python3Packages.meeko: 0.6.1 -> 0.7.1 (#472667)

{

  lib,

  stdenv,

  buildPythonPackage,

  fetchFromGitHub,

  # build-system

  setuptools,

  # dependencies

  gemmi,

  numpy,

  pytestCheckHook,

  pythonOlder,

  rdkit,

  scipy,

  # tests

  pytestCheckHook,

}:

buildPythonPackage rec {

  pname = "meeko";

  version = "0.6.1";

  format = "setuptools";

  disabled = pythonOlder "3.5";

  version = "0.7.1";

  pyproject = true;

  src = fetchFromGitHub {

    owner = "forlilab";

    repo = "Meeko";

    tag = "v${version}";

    hash = "sha256-ViIBiczwxTwraYn8UnFAZFCFT28v3WEYm04W2YpU/4g=";

    hash = "sha256-ObGUUNzfK2k37uJ/aY3DHf9BlJ1nzqTe6tHvV2rj1og=";

  };

  propagatedBuildInputs = [

    # setup.py only requires numpy but others are needed at runtime

  build-system = [

    setuptools

  ];

  dependencies = [

    gemmi

    numpy

    rdkit

  nativeCheckInputs = [ pytestCheckHook ];

  disabledTests = [

    # Require internet connection

    "test_add_variants"

    "test_build_noncovalent_CC"

    # AssertionError: assert {'chosen_by_d...ond': [], ...} == {'chosen_by_d...ond': [], ...}

    "test_polymer_encoding_decoding"

  ]

  ++ lib.optionals stdenv.hostPlatform.isDarwin [

    # AssertionError: assert 'altloc' in 'updated 1 h positions but deleted 11

    "test_AHHY_all_static_residues"

    "test_AHHY_flex_residues"

    "test_AHHY_flexibilize_then_parameterize"

    "test_AHHY_mk_prep_and_export"

    "test_AHHY_mutate_residues"

    "test_AHHY_padding"

    "test_disulfide_adjacent"

    "test_disulfides"

    "test_export_sidechains_no_idxmap"

    "test_insertion_code"

    "test_just_three_padded_mol"

    "test_monomer_encoding_decoding"

    "test_pdbqt_writing_from_decoded_polymer"

    "test_rdkit_molsetup_encoding_decoding"

    "test_residue_chem_templates_encoding_decoding"

    "test_residue_padder_encoding_decoding"

    "test_residue_template_encoding_decoding"

    "test_stitch_polymer"

    "test_write_pdb_1igy"

    "test_write_pdb_AHHY"

    # RuntimeError: Updated 1 H positions but deleted 10

    "test_altloc"

  ];

  pythonImportsCheck = [ "meeko" ];

  meta = {