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6ca3d33d79
Diff: https://github.com/openvax/mhcflurry/compare/v2.2.0...v2.2.1 Changelog: https://github.com/openvax/mhcflurry/releases/tag/v2.2.1
107 lines
2.5 KiB
Nix
107 lines
2.5 KiB
Nix
{
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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# build-system
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setuptools,
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# dependencies
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appdirs,
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mhcgnomes,
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numpy,
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pandas,
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pyyaml,
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scikit-learn,
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torch,
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tqdm,
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# tests
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pytestCheckHook,
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}:
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buildPythonPackage (finalAttrs: {
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pname = "mhcflurry";
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version = "2.2.1";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "openvax";
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repo = "mhcflurry";
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tag = "v${finalAttrs.version}";
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hash = "sha256-Vtlj6aK4o7rjhWeTaso/RBZWZFdoZy54AlTrYWUoGfE=";
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};
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build-system = [
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setuptools
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];
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# keras and tensorflow are not in the official setup.py requirements but are required for the CLI utilities to run.
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dependencies = [
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appdirs
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mhcgnomes
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numpy
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pandas
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pyyaml
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scikit-learn
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torch
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tqdm
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];
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nativeCheckInputs = [
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pytestCheckHook
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];
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disabledTests = [
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# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
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"test_a1_mage_epitope_downloaded_models"
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"test_a1_titin_epitope_downloaded_models"
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"test_a2_hiv_epitope_downloaded_models"
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"test_allele_specific_affinity_predictions"
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"test_basic"
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"test_caching"
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"test_class1_neural_network_a0205_training_accuracy"
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"test_commandline_sequences"
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"test_correlation"
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"test_csv"
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"test_downloaded_predictor"
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"test_downloaded_predictor_gives_percentile_ranks"
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"test_downloaded_predictor_invalid_peptides"
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"test_downloaded_predictor_is_savable"
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"test_downloaded_predictor_is_serializable"
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"test_downloaded_predictor_small"
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"test_fasta"
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"test_fasta_50nm"
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"test_fasta_best"
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"test_merge"
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"test_no_csv"
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"test_on_hpv"
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"test_pan_allele_affinity_predictions"
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"test_presentation_predictions"
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"test_run_cluster_parallelism"
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"test_run_parallel"
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"test_run_serial"
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"test_selected_peptides_mhcflurry_matches_csv"
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"test_selected_peptides_netmhcpan_affinity_close"
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"test_speed_allele_specific"
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"test_speed_pan_allele"
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];
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disabledTestPaths = [
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# RuntimeError: Missing MHCflurry downloadable file: /homeless-shelter/.local...
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"test/test_changing_allele_representations.py"
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"test/test_class1_affinity_predictor.py"
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"test/test_class1_pan.py"
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];
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pythonImportsCheck = [ "mhcflurry" ];
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meta = {
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description = "Peptide-MHC I binding affinity prediction";
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homepage = "https://github.com/openvax/mhcflurry";
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changelog = "https://github.com/openvax/mhcflurry/releases/tag/${finalAttrs.src.tag}";
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license = lib.licenses.asl20;
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maintainers = with lib.maintainers; [ samuela ];
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};
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})
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