Unverified Commit 9f7ea2b7 authored by kirillrdy's avatar kirillrdy Committed by GitHub
Browse files

python3Packages.mhcflurry: 2.1.5 -> 2.2.0 (#503862)

parents d75bdbcc 8ee204ce

pkgs/development/python-modules/mhcflurry/default.nix

+21 −21
Original line number Diff line number Diff line
@@ -3,53 +3,48 @@ 
  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

  ];
@@ -62,27 +57,32 @@ buildPythonPackage rec { 
    "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"

  ];
@@ -99,8 +99,8 @@ buildPythonPackage rec { 
  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 ];

  };

}
 
})

pkgs/development/python-modules/mhcgnomes/default.nix

+26 −12
Original line number Diff line number Diff line 
{

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  lib,



  # build-system

  setuptools,



  # dependencies

  pandas,

  pyyaml,

  serializable,

  numpy,



  # tests

  pytestCheckHook,

}:



buildPythonPackage {

buildPythonPackage (finalAttrs: {

  pname = "mhcgnomes";

  version = "1.8.6";

  format = "setuptools";

  version = "3.15.1";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "pirl-unc";

    repo = "mhcgnomes";

    # See https://github.com/pirl-unc/mhcgnomes/issues/20. As of 2023-07-13,

    # they do no have version tags.

    rev = "c7e779b60e35a031f6e0f0ea6ae70e8a8e7671c6";

    hash = "sha256-KKiBlnFlavRnaQnOpAzG0dyxmFB+zF9L6t/H05LkFZE=";

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

    hash = "sha256-tcJfGIJsbCdN+U/+2zsYBhKEJNy55QMf7eu9Z4nuXlk=";

  };



  propagatedBuildInputs = [

  build-system = [

    setuptools

  ];



  dependencies = [

    pandas

    pyyaml

    serializable

    numpy

  ];



  pythonImportsCheck = [ "mhcgnomes" ];



  nativeCheckInputs = [

    pytestCheckHook

  ];



  meta = {

    description = "Parsing MHC nomenclature in the wild";

    homepage = "https://github.com/pirl-unc/mhcgnomes";

    license = lib.licenses.asl20;

    maintainers = with lib.maintainers; [ samuela ];

  };

}
 
})