Merge pull request #308478 from natsukium/htseq/update

python311Packages.htseq: 0.12.4 -> 2.0.4

pkgs/development/python-modules/htseq/default.nix

@@ -1,29 +1,79 @@
-{ lib, buildPythonPackage, fetchFromGitHub, cython, numpy, pysam, matplotlib, python, isPy27, isPy3k }:
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  fetchpatch,
+  swig,
+  cython,
+  matplotlib,
+  numpy,
+  pandas,
+  pysam,
+  setuptools,
+  pytestCheckHook,
+  nix-update-script,
+}:
 buildPythonPackage rec {
-  version = "0.12.4";
-  format = "setuptools";
   pname = "htseq";
+  version = "2.0.4";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "htseq";
     repo = "htseq";
     rev = "release_${version}";
-    sha256 = "0y7vh249sljqjnv81060w4xkdx6f1y5zdqkh38yk926x6v9riijm";
+    hash = "sha256-7ocrmuj9LOtPz9XbI5rKGcdE5JbFz/pZh00Nie65XxE=";
   };
 
-  nativeBuildInputs = [ cython ];
-  propagatedBuildInputs = [ numpy pysam matplotlib ];
+  patches = [
+    # https://github.com/htseq/htseq/pull/84
+    (fetchpatch {
+      name = "replace-distutils-with-sysconfig.patch";
+      url = "https://github.com/htseq/htseq/commit/f0f1e464ee9aee56f0b44f905e7b3355b0bb8f29.patch";
+      hash = "sha256-yDYkXCPy+YFgnk1rnXwCB998aZwVd5nJeejZIgeEzAo=";
+     })
+  ];
 
-  checkPhase = lib.optionalString isPy27 ''
-    ${python.interpreter} python2/test/test_general.py
-  '' + lib.optionalString isPy3k ''
-    ${python.interpreter} python3/test/test_general.py
+  nativeBuildInputs = [ swig ];
+
+  build-system = [
+    cython
+    numpy
+    pysam
+    setuptools
+  ];
+
+  dependencies = [
+    numpy
+    pysam
+  ];
+
+  optional-dependencies = {
+    htseq-qa = [ matplotlib ];
+  };
+
+  pythonImportsCheck = [ "HTSeq" ];
+
+  nativeCheckInputs = [
+    pandas
+    pytestCheckHook
+  ] ++ optional-dependencies.htseq-qa;
+
+  preCheck = ''
+    rm -r src HTSeq
+    export PATH=$out/bin:$PATH
   '';
 
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "release_(.+)"
+    ];
+  };
+
   meta = with lib; {
     homepage = "https://htseq.readthedocs.io/";
     description = "A framework to work with high-throughput sequencing data";
     maintainers = with maintainers; [ unode ];
-    platforms = platforms.unix;
   };
 }