqwish smoothxg - ;tabix vcfbub vcflib vg -- cgit v1.2.3 From 0aaadc958165761b467be003b4ab4de59028414a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 11:00:08 +0300 Subject: rtg-tools: Use a smaller java implementation --- gn/packages/java.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gn/packages/java.scm b/gn/packages/java.scm index c8e1e9b..f39c5c7 100644 --- a/gn/packages/java.scm +++ b/gn/packages/java.scm @@ -32,12 +32,20 @@ #:use-module (gnu packages bioinformatics) #:use-module (gnu packages certs) #:use-module (gnu packages compression) + #:use-module (gnu packages cups) #:use-module (gnu packages gcc) #:use-module (gnu packages java) #:use-module (gnu packages java-compression) #:use-module (gnu packages perl) #:use-module (srfi srfi-1)) +;; This is an attempt to make a smaller version of openjdk +(define openjdk11-minimal + (package/inherit openjdk11 + (inputs + (modify-inputs (package-inputs openjdk11) + (replace "cups" cups-minimal))))) + ;; ---------------------------------------------------------------------------- ;; WORKING PACKAGES ;; ---------------------------------------------------------------------------- @@ -316,7 +324,8 @@ piece of information.") (base32 "13fjhhcjgnynxscaymkn3rpdciplbg2m2qmihc7fxsylgn4m6gxk")))) (build-system ant-build-system) (arguments - `(#:build-target "zip-nojre" + `(#:jdk ,openjdk11-minimal + #:build-target "zip-nojre" #:test-target "runalltests" #:phases (modify-phases %standard-phases -- cgit v1.2.3 From 08c989ee9a328ce5a26cc34a95d71a5c92cfa09e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 12:16:19 +0300 Subject: pggb: Remove python-pycairo --- gn/packages/bioinformatics.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 969f11c..c4463a2 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2572,7 +2572,6 @@ multiple sequence alignment.") parallel pigz python-igraph - python-pycairo python-wrapper r-data-table rtg-tools -- cgit v1.2.3 From d73c21e18365433b78ae5f92d80919ed8f6caa04 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 12:55:44 +0300 Subject: seqwish: Link with sdsl-lib --- gn/packages/bioinformatics.scm | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index c4463a2..a043358 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1637,6 +1637,19 @@ runApp(launch.browser=0, port=4208)~%\n" (else '()))) #:phases (modify-phases %standard-phases + (add-after 'unpack 'link-with-some-shared-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("CMakeLists.txt" + "deps/mmmulti/CMakeLists.txt") + (("\".*libsdsl\\.a\"") "\"-lsdsl\"") + (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") + (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\\$\\{sdsl-lite_INCLUDE\\}") + (string-append (assoc-ref inputs "sdsl-lite") + "/include/sdsl")) + (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") + (string-append (assoc-ref inputs "libdivsufsort") + "/include"))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) ;; Add seqwish to the PATH for the tests. @@ -1646,6 +1659,9 @@ runApp(launch.browser=0, port=4208)~%\n" (invoke "make")))))))) (inputs (list jemalloc + libdivsufsort + openmpi + sdsl-lite zlib)) (native-inputs (list perl)) -- cgit v1.2.3 From a295df1e9e233df66e4e70b55af01909c5cc9b06 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 13:06:48 +0300 Subject: smoothxg: Link with sdsl-lite --- gn/packages/bioinformatics.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a043358..c833e6a 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1705,6 +1705,19 @@ dictionaries to record a queryable version of the graph.") #~(list (string-append "CC = " #$(cc-for-target))) #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'link-with-some-shared-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("CMakeLists.txt" + "deps/mmmulti/CMakeLists.txt" + "deps/odgi/deps/mmmulti/CMakeLists.txt") + (("\".*libsdsl\\.a\"") "\"-lsdsl\"") + (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") + (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\\$\\{sdsl-lite_INCLUDE\\}") + (search-input-directory inputs "/include/sdsl")) + (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") + (dirname + (search-input-file inputs "/include/divsufsort.h")))))) (add-before 'build 'build-abPOA (lambda* (#:key make-flags #:allow-other-keys) ;; This helps with portability to other architectures. @@ -1715,9 +1728,11 @@ dictionaries to record a queryable version of the graph.") (apply invoke "make" "libabpoa" make-flags))))))) (inputs (list jemalloc + libdivsufsort openmpi pybind11 python + sdsl-lite zlib (list zstd "lib"))) (native-inputs -- cgit v1.2.3 From ac6c844f497f9e52887336a35542483053df6ce7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 13:50:14 +0300 Subject: smoothxg: Link with odgi --- gn/packages/bioinformatics.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index c833e6a..c2a2e09 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1713,11 +1713,14 @@ dictionaries to record a queryable version of the graph.") (("\".*libsdsl\\.a\"") "\"-lsdsl\"") (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\".*libodgi\\.a\"") "\"-lodgi\"") (("\\$\\{sdsl-lite_INCLUDE\\}") (search-input-directory inputs "/include/sdsl")) (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") (dirname - (search-input-file inputs "/include/divsufsort.h")))))) + (search-input-file inputs "/include/divsufsort.h"))) + (("\\$\\{odgi_INCLUDE\\}") + (search-input-directory inputs "/include/odgi"))))) (add-before 'build 'build-abPOA (lambda* (#:key make-flags #:allow-other-keys) ;; This helps with portability to other architectures. @@ -1729,6 +1732,7 @@ dictionaries to record a queryable version of the graph.") (inputs (list jemalloc libdivsufsort + odgi openmpi pybind11 python -- cgit v1.2.3 From 10f65dc422f98e2d679754e194ea7c70328b7784 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 15:23:03 +0300 Subject: Provide copy of sdsl-lite with glibc-hwcaps --- gn/packages/datastructures.scm | 117 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 117 insertions(+) create mode 100644 gn/packages/datastructures.scm diff --git a/gn/packages/datastructures.scm b/gn/packages/datastructures.scm new file mode 100644 index 0000000..1744420 --- /dev/null +++ b/gn/packages/datastructures.scm @@ -0,0 +1,117 @@ +;; Datastructures module + +(define-module (gn packages datastructures) + #:use-module (guix packages) + #:use-module (guix gexp) + #:use-module (guix utils) + #:use-module (gnu packages datastructures)) + +(define sdsl-lite-x86-64-v2 + (package/inherit sdsl-lite + (name "sdsl-lite-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:configure-flags flags #~'()) + #~(append (list "-DCMAKE_CXX_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/include")))) + (replace 'install-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libsdsl.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (copy-file "lib/libsdsl_static.a" + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define sdsl-lite-x86-64-v3 + (package/inherit sdsl-lite + (name "sdsl-lite-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:configure-flags flags #~'()) + #~(append (list "-DCMAKE_CXX_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/include")))) + (replace 'install-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libsdsl.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (copy-file "lib/libsdsl_static.a" + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define sdsl-lite-x86-64-v4 + (package/inherit sdsl-lite + (name "sdsl-lite-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:configure-flags flags #~'()) + #~(append (list "-DCMAKE_CXX_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/include")))) + (replace 'install-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libsdsl.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (copy-file "lib/libsdsl_static.a" + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public sdsl-lite-hwcaps + (package/inherit sdsl-lite + (name "sdsl-lite-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "sdsl-lite-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "sdsl-lite-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "sdsl-lite-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs sdsl-lite) + (append sdsl-lite-x86-64-v2 + sdsl-lite-x86-64-v3 + sdsl-lite-x86-64-v4))) + (properties `((tunable? . #f))))) -- cgit v1.2.3 From bc0bc49230c7bfbf2343301345da79a04bff43c9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 15:24:17 +0300 Subject: pggb: Provide version with glibc-hwcaps. --- gn/packages/bioinformatics.scm | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index c2a2e09..1fb8844 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -20,6 +20,7 @@ #:use-module (guix build-system waf) #:use-module (gnu packages) #:use-module (gn packages crates-io) + #:use-module (gn packages datastructures) #:use-module (gn packages java) #:use-module (gn packages ocaml) #:use-module (gn packages python) @@ -2602,7 +2603,7 @@ multiple sequence alignment.") fastix multiqc mummer - odgi-hwcaps + odgi pafplot parallel pigz @@ -2616,7 +2617,7 @@ multiple sequence alignment.") vcfbub vcflib vg - wfmash-hwcaps)) + wfmash)) (home-page "https://doi.org/10.1101/2023.04.05.535718") (synopsis "PanGenome Graph Builder") (description "@command{pggb} builds @@ -2646,6 +2647,19 @@ Reference Consortium, HPRC} as a method to build a graph from the @url{https://doi.org/10.1101/2022.07.09.499321, draft human pangenome}.") (license license:expat)))) +(define use-glibc-hwcaps + (package-input-rewriting/spec + ;; Replace some packages with ones built targeting custom packages build + ;; with glibc-hwcaps support. + `(("sdsl-lite" . ,(const sdsl-lite-hwcaps)) + ("odgi" . ,(const odgi-hwcaps)) + ("wfmash" . ,(const wfmash-hwcaps))))) + +(define-public pggb-with-hwcaps + (package + (inherit (use-glibc-hwcaps pggb)) + (name "pggb-with-hwcaps"))) + (define-public ucsc-genome-browser (package (name "ucsc-genome-browser") -- cgit v1.2.3 From 98eb79fc72ab4b6620eb13b7c021ce4975bc2a71 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 15:52:41 +0300 Subject: pggb: Fix typo. --- gn/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 1fb8844..89766bb 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2561,7 +2561,9 @@ multiple sequence alignment.") (wrap-script file `("PATH" ":" prefix ,(map (lambda (input) (string-append input "/bin")) - '#$(map (lambda (label) (this-package-input label)) + '#$(map (lambda (label) + (or (this-package-input (string-append label "-hwcaps")) + (this-package-input label))) (list "bcftools" "bedtools" "gfaffix" @@ -2569,7 +2571,7 @@ multiple sequence alignment.") "fastix" "multiqc" "mummer" - "odgi-hwcaps" + "odgi" "pafplot" "parallel" "pigz" @@ -2581,7 +2583,7 @@ multiple sequence alignment.") "vcfbub" "vcflib" "vg" - "wfmash-hwcaps")))))) + "wfmash")))))) (list (string-append out "/bin/pggb") (string-append out "/bin/partition-before-pggb") (string-append out "/bin/gfa2evaluation.sh") -- cgit v1.2.3 From 5676b7bb6c6d80a9364c61260aa7aaa2b4baf21e Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 25 Sep 2023 13:33:32 +0300 Subject: Delete python-mypy-0.981. * gn/packages/python.scm (python-mypy-0.981): Delete it. * gn/packages/genenetwork.scm (genenetwork3)[native-inputs]: Replace python-mypy-0.981 with upstream's python-mypy. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 2 +- gn/packages/python.scm | 25 +------------------------ 2 files changed, 2 insertions(+), 25 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5cd663e..4ce207d 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -129,7 +129,7 @@ (list python-click)) (native-inputs `(("python-hypothesis" ,python-hypothesis) - ("python-mypy" ,python-mypy-0.981) + ("python-mypy" ,python-mypy) ("python-mypy-extensions" ,python-mypy-extensions) ("python-pylint" ,python-pylint) ("python-pytest" ,python-pytest) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index d728ef3..020a6a9 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1899,27 +1899,4 @@ concepts.") (base32 "1al030ix0w63hr4s3mqry6s0mlqdj8p242pdqks06br7c25nx3yj")))) (propagated-inputs (modify-inputs (package-propagated-inputs yoyo-migrations) - (append python-importlib-metadata))))) - -(define-public python-mypy-0.981 - (package - (inherit python-mypy) - (name "python-mypy") - (version "0.981") - (source - (origin - ;; Because of https://github.com/python/mypy/issues/9584, the - ;; mypyc/analysis directory is missing in the PyPI archive, leading to - ;; test failures. - (method git-fetch) - (uri (git-reference - (url "https://github.com/python/mypy") - (commit (string-append "v" version)) - ;; Fetch git submodules otherwise typeshed is not fetched. - ;; Typeshed is a collection of Python sources type annotation - ;; (data) files. - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0awigl51an7466yk236f9vsbqpz2jzd6dsg9v5a4cia37vz4li0a")))))) + (append python-importlib-metadata))))) -- cgit v1.2.3 From 2dfb781a7f9292cc171e4063b0fd746244381566 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 24 Sep 2023 17:15:37 +0300 Subject: vg: Link with some shared libraries. --- gn/packages/bioinformatics.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 89766bb..afffcd4 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2372,6 +2372,20 @@ in-memory footprint at the cost of packing and unpacking.") (string-append " " (assoc-ref inputs "raptor2") "/lib/libraptor2.so")) ((" \\$\\(BIN_DIR\\)/rapper") (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))))) + (add-after 'unpack 'link-with-some-shared-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("deps/mmmultimap/CMakeLists.txt" + "deps/xg/CMakeLists.txt" + "deps/xg/deps/mmmulti/CMakeLists.txt") + (("\".*libsdsl\\.a\"") "\"-lsdsl\"") + (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") + (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\\$\\{sdsl-lite_INCLUDE\\}") + (string-append (assoc-ref inputs "sdsl-lite") + "/include/sdsl")) + (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") + (string-append (assoc-ref inputs "libdivsufsort") + "/include"))))) #; (add-before 'patch-source 'use-shared-libvg (lambda* (#:key inputs outputs #:allow-other-keys) -- cgit v1.2.3 From 3eb44711f16cd57ce625ce1011041390c7c270da Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 25 Sep 2023 22:03:12 +0300 Subject: seqwish: Make package tunable. --- gn/packages/bioinformatics.scm | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index afffcd4..285b01d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1613,7 +1613,8 @@ runApp(launch.browser=0, port=4208)~%\n" (snippet #~(begin (use-modules (guix build utils)) - (substitute* '("deps/atomic_queue/Makefile" + (substitute* '("CMakeLists.txt" + "deps/atomic_queue/Makefile" "deps/mmmulti/deps/DYNAMIC/CMakeLists.txt" "deps/mmmulti/deps/atomic_queue/Makefile" "deps/mmmulti/deps/ips4o/CMakeLists.txt") @@ -1625,17 +1626,12 @@ runApp(launch.browser=0, port=4208)~%\n" (build-system cmake-build-system) (arguments `(#:configure-flags - '(,@(cond ((target-x86-64?) - ;; This seems to be about the minimum - '("-DEXTRA_FLAGS=-march=x86-64-v2")) - ((target-aarch64?) - '("-DEXTRA_FLAGS=-march=armv8-a")) - ((target-riscv64?) - '("-DEXTRA_FLAGS=-march=rv64imafdc")) - ((target-ppc64le?) - '("-DEXTRA_FLAGS=-mcpu=power8")) - ;; The default case is '-march=native' - (else '()))) + '(,@(if (target-x86?) + ;; This is the minimum needed to compile on x86_64, and is a + ;; subset of any other optimizations which might be applied. + '("-DCMAKE_C_FLAGS=-mcx16" + "-DCMAKE_CXX_FLAGS=-mcx16") + '())) #:phases (modify-phases %standard-phases (add-after 'unpack 'link-with-some-shared-libraries @@ -1678,6 +1674,7 @@ large inputs that are commonly encountered when working with large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.") + (properties `((tunable? . #t))) (license license:expat))) (define-public smoothxg -- cgit v1.2.3 From 6ee7dfd989d93a083b13a0463e486b5c85ca1ac9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 26 Sep 2023 10:37:16 +0300 Subject: seqwish: Build and link against shared library. --- gn/packages/bioinformatics.scm | 32 ++++--- seqwish-shared-library.diff | 195 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 216 insertions(+), 11 deletions(-) create mode 100644 seqwish-shared-library.diff diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 285b01d..50c207d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1609,7 +1609,8 @@ runApp(launch.browser=0, port=4208)~%\n" (file-name (git-file-name name version)) (sha256 (base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x")) - (patches (search-patches "seqwish-paryfor-riscv.diff")) + (patches (search-patches "seqwish-paryfor-riscv.diff" + "seqwish-shared-library.diff")) (snippet #~(begin (use-modules (guix build utils)) @@ -1626,14 +1627,24 @@ runApp(launch.browser=0, port=4208)~%\n" (build-system cmake-build-system) (arguments `(#:configure-flags - '(,@(if (target-x86?) - ;; This is the minimum needed to compile on x86_64, and is a - ;; subset of any other optimizations which might be applied. - '("-DCMAKE_C_FLAGS=-mcx16" - "-DCMAKE_CXX_FLAGS=-mcx16") - '())) + (cons* ,@(if (target-x86?) + ;; This is the minimum needed to compile on x86_64, and is a + ;; subset of any other optimizations which might be applied. + '("-DCMAKE_C_FLAGS=-mcx16" + "-DCMAKE_CXX_FLAGS=-mcx16") + '()) + '("-DSEQWISH_LINK_SHARED_LIBRARY=ON")) #:phases (modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + ;; This stashes the build version in the executable. + (mkdir "include") + (substitute* "CMakeLists.txt" + (("^execute_process") "#execute_process")) + (with-output-to-file "include/seqwish_git_version.hpp" + (lambda () + (format #t "#define SEQWISH_GIT_VERSION \"~a\"~%" ,version))))) (add-after 'unpack 'link-with-some-shared-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("CMakeLists.txt" @@ -1642,11 +1653,10 @@ runApp(launch.browser=0, port=4208)~%\n" (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") (("\\$\\{sdsl-lite_INCLUDE\\}") - (string-append (assoc-ref inputs "sdsl-lite") - "/include/sdsl")) + (search-input-directory inputs "/include/sdsl")) (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") - (string-append (assoc-ref inputs "libdivsufsort") - "/include"))))) + (dirname + (search-input-file inputs "/include/divsufsort.h")))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) ;; Add seqwish to the PATH for the tests. diff --git a/seqwish-shared-library.diff b/seqwish-shared-library.diff new file mode 100644 index 0000000..be982de --- /dev/null +++ b/seqwish-shared-library.diff @@ -0,0 +1,195 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 09eafb5..a39f90f 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -7,6 +7,8 @@ project(seqwish) + # We build using c++14 + set(CMAKE_CXX_STANDARD 14) + ++include(GNUInstallDirs) ++ + set(THREADS_PREFER_PTHREAD_FLAG ON) + find_package(Threads REQUIRED) + +@@ -26,6 +28,8 @@ if(NOT DEFINED EXTRA_FLAGS) + "Extra compilation flags for C and CXX." FORCE) + endif() + ++set(SEQWISH_LINK_SHARED_LIBRARY OFF CACHE BOOL "Do not link against the libseqwish shared library") ++ + if (${CMAKE_BUILD_TYPE} MATCHES Release) + set(EXTRA_FLAGS "-Ofast ${EXTRA_FLAGS}") + set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast +@@ -82,7 +86,7 @@ include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) + # sdsl-lite (full build using its cmake config) + ExternalProject_Add(sdsl-lite + SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite" +- CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=" ++ CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_CXX_FLAGS=-fPIC;-DCMAKE_C_FLAGS=-fPIC;-DCMAKE_INSTALL_PREFIX=" + UPDATE_COMMAND "" + INSTALL_COMMAND "") + ExternalProject_Get_property(sdsl-lite INSTALL_DIR) +@@ -203,27 +207,125 @@ set(mio_INCLUDE "${SOURCE_DIR}/include") + #set(CMAKE_BUILD_TYPE Debug) + set(CMAKE_BUILD_TYPE Release) + ++# set up our target libraries and specify its dependencies and includes ++add_library( libseqwish_static ++ ${CMAKE_SOURCE_DIR}/src/utils.cpp ++ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp ++ ${CMAKE_SOURCE_DIR}/src/main.cpp ++ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp ++ ${CMAKE_SOURCE_DIR}/src/paf.cpp ++ ${CMAKE_SOURCE_DIR}/src/sxs.cpp ++ ${CMAKE_SOURCE_DIR}/src/cigar.cpp ++ ${CMAKE_SOURCE_DIR}/src/alignments.cpp ++ ${CMAKE_SOURCE_DIR}/src/pos.cpp ++ ${CMAKE_SOURCE_DIR}/src/match.cpp ++ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp ++ ${CMAKE_SOURCE_DIR}/src/links.cpp ++ ${CMAKE_SOURCE_DIR}/src/compact.cpp ++ ${CMAKE_SOURCE_DIR}/src/dna.cpp ++ ${CMAKE_SOURCE_DIR}/src/gfa.cpp ++ ${CMAKE_SOURCE_DIR}/src/vgp.cpp ++ ${CMAKE_SOURCE_DIR}/src/exists.cpp ++ ${CMAKE_SOURCE_DIR}/src/time.cpp ++ ${CMAKE_SOURCE_DIR}/src/mmap.cpp ++ ) ++add_dependencies(libseqwish_static tayweeargs) ++add_dependencies(libseqwish_static sdsl-lite) ++add_dependencies(libseqwish_static gzipreader) ++add_dependencies(libseqwish_static mmmulti) ++add_dependencies(libseqwish_static iitii) ++add_dependencies(libseqwish_static ips4o) ++add_dependencies(libseqwish_static bbhash) ++add_dependencies(libseqwish_static atomicbitvector) ++add_dependencies(libseqwish_static atomicqueue) ++add_dependencies(libseqwish_static ska) ++add_dependencies(libseqwish_static paryfor) ++add_dependencies(libseqwish_static mio) ++target_include_directories(libseqwish_static PUBLIC ++ "${sdsl-lite_INCLUDE}" ++ "${sdsl-lite-divsufsort_INCLUDE}" ++ "${tayweeargs_INCLUDE}" ++ "${gzipreader_INCLUDE}" ++ "${ips4o_INCLUDE}" ++ "${mmmulti_INCLUDE}" ++ "${iitii_INCLUDE}" ++ "${bbhash_INCLUDE}" ++ "${atomicbitvector_INCLUDE}" ++ "${atomicqueue_INCLUDE}" ++ "${ska_INCLUDE}" ++ "${paryfor_INCLUDE}" ++ "${mio_INCLUDE}") ++target_link_libraries(libseqwish_static ++ "${sdsl-lite_LIB}/libsdsl.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" ++ "-latomic" ++ Threads::Threads ++ jemalloc ++ z) ++set_target_properties(libseqwish_static PROPERTIES OUTPUT_NAME "seqwish") ++ ++add_library( libseqwish SHARED ++ ${CMAKE_SOURCE_DIR}/src/utils.cpp ++ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp ++ ${CMAKE_SOURCE_DIR}/src/main.cpp ++ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp ++ ${CMAKE_SOURCE_DIR}/src/paf.cpp ++ ${CMAKE_SOURCE_DIR}/src/sxs.cpp ++ ${CMAKE_SOURCE_DIR}/src/cigar.cpp ++ ${CMAKE_SOURCE_DIR}/src/alignments.cpp ++ ${CMAKE_SOURCE_DIR}/src/pos.cpp ++ ${CMAKE_SOURCE_DIR}/src/match.cpp ++ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp ++ ${CMAKE_SOURCE_DIR}/src/links.cpp ++ ${CMAKE_SOURCE_DIR}/src/compact.cpp ++ ${CMAKE_SOURCE_DIR}/src/dna.cpp ++ ${CMAKE_SOURCE_DIR}/src/gfa.cpp ++ ${CMAKE_SOURCE_DIR}/src/vgp.cpp ++ ${CMAKE_SOURCE_DIR}/src/exists.cpp ++ ${CMAKE_SOURCE_DIR}/src/time.cpp ++ ${CMAKE_SOURCE_DIR}/src/mmap.cpp ++ ${CMAKE_SOURCE_DIR}/src/version.cpp ++ ) ++add_dependencies(libseqwish tayweeargs) ++add_dependencies(libseqwish sdsl-lite) ++add_dependencies(libseqwish gzipreader) ++add_dependencies(libseqwish mmmulti) ++add_dependencies(libseqwish iitii) ++add_dependencies(libseqwish ips4o) ++add_dependencies(libseqwish bbhash) ++add_dependencies(libseqwish atomicbitvector) ++add_dependencies(libseqwish atomicqueue) ++add_dependencies(libseqwish ska) ++add_dependencies(libseqwish paryfor) ++add_dependencies(libseqwish mio) ++target_include_directories(libseqwish PUBLIC ++ "${sdsl-lite_INCLUDE}" ++ "${sdsl-lite-divsufsort_INCLUDE}" ++ "${tayweeargs_INCLUDE}" ++ "${gzipreader_INCLUDE}" ++ "${ips4o_INCLUDE}" ++ "${mmmulti_INCLUDE}" ++ "${iitii_INCLUDE}" ++ "${bbhash_INCLUDE}" ++ "${atomicbitvector_INCLUDE}" ++ "${atomicqueue_INCLUDE}" ++ "${ska_INCLUDE}" ++ "${paryfor_INCLUDE}" ++ "${mio_INCLUDE}") ++target_link_libraries(libseqwish ++ "${sdsl-lite_LIB}/libsdsl.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" ++ "-latomic" ++ Threads::Threads ++ jemalloc ++ z) ++set_target_properties(libseqwish PROPERTIES OUTPUT_NAME "seqwish") ++ + # set up our target executable and specify its dependencies and includes + add_executable(seqwish +- ${CMAKE_SOURCE_DIR}/src/utils.cpp +- ${CMAKE_SOURCE_DIR}/src/tempfile.cpp + ${CMAKE_SOURCE_DIR}/src/main.cpp +- ${CMAKE_SOURCE_DIR}/src/seqindex.cpp +- ${CMAKE_SOURCE_DIR}/src/paf.cpp +- ${CMAKE_SOURCE_DIR}/src/sxs.cpp +- ${CMAKE_SOURCE_DIR}/src/cigar.cpp +- ${CMAKE_SOURCE_DIR}/src/alignments.cpp +- ${CMAKE_SOURCE_DIR}/src/pos.cpp +- ${CMAKE_SOURCE_DIR}/src/match.cpp +- ${CMAKE_SOURCE_DIR}/src/transclosure.cpp +- ${CMAKE_SOURCE_DIR}/src/links.cpp +- ${CMAKE_SOURCE_DIR}/src/compact.cpp +- ${CMAKE_SOURCE_DIR}/src/dna.cpp +- ${CMAKE_SOURCE_DIR}/src/gfa.cpp +- ${CMAKE_SOURCE_DIR}/src/vgp.cpp +- ${CMAKE_SOURCE_DIR}/src/exists.cpp +- ${CMAKE_SOURCE_DIR}/src/time.cpp +- ${CMAKE_SOURCE_DIR}/src/mmap.cpp + ${CMAKE_SOURCE_DIR}/src/version.cpp + ) + add_dependencies(seqwish tayweeargs) +@@ -252,6 +354,11 @@ target_include_directories(seqwish PUBLIC + "${ska_INCLUDE}" + "${paryfor_INCLUDE}" + "${mio_INCLUDE}") ++if( SEQWISH_LINK_SHARED_LIBRARY ) ++ target_link_libraries( seqwish libseqwish ) ++else() ++ target_link_libraries( seqwish libseqwish_static ) ++endif() + target_link_libraries(seqwish + "${sdsl-lite_LIB}/libsdsl.a" + "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" +@@ -269,4 +376,6 @@ endif() + file(MAKE_DIRECTORY ${CMAKE_SOURCE_DIR}/include) + execute_process(COMMAND bash ${CMAKE_SOURCE_DIR}/scripts/generate_git_version.sh ${CMAKE_SOURCE_DIR}/include) + +-install(TARGETS seqwish DESTINATION bin) ++install(TARGETS seqwish DESTINATION "${CMAKE_INSTALL_BIDIR}") ++install(TARGETS libseqwish LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") ++install(TARGETS libseqwish_static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}") -- cgit v1.2.3 From 65a7e2f8a9308ca171013c8533f41e3c8bdba71a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 26 Sep 2023 11:36:44 +0300 Subject: seqwish: Provide glibc-hwcaps version --- gn/packages/bioinformatics.scm | 119 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 119 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 50c207d..15d8811 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1687,6 +1687,124 @@ dictionaries to record a queryable version of the graph.") (properties `((tunable? . #t))) (license license:expat))) +(define-public seqwish-x86-64-v2 + (package/inherit seqwish + (name "seqwish-x86-64-v2") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public seqwish-x86-64-v3 + (package/inherit seqwish + (name "seqwish-x86-64-v3") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public seqwish-x86-64-v4 + (package/inherit seqwish + (name "seqwish-x86-64-v4") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +;; This copy of seqwish will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public seqwish-hwcaps + (package/inherit seqwish + (name "seqwish-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs seqwish) + (append seqwish-x86-64-v2 + seqwish-x86-64-v3 + seqwish-x86-64-v4))) + (properties `((tunable? . #f))))) + (define-public smoothxg (package (name "smoothxg") @@ -2675,6 +2793,7 @@ Reference Consortium, HPRC} as a method to build a graph from the ;; Replace some packages with ones built targeting custom packages build ;; with glibc-hwcaps support. `(("sdsl-lite" . ,(const sdsl-lite-hwcaps)) + ("seqwish" . ,(const seqwish-hwcaps)) ("odgi" . ,(const odgi-hwcaps)) ("wfmash" . ,(const wfmash-hwcaps))))) -- cgit v1.2.3 From 01ebd8c995a6bbd45e427ae849cb7e08e84ab6b8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 26 Sep 2023 12:46:26 +0300 Subject: vg: Update package definition --- gn/packages/bioinformatics.scm | 65 +++++++++++++++++++++++------------------- 1 file changed, 36 insertions(+), 29 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 15d8811..9886e3f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2438,65 +2438,69 @@ in-memory footprint at the cost of packing and unpacking.") (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a") ((" \\$\\(LIB_DIR\\)/libtabixpp\\.a") - (string-append " " (assoc-ref inputs "tabixpp") "/lib/libtabixpp.so")) + (string-append " " (search-input-file inputs "/lib/libtabixpp.so"))) (("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc") - (string-append " " (assoc-ref inputs "tabixpp") "/lib/pkgconfig/tabixpp.pc")) + (string-append " " (search-input-file inputs "/lib/pkgconfig/tabixpp.pc"))) (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a") ((" \\$\\(LIB_DIR\\)/libhts\\.a") - (string-append " " (assoc-ref inputs "htslib") "/lib/libhts.so")) + (string-append " " (search-input-file inputs "/lib/libhts.so"))) (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") - (string-append " " (assoc-ref inputs "htslib") "/lib/pkgconfig/htslib.pc")) + (string-append " " (search-input-file inputs "/lib/pkgconfig/htslib.pc"))) (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a") ((" \\$\\(LIB_DIR\\)/libdeflate\\.a") - (string-append " " (assoc-ref inputs "libdeflate") "/lib/libdeflate.so")) + (string-append " " (search-input-file inputs "/lib/libdeflate.so"))) ((" \\$\\(LIB_DIR\\)/libvcflib.a") - (string-append " " (assoc-ref inputs "vcflib") "/lib/libvcflib.so")) + (string-append " " (search-input-file inputs "/lib/libvcflib.so"))) ((" \\$\\(BIN_DIR\\)/vcf2tsv") - (string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv")) + (string-append " " (search-input-file inputs "/bin/vcf2tsv"))) ((" \\$\\(FASTAHACK_DIR\\)/fastahack") - (string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) + (string-append " " (search-input-file inputs "/bin/fastahack"))) (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o") - (string-append "+= " (assoc-ref inputs "fastahack") "/lib/libfastahack.so")) + (string-append "+= " (search-input-file inputs "/lib/libfastahack.so"))) ((" \\$\\(LIB_DIR\\)/libsnappy.a") - (string-append " " (assoc-ref inputs "snappy") "/lib/libsnappy.so")) + (string-append " " (search-input-file inputs "/lib/libsnappy.so"))) ;; Only link against the libraries in the elfutils package. (("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf") ((" \\$\\(LIB_DIR\\)/libelf.a") - (string-append " " (assoc-ref inputs "elfutils") "/lib/libelf.so")) + (string-append " " (search-input-file inputs "/lib/libelf.so"))) ((" \\$\\(LIB_DIR\\)/libdw.a") - (string-append " " (assoc-ref inputs "elfutils") "/lib/libdw.so")) + (string-append " " (search-input-file inputs "/lib/libdw.so"))) ;; We need the Make.helper file in SDSL_DIR for gcsa2 ;((" \\$\\(LIB_DIR\\)/libsdsl.a") - ; (string-append " " (assoc-ref inputs "sdsl-lite") "/lib/libsdsl.so")) + ; (string-append " " (search-input-file inputs "/lib/libsdsl.so"))) ((" \\$\\(LIB_DIR\\)/%divsufsort.a") - (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/%divsufsort.so")) + (string-append " " (dirname + (search-input-file inputs "/lib/libdivsufsort.so")) + "%divsufsort.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort.a") - (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort.so")) + (string-append " " (search-input-file inputs "/lib/libdivsufsort.so"))) ((" \\$\\(LIB_DIR\\)/%divsufsort64.a") - (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/%divsufsort64.so")) + (string-append " " (dirname + (search-input-file inputs "/lib/libdivsufsort64.so")) + "%divsufsort64.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a") - (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort64.so")) + (string-append " " (search-input-file inputs "/lib/libdivsufsort64.so"))) ((" \\$\\(LIB_DIR\\)/libjemalloc.a") - (string-append " " (assoc-ref inputs "jemalloc") "/lib/libjemalloc.a")) + (string-append " " (search-input-file inputs "/lib/libjemalloc.a"))) ((" \\$\\(INC_DIR\\)/sparsehash") - (string-append " " (assoc-ref inputs "sparsehash") "/include/sparsehash")) + (string-append " " (search-input-directory inputs "/include/sparsehash"))) ((" \\$\\(INC_DIR\\)/raptor2") - (string-append " " (assoc-ref inputs "raptor2") "/include/raptor2")) + (string-append " " (search-input-directory inputs "/include/raptor2"))) ((" \\$\\(LIB_DIR\\)/libraptor2.a") - (string-append " " (assoc-ref inputs "raptor2") "/lib/libraptor2.so")) + (string-append " " (search-input-file inputs "/lib/libraptor2.so"))) ((" \\$\\(BIN_DIR\\)/rapper") - (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))))) + (string-append " " (search-input-file inputs "/bin/rapper")))))) (add-after 'unpack 'link-with-some-shared-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("deps/mmmultimap/CMakeLists.txt" @@ -2506,11 +2510,10 @@ in-memory footprint at the cost of packing and unpacking.") (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") (("\\$\\{sdsl-lite_INCLUDE\\}") - (string-append (assoc-ref inputs "sdsl-lite") - "/include/sdsl")) + (search-input-directory inputs "/include/sdsl")) (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") - (string-append (assoc-ref inputs "libdivsufsort") - "/include"))))) + (dirname + (search-input-file inputs "/include/divsufsort.h")))))) #; (add-before 'patch-source 'use-shared-libvg (lambda* (#:key inputs outputs #:allow-other-keys) @@ -2568,14 +2571,18 @@ in-memory footprint at the cost of packing and unpacking.") (substitute* "test/t/02_vg_construct.t" (("../deps/fastahack/fastahack") (which "fastahack")) (("../bin/vcf2tsv") (which "vcf2tsv"))) - ;; Lets skip the 7 failing tests for now. They fail with our + ;; Lets skip the 9 failing tests for now. They fail with our ;; bash-tap and the bundled one. (substitute* "test/t/02_vg_construct.t" - ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n") - ((".*the graph contains.*") "is $(true) \"\" \"\"\n")) + ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n")) + (substitute* "test/t/07_vg_map.t" + ;; Change in fasta's output + (("identity\\) 1 \"") "identity) 1.0 \"")) (substitute* '("test/t/07_vg_map.t" "test/t/33_vg_mpmap.t") ((".*node id.*") "is $(true) \"\" \"\"\n")) + (substitute* "test/t/48_vg_convert.t" + (("true \"vg.*") "true \"true\"\n")) (substitute* "test/t/50_vg_giraffe.t" ((".*A long read can.*") "is $(true) \"\" \"\"\n") ((".*A long read has.*") "is $(true) \"\" \"\"\n") -- cgit v1.2.3 From a848475c6bf6321dde971528f7c8d0c4d6e9e0d5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 26 Sep 2023 13:54:28 +0300 Subject: gsl: Provide glibc-hwcaps version. --- gn/packages/bioinformatics.scm | 4 +- gn/packages/maths.scm | 108 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 111 insertions(+), 1 deletion(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 9886e3f..95dda00 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -22,6 +22,7 @@ #:use-module (gn packages crates-io) #:use-module (gn packages datastructures) #:use-module (gn packages java) + #:use-module (gn packages maths) #:use-module (gn packages ocaml) #:use-module (gn packages python) #:use-module (gnu packages algebra) @@ -2799,7 +2800,8 @@ Reference Consortium, HPRC} as a method to build a graph from the (package-input-rewriting/spec ;; Replace some packages with ones built targeting custom packages build ;; with glibc-hwcaps support. - `(("sdsl-lite" . ,(const sdsl-lite-hwcaps)) + `(;("gsl" . ,(const gsl-hwcaps)) ; Causes too many rebuilds through multiqc + ("sdsl-lite" . ,(const sdsl-lite-hwcaps)) ("seqwish" . ,(const seqwish-hwcaps)) ("odgi" . ,(const odgi-hwcaps)) ("wfmash" . ,(const wfmash-hwcaps))))) diff --git a/gn/packages/maths.scm b/gn/packages/maths.scm index 1c1c1ae..7dfb896 100644 --- a/gn/packages/maths.scm +++ b/gn/packages/maths.scm @@ -3,6 +3,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) + #:use-module (guix gexp) #:use-module (gnu packages gcc) #:use-module (gnu packages gperf) #:use-module (gnu packages maths) @@ -131,3 +132,110 @@ (inputs `(,@(fold alist-delete (package-inputs suitesparse) '("metis")))))) + +(define-public gsl-x86-64-v2 + (package/inherit gsl + (name "gsl-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:make-flags flags #~'()) + #~(append (list "CFLAGS=-march=x86-64-v2" + "CXXFLAGS=-march=x86-64-v2") + #$flags)) + ((#:configure-flags flags #~'()) + #~(append (list (string-append "--libdir=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public gsl-x86-64-v3 + (package/inherit gsl + (name "gsl-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:make-flags flags #~'()) + #~(append (list "CFLAGS=-march=x86-64-v3" + "CXXFLAGS=-march=x86-64-v3") + #$flags)) + ((#:configure-flags flags #~'()) + #~(append (list (string-append "--libdir=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public gsl-x86-64-v4 + (package/inherit gsl + (name "gsl-x86-64-v4") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:make-flags flags #~'()) + #~(append (list "CFLAGS=-march=x86-64-v4" + "CXXFLAGS=-march=x86-64-v4") + #$flags)) + ((#:configure-flags flags #~'()) + #~(append (list (string-append "--libdir=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +;; This copy of gsl will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public gsl-hwcaps + (package/inherit gsl + (name "gsl-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "gsl-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "gsl-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "gsl-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs gsl) + (append gsl-x86-64-v2 + gsl-x86-64-v3 + gsl-x86-64-v4))) + (properties `((tunable? . #f))))) -- cgit v1.2.3 From 0d8ed9f6c2ca7804a73028c947db0a2a6a61e7cb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 26 Sep 2023 16:18:12 +0300 Subject: pggb: wrap with more packages --- gn/packages/bioinformatics.scm | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 95dda00..535018b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2692,7 +2692,11 @@ multiple sequence alignment.") ("scripts" "bin/scripts")) #:phases #~(modify-phases %standard-phases - (add-before 'install 'patch-binary-path + (add-after 'unpack 'force-python3 + (lambda _ + (substitute* (find-files "scripts" "\\.py$") + (("/usr/bin/python") "/usr/bin/python3")))) + (add-before 'install 'patch-and-wrap-scripts (lambda* (#:key inputs #:allow-other-keys) (substitute* "scripts/vcf_preprocess.sh" (("bcftools ") @@ -2706,6 +2710,8 @@ multiple sequence alignment.") (for-each (lambda (file) (wrap-script file + `("R_LIBS_SITE" ":" prefix + (,(getenv "R_LIBS_SITE"))) `("PATH" ":" prefix ,(map (lambda (input) (string-append input "/bin")) '#$(map (lambda (label) @@ -2722,7 +2728,9 @@ multiple sequence alignment.") "pafplot" "parallel" "pigz" + "python" "r-data-table" + "r-minimal" "rtg-tools" "samtools" "seqwish" @@ -2756,9 +2764,10 @@ multiple sequence alignment.") pafplot parallel pigz + python python-igraph - python-wrapper r-data-table + r-minimal rtg-tools samtools seqwish -- cgit v1.2.3 From 29633fd3a8bafce405bba487802cd3720e642d11 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 26 Sep 2023 17:11:58 +0300 Subject: pggb: Add missing inputs --- gn/packages/bioinformatics.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 535018b..9de6ad8 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2717,7 +2717,8 @@ multiple sequence alignment.") '#$(map (lambda (label) (or (this-package-input (string-append label "-hwcaps")) (this-package-input label))) - (list "bcftools" + (list "bc" + "bcftools" "bedtools" "gfaffix" "htslib" @@ -2735,6 +2736,7 @@ multiple sequence alignment.") "samtools" "seqwish" "smoothxg" + "time" "vcfbub" "vcflib" "vg" @@ -2752,7 +2754,8 @@ multiple sequence alignment.") (("/usr/local/bin/nucmer2vcf.R") (string-append out "/bin/nucmer2vcf.R"))))))))) (inputs - (list bcftools + (list bc + bcftools bedtools gfaffix guile-3.0 ; for wrap-script @@ -2772,6 +2775,7 @@ multiple sequence alignment.") samtools seqwish smoothxg + time vcfbub vcflib vg -- cgit v1.2.3 From de23151c31cd078d40d715e63daf2529d8e35a12 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 12:43:03 +0300 Subject: gn-auth: Update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4ce207d..4768ca8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd"))) + (commit "a8ebba8266618ec53fe485ee84d09d0cdff898a1"))) (hash (content-hash (base32 - "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) + "0ksdzkrb9z9br9mca9dxprfp57wj7ffd9gqnbsxg2gq0yj1ri9af"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 9e8f9d8e65290d8fdee9b15cb1afddf1a4f01466 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 12:54:32 +0300 Subject: gn-auth: Update commit and hash * Update the commit hash and the hash of the files after updating the guix-bioinformatics channel configurations for the gn-auth channel. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4768ca8..40c8857 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "a8ebba8266618ec53fe485ee84d09d0cdff898a1"))) + (commit "51534a303c22f919ec5b237f7bcc948e66978fdc"))) (hash (content-hash (base32 - "0ksdzkrb9z9br9mca9dxprfp57wj7ffd9gqnbsxg2gq0yj1ri9af"))))) + "0gp1lyx3r227s078hab079dckc8iambvnq1yd84qr03yi4ch8q19"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 9be94892e0a2446f104a72f680a926020ad8578c Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 13:04:22 +0300 Subject: gn-auth: Use upstream python-mypy --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 40c8857..d2b59c5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "51534a303c22f919ec5b237f7bcc948e66978fdc"))) + (commit "f4b9e51192a8dea3399ca83226a47a518b3ea5c5"))) (hash (content-hash (base32 - "0gp1lyx3r227s078hab079dckc8iambvnq1yd84qr03yi4ch8q19"))))) + "054i9va4850dcfiwzz79r4w4h2cinh3d6l1l4jc8s4sy7bjb50zp"))))) (build-system python-build-system) (arguments (list @@ -490,7 +490,7 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy-0.981) + `(("python-mypy" ,python-mypy) ("python-pytest" ,python-pytest) ("python-pylint" ,python-pylint) ("python-hypothesis" ,python-hypothesis) -- cgit v1.2.3 From 761a61bd77d1a4ade316bebe30aee1a136071025 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 13:42:13 +0300 Subject: gn-auth: Use newer setup.py Use updated setup.py to try and fix issues with the `sanity-check` phase. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d2b59c5..69d2e23 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "f4b9e51192a8dea3399ca83226a47a518b3ea5c5"))) + (commit "971c15423bbc3c090c28eca7a50caf90a5ad5411"))) (hash (content-hash (base32 - "054i9va4850dcfiwzz79r4w4h2cinh3d6l1l4jc8s4sy7bjb50zp"))))) + "07lkbdjhqr0qfw8v4rzqw1phyi63qxknzyyavsqmimrvx8wkq4nd"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 31bc467225bab461ba758e2e31299eb47c8e5c44 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 14:33:27 +0300 Subject: gn-auth: List packages to install List all packages to install to hopefully fix failure in `sanity-check` phase. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 69d2e23..42296c0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "971c15423bbc3c090c28eca7a50caf90a5ad5411"))) + (commit "9961237078834c342e5bf7d7d6ffd7f27be09c67"))) (hash (content-hash (base32 - "07lkbdjhqr0qfw8v4rzqw1phyi63qxknzyyavsqmimrvx8wkq4nd"))))) + "1nmwcwa897gv4dmn16swk7g9lsnl7jnzlb6qbsg38pgiwhyh6mrk"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From c094f4635a6bcdeed697875ea991f91b670e675e Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 27 Sep 2023 17:49:28 +0300 Subject: gn-auth: Fix missing import --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 42296c0..eaab3cd 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -475,11 +475,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "9961237078834c342e5bf7d7d6ffd7f27be09c67"))) + (commit "acd1a3d29900cff70ccc82dbe8ad1dc4b4c0fe8e"))) (hash (content-hash (base32 - "1nmwcwa897gv4dmn16swk7g9lsnl7jnzlb6qbsg38pgiwhyh6mrk"))))) + "19c0qshj511w4rhfbj5d9gvcscnbsjhk6xnr10ajjvr61w42qmq4"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 100148937e86311c24a41e97f6e7f0082fdacc33 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 4 Oct 2023 14:14:04 +0300 Subject: gn: javascript: Replace htmx.min.js with htmx.js. * gn/packages/javascript.scm (javascript-htmx) [arguments]: Replace "dist/htmx.min.js" with "dist/htmx.js" since we already are using the minify-build-system. Signed-off-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index a2db29b..9398bf2 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1899,7 +1899,7 @@ vector graphics.") "14m9wan8sp5lzblfzbi1hln621p7ld3npajxrhq1a19zm5bcrz3y")))) (build-system minify-build-system) (arguments - `(#:javascript-files '("dist/htmx.min.js"))) + `(#:javascript-files '("dist/htmx.js"))) (home-page "https://htmx.org/") (synopsis "High Power Tools for HTML") (description -- cgit v1.2.3 From 51931f0b587749d31825cee74d0ff76c5aedf6eb Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 6 Oct 2023 12:54:57 +0300 Subject: genenetwork3: Add python-pyld to propagated-inputs. * gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add python-ld. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index eaab3cd..ac26fd0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -153,6 +153,7 @@ ;; python-pingouin << build failing ("python-pingouin-without-tests" ,python-pingouin-without-tests) ("python-plotly" ,python-plotly) + ("python-pyld" ,python-pyld) ("python-scikit-learn" ,python-scikit-learn) ("python-pymonad" ,python-pymonad) ("python-redis" ,python-redis) -- cgit v1.2.3 From dab19f78848da9c176238cc1eec486964a54dfca Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 19 Oct 2023 13:32:19 +0100 Subject: Remove bh20-seq-resource. The package is broken, some of its inputs have been removed from upstream Guix, and we no longer need this package. * gn/packages/bioinformatics.scm (bh20-seq-resource): Delete variable. * gn/services/bh20-seq-resource-container.scm: Delete file. --- gn/packages/bioinformatics.scm | 73 ------------------ gn/services/bh20-seq-resource-container.scm | 110 ---------------------------- 2 files changed, 183 deletions(-) delete mode 100644 gn/services/bh20-seq-resource-container.scm diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 9de6ad8..2832ea6 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2096,79 +2096,6 @@ reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.") (license license:expat))) -(define-public bh20-seq-resource - (let ((commit "2ae71911cd87ce4f2eabdff21e538267b3270d45") - (revision "4")) - (package - (name "bh20-seq-resource") - (version (git-version "1.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pubseq/bh20-seq-resource") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1k6cc88hrcm77jwpdk2084q0zirv2vlbz3c07nmpbhk1lhqk5x0n")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file "gittaggers.py"))))) - (build-system python-build-system) - (arguments - (list - #:tests? #f ; Tests can't find pytest - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'patch-program-calls - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "bh20sequploader/qc_fasta.py" - (("\"minimap2\"") - (string-append "\"" (search-input-file - inputs "/bin/minimap2") - "\"")))))))) - (propagated-inputs - (list python-arvados-python-client - python-schema-salad - python-magic - python-pyshex - python-pyshexc-0.7 - python-py-dateutil - - ;; for the web - python-flask - python-pyyaml - python-redis - - ;; and for the service - python - gunicorn)) - (inputs - (list minimap2)) - (native-inputs - (list python-pytest-4 ; < 6 - python-pytest-runner-4)) ; < 5 - (home-page "https://github.com/pubseq/bh20-seq-resource") - (synopsis - "Tool to upload SARS-CoV-19 sequences and service to kick off analysis") - (description "This repository provides a sequence uploader for the -COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use -it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely -available to other researchers.") - (license license:asl2.0)))) - -;; This version has no profile collisions. -(define-public bh20-seq-resource-for-service - (package - ;(inherit (fix-profile-collisions-for-bh20 bh20-seq-resource)) - (inherit - ((package-input-rewriting/spec - `(("python-google-api-core" . ,(const python-google-api-core-1)) - ("python-google-auth" . ,(const python-google-auth-1)) - ("python-pyparsing" . ,(const python-pyparsing-2.4.7)))) - bh20-seq-resource)) - (properties `((hidden? . #t))))) - (define-public python-scanpy-git (let ((commit "590d42309f9ed6550d7b887039990edfc1ac7648") ; April 22, 2020 (revision "1")) diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm deleted file mode 100644 index e0eccf7..0000000 --- a/gn/services/bh20-seq-resource-container.scm +++ /dev/null @@ -1,110 +0,0 @@ -(define-module (gn services bh20-seq-resource-container)) - -(use-modules (gnu) - (gn packages bioinformatics) - (guix modules) - ((guix packages) #:select (package-source)) - (guix records) - (guix build-system python) ; for python-version from guix/build/python-build-system.scm - (ice-9 match)) -(use-service-modules shepherd) -(use-package-modules compression python python-web) - -(define-record-type* - covid19-pubseq-configuration - make-covid19-pubseq-configuration - covid19-pubseq-configuration? - (package covid19-pubseq-configuration-package ; package - (default bh20-seq-resource-for-service)) - (deploy-directory covid19-pubseq-deploy-directory ; string - (default "/srv/http")) - (port covid19-pubseq-configuration-port ; string - (default "5000"))) - -(define covid19-pubseq-activation-service - (match-lambda - (($ package deploy-directory port) - #~(begin - (let ((pkg-src #$(package-source package))) - (when (file-exists? #$deploy-directory) - (delete-file-recursively (mkdir-p #$deploy-directory))) - (mkdir-p #$deploy-directory) - (if (file-is-directory? pkg-src) - (copy-recursively pkg-src #$deploy-directory) - (begin - (copy-file pkg-src #$(string-append deploy-directory - "/src.tar.xz")) - (with-directory-excursion #$deploy-directory - (invoke #$(file-append xz "/bin/xz") "-d" "src.tar.xz") - (invoke #$(file-append tar "/bin/tar") "xvf" "src.tar" - "--strip-components=1"))))))))) - -(define covid19-pubseq-shepherd-service - (match-lambda - (($ package deploy-directory port) - (with-imported-modules (source-module-closure - '((gnu build shepherd) - (gnu system file-systems))) - (list (shepherd-service - (provision '(covid19-pubseq)) - (requirement '(networking)) - (modules '((gnu build shepherd) - (gnu system file-systems))) - ;(start #~(make-forkexec-constructor/container - (start #~(make-forkexec-constructor - (list - #$(file-append gunicorn "/bin/gunicorn") - (string-append "-blocalhost:" #$port) - "bh20simplewebuploader.main:app") - #:directory #$deploy-directory - #:log-file "/var/log/covid19-pubseq.log" - #:environment-variables - ;(let (pyversion (python-version (@ (gnu packages python) python))) - '("TMPDIR=/export/tmp" - "PYTHONPATH=/run/current-system/profile/lib/python3.9/site-packages") - ; (string-append "PYTHONPATH=/run/current-system/profile/lib/python" pyversion "/site-packages"))) - ;#:mappings - ;(list (file-system-mapping - ; (source "/export/tmp") - ; (target source) - ; (writable? #t)) - ; (file-system-mapping - ; ;; TODO: Don't hardcode python version! - ; (source "/run/current-system/profile/lib/python3.9/site-packages") - ; (target source))) - )) - (stop #~(make-kill-destructor)))))))) - -(define covid19-pubseq-service-type - (service-type - (name 'covid19-pubseq) - (extensions - (list - (service-extension shepherd-root-service-type - covid19-pubseq-shepherd-service) - (service-extension activation-service-type - covid19-pubseq-activation-service) - (service-extension profile-service-type - (compose list - covid19-pubseq-configuration-package)))) - (default-value (covid19-pubseq-configuration)) - (description - "Run a COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource Webserver."))) - -(operating-system - (host-name "covid19-pubseq") - (timezone "Etc/UTC") - (locale "en_US.utf8") - - (bootloader (bootloader-configuration - (bootloader grub-bootloader) - (targets '("does-not-matter")))) - (file-systems %base-file-systems) - ;; No firmware for VMs. - (firmware '()) - ;; We don't need any packages inside the container. - (packages '()) - - (services (list (service covid19-pubseq-service-type)))) - -;; guix system container /home/shepherd/guix-bioinformatics/gn/services/bh20-seq-resource-container.scm --share=/export/tmp=/export/tmp --network -- cgit v1.2.3 From d523b0ef610ff0e3cd3c0a53f74461c377686983 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 19 Oct 2023 15:14:48 +0100 Subject: Remove python-arvados-python-client. The package is broken, some of its inputs have been removed from upstream Guix, and we no longer need this package. Restore it later if necessary. * gn/packages/python.scm (python-arvados-python-client): Delete variable. --- gn/packages/python.scm | 44 -------------------------------------------- 1 file changed, 44 deletions(-) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 020a6a9..c23d894 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -864,50 +864,6 @@ spreadsheets without the need for COM objects.") (description "Extensions to the standard Python datetime module") (license license:bsd-3))) -(define-public python-arvados-python-client - (package - (name "python-arvados-python-client") - (version "2.5.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "arvados-python-client" version)) - (sha256 - (base32 "1j08aykj0v2z2bqwr5nfnbjgc1yzdnfdafcnxbf2jbwqh8kx7zc9")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "setup.py" - ;; Don't set a maximum version of pycurl. - (("(pycurl >=([[:digit:]]+\\.?)+),.*" _ pycurl) - (string-append pycurl "',\n"))))))) - (build-system python-build-system) - (arguments - `(#:tests? #f)) ; tests not included? - (propagated-inputs - (list python-ciso8601 - python-future - python-google-api-client - python-google-api-core-1 - python-google-auth-1 - python-httplib2 - python-protobuf - python-pycurl - python-pyparsing-2.4.7 ; < 3 - python-ruamel.yaml - python-ws4py)) - (native-inputs - (list python-mock - python-pbr-1.6.0 - python-pyyaml)) - (home-page "https://arvados.org") - (synopsis "Arvados client library") - (description "This package provides the arvados module, an API client for -Arvados. It also includes higher-level functions to help you write Crunch -scripts, and command-line tools to store and retrieve data in the Keep storage -server.") - (license license:asl2.0))) - (define-public python-pyshex (package (name "python-pyshex") -- cgit v1.2.3 From 7e69491db5ca59b7c53684b66ef82d597c353e67 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 19 Oct 2023 10:44:16 +0100 Subject: Upgrade guix channel to 330b94e. --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index 48fa53b..d3d0030 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "8d70ff3a49f7cdf0eab93b3a1c54ec2f016afc4a") + (commit "330b94e8bd88baf903d2bc11bf96e23b119e0fe5") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 53d19fd513a98d6215fd41e368559162721e9802 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 26 Oct 2023 18:22:26 +0300 Subject: gn: htmx: Replace minify with trivial build system. Esbuild system has no support for ES5 and will lead to a build failure with the following output: `dist/htmx.js:1979:20: error: Transforming let to the configured target environment ("es5") is not supported yet` Signed-off-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 9398bf2..9b5c34b 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1891,15 +1891,23 @@ vector graphics.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/bigskysoftware/htmx") - (commit (string-append "v" version)))) + (url "https://github.com/bigskysoftware/htmx") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "14m9wan8sp5lzblfzbi1hln621p7ld3npajxrhq1a19zm5bcrz3y")))) - (build-system minify-build-system) + (base32 + "14m9wan8sp5lzblfzbi1hln621p7ld3npajxrhq1a19zm5bcrz3y")))) + (build-system trivial-build-system) (arguments - `(#:javascript-files '("dist/htmx.js"))) + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((source (assoc-ref %build-inputs "source")) + (out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/genenetwork2/javascript"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/htmx.min.js")))))) (home-page "https://htmx.org/") (synopsis "High Power Tools for HTML") (description -- cgit v1.2.3 From d55876c9480b058541c586e5cf29064ae5e0dfef Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 27 Oct 2023 09:45:27 +0300 Subject: Update dependencies: genenetwork3 and gn-auth * genenetwork3: Remove `yoyo-migrations` as a dependency * gn-auth: Use the upstream `yoyo-migrations` * Remove temporary local definition for yoyo-migrations. --- gn/packages/genenetwork.scm | 5 ++--- gn/packages/python.scm | 20 -------------------- 2 files changed, 2 insertions(+), 23 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ac26fd0..4fb8908 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -170,8 +170,7 @@ ("r-wgcna" ,r-wgcna) ("r-ctl" ,r-ctl) ("rust-qtlreaper" ,rust-qtlreaper) - ("diffutils" ,diffutils) - ("yoyo-migrations" ,yoyo-migrations-8.2.0))) + ("diffutils" ,diffutils))) (build-system python-build-system) (arguments (list #:phases @@ -503,7 +502,7 @@ ("python-redis" ,python-redis) ("python-authlib" ,python-authlib) ("python-pymonad" ,python-pymonad) - ("yoyo-migrations" ,yoyo-migrations-8.2.0) + ("yoyo-migrations" ,yoyo-migrations) ("python-bcrypt" ,python-bcrypt) ;; remove after removing all references ("python-mysqlclient" ,python-mysqlclient) ("python-argon2-cffi" ,python-argon2-cffi) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index c23d894..db2f4c9 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1836,23 +1836,3 @@ complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.") (license license:bsd-3))) - -(define-public yoyo-migrations-8.2.0 - (package - (inherit yoyo-migrations) - (name "yoyo-migrations") - (version "8.2.0") - (source - (origin - ;; We use the upstream repository, as the tests are not included in the - ;; PyPI releases. - (method hg-fetch) - (uri (hg-reference - (url "https://hg.sr.ht/~olly/yoyo") - (changeset (string-append "v" version "-release")))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 "1al030ix0w63hr4s3mqry6s0mlqdj8p242pdqks06br7c25nx3yj")))) - (propagated-inputs - (modify-inputs (package-propagated-inputs yoyo-migrations) - (append python-importlib-metadata))))) -- cgit v1.2.3 From 61f9525a81e4635162b1102a6fd8ef1ed7684055 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 3 Nov 2023 18:33:29 +0300 Subject: gn: javascript: Copy the right htmx.min.js from the source. * gn/packages/javascript.scm (javascript-htmx): Copy "/dist/htmx.min.js" to the targetdir. Signed-off-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 9b5c34b..68cb984 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1907,7 +1907,8 @@ vector graphics.") (out (assoc-ref %outputs "out")) (targetdir (string-append out "/share/genenetwork2/javascript"))) (mkdir-p targetdir) - (copy-file source (string-append targetdir "/htmx.min.js")))))) + (copy-file (string-append source "/dist/htmx.min.js") + (string-append targetdir "/htmx.min.js")))))) (home-page "https://htmx.org/") (synopsis "High Power Tools for HTML") (description -- cgit v1.2.3 From fea0ff23da6c9e5db6540eb87d1ade4833d797c2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 8 Nov 2023 10:11:57 +0200 Subject: gn: lizardfs: Fix building. * gn/packages/file-systems.scm (lizardfs)[source]: Add patch. [arguments]: Remove trailing #t from phases. [inputs]: Remove labels. Use fuse-2. * lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch: New file. --- gn/packages/file-systems.scm | 27 +++-- ...fs-issues-found-on-Fedora-34-using-GCC-11.patch | 111 +++++++++++++++++++++ 2 files changed, 123 insertions(+), 15 deletions(-) create mode 100644 lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch diff --git a/gn/packages/file-systems.scm b/gn/packages/file-systems.scm index 709754a..bf92ed9 100644 --- a/gn/packages/file-systems.scm +++ b/gn/packages/file-systems.scm @@ -28,7 +28,8 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0zk73wmx82ari3m2mv0zx04x1ggsdmwcwn7k6bkl5c0jnxffc4ax")))) + "0zk73wmx82ari3m2mv0zx04x1ggsdmwcwn7k6bkl5c0jnxffc4ax")) + (patches (search-patches "lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -58,8 +59,7 @@ (("etc/mfs") "/etc/lizardfs")) ;; Then adjust the install instructions. (substitute* "src/data/CMakeLists.txt" - (("^install.*") "")) - #t)) + (("^install.*") "")))) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (let ((gtest (assoc-ref inputs "googletest")) @@ -99,9 +99,7 @@ ;; fix FTBFS with glibc-2.28; for makedev ;; https://github.com/lizardfs/lizardfs/issues/655 (substitute* "src/chunkserver/iostat.h" - (("sys/stat.h>") "sys/stat.h>\n#include ")) - - #t))) + (("sys/stat.h>") "sys/stat.h>\n#include "))))) (add-after 'install 'install-extras ;; This got broken by changing the directories above. (lambda* (#:key outputs #:allow-other-keys) @@ -120,16 +118,15 @@ (lambda (file) (copy-file file (string-append etc "/" (basename file) ".dist"))) - (find-files data "\\.cfg(\\.in)?$")) - #t))))))) + (find-files data "\\.cfg(\\.in)?$"))))))))) (inputs - `(("bdb" ,bdb) - ("boost" ,boost) - ("fuse" ,fuse) - ("linux-pam" ,linux-pam) - ("python" ,python-2) - ("spdlog" ,spdlog) - ("zlib" ,zlib))) + (list bdb + boost + fuse-2 + linux-pam + python-2 + spdlog + zlib)) (native-inputs `(("asciidoc" ,asciidoc) ("googletest" ,(package-source googletest-1.7)) diff --git a/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch b/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch new file mode 100644 index 0000000..55036a7 --- /dev/null +++ b/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch @@ -0,0 +1,111 @@ +From 1da538a07974b8b1afd2580af2828418cbdad42b Mon Sep 17 00:00:00 2001 +Message-ID: <1da538a07974b8b1afd2580af2828418cbdad42b.1699426938.git.efraim@flashner.co.il> +From: Marcin Konarski +Date: Fri, 21 May 2021 12:36:56 +0200 +Subject: [PATCH] all: Fix build issues found on Fedora 34 using GCC 11.1.1 + +Change-Id: I1c20e914d249d367d0a058de1102ae62dcaf6054 +--- + src/common/ec_read_plan.h | 2 +- + src/common/flat_set_unittest.cc | 4 ++-- + src/common/vector_range.h | 1 + + src/data/CMakeLists.txt | 25 +++++++++++++++++++++++ + src/master/goal_config_loader_unittest.cc | 4 ++-- + 5 files changed, 31 insertions(+), 5 deletions(-) + +diff --git a/src/common/ec_read_plan.h b/src/common/ec_read_plan.h +index c96413cb..bda10cb5 100644 +--- a/src/common/ec_read_plan.h ++++ b/src/common/ec_read_plan.h +@@ -132,7 +132,7 @@ protected: + } + } + +- for (const auto op : read_operations) { ++ for (auto const& op : read_operations) { + data_parts[op.first.getSlicePart()] = buffer + op.second.buffer_offset; + } + +diff --git a/src/common/flat_set_unittest.cc b/src/common/flat_set_unittest.cc +index 9ad760c4..e50308eb 100644 +--- a/src/common/flat_set_unittest.cc ++++ b/src/common/flat_set_unittest.cc +@@ -62,9 +62,9 @@ TEST(FlatSet, RedundantInsert) { + // const & + std::initializer_list elems2 = {"0", "1", "2", "3", "4"}; + flat_set cs2(elems2); +- for (const std::string &i : {"2", "4"}) { ++ for (char const* s : {"2", "4"}) { + EXPECT_EQ(cs2.size(), elems2.size()); +- cs2.insert(i); ++ cs2.insert(s); + EXPECT_EQ(cs2.size(), elems2.size()); + } + } +diff --git a/src/common/vector_range.h b/src/common/vector_range.h +index f336e1ec..57bba8dd 100644 +--- a/src/common/vector_range.h ++++ b/src/common/vector_range.h +@@ -22,6 +22,7 @@ + + #include + #include ++#include + #include + + /*! \brief Class providing std::vector like interface to subrange of vector. */ +diff --git a/src/data/CMakeLists.txt b/src/data/CMakeLists.txt +index 88c20d5d..bf69a5e2 100644 +--- a/src/data/CMakeLists.txt ++++ b/src/data/CMakeLists.txt +@@ -16,3 +16,28 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/mfschunkserver.cfg DESTINATION ${ETC_S + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/mfsmetalogger.cfg DESTINATION ${ETC_SUBDIR} RENAME mfsmetalogger.cfg.dist) + + install(FILES lizardfs.completion DESTINATION etc/bash_completion.d RENAME lizardfs) ++ ++if(BUILD_TESTS) ++ # Create a mock include dir. ++ # We do this because we want to preserve the proper include directives in the example code ++ # and still build this example program in the build step before the needed headers are installed. ++ file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs) ++ add_custom_command( ++ OUTPUT ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_c_api.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_error_codes.h ++ COMMAND ${CMAKE_COMMAND} -E create_symlink ++ ${CMAKE_SOURCE_DIR}/src/mount/client/lizardfs_c_api.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_c_api.h ++ COMMAND ${CMAKE_COMMAND} -E create_symlink ++ ${CMAKE_SOURCE_DIR}/src/common/lizardfs_error_codes.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_error_codes.h ++ ) ++ add_executable(c-client-example ++ liblizardfs-client-example.c ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_c_api.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_error_codes.h) ++ target_include_directories(c-client-example PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/include) ++ target_link_libraries(c-client-example lizardfs-client stdc++) ++ install(TARGETS c-client-example RUNTIME DESTINATION ${BIN_SUBDIR}) ++endif() +diff --git a/src/master/goal_config_loader_unittest.cc b/src/master/goal_config_loader_unittest.cc +index 050e8a52..a236dba9 100644 +--- a/src/master/goal_config_loader_unittest.cc ++++ b/src/master/goal_config_loader_unittest.cc +@@ -41,8 +41,8 @@ Goal::Slice createSlice(int type, + std::vector> part_list) { + Goal::Slice slice{Goal::Slice::Type(type)}; + int part_index = 0; +- for (const auto &part : part_list) { +- for (const auto label : part) { ++ for (auto const& part : part_list) { ++ for (auto const& label : part) { + slice[part_index][MediaLabel(label.first)] += label.second; + } + ++part_index; + +base-commit: 6f6fd530f8fa286fbfb6a050cacbba73e928bd26 +-- +Efraim Flashner רנשלפ םירפא +GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 +Confidentiality cannot be guaranteed on emails sent or received unencrypted + -- cgit v1.2.3 From 638abbad22c4942f273bf75aaf2f69a200bf58af Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Tue, 7 Nov 2023 16:12:52 +0300 Subject: gn: javascript: Add javascript-marked. * gn/packages/javascript.scm (javascript-marked): New package. Reviewed-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 68cb984..3d4c7e5 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1914,3 +1914,35 @@ vector graphics.") (description "htmx allows you to access AJAX, CSS Transitions, WebSockets and Server Sent Events directly in HTML, using attributes, so you can build modern user interfaces with the simplicity and power of hypertext") (license license:expat))) + +(define-public javascript-marked + (package + (name "javascript-marked") + (version "9.1.5") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdnjs.cloudflare.com/ajax/libs/marked/" version + "/marked.min.js")) + (file-name "marked.min.js") + (sha256 + (base32 + "1f4hw8yjdm99hgw0bq62099d3kv23awsm8r7969m7lv84n2wid8y")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/marked")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/marked.min.js")))))) + (native-inputs `(("source" ,source))) + (home-page "https://marked.js.org/") + (synopsis "A markdown parser and compiler. Built for speed.") + (description + "A low-level markdown compiler for parsing markdown without caching or blocking for long periods of time.") + (license license:expat))) -- cgit v1.2.3 From 35f3f75aa945728868a5df1bfe0164cd917e9d4b Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Tue, 7 Nov 2023 16:30:46 +0300 Subject: gn: javascript: Add javascript-marked-highlight. * gn/packages/javascript.scm (javascript-marked-highlight): New package. Reviewed-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 3d4c7e5..05706ce 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1946,3 +1946,33 @@ vector graphics.") (description "A low-level markdown compiler for parsing markdown without caching or blocking for long periods of time.") (license license:expat))) + +(define-public javascript-marked-highlight + (package + (name "javascript-marked-highlight") + (version "2.0.6") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdn.jsdelivr.net/npm/marked-highlight@" version "/lib/index.umd.min.js")) + (sha256 + (base32 + "087qcy77fm3r7dl6w0mxsqygmdpimrmksw78r4wkkkjdx9x9dshf")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/marked")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/marked-highlight.js")))))) + (native-inputs `(("source" ,source))) + (home-page "https://github.com/markedjs/marked-highlight") + (synopsis "Highlight code blocks.") + (description + "Add code highlighting to marked.") + (license license:expat))) -- cgit v1.2.3 From dab09fb41a2ad47b1ef337a006bf270cbc1672f4 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Fri, 10 Nov 2023 16:35:11 +0300 Subject: gn: javascript: Add javascript-ace * gn/packages/javascript.scm (javascript-ace): New package. Reviewed-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 05706ce..6471d65 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1976,3 +1976,34 @@ vector graphics.") (description "Add code highlighting to marked.") (license license:expat))) + +(define-public javascript-ace + (package + (name "javascript-ace") + (version "1.31.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ajaxorg/ace-builds.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08rfyrjfjjgb42x4if5qqfyvv8ag2qmf6vsbs7qrcnzgrac66m35")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/genenetwork2/javascript/ace")) + (source (assoc-ref %build-inputs "source")) + (dist (string-append source "/src-min-noconflict"))) + (copy-recursively dist targetdir))))) + (native-inputs `(("source" ,source))) + (home-page "https://github.com/ajaxorg/ace-builds") + (synopsis "Ace is a code editor written in JavaScript.") + (description + "Ace is a code editor written in JavaScript. ") + (license license:expat))) -- cgit v1.2.3 From dac05a9487e8cc924066e9cf79059f09a85e3fa0 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sat, 12 Aug 2023 10:37:56 +0200 Subject: Added note on move to https://git.genenetwork.org/guix-bioinformatics/ --- README.org | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.org b/README.org index d1295b1..c5936fa 100644 --- a/README.org +++ b/README.org @@ -1,5 +1,7 @@ * guix-bioinformatics +IMPORTANT: this repository has moved to https://git.genenetwork.org/guix-bioinformatics/! + Bioinformatics packages for GNU Guix that are used in https://genenetwork.org/ and some other places. See [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for installing and hacking GNU Guix. Other channels of bioinformatics -- cgit v1.2.3 From 50a7bc10fb80bd9396a613ffd69d2b84d184a53d Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 16 Nov 2023 19:05:39 +0100 Subject: Updated lizardfs to latest version on git. * gn/packages/file-systems.scm (lizardfs)[arguments]: updated and disabled tests in CMake --- gn/packages/file-systems.scm | 74 +++++++++++++++++++++++--------------------- 1 file changed, 38 insertions(+), 36 deletions(-) diff --git a/gn/packages/file-systems.scm b/gn/packages/file-systems.scm index bf92ed9..c145e1a 100644 --- a/gn/packages/file-systems.scm +++ b/gn/packages/file-systems.scm @@ -13,37 +13,38 @@ #:use-module (gnu packages linux) #:use-module (gnu packages logging) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pretty-print) #:use-module (gnu packages python)) + (define-public lizardfs - (package - (name "lizardfs") - (version "3.12.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/lizardfs/lizardfs") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0zk73wmx82ari3m2mv0zx04x1ggsdmwcwn7k6bkl5c0jnxffc4ax")) - (patches (search-patches "lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch")))) - (build-system cmake-build-system) - (arguments - `(#:configure-flags - (list "-DENABLE_CLIENT_LIB=YES" - "-DENABLE_TESTS=YES" - "-DENABLE_STATIC=NO" - "-DENABLE_VERBOSE_ASCIIDOC=YES" - "-DENABLE_TCMALLOC=NO" - ;"-DLIB_SUBDIR=lib" ; no 64 suffix - ;; Some directories need to be changed - ;"-DRUN_SUBDIR=/var/run/lizardfs" - ;"-DDATA_SUBDIR=/var/lib/lizardfs" - ;"-DETC_SUBDIR=/etc/lizardfs" - "-DENABLE_UTILS=YES") + (let ((commit "b1e97f974fc3a4046edaf9fdc3962264d4cd24fa")) + (package + (name "lizardfs") + (version (string-append "3.12.1-" (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lizardfs/lizardfs") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1jh5alwgaalsnnn53clp3zr5rhzqlbd6apiqvvm6gdxw6ja3f4s1")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DENABLE_CLIENT_LIB=YES" + "-DENABLE_TESTS=NO" + "-DENABLE_STATIC=NO" + "-DENABLE_VERBOSE_ASCIIDOC=YES" + "-DENABLE_TCMALLOC=NO" + ;"-DLIB_SUBDIR=lib" ; no 64 suffix + ;; Some directories need to be changed + ;"-DRUN_SUBDIR=/var/run/lizardfs" + ;"-DDATA_SUBDIR=/var/lib/lizardfs" + ;"-DETC_SUBDIR=/etc/lizardfs" + "-DENABLE_UTILS=YES") ;; Tests involve setting up a lizardfs instance and run as root. ;; We will make do with just building the tests. #:tests? #f @@ -120,13 +121,14 @@ (string-append etc "/" (basename file) ".dist"))) (find-files data "\\.cfg(\\.in)?$"))))))))) (inputs - (list bdb - boost - fuse-2 - linux-pam - python-2 - spdlog - zlib)) + `(("bdb" ,bdb) + ("boost" ,boost) + ("fuse" ,fuse) + ("fmt" ,fmt) + ("linux-pam" ,linux-pam) + ("python" ,python-2) + ("spdlog" ,spdlog) + ("zlib" ,zlib))) (native-inputs `(("asciidoc" ,asciidoc) ("googletest" ,(package-source googletest-1.7)) @@ -144,7 +146,7 @@ any downtime. The system will automatically move data across to the newly added servers, as it continuously takes care of balancing disk usage across all connected nodes.") (license (list license:asl2.0 ; external/crcutil - license:gpl3)))) + license:gpl3))))) (define-public googletest-1.7 ;; Source only package -- cgit v1.2.3 From e5bff14a977277fabe1c97db38407f490fd06a75 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Fri, 1 Dec 2023 13:23:12 -0600 Subject: roll-back on lizardfs because fuse3 issues --- gn/packages/file-systems.scm | 74 +++++++++++++++++++++----------------------- 1 file changed, 36 insertions(+), 38 deletions(-) diff --git a/gn/packages/file-systems.scm b/gn/packages/file-systems.scm index c145e1a..bf92ed9 100644 --- a/gn/packages/file-systems.scm +++ b/gn/packages/file-systems.scm @@ -13,38 +13,37 @@ #:use-module (gnu packages linux) #:use-module (gnu packages logging) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages pretty-print) #:use-module (gnu packages python)) - (define-public lizardfs - (let ((commit "b1e97f974fc3a4046edaf9fdc3962264d4cd24fa")) - (package - (name "lizardfs") - (version (string-append "3.12.1-" (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/lizardfs/lizardfs") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "1jh5alwgaalsnnn53clp3zr5rhzqlbd6apiqvvm6gdxw6ja3f4s1")))) - (build-system cmake-build-system) - (arguments - `(#:configure-flags - (list "-DENABLE_CLIENT_LIB=YES" - "-DENABLE_TESTS=NO" - "-DENABLE_STATIC=NO" - "-DENABLE_VERBOSE_ASCIIDOC=YES" - "-DENABLE_TCMALLOC=NO" - ;"-DLIB_SUBDIR=lib" ; no 64 suffix - ;; Some directories need to be changed - ;"-DRUN_SUBDIR=/var/run/lizardfs" - ;"-DDATA_SUBDIR=/var/lib/lizardfs" - ;"-DETC_SUBDIR=/etc/lizardfs" - "-DENABLE_UTILS=YES") + (package + (name "lizardfs") + (version "3.12.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lizardfs/lizardfs") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0zk73wmx82ari3m2mv0zx04x1ggsdmwcwn7k6bkl5c0jnxffc4ax")) + (patches (search-patches "lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DENABLE_CLIENT_LIB=YES" + "-DENABLE_TESTS=YES" + "-DENABLE_STATIC=NO" + "-DENABLE_VERBOSE_ASCIIDOC=YES" + "-DENABLE_TCMALLOC=NO" + ;"-DLIB_SUBDIR=lib" ; no 64 suffix + ;; Some directories need to be changed + ;"-DRUN_SUBDIR=/var/run/lizardfs" + ;"-DDATA_SUBDIR=/var/lib/lizardfs" + ;"-DETC_SUBDIR=/etc/lizardfs" + "-DENABLE_UTILS=YES") ;; Tests involve setting up a lizardfs instance and run as root. ;; We will make do with just building the tests. #:tests? #f @@ -121,14 +120,13 @@ (string-append etc "/" (basename file) ".dist"))) (find-files data "\\.cfg(\\.in)?$"))))))))) (inputs - `(("bdb" ,bdb) - ("boost" ,boost) - ("fuse" ,fuse) - ("fmt" ,fmt) - ("linux-pam" ,linux-pam) - ("python" ,python-2) - ("spdlog" ,spdlog) - ("zlib" ,zlib))) + (list bdb + boost + fuse-2 + linux-pam + python-2 + spdlog + zlib)) (native-inputs `(("asciidoc" ,asciidoc) ("googletest" ,(package-source googletest-1.7)) @@ -146,7 +144,7 @@ any downtime. The system will automatically move data across to the newly added servers, as it continuously takes care of balancing disk usage across all connected nodes.") (license (list license:asl2.0 ; external/crcutil - license:gpl3))))) + license:gpl3)))) (define-public googletest-1.7 ;; Source only package -- cgit v1.2.3 From 4914e019ce278bdf0eed3fb708e2f6bdd5b3d4ad Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Dec 2023 16:45:05 +0300 Subject: gn-auth: Remove bcrypt dependency --- gn/packages/genenetwork.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4fb8908..3e90ecb 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -503,7 +503,6 @@ ("python-authlib" ,python-authlib) ("python-pymonad" ,python-pymonad) ("yoyo-migrations" ,yoyo-migrations) - ("python-bcrypt" ,python-bcrypt) ;; remove after removing all references ("python-mysqlclient" ,python-mysqlclient) ("python-argon2-cffi" ,python-argon2-cffi) ("python-email-validator" ,python-email-validator))) -- cgit v1.2.3 From 62acd7e5e33e018ec3af2fcff556c55e73f308f5 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Dec 2023 16:45:29 +0300 Subject: gn-auth: add flask-cors dependency. --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 3e90ecb..4cf4612 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -503,6 +503,7 @@ ("python-authlib" ,python-authlib) ("python-pymonad" ,python-pymonad) ("yoyo-migrations" ,yoyo-migrations) + ("python-flask-cors" ,python-flask-cors) ("python-mysqlclient" ,python-mysqlclient) ("python-argon2-cffi" ,python-argon2-cffi) ("python-email-validator" ,python-email-validator))) -- cgit v1.2.3 From b97e14ca2990d9d861648d998a90bb36959f3555 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Fri, 29 Dec 2023 13:18:59 +0100 Subject: Ruby lmdb builds for ruby 2.7. We are not going to use it though --- gn/packages/ruby.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm index e2c4164..befb550 100644 --- a/gn/packages/ruby.scm +++ b/gn/packages/ruby.scm @@ -5983,13 +5983,17 @@ Simple gem that adds various color methods to String class, and can be used as f (base32 "0yzlf56ynj545ln5dxl422rpi8r6h11cr6rag5hk2qpbkzs6l9c2")))) (build-system ruby-build-system) + (inputs + (list lmdb)) (native-inputs `(("ruby-rake" ,ruby-rake) ("ruby-rake-compiler" ,ruby-rake-compiler) - ("ruby-rspec" ,ruby-rspec) ("ruby-rspec" ,ruby-rspec))) + ("ruby-rspec" ,ruby-rspec) + ("ruby-ruby-memcheck" ,ruby-ruby-memcheck) + )) (arguments - `(#:tests? #f ; There are no tests. - )) (synopsis "lmdb is a Ruby binding to OpenLDAP Lightning MDB.") + `(#:tests? #f)) + (synopsis "lmdb is a Ruby binding to OpenLDAP Lightning MDB.") (description "lmdb is a Ruby binding to OpenLDAP Lightning MDB.") (home-page "https://github.com/doriantaylor/rb-lmdb") (license license:expat))) -- cgit v1.2.3 From 7a4bf91e019fe084f92a90535cbfffb7c119b9a7 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 29 Dec 2023 19:06:01 +0000 Subject: gn: genenetwork3: Update to 0.1.0-4.093163e. --- gn/packages/genenetwork.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4cf4612..ff87f99 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -111,10 +111,11 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "f52247c15f3694f3dd5fd0fd79c3e15376137e07")) + (let ((commit "093163ebd511700078f998fa754e786435a81d1b") + (revision "4")) (package (name "genenetwork3") - (version (git-version "0.1.0" "3" commit)) + (version (git-version "0.1.0" revision commit)) (source (origin (method git-fetch) @@ -124,7 +125,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0ac0dr8dny65x4xvm8gw6ap3g8g0j933ipy9116idcws31rk2adk")))) + "06vfrfw1p60scrnxwfd2daxr8hdd6bjd27pdppwxs7k65nvync4s")))) (inputs (list python-click)) (native-inputs @@ -688,3 +689,5 @@ ; (directory-union ; "genenetwork2" ; (list genenetwork2 genenetwork-graph dag-svg-file))) + +genenetwork3 -- cgit v1.2.3 From 9d8990a85f1c321397bef6e879845479e5c4a403 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 2 Jan 2024 10:53:46 +0300 Subject: gnqc-py: New package --- gn/packages/genenetwork.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ff87f99..139b46c 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -467,6 +467,48 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public gnqc-py + (package + (name "gnqc-py") + (version "0.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/fredmanglis/gnqc_py.git") + (commit "c81a3d948b3bc0db20a530fa1aa428b35b5d6145"))) + (hash + (content-hash + (base32 + "1101pql7zpijn36i9phcakfx1r5dcvdf6ix0v4ndjzmzx3d0xyi2"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) + (native-inputs + `(("python-mypy" ,python-mypy + "python-pylint" ,python-pylint + "python-pytest" ,python-pytest + "python-hypothesis" ,python-hypothesis))) + (propagated-inputs + `(("gunicorn" ,gunicorn + "python-redis" ,python-redis + "python-flask" ,python-flask + "python-pyyaml" ,python-pyyaml + "python-jsonpickle" ,python-jsonpickle + "python-mysqlclient" ,python-mysqlclient))) + (synopsis "GeneNetwork Quality Control Application") + (description + "GeneNetwork qc is a quality control application for the data files that + eventually are used to add to the data in the GeneNetwork project.") + (home-page "https://gitlab.com/fredmanglis/gnqc_py") + (license license:agpl3+))) + (define-public gn-auth (package (name "gn-auth") -- cgit v1.2.3 From 72b54fdd4aa582fee3e4e6d1bf3f46c9f44764c8 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 30 Dec 2023 09:23:07 +0000 Subject: gn: genenetwork2: Substitute new path to default_settings.py. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 139b46c..0dafb3c 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -341,7 +341,7 @@ (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) ) - (substitute* '("etc/default_settings.py") + (substitute* '("gn2/default_settings.py") ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) -- cgit v1.2.3 From bc88ac43051bcb5d5fdf7975c47d805601200be8 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 13:55:52 +0000 Subject: gn: genenetwork2: Update to 3.11-3.ff67963. * gn/packages/genenetwork.scm (genenetwork2): Update to 3.11-3.ff67963. --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 0dafb3c..8b1216b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,10 +186,10 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "bfe557dc1e537dc78a82a30817ecf2ca3004d978")) + (let ((commit "ff679636d3ee9ae2388fab3fe5d091ef2f00a8e3")) (package (name "genenetwork2") - (version (git-version "3.11" "2" commit)) + (version (git-version "3.11" "3" commit)) (source (origin (method git-fetch) (uri (git-reference @@ -198,7 +198,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "1bn0j0fpk4hcicgfird62x5wq2n6lj4rs1ggw69dcxyf4qdxbk5d")))) + "0ap7q7v42c5sg4kjy76zdn6h6w5a3f534i5644rya5a1akmss7hg")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 8c75815e1ba02dcad7500e56b2dfe0987105b3db Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 13:56:35 +0000 Subject: Remove genenetwork3 return. This was introduced accidentally in 7a4bf91e019fe084f92a90535cbfffb7c119b9a7. * gn/packages/genenetwork.scm: Remove genenetwork3 return. --- gn/packages/genenetwork.scm | 2 -- 1 file changed, 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 8b1216b..890d7e5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -731,5 +731,3 @@ ; (directory-union ; "genenetwork2" ; (list genenetwork2 genenetwork-graph dag-svg-file))) - -genenetwork3 -- cgit v1.2.3 From 05dd63817302e890a16a33fc3b5f88fa07a8184d Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 16:55:32 +0000 Subject: gn: genenetwork2: Use G-expressions. * gn/packages/genenetwork.scm (genenetwork2): Use G-expressions. --- gn/packages/genenetwork.scm | 387 +++++++++++++++----------------------------- 1 file changed, 126 insertions(+), 261 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 890d7e5..6be016e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -202,270 +202,135 @@ (native-inputs (list graphviz)) (propagated-inputs - `(("genenetwork3" ,genenetwork3) - ("parallel" ,parallel) ;; GNU parallel - ("coreutils" ,coreutils) - ("git" ,git) - ("which" ,which) - ("grep" ,grep) - ("r" ,r) - ("r-ctl" ,r-ctl) - ("r-qtl" ,r-qtl) - ("r-wgcna" ,r-wgcna) - ("redis" ,redis) - ("mariadb" ,mariadb) - ("gemma" ,gemma-gn2) - ("gemma-wrapper" ,gemma-wrapper) - ("plink-ng-gn" ,plink-ng-gn) - ("rust-qtlreaper" ,rust-qtlreaper) - ("gn-rust-correlation" ,gn-rust-correlation) - ("glibc-utf8-locales" ,glibc-utf8-locales) - ("nginx" ,nginx) - ("python" ,python-wrapper) - ("python-pillow" ,python-pillow) - ("python-coverage" ,python-coverage) - ("python-configparser" ,python-configparser) ;; maintenance/scripts - ("python-flask" ,python-flask) - ("gunicorn" ,gunicorn) - ("python-autopep8" ,python-autopep8) - ("python-cssselect" ,python-cssselect) - ("python-flask-debugtoolbar" ,python-flask-debugtoolbar) - ("python-htmlgen" ,python-htmlgen) - ("python-ijson" ,python-ijson) - ("python-jinja2" ,python-jinja2) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-scipy" ,python-scipy) - ("python-lxml" ,python-lxml) - ("python-mysqlclient" ,python-mysqlclient) - ("python-mypy" ,python-mypy) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pylint" ,python-pylint) - ("python-pymonad" ,python-pymonad) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-simplejson" ,python-simplejson) - ("python-markdown" ,python-markdown) - ("python-rdflib" ,python-rdflib) - ("python-authlib" ,python-authlib) - ("python-flask-session" ,python-flask-session) - ;; TODO: Get rid of Python R bindings - ("python-rpy2" ,python-rpy2) - ("python-beautifulsoup4" ,python-beautifulsoup4) - ;; Disable for now. Build fails on Penguin2 - ;; ("python-flask-socketio" ,python-flask-socketio) - ("python-xlsxwriter" ,python-xlsxwriter) - ;; All the external js dependencies - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - ("javascript-chroma" ,javascript-chroma) - ("javascript-d3-tip" ,javascript-d3-tip) - ("javascript-jscolor" ,javascript-jscolor) - ("javascript-colorbox" ,javascript-colorbox) - ("javascript-jszip" ,javascript-jszip) - ("js-jstat" ,js-jstat) - ("js-md5" ,js-md5) - ("js-parsley" ,js-parsley) - ("javascript-plotly" ,javascript-plotly) - ("javascript-typeahead" ,javascript-typeahead) - ("js-underscore" ,js-underscore) - ("js-smart-time-ago" ,js-smart-time-ago) - ("javascript-nouislider" ,javascript-nouislider) - ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser) - ("javascript-ckeditor" ,javascript-ckeditor) - ("javascript-datatables" ,javascript-datatables) - ("javascript-datatables-scroller" ,javascript-datatables-scroller) - ("javascript-datatables-buttons" ,javascript-datatables-buttons) - ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap) - ("javascript-datatables-plugins" ,javascript-datatables-plugins) - ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder) - ("javascript-datatables-col-resize" ,javascript-datatables-col-resize) - ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) - ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) - ("javascript-underscore-string" ,javascript-underscore-string) - ("javascript-htmx" ,javascript-htmx) - ("javascript-qtip2" ,javascript-qtip2) - ("javascript-d3js" ,javascript-d3js) - ("javascript-nvd3" ,javascript-nvd3) - ("javascript-bootstrap" ,javascript-bootstrap) - ("javascript-jquery" ,javascript-jquery) - ("javascript-zxcvbn" ,javascript-zxcvbn) - ("javascript-jquery-ui" ,javascript-jquery-ui) - ("javascript-jquery-cookie" ,javascript-jquery-cookie) - ("javascript-xterm" ,javascript-xterm) - ("javascript-xterm-style" ,javascript-xterm-style) - ("javascript-xterm-addon-fit",javascript-xterm-addon-fit) - ("javascript-font-awesome" ,javascript-font-awesome))) + (list genenetwork3 + parallel + coreutils + git + which + grep + r + r-ctl + r-qtl + r-wgcna + redis + mariadb + gemma + gemma-wrapper + plink-ng-gn + rust-qtlreaper + gn-rust-correlation + glibc-utf8-locales + nginx + python-wrapper + python-pillow + python-coverage + python-configparser + python-flask + gunicorn + python-autopep8 + python-cssselect + python-flask-debugtoolbar + python-htmlgen + python-ijson + python-jinja2 + python-pytest + python-pytest-mock + python-sqlalchemy + python-setuptools + python-scipy + python-lxml + python-mysqlclient + python-mypy + python-numpy + python-pandas + python-pylint + python-pymonad + python-redis + python-requests + python-simplejson + python-markdown + python-rdflib + python-authlib + python-flask-session + python-rpy2 + python-beautifulsoup4 + python-xlsxwriter + javascript-twitter-post-fetcher + javascript-cytoscape + javascript-cytoscape-panzoom + javascript-cytoscape-qtip + javascript-chroma + javascript-d3-tip + javascript-jscolor + javascript-colorbox + javascript-jszip + js-jstat + js-md5 + js-parsley + javascript-plotly + javascript-typeahead + js-underscore + js-smart-time-ago + javascript-nouislider + javascript-purescript-genome-browser + javascript-ckeditor + javascript-datatables + javascript-datatables-scroller + javascript-datatables-buttons + javascript-datatables-buttons-bootstrap + javascript-datatables-plugins + javascript-datatables-col-reorder + javascript-datatables-col-resize + javascript-datatables-buttons-styles + javascript-shapiro-wilk + javascript-underscore-string + javascript-htmx + javascript-qtip2 + javascript-d3js + javascript-nvd3 + javascript-bootstrap + javascript-jquery + javascript-zxcvbn + javascript-jquery-ui + javascript-jquery-cookie + javascript-xterm + javascript-xterm-style + javascript-xterm-addon-fit + javascript-font-awesome)) (inputs - `(("javascript-colorbox" ,(package-source javascript-colorbox)))) + (list javascript-colorbox)) (build-system python-build-system) (arguments - `(#:tests? #f ; no 'setup.py test' - #:phases - (modify-phases %standard-phases - (delete 'reset-gzip-timestamps) - (add-after 'unpack 'fix-paths-scripts - (lambda _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python3") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))) - #t)) - ; (add-after 'unpack 'patch-javascript - ; (lambda* (#:key inputs #:allow-other-keys) - ; (let ((colorbox (assoc-ref inputs "javascript-colorbox")) - ; (gn2 "/share/genenetwork2/javascript/")) - ; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") - ; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") - ; #t))) - (add-before 'install 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ( - ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) - ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) - - (substitute* '("gn2/default_settings.py") - ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) - (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) - ) - ))) - ; (add-after 'install 'generate-graph - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (call-with-output-file - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages" - ; "/wqflask/dependency-graph.html") - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %d3js-backend))))))))))) - ;(add-after 'install 'generate-dag-svg-file - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let* ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/")) - ; (dot-file - ; (string-append - ; output-dir - ; "dependency-graph.dot")) - ; (svg-file - ; (string-append - ; output-dir - ; "dependency-graph.svg"))) - ; (begin - ; (call-with-output-file - ; dot-file - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %graphviz-backend))))))))) - ; (invoke "dot" "-Tsvg" "-o" svg-file dot-file))))) - - ;; TODO: Use this to replace the two previous phases. - ;(add-after 'install 'install-generated-files - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/"))) - ; (install-file (string-append %dag-svg-file "/dependency-graph.dot") output-dir) - ; (install-file (string-append %dag-svg-file "/dependency-graph.svg") output-dir) - ; (install-file (string-append %genenetwork-graph "/dependency-graph.html") output-dir) - ; #t))) - - #! - (add-after 'install 'generate-dependency-file - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file - (string-append - (assoc-ref outputs "out") - "/lib/python" - (python-version (assoc-ref inputs "python")) - "/site-packages" - "/wqflask/DEPENDENCIES.md" - ) - (lambda (port) - (format - port " -#### System Inputs (generated from ~a package defined in ~a) -|Name | Description | -|-----|-------------| -~a -" - ,(package-name this-package) - (string-append - "[genenetwork.scm]" - "(http://git.genenetwork.org/" - "guix-bioinformatics/guix-bioinformatics" - "/src/branch/master/gn/packages/" - "genenetwork.scm)") - ,(apply - string-append - (map - (lambda (input) - (let* ((pkg (cadr input)) - (name (package-name pkg)) - (version (package-version pkg)) - (home-page (package-home-page pkg)) - (description (package-synopsis pkg))) - (string-append - "| **[" name "](" home-page ")** v" - version"| " - description " |\n"))) - (package-propagated-inputs this-package)))))))) - !# - ))) - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'reset-gzip-timestamps) + (add-after 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python3") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which"))))) + (add-before 'install 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) + (substitute* '("gn2/default_settings.py") + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))))))))) + (home-page "http://genenetwork.org/") + (synopsis "Full genenetwork services") + (description "Genenetwork installation sumo.") + (license license:agpl3+)))) (define-public gnqc-py (package -- cgit v1.2.3 From 7a4299e73635f0b68f548105f05cfdd6ecb234bd Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 16:57:24 +0000 Subject: gn: genenetwork2: Install bundled fonts. * gn/packages/genenetwork.scm (genenetwork2)[arguments]: Add install-bundled-fonts and fix-font-paths phases. --- gn/packages/genenetwork.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 6be016e..d499d8a 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -305,6 +305,19 @@ #:phases #~(modify-phases %standard-phases (delete 'reset-gzip-timestamps) + (add-after 'install 'install-bundled-fonts + (lambda _ + ;; Install bundled fonts. + (for-each (lambda (font-file) + (install-file font-file (string-append #$output "/share/fonts/"))) + (find-files "gn2/wqflask/static/fonts" + "\\.ttf$")))) + (add-after 'unpack 'fix-font-paths + (lambda _ + ;; Set absolute store paths to installed bundled fonts. + (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" + (("\\./gn2/wqflask/static/fonts") + (string-append #$output "/gn2/wqflask/static/fonts"))))) (add-after 'unpack 'fix-paths-scripts (lambda _ (substitute* "bin/genenetwork2" -- cgit v1.2.3 From 22cb97904b4efed9f51b5699f0a25648c7e995f6 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 2 Jan 2024 17:15:39 +0000 Subject: gn: genenetwork2: Fix path to installed bundled fonts. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d499d8a..f6c45b4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -317,7 +317,7 @@ ;; Set absolute store paths to installed bundled fonts. (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" (("\\./gn2/wqflask/static/fonts") - (string-append #$output "/gn2/wqflask/static/fonts"))))) + (string-append #$output "/share/fonts"))))) (add-after 'unpack 'fix-paths-scripts (lambda _ (substitute* "bin/genenetwork2" -- cgit v1.2.3 From 4ba4df365b6c5764c90e3ff939648f11110e04e5 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 3 Jan 2024 00:30:21 +0000 Subject: gn: genenetwork3: Update to 0.1.0-5.6bb4a5f. * gn/packages/genenetwork.scm (genenetwork3): Update to 0.1.0-5.6bb4a5f. --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index f6c45b4..ec0426b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -111,8 +111,8 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "093163ebd511700078f998fa754e786435a81d1b") - (revision "4")) + (let ((commit "6bb4a5f05c1a2c96b7da1780ae4a1d70c7cc4afb") + (revision "5")) (package (name "genenetwork3") (version (git-version "0.1.0" revision commit)) @@ -125,7 +125,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "06vfrfw1p60scrnxwfd2daxr8hdd6bjd27pdppwxs7k65nvync4s")))) + "13nvi2gwwb0shra0d9rsfhppa9ky4bhgh1zgb34790ax0g9lwa97")))) (inputs (list python-click)) (native-inputs -- cgit v1.2.3 From 250f5bb11be7596d77cb8993afb3cc7e741530d3 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 3 Jan 2024 00:33:25 +0000 Subject: gn: genenetwork2: Update to 3.11-4.c1d377e. * gn/packages/genenetwork.scm (genenetwork2): Update to 3.11-4.c1d377e. --- gn/packages/genenetwork.scm | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ec0426b..1ad63c0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,10 +186,11 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "ff679636d3ee9ae2388fab3fe5d091ef2f00a8e3")) + (let ((commit "c1d377ec86b902f76e47fc4506a9ff260d788082") + (revision "4")) (package (name "genenetwork2") - (version (git-version "3.11" "3" commit)) + (version (git-version "3.11" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -198,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "0ap7q7v42c5sg4kjy76zdn6h6w5a3f534i5644rya5a1akmss7hg")))) + "03l01nr0pg52pdnc6sajnsvylw61j68x6zz6mi5ygkimbj4093sa")))) (native-inputs (list graphviz)) (propagated-inputs @@ -305,19 +306,17 @@ #:phases #~(modify-phases %standard-phases (delete 'reset-gzip-timestamps) - (add-after 'install 'install-bundled-fonts - (lambda _ - ;; Install bundled fonts. - (for-each (lambda (font-file) - (install-file font-file (string-append #$output "/share/fonts/"))) - (find-files "gn2/wqflask/static/fonts" - "\\.ttf$")))) - (add-after 'unpack 'fix-font-paths - (lambda _ - ;; Set absolute store paths to installed bundled fonts. + (add-after 'unpack 'fix-paths-to-static-files + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Set absolute store paths to installed static files. (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" (("\\./gn2/wqflask/static/fonts") - (string-append #$output "/share/fonts"))))) + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/fonts"))) + (substitute* "gn2/wqflask/views.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))))) (add-after 'unpack 'fix-paths-scripts (lambda _ (substitute* "bin/genenetwork2" -- cgit v1.2.3 From 25cb9ad70155a08c088ff28bf54c06e12293105b Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 3 Jan 2024 14:56:04 +0300 Subject: gnqc-py: Fix syntax error. --- gn/packages/genenetwork.scm | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1ad63c0..4e3dc21 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -368,17 +368,17 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy - "python-pylint" ,python-pylint - "python-pytest" ,python-pytest - "python-hypothesis" ,python-hypothesis))) + `(("python-mypy" ,python-mypy) + ("python-pylint" ,python-pylint) + ("python-pytest" ,python-pytest) + ("python-hypothesis" ,python-hypothesis))) (propagated-inputs - `(("gunicorn" ,gunicorn - "python-redis" ,python-redis - "python-flask" ,python-flask - "python-pyyaml" ,python-pyyaml - "python-jsonpickle" ,python-jsonpickle - "python-mysqlclient" ,python-mysqlclient))) + `(("gunicorn" ,gunicorn) + ("python-redis" ,python-redis) + ("python-flask" ,python-flask) + ("python-pyyaml" ,python-pyyaml) + ("python-jsonpickle" ,python-jsonpickle) + ("python-mysqlclient" ,python-mysqlclient))) (synopsis "GeneNetwork Quality Control Application") (description "GeneNetwork qc is a quality control application for the data files that -- cgit v1.2.3 From 187b4f441aa45a0e49b71c03716025965091fe68 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 1 Feb 2024 19:52:45 +0300 Subject: gn: Update javascript-ckeditor. * gn/packages/javascript.scm (javascript-ckeditor): Copy entire directory structure of ckeditor to the store. ckeditor.js requires some CSS and other js files in the unzipped source to be able to be fully functional. Signed-off-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 39 ++++++++++++++++++++++----------------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 6471d65..81558fe 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1319,32 +1319,37 @@ a sample function, allowing for more complex calculations.") (arguments `(#:javascript-files '("dist/jstat.js"))) (build-system minify-build-system))) -(define-public javascript-ckeditor ; version 4 +(define-public javascript-ckeditor ; version 4 (package (name "javascript-ckeditor") - (version "4.13.0") ; Sept. 26, 2019 + (version "4.13.0") ; Sept. 26, 2019 (source (origin (method url-fetch) - (uri (string-append "https://cdn.ckeditor.com/" version - "/standard/ckeditor.js")) - (file-name (string-append "ckeditor-" version ".js")) + (uri (string-append "http://download.cksource.com/CKEditor/CKEditor/CKEditor%20" version + "/ckeditor_4.13.0_standard.zip")) (sha256 - (base32 - "0cvf1qdva5h2dh8y10c9v7dxrd82siswxx7h6cq0mf46ssjdygd0")))) + (base32 + "1n2xynmbr2v4wm2g2vqcqd16n93phsbq4sqrnljzb7wzjq9svl36")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) #:builder (begin - (use-modules (guix build utils)) - (let* ((out (assoc-ref %outputs "out")) - (targetdir - (string-append out "/share/genenetwork2/javascript/ckeditor")) - (source (assoc-ref %build-inputs "source"))) - (mkdir-p targetdir) - (copy-file source (string-append targetdir "/ckeditor.js")))))) - (native-inputs `(("source" ,source))) + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (name "ckeditor") + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip")) + (targetdir + (string-append (string-append out "/share/genenetwork2/javascript/" name))) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (invoke unzip source) + (copy-recursively "ckeditor" targetdir))))) + (native-inputs + `(("source" ,source) + ("unzip" ,unzip))) (home-page "https://ckeditor.com/") (synopsis "Smart WYSIWYG HTML editor") (description @@ -1358,8 +1363,8 @@ browser compatibility, including legacy browsers. @item Long-term support (LTS) until 2023. @end enumerate") (license (list license:gpl2+ - license:lgpl2.1+ - license:mpl1.1)))) ; Any of these three + license:lgpl2.1+ + license:mpl1.1)))) ; Any of these three (define-public javascript-parsley (package -- cgit v1.2.3 From e947a1e5c330595eee3a27185e042cf3b73689da Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Thu, 15 Feb 2024 13:59:30 +0300 Subject: gn: javascript: Add javascript-uikit. * gn/packages/javascript.scm: (javascript-uikit): New package. * gn/packages/javascript.scm: (genenetwork2) [propagated-inputs]:Add javascript-uikit. --- gn/packages/genenetwork.scm | 1 + gn/packages/javascript.scm | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 35 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4e3dc21..8d690f2 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -271,6 +271,7 @@ javascript-plotly javascript-typeahead js-underscore + javascript-uikit js-smart-time-ago javascript-nouislider javascript-purescript-genome-browser diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 81558fe..e24990b 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -2012,3 +2012,37 @@ vector graphics.") (description "Ace is a code editor written in JavaScript. ") (license license:expat))) + +(define-public javascript-uikit + (package + (name "javascript-uikit") + (version "3.7.4") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/uikit/uikit/releases/download/v" + version "/uikit" "-" version ".zip")) + (sha256 + (base32 "1qhhz3iki1nbyffg6qa7x2937708hjr9gf6mkn4v4cdl9j0mgyv0")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip")) + (targetdir (string-append out "/share/genenetwork2/javascript/uikit")) + (source (assoc-ref %build-inputs "source"))) + (invoke unzip source) + (copy-recursively "." targetdir))))) + (native-inputs + `(("source" ,source) + ("unzip" ,unzip))) + (home-page "https://getuikit.com/") + (synopsis "UIkit is a lightweight and modular front-end framework +for developing fast and powerful web interfaces.") + (description "UIkit is a lightweight and modular front-end framework +for developing fast and powerful web interfaces.") + (license license:bsd-3))) -- cgit v1.2.3 From b8348147e422a6499d2fd5992a349e4a29780ed0 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 15 Feb 2024 16:59:16 +0300 Subject: Bump down font-awesome to v4.7.0. * gn/packages/javascript.scm (javascript-font-awesome): Update to v4.7.0 which is the exact version we use in the genenetwork website. Signed-off-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index e24990b..349fa66 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -1854,7 +1854,7 @@ Popper will automatically put the tooltip in the right place near the button.") (define-public javascript-font-awesome (package (name "javascript-font-awesome") - (version "5.15.2") + (version "v4.7.0") (source (origin (method git-fetch) @@ -1863,7 +1863,7 @@ Popper will automatically put the tooltip in the right place near the button.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1jin0qlf5lv4l9gj8qc1pp34mxyvyj6gma4qnjqiah1bzcfn635l")))) + (base32 "0w30y26jp8nvxa3iiw7ayl6rkza1rz62msl9xw3srvxya1c77grc")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -1873,13 +1873,11 @@ Popper will automatically put the tooltip in the right place near the button.") (let* ((out (assoc-ref %outputs "out")) (targetdir (string-append out "/share/genenetwork2/javascript/fontawesome")) (source (assoc-ref %build-inputs "source")) - (js-dir (string-append source "/js")) (css-dir (string-append source "/css")) - (fonts-dir (string-append source "/webfonts"))) + (fonts-dir (string-append source "/fonts"))) (copy-recursively css-dir (string-append targetdir "/css")) - (copy-recursively js-dir (string-append targetdir "/js")) (copy-recursively fonts-dir - (string-append targetdir "/webfonts")))))) + (string-append targetdir "/fonts")))))) (native-inputs `(("source" ,source))) (home-page "https://fontawesome.com/") (synopsis "Font that contains a rich iconset") -- cgit v1.2.3 From c50c78496f11c6e925d279ae7f75a0a8bf59f475 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 22 Feb 2024 13:18:41 +0000 Subject: Upgrade guix channel to 58233e6. --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index d3d0030..bff677d 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "330b94e8bd88baf903d2bc11bf96e23b119e0fe5") + (commit "58233e6c21307be41e0636de61960e9376d3d82e") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 81e1e04973f22b00296fef38ecaa98e2c5cf016e Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 22 Feb 2024 23:20:46 +0000 Subject: gn: Add ocaml4.07-gsl-1. ocaml4.07-gsl-1 has been removed from upstream Guix. * gn/packages/ocaml.scm (ocaml4.07-gsl-1): New variable. --- gn/packages/ocaml.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/gn/packages/ocaml.scm b/gn/packages/ocaml.scm index 4aa2543..7c6020a 100644 --- a/gn/packages/ocaml.scm +++ b/gn/packages/ocaml.scm @@ -1,9 +1,11 @@ (define-module (gn packages ocaml) #:use-module (guix packages) + #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system ocaml) #:use-module (gnu packages) - #:use-module (gnu packages ocaml)) + #:use-module (gnu packages ocaml) + #:use-module (gnu packages maths)) ;; This is the last version supported by ocaml-4.07. (define-public ocaml4.07-lwt-5.5.0 @@ -23,5 +25,26 @@ "1jbjz2rsz3j56k8vh5qlmm87hhkr250bs2m3dvpy9vsri8rkzj9z")))) (properties '())))) +(define-public ocaml4.07-gsl-1 + (package-with-ocaml4.07 + (package + (inherit ocaml-gsl) + (version "1.19.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/mmottl/gsl-ocaml" + "/releases/download/v" + version "/gsl-ocaml-" version ".tar.gz")) + (sha256 + (base32 + "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh")))) + (build-system ocaml-build-system) + (inputs + `(("gsl" ,gsl-static))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild))) + (arguments '()) + (propagated-inputs '())))) + (define-public build-with-ocaml4.07 (package-input-rewriting/spec `(("ocaml4.07-lwt" . ,(const ocaml4.07-lwt-5.5.0))))) -- cgit v1.2.3 From d2ee9dc81af5ee64ebbb1bff3d8de8ef878a845c Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 23 Feb 2024 17:32:32 +0000 Subject: Upgrade guix channel to e7990b1. --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index bff677d..26ad673 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "58233e6c21307be41e0636de61960e9376d3d82e") + (commit "e7990b12170eec0c35541196f948be26a9e4a519") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From 73f615b37829354a90a015caf8880e1c49503ddd Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 23 Feb 2024 21:27:09 +0000 Subject: gn: Add r-rrbgen. * gn/packages/bioinformatics.scm (r-rrbgen): New variable. --- gn/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 2832ea6..c3e5020 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4460,3 +4460,28 @@ automatically vectorize for different architectures without adapting the code.") (substitute-keyword-arguments (package-arguments wfa2-lib) ((#:make-flags flags ''()) #~(cons "CC_FLAGS+=-static" #$flags)))))) + +(define-public r-rrbgen + (package + (name "r-stitch") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/rwdavies/rrbgen/releases/download/" + version "/rrbgen_" version ".tar.gz")) + (sha256 + (base32 + "1vhqy8licl2pkzar4aag0q5fhnb3fdch8acyjh9445ia42z01z9c")))) + (build-system r-build-system) + (propagated-inputs + (list r-rcpp + r-rcpparmadillo)) + (home-page "https://github.com/rwdavies/rrbgen") + (synopsis "Lightweight limited functionality R bgen read/write library") + (description "@code{r-rrbgen} supports v1.3 of the bgen format. It supports reading +and writing using 8, 16, 24 or 32 bits per probability, using Layout = +2 and CompressedSNPBlocks = 1, for bi-allelic SNPs with samples of +ploidy 2. Any other format specification may crash unexpectedly +without a properly defined error.") + (license license:gpl3))) -- cgit v1.2.3 From 8de10edc74100b49589949778c5bd84c72e83deb Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 23 Feb 2024 21:28:00 +0000 Subject: gn: Add seqlib. * gn/packages/bioinformatics.scm (seqlib): New variable. --- gn/packages/bioinformatics.scm | 65 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index c3e5020..b0590ca 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4485,3 +4485,68 @@ and writing using 8, 16, 24 or 32 bits per probability, using Layout = ploidy 2. Any other format specification may crash unexpectedly without a properly defined error.") (license license:gpl3))) + +(define-public seqlib + (package + (name "seqlib") + (version "0.1.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Zilong-Li/SeqLib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hczg1swghnxm6af74l09crdgf7l282jabmyck9mi5bk6vg9s1pn")))) + (build-system gnu-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + ;; Patch build scripts to unbundle htslib and build a + ;; seqlib shared library using libtool. + (add-after 'unpack 'patch-build-scripts + (lambda _ + ;; Initialize libtool. + (substitute* "configure.ac" + (("AM_INIT_AUTOMAKE\\(foreign\\)\n" all) + (string-append all "LT_INIT\n"))) + (substitute* "Makefile.am" + ;; Install headers + (("^SUBDIRS" all) + (string-append "nobase_include_HEADERS = " + (string-join (find-files "SeqLib")) + "\n" all)) + ;; Do not recurse into htslib submodule. + (("htslib") "") + ;; Remove install target override. + (("^install:") "") + (("^\tmkdir -p lib && cp src/libseqlib.a /libhts.a lib") "")) + (substitute* "src/Makefile.am" + ;; Build libtool library. + (("noinst_LIBRARIES = libseqlib\\.a") + "lib_LTLIBRARIES = libseqlib.la\nlibseqlib_la_LIBADD = -ljsoncpp") + (("libseqlib\\.a") "libseqlib.la") + (("libseqlib_a") "libseqlib_la")) + (substitute* (list "SeqLib/BamHeader.h" + "SeqLib/BamRecord.h" + "SeqLib/RefGenome.h" + "src/ReadFilter.cpp") + ;; Patch path to htslib headers. + (("\"htslib/htslib/([^\"]*)\"" all header) + (string-append "")))))))) + (inputs + (list zlib)) + (native-inputs + (list autoconf automake libtool)) + ;; seqlib headers include headers from htslib and jsoncpp. So, + ;; they are propagated inputs. + (propagated-inputs + (list htslib jsoncpp)) + (home-page "https://github.com/Zilong-Li/SeqLib") + (synopsis "C++ htslib interface for manipulating sequence data and VCF") + (description "@code{seqlib} is a C++ htslib interface for manipulating sequence data +and VCF files.") + (license (list license:expat ; SeqLib/IntervalTree.h, SeqLib/aho_corasick.hpp, + ; json/json-forwards.h, json/json.h, src/jsoncpp.cpp, src/ssw.c, + license:asl2.0)))) ; main license -- cgit v1.2.3 From 9f4c479e6d21e7bb2d3590cbb2df5906060d2781 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 23 Feb 2024 21:28:12 +0000 Subject: gn: Add vcfpp. * gn/packages/bioinformatics.scm (vcfpp): New variable. --- gn/packages/bioinformatics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b0590ca..8141ada 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4550,3 +4550,24 @@ and VCF files.") (license (list license:expat ; SeqLib/IntervalTree.h, SeqLib/aho_corasick.hpp, ; json/json-forwards.h, json/json.h, src/jsoncpp.cpp, src/ssw.c, license:asl2.0)))) ; main license + +(define-public vcfpp + (package + (name "vcfpp") + (version "0.3.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/Zilong-Li/vcfpp/releases/download/v" + version "/vcfpp.h")) + (sha256 + (base32 + "1wq76wz81y09ic37z30vljqnczhwx2qijav0nfvg6xi8wd2c75n3")))) + (build-system copy-build-system) + (arguments + (list #:install-plan #~'(("vcfpp.h" "include/vcfpp/vcfpp.h")))) + (home-page "https://github.com/Zilong-Li/vcfpp") + (synopsis "C++ API of htslib") + (description "@code{vcfpp} is a single C++ file as +interface to the basic htslib. It can be easily included in a C++ +program for scripting high-performance genomic analyses.") + (license license:asl2.0))) -- cgit v1.2.3 From e1888bca8136a05438fcf33bc995531514e6cde0 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 23 Feb 2024 21:28:22 +0000 Subject: gn: Add r-stitch. * gn/packages/bioinformatics.scm (r-stitch): New variable. --- gn/packages/bioinformatics.scm | 48 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 8141ada..b5fac4d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4571,3 +4571,51 @@ and VCF files.") interface to the basic htslib. It can be easily included in a C++ program for scripting high-performance genomic analyses.") (license license:asl2.0))) + +(define-public r-stitch + (package + (name "r-stitch") + (version "1.6.10") + (source + ;; The release tarball bundles dependencies. So, use git-fetch. + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rwdavies/STITCH") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0iy5fq2l5a35xdxqaf9ypj56da57qmwppwqmh9nflbvmbc7kgbkf")))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "STITCH"))) + (add-after 'chdir 'patch-build-system + (lambda _ + (substitute* "src/Makevars" + (("\\$\\(SEQLIB_ROOT\\)/src/libseqlib.a") "-lseqlib") + (("\\$\\(SEQLIB_ROOT\\)/htslib/libhts.a") "-lhts") + ((": SeqLib") ":"))))))) + (inputs + (list curl htslib seqlib zlib)) + (native-inputs + (list autoconf automake vcfpp)) + (propagated-inputs + (list r-data-table r-rrbgen + ;; FIXME: These should be inputs that are substituted into + ;; the source. But, for some reason, the reference scanner + ;; does not pick them up that way. + coreutils findutils htslib rsync)) + (home-page "https://github.com/rwdavies/STITCH") + (synopsis "Sequencing to imputation through constructing haplotypes") + (description "@code{r-stitch} is an R program for reference panel free, +read aware, low coverage sequencing genotype imputation. STITCH runs +on a set of samples with sequencing reads in BAM format, as well as a +list of positions to genotype, and outputs imputed genotypes in VCF +format.") + (license license:gpl3))) -- cgit v1.2.3 From d3b01e82a43507f7388e6b0397c324ebdf44bcf7 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 23 Feb 2024 21:32:28 +0000 Subject: gn: bioinformatics: Import (guix build-system r). --- gn/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b5fac4d..82caab9 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -16,6 +16,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system python) + #:use-module (guix build-system r) #:use-module (guix build-system trivial) #:use-module (guix build-system waf) #:use-module (gnu packages) -- cgit v1.2.3 From 336799a9ea0d495693336283961f8853cf1cb614 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 26 Feb 2024 11:44:42 +0000 Subject: gn: gn-auth: Use list-style inputs. * gn/packages/genenetwork.scm (gn-auth)[native-inputs, propagated-inputs]: List them directly instead of using an association list. --- gn/packages/genenetwork.scm | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 8d690f2..a316464 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -411,23 +411,23 @@ (when tests? (invoke "pytest" "-k" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy) - ("python-pytest" ,python-pytest) - ("python-pylint" ,python-pylint) - ("python-hypothesis" ,python-hypothesis) - ("python-pytest-mock" ,python-pytest-mock) - ("python-mypy-extensions" ,python-mypy-extensions))) + (list python-hypothesis + python-mypy + python-mypy-extensions + python-pylint + python-pytest + python-pytest-mock)) (propagated-inputs - `(("gunicorn" ,gunicorn) - ("python-flask" ,python-flask) - ("python-redis" ,python-redis) - ("python-authlib" ,python-authlib) - ("python-pymonad" ,python-pymonad) - ("yoyo-migrations" ,yoyo-migrations) - ("python-flask-cors" ,python-flask-cors) - ("python-mysqlclient" ,python-mysqlclient) - ("python-argon2-cffi" ,python-argon2-cffi) - ("python-email-validator" ,python-email-validator))) + (list gunicorn + python-argon2-cffi + python-authlib + python-email-validator + python-flask + python-flask-cors + python-mysqlclient + python-pymonad + python-redis + yoyo-migrations)) (home-page "https://github.com/genenetwork/gn-auth") (synopsis "Authentication and Authorisation server for GeneNetwork services") (description "Authentication and Authorisation server for GeneNetwork services.") -- cgit v1.2.3 From 08df252121f5167966e4e8a3c8e34dddedf7bc57 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 26 Feb 2024 11:45:28 +0000 Subject: gn: gn-auth: Update to commit 10ec3b1. * gn/packages/genenetwork.scm (gn-auth): Update to commit 10ec3b1. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index a316464..99423f7 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -396,11 +396,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "acd1a3d29900cff70ccc82dbe8ad1dc4b4c0fe8e"))) + (commit "10ec3b1f851897c2cce89356b4404c18f9f11a2f"))) (hash (content-hash (base32 - "19c0qshj511w4rhfbj5d9gvcscnbsjhk6xnr10ajjvr61w42qmq4"))))) + "1p7mcimg1fhdxjmhi6p6snpq73h5h8h6ya2lx9c9kr8r3zn67pb5"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From eb6c7c0607e3c7ffdf9198b7fe9c5960e63e37e3 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 28 Feb 2024 23:33:43 +0000 Subject: Upgrade guix channel to aeaa390. --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index 26ad673..00b4bf3 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "e7990b12170eec0c35541196f948be26a9e4a519") + (commit "aeaa390b71a15335bef03f83bd9dc946fa535398") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From a490ca06e186f5057bcdda17266ad93763cc0c2f Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 29 Feb 2024 00:31:32 +0000 Subject: gn: crates-io: Import (gnu packages crates-windows) for rust-dunce-1. --- gn/packages/crates-io.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index 331a179..4cebb33 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -7,6 +7,7 @@ #:use-module (guix build-system cargo) #:use-module (gnu packages crates-graphics) #:use-module (gnu packages crates-io) + #:use-module (gnu packages crates-windows) #:use-module (gnu packages maths) #:use-module (gnu packages python)) -- cgit v1.2.3 From c7641ce85b216bf1b9d337a35de8e9a85228a6f3 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 29 Feb 2024 01:12:46 +0000 Subject: gn: Add python-globus-sdk. * gn/packages/globus.scm (python-globus-sdk): New variable. --- gn/packages/globus.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 gn/packages/globus.scm diff --git a/gn/packages/globus.scm b/gn/packages/globus.scm new file mode 100644 index 0000000..43a8f7a --- /dev/null +++ b/gn/packages/globus.scm @@ -0,0 +1,29 @@ +(define-module (gn packages globus) + #:use-module (gnu packages python-build) + #:use-module (gnu packages python-crypto) + #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) + #:use-module (guix build-system pyproject) + #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages)) + +(define-public python-globus-sdk + (package + (name "python-globus-sdk") + (version "3.37.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "globus-sdk" version)) + (sha256 + (base32 + "19w3pjzfycaqvvr11nq8c91i6pkkkic95yf170hr39dwj70lrkc7")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-cryptography python-pyjwt python-requests + python-typing-extensions)) + (home-page "https://github.com/globus/globus-sdk-python") + (synopsis "Globus SDK for Python") + (description "@code{python-globus-sdk} provides a convenient Pythonic interface to +Globus APIs.") + (license license:asl2.0))) -- cgit v1.2.3 From b8eac8a000f1c2de203281b3c016fe959fcff7a4 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 29 Feb 2024 01:14:17 +0000 Subject: gnu: Add python-click-type-test. * gn/packages/globus.scm (python-click-type-test): New variable. --- gn/packages/globus.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gn/packages/globus.scm b/gn/packages/globus.scm index 43a8f7a..af296f3 100644 --- a/gn/packages/globus.scm +++ b/gn/packages/globus.scm @@ -1,4 +1,5 @@ (define-module (gn packages globus) + #:use-module (gnu packages check) #:use-module (gnu packages python-build) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) @@ -27,3 +28,22 @@ (description "@code{python-globus-sdk} provides a convenient Pythonic interface to Globus APIs.") (license license:asl2.0))) + +(define-public python-click-type-test + (package + (name "python-click-type-test") + (version "0.0.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "click-type-test" version)) + (sha256 + (base32 + "1i3z7akiz7s8jy6x0vzrak88m55ac1spq88vziwryzr7355y3hgq")))) + (build-system pyproject-build-system) + (native-inputs (list python-pytest)) + (propagated-inputs (list python-click)) + (home-page "https://github.com/sirosen/click-type-test") + (synopsis "Test that type annotations match click parameter types") + (description "@code{python-click-type-test} allows you to test that your click +options and arguments match your type annotations.") + (license license:expat))) -- cgit v1.2.3 From 2c1db30bc59441fc3e964bd30de55667ecd752c9 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 29 Feb 2024 01:14:44 +0000 Subject: gnu: Add globus-cli. * gn/packages/globus.scm (globus-cli): New variable. --- gn/packages/globus.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gn/packages/globus.scm b/gn/packages/globus.scm index af296f3..56d2c35 100644 --- a/gn/packages/globus.scm +++ b/gn/packages/globus.scm @@ -47,3 +47,30 @@ Globus APIs.") (description "@code{python-click-type-test} allows you to test that your click options and arguments match your type annotations.") (license license:expat))) + +(define-public globus-cli + (package + (name "globus-cli") + (version "3.25.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "globus-cli" version)) + (sha256 + (base32 + "05div2psajmqdy9md804q4x6ha4yfp4w6yrxz0ynsq3i62a6cl5v")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) + (propagated-inputs + (list python-click + python-cryptography + python-globus-sdk + python-jmespath + python-packaging + python-requests + python-typing-extensions)) + (home-page "https://docs.globus.org/cli") + (synopsis "Globus CLI") + (description "@code{python-globus-sdk} provides a command-line interface to +Globus APIs.") + (license license:asl2.0))) -- cgit v1.2.3 From ec4abbab4a2c298f56d3273cfa677ab19c172841 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 29 Feb 2024 20:54:21 +0000 Subject: Fix Globus CLI description. --- gn/packages/globus.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/globus.scm b/gn/packages/globus.scm index 56d2c35..6cc5d9e 100644 --- a/gn/packages/globus.scm +++ b/gn/packages/globus.scm @@ -71,6 +71,6 @@ options and arguments match your type annotations.") python-typing-extensions)) (home-page "https://docs.globus.org/cli") (synopsis "Globus CLI") - (description "@code{python-globus-sdk} provides a command-line interface to + (description "@code{globus-cli} provides a command-line interface to Globus APIs.") (license license:asl2.0))) -- cgit v1.2.3 From 5fa3e2bcaafb498ec3bca51f72545f5a16b5a527 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 1 Mar 2024 11:15:13 +0000 Subject: gn: gn-auth: Update to commit 8a20071. * gn/packages/genenetwork.scm (gn-auth): Update to commit 8a20071. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 99423f7..1084a63 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -396,11 +396,11 @@ (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "10ec3b1f851897c2cce89356b4404c18f9f11a2f"))) + (commit "8a20071dc8009b5b9439d10e17a2a57883b7b363"))) (hash (content-hash (base32 - "1p7mcimg1fhdxjmhi6p6snpq73h5h8h6ya2lx9c9kr8r3zn67pb5"))))) + "1p8vcdpj9wlkfaxzmg3b6372zad9m2byrz7rzg6fdl26v95wd4qm"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 60a524a955455b2f36fd82e95926f50220608ab0 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Sat, 2 Mar 2024 16:20:48 +0300 Subject: gn-auth: Update the commit and hash. --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1084a63..7030515 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -390,17 +390,17 @@ (define-public gn-auth (package (name "gn-auth") - (version "1.0.0") + (version "1.0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/genenetwork/gn-auth.git") - (commit "8a20071dc8009b5b9439d10e17a2a57883b7b363"))) + (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) (hash (content-hash (base32 - "1p8vcdpj9wlkfaxzmg3b6372zad9m2byrz7rzg6fdl26v95wd4qm"))))) + "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 2c3dc85ef14c1d9c1f8e69daf9bcda0dadb308ff Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 3 Mar 2024 07:05:40 -0600 Subject: gn: xterm: comment out xterm.js package because of suspect sources - the hash value changed. Also needs fixing of the code that uses it in gn2. * gn/packages/genenetwork.scm (xterm.js): Comment out packages --- gn/packages/genenetwork.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 7030515..b7e3f6f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -295,9 +295,9 @@ javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie - javascript-xterm - javascript-xterm-style - javascript-xterm-addon-fit + ; javascript-xterm -- disabled until we know what to do with it, not working on production + ; javascript-xterm-style + ; javascript-xterm-addon-fit javascript-font-awesome)) (inputs (list javascript-colorbox)) -- cgit v1.2.3 From b27452660632d72e1b066acff9072f4a5b645c3e Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 4 Mar 2024 08:11:10 +0300 Subject: genenetwork2: Update commit and hash to build with missing templates --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b7e3f6f..ad27cb0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "c1d377ec86b902f76e47fc4506a9ff260d788082") + (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "03l01nr0pg52pdnc6sajnsvylw61j68x6zz6mi5ygkimbj4093sa")))) + "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 2356005a27de00613f9ae29dde021953cd05fc1f Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Mar 2024 06:52:10 +0300 Subject: genenetwork2: Update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ad27cb0..9d545fb 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") + (let ((commit "084ce21fb1d8263e9d8f50ed1fe74799af10fb52") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) + "02x47kilmi8a00vd1bbcvzsgxnhyxjx4wva64b1jv2ijjgypbbgk")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 768d3b78aeeb12e84edd3b7e64270bf946df1c55 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Mar 2024 07:08:07 +0300 Subject: genenetwork2: Fix commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 9d545fb..ad27cb0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "084ce21fb1d8263e9d8f50ed1fe74799af10fb52") + (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "02x47kilmi8a00vd1bbcvzsgxnhyxjx4wva64b1jv2ijjgypbbgk")))) + "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From c6a011042bc7dec4476d4b66d035930416d3561a Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 5 Mar 2024 07:50:34 +0300 Subject: genenetwork2: update commit and hash to fetch configs from app --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ad27cb0..dda9bf8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "a0b8e0a2d0c35542a47f906192d08d39bff290ff") + (let ((commit "9983b4273622dc5fd8b7d43d10d935f07e3c9eb6") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "0awspvn2fyllr5dkyskf62zxr38m2dhn8jiyzh8rq036mmd4ixya")))) + "1ihjx5a1k8nsd88i85simv09k393jcrijy024ds5pb48k5hc9sff")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 645cfb51a968e58b286e8af7a6fa3fefa6b512a8 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 6 Mar 2024 06:00:17 +0300 Subject: genenetwork2: update commit and hash Removes use of configs from `gn2.utility.tools` module since they are not up to date. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dda9bf8..5298490 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -186,7 +186,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "9983b4273622dc5fd8b7d43d10d935f07e3c9eb6") + (let ((commit "1e81c74ee8752ad2913b4e610ba7575638755385") (revision "4")) (package (name "genenetwork2") @@ -199,7 +199,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "1ihjx5a1k8nsd88i85simv09k393jcrijy024ds5pb48k5hc9sff")))) + "18g4dd3h737slqmp1ql2jqqzmzql3mx3b4xy72d7qwhwwhc7hcgv")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From 3414d825a9799f30d92e5188378cb7ad69db0eb0 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 8 Mar 2024 02:55:29 +0300 Subject: gn-uploader: Update package definition --- gn/packages/genenetwork.scm | 85 +++++++++++++++++++++++---------------------- 1 file changed, 44 insertions(+), 41 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5298490..dae4b54 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -345,47 +345,50 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) -(define-public gnqc-py - (package - (name "gnqc-py") - (version "0.0.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/fredmanglis/gnqc_py.git") - (commit "c81a3d948b3bc0db20a530fa1aa428b35b5d6145"))) - (hash - (content-hash - (base32 - "1101pql7zpijn36i9phcakfx1r5dcvdf6ix0v4ndjzmzx3d0xyi2"))))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-k" "unit_test"))))))) - (native-inputs - `(("python-mypy" ,python-mypy) - ("python-pylint" ,python-pylint) - ("python-pytest" ,python-pytest) - ("python-hypothesis" ,python-hypothesis))) - (propagated-inputs - `(("gunicorn" ,gunicorn) - ("python-redis" ,python-redis) - ("python-flask" ,python-flask) - ("python-pyyaml" ,python-pyyaml) - ("python-jsonpickle" ,python-jsonpickle) - ("python-mysqlclient" ,python-mysqlclient))) - (synopsis "GeneNetwork Quality Control Application") - (description - "GeneNetwork qc is a quality control application for the data files that - eventually are used to add to the data in the GeneNetwork project.") - (home-page "https://gitlab.com/fredmanglis/gnqc_py") - (license license:agpl3+))) +(define-public gn-uploader + (let ((commit "6ced7085193affa636f229e72dc19175a3a06cfe") + (version "0.0.1")) + (package + (name "gn-uploader") + (version (string-append version (string-take commit 8))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) + (hash + (content-hash + (base32 + "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) + (native-inputs + `(("python-mypy" ,python-mypy) + ("python-pylint" ,python-pylint) + ("python-pytest" ,python-pytest) + ("python-hypothesis" ,python-hypothesis))) + (propagated-inputs + `(("gunicorn" ,gunicorn) + ("python-redis" ,python-redis) + ("python-flask" ,python-flask) + ("python-pyyaml" ,python-pyyaml) + ("python-jsonpickle" ,python-jsonpickle) + ("python-mysqlclient" ,python-mysqlclient))) + (synopsis "GeneNetwork Quality Control Application") + (description + "gn-uploader is a service allowing upload of new data into GeneNetwork, + that does quality control for the data files that is being uploaded to ensure + it fulfils all conditions before it can be accepted.") + (home-page "https://git.genenetwork.org/gn-uploader") + (license license:agpl3+)))) (define-public gn-auth (package -- cgit v1.2.3 From 869598d39a532c6acc83bb0b9d21baaa79476973 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 8 Mar 2024 10:10:08 +0300 Subject: gn-uploader: Use more modern list-style inputs. Fix version number. --- gn/packages/genenetwork.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dae4b54..98d92ac 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -350,7 +350,7 @@ (version "0.0.1")) (package (name "gn-uploader") - (version (string-append version (string-take commit 8))) + (version (string-append version "-" (string-take commit 8))) (source (origin (method git-fetch) @@ -371,17 +371,17 @@ (when tests? (invoke "pytest" "-m" "unit_test"))))))) (native-inputs - `(("python-mypy" ,python-mypy) - ("python-pylint" ,python-pylint) - ("python-pytest" ,python-pytest) - ("python-hypothesis" ,python-hypothesis))) + (list python-mypy + python-pylint + python-pytest + python-hypothesis)) (propagated-inputs - `(("gunicorn" ,gunicorn) - ("python-redis" ,python-redis) - ("python-flask" ,python-flask) - ("python-pyyaml" ,python-pyyaml) - ("python-jsonpickle" ,python-jsonpickle) - ("python-mysqlclient" ,python-mysqlclient))) + (list gunicorn + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, -- cgit v1.2.3 From be336001a7665cb32abdf29b888651740322bb3d Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 02:19:45 +0000 Subject: Upgrade guix channel to b0b988c. --- .guix-channel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-channel b/.guix-channel index 00b4bf3..e7e9a9a 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "aeaa390b71a15335bef03f83bd9dc946fa535398") + (commit "b0b988c41c9e0e591274495a1b2d6f27fcdae15a") (introduction (channel-introduction (version 0) -- cgit v1.2.3 From e8e9acbbc24ee29781df50832f3b979106c41415 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 02:42:18 +0000 Subject: gn: Add python-rdflib-jsonld. python-rdflib-jsonld has been removed from upstream Guix. * gn/packages/python.scm (python-rdflib-jsonld): New variable. --- gn/packages/python.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index db2f4c9..2e0fab7 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1773,6 +1773,30 @@ file format spec.") (license:fsf-free (string-append "https://web.archive.org/web/20190211105114/" "http://www.repoze.org/LICENSE.txt"))))) +;; Note: This package is only needed for rdflib < 6.0; supersede when +;; the above are removed. +(define-public python-rdflib-jsonld + (package + (name "python-rdflib-jsonld") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rdflib-jsonld" version)) + (sha256 + (base32 + "0qrshlqzv5g5bign7kjja3xf7hyk7xgayr3yd0qlqda1kl0x6z0h")))) + (build-system python-build-system) + (native-inputs + (list python-nose)) + (propagated-inputs + (list python-rdflib)) + (home-page "https://github.com/RDFLib/rdflib-jsonld") + (synopsis "rdflib extension adding JSON-LD parser and serializer") + (description "This package provides an rdflib extension adding JSON-LD +parser and serializer.") + (license license:bsd-3))) + (define-public python-rdflib-shim (package (name "python-rdflib-shim") -- cgit v1.2.3 From 7a62aae3fda55385dbc1e8f2dc826c8e4ca14be6 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 19:05:23 +0000 Subject: gn: Add python-typing-extensions-4.10. * gn/packages/python.scm (python-typing-extensions-4.10): New variable. --- gn/packages/python.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 2e0fab7..11f2762 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1860,3 +1860,14 @@ complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.") (license license:bsd-3))) + +(define-public python-typing-extensions-4.10 + (package + (inherit python-typing-extensions) + (version "4.10.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "typing_extensions" version)) + (sha256 + (base32 + "1jxkj4pni8pdyrn79sq441lsp40xzw363n0qvfc6zfcgkv4dgaxh")))))) -- cgit v1.2.3 From 88bbef10dfd95637c65a2392b54b426dbed78c4c Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 19:05:37 +0000 Subject: gn: Add python-addict. * gn/packages/python.scm (python-addict): New variable. --- gn/packages/python.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 11f2762..9ea3c81 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -36,6 +36,7 @@ #:use-module (guix hg-download) #:use-module (guix gexp) #:use-module (guix utils) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (srfi srfi-1)) @@ -1871,3 +1872,20 @@ concepts.") (sha256 (base32 "1jxkj4pni8pdyrn79sq441lsp40xzw363n0qvfc6zfcgkv4dgaxh")))))) + +(define-public python-addict + (package + (name "python-addict") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "addict" version)) + (sha256 + (base32 + "1574sicy5ydx9pvva3lbx8qp56z9jbdwbj26aqgjhyh61q723cmk")))) + (build-system pyproject-build-system) + (home-page "https://github.com/mewwts/addict") + (synopsis "Python dictionary with attribute accessible values") + (description "@code{python-addict} provides dictionaries whose items can +be get and set using both attribute and item syntax.") + (license license:expat))) -- cgit v1.2.3 From e84620e6d91e2cbd7aa683846ccb9664ae9137eb Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 19:05:58 +0000 Subject: gn: Add python-enlighten. * gn/packages/python.scm (python-enlighten): New variable. --- gn/packages/python.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 9ea3c81..da0cdc6 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1889,3 +1889,25 @@ concepts.") (description "@code{python-addict} provides dictionaries whose items can be get and set using both attribute and item syntax.") (license license:expat))) + +(define-public python-enlighten + (package + (name "python-enlighten") + (version "1.12.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "enlighten" version)) + (sha256 + (base32 + "0psvglhi0c7d7pdk9rfb8scnv3xbq2fz78619x2mxvz094mxkwvm")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-blessed python-prefixed)) + (home-page "https://github.com/Rockhopper-Technologies/enlighten") + (synopsis "Console progress bar library") + (description "@code{python-enlighten} is a console progress bar library +for Python. The main advantage of Enlighten is that it allows writing to +stdout and stderr without any redirection or additional code---just print or +log as you normally would. Enlighten also includes experimental support for +Jupyter Notebooks.") + (license license:mpl2.0))) -- cgit v1.2.3 From fc04f7328522c4ca8b728bd129c53f26d2857d37 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 19:06:08 +0000 Subject: gn: Add python-pypubsub. * gn/packages/python.scm (python-pypubsub): New variable. --- gn/packages/python.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index da0cdc6..a9cd5be 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1911,3 +1911,29 @@ stdout and stderr without any redirection or additional code---just print or log as you normally would. Enlighten also includes experimental support for Jupyter Notebooks.") (license license:mpl2.0))) + +(define-public python-pypubsub + (package + (name "python-pypubsub") + (version "4.0.3") + ;; There is no source tarball on PyPI. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/schollii/pypubsub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02j74w28wzmdvxkk8i561ywjgizjifq3hgcl080yj0rvkd3wivlb")))) + (build-system python-build-system) + (home-page "https://github.com/schollii/pypubsub") + (synopsis "Python publish-subscribe library") + (description "@code{python-pypubsub} provides a pure Python +publish-subscribe API to facilitate event-based or message-based architecture +in a single-process application. It is centered on the notion of a topic; +senders publish messages of a given topic, and listeners subscribe to messages +of a given topic, all inside the same process. The package also supports a +variety of advanced features that facilitate debugging and maintaining topics +and messages in larger desktop or server-based applications.") + (license license:bsd-2))) -- cgit v1.2.3 From a32299d4d002485e8b8142a14b21d46d2bb3f989 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 19:06:15 +0000 Subject: gn: Add python-prefixed. * gn/packages/python.scm (python-prefixed): New variable. --- gn/packages/python.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index a9cd5be..e7cfdd7 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1937,3 +1937,21 @@ of a given topic, all inside the same process. The package also supports a variety of advanced features that facilitate debugging and maintaining topics and messages in larger desktop or server-based applications.") (license license:bsd-2))) + +(define-public python-prefixed + (package + (name "python-prefixed") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "prefixed" version)) + (sha256 + (base32 + "1sdvxwy4kvcxvnq1nx70j1ccx5ga6wdb478vqd5azf1fc1gd2m0b")))) + (build-system pyproject-build-system) + (home-page "https://github.com/Rockhopper-Technologies/prefixed") + (synopsis "Prefixed alternative numeric library") + (description "@code{python-prefixed} provides an alternative +implementation of the built-in float which supports formatted output with +SI (decimal) and IEC (binary) prefixes.") + (license license:mpl2.0))) -- cgit v1.2.3 From 4a177f3666b4bc3936a1d6e94f888feddcaa3d31 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 19:07:08 +0000 Subject: gn: Add python-cwltool. * gn/packages/cwl.scm (python-cwltool): New variable. --- gn/packages/cwl.scm | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index a327187..96dad02 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -4,7 +4,8 @@ #:use-module (guix packages) #:use-module (guix build-system python) #:use-module (gnu packages) - #:use-module (gnu packages bioinformatics)) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages node) (define-public cwl-runner @@ -28,3 +29,15 @@ "Common workflow language alternate entry point to allow cwl-runner script as an implementation-agnostic script interpreter.") (license license:asl2.0))) + +;; python-toil tightly integrates with cwltool using it as a library. So, +;; create a library version of cwltool where inputs become propagated inputs. +(define-public python-cwltool + (package + (inherit cwltool) + (name "python-cwltool") + (inputs + (list node)) + (propagated-inputs + (modify-inputs (package-inputs cwltool) + (delete "node"))))) -- cgit v1.2.3 From d68beff869e887cd0afbde6079b2f41a61053c42 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Mon, 11 Mar 2024 19:07:16 +0000 Subject: gn: Add python-toil. * gn/packages/cwl.scm (python-toil): New variable. --- gn/packages/cwl.scm | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 96dad02..fe5fcb2 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -1,11 +1,19 @@ (define-module (gn packages cwl) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix packages) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages docker) #:use-module (gnu packages node) + #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) + #:use-module (gnu packages serialization) + #:use-module (gnu packages time) + #:use-module (gn packages python)) (define-public cwl-runner @@ -41,3 +49,64 @@ script as an implementation-agnostic script interpreter.") (propagated-inputs (modify-inputs (package-inputs cwltool) (delete "node"))))) + +(define-public python-toil + (package + (name "python-toil") + (version "6.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "toil" version)) + (sha256 + (base32 + "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'disable-optional-features + (lambda _ + (substitute* "requirements-cwl.txt" + ;; Loosen version restrictions on ruamel.yaml. + (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n") + ;; Remove optional dependency on galaxy-util and + ;; galaxy-tool-util. TODO: Package these and restore these + ;; dependencies. + (("galaxy-util[^\n]*") "") + (("galaxy-tool-util[^\n]*") "")) + ;; Disable optional wdl, wes and mesos features. We don't yet + ;; have dependencies packaged for them. TODO: Package these + ;; dependencies and enable these features. + (substitute* "setup.py" + (("\"wdl\",") "") + (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]") + "toil-cwl-runner = toil.cwl.cwltoil:main") + (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "") + (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "") + (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") ""))))))) + (propagated-inputs + (list python-addict + python-cachecontrol + python-configargparse + python-cwltool + python-dateutil + python-dill + python-docker + python-enlighten + python-psutil + python-pypubsub + python-pytz + python-pyyaml + python-requests + python-ruamel.yaml + python-typing-extensions-4.10 + python-urllib3)) + (home-page "https://github.com/DataBiosphere/toil") + (synopsis "Scalable, efficient and cross-platform workflow engine") + (description "Toil is a scalable, efficient, cross-platform pipeline +management system, written entirely in Python, and designed around the +principles of functional programming.") + (license (list license:asl2.0 ;; main license + license:expat)))) ;; src/toil/batchSystems/lsf.py and + ;; src/toil/batchSystems/lsfHelper.py -- cgit v1.2.3 From 36b5aadb6017cbadbddf3fa7b270c9cb4797fc24 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 11 Mar 2024 17:08:21 -0500 Subject: gn: Add genenetwork2-production variant * gn/packages/genenetwork.scm (genenetwork-stable): New variable. --- gn/packages/genenetwork.scm | 89 ++++++++++++++++++++++++++------------------- 1 file changed, 51 insertions(+), 38 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 98d92ac..38b66b2 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -5,6 +5,7 @@ #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git) #:use-module (guix git-download) #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) @@ -345,50 +346,62 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public genenetwork2-stable + (let ((commit "2c122f99098cf84d4b67953f2a3ef05dab762c9c") + (revision "1")) + (package + (inherit genenetwork2) + (name "genenetwork2-stable") + (version (string-append "stable-" (git-version "3.11" revision commit))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork2") + (branch "prod")))))) + (define-public gn-uploader (let ((commit "6ced7085193affa636f229e72dc19175a3a06cfe") (version "0.0.1")) (package - (name "gn-uploader") - (version (string-append version "-" (string-take commit 8))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.genenetwork.org/gn-uploader") - (commit commit))) - (hash - (content-hash - (base32 - "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-m" "unit_test"))))))) - (native-inputs - (list python-mypy - python-pylint - python-pytest - python-hypothesis)) - (propagated-inputs - (list gunicorn - python-redis - python-flask - python-pyyaml - python-jsonpickle - python-mysqlclient)) - (synopsis "GeneNetwork Quality Control Application") - (description - "gn-uploader is a service allowing upload of new data into GeneNetwork, + (name "gn-uploader") + (version (string-append version "-" (string-take commit 8))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) + (hash + (content-hash + (base32 + "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) + (native-inputs + (list python-mypy + python-pylint + python-pytest + python-hypothesis)) + (propagated-inputs + (list gunicorn + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) + (synopsis "GeneNetwork Quality Control Application") + (description + "gn-uploader is a service allowing upload of new data into GeneNetwork, that does quality control for the data files that is being uploaded to ensure it fulfils all conditions before it can be accepted.") - (home-page "https://git.genenetwork.org/gn-uploader") - (license license:agpl3+)))) + (home-page "https://git.genenetwork.org/gn-uploader") + (license license:agpl3+)))) (define-public gn-auth (package -- cgit v1.2.3 From 6585db1b6af0ed66feb4425121ff3885e6381a98 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 13 Mar 2024 04:59:29 +0300 Subject: genenetwork2: Update commit and hash - get commit with bugfixes. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 38b66b2..9a15bc0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -187,7 +187,7 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "1e81c74ee8752ad2913b4e610ba7575638755385") + (let ((commit "b9e04ad79e0039edba25d58f8bc03e4d2a17583b") (revision "4")) (package (name "genenetwork2") @@ -200,7 +200,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "18g4dd3h737slqmp1ql2jqqzmzql3mx3b4xy72d7qwhwwhc7hcgv")))) + "1ri56g5hl2n0q7cz15sbvjmrr5pmsrp274frkvvcgr9ddxjlzd9p")))) (native-inputs (list graphviz)) (propagated-inputs -- cgit v1.2.3 From e03c9118ed42d69fbadad23ff41ad7922e84f701 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 13 Mar 2024 05:14:25 +0300 Subject: gn-uploader: Update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 9a15bc0..477bbd8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -359,7 +359,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "6ced7085193affa636f229e72dc19175a3a06cfe") + (let ((commit "13bc6684cc2f90b1fdac306a2ce9a8849911b43f") (version "0.0.1")) (package (name "gn-uploader") @@ -373,7 +373,7 @@ (hash (content-hash (base32 - "09sy7kxdrf44m2yr4cqn0nx070mdnqb76888ghrwpqzgd2phfhjp"))))) + "1ckbp9hy1yi779iism7hw2bgc8bmw7fkjnyx6xalv4zh6cz4zzn0"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 03c9a8bb9716b48bd853b3be54be4cbd50bcc615 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 19 Mar 2024 05:32:50 +0300 Subject: gn-uploader: update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 477bbd8..f72d066 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -359,7 +359,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "13bc6684cc2f90b1fdac306a2ce9a8849911b43f") + (let ((commit "38227b8e482ea10f8bb111a1a90f22f8f019e2ab") (version "0.0.1")) (package (name "gn-uploader") @@ -373,7 +373,7 @@ (hash (content-hash (base32 - "1ckbp9hy1yi779iism7hw2bgc8bmw7fkjnyx6xalv4zh6cz4zzn0"))))) + "0vbys9icgwxx2i82mq5yk0lp9869zr0mnjfcdnna647g8cyxzyzq"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 612fa6ca7f5c78a8e652562306f6c93f12a6de00 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Mon, 18 Mar 2024 18:20:05 +0300 Subject: gn: javascript: Add javascript-linkify, javascript-linkify-html. * gn/packages/javascript.scm: (javascript-linkify): New package. (javascript-linkify-html): New package. Acked-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 58 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 349fa66..2d1668b 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -2044,3 +2044,61 @@ for developing fast and powerful web interfaces.") (description "UIkit is a lightweight and modular front-end framework for developing fast and powerful web interfaces.") (license license:bsd-3))) + +(define-public javascript-linkify + (package + (name "javascript-linkify") + (version "4.1.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdn.jsdelivr.net/npm/linkifyjs@" version "/dist/linkify.min.js")) + (sha256 + (base32 + "1cy1z4gin0qx3a04fw2biszz1sgns0zc1zbr6sbkr2dicgqxjpf3")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/linkify")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/linkify.min.js")))))) + (native-inputs `(("source" ,source))) + (home-page "https://linkify.js.org") + (synopsis "Find URLs and email addresses in plain text") + (description + "JavaScript plugin for finding links in plain-text and converting them to HTML tags") + (license license:expat))) + +(define-public javascript-linkify-html + (package + (inherit javascript-linkify) + (name "javascript-linkify-html") + (version "4.1.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdn.jsdelivr.net/npm/linkify-html@" version "/dist/linkify-html.min.js")) + (sha256 + (base32 + "1s3l4wnyws9c9qjgp9ivl88inhyy28cjrhqjayb6hm1hzkasgj2j")))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/linkify")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/linkify-html.min.js")))))) + (native-inputs `(("source" ,source))) + (description + "JavaScript plugin for finding links in plain-text and highlightinging links within strings that contain HTML markup.") + (license license:expat))) -- cgit v1.2.3 From df839ea519decf3693437f5556fa44bc5a994a9c Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Mon, 18 Mar 2024 18:20:06 +0300 Subject: Add javascript-linkify, javascript-linkify-html to genenetwork. * gn/packages/genenetwork.scm (genenetwork2) [propagated-inputs]: Add javacript-linkify and javascript-linkify-html. Acked-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index f72d066..a28075e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -296,6 +296,8 @@ javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie + javascript-linkify + javascript-linkify-html ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit -- cgit v1.2.3 From 2fdbf2445e5293ba9a12b154c58774e73dfeabe5 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 19 Mar 2024 15:20:36 +0300 Subject: gn-uploader: update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index a28075e..ffcd449 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -361,7 +361,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "38227b8e482ea10f8bb111a1a90f22f8f019e2ab") + (let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63") (version "0.0.1")) (package (name "gn-uploader") @@ -375,7 +375,7 @@ (hash (content-hash (base32 - "0vbys9icgwxx2i82mq5yk0lp9869zr0mnjfcdnna647g8cyxzyzq"))))) + "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 27970a971d821fc598eb5050f76585e83fefe2c0 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Tue, 19 Mar 2024 14:36:52 +0300 Subject: gn: genenetwork3: Add python-biopython. * gn/packages/genenetwork.scm (genenetwork3) [propated-inputs]: Add python-biopython. Signed-off-by: Munyoki Kilyungi --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ffcd449..b26c53e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -165,6 +165,7 @@ ("python-sparqlwrapper" ,python-sparqlwrapper) ("python-email-validator" ,python-email-validator) ("python-xapian-bindings" ,python-xapian-bindings) + ("python-biopython" ,python-biopython) ("r-optparse" ,r-optparse) ("r-qtl" ,r-qtl) ("r-rjson" ,r-rjson) -- cgit v1.2.3 From f95867933281683eab207b806550f8b637447608 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 24 Mar 2024 09:01:32 +0100 Subject: genenetwork-stable: fix URL problem R/qtl api --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b26c53e..91063b9 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -350,7 +350,7 @@ (license license:agpl3+)))) (define-public genenetwork2-stable - (let ((commit "2c122f99098cf84d4b67953f2a3ef05dab762c9c") + (let ((commit "42b37bba21530aab104bd2fbbddb27ce7cd7de7c") (revision "1")) (package (inherit genenetwork2) -- cgit v1.2.3 From 184ef672921b525dd542e44eff5f17a77952394a Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 11:37:46 +0200 Subject: gn: genenetwork3: reformat package list AND fix tabs2spaces * gn/packages/genenetwork.scm (genenetwork3) --- gn/packages/genenetwork.scm | 144 +++++++++++++++++++++----------------------- 1 file changed, 70 insertions(+), 74 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 91063b9..ce99066 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -130,50 +130,46 @@ (inputs (list python-click)) (native-inputs - `(("python-hypothesis" ,python-hypothesis) - ("python-mypy" ,python-mypy) - ("python-mypy-extensions" ,python-mypy-extensions) - ("python-pylint" ,python-pylint) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock))) + (list python-hypothesis + python-mypy + python-mypy-extensions + python-pylint + python-pytest + python-pytest-mock)) (propagated-inputs - `(("gemma-wrapper" ,gemma-wrapper) - ("python-wrapper" ,python-wrapper) - ("csvdiff" ,csvdiff) - ("gn-rust-correlation" ,gn-rust-correlation) - ;; Replace use of bcrypt with argon below - ("python-bcrypt" ,python-bcrypt) - ("python-argon2-cffi" ,python-argon2-cffi) - ("python-flask" ,python-flask) - ("python-flask-cors" ,python-flask-cors) - ;; Not working in Python > 3.8 - ;; python-ipfshttpclient - ("python-lmdb" ,python-lmdb) - ("python-mysqlclient" ,python-mysqlclient) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ;; python-pingouin << build failing - ("python-pingouin-without-tests" ,python-pingouin-without-tests) - ("python-plotly" ,python-plotly) - ("python-pyld" ,python-pyld) - ("python-scikit-learn" ,python-scikit-learn) - ("python-pymonad" ,python-pymonad) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-scipy" ,python-scipy) - ("python-authlib" ,python-authlib) - ("python-sparqlwrapper" ,python-sparqlwrapper) - ("python-email-validator" ,python-email-validator) - ("python-xapian-bindings" ,python-xapian-bindings) - ("python-biopython" ,python-biopython) - ("r-optparse" ,r-optparse) - ("r-qtl" ,r-qtl) - ("r-rjson" ,r-rjson) - ("r-stringi" ,r-stringi) - ("r-wgcna" ,r-wgcna) - ("r-ctl" ,r-ctl) - ("rust-qtlreaper" ,rust-qtlreaper) - ("diffutils" ,diffutils))) + (list gemma-wrapper + python-wrapper + csvdiff + gn-rust-correlation + python-bcrypt ;; Replace use of bcrypt with argon below + python-argon2-cffi + python-flask + python-flask-cors + python-lmdb + python-mysqlclient + python-numpy + python-pandas + python-pingouin-without-tests + python-plotly + python-pyld + python-scikit-learn + python-pymonad + python-redis + python-requests + python-scipy + python-authlib + python-sparqlwrapper + python-email-validator + python-xapian-bindings + python-biopython + r-optparse + r-qtl + r-rjson + r-stringi + r-wgcna + r-ctl + rust-qtlreaper + diffutils)) (build-system python-build-system) (arguments (list #:phases @@ -273,7 +269,7 @@ javascript-plotly javascript-typeahead js-underscore - javascript-uikit + javascript-uikit js-smart-time-ago javascript-nouislider javascript-purescript-genome-browser @@ -288,7 +284,7 @@ javascript-datatables-buttons-styles javascript-shapiro-wilk javascript-underscore-string - javascript-htmx + javascript-htmx javascript-qtip2 javascript-d3js javascript-nvd3 @@ -297,8 +293,8 @@ javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie - javascript-linkify - javascript-linkify-html + javascript-linkify + javascript-linkify-html ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit @@ -363,7 +359,7 @@ (define-public gn-uploader (let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63") - (version "0.0.1")) + (version "0.0.1")) (package (name "gn-uploader") (version (string-append version "-" (string-take commit 8))) @@ -371,33 +367,33 @@ (origin (method git-fetch) (uri (git-reference - (url "https://git.genenetwork.org/gn-uploader") - (commit commit))) + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) (hash - (content-hash - (base32 - "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) + (content-hash + (base32 + "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-m" "unit_test"))))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) (native-inputs (list python-mypy - python-pylint - python-pytest - python-hypothesis)) + python-pylint + python-pytest + python-hypothesis)) (propagated-inputs (list gunicorn - python-redis - python-flask - python-pyyaml - python-jsonpickle - python-mysqlclient)) + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, @@ -414,21 +410,21 @@ (origin (method git-fetch) (uri (git-reference - (url "https://github.com/genenetwork/gn-auth.git") - (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) + (url "https://github.com/genenetwork/gn-auth.git") + (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) (hash - (content-hash - (base32 - "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) + (content-hash + (base32 + "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-k" "unit_test"))))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) (native-inputs (list python-hypothesis python-mypy -- cgit v1.2.3 From 4a8d467bcf0024960f3b88842be32a64f610c022 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 11:42:19 +0200 Subject: gn: genenetwork3: sorted package names and added R to propagated inputs to make Rscript available on the path * gn/packages/genenetwork.scm (genenetwork3) [propagated-inputs]: Add r. --- gn/packages/genenetwork.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ce99066..e439fdd 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -140,9 +140,13 @@ (list gemma-wrapper python-wrapper csvdiff + diffutils gn-rust-correlation - python-bcrypt ;; Replace use of bcrypt with argon below + python-authlib python-argon2-cffi + python-bcrypt ;; Replace use of bcrypt with argon + python-biopython + python-email-validator python-flask python-flask-cors python-lmdb @@ -152,24 +156,21 @@ python-pingouin-without-tests python-plotly python-pyld - python-scikit-learn python-pymonad python-redis python-requests + python-scikit-learn python-scipy - python-authlib python-sparqlwrapper - python-email-validator python-xapian-bindings - python-biopython + r + r-ctl r-optparse r-qtl r-rjson r-stringi r-wgcna - r-ctl - rust-qtlreaper - diffutils)) + rust-qtlreaper)) (build-system python-build-system) (arguments (list #:phases -- cgit v1.2.3 From e200b1c3ea52776bbc701f9912d0fcbc86b79a2e Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 14:32:10 +0200 Subject: gn: Add genenetwork3-production variant * gn/packages/genenetwork.scm (genenetwork3-stable): New variable. --- gn/packages/genenetwork.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e439fdd..d89852d 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -346,6 +346,18 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public genenetwork3-stable + (let ((commit "25d3f3d7a13a9d94b561b1d824ba0b428a3fc006") + (revision "1")) + (package + (inherit genenetwork3) + (name "genenetwork3-stable") + (version (string-append "stable-" (git-version "3.11" revision commit))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork3") + (branch "prod")))))) + (define-public genenetwork2-stable (let ((commit "42b37bba21530aab104bd2fbbddb27ce7cd7de7c") (revision "1")) -- cgit v1.2.3 From 10f9f0f19a0bb8c354ee68f0479edf606e3a2dd1 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 15:17:17 +0200 Subject: gn: genenetwork3: sorted package names and moved python-test and python-test-mock into propagated inputs * gn/packages/genenetwork.scm (genenetwork3) [propagated-inputs]: add testing --- gn/packages/genenetwork.scm | 161 ++++++++++++++++++++++---------------------- 1 file changed, 81 insertions(+), 80 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d89852d..d05d9f5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -133,17 +133,14 @@ (list python-hypothesis python-mypy python-mypy-extensions - python-pylint - python-pytest - python-pytest-mock)) + python-pylint)) (propagated-inputs - (list gemma-wrapper - python-wrapper - csvdiff + (list csvdiff diffutils + gemma-wrapper gn-rust-correlation - python-authlib python-argon2-cffi + python-authlib python-bcrypt ;; Replace use of bcrypt with argon python-biopython python-email-validator @@ -157,11 +154,14 @@ python-plotly python-pyld python-pymonad + python-pytest + python-pytest-mock python-redis python-requests python-scikit-learn python-scipy python-sparqlwrapper + python-wrapper python-xapian-bindings r r-ctl @@ -203,103 +203,104 @@ (list graphviz)) (propagated-inputs (list genenetwork3 - parallel coreutils - git - which - grep - r - r-ctl - r-qtl - r-wgcna - redis - mariadb gemma gemma-wrapper - plink-ng-gn - rust-qtlreaper - gn-rust-correlation + git glibc-utf8-locales - nginx - python-wrapper - python-pillow - python-coverage - python-configparser - python-flask + gn-rust-correlation + grep gunicorn + javascript-bootstrap + javascript-chroma + javascript-ckeditor + javascript-colorbox + javascript-cytoscape + javascript-cytoscape-panzoom + javascript-cytoscape-qtip + javascript-d3-tip + javascript-d3js + javascript-datatables + javascript-datatables-buttons + javascript-datatables-buttons-bootstrap + javascript-datatables-buttons-styles + javascript-datatables-col-reorder + javascript-datatables-col-resize + javascript-datatables-plugins + javascript-datatables-scroller + javascript-font-awesome + javascript-htmx + javascript-jquery + javascript-jquery-cookie + javascript-jquery-ui + javascript-jscolor + javascript-jszip + javascript-linkify + javascript-linkify-html + javascript-nouislider + javascript-nvd3 + javascript-plotly + javascript-purescript-genome-browser + javascript-qtip2 + javascript-shapiro-wilk + javascript-twitter-post-fetcher + javascript-typeahead + javascript-uikit + javascript-underscore-string + javascript-zxcvbn + js-jstat + js-md5 + js-parsley + js-smart-time-ago + js-underscore + mariadb + nginx + parallel + plink-ng-gn + python-authlib python-autopep8 + python-beautifulsoup4 + python-configparser + python-coverage python-cssselect + python-flask python-flask-debugtoolbar + python-flask-session python-htmlgen python-ijson python-jinja2 - python-pytest - python-pytest-mock - python-sqlalchemy - python-setuptools - python-scipy python-lxml - python-mysqlclient + python-markdown python-mypy + python-mysqlclient python-numpy python-pandas + python-pillow python-pylint python-pymonad + python-pytest + python-pytest-mock + python-rdflib python-redis python-requests - python-simplejson - python-markdown - python-rdflib - python-authlib - python-flask-session python-rpy2 - python-beautifulsoup4 + python-scipy + python-setuptools + python-simplejson + python-sqlalchemy + python-wrapper python-xlsxwriter - javascript-twitter-post-fetcher - javascript-cytoscape - javascript-cytoscape-panzoom - javascript-cytoscape-qtip - javascript-chroma - javascript-d3-tip - javascript-jscolor - javascript-colorbox - javascript-jszip - js-jstat - js-md5 - js-parsley - javascript-plotly - javascript-typeahead - js-underscore - javascript-uikit - js-smart-time-ago - javascript-nouislider - javascript-purescript-genome-browser - javascript-ckeditor - javascript-datatables - javascript-datatables-scroller - javascript-datatables-buttons - javascript-datatables-buttons-bootstrap - javascript-datatables-plugins - javascript-datatables-col-reorder - javascript-datatables-col-resize - javascript-datatables-buttons-styles - javascript-shapiro-wilk - javascript-underscore-string - javascript-htmx - javascript-qtip2 - javascript-d3js - javascript-nvd3 - javascript-bootstrap - javascript-jquery - javascript-zxcvbn - javascript-jquery-ui - javascript-jquery-cookie - javascript-linkify - javascript-linkify-html + r + r-ctl + r-qtl + r-wgcna + redis + rust-qtlreaper + which ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit - javascript-font-awesome)) + )) (inputs (list javascript-colorbox)) (build-system python-build-system) -- cgit v1.2.3 From 467279ce30a02b9cbb6ddfca48ef15f117a6d85f Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 1 Apr 2024 15:21:57 +0200 Subject: gn: genenetwork3-stable: disable testing for now * gn/packages/genenetwork.scm (genenetwork3-stable) disable testing --- gn/packages/genenetwork.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d05d9f5..3e8a2ed 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -354,6 +354,9 @@ (inherit genenetwork3) (name "genenetwork3-stable") (version (string-append "stable-" (git-version "3.11" revision commit))) + (arguments + (list + #:tests? #f)) ; temporary disable on production setup (source (git-checkout (url "https://github.com/genenetwork/genenetwork3") -- cgit v1.2.3 From 3d3bdd5c74c41385f4c7fa00d12e25e44a04b4aa Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 2 Apr 2024 10:13:46 +0300 Subject: gn-uploader: update commit and hash. --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 3e8a2ed..efb0ea8 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -375,7 +375,7 @@ (branch "prod")))))) (define-public gn-uploader - (let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63") + (let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6") (version "0.0.1")) (package (name "gn-uploader") @@ -389,7 +389,7 @@ (hash (content-hash (base32 - "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) + "1q04viyf7d0q30k3424hrzsh9wxhhgs7hywlhzl3m68jki4zq1i7"))))) (build-system python-build-system) (arguments (list -- cgit v1.2.3 From 404a97f8973cf1199e147b7117ac562580a70634 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 2 Apr 2024 09:30:18 +0200 Subject: genenetwork3-stable: Update commit and hash. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index efb0ea8..2d7fab5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "25d3f3d7a13a9d94b561b1d824ba0b428a3fc006") + (let ((commit "b04458b6ff745c9d0d1101527bec6eeafd911d05") (revision "1")) (package (inherit genenetwork3) -- cgit v1.2.3 From 4bce9fa4e3ebc3036ec94207b392d0c5b5d869d1 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 2 Apr 2024 16:32:16 +0200 Subject: genenetwork3-stable: Update commit and hash. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2d7fab5..2053e78 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "b04458b6ff745c9d0d1101527bec6eeafd911d05") + (let ((commit "c094d2db352a39cc001b21ad4195fc32de24c863") (revision "1")) (package (inherit genenetwork3) -- cgit v1.2.3 From 5871a33c424510c9fad10a240d355dfb31b027e7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 04:08:07 -0500 Subject: genenetwork3-stable: patch path to R script --- gn/packages/genenetwork.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2053e78..a0c8a57 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "c094d2db352a39cc001b21ad4195fc32de24c863") + (let ((commit "8414f1d74f6b09205d3cfd09240c787323474626") (revision "1")) (package (inherit genenetwork3) @@ -356,7 +356,13 @@ (version (string-append "stable-" (git-version "3.11" revision commit))) (arguments (list - #:tests? #f)) ; temporary disable on production setup + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'update-paths + (lambda _ + (substitute* "gn3/api/rqtl.py" + (("scripts/rqtl_wrapper.R)" + (string-append #$output "/scripts/rqtl_wrapper.R")))))))) (source (git-checkout (url "https://github.com/genenetwork/genenetwork3") -- cgit v1.2.3 From 75ff5fe367f6de7d1bb7ad4c3fb29ed97d32bd10 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 04:47:55 -0500 Subject: genenetwork3-stable: patch path to R script - missing bracket --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index a0c8a57..20e91be 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -353,7 +353,7 @@ (package (inherit genenetwork3) (name "genenetwork3-stable") - (version (string-append "stable-" (git-version "3.11" revision commit))) + (version (string-append (git-version "3.11" revision commit))) (arguments (list #:phases @@ -361,7 +361,7 @@ (add-before 'build 'update-paths (lambda _ (substitute* "gn3/api/rqtl.py" - (("scripts/rqtl_wrapper.R)" + (("scripts/rqtl_wrapper.R)") (string-append #$output "/scripts/rqtl_wrapper.R")))))))) (source (git-checkout -- cgit v1.2.3 From fe1e3e87f25c34267c25e1cca1b6063660fb9236 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 04:57:09 -0500 Subject: genenetwork3-stable: copy R script into destination --- gn/packages/genenetwork.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 20e91be..af0fea3 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -356,13 +356,21 @@ (version (string-append (git-version "3.11" revision commit))) (arguments (list + #:tests? #f #:phases #~(modify-phases %standard-phases (add-before 'build 'update-paths (lambda _ (substitute* "gn3/api/rqtl.py" (("scripts/rqtl_wrapper.R)") - (string-append #$output "/scripts/rqtl_wrapper.R")))))))) + (string-append #$output "/scripts/rqtl_wrapper.R"))))) + (add-before 'install 'install-scripts + (lambda _ + (begin + (mkdir (string-append #$output "scripts")) + (install-file "scripts/rqtl_wrapper.R" + (string-append #$output "/scripts")))))))) + (source (git-checkout (url "https://github.com/genenetwork/genenetwork3") -- cgit v1.2.3 From 31e8932290d54ac8710fb3a496fa083ad640d39c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 05:08:35 -0500 Subject: genenetwork3-stable: copy other R scripts into destination --- gn/packages/genenetwork.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index af0fea3..5bd4c71 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -368,8 +368,13 @@ (lambda _ (begin (mkdir (string-append #$output "scripts")) - (install-file "scripts/rqtl_wrapper.R" - (string-append #$output "/scripts")))))))) + (for-each (lambda (fn) + (install-file fn + (string-append #$output "/scripts"))) + '("scripts/rqtl_wrapper.R" + "scripts/ctl_analysis.R" + "scripts/wgcna_analysis.R" + )))))))) (source (git-checkout -- cgit v1.2.3 From 65cb368fe12bd2604d6f36d5d50404ac58d08673 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 05:11:41 -0500 Subject: genenetwork3-stable: modify files using R scripts --- gn/packages/genenetwork.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5bd4c71..4ceac43 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -362,8 +362,8 @@ (add-before 'build 'update-paths (lambda _ (substitute* "gn3/api/rqtl.py" - (("scripts/rqtl_wrapper.R)") - (string-append #$output "/scripts/rqtl_wrapper.R"))))) + (("scripts/") + (string-append #$output "/scripts/"))))) (add-before 'install 'install-scripts (lambda _ (begin -- cgit v1.2.3 From 6303fe046b944a380704eb02144cca777fee689b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 06:14:59 -0500 Subject: genenetwork3-stable: modify files that use R scripts --- gn/packages/genenetwork.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4ceac43..c404c53 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "8414f1d74f6b09205d3cfd09240c787323474626") + (let ((commit "d8203aaa523895fd8b1ff6cc124f2e8a53932a07") (revision "1")) (package (inherit genenetwork3) @@ -361,9 +361,14 @@ #~(modify-phases %standard-phases (add-before 'build 'update-paths (lambda _ - (substitute* "gn3/api/rqtl.py" + (for-each (lambda (fn) + (substitute* (string-append "gn3/" fn) (("scripts/") - (string-append #$output "/scripts/"))))) + (string-append #$output "/scripts/")))) + '("api/rqtl.py" + "computations/wgcna.py" + "computations/ctl.py" + "api/general.py")))) (add-before 'install 'install-scripts (lambda _ (begin -- cgit v1.2.3 From 9dd4e53a93f7c3a9aa970b6e2a787e4122461c13 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 3 Apr 2024 06:43:34 -0500 Subject: genenetwork3-stable: update hash --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index c404c53..f7337c4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -348,7 +348,7 @@ (license license:agpl3+)))) (define-public genenetwork3-stable - (let ((commit "d8203aaa523895fd8b1ff6cc124f2e8a53932a07") + (let ((commit "e5569c3bb1c0d59ff7142273c5f51fe19f06cfe8") (revision "1")) (package (inherit genenetwork3) -- cgit v1.2.3 From 1a6522f3a5a7d0990e50fe5dd91f286f62e083e7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 4 Apr 2024 05:49:19 -0500 Subject: javascript-d3panels: add variable and add to genenetwork2 --- gn/packages/genenetwork.scm | 23 +++++++++++++++++++---- gn/packages/javascript.scm | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+), 4 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index f7337c4..e3ec17f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -220,6 +220,7 @@ javascript-cytoscape-qtip javascript-d3-tip javascript-d3js + javascript-d3panels javascript-datatables javascript-datatables-buttons javascript-datatables-buttons-bootstrap @@ -373,7 +374,7 @@ (lambda _ (begin (mkdir (string-append #$output "scripts")) - (for-each (lambda (fn) + (for-each (lambda (fn) (install-file fn (string-append #$output "/scripts"))) '("scripts/rqtl_wrapper.R" @@ -387,16 +388,30 @@ (branch "prod")))))) (define-public genenetwork2-stable - (let ((commit "42b37bba21530aab104bd2fbbddb27ce7cd7de7c") + (let ((commit "fd3de3dd7e0fac465bde193bd78085bd3434e885") (revision "1")) (package (inherit genenetwork2) (name "genenetwork2-stable") - (version (string-append "stable-" (git-version "3.11" revision commit))) + (version (string-append "stable-" (git-version "3.12" revision commit))) (source (git-checkout (url "https://github.com/genenetwork/genenetwork2") - (branch "prod")))))) + (branch "prod"))) + (arguments + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'update-font-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (for-each (lambda (fn) + (substitute* (string-append "gn2/" fn) + (("\\./gn2/wqflask/static/fonts/") + (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts/")))) + '("utility/Plot.py" + "wqflask/marker_regression/display_mapping_results.py")))) + )))))) (define-public gn-uploader (let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6") diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 2d1668b..f92ada9 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -433,6 +433,7 @@ tables with minimal effort.") (description "Scroller is a virtual rendering plug-in for DataTables which allows large datasets to be drawn on screen very quickly. Virtual rendering means is that only the visible portion of the table is drawn, while the scrolling container gives the visual impression that the whole table is visible, allowing excellent browser performance.") (license license:expat))) + (define-public javascript-xterm (package (name "javascript-xterm") @@ -805,6 +806,41 @@ without tying yourself to a proprietary framework, combining powerful visualization components and a data-driven approach to DOM manipulation.") (license license:bsd-3))) +(define-public javascript-d3panels + (package + (name "javascript-d3panels") + (version "1.8.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kbroman/d3panels.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pmv24x4k0iy2mbibwwk8f85c6mljyqj2qwn03sq3pg93r16a0b5")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/genenetwork2/javascript/d3panels")) + (source (assoc-ref %build-inputs "source"))) + (install-file (string-append source "/d3panels.js") targetdir) + (install-file (string-append source "/d3panels.min.js") targetdir) + (install-file (string-append source "/d3panels.css") targetdir) + (install-file (string-append source "/d3panels.min.css") targetdir) + (install-file (string-append source "/README.md") targetdir) + (install-file (string-append source "/NEWS.md") targetdir) + (install-file (string-append source "/LICENSE.md") targetdir) + )))) + (home-page "https://kbroman.org/d3panels") + (synopsis "d3panels for QTL mapping") + (description "This is a set of D3-based graphic panels, to be combined into larger multi-panel charts. They were developed for the R/qtlcharts package.") + (license license:expat))) + (define-public javascript-jquery (package (inherit web-jquery) -- cgit v1.2.3 From 914ae94d48bd8a7619102263eb654a764877dbc6 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 4 Apr 2024 11:14:18 -0500 Subject: Add recent javascript-d3 library --- gn/packages/genenetwork.scm | 3 ++- gn/packages/javascript.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e3ec17f..21de18a 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -219,7 +219,8 @@ javascript-cytoscape-panzoom javascript-cytoscape-qtip javascript-d3-tip - javascript-d3js + javascript-d3js ;; very old + javascript-d3js-7 javascript-d3panels javascript-datatables javascript-datatables-buttons diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index f92ada9..d8c9af9 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -894,6 +894,46 @@ visualization components and a data-driven approach to DOM manipulation.") (install-file "d3.min.js" targetdir) (install-file "LICENSE" (string-append out "/share/doc/d3js-" ,version)))))))) +(define-public javascript-d3js-7 + (package + (name "javascript-d3js-7") + (version "7.9.0") + (source + (origin + (method url-fetch) + ;; note that D3 no longer provides a prebuilt JS file - except through CDS + (uri (string-append "https://files.genenetwork.org/software/d3.v" version ".min.js.gz")) + (sha256 + (base32 "0k7g40zb65s12z1zchvimj5xibkrqff5sylbrhcwmwpcplpigid7")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (module-name "d3js-7") + (gzip (string-append (assoc-ref %build-inputs "gzip") + "/bin/gzip")) + (targetdir (string-append out "/share/genenetwork2/javascript/" module-name)) + (jsname (string-append "d3.v" "7.9.0" ".min.js")) + (gzname (string-append jsname ".gz")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file (pk source) (pk (string-append targetdir "/" gzname))) + (invoke gzip "-fd" (string-append targetdir "/" gzname)))))) + (native-inputs + `(("source" ,source) + ("gzip" ,gzip))) + (home-page "https://d3js.org/") + (synopsis "JavaScript library for visualizing data") + (description "D3.js is a JavaScript library for manipulating documents based +on data. D3 helps you bring data to life using HTML, SVG, and CSS. D3's +emphasis on web standards gives you the full capabilities of modern browsers +without tying yourself to a proprietary framework, combining powerful +visualization components and a data-driven approach to DOM manipulation.") + (license license:bsd-3))) + (define-public javascript-d3js-multi (package (name "javascript-d3js-multi") -- cgit v1.2.3 From 3aa257007eeb4169ab4c3357bd7d5b3bb80a89f8 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 5 Apr 2024 02:26:10 -0500 Subject: genenetwork2-stable: update hash --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 21de18a..ac9072a 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -389,7 +389,7 @@ (branch "prod")))))) (define-public genenetwork2-stable - (let ((commit "fd3de3dd7e0fac465bde193bd78085bd3434e885") + (let ((commit "95e634ca90d52922812b93df162686b348288651") (revision "1")) (package (inherit genenetwork2) -- cgit v1.2.3 From 3783f8b1865117e54c968ecc4dad0af5e57d5995 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 9 Apr 2024 13:11:42 +0300 Subject: gn: javascript: Fix failing javascript-xterm build. * gn/packages/javascript.scm (javascript-xterm): Update hash. [native-inputs]: Move this ... [propagated-inputs]: ... here. Signed-off-by: Munyoki Kilyungi --- gn/packages/javascript.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index d8c9af9..7f9f35d 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -446,7 +446,7 @@ tables with minimal effort.") (file-name (string-append "xterm.min" version ".js")) (sha256 (base32 - "18smra546ws5fhnfdhj9m6yhvfjqdwx44jyb19q3az780ifwj2lz")))) + "1ipk8l837pinl9151qcb39hfrjy5d7zzyf19nsfhv4wgavy8fcar")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -459,7 +459,7 @@ tables with minimal effort.") (source (assoc-ref %build-inputs "source"))) (mkdir-p targetdir) (copy-file source (string-append targetdir "/xterm.min.js")))))) - (native-inputs `(("source" ,source))) + (propagated-inputs `(("source" ,source))) (home-page "https://xtermjs.org/") (synopsis "Javascript library that allows apps to bring fully-featured terminals in browsers.") (description -- cgit v1.2.3 From 931c99dd43bd155013606cac563d203026d8d443 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 19 Apr 2024 17:16:33 +0100 Subject: gn: Add hifiasm. * gn/packages/bioinformatics.scm (hifiasm): New variable. --- gn/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 82caab9..ed6d4d4 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4620,3 +4620,41 @@ on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.") (license license:gpl3))) + +(define-public hifiasm + (package + (name "hifiasm") + (version "0.19.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chhylp123/hifiasm") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1g6m2qdc0224vjaic87669g7y9ky1yps07qbjkmbh1vakz4zmgvr")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "hifiasm" (string-append #$output "/bin")) + (install-file "hifiasm.1" (string-append #$output "/share/man/man1"))))))) + (inputs + (list zlib)) + (home-page "https://github.com/chhylp123/hifiasm") + (synopsis "haplotype-resolved assembler for accurate Hifi reads") + (description "Hifiasm is a fast haplotype-resolved de-novo assembler originally +designed for PacBio HiFi reads. Its latest release supports the +telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore +reads. Hifiasm produces arguably the best single-sample +telomere-to-telomere assemblies combing HiFi, ultralong and Hi-C +reads, and it is one of the best haplotype-resolved assemblers for the +trio-binning assembly given parental short reads. For a human genome, +hifiasm can produce the telomere-to-telomere assembly in one day.") + (license license:expat))) -- cgit v1.2.3 From 7f9908d03acd6d2c44733188122313036dc63b64 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 9 May 2024 18:34:00 +0300 Subject: Fix path to error GIFs. Co-authored-by: Alexander --- gn/packages/genenetwork.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index ac9072a..eab8a07 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -319,6 +319,10 @@ (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts"))) (substitute* "gn2/wqflask/views.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))) + (substitute* "gn2/wqflask/app_errors.py" (("\\./gn2/wqflask/static/gif/error") (string-append (site-packages inputs outputs) "/gn2/wqflask/static/gif/error"))))) -- cgit v1.2.3 From e09f102357ffe615d1043167c9e2bed3e2b6b418 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 12 Jun 2024 13:04:19 -0500 Subject: gn-uploader: Fix indentation. --- gn/packages/genenetwork.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index eab8a07..5801cb5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -445,16 +445,16 @@ (invoke "pytest" "-m" "unit_test"))))))) (native-inputs (list python-mypy - python-pylint - python-pytest - python-hypothesis)) + python-pylint + python-pytest + python-hypothesis)) (propagated-inputs (list gunicorn - python-redis - python-flask - python-pyyaml - python-jsonpickle - python-mysqlclient)) + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, -- cgit v1.2.3 From 9f5097a76eb87abb16006c0d9e6080c2231fdb3d Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 13 Jun 2024 09:09:47 -0500 Subject: gn-uploader: javascript-bootstrap: New dependency Bundle javascript-bootstrap with gn-uploader for styling. --- gn/packages/genenetwork.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 5801cb5..39bad71 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -454,7 +454,8 @@ python-flask python-pyyaml python-jsonpickle - python-mysqlclient)) + python-mysqlclient + javascript-bootstrap)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, -- cgit v1.2.3 From 22a779d83b39158459055b22a6d75e770054784c Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 14 Jun 2024 10:44:38 -0500 Subject: gn-uploader: (javascript-jquery): New dependency JQuery is needed to get the bootstrap plugins working correctly. --- gn/packages/genenetwork.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 39bad71..10619da 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -455,6 +455,7 @@ python-pyyaml python-jsonpickle python-mysqlclient + javascript-jquery javascript-bootstrap)) (synopsis "GeneNetwork Quality Control Application") (description -- cgit v1.2.3 From 0362ee068a39ce9a5fd6f0fba9cd5586211f07f1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 20 Jun 2024 07:18:07 -0500 Subject: genecup: use keras without tests --- gn/packages/ratspub.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm index 726bc0b..19b70c2 100644 --- a/gn/packages/ratspub.scm +++ b/gn/packages/ratspub.scm @@ -179,6 +179,20 @@ gene-keyword relationships are presented as an interactive graph and a table.") `(modify-phases ,phases (delete 'check)))))))) +(define-public python-keras-no-tests + (hidden-package + (package + (inherit python-keras) + (source + (origin + (inherit (package-source python-keras)))) + (arguments + (substitute-keyword-arguments (package-arguments python-keras) + ((#:phases phases) + `(modify-phases ,phases + (delete 'check)))))))) + + (define-public hrdp-project (package (name "hrdp-project") @@ -370,7 +384,7 @@ if __name__ == '__main__': ("inetutils" ,inetutils) ("python-bcrypt" ,python-bcrypt) ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) - ("python-keras" ,python-keras-for-ratspub) + ("python-keras" ,python-keras-no-tests) ("python-nltk" ,python-nltk) ("python-pandas" ,python-pandas) ("python-regex" ,python-regex) -- cgit v1.2.3