python3Packages.dendropy: 4.5.1 -> 5.0.2 (#326199)

{

  lib,

  stdenvNoCC,

  fetchurl,

  autoPatchelfHook,

  curl,

  gfortran,

  zlib,

}:

stdenvNoCC.mkDerivation {

  pname = "paup";

  version = "4.0a168";

  src = fetchurl {

    url = "http://phylosolutions.com/paup-test/paup4a168_centos64.gz";

    hash = "sha256-41dZswlrIQ05f1zJzId78DKmPf0QH1SfrexzvCAUxq8=";

  };

  unpackPhase = ''

    runHook preUnpack

    gunzip -c $src > paup

    runHook postUnpack

  '';

  nativeBuildInputs = [ autoPatchelfHook ];

  buildInputs = [

    curl

    gfortran

    zlib

  ];

  installPhase = ''

    runHook preInstall

    install -Dm755 paup -t $out/bin

    runHook postInstall

  '';

  meta = {

    description = "A software package for inferring evolutionary trees";

    homepage = "http://phylosolutions.com/paup-test/";

    license = lib.licenses.unfree;

    sourceProvenance = [ lib.sourceTypes.binaryNativeCode ];

    maintainers = with lib.maintainers; [ pandapip1 ];

    mainProgram = "paup";

    platforms = [ "x86_64-linux" ];

  };

}

{

  lib,

  stdenv,

  buildPythonPackage,

  fetchFromGitHub,

  pytestCheckHook,

  pythonOlder,

  nix-update-script,

  setuptools,

  paup,

  paupIntegration ? false,

}:

let

  paupPath = if paupIntegration then lib.getExe paup else "NONE";

in

buildPythonPackage rec {

  pname = "dendropy";

  version = "4.5.1";

  format = "setuptools";

  version = "5.0.2";

  disabled = pythonOlder "3.7";

  pyproject = true;

  build-system = [ setuptools ];

  src = fetchFromGitHub {

    owner = "jeetsukumaran";

    repo = pname;

    rev = "v${version}";

    hash = "sha256-FP0+fJkkFtSysPxoHXjyMgF8pPin7aRyzmHe9bH8LlM=";

    repo = "dendropy";

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

    hash = "sha256-OiFei/6226FDtL4w1XrXL2OVn3/hfQwnIhTzM4OneKc=";

  };

  nativeCheckInputs = [ pytestCheckHook ];

  postPatch = ''

    substituteInPlace setup.py \

      --replace '["pytest-runner"],' '[],'

  disabledTests = [

    # FileNotFoundError: [Errno 2] No such file or directory: 'paup'

    "test_basic_split_count_with_incorrect_rootings_raises_error"

    "test_basic_split_count_with_incorrect_weight_treatment_raises_error"

    "test_basic_split_counting_under_different_rootings"

    "test_group1"

    # AssertionError: 6 != 5

    "test_by_num_lineages"

    # AttributeError: module 'collections' has no attribute 'Iterable'

    "test_findall_multiple"

  ];

    substituteInPlace src/dendropy/interop/paup.py \

      --replace 'PAUP_PATH = os.environ.get(metavar.DENDROPY_PAUP_PATH_ENVAR, "paup")' 'PAUP_PATH = os.environ.get(metavar.DENDROPY_PAUP_PATH_ENVAR, "${paupPath}")'

  '';

  nativeCheckInputs = [ pytestCheckHook ];

  pythonImportsCheck = [ "dendropy" ];

  meta = with lib; {

  passthru.updateScript = nix-update-script { };

  meta = {

    description = "Python library for phylogenetic computing";

    homepage = "https://dendropy.org/";

    license = licenses.bsd3;

    maintainers = with maintainers; [ unode ];

    homepage = "https://jeetsukumaran.github.io/DendroPy/";

    license = lib.licenses.bsd3;

    maintainers = with lib.maintainers; [

      unode

      pandapip1

    ];

  };

}