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gnu: Add python-scikit-allel.

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* gnu/packages/python-science.scm (python-scikit-allel): New variable.
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Efraim Flashner 2022-03-16 13:36:35 +02:00
parent cab5f92836
commit 3e34b01b70
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51
gnu/packages/python-science.scm
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@ -3,7 +3,7 @@
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@ -35,6 +35,7 @@ (define-module (gnu packages python-science)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages cpp)
@ -304,6 +305,54 @@ (define-public python-scikit-image
"Scikit-image is a collection of algorithms for image processing.")
(license license:bsd-3)))
(define-public python-scikit-allel
(package
(name "python-scikit-allel")
(version "1.3.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scikit-allel" version))
(sha256
(base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "setup.py" "build_ext" "--inplace")
(invoke "python" "-m" "pytest" "-v" "allel"
;; AttributeError: 'Dataset' object has no attribute 'asstr'
"-k" (string-append
"not test_vcf_to_hdf5"
" and not test_vcf_to_hdf5_exclude"
" and not test_vcf_to_hdf5_rename"
" and not test_vcf_to_hdf5_group"
" and not test_vcf_to_hdf5_ann"))))))))
(propagated-inputs
(list python-dask
python-numpy))
(native-inputs
(list python-cython
;; The following are all needed for the tests
htslib
python-h5py
python-hmmlearn
python-numexpr
python-pytest
python-scipy
python-setuptools-scm
python-zarr))
(home-page "https://github.com/cggh/scikit-allel")
(synopsis "Explore and analyze genetic variation data")
(description
"This package provides utilities for exploratory analysis of large scale
genetic variation data.")
(license license:expat)))
(define-public python-sgp4
(package
(name "python-sgp4")