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{ appdirs
, buildPythonPackage
, fetchFromGitHub
, keras
, lib
, mhcgnomes
, nose
, pandas
, pytestCheckHook
, pyyaml
, scikit-learn
, tensorflow
, tqdm
}:
buildPythonPackage rec {
pname = "mhcflurry";
version = "2.1.0";
format = "setuptools";
src = fetchFromGitHub {
owner = "openvax";
repo = pname;
rev = "refs/tags/v${version}";
hash = "sha256-VyPHcNlZYgNJZb2UBFX55x+nE0GnHixkcsiTNjDCju0=";
};
# keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.
propagatedBuildInputs = [
appdirs
keras
mhcgnomes
pandas
pyyaml
scikit-learn
tensorflow
tqdm
];
nativeCheckInputs = [ nose pytestCheckHook ];
disabledTests = [
# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
"test_a1_mage_epitope_downloaded_models"
"test_a1_titin_epitope_downloaded_models"
"test_a2_hiv_epitope_downloaded_models"
"test_basic"
"test_caching"
"test_class1_neural_network_a0205_training_accuracy"
"test_commandline_sequences"
"test_correlation"
"test_csv"
"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_50nm"
"test_fasta_best"
"test_fasta"
"test_merge"
"test_no_csv"
"test_on_hpv"
"test_run_cluster_parallelism"
"test_run_parallel"
"test_run_serial"
"test_speed_allele_specific"
"test_speed_pan_allele"
];
disabledTestPaths = [
# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
"test/test_changing_allele_representations.py"
"test/test_class1_affinity_predictor.py"
"test/test_class1_pan.py"
];
pythonImportsCheck = [ "mhcflurry" ];
meta = with lib; {
description = "Peptide-MHC I binding affinity prediction";
homepage = "https://github.com/openvax/mhcflurry";
license = licenses.asl20;
maintainers = with maintainers; [ samuela ];
};
}
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