Unverified Commit 4c5e107d authored by Emily's avatar Emily Committed by GitHub
Browse files

Merge pull request #330744 from pyrox0/denose/bx-python 

python312Packages.bx-python: Drop nose dependency; modernize
parents 1f27835c a007b9f7

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

+26 −14
Original line number Diff line number Diff line
@@ -2,38 +2,50 @@ 
  lib,

  fetchFromGitHub,

  buildPythonPackage,

  pythonOlder,

  numpy,

  cython,

  zlib,

  python-lzo,

  nose,

  pytestCheckHook,

  setuptools,

  oldest-supported-numpy,

}:



buildPythonPackage rec {

  pname = "bx-python";

  version = "0.11.0";

  format = "setuptools";



  disabled = pythonOlder "3.8";

  version = "0.12.0";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "bxlab";

    repo = "bx-python";

    rev = "refs/tags/v${version}";

    hash = "sha256-evhxh/cCZFSK6EgMu7fC9/ZrPd2S1fZz89ItGYrHQck=";

    hash = "sha256-ZpZjh7OXdUY7rd692h7VYHzC3qCrDKFme6r+wuG7GP4=";

  };



  nativeBuildInputs = [ cython ];

  postPatch = ''

    # pytest-cython, which provides this option, isn't packaged

    substituteInPlace pytest.ini \

      --replace-fail "--doctest-cython" ""

  '';



  build-system = [

    setuptools

    cython

    oldest-supported-numpy

  ];



  buildInputs = [ zlib ];



  propagatedBuildInputs = [

    numpy

  dependencies = [ numpy ];



  nativeCheckInputs = [

    python-lzo

    pytestCheckHook

  ];



  nativeCheckInputs = [ nose ];

  # https://github.com/bxlab/bx-python/issues/101

  doCheck = false;



  postInstall = ''

    cp -r scripts/* $out/bin
@@ -45,12 +57,12 @@ buildPythonPackage rec { 
    ln -s $out/bin scripts

  '';



  meta = with lib; {

  meta = {

    description = "Tools for manipulating biological data, particularly multiple sequence alignments";

    homepage = "https://github.com/bxlab/bx-python";

    changelog = "https://github.com/bxlab/bx-python/releases/tag/v${version}";

    license = licenses.mit;

    maintainers = with maintainers; [ jbedo ];

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [ jbedo ];

    platforms = [ "x86_64-linux" ];

  };

}