1038 lines
39 KiB
Scheme
1038 lines
39 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2020, 2021 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, 2021 Vinicius Monego <monego@posteo.net>
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;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
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;;; Copyright © 2021 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
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;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
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;;; Copyright © 2021 Felix Gruber <felgru@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 databases)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages image-processing)
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#:use-module (gnu packages machine-learning)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-build)
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#:use-module (gnu packages python-crypto)
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#:use-module (gnu packages python-check)
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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 simulation)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages statistics)
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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 git-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 "1.6.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32 "0rh5b1rwdcvvagld8vpxnpaibszy1skpx39a0fwzd5gx5pwcjvfb"))))
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(build-system python-build-system)
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(propagated-inputs
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(list python-numpy python-matplotlib python-pyparsing))
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(inputs
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(list openblas pybind11))
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(native-inputs
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(list python-cython
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python-pytest
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python-sphinx
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python-numpydoc
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gfortran
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perl
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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-before 'build 'change-home-dir
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(lambda _
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;; Change from /homeless-shelter to /tmp for write permission.
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(setenv "HOME" "/tmp")
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#t))
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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 tests? inputs outputs #:allow-other-keys)
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(when tests?
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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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(native-inputs
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(list python2-cython
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python2-pytest
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python2-sphinx
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python2-numpydoc
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gfortran-7
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gcc-7
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perl
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which))))
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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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(list python2-numpy))
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(native-inputs
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(list 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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(list python-nose))
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(propagated-inputs
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(list python-networkx python-numpy 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 "0.18.1")
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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 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv"))))
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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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(add-before 'build 'change-home-dir
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(lambda _
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;; Change from /homeless-shelter to /tmp for write permission.
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(setenv "HOME" "/tmp")
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#t))
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(replace 'build
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(lambda _
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(invoke "make")))
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(replace 'check
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(lambda _
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;; The following tests require online data.
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(invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
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(string-append "not test_ndim"
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" and not test_skin")))))))
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;; See requirements/ for the list of build and run time requirements.
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;; NOTE: scikit-image has an optional dependency on python-pooch, however
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;; propagating it would enable many more tests that require online data.
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(propagated-inputs
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(list python-cloudpickle
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python-dask
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python-imageio
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python-matplotlib
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python-networkx
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python-numpy
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python-pillow
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python-pywavelets
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python-scipy
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python-tifffile))
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(native-inputs
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(list python-codecov
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python-cython
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python-flake8
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python-pytest
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python-pytest-cov
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python-pytest-localserver
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python-wheel))
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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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(list 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 "1.3.4")
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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 "1z3gm521wpm3j13rwhlb4f2x0645zvxkgxij37i3imdpy39iiam2"))))
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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-1)
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(srfi srfi-26))
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#:phases
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(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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(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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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(let ((build-directory
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(string-append
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(getcwd) "/build/"
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(first (scandir "build"
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(cut string-prefix? "lib." <>))))))
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(substitute* "pyproject.toml"
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;; Not all data files are distributed with the tarball.
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(("--strict-data-files ") ""))
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(with-directory-excursion build-directory
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(when tests?
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(invoke "pytest" "-vv" "pandas" "--skip-slow"
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"--skip-network"
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"-k"
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;; These tets access the internet:
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;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml]
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;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree]
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;; TODO: the excel tests fail for unknown reasons
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(string-append "not test_wrong_url"
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" and not test_excelwriter_fspath"
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" and not test_ExcelWriter_dispatch"
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;; TODO: Missing input
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" and not TestS3"
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" and not s3"))))))))))
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(propagated-inputs
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(list python-jinja2
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python-numpy
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python-openpyxl
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python-pytz
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python-dateutil
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python-xlrd))
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(inputs
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(list which xclip xsel))
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(native-inputs
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(list python-cython
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python-beautifulsoup4
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python-lxml
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python-html5lib
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python-nose
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python-pytest
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python-pytest-mock
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;; Needed to test clipboard support.
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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"
|
|
(("if 'NULL byte' in msg:")
|
|
"if 'NULL byte' in msg or 'line contains NUL' in msg:"))))))
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build python-build-system)
|
|
(ice-9 ftw)
|
|
(srfi srfi-26))
|
|
#:python ,python-2
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'patch-which
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((which (assoc-ref inputs "which")))
|
|
(substitute* "pandas/io/clipboard/__init__.py"
|
|
(("^CHECK_CMD = .*")
|
|
(string-append "CHECK_CMD = \"" which "\"\n"))))))
|
|
(replace 'check
|
|
(lambda _
|
|
(let ((build-directory
|
|
(string-append
|
|
(getcwd) "/build/"
|
|
(car (scandir "build"
|
|
(cut string-prefix? "lib." <>))))))
|
|
;; Disable the "strict data files" option which causes
|
|
;; the build to error out if required data files are
|
|
;; not available (as is the case with PyPI archives).
|
|
(substitute* "setup.cfg"
|
|
(("addopts = --strict-data-files") "addopts = "))
|
|
(with-directory-excursion build-directory
|
|
;; Delete tests that require "moto" which is not yet
|
|
;; in Guix.
|
|
(for-each delete-file
|
|
'("pandas/tests/io/conftest.py"
|
|
"pandas/tests/io/json/test_compression.py"
|
|
"pandas/tests/io/parser/test_network.py"
|
|
"pandas/tests/io/test_parquet.py"))
|
|
(invoke "pytest" "-vv" "pandas" "--skip-slow"
|
|
"--skip-network" "-k"
|
|
;; XXX: Due to the deleted tests above.
|
|
"not test_read_s3_jsonl"))))))))
|
|
(propagated-inputs
|
|
(list python2-numpy python2-openpyxl python2-pytz python2-dateutil
|
|
python2-xlrd))
|
|
(inputs
|
|
(list which))
|
|
(native-inputs
|
|
(list python2-cython
|
|
python2-beautifulsoup4
|
|
python2-lxml
|
|
python2-html5lib
|
|
python2-nose
|
|
python2-pytest
|
|
python2-pytest-mock)))))
|
|
|
|
(define-public python2-pyflow
|
|
(package
|
|
(name "python2-pyflow")
|
|
(version "1.1.20")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://github.com/Illumina/pyflow/releases/download/v"
|
|
version "/pyflow-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1bvfvviw58cndyn862qnv9nj3d9cd3a0dm4vc4sd9vwq8a6z1riv"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:tests? #f ; There is no test suite.
|
|
;; There is no official Python 3-compatible version and upstream is
|
|
;; dead. See https://github.com/Illumina/pyflow/issues/20.
|
|
#:python ,python-2))
|
|
(home-page "https://illumina.github.io/pyflow/")
|
|
(synopsis "Tool to manage tasks in a task dependency graph")
|
|
(description "This package is a Python module to manage tasks in the
|
|
context of a task dependency graph. It has some similarities to make.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public python-bottleneck
|
|
(package
|
|
(name "python-bottleneck")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "Bottleneck" version))
|
|
(sha256
|
|
(base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
|
|
(invoke "python" "setup.py" "pytest"))))))
|
|
(native-inputs
|
|
(list python-hypothesis python-pytest python-pytest-runner))
|
|
(propagated-inputs
|
|
(list python-numpy))
|
|
(home-page "https://github.com/pydata/bottleneck")
|
|
(synopsis "Fast NumPy array functions written in C")
|
|
(description
|
|
"Bottleneck is a collection of fast, NaN-aware NumPy array functions
|
|
written in C.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public python-baycomp
|
|
(package
|
|
(name "python-baycomp")
|
|
(version "1.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "baycomp" version))
|
|
(sha256
|
|
(base32 "1c1354a7b3g8slychjgyjxqdm8z40z9kviyl9n4g9kfpdg0p4d64"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-matplotlib python-numpy 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
|
|
(list python-setuptools-scm python-pytest))
|
|
(propagated-inputs
|
|
(list python-numpy 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
|
|
(list python-msgpack 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)))
|
|
|
|
(define-public python-ruffus
|
|
(package
|
|
(name "python-ruffus")
|
|
(version "2.8.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "ruffus" version))
|
|
(sha256
|
|
(base32
|
|
"1ai673k1s94s8b6pyxai8mk17p6zvvyi87rl236fs6ls8mpdklvc"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'check)
|
|
(add-after 'install 'check
|
|
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
|
|
(when tests?
|
|
(add-installed-pythonpath inputs outputs)
|
|
(with-directory-excursion "ruffus/test"
|
|
(invoke "bash" "run_all_unit_tests3.cmd"))))))))
|
|
(native-inputs
|
|
(list python-pytest))
|
|
(home-page "http://www.ruffus.org.uk")
|
|
(synopsis "Light-weight computational pipeline management")
|
|
(description
|
|
"Ruffus is designed to allow scientific and other analyses to be
|
|
automated with the minimum of fuss and the least effort.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-statannot
|
|
(package
|
|
(name "python-statannot")
|
|
(version "0.2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "statannot" version))
|
|
(sha256
|
|
(base32
|
|
"1f8c2sylzr7lpjbyqxsqlp9xi8rj3d8c9hfh98x4jbb83zxc4026"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-numpy python-seaborn python-matplotlib python-pandas
|
|
python-scipy))
|
|
(home-page
|
|
"https://github.com/webermarcolivier/statannot")
|
|
(synopsis "Add annotations to existing plots generated by seaborn")
|
|
(description
|
|
"This is a Python package to compute statistical test and add statistical
|
|
annotations on an existing boxplots and barplots generated by seaborn.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-upsetplot
|
|
(package
|
|
(name "python-upsetplot")
|
|
(version "0.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "UpSetPlot" version))
|
|
(sha256
|
|
(base32
|
|
"0kwljcmsvrxm33y3ssham2bwv4a5m31mv96y9h18va0cv7s3mqn1"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-versioning
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("pytest-cov<2.6") "pytest-cov"))))
|
|
(replace 'check
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(add-installed-pythonpath inputs outputs)
|
|
(invoke "pytest" "-v" "--doctest-modules"))))))
|
|
(propagated-inputs
|
|
(list python-matplotlib python-pandas))
|
|
(native-inputs
|
|
(list python-pytest-runner python-pytest-cov))
|
|
(home-page "https://upsetplot.readthedocs.io")
|
|
(synopsis "Draw UpSet plots with Pandas and Matplotlib")
|
|
(description
|
|
"This is a Python implementation of UpSet plots by Lex et al.
|
|
UpSet plots are used to visualize set overlaps; like Venn diagrams but more
|
|
readable.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-vedo
|
|
(package
|
|
(name "python-vedo")
|
|
(version "2021.0.3")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/marcomusy/vedo")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"18i3ajh5jzhpc86di15lwh4jv97jhm627ii877sa4yhv6abzjfpn"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'build 'mpi-setup
|
|
,%openmpi-setup)
|
|
(replace 'check
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(setenv "HOME" (getcwd))
|
|
(add-installed-pythonpath inputs outputs)
|
|
(with-directory-excursion "tests"
|
|
(for-each (lambda (dir)
|
|
(with-directory-excursion dir
|
|
(invoke "./run_all.sh")))
|
|
'("common" "dolfin")))
|
|
#t)))))
|
|
(inputs ; for the check phase
|
|
`(("dolfin" ,fenics)
|
|
("pkgconfig" ,python-pkgconfig)
|
|
("matplotlib" ,python-matplotlib)))
|
|
(native-inputs ; for python-pkgconfig
|
|
(list pkg-config))
|
|
(propagated-inputs
|
|
`(("numpy" ,python-numpy)
|
|
("vtk" ,vtk)))
|
|
(home-page "https://github.com/marcomusy/vedo")
|
|
(synopsis
|
|
"Analysis and visualization of 3D objects and point clouds")
|
|
(description
|
|
"@code{vedo} is a fast and lightweight python module for
|
|
scientific analysis and visualization. The package provides a wide
|
|
range of functionalities for working with three-dimensional meshes and
|
|
point clouds. It can also be used to generate high quality
|
|
two-dimensional renderings such as scatter plots and histograms.
|
|
@code{vedo} is based on @code{vtk} and @code{numpy}, with no other
|
|
dependencies.")
|
|
;; vedo is released under the Expat license. Included fonts are
|
|
;; covered by the OFL license and textures by the CC0 license.
|
|
;; The earth images are in the public domain.
|
|
(license (list license:expat
|
|
license:silofl1.1
|
|
license:cc0
|
|
license:public-domain))))
|
|
|
|
(define-public python-pandas-flavor
|
|
(package
|
|
(name "python-pandas-flavor")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "pandas_flavor" version))
|
|
(sha256
|
|
(base32
|
|
"12g4av8gpl6l83yza3h97j3f2jblqv69frlidrvdq8ny2rc6awbq"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-pandas python-xarray))
|
|
(home-page "https://github.com/Zsailer/pandas_flavor")
|
|
(synopsis "Write your own flavor of Pandas")
|
|
(description "Pandas 0.23 added a simple API for registering accessors
|
|
with Pandas objects. Pandas-flavor extends Pandas' extension API by
|
|
|
|
@itemize
|
|
@item adding support for registering methods as well
|
|
@item making each of these functions backwards compatible with older versions
|
|
of Pandas
|
|
@end itemize")
|
|
(license license:expat)))
|
|
|
|
(define-public python-pingouin
|
|
(package
|
|
(name "python-pingouin")
|
|
(version "0.5.0")
|
|
(source
|
|
;; The PyPI tarball does not contain the tests.
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/raphaelvallat/pingouin")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"01aaq023q4bymffrc2wm56af87da32wcvy5d5156i4g7qgvh346r"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
;; On loading, Pingouin uses the outdated package to check if a newer
|
|
;; version is available on PyPI. This check adds an extra dependency
|
|
;; and is irrelevant to Guix users. So, disable it.
|
|
(add-after 'unpack 'remove-outdated-check
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("'outdated',") ""))
|
|
(substitute* "pingouin/__init__.py"
|
|
(("^from outdated[^\n]*") "")
|
|
(("^warn_if_outdated[^\n]*") ""))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "pytest")))))))
|
|
(native-inputs
|
|
(list python-pytest python-pytest-cov))
|
|
(propagated-inputs
|
|
(list python-matplotlib
|
|
python-mpmath
|
|
python-numpy
|
|
python-pandas
|
|
python-pandas-flavor
|
|
python-scikit-learn
|
|
python-scipy
|
|
python-seaborn
|
|
python-statsmodels
|
|
python-tabulate))
|
|
(home-page "https://pingouin-stats.org/")
|
|
(synopsis "Statistical package for Python")
|
|
(description "Pingouin is a statistical package written in Python 3 and
|
|
based mostly on Pandas and NumPy. Its features include
|
|
|
|
@itemize
|
|
@item ANOVAs: N-ways, repeated measures, mixed, ancova
|
|
@item Pairwise post-hocs tests (parametric and non-parametric) and pairwise
|
|
correlations
|
|
@item Robust, partial, distance and repeated measures correlations
|
|
@item Linear/logistic regression and mediation analysis
|
|
@item Bayes Factors
|
|
@item Multivariate tests
|
|
@item Reliability and consistency
|
|
@item Effect sizes and power analysis
|
|
@item Parametric/bootstrapped confidence intervals around an effect size or a
|
|
correlation coefficient
|
|
@item Circular statistics
|
|
@item Chi-squared tests
|
|
@item Plotting: Bland-Altman plot, Q-Q plot, paired plot, robust correlation,
|
|
and more
|
|
@end itemize")
|
|
(license license:gpl3)))
|
|
|
|
(define-public python-distributed
|
|
(package
|
|
(name "python-distributed")
|
|
(version "2021.11.2")
|
|
(source
|
|
(origin
|
|
;; The test files are not included in the archive on pypi
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/dask/distributed")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1p20cbyabzl7rs8y3ydzszsskh4kw088m252ghgairhs0p2f95hl"))
|
|
;; Delete bundled copy of python-versioneer.
|
|
(snippet '(delete-file "versioneer.py"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'versioneer
|
|
(lambda _
|
|
(invoke "versioneer" "install")))
|
|
(add-after 'unpack 'fix-references
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(substitute* '("distributed/comm/tests/test_ucx_config.py"
|
|
"distributed/tests/test_client.py"
|
|
"distributed/tests/test_queues.py"
|
|
"distributed/tests/test_variable.py"
|
|
"distributed/cli/tests/test_tls_cli.py"
|
|
"distributed/cli/tests/test_dask_spec.py"
|
|
"distributed/cli/tests/test_dask_worker.py"
|
|
"distributed/cli/tests/test_dask_scheduler.py")
|
|
(("\"dask-scheduler\"")
|
|
(format #false "\"~a/bin/dask-scheduler\""
|
|
(assoc-ref outputs "out")))
|
|
(("\"dask-worker\"")
|
|
(format #false "\"~a/bin/dask-worker\""
|
|
(assoc-ref outputs "out"))))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(setenv "DISABLE_IPV6" "1")
|
|
(invoke "pytest" "-vv" "distributed"
|
|
"-m" "not slow and not gpu and not ipython and not avoid_ci"
|
|
"-k"
|
|
;; TODO: These tests fail for unknown reasons:
|
|
(string-append
|
|
;; TimeoutExpired
|
|
"not test_text"
|
|
;; AssertionError
|
|
" and not test_version_option"
|
|
;; "The 'distributed' distribution was not found"
|
|
" and not test_register_backend_entrypoint"
|
|
;; "AttributeError: module 'distributed.dashboard' has no attribute 'scheduler'"
|
|
" and not test_get_client_functions_spawn_clusters"))))))))
|
|
(propagated-inputs
|
|
(list python-click
|
|
python-cloudpickle
|
|
python-cryptography
|
|
python-dask
|
|
python-msgpack
|
|
python-psutil
|
|
python-pyyaml
|
|
python-setuptools
|
|
python-sortedcontainers
|
|
python-tblib
|
|
python-toolz
|
|
python-tornado-6
|
|
python-zict))
|
|
(native-inputs
|
|
(list python-pytest python-versioneer))
|
|
(home-page "https://distributed.dask.org")
|
|
(synopsis "Distributed scheduler for Dask")
|
|
(description "Dask.distributed is a lightweight library for distributed
|
|
computing in Python. It extends both the @code{concurrent.futures} and
|
|
@code{dask} APIs to moderate sized clusters.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-modin
|
|
(package
|
|
(name "python-modin")
|
|
(version "0.10.1")
|
|
(source
|
|
(origin
|
|
;; The archive on pypi does not include all required files.
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/modin-project/modin")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"128ghfb9ncmnn8km409xjcdppvn9nr9jqw8rkvsfavh7wnwlk509"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'make-files-writable
|
|
(lambda _
|
|
(for-each make-file-writable (find-files "."))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(setenv "MODIN_ENGINE" "dask")
|
|
(invoke "python" "-m" "pytest"
|
|
"modin/pandas/test/test_concat.py")
|
|
(setenv "MODIN_ENGINE" "python")
|
|
(invoke "python" "-m" "pytest"
|
|
"modin/pandas/test/test_concat.py")))))))
|
|
(propagated-inputs
|
|
(list python-cloudpickle
|
|
python-dask
|
|
python-distributed
|
|
python-numpy
|
|
python-packaging
|
|
python-pandas))
|
|
(native-inputs
|
|
(list python-coverage
|
|
python-jinja2
|
|
python-lxml
|
|
python-matplotlib
|
|
python-msgpack
|
|
python-openpyxl
|
|
python-psutil
|
|
python-pyarrow
|
|
python-pytest
|
|
python-pytest-benchmark
|
|
python-pytest-cov
|
|
python-pytest-xdist
|
|
python-scipy
|
|
python-sqlalchemy
|
|
python-tables
|
|
python-tqdm
|
|
python-xarray
|
|
python-xlrd))
|
|
(home-page "https://github.com/modin-project/modin")
|
|
(synopsis "Make your pandas code run faster")
|
|
(description
|
|
"Modin uses Ray or Dask to provide an effortless way to speed up your
|
|
pandas notebooks, scripts, and libraries. Unlike other distributed DataFrame
|
|
libraries, Modin provides seamless integration and compatibility with existing
|
|
pandas code.")
|
|
(license license:asl2.0)))
|