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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-05-01 00:35:14 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-05-05 22:38:16 +0200 |
| commit | 53b2fe29734c58c0cf4a5ef0ae51a595998d7fa3 (patch) | |
| tree | d78c4a56dceaa88f69a3eac76c4604403772ecaf /gnu/packages/bioinformatics.scm | |
| parent | e9d70b85ebc7088629d6b513da3d48a95e4ec75c (diff) | |
| download | guix-patches-53b2fe29734c58c0cf4a5ef0ae51a595998d7fa3.tar guix-patches-53b2fe29734c58c0cf4a5ef0ae51a595998d7fa3.tar.gz | |
gnu: python-scikit-bio: Update to 0.6.0.
* gnu/packages/patches/python-scikit-bio-1887.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.6.0.
[source]: Remove patch.
[arguments]: Disable skbio.diversity doctest; remove 'compatibility phase.
[propagated-inputs]: Add python-biom-format; remove python-ipython and
python-matplotlib.
Change-Id: I9bd9e0fd72f5f1b80ef6ff61c52da5fd56a715ed
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 20 |
1 files changed, 9 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4b6d85dfba..1d796e31a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5278,25 +5278,24 @@ and record oriented data modeling and the Semantic Web.") (define-public python-scikit-bio (package (name "python-scikit-bio") - (version "0.5.9") + (version "0.6.0") (source (origin (method url-fetch) (uri (pypi-uri "scikit-bio" version)) (sha256 (base32 - "0429060pkyq1pm19zb2n1la7czh7b633mp4a4h01j8zfigf49q3s")) - (patches (search-patches "python-scikit-bio-1887.patch")))) + "03y1n91p6m44hhxm3rpb355j6ddalydz49s94h85kbhm7iy5l40h")))) (build-system pyproject-build-system) (arguments (list + #:test-flags ;; Accuracy problem - #:test-flags '(list "-k" "not test_fisher_alpha") + '(list "-k" (string-append "not test_fisher_alpha" + ;; UNEXPECTED EXCEPTION: ValueError("could + ;; not convert string to float: 'gut'") + " and not skbio.diversity")) #:phases '(modify-phases %standard-phases - (add-after 'unpack 'compatibility - (lambda _ - (substitute* "skbio/diversity/__init__.py" - ((", numeric_only=True") "")))) (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. @@ -5306,11 +5305,10 @@ and record oriented data modeling and the Semantic Web.") (when tests? (apply invoke "python3" "-m" "skbio.test" test-flags))))))) (propagated-inputs - (list python-decorator + (list python-biom-format + python-decorator python-h5py python-hdmedians - python-ipython - python-matplotlib python-natsort python-numpy python-pandas |