diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 131 |
1 files changed, 117 insertions, 14 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 8df311baea..292f9dc11a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -3,13 +3,13 @@ ;;; 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> ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org> ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> -;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net> +;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2021 Greg Hogan <code@greghogan.com> ;;; Copyright © 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com> @@ -35,7 +35,10 @@ #: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) #:use-module (gnu packages databases) #:use-module (gnu packages gcc) #:use-module (gnu packages image-processing) @@ -58,6 +61,7 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xorg) #:use-module (guix packages) + #:use-module (guix gexp) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix utils) @@ -154,10 +158,7 @@ atlas_libs = openblas (tgt-dir (string-append html "/" dir))) (install-file file html))) (find-files "."))))))) - ;; Tests can only be run after the library has been installed and not - ;; within the source directory. - (delete 'check) - (add-after 'install 'check + (replace 'check (lambda* (#:key tests? inputs outputs #:allow-other-keys) (when tests? (add-installed-pythonpath inputs outputs) @@ -254,13 +255,13 @@ logic, also known as grey logic.") (define-public python-scikit-image (package (name "python-scikit-image") - (version "0.18.1") + (version "0.19.2") (source (origin (method url-fetch) (uri (pypi-uri "scikit-image" version)) (sha256 - (base32 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv")))) + (base32 "0vc6c78780jivsg79ja0cncn1ma2wysy9fyz97kik0kg59jb8cyl")))) (build-system python-build-system) (arguments `(#:phases @@ -290,23 +291,68 @@ logic, also known as grey logic.") python-networkx python-numpy python-pillow + python-pythran python-pywavelets python-scipy python-tifffile)) (native-inputs - (list python-codecov - python-cython - python-flake8 + (list python-cython python-pytest - python-pytest-cov - python-pytest-localserver - python-wheel)) + python-pytest-localserver)) (home-page "https://scikit-image.org/") (synopsis "Image processing in Python") (description "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") @@ -509,6 +555,63 @@ doing practical, real world data analysis in Python.") context of a task dependency graph. It has some similarities to make.") (license license:bsd-2))) +(define-public python-pythran + (package + (name "python-pythran") + (version "0.11.0") + (home-page "https://github.com/serge-sans-paille/pythran") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0cm7wfcyvkp1wmq7n1lyf2d3sj6158jf63bagjpjmfnjwij19n0p")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove bundled Boost and xsimd. + (delete-file-recursively "third_party"))))) + (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'do-not-install-third-parties + (lambda _ + (substitute* "setup.py" + (("third_parties = .*") + "third_parties = []\n")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Remove compiler flag that trips newer GCC: + ;; https://github.com/serge-sans-paille/pythran/issues/908 + (substitute* "pythran/tests/__init__.py" + (("'-Wno-absolute-value',") + "")) + (setenv "HOME" (getcwd)) + ;; This setup is modelled after the upstream CI system. + (call-with-output-file ".pythranrc" + (lambda (port) + (format port "[compiler]\nblas=openblas~%"))) + (invoke "pytest" "-vv" + (string-append "--numprocesses=" + (number->string + (parallel-job-count))) + "pythran/tests/test_cases.py"))))))) + (native-inputs + ;; For tests. + (list openblas python-pytest python-pytest-xdist)) + (propagated-inputs + (list boost xsimd ;headers need to be available + python-beniget python-gast python-numpy python-ply)) + (synopsis "Ahead of Time compiler for numeric kernels") + (description + "Pythran is an ahead of time compiler for a subset of the Python +language, with a focus on scientific computing. It takes a Python module +annotated with a few interface descriptions and turns it into a native +Python module with the same interface, but (hopefully) faster.") + (license license:bsd-3))) + (define-public python-bottleneck (package (name "python-bottleneck") |