python311Packages.scikit-bio: unbreak, refactor, run tests, adopt

{

  lib,

  buildPythonPackage,

  fetchPypi,

  fetchFromGitHub,

  setuptools,

  cython,

  lockfile,

  cachecontrol,

  oldest-supported-numpy,

  requests,

  decorator,

  h5py,

  ipython,

  matplotlib,

  natsort,

  numpy,

  pandas,

  scipy,

  h5py,

  hdmedians,

  scikit-learn,

  coverage,

  biom-format,

  python,

  isPy3k,

  pytestCheckHook,

}:

buildPythonPackage rec {

  version = "0.6.0";

  format = "setuptools";

  pname = "scikit-bio";

  disabled = !isPy3k;

  version = "0.6.0";

  pyproject = true;

  src = fetchPypi {

    inherit pname version;

    hash = "sha256-EBBafDwVrlkQJEkn8punqjUjSxnr5lE7hIRUc0OywQ8=";

  src = fetchFromGitHub {

    owner = "scikit-bio";

    repo = "scikit-bio";

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

    hash = "sha256-v8/r52pJpMi34SekPQBf7CqRbs+ZEyPR3WO5RBB7uKg=";

  };

  nativeBuildInputs = [ cython ];

  nativeCheckInputs = [ coverage ];

  propagatedBuildInputs = [

    lockfile

    cachecontrol

  build-system = [

    setuptools

    cython

    oldest-supported-numpy

  ];

  dependencies = [

    requests

    decorator

    ipython

    matplotlib

    natsort

    numpy

    pandas

    scipy

    h5py

    hdmedians

    scikit-learn

    biom-format

  ];

  # cython package not included for tests

  doCheck = false;

  nativeCheckInputs = [ pytestCheckHook ];

  checkPhase = ''

    ${python.interpreter} -m skbio.test

  '';

  # only the $out dir contains the built cython extensions, so we run the tests inside there

  pytestFlagsArray = [ "${placeholder "out"}/${python.sitePackages}/skbio" ];

  pythonImportsCheck = [ "skbio" ];

  meta = with lib; {

  meta = {

    homepage = "http://scikit-bio.org/";

    description = "Data structures, algorithms and educational resources for bioinformatics";

    license = licenses.bsd3;

    platforms = [

      "x86_64-linux"

      "x86_64-darwin"

    ];

    maintainers = [ ];

    license = lib.licenses.bsd3;

    maintainers = with lib.maintainers; [ tomasajt ];

  };

}