From 5d918e7041532293fcc2ff660e33f94d00c5607d Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 11 Oct 2022 22:04:40 +0300
Subject: gn: (gn-rust-correlation): Update to 0.1.4-0.b82a93b

* gn/packages/crates-io.scm (gn-rust-correlation): 0.1.4-0.b82a93b
---
 gn/packages/crates-io.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 1dc4f65..b90589f 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -371,7 +371,7 @@ or any combination.")
     (license license:gpl3+)))
 
 (define-public gn-rust-correlation
-  (let ((commit "fd85c0f75e03f170b97fcedba26317e0832d087e")
+  (let ((commit "b82a93b691bb86e9dcf4ed30a4011a159857bba5")
         (revision "0"))
     (package
       (name "gn-rust-correlation")
@@ -385,7 +385,7 @@ or any combination.")
           (file-name (git-file-name name version))
           (sha256
            (base32
-            "164z2abp8vassxi8bpf68wgiqjmafd6hzrkz4hj3wdhf4djiplrr"))))
+            "03jqxnv3f8gc8bd1sz4jgrzhrgisd7jwsayvn0njys7i0a715ps3"))))
       (build-system cargo-build-system)
       (native-inputs
        (list gsl))
-- 
cgit 1.4.1


From b44f584e027d6b427dd55a42187d306a431609d9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 24 Oct 2022 10:55:48 +0300
Subject: gn: Update crates for upstream changes

---
 gn/packages/crates-io.scm | 115 +++++++++++++++++++++++++++++++++++++++++++---
 gn/packages/pangenome.scm |  15 +-----
 2 files changed, 110 insertions(+), 20 deletions(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index b90589f..2ffd798 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -9,9 +9,39 @@
   #:use-module (gnu packages crates-io)
   #:use-module (gnu packages maths))
 
+(define-public rust-boomphf-0.5
+  (package
+    (name "rust-boomphf")
+    (version "0.5.9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "boomphf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "0braniw72g9yq5006sfgc1g8d4317bb524c694jw6nggizrvg3sf"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-crossbeam-utils" ,rust-crossbeam-utils-0.8)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-rayon" ,rust-rayon-1)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-wyhash" ,rust-wyhash-0.5))
+       #:cargo-development-inputs
+       (("rust-bencher" ,rust-bencher-0.1)
+        ("rust-quickcheck" ,rust-quickcheck-1))))
+    (home-page "https://github.com/10XGenomics/rust-boomphf")
+    (synopsis "Scalable and Efficient Minimal Perfect Hash Functions")
+    (description "This package provides a Rust implementation of
+@url{https://arxiv.org/abs/1702.03154, fast and scalable minimal perfect hashing
+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-handlegraph-0.7
   (package
-    (inherit rust-handlegraph-0.3)
     (name "rust-handlegraph")
     (version "0.7.0-alpha.9")
     (source
@@ -23,6 +53,7 @@
         (sha256
          (base32
           "1frlcdwhycjvizb0gfb0v36vxjdi0jxagl2l2v6dzdjxpaawv9rs"))))
+    (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-anyhow" ,rust-anyhow-1)
@@ -36,7 +67,79 @@
         ("rust-succinct" ,rust-succinct-0.5))
        #:cargo-development-inputs
        (("rust-quickcheck" ,rust-quickcheck-0.9)
-        ("rust-rand" ,rust-rand-0.7))))))
+        ("rust-rand" ,rust-rand-0.7))))
+    (home-page "https://github.com/chfi/rs-handlegraph")
+    (synopsis "Library for use in variation graphs")
+    (description
+     "This package provides a Rust implementation of VG handle graph.")
+    (license license:expat)))
+
+(define-public rust-handlegraph-0.3
+  (package
+    (inherit rust-handlegraph-0.7)
+    (name "rust-handlegraph")
+    (version "0.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "handlegraph" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1sj100w4lpj7798pws85qrfrzsily5hhzh6j118rwf56sgic1yml"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bstr" ,rust-bstr-0.2)
+        ("rust-gfa" ,rust-gfa-0.6))))))
+
+(define-public rust-kstring-1
+  (package
+    (name "rust-kstring")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "kstring" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "1r4n9fa5scikqvl736nxghcfa6s3b07xz61w43hyzs2qb3wmd3nk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(;#:skip-build? #t     ; Uses unstable features.
+       #:cargo-inputs
+       (("rust-document-features" ,rust-document-features-0.2)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-static-assertions" ,rust-static-assertions-1))
+       #:cargo-development-inputs
+       (("rust-criterion" ,rust-criterion-0.3)
+        ("rust-proptest" ,rust-proptest-1))))
+    (home-page "https://github.com/cobalt-org/kstring")
+    (synopsis "String optimized for map keys")
+    (description "Key String provides a Rust package optimized for map keys.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-succinct-0.5
+  (package
+    (name "rust-succinct")
+    (version "0.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "succinct" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "0654c9gq50x7djyf25zbzz3d2pc4x3z21wmjj3qbr6d9h4hbd63p"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-byteorder" ,rust-byteorder-1)
+        ("rust-num-traits" ,rust-num-traits-0.2))
+       #:cargo-development-inputs
+       (("rust-quickcheck" ,rust-quickcheck-0.9))))
+    (home-page "https://github.com/tov/succinct-rs")
+    (synopsis "Succinct data structures for Rust")
+    (description "This package provides succinct data structures for Rust.")
+    (license (list license:expat license:asl2.0))))
 
 (define-public rust-clap-for-jrep
   (package
@@ -236,7 +339,7 @@ or any combination.")
         ("rust-unicode-width" ,rust-unicode-width-0.1))
        #:cargo-development-inputs
        (("rust-criterion" ,rust-criterion-0.3)
-        ("rust-lipsum" ,rust-lipsum-0.8)
+        ;("rust-lipsum" ,rust-lipsum-0.8)
         ("rust-termion" ,rust-termion-1)
         ;("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9)
         ("rust-version-sync" ,rust-version-sync-0.9))))
@@ -260,9 +363,7 @@ or any combination.")
          (base32 "1rwa5nzq8c5zg7lqmpkf7hyib415yxshd9amp911y8w1zss4s38p"))))
     (build-system cargo-build-system)
     (arguments
-     `(;#:skip-build? #t     ; Not all inputs at correct versions?
-       ;#:tests? #f          ; Skip tests for now
-       #:cargo-inputs
+     `(#:cargo-inputs
        (("rust-backtrace" ,rust-backtrace-0.3)
         ("rust-concolor" ,rust-concolor-0.0.8)
         ("rust-content-inspector" ,rust-content-inspector-0.2)
@@ -302,7 +403,7 @@ or any combination.")
          (base32 "0wx4wd849bmkqj0gdi041gmpfpvlyhy2ha4zpin69yw9d9npl8cl"))))
     (build-system cargo-build-system)
     (arguments
-     `(;#:skip-build? #t     ; Not all inputs packaged
+     `(#:skip-build? #t     ; Not all inputs packaged
        ;#:tests? #f          ; Skip tests for now
        #:cargo-inputs
        (("rust-combine" ,rust-combine-4)
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 69e3d81..c66b594 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -1,23 +1,12 @@
-;; Bioinformatics module
+;; Pangenome module
 
 (define-module (gn packages pangenome)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
-  #:use-module (guix utils)
   #:use-module (guix download)
-  #:use-module (guix git-download)
   #:use-module (guix build-system cargo)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix graph)
-  #:use-module (guix scripts graph)
-  #:use-module (guix store)
-  #:use-module (guix gexp)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages base)
   #:use-module (gnu packages crates-io)
-  #:use-module (gnu packages rust)
-  #:use-module (gnu packages version-control)
-  #:use-module (srfi srfi-1))
+  #:use-module (gn packages crates-io))
 
 
 (define-public gfautil
-- 
cgit 1.4.1


From ea88896fb43c79b9b0ee8b6722adc61ebce247b0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 7 Nov 2022 10:19:59 +0200
Subject: gn: Add missing crate

---
 gn/packages/crates-io.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 2ffd798..8ea1765 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -40,6 +40,35 @@ 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-gfa-0.6
+  (package
+    (name "rust-gfa")
+    (version "0.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "gfa" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0ghmy4r0324s6vvmj9nmh326346nkwm7nybnpcpswnjvf02b85gw"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bstr" ,rust-bstr-0.2)
+        ("rust-bytemuck" ,rust-bytemuck-1)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-nom" ,rust-nom-5)
+        ("rust-regex" ,rust-regex-1)
+        ("rust-serde" ,rust-serde-1))
+        #:cargo-development-inputs
+        (("rust-criterion" ,rust-criterion-0.3))))
+    (home-page "https://github.com/chfi/rs-gfa")
+    (synopsis
+     "Library for working with graphs in the GFA (Graphical Fragment Assembly) format")
+    (description
+     "Library for working with graphs in the GFA (Graphical Fragment Assembly) format")
+    (license license:expat)))
+
 (define-public rust-handlegraph-0.7
   (package
     (name "rust-handlegraph")
-- 
cgit 1.4.1


From c6ec09ebb994e6b281a513be8465d81ed0dfc003 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 10 Nov 2022 17:56:36 +0200
Subject: gn: Add pgr-tk

---
 gn/packages/bioinformatics.scm | 111 +++++++++++++++++++++++++
 gn/packages/crates-io.scm      | 182 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 293 insertions(+)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 2d1b55f..4e3c92b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -54,6 +54,7 @@
   #:use-module (gnu packages java)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages llvm)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
@@ -510,6 +511,116 @@ reads.")
 collapses them into a non-redundant graph structure.")
     (license license:expat)))
 
+(define-public pgr-tk
+  (package
+    (name "pgr-tk")
+    (version "0.3.6")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/Sema4-Research/pgr-tk")
+               (commit (string-append "v" version))
+               (recursive? #t)))        ; agc, WFA
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "160ngqbi8cbgaafq8crhfqv039mxr9jgl8hxxpwz0fh8mrh4003y"))
+        (snippet
+         #~(begin
+             (use-modules (guix build utils))
+             (substitute* (find-files "." "Cargo.toml")
+               ;; Only use the major+minor version to decrease the number of
+               ;; special version crates.
+               (("(.*= \")([[:digit:]]+\\.[[:digit:]]+)\\.[[:digit:]]+(\".*)"
+                 _ name version tail)
+                (string-append name version tail))
+               ;; Then fix the version string for the actual package.
+               (("^version = \".*")
+                (string-append "version = \"" #$version "\"\n")))))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:install-source? #f
+       #:cargo-test-flags
+       (list "--release" "--"
+             "--skip=get_aln_segements"
+             "--skip=get_shmmr_dots"
+             "--skip=AGCFile"
+             "--skip=SeqIndexDB")
+       #:cargo-inputs
+       (("rust-bindgen" ,rust-bindgen-0.58)
+        ("rust-bgzip" ,rust-bgzip-0.2)
+        ("rust-byteorder" ,rust-byteorder-1)
+        ("rust-clap" ,rust-clap-3.1)
+        ("rust-cuckoofilter" ,rust-cuckoofilter-0.5)
+        ("rust-flate2" ,rust-flate2-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-petgraph" ,rust-petgraph-0.6)
+        ("rust-pyo3" ,rust-pyo3-0.14)
+        ("rust-rayon" ,rust-rayon-1)
+        ("rust-regex" ,rust-regex-1)
+        ("rust-rustc-hash" ,rust-rustc-hash-1)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-serde-json" ,rust-serde-json-1)
+        ("rust-simple-logger" ,rust-simple-logger-1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'insert-wfa-source
+           (lambda* (#:key inputs #:allow-other-keys)
+             (copy-recursively (assoc-ref inputs "wfa-src")
+                               "rs-wfa/WFA")))
+         (add-after 'unpack 'adjust-source
+           (lambda _
+             (substitute* '("pgr-bin/build.rs"
+                            "pgr-db/build.rs"
+                            "pgr-tk/build.rs")
+               (("git") "ls")
+               (("bioconda") "Guix"))
+             ;; Build with zlib, not zlib-ng
+             (substitute* '("pgr-bin/Cargo.toml"
+                            "pgr-db/Cargo.toml")
+               (("zlib-ng-compat") "zlib"))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (with-directory-excursion "target/release"
+                 (install-file "libpgrtk.so" (string-append out "/lib"))
+                 (for-each
+                   (lambda (file)
+                     (install-file file (string-append out "/bin")))
+                   (list "pgr-filter"
+                         "pgr-mdb"
+                         "pgr-multifilter"
+                         "pgr-probe-match"
+                         "pgr-shmmr-pair-count")))))))))
+    (inputs (list clang python zlib))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("wfa-src"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                  ;; forPYO3 branch, 14-03-2021
+                  (url "https://github.com/cschin/WFA")
+                  (commit "1f8c8d2905ed482cd2d306a1676d60c2a45cb098")))
+           (file-name "wfa-for-pgr-tk")
+           (sha256
+            (base32 "19h1cjp2bdlcfq5c6rsbk8bc0f8zn64b471dhj4xlfxd1prv2dpk"))))))
+    (home-page "https://github.com/Sema4-Research/pgr-tk")
+    (synopsis "Pangenome Research Tool Kit")
+    (description
+     "PGR-TK provides pangenome assembly management, query and
+@acronym{Minimizer Anchored Pangenome, MAP} Graph Generation.  It is a project
+to provide Python and Rust libraries to facilitate pangenomics analysis.
+Several algorithms and data structures used for the Peregrine Genome Assembler
+are useful for Pangenomics analysis as well.  This repo takes those algorithms
+and data structure, combining other handy 3rd party tools to expose them as a
+library in Python (with Rust code for those computing parts that need
+performance.)")
+    (license (license:non-copyleft
+               "file:///LICENSE"
+               "CC-BY-NC-SA 4.0"))))
+
 (define-public pangenie
   (let ((commit "e779076827022d1416ab9fabf99a03d8f4725956") ; September 2, 2021 from phasing-tests branch
         (revision "2"))
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 8ea1765..847b2ef 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -9,6 +9,31 @@
   #:use-module (gnu packages crates-io)
   #:use-module (gnu packages maths))
 
+(define-public rust-bgzip-0.2
+  (package
+    (name "rust-bgzip")
+    (version "0.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "bgzip" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1kssq4hp8csg27rhggabpfiyn9xp5rh5b8al63dghk11vqs7hk5j"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-flate2" ,rust-flate2-1)
+        ("rust-thiserror" ,rust-thiserror-1))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-csv" ,rust-csv-1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (home-page "https://github.com/informationsea/bgzip-rs")
+    (synopsis "Rust implementation of bgzip")
+    (description "Rust implementation of bgzip")
+    (license license:expat)))
+
 (define-public rust-boomphf-0.5
   (package
     (name "rust-boomphf")
@@ -40,6 +65,36 @@ 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-cuckoofilter-0.5
+  (package
+    (name "rust-cuckoofilter")
+    (version "0.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "cuckoofilter" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "067fkr9dc118rqddr72xdldq05d31yyipvvyrmj9yrrik52ah45q"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t     ; Not packaging dependencies
+       #:cargo-inputs
+       (("rust-byteorder" ,rust-byteorder-1)
+        ;("rust-clippy" ,rust-clippy-0.0.302)
+        ;("rust-farmhash" ,rust-farmhash-1)
+        ("rust-fnv" ,rust-fnv-1)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-serde-bytes" ,rust-serde-bytes-0.11)
+        ("rust-serde-derive" ,rust-serde-derive-1))
+       #:cargo-development-inputs
+       (("rust-serde-json" ,rust-serde-json-1))))
+    (home-page "http://axiom.co")
+    (synopsis "Cuckoo Filter: Practically Better Than Bloom")
+    (description "Cuckoo Filter: Practically Better Than Bloom")
+    (license license:expat)))
+
 (define-public rust-gfa-0.6
   (package
     (name "rust-gfa")
@@ -146,6 +201,133 @@ 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-pyo3-0.14
+  (package
+    (name "rust-pyo3")
+    (version "0.14.5")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "pyo3" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1j70b9bkncgpgnfxjxyvp4mk40rp55lk6qmacxm5c2k78y9hy41m"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-cfg-if" ,rust-cfg-if-1)
+        ("rust-hashbrown" ,rust-hashbrown-0.11)
+        ("rust-indexmap" ,rust-indexmap-1)
+        ("rust-indoc" ,rust-indoc-0.3)
+        ("rust-inventory" ,rust-inventory-0.1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-num-bigint" ,rust-num-bigint-0.4)
+        ("rust-num-complex" ,rust-num-complex-0.4)
+        ("rust-parking-lot" ,rust-parking-lot-0.11)
+        ("rust-paste" ,rust-paste-0.1)
+        ("rust-pyo3-build-config" ,rust-pyo3-build-config-0.14)
+        ("rust-pyo3-macros" ,rust-pyo3-macros-0.14)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-unindent" ,rust-unindent-0.1))
+       #:cargo-development-inputs
+       (("rust-assert-approx-eq" ,rust-assert-approx-eq-1)
+        ("rust-criterion" ,rust-criterion-0.3)
+        ("rust-proptest" ,rust-proptest-0.10)
+        ("rust-rustversion" ,rust-rustversion-1)
+        ("rust-serde-json" ,rust-serde-json-1)
+        ("rust-trybuild" ,rust-trybuild-1))))
+    (inputs (list python))
+    (home-page "https://github.com/pyo3/pyo3")
+    (synopsis "Rust bindings for the Python interpreter")
+    (description
+     "This package provides Rust bindings for Python, including tools for
+creating native Python extension modules.  Running and interacting with
+Python code from a Rust binary is also supported.")
+    (license license:asl2.0)))
+
+(define-public rust-pyo3-build-config-0.14
+  (package
+    (name "rust-pyo3-build-config")
+    (version "0.14.5")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "pyo3-build-config" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "13vkcl49b2x81azb613ss256k8pazrfc4fy4ny8pzgdciirn2afi"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-once-cell" ,rust-once-cell-1))))
+    (home-page "https://github.com/pyo3/pyo3")
+    (synopsis "Build configuration for the PyO3 ecosystem")
+    (description "Build configuration for the PyO3 ecosystem")
+    (license license:asl2.0)))
+
+(define-public rust-pyo3-macros-0.14
+  (package
+    (name "rust-pyo3-macros")
+    (version "0.14.5")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "pyo3-macros" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1a4fh24c5q85f31n2rwbqrai2bjprf9kzh6xvpgj8j3hblhwa2zw"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-pyo3-macros-backend" ,rust-pyo3-macros-backend-0.14)
+        ("rust-quote" ,rust-quote-1)
+        ("rust-syn" ,rust-syn-1))))
+    (home-page "https://github.com/pyo3/pyo3")
+    (synopsis "Proc macros for PyO3 package")
+    (description "Proc macros for PyO3 package")
+    (license license:asl2.0)))
+
+(define-public rust-pyo3-macros-backend-0.14
+  (package
+    (name "rust-pyo3-macros-backend")
+    (version "0.14.5")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "pyo3-macros-backend" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1ps068jqyq1275zxxbzn6hyz9lkfz35az8waj6mzlji2jg2kyqki"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1)
+        ("rust-pyo3-build-config" ,rust-pyo3-build-config-0.14)
+        ("rust-quote" ,rust-quote-1)
+        ("rust-syn" ,rust-syn-1))))
+    (home-page "https://github.com/pyo3/pyo3")
+    (synopsis "Code generation for PyO3 package")
+    (description "Code generation for PyO3 package")
+    (license license:asl2.0)))
+
+(define-public rust-quick-csv-0.1
+  (package
+    (name "rust-quick-csv")
+    (version "0.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "quick-csv" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "131k8zzlplk2h62wz813jbvm0sk7v3mixwhhq34y9lmp3mqbgx7d"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-rustc-serialize" ,rust-rustc-serialize-0.3))))
+    (home-page "https://github.com/tafia/quick-csv")
+    (synopsis "quick csv reader and decoder")
+    (description "quick csv reader and decoder")
+    (license license:expat)))
+
 (define-public rust-succinct-0.5
   (package
     (name "rust-succinct")
-- 
cgit 1.4.1


From cc8ee17a6e63cf20adc9374735a1322dd9c7f88e Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 16 Nov 2022 14:56:36 +0200
Subject: gn: Add graph-genotyper and dependent packages

---
 gn/packages/bioinformatics.scm | 133 ++++++++++++++++++++++++++++++++++++++++
 gn/packages/crates-io.scm      | 135 ++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 267 insertions(+), 1 deletion(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8f98b8e..76b93d9 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -512,6 +512,34 @@ reads.")
 collapses them into a non-redundant graph structure.")
     (license license:expat)))
 
+(define-public gafpack
+  (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6")     ; November 10, 2022
+        (revision "1"))
+    (package
+      (name "gafpack")
+      (version (git-version "0.0.0" revision commit))
+      (source
+        (origin
+          (method git-fetch)
+          (uri (git-reference
+                 (url "https://github.com/ekg/gafpack")
+                 (commit commit)))
+          (file-name (git-file-name name version))
+          (sha256
+           (base32 "0di2psh0ls7jlbnqs7k71p55f73pn23a09k1h3ril7gwjcrzr3rk"))))
+      (build-system cargo-build-system)
+      (arguments
+       `(#:install-source? #f
+         #:cargo-inputs
+         (("rust-clap" ,rust-clap-4)
+          ("rust-gfa" ,rust-gfa-0.10))))
+      (home-page "https://github.com/ekg/gafpack")
+      (synopsis "Convert variation graph alignments to coverage maps over nodes")
+      (description
+       "Gafpack converts alignments to pangenome variation graphs to coverage
+maps useful in haplotype-based genotyping.")
+      (license license:expat))))
+
 (define-public agc-for-pgr-tk
   (let ((commit "453c0afdc54b4aa00fa8e97a63f196931fdb81c4") ; April 26, 2022
         (revision "1"))
@@ -728,6 +756,61 @@ performance.)")
                "file:///LICENSE"
                "CC-BY-NC-SA 4.0"))))
 
+(define-public graph-genotyper
+  (let ((commit "e7cc6b43a5b1f389d76bf9aac7f2ee02f92caeaf") ; October 17, 2022
+        (revision "13"))
+    (package
+      (name "graph-genotyper")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/davidebolo1993/graph_genotyper")
+               (commit commit)))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1l8yjpkqamiqr1q5i7vr5z04aba7skpbcwyc9dx5fiklvljjfhcx"))))
+      (build-system copy-build-system)
+      (arguments
+       `(#:install-plan
+         '(("genotype.py" "bin/")
+           ("genotype.sh" "bin/"))
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'install 'wrap-genotype
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (wrap-script (string-append out "/bin/genotype.sh")
+                  `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
+                  `("PATH" ":" prefix
+                    ,(map (lambda (file-name)
+                            (string-append (assoc-ref inputs file-name) "/bin"))
+                          (list "gafpack"
+                                "odgi"
+                                "python"
+                                "samtools"
+                                "vg"))))))))))
+      (inputs
+       (list gafpack
+             guile-3.0
+             odgi
+             python
+             python-numpy
+             python-pandas
+             python-scipy
+             samtools
+             vg))
+      (home-page "https://bitbucket.org/jana_ebler")
+      (synopsis "Genotyping based on k-mers and pangenome graphs")
+      (description
+       "This package provides a genotyper for various types of genetic variants
+(such as SNPs, indels and structural variants).  Genotypes are computed based on
+read k-mer counts and a panel of known haplotypes.  A description of the method
+can be found @url{https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1,
+here}.")
+      (license (license:non-copyleft
+                 "No license listed")))))
+
 (define-public pangenie
   (let ((commit "e779076827022d1416ab9fabf99a03d8f4725956") ; September 2, 2021 from phasing-tests branch
         (revision "2"))
@@ -1811,6 +1894,56 @@ available to other researchers.")
                  (delete-file "scanpy/tests/test_pca.py")
                  #t)))))))))
 
+;; TODO: Unbundle everything
+(define-public odgi
+  (package
+    (name "odgi")
+    (version "0.8.1")
+    (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"))
+              (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")))))
+    (build-system cmake-build-system)
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list jemalloc
+           libdivsufsort
+           pybind11
+           python
+           sdsl-lite))
+    (home-page "https://github.com/vgteam/odgi")
+    (synopsis "Optimized Dynamic Genome/Graph Implementation")
+    (description "@acronym{Optimized Dynamic Genome/Graph Implementation, odgi}
+provides an efficient and succinct dynamic DNA sequence graph model, as well as
+a host of algorithms that allow the use of such graphs in bioinformatic
+analyses.
+
+Careful encoding of graph entities allows odgi to efficiently compute and
+transform pangenomes with minimal overheads.  @command{odgi} implements a
+dynamic data structure that leveraged multi-core CPUs and can be updated on the
+fly.
+
+The edges and path steps are recorded as deltas between the current node id and
+the target node id, where the node id corresponds to the rank in the global
+array of nodes.  Graphs built from biological data sets tend to have local
+partial order and, when sorted, the deltas be small.  This allows them to be
+compressed with a variable length integer representation, resulting in a small
+in-memory footprint at the cost of packing and unpacking.")
+    (properties '((tunable? . #t)))
+    (license license:expat)))
+
 (define-public vg
   (package
     (name "vg")
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 847b2ef..8b7bc4c 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -7,7 +7,8 @@
   #:use-module (guix build-system cargo)
   #:use-module (gnu packages crates-graphics)
   #:use-module (gnu packages crates-io)
-  #:use-module (gnu packages maths))
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages python))
 
 (define-public rust-bgzip-0.2
   (package
@@ -65,6 +66,25 @@ 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")
@@ -352,6 +372,51 @@ Python code from a Rust binary is also supported.")
     (description "This package provides succinct data structures for Rust.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-terminal-size-0.2
+  (package
+    (name "rust-terminal-size")
+    (version "0.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "terminal-size" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0yhza8sc6jkka6j0nq5sl749ckx1jagvxp3b38yhh4px6k291jj0"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       ;#:cargo-inputs
+       ;(("rust-rustix" ,rust-rustix-0.35)
+       ; ("rust-windows-sys" ,rust-windows-sys-0.42))
+       ))
+    (home-page "https://github.com/eminence/terminal-size")
+    (synopsis "Gets the size of your Linux or Windows terminal")
+    (description "Gets the size of your Linux or Windows terminal")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-unic-emoji-char-0.9
+  (package
+    (name "rust-unic-emoji-char")
+    (version "0.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "unic-emoji-char" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0ka9fr7s6lv0z43r9xphg9injn35pfxf9g9q18ki0wl9d0g241qb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-unic-char-property" ,rust-unic-char-property-0.9)
+        ("rust-unic-char-range" ,rust-unic-char-range-0.9)
+        ("rust-unic-ucd-version" ,rust-unic-ucd-version-0.9))))
+    (home-page "https://github.com/open-i18n/rust-unic/")
+    (synopsis "UNIC â Unicode Emoji â Emoji Character Properties")
+    (description "UNIC â Unicode Emoji â Emoji Character Properties")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-clap-for-jrep
   (package
     (name "rust-clap")
@@ -499,6 +564,48 @@ or any combination.")
       Argument Parser")
     (license (list license:expat license:asl2.0))))
 
+(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
+     `(#: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-0.2)
+        ("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))))
+
 ;; ready to upstream, WITH rust-clap-derive
 ;; replace fields with those from upstream.
 (define-public rust-clap-derive-3.1
@@ -527,6 +634,32 @@ or any combination.")
       "Parse command line argument by defining a struct, derive crate.")
     (license (list license:expat license:asl2.0))))
 
+(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-textwrap-0.15
   (package
     (name "rust-textwrap")
-- 
cgit 1.4.1


From f10212acf2cb89cccbc6c5053d7afe416e89495e Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 27 Nov 2022 11:02:52 +0200
Subject: gn: Fix guix pull.

---
 gn/packages/crates-io.scm | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 8b7bc4c..32394bf 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -577,7 +577,8 @@ or any combination.")
                 "1w0dxqzrh449s9l2k8g66pdsff02599bwi5mh0gny3227kcpsq1h"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs
+     `(#: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)
@@ -589,15 +590,16 @@ or any combination.")
         ("rust-terminal-size" ,rust-terminal-size-0.2)
         ("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))))
+       ;#: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")
-- 
cgit 1.4.1


From ad6055084e48faa7563615c78392fcf469100140 Mon Sep 17 00:00:00 2001
From: AlexanderKabui
Date: Mon, 28 Nov 2022 20:18:51 +0300
Subject: gn: (gn-rust-correlation): Update to 0.1.4-0.a22381e

* gn/packages/crates-io.scm (gn-rust-correlation): 0.1.4--0.a22381e
---
 gn/packages/crates-io.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 32394bf..60b6229 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -818,7 +818,7 @@ or any combination.")
     (license license:gpl3+)))
 
 (define-public gn-rust-correlation
-  (let ((commit "b82a93b691bb86e9dcf4ed30a4011a159857bba5")
+  (let ((commit "a22381e9830bac9a6848449279d258397217e251")
         (revision "0"))
     (package
       (name "gn-rust-correlation")
@@ -832,7 +832,7 @@ or any combination.")
           (file-name (git-file-name name version))
           (sha256
            (base32
-            "03jqxnv3f8gc8bd1sz4jgrzhrgisd7jwsayvn0njys7i0a715ps3"))))
+            "1cb197p8zmgxymzs9b7bygs0kg67809z6gc2svza909sxr9ac5ps"))))
       (build-system cargo-build-system)
       (native-inputs
        (list gsl))
-- 
cgit 1.4.1


From a8481f8fda599be8af4c14663cc57e538f8117c3 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 30 Nov 2022 10:54:03 +0200
Subject: gn: Remove upstreamed packages

---
 gn/packages/bioinformatics.scm |   4 +-
 gn/packages/crates-io.scm      | 151 -----------------------------------------
 2 files changed, 2 insertions(+), 153 deletions(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 76b93d9..19cc1ff 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -489,7 +489,7 @@ reads.")
     (arguments
      `(#:install-source? #f
        #:cargo-inputs
-       (("rust-clap" ,rust-clap-3.1)
+       (("rust-clap" ,rust-clap-3)
         ("rust-rustc-hash" ,rust-rustc-hash-1)
         ("rust-regex" ,rust-regex-1)
         ("rust-handlegraph" ,rust-handlegraph-0.7)
@@ -670,7 +670,7 @@ types of datasets: short genomes (viruses) as well as long (humans).")
        (("rust-bindgen" ,rust-bindgen-0.58)
         ("rust-bgzip" ,rust-bgzip-0.2)
         ("rust-byteorder" ,rust-byteorder-1)
-        ("rust-clap" ,rust-clap-3.1)
+        ("rust-clap" ,rust-clap-3)
         ("rust-cuckoofilter" ,rust-cuckoofilter-0.5)
         ("rust-flate2" ,rust-flate2-1)
         ("rust-libc" ,rust-libc-0.2)
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 60b6229..342aca4 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -372,51 +372,6 @@ Python code from a Rust binary is also supported.")
     (description "This package provides succinct data structures for Rust.")
     (license (list license:expat license:asl2.0))))
 
-(define-public rust-terminal-size-0.2
-  (package
-    (name "rust-terminal-size")
-    (version "0.2.2")
-    (source (origin
-              (method url-fetch)
-              (uri (crate-uri "terminal-size" version))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0yhza8sc6jkka6j0nq5sl749ckx1jagvxp3b38yhh4px6k291jj0"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:skip-build? #t
-       ;#:cargo-inputs
-       ;(("rust-rustix" ,rust-rustix-0.35)
-       ; ("rust-windows-sys" ,rust-windows-sys-0.42))
-       ))
-    (home-page "https://github.com/eminence/terminal-size")
-    (synopsis "Gets the size of your Linux or Windows terminal")
-    (description "Gets the size of your Linux or Windows terminal")
-    (license (list license:expat license:asl2.0))))
-
-(define-public rust-unic-emoji-char-0.9
-  (package
-    (name "rust-unic-emoji-char")
-    (version "0.9.0")
-    (source (origin
-              (method url-fetch)
-              (uri (crate-uri "unic-emoji-char" version))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0ka9fr7s6lv0z43r9xphg9injn35pfxf9g9q18ki0wl9d0g241qb"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs
-       (("rust-unic-char-property" ,rust-unic-char-property-0.9)
-        ("rust-unic-char-range" ,rust-unic-char-range-0.9)
-        ("rust-unic-ucd-version" ,rust-unic-ucd-version-0.9))))
-    (home-page "https://github.com/open-i18n/rust-unic/")
-    (synopsis "UNIC â Unicode Emoji â Emoji Character Properties")
-    (description "UNIC â Unicode Emoji â Emoji Character Properties")
-    (license (list license:expat license:asl2.0))))
-
 (define-public rust-clap-for-jrep
   (package
     (name "rust-clap")
@@ -520,50 +475,6 @@ or any combination.")
       (description "Rust CLI tools for manipulation of Jupyter Notebooks.")
       (license #f)))) ; There is no license.
 
-;; replace fields with those from upstream
-(define-public rust-clap-3.1
-  (package
-    (name "rust-clap")
-    (version "3.1.6")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "clap" version))
-        (file-name (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "08q1hkksfixybnrwrpm44xq028wbn9yr2hnzrax9hihyq8v39jfq"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#: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-3.1)
-        ("rust-indexmap" ,rust-indexmap-1)
-        ("rust-lazy-static" ,rust-lazy-static-1)
-        ("rust-os-str-bytes" ,rust-os-str-bytes-6)
-        ("rust-regex" ,rust-regex-1)
-        ("rust-strsim" ,rust-strsim-0.10)
-        ("rust-termcolor" ,rust-termcolor-1)
-        ("rust-terminal-size" ,rust-terminal-size-0.1)
-        ("rust-textwrap" ,rust-textwrap-0.15)
-        ("rust-unicase" ,rust-unicase-2)
-        ("rust-yaml-rust" ,rust-yaml-rust-0.4))
-       #:cargo-development-inputs
-       (("rust-criterion" ,rust-criterion-0.3)
-        ("rust-lazy-static" ,rust-lazy-static-1)
-        ("rust-regex" ,rust-regex-1)
-        ("rust-rustversion" ,rust-rustversion-1)
-        ("rust-trybuild" ,rust-trybuild-1)
-        ("rust-trycmd" ,rust-trycmd-0.12))))
-    (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-4
   (package
     (name "rust-clap")
@@ -608,34 +519,6 @@ or any combination.")
       Argument Parser")
     (license (list license:expat license:asl2.0))))
 
-;; ready to upstream, WITH rust-clap-derive
-;; replace fields with those from upstream.
-(define-public rust-clap-derive-3.1
-  (package
-    (name "rust-clap-derive")
-    (version "3.1.4")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "clap-derive" version))
-        (file-name (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "05mz2y6k73wc1gvv9r4mllfqslzvlwkvx77lk7769ag1xlwd15fs"))))
-    (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-clap-derive-4
   (package
     (name "rust-clap-derive")
@@ -662,40 +545,6 @@ or any combination.")
       "Parse command line argument by defining a struct, derive crate.")
     (license (list license:expat license:asl2.0))))
 
-(define-public rust-textwrap-0.15
-  (package
-    (name "rust-textwrap")
-    (version "0.15.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "textwrap" version))
-        (file-name (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "1yw513k61lfiwgqrfvsjw1a5wpvm0azhpjr2kr0jhnq9c56is55i"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:skip-build? #t     ; Not all inputs packaged
-       ;#:tests? #f          ; Skip tests for now
-       #:cargo-inputs
-       (("rust-hyphenation" ,rust-hyphenation-0.8)
-        ("rust-smawk" ,rust-smawk-0.3)
-        ("rust-terminal-size" ,rust-terminal-size-0.1)
-        ("rust-unicode-linebreak" ,rust-unicode-linebreak-0.1)
-        ("rust-unicode-width" ,rust-unicode-width-0.1))
-       #:cargo-development-inputs
-       (("rust-criterion" ,rust-criterion-0.3)
-        ;("rust-lipsum" ,rust-lipsum-0.8)
-        ("rust-termion" ,rust-termion-1)
-        ;("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9)
-        ("rust-version-sync" ,rust-version-sync-0.9))))
-    (home-page "https://github.com/mgeisler/textwrap")
-    (synopsis
-      "Powerful library for word wrapping, indenting, and dedenting strings")
-    (description
-      "Powerful library for word wrapping, indenting, and dedenting strings")
-    (license license:expat)))
-
 (define-public rust-trycmd-0.12
   (package
     (name "rust-trycmd")
-- 
cgit 1.4.1


From fb631515ccf985e6e89c6cb03a86833aa3b963c6 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 6 Dec 2022 04:50:00 +0300
Subject: gn: rust-quick-csv-0.1: remove duplicated package

* gn/packages/crates-io.scm (rust-quick-csv-0.1): Remove package that
  is also defined in mainline guix
---
 gn/packages/crates-io.scm | 19 -------------------
 1 file changed, 19 deletions(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 342aca4..98c0e40 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -329,25 +329,6 @@ Python code from a Rust binary is also supported.")
     (description "Code generation for PyO3 package")
     (license license:asl2.0)))
 
-(define-public rust-quick-csv-0.1
-  (package
-    (name "rust-quick-csv")
-    (version "0.1.6")
-    (source (origin
-              (method url-fetch)
-              (uri (crate-uri "quick-csv" version))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "131k8zzlplk2h62wz813jbvm0sk7v3mixwhhq34y9lmp3mqbgx7d"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs (("rust-rustc-serialize" ,rust-rustc-serialize-0.3))))
-    (home-page "https://github.com/tafia/quick-csv")
-    (synopsis "quick csv reader and decoder")
-    (description "quick csv reader and decoder")
-    (license license:expat)))
-
 (define-public rust-succinct-0.5
   (package
     (name "rust-succinct")
-- 
cgit 1.4.1


From 217b73be4fb872380cabd0756352188011d58b84 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 6 Dec 2022 05:39:27 +0300
Subject: gn: (rust-clap-4): Update dependency

* gn/packages/crates-io.scm (rust-clap-4): Change from
  rust-terminal-size-0.2 which is undefined to rust-terminal-size-0.1
---
 gn/packages/crates-io.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 98c0e40..112eaf4 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -479,7 +479,7 @@ or any combination.")
         ("rust-once-cell" ,rust-once-cell-1)
         ("rust-strsim" ,rust-strsim-0.10)
         ("rust-termcolor" ,rust-termcolor-1)
-        ("rust-terminal-size" ,rust-terminal-size-0.2)
+        ("rust-terminal-size" ,rust-terminal-size-0.1)
         ("rust-unicase" ,rust-unicase-2)
         ("rust-unicode-width" ,rust-unicode-width-0.1))
        ;#:cargo-development-inputs
-- 
cgit 1.4.1


From 4a94d82150bae9ca7a9f3926125b6a1974b229d0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Fri, 9 Dec 2022 09:21:21 +0200
Subject: Revert "gn: rust-quick-csv-0.1: remove duplicated package"

This reverts commit fb631515ccf985e6e89c6cb03a86833aa3b963c6.

rust-quick-csv-0.1 isn't actually in Guix yet.
---
 gn/packages/crates-io.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

(limited to 'gn/packages/crates-io.scm')

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 112eaf4..e500d86 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -329,6 +329,25 @@ Python code from a Rust binary is also supported.")
     (description "Code generation for PyO3 package")
     (license license:asl2.0)))
 
+(define-public rust-quick-csv-0.1
+  (package
+    (name "rust-quick-csv")
+    (version "0.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "quick-csv" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "131k8zzlplk2h62wz813jbvm0sk7v3mixwhhq34y9lmp3mqbgx7d"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-rustc-serialize" ,rust-rustc-serialize-0.3))))
+    (home-page "https://github.com/tafia/quick-csv")
+    (synopsis "quick csv reader and decoder")
+    (description "quick csv reader and decoder")
+    (license license:expat)))
+
 (define-public rust-succinct-0.5
   (package
     (name "rust-succinct")
-- 
cgit 1.4.1