From d4ebd06e80f226ffb736f5b494077cb691fb2c9e Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Fri, 2 Jan 2026 23:56:39 +0000
Subject: [PATCH] gnu: python-pomegranate: Update to 1.1.0.

* gnu/packages/python-xyz.scm (python-pomegranate): Update to 1.1.0.
[source]: Switch to git-fetch providing tests.
[arguments] <tests?, test-flags>: Enable them.
[propagated-inputs]: Remove python-joblib and python-pyyaml; add
python-apricot-select, python-scikit-learn, and python-pytorch.
[native-inputs]: Remove python-pandas and python-wheel; add
python-pytest.

Change-Id: Idf53aff2124c98fd7dc1172a31028a57347d2a4b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
---
 gnu/packages/python-xyz.scm | 75 +++++++++++++++++++++++++------------
 1 file changed, 52 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f4c6edec0465336005e2d7122ffb240159038f8c..2811789841487b84d360a6eaa45d61fadedcae5d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7459,34 +7459,63 @@ a certain expected condition.")
 (define-public python-pomegranate
   (package
     (name "python-pomegranate")
-    (version "0.14.8")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pomegranate" version))
-              (sha256
-               (base32
-                "0gb9srkbxzlkjyfizvxkw5y0bvnfcyiaxapz0hrdaba8j096b5i2"))
-              (modules '((guix build utils)))
-              ;; Delete generated Cython C files.
-              (snippet
-               '(for-each delete-file (find-files "." "\\.c$")))))
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/jmschrei/pomegranate")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0arx5wik4ywna7k7g5y3ggwz98fl1hgap0278pph3c77ap8afqd7"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; XXX: Update to python@3.11 broke some python-nose functionality.
-      ;; Tests are broken but the package itself is most likely fine.
-      #:tests? #f))
-    (propagated-inputs
-     (list python-joblib
-           python-networkx
-           python-numpy
-           python-pyyaml
-           python-scipy))
+      ;; tests: 830 passed, 19 deselected, 529 warnings
+      #:test-flags
+      #~(list #$@(map (lambda (test) (string-append "--deselect="
+                                                    "tests/distributions/"
+                                                    test))
+                      ;; _pickle.UnpicklingError: Weights only load failed.
+                      (list "test_bernoulli.py::test_serialization"
+                            "test_categorical.py::test_serialization"
+                            "test_exponential.py::test_serialization"
+                            "test_gamma.py::test_serialization"
+                            "test_independent_component.py::test_serialization"
+                            "test_normal_diagonal.py::test_serialization"
+                            "test_normal_full.py::test_serialization"
+                            "test_poisson.py::test_serialization"
+                            "test_student_t.py::test_serialization"
+                            "test_uniform.py::test_serialization"
+                            ;; Arrays are not almost equal to 3 decimals
+                            "test_categorical.py::test_sample"
+                            "test_independent_component.py::test_sample"
+                            "test_joint_categorical.py::test_sample"
+                            "test_joint_categorical.py::test_sample"))
+              #$@(map (lambda (test) (string-append "--deselect="
+                                                    "tests/"
+                                                    test))
+                      ;; _pickle.UnpicklingError: Weights only load failed.
+                      (list "test_bayes_classifier.py::test_serialization"
+                            "test_gmm.py::test_serialization"
+                            "test_kmeans.py::test_serialization"
+                            ;; Arrays are not almost equal to 3 decimals
+                            "test_bayesian_network.py::test_sample"
+                            "test_gmm.py::test_sample"
+                            "test_markov_chain.py::test_sample"
+                            "test_markov_chain.py::test_sample")))))
     (native-inputs
      (list python-cython
-           python-pandas
-           python-setuptools
-           python-wheel))
+           python-pytest
+           python-setuptools))
+    (propagated-inputs
+     (list python-apricot-select
+	   python-networkx
+	   python-numpy
+	   python-scikit-learn
+	   python-scipy
+	   python-pytorch))
     (home-page "https://pypi.python.org/pypi/pomegranate/")
     (synopsis "Graphical models library for Python")
     (description