guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 4a8c546ab8778fa4072511b4f8216576f3436e95
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Tue Jul 7 12:45:32 2026 +0100
gnu: python-biom-format: Update to 2.1.17-0.0f3855c.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to
0f3855c4af5dd5f33766badd8a6ba2dbdccf29dd commit.
[propagated-inputs]: Remove python-anndata.
---
gnu/packages/bioinformatics.scm | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d87d0db677..31c88bf51d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4286,20 +4286,27 @@ use-case, we encourage users to compose functions to
achieve their goals.")
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.17")
+ ;; 2.1.17 (2025-08-26); the latest changes provide support for fresh NumPy
+ ;; and Pandas., see: <https://github.com/biocore/biom-format/issues/1003>,
+ ;; <https://github.com/biocore/biom-format/issues/1001>.
+ (properties '((commit . "0f3855c4af5dd5f33766badd8a6ba2dbdccf29dd")
+ (revision . "0")))
+ (version (git-version "2.1.17"
+ (assoc-ref properties 'revision)
+ (assoc-ref properties 'commit)))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/biocore/biom-format";)
- (commit version)))
+ (commit (assoc-ref properties 'commit))))
(file-name (git-file-name name version))
(sha256
- (base32 "0fmlrxcn8bgh8wccs2qzz5q08ivd3r3zva9h8zzr1jsbff7904fz"))))
+ (base32 "1hqihr1hkx3g0p71vkzx5sk2k1cwrxhskxzxss6z9vxg1hwn27k0"))))
(build-system pyproject-build-system)
(arguments
(list
- ;; tests: 380 passed, 4 skipped, 16 warnings
+ ;; tests: 378 passed, 7 skipped, 7 warnings
#:test-flags
;; Doctests depend on Nose.
#~(list "--ignore=doc/sphinxext/numpydoc/numpydoc/tests/")
@@ -4322,9 +4329,7 @@ use-case, we encourage users to compose functions to
achieve their goals.")
python-h5py
python-numpy
python-pandas
- python-scipy
- ;; [optional]
- python-anndata))
+ python-scipy))
(home-page "https://www.biom-format.org";)
(synopsis "Biological Observation Matrix (BIOM) format utilities")
(description
