diff options
| -rw-r--r-- | gnu/packages/python-science.scm | 51 |
1 files changed, 50 insertions, 1 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index e4aacdc072..292f9dc11a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -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 @@ #: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 @@ logic, also known as grey logic.") "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") |