gnu: Add python-scikit-bio.
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
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@ -2978,6 +2978,71 @@ (define-public python-schema-salad
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and record oriented data modeling and the Semantic Web.")
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(license license:asl2.0)))
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(define-public python-scikit-bio
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(package
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(name "python-scikit-bio")
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(version "0.5.7")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "scikit-bio" version))
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(sha256
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(base32
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"1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:phases
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'(modify-phases %standard-phases
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;; See https://github.com/biocore/scikit-bio/pull/1826
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(add-after 'unpack 'compatibility
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(lambda _
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(substitute* "skbio/sequence/tests/test_sequence.py"
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(("def test_concat_strict_many")
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"def _do_not_test_concat_strict_many"))
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(substitute* "skbio/stats/distance/_mantel.py"
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(("from scipy.stats import PearsonRConstantInputWarning")
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"from scipy.stats import ConstantInputWarning")
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(("from scipy.stats import PearsonRNearConstantInputWarning")
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"from scipy.stats import NearConstantInputWarning")
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(("from scipy.stats import SpearmanRConstantInputWarning") "")
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(("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)")
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"warnings.warn(ConstantInputWarning())")
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(("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)")
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"warnings.warn(NearConstantInputWarning())")
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(("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)")
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"warnings.warn(ConstantInputWarning())"))
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(substitute* "skbio/diversity/alpha/tests/test_base.py"
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(("self.assertEqual\\(pielou_e")
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"self.assertAlmostEqual(pielou_e"))))
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(add-before 'check 'build-extensions
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(lambda _
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;; Cython extensions have to be built before running the tests.
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(invoke "python3" "setup.py" "build_ext" "--inplace")))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests? (invoke "python3" "-m" "skbio.test")))))))
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(propagated-inputs
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(list python-cachecontrol
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python-decorator
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python-h5py
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python-hdmedians
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python-ipython
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python-lockfile
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python-matplotlib
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python-natsort
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python-numpy
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python-pandas
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python-scikit-learn
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python-scipy))
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(native-inputs
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(list python-coverage python-pytest))
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(home-page "https://scikit-bio.org")
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(synopsis "Data structures, algorithms and educational resources for bioinformatics")
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(description
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"This package provides data structures, algorithms and educational
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resources for bioinformatics.")
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(license license:bsd-3)))
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(define-public cwltool
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(package
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(name "cwltool")
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