python3Packages.mhcflurry: 2.1.5 -> 2.2.0

  buildPythonPackage,

  fetchFromGitHub,

  # build-system

  setuptools,

  # dependencies

  appdirs,

  keras,

  mhcgnomes,

  numpy,

  pandas,

  pyyaml,

  scikit-learn,

  tensorflow,

  tf-keras,

  torch,

  tqdm,

  # tests

  pytestCheckHook,

}:

buildPythonPackage rec {

buildPythonPackage (finalAttrs: {

  pname = "mhcflurry";

  version = "2.1.5";

  version = "2.2.0";

  pyproject = true;

  src = fetchFromGitHub {

    owner = "openvax";

    repo = "mhcflurry";

    tag = "v${version}";

    hash = "sha256-TNb3oKZvgBuXoSwsTuEJjFKEVZyHynazuPInj7wVKs8=";

    tag = "v${finalAttrs.version}";

    hash = "sha256-xtxPQg4Hsu7PzbXdjf0MlEaOYeAZaMG3gSNsa6l9RiM=";

  };

  # pipes has been removed in python 3.13

  postPatch = ''

    substituteInPlace mhcflurry/downloads.py \

      --replace-fail \

        "from pipes import quote" \

        "from shlex import quote"

  '';

  build-system = [

    setuptools

  ];

  # keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.

  dependencies = [

    appdirs

    keras

    mhcgnomes

    numpy

    pandas

    pyyaml

    scikit-learn

    tensorflow

    tf-keras

    torch

    tqdm

  ];

    "test_a1_mage_epitope_downloaded_models"

    "test_a1_titin_epitope_downloaded_models"

    "test_a2_hiv_epitope_downloaded_models"

    "test_allele_specific_affinity_predictions"

    "test_basic"

    "test_caching"

    "test_class1_neural_network_a0205_training_accuracy"

    "test_commandline_sequences"

    "test_correlation"

    "test_csv"

    "test_downloaded_predictor"

    "test_downloaded_predictor_gives_percentile_ranks"

    "test_downloaded_predictor_invalid_peptides"

    "test_downloaded_predictor_is_savable"

    "test_downloaded_predictor_is_serializable"

    "test_downloaded_predictor_small"

    "test_downloaded_predictor"

    "test_fasta"

    "test_fasta_50nm"

    "test_fasta_best"

    "test_fasta"

    "test_merge"

    "test_no_csv"

    "test_on_hpv"

    "test_pan_allele_affinity_predictions"

    "test_presentation_predictions"

    "test_run_cluster_parallelism"

    "test_run_parallel"

    "test_run_serial"

    "test_selected_peptides_mhcflurry_matches_csv"

    "test_selected_peptides_netmhcpan_affinity_close"

    "test_speed_allele_specific"

    "test_speed_pan_allele"

  ];

  meta = {

    description = "Peptide-MHC I binding affinity prediction";

    homepage = "https://github.com/openvax/mhcflurry";

    changelog = "https://github.com/openvax/mhcflurry/releases/tag/v${version}";

    changelog = "https://github.com/openvax/mhcflurry/releases/tag/${finalAttrs.src.tag}";

    license = lib.licenses.asl20;

    maintainers = with lib.maintainers; [ samuela ];

  };

}

})