diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-12-29 14:47:42 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:19:47 +0100 |
| commit | 9d660798bd5af0b8fed6ab28e4675e5f4bde400f (patch) | |
| tree | af3c2ee6b4225c9a1b10c0d115bb10fec55747f5 /gnu | |
| parent | af61727fd2ae33aa8b4b32b3853deb9eb1ff8805 (diff) | |
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
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 19 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 42a18fafabc..db20d741052 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6832,44 +6832,40 @@ 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 |