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

   1 {
   2   lib,
   3   buildPythonPackage,
   4   fetchFromGitHub,
   5
   6   # dependencies
   7   appdirs,
   8   keras,
   9   mhcgnomes,
  10   pandas,
  11   pyyaml,
  12   scikit-learn,
  13   tensorflow,
  14   tf-keras,
  15   tqdm,
  16
  17   # tests
  18   pytestCheckHook,
  19 }:
  20
  21 buildPythonPackage rec {
  22   pname = "mhcflurry";
  23   version = "2.1.4";
  24   pyproject = true;
  25
  26   src = fetchFromGitHub {
  27     owner = "openvax";
  28     repo = "mhcflurry";
  29     rev = "refs/tags/v${version}";
  30     hash = "sha256-dxCGCPnk1IFKg8ZVqMJsojQL0KlNirKlHJoaaOYIzMU=";
  31   };
  32
  33   # keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.
  34   dependencies = [
  35     appdirs
  36     keras
  37     mhcgnomes
  38     pandas
  39     pyyaml
  40     scikit-learn
  41     tensorflow
  42     tf-keras
  43     tqdm
  44   ];
  45
  46   # Tests currently depend on nose; see
  47   # <https://github.com/openvax/mhcflurry/pull/244>.
  48   nativeCheckInputs = [
  49     pytestCheckHook
  50   ];
  51
  52   disabledTests = [
  53     # RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
  54     "test_a1_mage_epitope_downloaded_models"
  55     "test_a1_titin_epitope_downloaded_models"
  56     "test_a2_hiv_epitope_downloaded_models"
  57     "test_basic"
  58     "test_caching"
  59     "test_class1_neural_network_a0205_training_accuracy"
  60     "test_commandline_sequences"
  61     "test_correlation"
  62     "test_csv"
  63     "test_downloaded_predictor_gives_percentile_ranks"
  64     "test_downloaded_predictor_invalid_peptides"
  65     "test_downloaded_predictor_is_savable"
  66     "test_downloaded_predictor_is_serializable"
  67     "test_downloaded_predictor_small"
  68     "test_downloaded_predictor"
  69     "test_fasta_50nm"
  70     "test_fasta_best"
  71     "test_fasta"
  72     "test_merge"
  73     "test_no_csv"
  74     "test_on_hpv"
  75     "test_run_cluster_parallelism"
  76     "test_run_parallel"
  77     "test_run_serial"
  78     "test_speed_allele_specific"
  79     "test_speed_pan_allele"
  80   ];
  81
  82   disabledTestPaths = [
  83     # RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
  84     "test/test_changing_allele_representations.py"
  85     "test/test_class1_affinity_predictor.py"
  86     "test/test_class1_pan.py"
  87   ];
  88
  89   pythonImportsCheck = [ "mhcflurry" ];
  90
  91   meta = {
  92     description = "Peptide-MHC I binding affinity prediction";
  93     homepage = "https://github.com/openvax/mhcflurry";
  94     changelog = "https://github.com/openvax/mhcflurry/releases/tag/v${version}";
  95     license = lib.licenses.asl20;
  96     maintainers = with lib.maintainers; [ samuela ];
  97     # Requires a recent version of tensorflow
  98     broken = lib.versionOlder tensorflow.version "2.15.0";
  99   };
 100 }