python311Packages.biom-format: init at 2.1.15

{

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  fetchpatch,

  setuptools,

  cython,

  click,

  numpy,

  scipy,

  pandas,

  h5py,

  pytestCheckHook,

}:

buildPythonPackage rec {

  pname = "biom-format";

  version = "2.1.15";

  pyproject = true;

  src = fetchFromGitHub {

    owner = "biocore";

    repo = "biom-format";

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

    hash = "sha256-WRBc+C/UWme7wYogy4gH4KTIdIqU3KmBm2jWzGNxGQg=";

  };

  patches = [

    # fixes a test, can be removed in next version after 2.1.15

    (fetchpatch {

      name = "fix-dataframe-comparison.patch";

      url = "https://github.com/biocore/biom-format/commit/5d1c921ca2cde5d7332508503ce990a7209d1fdc.patch";

      hash = "sha256-nyHi469ivjJSQ01yIk/6ZMXFdoo9wVuazJHnFdy2nBg=";

    })

  ];

  build-system = [

    setuptools

    cython

    numpy

  ];

  dependencies = [

    click

    numpy

    scipy

    pandas

    h5py

  ];

  # make pytest resolve the package from $out

  # some tests don't work if we change the level of directory nesting

  preCheck = ''

    mkdir biom_tests

    mv biom/tests biom_tests/tests

    rm -r biom

  '';

  nativeCheckInputs = [ pytestCheckHook ];

  pytestFlagsArray = [ "biom_tests/tests" ];

  pythonImportsCheck = [ "biom" ];

  meta = {

    homepage = "http://biom-format.org/";

    description = "Biological Observation Matrix (BIOM) format";

    license = lib.licenses.bsd3;

    maintainers = with lib.maintainers; [ tomasajt ];

  };

}

  binwalk-full = self.binwalk.override { visualizationSupport = true; };

  biom-format = callPackage ../development/python-modules/biom-format { };

  biopandas = callPackage ../development/python-modules/biopandas { };

  biopython = callPackage ../development/python-modules/biopython { };