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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09b1910580..0fed480b32 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2978,6 +2978,71 @@ generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.") (license license:asl2.0))) +(define-public python-scikit-bio + (package + (name "python-scikit-bio") + (version "0.5.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "scikit-bio" version)) + (sha256 + (base32 + "1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; See https://github.com/biocore/scikit-bio/pull/1826 + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "skbio/sequence/tests/test_sequence.py" + (("def test_concat_strict_many") + "def _do_not_test_concat_strict_many")) + (substitute* "skbio/stats/distance/_mantel.py" + (("from scipy.stats import PearsonRConstantInputWarning") + "from scipy.stats import ConstantInputWarning") + (("from scipy.stats import PearsonRNearConstantInputWarning") + "from scipy.stats import NearConstantInputWarning") + (("from scipy.stats import SpearmanRConstantInputWarning") "") + (("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)") + "warnings.warn(ConstantInputWarning())") + (("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)") + "warnings.warn(NearConstantInputWarning())") + (("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)") + "warnings.warn(ConstantInputWarning())")) + (substitute* "skbio/diversity/alpha/tests/test_base.py" + (("self.assertEqual\\(pielou_e") + "self.assertAlmostEqual(pielou_e")))) + (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? #:allow-other-keys) + (when tests? (invoke "python3" "-m" "skbio.test"))))))) + (propagated-inputs + (list python-cachecontrol + python-decorator + python-h5py + python-hdmedians + python-ipython + python-lockfile + python-matplotlib + python-natsort + python-numpy + python-pandas + python-scikit-learn + python-scipy)) + (native-inputs + (list python-coverage python-pytest)) + (home-page "https://scikit-bio.org") + (synopsis "Data structures, algorithms and educational resources for bioinformatics") + (description + "This package provides data structures, algorithms and educational +resources for bioinformatics.") + (license license:bsd-3))) + (define-public cwltool (package (name "cwltool") |