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{
lib,
buildPythonPackage,
fetchFromGitHub,
# dependencies
appdirs,
keras,
mhcgnomes,
numpy,
pandas,
pyyaml,
scikit-learn,
tensorflow,
tf-keras,
tqdm,
# tests
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "mhcflurry";
version = "2.1.5";
pyproject = true;
src = fetchFromGitHub {
owner = "openvax";
repo = "mhcflurry";
tag = "v${version}";
hash = "sha256-TNb3oKZvgBuXoSwsTuEJjFKEVZyHynazuPInj7wVKs8=";
};
# pipes has been removed in python 3.13
postPatch = ''
substituteInPlace mhcflurry/downloads.py \
--replace-fail \
"from pipes import quote" \
"from shlex import quote"
'';
# keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.
dependencies = [
appdirs
keras
mhcgnomes
numpy
pandas
pyyaml
scikit-learn
tensorflow
tf-keras
tqdm
];
nativeCheckInputs = [
pytestCheckHook
];
disabledTests = [
# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
"test_a1_mage_epitope_downloaded_models"
"test_a1_titin_epitope_downloaded_models"
"test_a2_hiv_epitope_downloaded_models"
"test_basic"
"test_caching"
"test_class1_neural_network_a0205_training_accuracy"
"test_commandline_sequences"
"test_correlation"
"test_csv"
"test_downloaded_predictor_gives_percentile_ranks"
"test_downloaded_predictor_invalid_peptides"
"test_downloaded_predictor_is_savable"
"test_downloaded_predictor_is_serializable"
"test_downloaded_predictor_small"
"test_downloaded_predictor"
"test_fasta_50nm"
"test_fasta_best"
"test_fasta"
"test_merge"
"test_no_csv"
"test_on_hpv"
"test_run_cluster_parallelism"
"test_run_parallel"
"test_run_serial"
"test_speed_allele_specific"
"test_speed_pan_allele"
];
disabledTestPaths = [
# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
"test/test_changing_allele_representations.py"
"test/test_class1_affinity_predictor.py"
"test/test_class1_pan.py"
];
pythonImportsCheck = [ "mhcflurry" ];
meta = {
description = "Peptide-MHC I binding affinity prediction";
homepage = "https://github.com/openvax/mhcflurry";
changelog = "https://github.com/openvax/mhcflurry/releases/tag/v${version}";
license = lib.licenses.asl20;
maintainers = with lib.maintainers; [ samuela ];
};
}
|
