python3Packages.mhcflurry: 2.1.5 -> 2.2.0 (#503862)

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

@@ -3,53 +3,48 @@
   buildPythonPackage,
   fetchFromGitHub,
 
+  # build-system
+  setuptools,
+
   # dependencies
   appdirs,
-  keras,
   mhcgnomes,
   numpy,
   pandas,
   pyyaml,
   scikit-learn,
-  tensorflow,
-  tf-keras,
+  torch,
   tqdm,
 
   # tests
   pytestCheckHook,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "mhcflurry";
-  version = "2.1.5";
+  version = "2.2.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "openvax";
     repo = "mhcflurry";
-    tag = "v${version}";
-    hash = "sha256-TNb3oKZvgBuXoSwsTuEJjFKEVZyHynazuPInj7wVKs8=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-xtxPQg4Hsu7PzbXdjf0MlEaOYeAZaMG3gSNsa6l9RiM=";
   };
 
-  # pipes has been removed in python 3.13
-  postPatch = ''
-    substituteInPlace mhcflurry/downloads.py \
-      --replace-fail \
-        "from pipes import quote" \
-        "from shlex import quote"
-  '';
+  build-system = [
+    setuptools
+  ];
 
   # 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
+    torch
     tqdm
   ];
 
@@ -62,27 +57,32 @@ buildPythonPackage rec {
     "test_a1_mage_epitope_downloaded_models"
     "test_a1_titin_epitope_downloaded_models"
     "test_a2_hiv_epitope_downloaded_models"
+    "test_allele_specific_affinity_predictions"
     "test_basic"
     "test_caching"
     "test_class1_neural_network_a0205_training_accuracy"
     "test_commandline_sequences"
     "test_correlation"
     "test_csv"
+    "test_downloaded_predictor"
     "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"
     "test_fasta_50nm"
     "test_fasta_best"
-    "test_fasta"
     "test_merge"
     "test_no_csv"
     "test_on_hpv"
+    "test_pan_allele_affinity_predictions"
+    "test_presentation_predictions"
     "test_run_cluster_parallelism"
     "test_run_parallel"
     "test_run_serial"
+    "test_selected_peptides_mhcflurry_matches_csv"
+    "test_selected_peptides_netmhcpan_affinity_close"
     "test_speed_allele_specific"
     "test_speed_pan_allele"
   ];
@@ -99,8 +99,8 @@ buildPythonPackage rec {
   meta = {
     description = "Peptide-MHC I binding affinity prediction";
     homepage = "https://github.com/openvax/mhcflurry";
-    changelog = "https://github.com/openvax/mhcflurry/releases/tag/v${version}";
+    changelog = "https://github.com/openvax/mhcflurry/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ samuela ];
   };
-}
+})

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

@@ -1,38 +1,52 @@
 {
+  lib,
   buildPythonPackage,
   fetchFromGitHub,
-  lib,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   pandas,
   pyyaml,
-  serializable,
+  numpy,
+
+  # tests
+  pytestCheckHook,
 }:
 
-buildPythonPackage {
+buildPythonPackage (finalAttrs: {
   pname = "mhcgnomes";
-  version = "1.8.6";
-  format = "setuptools";
+  version = "3.15.1";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "pirl-unc";
     repo = "mhcgnomes";
-    # 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=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-tcJfGIJsbCdN+U/+2zsYBhKEJNy55QMf7eu9Z4nuXlk=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [
+    setuptools
+  ];
+
+  dependencies = [
     pandas
     pyyaml
-    serializable
+    numpy
   ];
 
   pythonImportsCheck = [ "mhcgnomes" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
   meta = {
     description = "Parsing MHC nomenclature in the wild";
     homepage = "https://github.com/pirl-unc/mhcgnomes";
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ samuela ];
   };
-}
+})