python3Packages.pomegranate: fix for cnvkit tests.

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

@@ -3,20 +3,15 @@
   stdenv,
   buildPythonPackage,
   fetchFromGitHub,
-
-  # build-system
+  fetchpatch,
+  pytestCheckHook,
   setuptools,
-
-  # dependencies
   apricot-select,
   networkx,
   numpy,
   scikit-learn,
   scipy,
   torch,
-
-  # tests
-  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
@@ -27,34 +22,10 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     repo = "pomegranate";
     owner = "jmschrei";
-    # tag = "v${version}";
-    # No tag for 1.1.2
-    rev = "e9162731f4f109b7b17ecffde768734cacdb839b";
-    hash = "sha256-vVoAoZ+mph11ZfINT+yxRyk9rXv6FBDgxBz56P2K95Y=";
+    tag = "v${version}";
+    hash = "sha256-p2Gn0FXnsAHvRUeAqx4M1KH0+XvDl3fmUZZ7MiMvPSs=";
   };
 
-  # _pickle.UnpicklingError: Weights only load failed.
-  # https://pytorch.org/docs/stable/generated/torch.load.html
-  postPatch = ''
-    substituteInPlace \
-      tests/distributions/test_bernoulli.py \
-      tests/distributions/test_categorical.py \
-      tests/distributions/test_exponential.py \
-      tests/distributions/test_gamma.py \
-      tests/distributions/test_independent_component.py \
-      tests/distributions/test_normal_diagonal.py \
-      tests/distributions/test_normal_full.py \
-      tests/distributions/test_poisson.py \
-      tests/distributions/test_student_t.py \
-      tests/distributions/test_uniform.py \
-      tests/test_bayes_classifier.py \
-      tests/test_gmm.py \
-      tests/test_kmeans.py \
-      --replace-fail \
-        'torch.load(".pytest.torch")' \
-        'torch.load(".pytest.torch", weights_only=False)'
-  '';
-
   build-system = [ setuptools ];
 
   dependencies = [
@@ -72,11 +43,20 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  disabledTestPaths = lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64) [
+  patches = [
+    # Fix tests for pytorch 2.6
+    (fetchpatch {
+      name = "python-2.6.patch";
+      url = "https://github.com/jmschrei/pomegranate/pull/1142/commits/9ff5d5e2c959b44e569937e777b26184d1752a7b.patch";
+      hash = "sha256-BXsVhkuL27QqK/n6Fa9oJCzrzNcL3EF6FblBeKXXSts=";
+    })
+  ];
+
+  pytestFlagsArray = lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64) [
     # AssertionError: Arrays are not almost equal to 6 decimals
-    "=tests/distributions/test_normal_full.py::test_fit"
-    "=tests/distributions/test_normal_full.py::test_from_summaries"
-    "=tests/distributions/test_normal_full.py::test_serialization"
+    "--deselect=tests/distributions/test_normal_full.py::test_fit"
+    "--deselect=tests/distributions/test_normal_full.py::test_from_summaries"
+    "--deselect=tests/distributions/test_normal_full.py::test_serialization"
   ];
 
   disabledTests = [