From 752be79bf3b0f8de886304f8280e68b9584cafa7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 16 Aug 2022 10:22:34 +0200
Subject: gnu: htseq: Update to 2.0.2.

* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.2.
[source]: Fetch from git repository.
[arguments]: Delete 'build phase; run tests with pytest in 'check phase.
[propagated-inputs]: Add python-matplotlib and python-pysam.
[inputs]: Remove python-matplotlib and python-pysam.
[native-inputs]: Add python-pandas, python-pytest, python-scipy, and swig.
[synopsis]: Update.
[description]: Update.
---
 gnu/packages/bioinformatics.scm | 46 ++++++++++++++++++++++++++++-------------
 1 file changed, 32 insertions(+), 14 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 38b9fe6cf6..9c18737ade 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3985,26 +3985,44 @@ (define-public hmmer
 (define-public htseq
   (package
     (name "htseq")
-    (version "0.12.3")
+    (version "2.0.2")
+    ;; Sources on pypi do not include everything needed to run the tests.
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "HTSeq" version))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/htseq/htseq")
+                    (commit (string-append "release_" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b"))))
+                "1kbr4ydjjhizz6r5m3xd4f0wj7qnn8zs0vnzghhgaa0yhbya5r19"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-cython))
-    ;; Numpy needs to be propagated when htseq is used as a Python library.
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; Avoid rebuilding the extension.  Everything is built during the
+         ;; 'install phase anyway.
+         (delete 'build)
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "pytest" "-v")))))))
     (propagated-inputs
-     (list python-numpy))
-    (inputs
-     (list python-pysam python-matplotlib))
-    (home-page "https://htseq.readthedocs.io/")
-    (synopsis "Analysing high-throughput sequencing data with Python")
+     (list python-matplotlib
+           python-numpy
+           python-pysam))
+    (native-inputs
+     (list python-cython
+           python-pandas
+           python-pytest
+           python-scipy
+           swig))
+    (home-page "https://github.com/htseq")
+    (synopsis "Framework for analyzing high-throughput sequencing data")
     (description
-     "HTSeq is a Python package that provides infrastructure to process data
-from high-throughput sequencing assays.")
+     "This package provides a framework to process and analyze data from
+high-throughput sequencing (HTS) assays")
     (license license:gpl3+)))
 
 (define-public java-htsjdk
-- 
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