guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 18aaa982c1aacc3d52775a6dc6d2c9e028b3765b
Author: Hartmut Goebel <[email protected]>
AuthorDate: Sun Oct 19 16:35:35 2025 +0200
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
