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07/08: gnu: Add python-scikit-bio.
From: |
guix-commits |
Subject: |
07/08: gnu: Add python-scikit-bio. |
Date: |
Fri, 2 Dec 2022 15:48:00 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit b93e21a213827afaf635e6c7f6749bd2f5e329dc
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Dec 2 21:39:56 2022 +0100
gnu: Add python-scikit-bio.
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
---
gnu/packages/bioinformatics.scm | 65 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 65 insertions(+)
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")
- branch master updated (9ef6286bc3 -> fd44d489b5), guix-commits, 2022/12/02
- 01/08: gnu: python-cellbender: Update to 0.2.2., guix-commits, 2022/12/02
- 04/08: gnu: python-pairtools: Run tests conditionally., guix-commits, 2022/12/02
- 02/08: gnu: python-htsget: Update to 0.2.6., guix-commits, 2022/12/02
- 05/08: gnu: python-pairtools: Update to 1.0.2., guix-commits, 2022/12/02
- 03/08: gnu: python-pybedtools: Use pyproject-build-system., guix-commits, 2022/12/02
- 06/08: gnu: Add python-hdmedians., guix-commits, 2022/12/02
- 07/08: gnu: Add python-scikit-bio.,
guix-commits <=
- 08/08: gnu: python-biom-format: Update to 2.1.12., guix-commits, 2022/12/02