mirror of
https://git.savannah.gnu.org/git/guix.git
synced 2025-02-07 19:39:34 +01:00
ec1224a73b
* gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from here... * gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here. * gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm, gnu/packages/statistics.scm: Adjust module imports.
193 lines
7.7 KiB
Scheme
193 lines
7.7 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
|
|
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
|
|
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
|
|
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
|
|
;;; Copyright © 2016, 2018 Marius Bakke <mbakke@fastmail.com>
|
|
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
|
|
;;;
|
|
;;; This file is part of GNU Guix.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
|
;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(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 check)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages perl)
|
|
#:use-module (gnu packages python)
|
|
#:use-module (gnu packages python-xyz)
|
|
#:use-module (gnu packages sphinx)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix download)
|
|
#:use-module (guix utils)
|
|
#:use-module (guix build-system python))
|
|
|
|
(define-public python-scipy
|
|
(package
|
|
(name "python-scipy")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "scipy" version))
|
|
(sha256
|
|
(base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-matplotlib" ,python-matplotlib)
|
|
("python-pyparsing" ,python-pyparsing)))
|
|
(inputs
|
|
`(("lapack" ,lapack)
|
|
("openblas" ,openblas)))
|
|
(native-inputs
|
|
`(("python-cython" ,python-cython)
|
|
("python-pytest" ,python-pytest)
|
|
("python-sphinx" ,python-sphinx)
|
|
("python-numpydoc" ,python-numpydoc)
|
|
("gfortran" ,gfortran)
|
|
("perl" ,perl)
|
|
("which" ,which)))
|
|
(outputs '("out" "doc"))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'disable-broken-tests
|
|
(lambda _
|
|
(substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
|
|
(("^( +)def test_threads_parallel\\(self\\):" m indent)
|
|
(string-append indent
|
|
"@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
|
|
m)))
|
|
(substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
|
|
(("^def test_parallel_threads\\(\\):" m)
|
|
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
|
|
m)))
|
|
#t))
|
|
(add-before 'build 'configure-openblas
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(call-with-output-file "site.cfg"
|
|
(lambda (port)
|
|
(format port
|
|
"[blas]
|
|
libraries = openblas
|
|
library_dirs = ~a/lib
|
|
include_dirs = ~a/include
|
|
|
|
# backslash-n to make emacs happy
|
|
\n[atlas]
|
|
library_dirs = ~a/lib
|
|
atlas_libs = openblas
|
|
"
|
|
(assoc-ref inputs "openblas")
|
|
(assoc-ref inputs "openblas")
|
|
(assoc-ref inputs "openblas"))))
|
|
#t))
|
|
(add-after 'install 'install-doc
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
|
|
(doc (string-append data "/doc/" ,name "-" ,version))
|
|
(html (string-append doc "/html"))
|
|
(pyver ,(string-append "PYVER=" (version-major+minor
|
|
(package-version python))))
|
|
;; By default it tries to run sphinx-build through the Python
|
|
;; interpreter which won't work with our shell wrapper.
|
|
(sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
|
|
;; Make installed package available for building the
|
|
;; documentation
|
|
(add-installed-pythonpath inputs outputs)
|
|
(with-directory-excursion "doc"
|
|
;; Fix generation of images for mathematical expressions.
|
|
(substitute* (find-files "source" "conf\\.py")
|
|
(("pngmath_use_preview = True")
|
|
"pngmath_use_preview = False"))
|
|
(mkdir-p html)
|
|
(invoke "make" "html" pyver sphinxbuild)
|
|
(with-directory-excursion "build/html"
|
|
(for-each (lambda (file)
|
|
(let* ((dir (dirname file))
|
|
(tgt-dir (string-append html "/" dir)))
|
|
(install-file file html)))
|
|
(find-files "." ".*")))))
|
|
#t))
|
|
;; Tests can only be run after the library has been installed and not
|
|
;; within the source directory.
|
|
(delete 'check)
|
|
(add-after 'install 'check
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(add-installed-pythonpath inputs outputs)
|
|
(with-directory-excursion "/tmp"
|
|
(invoke "python" "-c"
|
|
"import scipy; scipy.test(verbose=2)")))))))
|
|
(home-page "https://www.scipy.org/")
|
|
(synopsis "The Scipy library provides efficient numerical routines")
|
|
(description "The SciPy library is one of the core packages that make up
|
|
the SciPy stack. It provides many user-friendly and efficient numerical
|
|
routines such as routines for numerical integration and optimization.")
|
|
(properties `((python2-variant . ,(delay python2-scipy))))
|
|
(license license:bsd-3)))
|
|
|
|
;; Version 1.2.2 is the last version to support Python 2
|
|
(define-public python2-scipy
|
|
(package
|
|
(inherit (package-with-python2
|
|
(strip-python2-variant python-scipy)))
|
|
(version "1.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "scipy" version))
|
|
(sha256
|
|
(base32
|
|
"1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
|
|
|
|
(define-public python-scikit-image
|
|
(package
|
|
(name "python-scikit-image")
|
|
(version "0.14.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "scikit-image" version))
|
|
(sha256
|
|
(base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
;; TODO: Some tests require running X11 server. Disable them?
|
|
'(#:tests? #f))
|
|
;; See DEPENDS.txt for the list of build and run time requiremnts
|
|
(propagated-inputs
|
|
`(("python-cloudpickle" ,python-cloudpickle)
|
|
("python-dask" ,python-dask)
|
|
("python-matplotlib" ,python-matplotlib)
|
|
("python-networkx" ,python-networkx)
|
|
("python-numpy" ,python-numpy)
|
|
("python-pillow" ,python-pillow)
|
|
("python-pywavelets" ,python-pywavelets)
|
|
("python-scipy" ,python-scipy)
|
|
("python-six" ,python-six)))
|
|
(native-inputs
|
|
`(("python-cython" ,python-cython)))
|
|
(home-page "http://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 python2-scikit-image
|
|
(package-with-python2 python-scikit-image))
|