From 18aaa982c1aacc3d52775a6dc6d2c9e028b3765b Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Sun, 19 Oct 2025 16:35:35 +0200
Subject: [PATCH] gnu: python-omnipath: Update to 1.0.10.

* gnu/packages/python-web.scm (python-omnipath): Update to 1.0.10. Style package.
[arguments][test-flags]: Enable now passing test.
[arguments][phase]: Remove custom phase pretend-version.
[native-inputs]: Remove python-setuptools, python-setuptools-scm, python-tox, and
python-wheel; add python-hatchling.

Change-Id: Ia209644349a18ceabb37b9c3c557288a627f6aa7
---
 gnu/packages/python-web.scm | 112 +++++++++++++++---------------------
 1 file changed, 47 insertions(+), 65 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0675386675..0beff7d6e0 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -4140,72 +4140,54 @@ Python’s.")
     (license license:bsd-3)))
 
 (define-public python-omnipath
-  ;; The latest release is incompatible with Numpy 2 and pretty old.  A new
-  ;; release is expected soon.
-  (let ((commit "3d1613493aa1554618fb2d7297f82e034b7694ce")
-        (revision "0"))
-    (package
-      (name "python-omnipath")
-      (version (git-version "1.0.8" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/saezlab/omnipath/")
-                      (commit commit)))
-                (file-name (git-file-name name commit))
-                (sha256
-                 (base32
-                  "03lqbgqihglh9mmp7lwmar26fcnsb1qaidrzbmp0z2wvsrgi4fg7"))))
-      (build-system pyproject-build-system)
-      (arguments
-       (list
-        #:test-flags
-        '(list "-k"
-               (string-append
-                ;; These require internet access
-                "not test_download_homologene"
-                " and not test_complex_genes"
-                ;; Arrays are not equal: Mismatched elements: 4759 / 255465 (1.86%)
-                " and not test_import_intercell_network"))
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-before 'build 'pretend-version
-              ;; The version string is usually derived via setuptools-scm, but
-              ;; without the git metadata available, the version string is set
-              ;; to '0.0.0'.
-              (lambda _
-                (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
-                        #$(version-major+minor (package-version this-package)))))
-            (add-after 'unpack 'set-home
-              (lambda _ (setenv "HOME" "/tmp"))))))
-      (propagated-inputs
-       (list python-attrs
-             python-docrep
-             python-inflect
-             python-networkx
-             python-packaging
-             python-pandas
-             python-requests
-             python-tqdm
-             python-typing-extensions
-             python-urllib3
-             python-wrapt))
-      (native-inputs
-       (list nss-certs-for-test
-             python-bump2version
-             python-pytest
-             python-pytest-mock
-             python-pytest-socket
-             python-requests-mock
-             python-setuptools
-             python-setuptools-scm
-             python-tox
-             python-wheel))
-      (home-page "https://omnipathdb.org/")
-      (synopsis "Python client for the OmniPath web service")
-      (description "This package provides a Python client for the OmniPath web
+  (package
+    (name "python-omnipath")
+    (version "1.0.10")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/saezlab/omnipath/")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0jnc7nsn6n5hqx5wlk928b7xmg0mpfqy8al9w2p707ihcwh4s1rf"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags '(list "-k"
+                          (string-append
+                           ;; These require internet access
+                           "not test_download_homologene"
+                           " and not test_complex_genes"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-home
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
+    (propagated-inputs (list python-attrs
+                             python-docrep
+                             python-inflect
+                             python-networkx
+                             python-packaging
+                             python-pandas
+                             python-requests
+                             python-tqdm
+                             python-typing-extensions
+                             python-urllib3
+                             python-wrapt))
+    (native-inputs (list nss-certs-for-test
+                         python-bump2version
+                         python-hatchling
+                         python-pytest
+                         python-pytest-mock
+                         python-pytest-socket
+                         python-requests-mock))
+    (home-page "https://omnipathdb.org/")
+    (synopsis "Python client for the OmniPath web service")
+    (description "This package provides a Python client for the OmniPath web
 service.")
-      (license license:expat))))
+    (license license:expat)))
 
 (define-public python-openai
   (package