move patches

17 files changed, 0 insertions, 422 deletions

diff --git a/gn/packages/edash.scm b/gn/packages/edash.scm
deleted file mode 100644
index 8781bfc..0000000
--- a/gn/packages/edash.scm
+++ /dev/null
@@ -1,372 +0,0 @@
-(define-module (gn packages edash)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix build-system trivial)
-  #:use-module (guix build-system python)
-  #:use-module (gnu packages web)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages python-build)
-  #:use-module (gnu packages python-check)
-  #:use-module (gnu packages python-web)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages python-crypto)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages time)
-  #:use-module (gnu packages databases)
-  #:use-module (gnu packages check)
-  #:use-module (gn packages web)
-  #:use-module (gnu packages sqlite)
-  #:use-module (gn packages python)
-  #:use-module (past packages python27))
-
-(define-public python-s3transfer-0.1.13
-  (package
-  (name "python-s3transfer")
-  (version "0.1.13")
-  (source
-    (origin
-      (method url-fetch)
-      (uri (pypi-uri "s3transfer" version))
-      (sha256
-        (base32
-          "1harvyn1s8v54n1w5h7c0lg4bgjh68aylhg28s8n174q53h1ip4h"))))
-  (build-system python-build-system)
-  (arguments
-   `(#:tests? #f))
-  (home-page "https://github.com/boto/s3transfer")
-  (synopsis "Amazon S3 Transfer Manager")
-  (description "S3transfer is a Python library for managing Amazon S3
-transfers.")
-  (license license:asl2.0)))
-
-(define-public python-botocore-1.10.48
-  (package
-    (name "python-botocore")
-    (version "1.10.48")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "botocore" version))
-       (sha256
-        (base32
-	 "1432drc7482nwrppwkk1i6ars3wz9w2g9rsxkz5nlxmyf9qm260j"))))
-    (build-system python-build-system)
-    (arguments
-    ;; FIXME: Many tests are failing.
-    '(#:tests? #f))
-    (propagated-inputs
-     `(("python-dateutil" ,python-dateutil)
-       ("python-docutils" ,python-docutils)
-       ("python-jmespath" ,python-jmespath)))
-    (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-nose" ,python-nose)
-       ("behave" ,behave)
-       ("python-tox" ,python-tox)
-       ("python-wheel" ,python-wheel)))
-    (home-page "https://github.com/boto/botocore")
-    (synopsis "Low-level interface to AWS")
-    (description "Botocore is a Python library that provides a low-level
-interface to the Amazon Web Services (AWS) API.")
-    (license license:asl2.0)))
-
-(define-public python-speaklater
-  (package
-  (name "python-speaklater")
-  (version "1.3")
-  (source
-    (origin
-      (method url-fetch)
-      (uri (pypi-uri "speaklater" version))
-      (sha256
-        (base32
-          "1ab5dbfzzgz6cnz4xlwx79gz83id4bhiw67k1cgqrlzfs0va7zjr"))))
-  (build-system python-build-system)
-  (home-page
-    "http://github.com/mitsuhiko/speaklater")
-  (synopsis
-    "implements a lazy string for python useful for use with gettext")
-  (description
-    "implements a lazy string for python useful for use with gettext")
-  (license license:bsd-3)))
-
-(define-public python-flask-mail
-  (package
-   (name "python-flask-mail")
-   (version "0.9.1")
-   (source
-    (origin
-     (method url-fetch)
-     (uri (pypi-uri "flask-mail" version))
-     (sha256
-      (base32
-       "0hazjc351s3gfbhk975j8k65cg4gf31yq404yfy0gx0bjjdfpr92"))))
-   (build-system python-build-system)
-   (propagated-inputs
-    `(("python-mock" ,python-mock)
-      ("python-nose" ,python-nose)
-      ("python-flask" ,python-flask)
-      ("python-blinker" ,python-blinker)
-      ("python-speaklater" ,python-speaklater)))
-   (home-page
-    "https://github.com/rduplain/flask-mail")
-   (synopsis "Flask extension for sending email")
-   (description "Flask extension for sending email")
-   (license license:bsd-3)))
-
-(define-public python-python-version
-  (package
-   (name "python-python-version")
-   (version "0.0.2")
-   (source
-    (origin
-     (method url-fetch)
-     (uri (pypi-uri "python_version" version))
-     (sha256
-      (base32
-       "0rzy0jzh1w7rx7swgjb5qv7b7dhblbsyhs7l3ii19mpjqxbxw5jw"))))
-   (build-system python-build-system)
-   (home-page
-    "https://gitlab.com/halfak/python_version")
-   (synopsis
-    "Provides a simple utility for checking the python version.")
-   (description
-    "Provides a simple utility for checking the python version.")
-   (license license:expat)))
-
-(define-public python-tests
-  (package
-    (name "python-tests")
-    (version "0.007")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "tests" version ".zip"))
-       (sha256
-        (base32
-         "09nfrysnqivqhs7znync8k87v16anvnb02j9ikmr3i6hdqxjcd31"))))
-    (build-system python-build-system)
-    (inputs
-     `(("unzip" ,unzip)))
-    (home-page "http://www.propython.com/")
-    (synopsis "UNKNOWN")
-    (description "UNKNOWN")
-    (license #f)))
-
-(define-public python-clickclick
-  (package
-    (name "python-clickclick")
-    (version "1.2.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "clickclick" version))
-       (sha256
-        (base32
-         "08vd1whzr1gz3cfb9iqs200rgj1x9srlwaa6sjmwz41rkjm0m2aa"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-six" ,python-six)
-       ("python-click" ,python-click)
-       ("python-pyyaml" ,python-pyyaml)
-       ("python-pytest" ,python-pytest)
-       ("python-pyflakes" ,python-pyflakes)
-       ("python-flake8" ,python-flake8)
-       ("python-pytest-cov" ,python-pytest-cov)))
-    (arguments `(#:tests? #f))
-    (home-page
-     "https://github.com/zalando/python-clickclick")
-    (synopsis "Click utility functions")
-    (description "Utility functions (Python 3 only) for the wonderful
-Click library.  Click is a Python package for creating beautiful
-command line interfaces in a composable way with as little code as
-necessary.")
-    (license license:asl2.0)))
-
-(define-public python-aiohttp-jinja2
-  (package
-    (name "python-aiohttp-jinja2")
-    (version "1.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "aiohttp-jinja2" version))
-       (sha256
-        (base32
-         "031djiddn2yg50mkw60x1ql1qwqxnmghk46902nq48cnbxcvdydf"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-jinja2" ,python-jinja2)
-       ("python-aiohttp" ,python-aiohttp)))
-    (arguments `(#:tests? #f))
-    (home-page
-     "https://github.com/aio-libs/aiohttp_jinja2/")
-    (synopsis
-     "jinja2 template renderer for aiohttp.web (http server for asyncio)")
-    (description
-     "jinja2 template renderer for aiohttp.web (http server for asyncio)")
-    (license license:asl2.0)))
-
-(define-public python-swagger-ui-bundle
-  (package
-    (name "python-swagger-ui-bundle")
-    (version "0.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "swagger_ui_bundle" version))
-       (sha256
-        (base32
-         "0kk6y8p1fhmnjnxfafdw6dm1xc5wj8101y5h7hcy3rb2bxc1i94q"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-tox" ,python-tox)
-       ("python-jinja2" ,python-jinja2)
-       ("python-pyflakes" ,python-pyflakes)
-       ("python-flake8" ,python-flake8)
-       ("python-pytest-cov" ,python-pytest-cov)
-       ("python-pytest-pycodestyle" ,python-pytest-pycodestyle)
-;;       ("python-pytest-flakes" ,python-pytest-flakes)
-       ))
-    (arguments `(#:tests? #f))
-    (home-page
-     "https://github.com/dtkav/swagger_ui_bundle")
-    (synopsis
-     "swagger_ui_bundle - swagger-ui files in a pip package")
-    (description
-     "swagger_ui_bundle - swagger-ui files in a pip package")
-    (license license:asl2.0)))
-
-(define-public python-connexion
-  (package
-  (name "python-connexion")
-  (version "2.1.0")
-  (source
-    (origin
-      (method url-fetch)
-      (uri (pypi-uri "connexion" version))
-      (sha256
-        (base32
-          "08xkjlvj8gb6sz4p4wjab6dag2sdvlfpaz4053k9nf7zj766j0bg"))))
-  (build-system python-build-system)
-  (propagated-inputs
-    `(;; ("python-six" ,python-six)
-      ;; ("python-mock" ,python-mock)
-      ("python-ujson" ,python-ujson)
-      ("python-flask" ,python-flask)
-      ;; ("python-tests" ,python-tests)
-      ;; ("python-pyyaml" ,python-pyyaml)
-      ;; ("python-pytest" ,python-pytest)
-      ;; ("python-typing" ,python-typing)
-      ;; ("python-pathlib" ,python-pathlib)
-      ("python-aiohttp" ,python-aiohttp)
-      ("python-requests" ,python-requests)
-      ;; ("python-pyflakes" ,python-pyflakes)
-      ("python-flake8" ,python-flake8)
-      ("python-decorator" ,python-decorator)
-      ("python-inflection" ,python-inflection)
-      ;; ("python-jsonschema" ,python-jsonschema)
-      ;; ("python-pytest-cov" ,python-pytest-cov)
-      ("python-clickclick" ,python-clickclick)
-      ("python-testfixtures" ,python-testfixtures)
-      ;; ("python-python-version" ,python-python-version)
-      ("python-pytest-aiohttp" ,python-pytest-aiohttp)
-      ("python-aiohttp-jinja2" ,python-aiohttp-jinja2)
-      ("python-swagger-ui-bundle" ,python-swagger-ui-bundle)
-      ("python-openapi-spec-validator" ,python-openapi-spec-validator)
-      ))
-  (arguments `(#:tests? #f))
-  (home-page
-    "https://github.com/zalando/connexion")
-  (synopsis
-    "Connexion - API first applications with OpenAPI/Swagger and Flask")
-  (description
-    "Connexion - API first applications with OpenAPI/Swagger and Flask")
-  (license license:asl2.0)))
-
-(define-public edash
-  (let ((md5 "93e745e9c"))
-    (package
-    (name "edash")
-    (version "0.0.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri "http://biogems.info/genenetwork2-2.0-a8fcff4.svg") ; any old file
-       (file-name (string-append name "-" md5))
-       (sha256
-        (base32 "0rir1mcn3a8i1mbw3ppgnjl7wg71mapljik7n3v5i8j5ic95mqr5"))))
-    (build-system trivial-build-system)
-    (native-inputs `(("unzip" ,unzip)
-                     ("source" ,source)))
-    ;;(inputs `(("sassc" ,sassc)))
-    (propagated-inputs
-     `(("python" ,python)
-       ("glibc-locales" ,glibc-locales)
-       ("gunicorn" ,gunicorn)
-       ("python-wrapper" ,python-wrapper)
-       ("python-elasticsearch" ,python-elasticsearch)
-       ("python-flask" ,python-flask)
-       ("python-jinja2" ,python-jinja2)
-       ("python-markdown" ,python-markdown)
-       ("python-misaka" ,python-misaka)
-       ;; ("python-pygit2" ,python-pygit2)
-       ("web-bootstrap" ,web-bootstrap)
-       ;;("sassc" ,sassc)
-       ("python-boto3" ,python-boto3)
-       ("python-pytest" ,python-pytest)
-       ("python-flask-login" ,python-flask-login)
-       ("python-passlib" ,python-passlib)
-       ("python-pyjwt" ,python-pyjwt)
-       ("python-sqlalchemy" ,python-sqlalchemy)
-       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
-       ("python-flask-mail" ,python-flask-mail)
-       ("python-flask-wtf" ,python-flask-wtf)
-       ("sqlite" ,sqlite)
-       ;; ("python-ipython" ,python-ipython)
-       ("python-swagger-ui-bundle" ,python-swagger-ui-bundle)
-       ("python-connexion" ,python-connexion)
-       ("python-schedule" ,python-schedule)
-       ("python-flask-cors" ,python-flask-cors)))
-    (arguments
-     `(#:modules ((guix build utils))
-       #:builder
-       (begin
-         (use-modules (guix build utils))
-         (let ((target (string-append (assoc-ref %outputs "out")
-                                      "/share")))
-             (write target)
-             (mkdir-p target)
-             ; (copy-recursively (assoc-ref %build-inputs "source") target)
-             #t))))
-
-    (home-page "https://gitlab.com/unless-emtec/live-service")
-    (synopsis "EMTech's edash service")
-    (description "EMTech's edash service package.")
-    (license license:agpl3+))))
-
-(define-public python-flask-cors
-  (package
-    (name "python-flask-cors")
-    (version "3.0.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "Flask-Cors" version))
-       (sha256
-        (base32
-         "1v6gq4vjgyxi8q8lxawpdfhq01adb4bznnabp08ks5nzbwibz43y"))))
-    (build-system python-build-system)
-    (inputs
-     `(("python-flask" ,python-flask)
-       ("python-six" ,python-six)
-       ("python-nose" ,python-nose)))
-    (home-page
-     "https://github.com/corydolphin/flask-cors")
-    (synopsis
-     "A Flask extension adding a decorator for CORS support")
-    (description
-     "A Flask extension adding a decorator for CORS support")
-    (license license:expat)))
diff --git a/arrayfire-lapack-detection.patch b/gn/packages/patches/arrayfire-lapack-detection.patch
index 1925122..1925122 100644
--- a/arrayfire-lapack-detection.patch
+++ b/gn/packages/patches/arrayfire-lapack-detection.patch
diff --git a/arrayfire-newer-boost-compute.patch b/gn/packages/patches/arrayfire-newer-boost-compute.patch
index b08c121..b08c121 100644
--- a/arrayfire-newer-boost-compute.patch
+++ b/gn/packages/patches/arrayfire-newer-boost-compute.patch
diff --git a/blist-stopiteration.patch b/gn/packages/patches/blist-stopiteration.patch
index 198bef4..198bef4 100644
--- a/blist-stopiteration.patch
+++ b/gn/packages/patches/blist-stopiteration.patch
diff --git a/delly-use-system-libraries.patch b/gn/packages/patches/delly-use-system-libraries.patch
index 3ce817f..3ce817f 100644
--- a/delly-use-system-libraries.patch
+++ b/gn/packages/patches/delly-use-system-libraries.patch
diff --git a/gnulib-gets.patch b/gn/packages/patches/gnulib-gets.patch
index cccb55a..cccb55a 100644
--- a/gnulib-gets.patch
+++ b/gn/packages/patches/gnulib-gets.patch
diff --git a/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch b/gn/packages/patches/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch
index 55036a7..55036a7 100644
--- a/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch
+++ b/gn/packages/patches/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch
diff --git a/octave-nested-class.patch b/gn/packages/patches/octave-nested-class.patch
index 6d835cb..6d835cb 100644
--- a/octave-nested-class.patch
+++ b/gn/packages/patches/octave-nested-class.patch
diff --git a/plink-ng-Makefile-zlib.patch b/gn/packages/patches/plink-ng-Makefile-zlib.patch
index f3bb269..f3bb269 100644
--- a/plink-ng-Makefile-zlib.patch
+++ b/gn/packages/patches/plink-ng-Makefile-zlib.patch
diff --git a/python-twint-mentions.patch b/gn/packages/patches/python-twint-mentions.patch
index f792786..f792786 100644
--- a/python-twint-mentions.patch
+++ b/gn/packages/patches/python-twint-mentions.patch
diff --git a/python-twint-token.patch b/gn/packages/patches/python-twint-token.patch
index 570ca8b..570ca8b 100644
--- a/python-twint-token.patch
+++ b/gn/packages/patches/python-twint-token.patch
diff --git a/python-twint-userlist.patch b/gn/packages/patches/python-twint-userlist.patch
index 1d5b860..1d5b860 100644
--- a/python-twint-userlist.patch
+++ b/gn/packages/patches/python-twint-userlist.patch
diff --git a/python2-htmlgen-Applied-Deb-patch.patch b/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch
index d6a957c..d6a957c 100644
--- a/python2-htmlgen-Applied-Deb-patch.patch
+++ b/gn/packages/patches/python2-htmlgen-Applied-Deb-patch.patch
diff --git a/python2-htmlgen-Fix-test-for-random.patch b/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch
index 279a82f..279a82f 100644
--- a/python2-htmlgen-Fix-test-for-random.patch
+++ b/gn/packages/patches/python2-htmlgen-Fix-test-for-random.patch
diff --git a/quast.patch b/gn/packages/patches/quast.patch
index 31e5460..31e5460 100644
--- a/quast.patch
+++ b/gn/packages/patches/quast.patch
diff --git a/vcflib-use-system-fastahack-smithwaterman.patch b/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch
index 91f372c..91f372c 100644
--- a/vcflib-use-system-fastahack-smithwaterman.patch
+++ b/gn/packages/patches/vcflib-use-system-fastahack-smithwaterman.patch
diff --git a/gn/packages/tcl.scm b/gn/packages/tcl.scm
deleted file mode 100644
index d71c1c6..0000000
--- a/gn/packages/tcl.scm
+++ /dev/null
@@ -1,50 +0,0 @@
-
-(define-module (gn packages tcl)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system perl)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages tcl)
-  #:use-module (gnu packages image)
-  #:use-module (gnu packages fontutils)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages xorg)
-  #:use-module (guix licenses))
-
-(define-public environment-modules ; guix: fix DL and tests
-  (package
-    (name "environment-modules")
-    (version "3.2.10")
-    (source
-     (origin
-      (method url-fetch)
-      ;; Would be nice to have a versioned download URL
-      (uri "http://sourceforge.net/projects/modules/files/latest/download?source=directory")
-      (sha256
-       (base32
-        "0m9rn1vr9acvc3qh9rdwnxlkzchdrbqajdvpv6hhay27hcmch1gv"))))
-    (build-system gnu-build-system)
-    (inputs
-     `(("tcl" ,tcl)))
-    (arguments
-     '(#:configure-flags
-       (let ((out (assoc-ref %outputs "out"))
-             (tcl (assoc-ref %build-inputs "tcl")))
-         (list (string-append "--with-tcl=" tcl "/lib")
-               (string-append "--with-tclinclude=" tcl "/include")
-               (string-append "--exec-prefix=" out)
-               (string-append "--disable-versioning")
-               (string-append "--mandir=" out "/share/man")
-               "CPPFLAGS=-DUSE_INTERP_ERRORLINE"))
-       #:tests? #f))
-
-    (home-page "")
-    (synopsis "Tool for managing the shell environment")
-    (description
-     "The Environment Modules system is a tool to help users manage
-their Unix or Linux shell environment, by allowing groups of related
-environment-variable settings to be made or removed dynamically.")
-    (license gpl2)))
-