Merge pull request #308478 from natsukium/htseq/update

{ 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;

  };

}