Merge pull request #243406 from samuela/samuela/mhcflurry

python3Packages.mhcflurry: init at 2.0.6

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

@@ -0,0 +1,99 @@
+{ appdirs
+, buildPythonPackage
+, fetchFromGitHub
+, keras
+, lib
+, mhcgnomes
+, nose
+, pandas
+, pytestCheckHook
+, pythonRelaxDepsHook
+, pyyaml
+, scikit-learn
+, tensorflow
+, tqdm
+}:
+
+buildPythonPackage rec {
+  pname = "mhcflurry";
+  version = "2.0.6";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "openvax";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-Cr7L6uo6Kc1PSeG5nK6zQSD7eeCFcUJUzhsX+waz7og=";
+  };
+
+  nativeBuildInputs = [ pythonRelaxDepsHook ];
+
+  pythonRemoveDeps = [
+    # See https://github.com/openvax/mhcflurry/issues/216.
+    "np-utils"
+  ];
+
+  # 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"
+
+    # See https://github.com/openvax/mhcflurry/issues/217
+    "test_more"
+    "test_small"
+  ];
+
+  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 ];
+  };
+}

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

@@ -0,0 +1,33 @@
+{ buildPythonPackage
+, fetchFromGitHub
+, lib
+, pandas
+, pyyaml
+, serializable
+}:
+
+buildPythonPackage rec {
+  pname = "mhcgnomes";
+  version = "1.8.6";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "pirl-unc";
+    repo = pname;
+    # 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=";
+  };
+
+  propagatedBuildInputs = [ pandas pyyaml serializable ];
+
+  pythonImportsCheck = [ "mhcgnomes" ];
+
+  meta = with lib; {
+    description = "Parsing MHC nomenclature in the wild";
+    homepage = "https://github.com/pirl-unc/mhcgnomes";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ samuela ];
+  };
+}

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

@@ -0,0 +1,33 @@
+{ buildPythonPackage
+, fetchFromGitHub
+, lib
+, simplejson
+, six
+, typechecks
+}:
+
+buildPythonPackage rec {
+  pname = "serializable";
+  version = "unstable-2023-07-13";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "iskandr";
+    repo = pname;
+    # See https://github.com/iskandr/serializable/issues/7. As of 2023-07-13,
+    # they do no have version tags.
+    rev = "ed309a6f8f2590b525fc0f93c00549223c8c944f";
+    hash = "sha256-AXlgIc1B7bkR+joXn6ZSxk/t848CWlgVZp8WIsSZFKQ=";
+  };
+
+  propagatedBuildInputs = [ simplejson six typechecks ];
+
+  pythonImportsCheck = [ "serializable" ];
+
+  meta = with lib; {
+    description = "Base class with serialization methods for user-defined Python objects";
+    homepage = "https://github.com/iskandr/serializable";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ samuela ];
+  };
+}

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

@@ -0,0 +1,28 @@
+{ buildPythonPackage
+, fetchFromGitHub
+, lib
+}:
+
+buildPythonPackage rec {
+  pname = "typechecks";
+  version = "unstable-2023-07-13";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "openvax";
+    repo = pname;
+    # See https://github.com/openvax/typechecks/issues/2. As of 2023-07-13,
+    # they do no have version tags.
+    rev = "5340b4e8a2f419b3a7aa816a5b19e2e0a6ce0679";
+    hash = "sha256-GdmBtkyuzLfpk6oneWgJ5M1bnhGJ5/lSbGliwoAQWZs=";
+  };
+
+  pythonImportsCheck = [ "typechecks" ];
+
+  meta = with lib; {
+    description = "Type checking helpers for Python";
+    homepage = "https://github.com/openvax/typechecks";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ samuela ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -6377,6 +6377,10 @@ self: super: with self; {
 
   mf2py = callPackage ../development/python-modules/mf2py { };
 
+  mhcflurry = callPackage ../development/python-modules/mhcflurry { };
+
+  mhcgnomes = callPackage ../development/python-modules/mhcgnomes { };
+
   micawber = callPackage ../development/python-modules/micawber { };
 
   microdata = callPackage ../development/python-modules/microdata { };
@@ -11327,6 +11331,8 @@ self: super: with self; {
 
   serialio = callPackage ../development/python-modules/serialio { };
 
+  serializable = callPackage ../development/python-modules/serializable { };
+
   serpent = callPackage ../development/python-modules/serpent { };
 
   serpy = callPackage ../development/python-modules/serpy { };
@@ -12789,6 +12795,8 @@ self: super: with self; {
 
   txzmq = callPackage ../development/python-modules/txzmq { };
 
+  typechecks = callPackage ../development/python-modules/typechecks { };
+
   typecode = callPackage ../development/python-modules/typecode { };
 
   typecode-libmagic = callPackage ../development/python-modules/typecode/libmagic.nix {