guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 7bd496fe221391bbc80c1f2278e1737486ca9c12
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 29 14:47:42 2025 +0000
gnu: python-scikit-bio: Update to 0.7.1.post1.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to
0.7.1.post1.
[arguments] <test-backend, test-flags>: Use 'custom, run all tests.
<phases>: Remove 'build-extensions; use default 'check; add
'remove-local-source.
[propagated-inputs]: Remove python-hdmedians; add
python-array-api-compat, python-patsy, and python-statsmodels.
[native-inputs]: Remove python-coverage; add python-cython and
python-setuptools.
Change-Id: I460ba8dd7362f5d4bbf16a5923403ecbf5fc2026
---
gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++----------------------
1 file changed, 19 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cd9b7d03ce..b2c87d022e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6831,44 +6831,40 @@ and record oriented data modeling and the Semantic
Web.")
(define-public python-scikit-bio
(package
(name "python-scikit-bio")
- (version "0.6.0")
+ (version "0.7.1.post1")
(source (origin
(method url-fetch)
- (uri (pypi-uri "scikit-bio" version))
+ (uri (pypi-uri "scikit_bio" version))
(sha256
(base32
- "03y1n91p6m44hhxm3rpb355j6ddalydz49s94h85kbhm7iy5l40h"))))
+ "15czagyilqxj68ivqi9slnz2brs0nn4a18swx8vjhj8inwc29nfb"))))
(build-system pyproject-build-system)
(arguments
(list
- #:test-flags
- ;; Accuracy problem
- '(list "-k" (string-append "not test_fisher_alpha"
- ;; UNEXPECTED EXCEPTION: ValueError("could
- ;; not convert string to float: 'gut'")
- " and not skbio.diversity"))
+ ;; tests: 3336 passed, 105 skipped, 73 warnings
+ #:test-backend #~'custom
+ #:test-flags #~(list "-m" "skbio.test")
#:phases
- '(modify-phases %standard-phases
- (add-before 'check 'build-extensions
- (lambda _
- ;; Cython extensions have to be built before running the tests.
- (invoke "python3" "setup.py" "build_ext" "--inplace")))
- (replace 'check
- (lambda* (#:key tests? test-flags #:allow-other-keys)
- (when tests?
- (apply invoke "python3" "-m" "skbio.test" test-flags)))))))
+ #~(modify-phases %standard-phases
+ (add-before 'check 'remove-local-source
+ (lambda _
+ (delete-file-recursively "skbio"))))))
+ (native-inputs
+ (list python-cython
+ python-pytest
+ python-setuptools))
(propagated-inputs
- (list python-biom-format
+ (list python-array-api-compat
+ python-biom-format
python-decorator
python-h5py
- python-hdmedians
python-natsort
python-numpy
python-pandas
+ python-patsy
python-requests
- python-scipy))
- (native-inputs
- (list python-coverage python-pytest))
+ python-scipy
+ python-statsmodels))
(home-page "https://scikit-bio.org";)
(synopsis "Data structures, algorithms and educational resources for
bioinformatics")
(description
