Merge pull request #309586 from TomaSajt/scikit-bio

{

  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 ];

  };

}

{ lib

, buildPythonPackage

, fetchPypi

, cython

, lockfile

, cachecontrol

, decorator

, h5py

, ipython

, matplotlib

, natsort

, numpy

, pandas

, scipy

, hdmedians

, scikit-learn

, coverage

, python

, isPy3k

{

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  setuptools,

  cython,

  oldest-supported-numpy,

  requests,

  decorator,

  natsort,

  numpy,

  pandas,

  scipy,

  h5py,

  hdmedians,

  biom-format,

  python,

  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 decorator ipython matplotlib natsort numpy pandas scipy h5py hdmedians scikit-learn ];

  build-system = [

    setuptools

    cython

    oldest-supported-numpy

  ];

  dependencies = [

    requests

    decorator

    natsort

    numpy

    pandas

    scipy

    h5py

    hdmedians

    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 ];

  };

}

  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 { };