527 lines
20 KiB
Scheme
527 lines
20 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2020 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
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;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
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;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
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;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
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;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
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;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages python-science)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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#:use-module (gnu packages check)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages time)
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#:use-module (gnu packages xdisorg)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages xorg)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix utils)
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#:use-module (guix build-system python))
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(define-public python-scipy
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(package
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(name "python-scipy")
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(version "1.3.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-numpy" ,python-numpy)
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("python-matplotlib" ,python-matplotlib)
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("python-pyparsing" ,python-pyparsing)))
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(inputs
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`(("lapack" ,lapack)
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("openblas" ,openblas)))
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(native-inputs
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`(("python-cython" ,python-cython)
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("python-pytest" ,python-pytest)
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("python-sphinx" ,python-sphinx)
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("python-numpydoc" ,python-numpydoc)
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("gfortran" ,gfortran)
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("perl" ,perl)
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("which" ,which)))
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(outputs '("out" "doc"))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'disable-broken-tests
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(lambda _
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(substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
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(("^( +)def test_threads_parallel\\(self\\):" m indent)
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(string-append indent
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"@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))
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(substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
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(("^def test_parallel_threads\\(\\):" m)
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(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))
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#t))
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(add-before 'build 'configure-openblas
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(lambda* (#:key inputs #:allow-other-keys)
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(call-with-output-file "site.cfg"
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(lambda (port)
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(format port
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"[blas]
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libraries = openblas
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library_dirs = ~a/lib
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include_dirs = ~a/include
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# backslash-n to make emacs happy
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\n[atlas]
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library_dirs = ~a/lib
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atlas_libs = openblas
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"
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas"))))
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#t))
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(add-after 'install 'install-doc
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
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(doc (string-append data "/doc/" ,name "-" ,version))
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(html (string-append doc "/html"))
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(pyver ,(string-append "PYVER=" (version-major+minor
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(package-version python))))
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;; By default it tries to run sphinx-build through the Python
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;; interpreter which won't work with our shell wrapper.
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(sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
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;; Make installed package available for building the
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;; documentation
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(add-installed-pythonpath inputs outputs)
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(with-directory-excursion "doc"
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;; Fix generation of images for mathematical expressions.
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(substitute* (find-files "source" "conf\\.py")
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(("pngmath_use_preview = True")
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"pngmath_use_preview = False"))
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(mkdir-p html)
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(invoke "make" "html" pyver sphinxbuild)
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(with-directory-excursion "build/html"
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(for-each (lambda (file)
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(let* ((dir (dirname file))
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(tgt-dir (string-append html "/" dir)))
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(install-file file html)))
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(find-files "." ".*")))))
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#t))
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;; Tests can only be run after the library has been installed and not
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;; within the source directory.
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(delete 'check)
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(add-after 'install 'check
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(add-installed-pythonpath inputs outputs)
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(with-directory-excursion "/tmp"
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(invoke "python" "-c"
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"import scipy; scipy.test(verbose=2)")))))))
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(home-page "https://www.scipy.org/")
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(synopsis "The Scipy library provides efficient numerical routines")
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(description "The SciPy library is one of the core packages that make up
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the SciPy stack. It provides many user-friendly and efficient numerical
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routines such as routines for numerical integration and optimization.")
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(properties `((python2-variant . ,(delay python2-scipy))))
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(license license:bsd-3)))
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;; Version 1.2.2 is the last version to support Python 2
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(define-public python2-scipy
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(package
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(inherit (package-with-python2
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(strip-python2-variant python-scipy)))
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(version "1.2.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32
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"1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
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(define-public python2-weave
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(package
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(name "python2-weave")
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(version "0.16.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "weave" version))
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(sha256
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(base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2
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#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda _
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(invoke "nosetests" "-v"
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"--exclude"
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"test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
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(propagated-inputs
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`(("python-numpy" ,python2-numpy)))
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(native-inputs
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`(("python-nose" ,python2-nose)))
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(home-page "https://www.scipy.org/")
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(synopsis "Tools for including C/C++ code within Python code")
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(description "Weave is the stand-alone version of the obsolete Scipy
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submodule @code{scipy.weave}. It is Python 2.x only, and is provided for
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users that need new versions of Scipy but have existing code that still
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depends on @code{scipy.weave}. For new code, users are recommended to use
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Cython.")
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(license license:bsd-3)))
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(define-public python-scikit-fuzzy
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(package
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(name "python-scikit-fuzzy")
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(version "0.4.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scikit-fuzzy" version))
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(sha256
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(base32 "0bp1n771fj44kdp7a00bcvfwirvv2rc803b7g6yf3va7v0j29c8s"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda _
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(invoke "nosetests" "-s" "-v" "skfuzzy")
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#t)))))
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(native-inputs
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`(("python-nose" ,python-nose)))
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(propagated-inputs
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`(("python-networkx" ,python-networkx)
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("python-numpy" ,python-numpy)
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("python-scipy" ,python-scipy)))
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(home-page "https://github.com/scikit-fuzzy/scikit-fuzzy")
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(synopsis "Fuzzy logic toolkit for SciPy")
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(description
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"This package implements many useful tools for projects involving fuzzy
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logic, also known as grey logic.")
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(license license:bsd-3)))
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(define-public python-scikit-image
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(package
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(name "python-scikit-image")
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(version "0.17.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scikit-image" version))
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(sha256
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(base32 "1cyqqbcbrg3prc36wis0sm3q5rjhd7h9bp33jwfyixzhi02lr5dx"))))
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(build-system python-build-system)
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(arguments
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;; TODO: Some tests require running X11 server. Disable them?
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'(#:tests? #f))
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;; See DEPENDS.txt for the list of build and run time requiremnts
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(propagated-inputs
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`(("python-cloudpickle" ,python-cloudpickle)
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("python-dask" ,python-dask)
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("python-imageio" ,python-imageio)
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("python-matplotlib" ,python-matplotlib)
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("python-networkx" ,python-networkx)
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("python-numpy" ,python-numpy)
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("python-pillow" ,python-pillow)
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("python-pywavelets" ,python-pywavelets)
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("python-scipy" ,python-scipy)
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("python-six" ,python-six)
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("python-tifffile" ,python-tifffile)))
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(native-inputs
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`(("python-cython" ,python-cython)))
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(home-page "https://scikit-image.org/")
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(synopsis "Image processing in Python")
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(description
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"Scikit-image is a collection of algorithms for image processing.")
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(license license:bsd-3)))
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(define-public python-sgp4
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(package
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(name "python-sgp4")
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(version "2.12")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "sgp4" version))
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(sha256
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(base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-numpy" ,python-numpy)))
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(home-page "https://github.com/brandon-rhodes/python-sgp4")
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(synopsis "Track earth satellite TLE orbits using SGP4")
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(description
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"This package provides a Python implementation of the most recent version
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of the SGP4 satellite tracking algorithm.")
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(license license:expat)))
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(define-public python-pandas
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(package
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(name "python-pandas")
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(version "1.0.5")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "pandas" version))
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(sha256
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(base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
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(build-system python-build-system)
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(arguments
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`(#:modules ((guix build utils)
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(guix build python-build-system)
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(ice-9 ftw)
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(srfi srfi-26))
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#:phases (modify-phases %standard-phases
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(add-after 'unpack 'patch-which
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((which (assoc-ref inputs "which")))
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(substitute* "pandas/io/clipboard/__init__.py"
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(("^WHICH_CMD = .*")
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(string-append "WHICH_CMD = \"" which "\"\n"))))
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#t))
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(add-before 'check 'prepare-x
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(lambda _
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(system "Xvfb &")
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(setenv "DISPLAY" ":0")
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;; xsel needs to write a log file.
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(setenv "HOME" "/tmp")
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#t))
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(replace 'check
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(lambda _
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(let ((build-directory
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(string-append
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(getcwd) "/build/"
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(car (scandir "build"
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(cut string-prefix? "lib." <>))))))
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;; Disable the "strict data files" option which causes
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;; the build to error out if required data files are
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;; not available (as is the case with PyPI archives).
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(substitute* "setup.cfg"
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(("addopts = --strict-data-files") "addopts = "))
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(with-directory-excursion build-directory
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(invoke "pytest" "-vv" "pandas" "--skip-slow"
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"--skip-network"))))))))
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(propagated-inputs
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`(("python-jinja2" ,python-jinja2)
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("python-numpy" ,python-numpy)
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("python-openpyxl" ,python-openpyxl)
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("python-pytz" ,python-pytz)
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("python-dateutil" ,python-dateutil)
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("python-xlrd" ,python-xlrd)))
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(inputs
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`(("which" ,which)
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("xclip" ,xclip)
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("xsel" ,xsel)))
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(native-inputs
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`(("python-cython" ,python-cython)
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("python-beautifulsoup4" ,python-beautifulsoup4)
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("python-lxml" ,python-lxml)
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("python-html5lib" ,python-html5lib)
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("python-nose" ,python-nose)
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("python-pytest" ,python-pytest)
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("python-pytest-mock" ,python-pytest-mock)
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;; Needed to test clipboard support.
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("xorg-server" ,xorg-server-for-tests)))
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(home-page "https://pandas.pydata.org")
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(synopsis "Data structures for data analysis, time series, and statistics")
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(description
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"Pandas is a Python package providing fast, flexible, and expressive data
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structures designed to make working with structured (tabular,
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multidimensional, potentially heterogeneous) and time series data both easy
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and intuitive. It aims to be the fundamental high-level building block for
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doing practical, real world data analysis in Python.")
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(properties `((python2-variant . ,(delay python2-pandas))))
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(license license:bsd-3)))
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(define-public python-pandas-0.25
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(package
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(inherit python-pandas)
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(version "0.25.3")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "pandas" version))
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(sha256
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(base32
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"191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
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(arguments
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(substitute-keyword-arguments (package-arguments python-pandas)
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((#:phases phases)
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`(modify-phases ,phases
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(replace 'patch-which
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((which (assoc-ref inputs "which")))
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(substitute* "pandas/io/clipboard/__init__.py"
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(("^CHECK_CMD = .*")
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(string-append "CHECK_CMD = \"" which "\"\n"))))
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#t))
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(delete 'prepare-x)))))))
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;; Pandas 0.24.x are the last versions that support Python 2.
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(define-public python2-pandas
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(let ((pandas (package-with-python2
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(strip-python2-variant python-pandas-0.25))))
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(package
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(inherit pandas)
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(version "0.24.2")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "pandas" version))
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|
(sha256
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|
(base32
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"18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
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(modules '((guix build utils)))
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|
(snippet
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'(begin
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;; Adjust for renamed error message in Python 2.7.17. Taken
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;; from <https://github.com/pandas-dev/pandas/pull/29294>.
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(substitute* "pandas/io/parsers.py"
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(("if 'NULL byte' in msg:")
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"if 'NULL byte' in msg or 'line contains NUL' in msg:"))
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#t)))))))
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(define-public python-bottleneck
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(package
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(name "python-bottleneck")
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(version "1.3.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "Bottleneck" version))
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(sha256
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(base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda _
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(invoke "python" "setup.py" "pytest"))))))
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(native-inputs
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`(("python-hypothesis" ,python-hypothesis)
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("python-pytest" ,python-pytest)
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("python-pytest-runner" ,python-pytest-runner)))
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(propagated-inputs
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`(("python-numpy" ,python-numpy)))
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(home-page "https://github.com/pydata/bottleneck")
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(synopsis "Fast NumPy array functions written in C")
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(description
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"Bottleneck is a collection of fast, NaN-aware NumPy array functions
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written in C.")
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(license license:bsd-2)))
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(define-public python-baycomp
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(package
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(name "python-baycomp")
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(version "1.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "baycomp" version))
|
|
(sha256
|
|
(base32 "1c1354a7b3g8slychjgyjxqdm8z40z9kviyl9n4g9kfpdg0p4d64"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
`(("python-matplotlib" ,python-matplotlib)
|
|
("python-numpy" ,python-numpy)
|
|
("python-scipy" ,python-scipy)))
|
|
(home-page "https://github.com/janezd/baycomp")
|
|
(synopsis "Library for comparison of Bayesian classifiers")
|
|
(description
|
|
"Baycomp is a library for Bayesian comparison of classifiers. Functions
|
|
in the library compare two classifiers on one or on multiple data sets. They
|
|
compute three probabilities: the probability that the first classifier has
|
|
higher scores than the second, the probability that differences are within the
|
|
region of practical equivalence (rope), or that the second classifier has
|
|
higher scores.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-xarray
|
|
(package
|
|
(name "python-xarray")
|
|
(version "0.15.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "xarray" version))
|
|
(sha256
|
|
(base32
|
|
"1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
`(("python-setuptools-scm" ,python-setuptools-scm)
|
|
("python-pytest" ,python-pytest)))
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-pandas" ,python-pandas)))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
|
|
(invoke "pytest"))))))
|
|
(home-page "https://github.com/pydata/xarray")
|
|
(synopsis "N-D labeled arrays and datasets")
|
|
(description "Xarray (formerly xray) makes working with labelled
|
|
multi-dimensional arrays simple, efficient, and fun!
|
|
|
|
Xarray introduces labels in the form of dimensions, coordinates and attributes
|
|
on top of raw NumPy-like arrays, which allows for a more intuitive, more
|
|
concise, and less error-prone developer experience. The package includes a
|
|
large and growing library of domain-agnostic functions for advanced analytics
|
|
and visualization with these data structures.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public python-msgpack-numpy
|
|
(package
|
|
(name "python-msgpack-numpy")
|
|
(version "0.4.6.post0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "msgpack-numpy" version))
|
|
(sha256
|
|
(base32
|
|
"0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
`(("python-msgpack" ,python-msgpack)
|
|
("python-numpy" ,python-numpy)))
|
|
(home-page "https://github.com/lebedov/msgpack-numpy")
|
|
(synopsis
|
|
"Numpy data serialization using msgpack")
|
|
(description
|
|
"This package provides encoding and decoding routines that enable the
|
|
serialization and deserialization of numerical and array data types provided
|
|
by numpy using the highly efficient @code{msgpack} format. Serialization of
|
|
Python's native complex data types is also supported.")
|
|
(license license:bsd-3)))
|