2197 lines
85 KiB
Scheme
2197 lines
85 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023 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, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
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;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2019, 2021, 2022, 2023 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, 2022, 2023 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, 2023 Felix Gruber <felgru@posteo.net>
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;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes@gmail.com>
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;;; Copyright © 2022 Guillaume Le Vaillant <glv@posteo.net>
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;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
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;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
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;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
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;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
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;;; Copyright © 2022 jgart <jgart@dismail.de>
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;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
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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 bioinformatics)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages build-tools)
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#:use-module (gnu packages check)
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|
#:use-module (gnu packages cpp)
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|
#:use-module (gnu packages crypto)
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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 geo)
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#:use-module (gnu packages image)
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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 pcre)
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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)
|
|
#:use-module (gnu packages xorg)
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|
#:use-module (guix packages)
|
|
#:use-module (guix gexp)
|
|
#: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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#:use-module (guix build-system pyproject))
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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 "1.10.1")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32 "19gk88nvrxl050nasz25qpmmqvbdk247bkj09jx8jibv1awdzy9c"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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;; FIXME: The default 'mesonpy' build system doesn't seem to work with
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;; our pyproject-build-system, errors with: AttributeError: 'list'
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;; object has no attribute 'items' (see:
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;; https://issues.guix.gnu.org/62781).
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#:build-backend "setuptools.build_meta"
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#:phases
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#~(modify-phases %standard-phases
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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;; Step out of the source directory to avoid interference.
|
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(with-directory-excursion "/tmp"
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(invoke "python" "-c"
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(string-append
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"import scipy; scipy.test('fast', parallel="
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(number->string (parallel-job-count))
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", verbose=2)"))))))
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(add-after 'check 'install-doc
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(lambda* (#:key outputs #:allow-other-keys)
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;; FIXME: Documentation cannot be built because it requires
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;; a newer version of pydata-sphinx-theme, which currently
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;; cannot build without internet access:
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;; <https://github.com/pydata/pydata-sphinx-theme/issues/628>.
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;; Keep the phase for easy testing.
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(let ((sphinx-build (false-if-exception
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(search-input-file input "bin/sphinx-build"))))
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(if sphinx-build
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(let* ((doc (assoc-ref outputs "doc"))
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(data (string-append doc "/share"))
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(docdir (string-append
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data "/doc/"
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#$(package-name this-package) "-"
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#$(package-version this-package)))
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(html (string-append docdir "/html")))
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(with-directory-excursion "doc"
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;; Build doc.
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(invoke "make" "html"
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;; Building the documentation takes a very long time.
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;; Parallelize it.
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(string-append "SPHINXOPTS=-j"
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(number->string (parallel-job-count))))
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;; Install doc.
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(mkdir-p html)
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(copy-recursively "build/html" html)))
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(format #t "sphinx-build not found, skipping~%"))))))))
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(propagated-inputs
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(list python-numpy python-matplotlib python-pyparsing python-pythran))
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(inputs (list openblas pybind11))
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(native-inputs
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(list gfortran
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;; XXX: Adding gfortran shadows GCC headers, causing a compilation
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;; failure. Somehow also providing GCC works around it ...
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gcc
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meson-python
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pkg-config
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python-cython
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python-pytest
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python-pytest-xdist
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python-threadpoolctl))
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(home-page "https://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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(license license:bsd-3)))
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(define-public python-scikit-allel
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(package
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(name "python-scikit-allel")
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(version "1.3.5")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scikit-allel" version))
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(sha256
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(base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
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(build-system pyproject-build-system)
|
|
(arguments
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|
(list
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#:test-flags
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'(list "-k"
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(string-append
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;; AttributeError: 'Dataset' object has no attribute 'asstr'
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"not test_vcf_to_hdf5"
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" and not test_vcf_to_hdf5_exclude"
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|
" and not test_vcf_to_hdf5_rename"
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|
" and not test_vcf_to_hdf5_group"
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" and not test_vcf_to_hdf5_ann"
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|
;; Does not work with recent hmmlearn
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" and not test_roh_mhmm_0pct"
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" and not test_roh_mhmm_100pct"))
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#:phases
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'(modify-phases %standard-phases
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(add-before 'check 'build-ext
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(lambda _
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(invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
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(propagated-inputs
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|
(list python-dask
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python-numpy))
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(native-inputs
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(list python-cython
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;; The following are all needed for the tests
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htslib
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|
python-h5py
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|
python-hmmlearn
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|
python-numexpr
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python-pytest
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|
python-scipy
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|
python-setuptools-scm
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|
python-zarr))
|
|
(home-page "https://github.com/cggh/scikit-allel")
|
|
(synopsis "Explore and analyze genetic variation data")
|
|
(description
|
|
"This package provides utilities for exploratory analysis of large scale
|
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genetic variation data.")
|
|
(license license:expat)))
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|
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(define-public python-scikit-fem
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(package
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(name "python-scikit-fem")
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(version "8.1.0")
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(source (origin
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(method git-fetch) ; no tests in PyPI
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(uri (git-reference
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(url "https://github.com/kinnala/scikit-fem")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
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|
(base32
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|
"1zpn0wpsvls5nkrav5a43z77yg9nc09dpyy9ri0dpmpm2ndh2mhs"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
;; Examples below require python-autograd and python-pyamg.
|
|
(list #:test-flags #~(list "-k" "not TestEx32 and not TestEx45")))
|
|
(propagated-inputs (list python-meshio python-numpy python-scipy))
|
|
(native-inputs (list python-pytest))
|
|
(home-page "https://scikit-fem.readthedocs.io/en/latest/")
|
|
(synopsis "Library for performing finite element assembly")
|
|
(description
|
|
"@code{scikit-fem} is a library for performing finite element assembly.
|
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Its main purpose is the transformation of bilinear forms into sparse matrices
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and linear forms into vectors.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-scikit-fuzzy
|
|
(package
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|
(name "python-scikit-fuzzy")
|
|
(version "0.4.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "scikit-fuzzy" version))
|
|
(sha256
|
|
(base32 "0bp1n771fj44kdp7a00bcvfwirvv2rc803b7g6yf3va7v0j29c8s"))))
|
|
(build-system python-build-system)
|
|
(arguments '(#:tests? #f)) ;XXX: not compatible with newer numpy.testing
|
|
(native-inputs
|
|
(list python-nose))
|
|
(propagated-inputs
|
|
(list python-networkx python-numpy python-scipy))
|
|
(home-page "https://github.com/scikit-fuzzy/scikit-fuzzy")
|
|
(synopsis "Fuzzy logic toolkit for SciPy")
|
|
(description
|
|
"This package implements many useful tools for projects involving fuzzy
|
|
logic, also known as grey logic.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-scikit-image
|
|
(package
|
|
(name "python-scikit-image")
|
|
(version "0.19.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "scikit-image" version))
|
|
(sha256
|
|
(base32 "0l645smf7w1kail70z8d9r3xmvz7qh6g7n3d2bpacbbnw5ykdd94"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'build 'change-home-dir
|
|
(lambda _
|
|
;; Change from /homeless-shelter to /tmp for write permission.
|
|
(setenv "HOME" "/tmp")
|
|
#t))
|
|
(replace 'build
|
|
(lambda _
|
|
(invoke "make")))
|
|
(replace 'check
|
|
(lambda _
|
|
;; The following tests require online data.
|
|
(invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
|
|
(string-append "not test_ndim"
|
|
" and not test_skin")))))))
|
|
;; See requirements/ for the list of build and run time requirements.
|
|
;; NOTE: scikit-image has an optional dependency on python-pooch, however
|
|
;; propagating it would enable many more tests that require online data.
|
|
(propagated-inputs
|
|
(list python-cloudpickle
|
|
python-dask
|
|
python-imageio
|
|
python-matplotlib
|
|
python-networkx
|
|
python-numpy
|
|
python-pillow
|
|
python-pythran
|
|
python-pywavelets
|
|
python-scipy
|
|
python-tifffile))
|
|
(native-inputs
|
|
(list python-cython
|
|
python-pytest
|
|
python-pytest-localserver))
|
|
(home-page "https://scikit-image.org/")
|
|
(synopsis "Image processing in Python")
|
|
(description
|
|
"Scikit-image is a collection of algorithms for image processing.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-scikit-optimize
|
|
(package
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|
(name "python-scikit-optimize")
|
|
(version "0.9.0")
|
|
(source (origin
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|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/scikit-optimize/scikit-optimize")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0hsq6pmryimxc275yrcy4bv217bx7ma6rz0q6m4138bv4zgq18d1"))
|
|
(patches
|
|
;; These are for compatibility with more recent versions of
|
|
;; numpy and scikit-learn.
|
|
(search-patches "python-scikit-optimize-1148.patch"
|
|
"python-scikit-optimize-1150.patch"))))
|
|
(build-system pyproject-build-system)
|
|
(propagated-inputs
|
|
(list python-joblib
|
|
python-matplotlib
|
|
python-numpy
|
|
python-pyaml
|
|
python-scikit-learn
|
|
python-scipy))
|
|
(native-inputs
|
|
(list python-pytest))
|
|
(home-page "https://scikit-optimize.github.io/")
|
|
(synopsis "Sequential model-based optimization toolbox")
|
|
(description "Scikit-Optimize, or @code{skopt}, is a simple and efficient
|
|
library to minimize (very) expensive and noisy black-box functions. It
|
|
implements several methods for sequential model-based optimization.
|
|
@code{skopt} aims to be accessible and easy to use in many contexts.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-tdda
|
|
(package
|
|
(name "python-tdda")
|
|
(version "2.0.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "tdda" version))
|
|
(sha256
|
|
(base32 "1xs91s8b7cshjcqw88qsrjh10xly799k5rf2ycawqfz2mw8sy3br"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
'(#:phases (modify-phases %standard-phases
|
|
(add-after 'unpack 'relax-requirements
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("pandas>=1.5.2")
|
|
"pandas"))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "tdda" "test")))))))
|
|
(native-inputs (list python-numpy python-pandas))
|
|
(home-page "https://www.stochasticsolutions.com")
|
|
(synopsis "Test-driven data analysis library for Python")
|
|
(description
|
|
"The TDDA Python module provides command-line and Python API support
|
|
for the overall process of data analysis, through tools that peform
|
|
reference testing, constraint discovery for data, automatic inference
|
|
of regular expressions from text data and automatic test generation.")
|
|
(license license:expat))) ; MIT License
|
|
|
|
(define-public python-trimesh
|
|
(package
|
|
(name "python-trimesh")
|
|
(version "3.23.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "trimesh" version))
|
|
(sha256
|
|
(base32 "08967axlnmfv98n05dhrkynyrmcc814hl8184gzzmcy4rjg6dzdx"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-numpy))
|
|
(native-inputs
|
|
(list python-coveralls
|
|
python-pyinstrument
|
|
python-pytest
|
|
python-pytest-cov))
|
|
(arguments
|
|
`(;; TODO: Get tests to work.
|
|
#:tests? #f
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-build
|
|
(lambda _
|
|
(substitute* "trimesh/resources/templates/blender_boolean.py.tmpl"
|
|
(("\\$MESH_PRE")
|
|
"'$MESH_PRE'")))))))
|
|
(home-page "https://github.com/mikedh/trimesh")
|
|
(synopsis "Python library for loading and using triangular meshes")
|
|
(description
|
|
"Trimesh is a pure Python library for loading and using triangular meshes
|
|
with an emphasis on watertight surfaces. The goal of the library is to provide
|
|
a full featured and well tested Trimesh object which allows for easy
|
|
manipulation and analysis, in the style of the Polygon object in the Shapely
|
|
library.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-meshzoo
|
|
(package
|
|
(name "python-meshzoo")
|
|
(version "0.9.4")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/diego-hayashi/meshzoo")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "107byfppbq16fqyp2hw7ydcvvahspzq0hzvlvzqg2zxi1aigbr68"))))
|
|
(build-system pyproject-build-system)
|
|
(propagated-inputs
|
|
(list python-numpy))
|
|
(native-inputs (list python-flit-core python-matplotlib python-pytest))
|
|
(home-page "https://github.com/diego-hayashi/meshzoo")
|
|
(synopsis "Mesh generator for simple geometries")
|
|
(description
|
|
"@code{meshzoo} is a mesh generator for finite element or finite
|
|
volume computations for simple domains like regular polygons, disks,
|
|
spheres, cubes, etc.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public python-tspex
|
|
(package
|
|
(name "python-tspex")
|
|
(version "0.6.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "tspex" version))
|
|
(sha256
|
|
(base32
|
|
"0x64ki1nzhms2nb8xpng92bzh5chs850dvapr93pkg05rk22m6mv"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-matplotlib python-numpy python-pandas python-xlrd))
|
|
(home-page "https://apcamargo.github.io/tspex/")
|
|
(synopsis "Calculate tissue-specificity metrics for gene expression")
|
|
(description
|
|
"This package provides a Python package for calculating
|
|
tissue-specificity metrics for gene expression.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public python-pandas
|
|
(package
|
|
(name "python-pandas")
|
|
(version "1.4.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "pandas" version))
|
|
(sha256
|
|
(base32 "0ryv66s9cvd27q6a985vv556k2qlnlrdna2z7qc7bdhphrrhsv5b"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build python-build-system)
|
|
(ice-9 ftw)
|
|
(srfi srfi-1)
|
|
(srfi srfi-26))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'enable-parallel-build
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("\"-j\", type=int, default=1")
|
|
(format #f "\"-j\", type=int, default=~a"
|
|
(parallel-job-count))))))
|
|
(add-after 'unpack 'patch-which
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((which (assoc-ref inputs "which")))
|
|
(substitute* "pandas/io/clipboard/__init__.py"
|
|
(("^WHICH_CMD = .*")
|
|
(string-append "WHICH_CMD = \"" which "\"\n"))))))
|
|
(add-before 'check 'prepare-x
|
|
(lambda _
|
|
(system "Xvfb &")
|
|
(setenv "DISPLAY" ":0")
|
|
;; xsel needs to write a log file.
|
|
(setenv "HOME" "/tmp")))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(let ((build-directory
|
|
(string-append
|
|
(getcwd) "/build/"
|
|
(first (scandir "build"
|
|
(cut string-prefix? "lib." <>))))))
|
|
(substitute* "pyproject.toml"
|
|
;; Not all data files are distributed with the tarball.
|
|
(("--strict-data-files ") ""))
|
|
(with-directory-excursion build-directory
|
|
(when tests?
|
|
(invoke "pytest" "-vv" "pandas" "--skip-slow"
|
|
"--skip-network"
|
|
"-n" (number->string (parallel-job-count))
|
|
"-k"
|
|
(string-append
|
|
;; These test access the internet (see:
|
|
;; https://github.com/pandas-dev/pandas/issues/45085).:
|
|
;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml]
|
|
;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree]
|
|
"not test_wrong_url"
|
|
;; TODO: Missing input
|
|
" and not TestS3"
|
|
" and not s3"
|
|
;; This test fails when run with pytest-xdist
|
|
;; (see:
|
|
;; https://github.com/pandas-dev/pandas/issues/39096).
|
|
" and not test_memory_usage"))))))))))
|
|
(propagated-inputs
|
|
(list python-jinja2
|
|
python-numpy
|
|
python-openpyxl
|
|
python-pytz
|
|
python-dateutil
|
|
python-xlrd
|
|
python-xlsxwriter))
|
|
(inputs
|
|
(list which xclip xsel))
|
|
(native-inputs
|
|
(list python-cython
|
|
python-beautifulsoup4
|
|
python-lxml
|
|
python-html5lib
|
|
python-pytest
|
|
python-pytest-mock
|
|
python-pytest-xdist
|
|
;; Needed to test clipboard support.
|
|
xorg-server-for-tests))
|
|
(home-page "https://pandas.pydata.org")
|
|
(synopsis "Data structures for data analysis, time series, and statistics")
|
|
(description
|
|
"Pandas is a Python package providing fast, flexible, and expressive data
|
|
structures designed to make working with structured (tabular,
|
|
multidimensional, potentially heterogeneous) and time series data both easy
|
|
and intuitive. It aims to be the fundamental high-level building block for
|
|
doing practical, real world data analysis in Python.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-pythran
|
|
(package
|
|
(name "python-pythran")
|
|
(version "0.11.0")
|
|
(home-page "https://github.com/serge-sans-paille/pythran")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference (url home-page) (commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "0cm7wfcyvkp1wmq7n1lyf2d3sj6158jf63bagjpjmfnjwij19n0p"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
;; Remove bundled Boost and xsimd.
|
|
(delete-file-recursively "third_party")))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
(list #:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'do-not-install-third-parties
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("third_parties = .*")
|
|
"third_parties = []\n"))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
;; Remove compiler flag that trips newer GCC:
|
|
;; https://github.com/serge-sans-paille/pythran/issues/908
|
|
(substitute* "pythran/tests/__init__.py"
|
|
(("'-Wno-absolute-value',")
|
|
""))
|
|
(setenv "HOME" (getcwd))
|
|
;; This setup is modelled after the upstream CI system.
|
|
(call-with-output-file ".pythranrc"
|
|
(lambda (port)
|
|
(format port "[compiler]\nblas=openblas~%")))
|
|
(invoke "pytest" "-vv"
|
|
(string-append "--numprocesses="
|
|
(number->string
|
|
(parallel-job-count)))
|
|
"pythran/tests/test_cases.py")))))))
|
|
(native-inputs
|
|
;; For tests.
|
|
(list openblas python-pytest python-pytest-xdist))
|
|
(propagated-inputs
|
|
(list boost xsimd ;headers need to be available
|
|
python-beniget python-gast python-numpy python-ply))
|
|
(synopsis "Ahead of Time compiler for numeric kernels")
|
|
(description
|
|
"Pythran is an ahead of time compiler for a subset of the Python
|
|
language, with a focus on scientific computing. It takes a Python module
|
|
annotated with a few interface descriptions and turns it into a native
|
|
Python module with the same interface, but (hopefully) faster.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-pyts
|
|
(package
|
|
(name "python-pyts")
|
|
(version "0.12.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "pyts" version))
|
|
(sha256
|
|
(base32
|
|
"1cb5jwp8g52a3hxay6mxbfzk16ly6yj6rphq8cwbwk1k2jdf11dg"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
'(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "pytest" "-v"
|
|
;; XXX: This test fails for unknown reasons
|
|
;; Expected:
|
|
;; (40, 9086)
|
|
;; Got:
|
|
;; (40, 9088)
|
|
"-k"
|
|
"not pyts.multivariate.transformation.weasel_muse.WEASELMUSE")))))))
|
|
(propagated-inputs
|
|
(list python-joblib
|
|
python-matplotlib
|
|
python-numba
|
|
python-numpy
|
|
python-scikit-learn
|
|
python-scipy))
|
|
(native-inputs
|
|
(list python-pytest python-pytest-cov))
|
|
(home-page "https://github.com/johannfaouzi/pyts")
|
|
(synopsis "Python package for time series classification")
|
|
(description
|
|
"This package provides a Python package for time series classification.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-bottleneck
|
|
(package
|
|
(name "python-bottleneck")
|
|
(version "1.3.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "Bottleneck" version))
|
|
(sha256
|
|
(base32 "1y410r3scfhs6s1j1jpxig01qlyn2hr2izyh1qsdlsfl78vpwip1"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(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-numpoly
|
|
(package
|
|
(name "python-numpoly")
|
|
(version "1.2.11")
|
|
(source (origin
|
|
(method git-fetch) ;; PyPI is missing some Pytest fixtures
|
|
(uri (git-reference
|
|
(url "https://github.com/jonathf/numpoly")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"01g21v91f4d66xd0bvap0n6d6485w2fnq1636gx6h2s42550rlbd"))))
|
|
(build-system pyproject-build-system)
|
|
(propagated-inputs (list python-importlib-metadata python-numpy))
|
|
(native-inputs (list python-pytest python-sympy))
|
|
(home-page "https://numpoly.readthedocs.io/en/master/")
|
|
(synopsis "Polynomials as a numpy datatype")
|
|
(description "Numpoly is a generic library for creating, manipulating and
|
|
evaluating arrays of polynomials based on @code{numpy.ndarray objects}.")
|
|
;; Tests fail with dtype mismatches on 32-bit architectures, suggesting
|
|
;; that numpoly only supports 64 bit platforms.
|
|
(supported-systems '("x86_64-linux" "aarch64-linux" "powerpc64le-linux"))
|
|
(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-fbpca
|
|
(package
|
|
(name "python-fbpca")
|
|
(version "1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fbpca" version))
|
|
(sha256
|
|
(base32
|
|
"1lbjqhqsdmqk86lb86q3ywf7561zmdny1dfvgwqkyrkr4ij7f1hm"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-numpy python-scipy))
|
|
(home-page "https://fbpca.readthedocs.io/")
|
|
(synopsis "Functions for principal component analysis and accuracy checks")
|
|
(description
|
|
"This package provides fast computations for @dfn{principal component
|
|
analysis} (PCA), SVD, and eigendecompositions via randomized methods")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-geosketch
|
|
(package
|
|
(name "python-geosketch")
|
|
(version "1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "geosketch" version))
|
|
(sha256
|
|
(base32
|
|
"0knch5h0p8xpm8bi3b5mxyaf1ywwimrsdmbnc1xr5icidcv9gzmv"))))
|
|
(build-system python-build-system)
|
|
(arguments '(#:tests? #false)) ;there are none
|
|
(propagated-inputs (list python-fbpca python-numpy python-scikit-learn))
|
|
(home-page "https://github.com/brianhie/geosketch")
|
|
(synopsis "Geometry-preserving random sampling")
|
|
(description "geosketch is a Python package that implements the geometric
|
|
sketching algorithm described by Brian Hie, Hyunghoon Cho, Benjamin DeMeo,
|
|
Bryan Bryson, and Bonnie Berger in \"Geometric sketching compactly summarizes
|
|
the single-cell transcriptomic landscape\", Cell Systems (2019). This package
|
|
provides an example implementation of the algorithm as well as scripts
|
|
necessary for reproducing the experiments in the paper.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-einops
|
|
(package
|
|
(name "python-einops")
|
|
(version "0.6.1")
|
|
(source (origin
|
|
(method git-fetch) ;PyPI misses .ipynb files required for tests
|
|
(uri (git-reference
|
|
(url "https://github.com/arogozhnikov/einops")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1h8p39kd7ylg99mh620xr20hg7v78x1jnj6vxwk31rlw2dmv2dpr"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list #:phases #~(modify-phases %standard-phases
|
|
(add-after 'unpack 'set-backend
|
|
(lambda _
|
|
;; Einops supports different backends, but we test
|
|
;; only NumPy for availability and simplicity.
|
|
(setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
|
|
(native-inputs (list jupyter
|
|
python-hatchling
|
|
python-nbconvert
|
|
python-nbformat
|
|
python-parameterized
|
|
python-pytest))
|
|
(propagated-inputs (list python-numpy))
|
|
(home-page "https://einops.rocks/")
|
|
(synopsis "Tensor operations for different backends")
|
|
(description "Einops provides a set of tensor operations for NumPy and
|
|
multiple deep learning frameworks.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-xarray
|
|
(package
|
|
(name "python-xarray")
|
|
(version "2023.6.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "xarray" version))
|
|
(sha256
|
|
(base32
|
|
"1339fz5gxkizq02h6vn19546x9p4c3nd9ipzpcg39h7gwhg26yi6"))))
|
|
(build-system pyproject-build-system)
|
|
(native-inputs
|
|
(list python-setuptools-scm python-pytest))
|
|
(propagated-inputs
|
|
(list python-numpy python-pandas))
|
|
(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-xarray-einstats
|
|
(package
|
|
(name "python-xarray-einstats")
|
|
(version "0.5.1")
|
|
(source (origin
|
|
(method git-fetch) ; no tests in PyPI
|
|
(uri (git-reference
|
|
(url "https://github.com/arviz-devs/xarray-einstats")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1gg7p2lq7zxic64nbr6a8ynizs8rjzb29fnqib7hw3lmp13wsfm0"))))
|
|
(build-system pyproject-build-system)
|
|
(native-inputs (list python-einops python-flit-core python-numba
|
|
python-pytest))
|
|
(propagated-inputs (list python-numpy python-scipy python-xarray))
|
|
(home-page "https://einstats.python.arviz.org/en/latest/")
|
|
(synopsis "Stats, linear algebra and einops for xarray")
|
|
(description
|
|
"@code{xarray_einstats} provides wrappers around some NumPy and SciPy
|
|
functions and around einops with an API and features adapted to xarray.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public python-pytensor
|
|
(package
|
|
(name "python-pytensor")
|
|
(version "2.18.1")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/pymc-devs/pytensor")
|
|
(commit (string-append "rel-" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0qa0y13xfm6w7ry7gp0lv84c8blyg34a9ns7ynwqyhf9majq08s5"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
;; Replace version manually because pytensor uses
|
|
;; versioneer, which requires git metadata.
|
|
(add-after 'unpack 'versioneer
|
|
(lambda _
|
|
(with-output-to-file "setup.cfg"
|
|
(lambda ()
|
|
(display "\
|
|
[versioneer]
|
|
VCS = git
|
|
style = pep440
|
|
versionfile_source = pytensor/_version.py
|
|
versionfile_build = pytensor/_version.py
|
|
tag_prefix =
|
|
parentdir_prefix = pytensor-
|
|
")))
|
|
(invoke "versioneer" "install")
|
|
(substitute* "setup.py"
|
|
(("versioneer.get_version\\(\\)")
|
|
(string-append "\"" #$version "\"")))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(setenv "HOME" "/tmp") ; required for most tests
|
|
;; Test discovery fails, have to call pytest by hand.
|
|
;; test_tensor_basic.py file requires JAX.
|
|
(invoke "python" "-m" "pytest" "-vv"
|
|
"--ignore" "tests/link/jax/test_tensor_basic.py"
|
|
;; Skip benchmark tests.
|
|
"-k" (string-append
|
|
"not test_elemwise_speed"
|
|
" and not test_logsumexp_benchmark"
|
|
" and not test_fused_elemwise_benchmark"
|
|
" and not test_scan_multiple_output"
|
|
" and not test_vector_taps_benchmark"
|
|
" and not test_cython_performance")
|
|
;; Skip computationally intensive tests.
|
|
"--ignore" "tests/scan/"
|
|
"--ignore" "tests/tensor/"
|
|
"--ignore" "tests/sandbox/"
|
|
"--ignore" "tests/sparse/sandbox/")))))))
|
|
(native-inputs (list python-cython
|
|
python-pytest
|
|
python-pytest-mock
|
|
python-versioneer))
|
|
(propagated-inputs (list python-cons
|
|
python-etuples
|
|
python-filelock
|
|
python-logical-unification
|
|
python-minikanren
|
|
python-numba
|
|
python-numpy
|
|
python-scipy
|
|
python-typing-extensions))
|
|
(home-page "https://pytensor.readthedocs.io/en/latest/")
|
|
(synopsis
|
|
"Library for mathematical expressions in multi-dimensional arrays")
|
|
(description
|
|
"PyTensor is a Python library that allows one to define, optimize, and
|
|
efficiently evaluate mathematical expressions involving multi-dimensional
|
|
arrays. It is a fork of the Aesara library.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-msgpack-numpy
|
|
(package
|
|
(name "python-msgpack-numpy")
|
|
(version "0.4.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "msgpack-numpy" version))
|
|
(sha256
|
|
(base32
|
|
"0sbfanbkfs6c77np4vz0ayrwnv99bpn5xgj5fnf2yhhk0lcd6ry6"))))
|
|
(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 "0.6.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "UpSetPlot" version))
|
|
(sha256
|
|
(base32
|
|
"11zrykwnb00w5spx4mnsnm0f9gwrphdczainpmwkyyi50vipaa2l"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Patch for compatibility with newer setuptools:
|
|
;; https://github.com/jnothman/UpSetPlot/pull/178
|
|
'(substitute* "upsetplot/data.py"
|
|
(("import distutils")
|
|
"from distutils.version import LooseVersion")
|
|
(("if distutils\\.version\\.LooseVersion")
|
|
"if LooseVersion")))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(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 "2022.2.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/marcomusy/vedo")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1hhv4xc4bphhd1zrnf7r6fpf65xvkdqmb1lh51qg1xpv91h2az0h"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-tests
|
|
;; These tests require online data.
|
|
(lambda _
|
|
(substitute* "tests/common/test_actors.py"
|
|
(("^st = .*") "")
|
|
(("^assert isinstance\\(st\\.GetTexture\\(\\), .*") ""))
|
|
(delete-file "tests/common/test_pyplot.py")))
|
|
(add-after 'build 'mpi-setup
|
|
,%openmpi-setup)
|
|
(replace 'check
|
|
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
|
|
(when tests?
|
|
(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"))))))
|
|
;; Disable the sanity check, which fails with the following error:
|
|
;;
|
|
;; ...checking requirements: ERROR: vedo==2022.2.0 DistributionNotFound(Requirement.parse('vtk<9.1.0'), {'vedo'})
|
|
(delete 'sanity-check))))
|
|
(native-inputs
|
|
(list pkg-config
|
|
python-pkgconfig))
|
|
(propagated-inputs
|
|
(list fenics
|
|
python-deprecated
|
|
python-matplotlib
|
|
python-numpy
|
|
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}.")
|
|
;; 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 "0.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "pandas_flavor" version))
|
|
(sha256
|
|
(base32
|
|
"0473lkbdnsag3w5x65sxwjlyq0i7z938ssxqwn2cpcml282vksx1"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-lazy-loader python-packaging python-pandas python-xarray))
|
|
(home-page "https://github.com/pyjanitor-devs/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 "0.5.2")
|
|
(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
|
|
"0czy7cpn6xx9fs6wbz6rq2lpkb1a89bzxj1anf2f9in1m5qyrh83"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'loosen-requirements
|
|
(lambda _
|
|
(substitute* '("requirements.txt" "setup.py")
|
|
;; Remove sklearn pinning since it works fine with 1.1.2:
|
|
;; https://github.com/raphaelvallat/pingouin/pull/300
|
|
(("scikit-learn<1\\.1\\.0")
|
|
"scikit-learn"))))
|
|
;; 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-pyglm
|
|
(package
|
|
(name "python-pyglm")
|
|
(version "2.5.7")
|
|
(source
|
|
(origin
|
|
;; Test files are not included in the archive in pypi.
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/Zuzu-Typ/PyGLM")
|
|
(commit version)
|
|
;; Checkout the bundled `glm` submodule. PyGLM uses the
|
|
;; currently unreleased GLM_EXT_matrix_integer feature. Can
|
|
;; maybe unbundle once glm@0.9.9.9 is released.
|
|
(recursive? #t)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"08v0cgkwsf8rxscx5g9c5p1dy38rvak2fy3q6hg985if1nj6d9ks"))))
|
|
(build-system python-build-system)
|
|
(home-page "https://github.com/Zuzu-Typ/PyGLM")
|
|
(synopsis "OpenGL Mathematics library for Python")
|
|
(description "PyGLM is a Python extension library which brings the OpenGL
|
|
Mathematics (GLM) library to Python.")
|
|
(license license:zlib)))
|
|
|
|
(define-public python-distributed
|
|
(package
|
|
(name "python-distributed")
|
|
(version "2023.7.0")
|
|
(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
|
|
"0b93fpwz7kw31pkzfyihpkw8mzbqshzd6rw5vcwld7n3z2aaaxxb"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:test-flags
|
|
'(list "-x" "-m"
|
|
(string-append "not slow"
|
|
" and not flaky"
|
|
" and not gpu"
|
|
" and not ipython"
|
|
" and not avoid_ci")
|
|
"-k"
|
|
(string-append
|
|
;; These fail because they require network access,
|
|
;; specifically access to 8.8.8.8.
|
|
"not "
|
|
(string-join
|
|
(list
|
|
"TestClientSecurityLoader.test_security_loader"
|
|
"test_BatchedSend"
|
|
"test_allowed_failures_config"
|
|
"test_async_context_manager"
|
|
"test_async_with"
|
|
"test_client_repr_closed_sync"
|
|
"test_client_is_quiet_cluster_close"
|
|
"test_close_closed"
|
|
"test_close_fast_without_active_handlers"
|
|
"test_close_grace_period_for_handlers"
|
|
"test_close_loop_sync"
|
|
"test_close_properly"
|
|
"test_close_twice"
|
|
"test_compression"
|
|
"test_connection_pool"
|
|
"test_connection_pool_close_while_connecting"
|
|
"test_connection_pool_detects_remote_close"
|
|
"test_connection_pool_outside_cancellation"
|
|
"test_connection_pool_remove"
|
|
"test_connection_pool_respects_limit"
|
|
"test_connection_pool_tls"
|
|
"test_counters"
|
|
"test_dashboard_host"
|
|
"test_dashboard_link_cluster"
|
|
"test_dashboard_link_inproc"
|
|
"test_deserialize_error"
|
|
"test_dont_override_default_get"
|
|
"test_ensure_no_new_clients"
|
|
"test_errors"
|
|
"test_fail_to_pickle_target_2"
|
|
"test_failure_doesnt_crash"
|
|
"test_file_descriptors_dont_leak"
|
|
"test_finished"
|
|
"test_freeze_batched_send"
|
|
"test_get_client_functions_spawn_clusters"
|
|
"test_host_uses_scheduler_protocol"
|
|
"test_identity_inproc"
|
|
"test_identity_tcp"
|
|
"test_large_packets_inproc"
|
|
"test_locked_comm_drop_in_replacement"
|
|
"test_locked_comm_intercept_read"
|
|
"test_locked_comm_intercept_write"
|
|
"test_mixing_clients_different_scheduler"
|
|
"test_multiple_listeners"
|
|
"test_no_dangling_asyncio_tasks"
|
|
"test_plugin_exception"
|
|
"test_plugin_internal_exception"
|
|
"test_plugin_multiple_exceptions"
|
|
"test_ports"
|
|
"test_preload_import_time"
|
|
"test_queue_in_task"
|
|
"test_quiet_client_close"
|
|
"test_rebalance_sync"
|
|
"test_repr_localcluster"
|
|
"test_require_encryption"
|
|
"test_rpc_default"
|
|
"test_rpc_inproc"
|
|
"test_rpc_message_lifetime_default"
|
|
"test_rpc_message_lifetime_inproc"
|
|
"test_rpc_message_lifetime_tcp"
|
|
"test_rpc_serialization"
|
|
"test_rpc_tcp"
|
|
"test_rpc_tls"
|
|
"test_rpc_with_many_connections_inproc"
|
|
"test_rpc_with_many_connections_tcp"
|
|
"test_scheduler_file"
|
|
"test_security_dict_input_no_security"
|
|
"test_security_loader"
|
|
"test_security_loader_ignored_if_explicit_security_provided"
|
|
"test_security_loader_ignored_if_returns_none"
|
|
"test_send_after_stream_start"
|
|
"test_send_before_close"
|
|
"test_send_before_start"
|
|
"test_send_recv_args"
|
|
"test_send_recv_cancelled"
|
|
"test_sending_traffic_jam"
|
|
"test_serializers"
|
|
"test_server"
|
|
"test_server_comms_mark_active_handlers"
|
|
"test_shutdown"
|
|
"test_shutdown_localcluster"
|
|
"test_teardown_failure_doesnt_crash_scheduler"
|
|
"test_threadpoolworkers_pick_correct_ioloop"
|
|
"test_tls_listen_connect"
|
|
"test_tls_temporary_credentials_functional"
|
|
"test_variable_in_task"
|
|
"test_worker_preload_text"
|
|
"test_worker_uses_same_host_as_nanny"
|
|
"test_nanny_timeout") ; access to 127.0.0.1
|
|
" and not ")
|
|
|
|
;; These fail because it doesn't find dask[distributed]
|
|
" and not test_quiet_close_process"
|
|
|
|
;; There is no distributed.__git_revision__ property.
|
|
" and not test_git_revision"
|
|
|
|
;; The system monitor did not return a dictionary containing
|
|
;; "host_disk_io.read_bps".
|
|
" and not test_disk_config"
|
|
|
|
;; These fail because the exception text format
|
|
;; appears to have changed.
|
|
" and not test_exception_text"
|
|
" and not test_worker_bad_args"
|
|
|
|
;; These time out
|
|
" and not test_nanny_timeout"
|
|
|
|
;; These tests are rather flaky
|
|
" and not test_quiet_quit_when_cluster_leaves"
|
|
" and not multiple_clients_restart"
|
|
" and not test_steal_twice"))
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'versioneer
|
|
(lambda _
|
|
;; Our version of versioneer needs setup.cfg. This is adapted
|
|
;; from pyproject.toml.
|
|
(with-output-to-file "setup.cfg"
|
|
(lambda ()
|
|
(display "\
|
|
[versioneer]
|
|
VCS = git
|
|
style = pep440
|
|
versionfile_source = distributed/_version.py
|
|
versionfile_build = distributed/_version.py
|
|
tag_prefix =
|
|
parentdir_prefix = distributed-
|
|
")))
|
|
(invoke "versioneer" "install")
|
|
(substitute* "setup.py"
|
|
(("versioneer.get_version\\(\\)")
|
|
(string-append "\"" #$version "\"")))))
|
|
(add-after 'unpack 'fix-pytest-config
|
|
(lambda _
|
|
;; This option is not supported by our version of pytest.
|
|
(substitute* "pyproject.toml"
|
|
(("--cov-config=pyproject.toml.*") ""))))
|
|
(add-after 'unpack 'fix-references
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(substitute* '("distributed/comm/tests/test_ucx_config.py"
|
|
"distributed/tests/test_client.py"
|
|
"distributed/tests/test_queues.py"
|
|
"distributed/tests/test_variable.py"
|
|
"distributed/cli/tests/test_tls_cli.py"
|
|
"distributed/cli/tests/test_dask_spec.py"
|
|
"distributed/cli/tests/test_dask_worker.py"
|
|
"distributed/cli/tests/test_dask_scheduler.py")
|
|
(("\"dask-scheduler\"")
|
|
(format #false "\"~a/bin/dask-scheduler\"" #$output))
|
|
(("\"dask-worker\"")
|
|
(format #false "\"~a/bin/dask-worker\"" #$output)))))
|
|
(add-before 'check 'pre-check
|
|
(lambda _
|
|
(setenv "DISABLE_IPV6" "1")
|
|
;; The integration tests are all problematic to some
|
|
;; degree. They either require network access or some
|
|
;; other setup. We only run the tests in
|
|
;; distributed/tests.
|
|
(for-each (lambda (dir)
|
|
(delete-file-recursively
|
|
(string-append "distributed/" dir "/tests")))
|
|
(list "cli" "comm" "dashboard" "deploy" "diagnostics"
|
|
"http" "http/scheduler" "http/worker"
|
|
"protocol" "shuffle"))))
|
|
;; We need to use "." here.
|
|
(replace 'check
|
|
(lambda* (#:key tests? test-flags #:allow-other-keys)
|
|
(when tests?
|
|
(apply invoke "python" "-m" "pytest" "." "-vv" test-flags)))))))
|
|
(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-urllib3
|
|
python-zict))
|
|
(native-inputs
|
|
(list python-importlib-metadata
|
|
python-pytest
|
|
python-pytest-timeout
|
|
python-flaky
|
|
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 "0.15.1")
|
|
(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
|
|
"0nf2pdqna2vn7vq7q7b51f3cfbrxfn77pyif3clibjsxzvfm9k03"))))
|
|
(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 "."))))
|
|
(add-after 'unpack 'loosen-requirements
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
;; Don't depend on a specific version of Pandas.
|
|
(("pandas==")
|
|
"pandas>="))))
|
|
(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)))
|
|
|
|
(define-public python-numpy-groupies
|
|
(package
|
|
(name "python-numpy-groupies")
|
|
(version "0.9.14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "numpy_groupies" version))
|
|
(sha256
|
|
(base32 "000qz0z78rs3l6y0dd2vzvd2lx3mczm2762whwsdnhz6c35axdq1"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
(list python-pytest
|
|
python-pytest-runner
|
|
python-numba
|
|
python-numpy))
|
|
(home-page "https://github.com/ml31415/numpy-groupies")
|
|
(synopsis "Tools for group-indexing operations: aggregated sum and more")
|
|
(description
|
|
"This package provides optimized tools for group-indexing operations:
|
|
aggregated sum and more.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-plotnine
|
|
(package
|
|
(name "python-plotnine")
|
|
;; XXX Version 0.12.x exists, but we can't build it because we're still at
|
|
;; matplotlib 3.5. We'd need at least 3.6.
|
|
(version "0.10.1")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/has2k1/plotnine")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0lg53wcm00lj8zbb4q9yj4a0n0fqaqq7c7vj18bda0k56gg0fpwl"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:test-flags
|
|
;; These all fail because the images are considered to be too different,
|
|
;; though they really do look fine.
|
|
'(list "-k" (string-append
|
|
"not TestThemes"
|
|
(string-join
|
|
(list
|
|
;; Image tests
|
|
"test_adjust_text"
|
|
"test_annotation_logticks_coord_flip_discrete"
|
|
"test_annotation_logticks_faceting"
|
|
"test_arrow"
|
|
"test_aslabeller_dict_0tag"
|
|
"test_caption_simple"
|
|
"test_continuous_x"
|
|
"test_continuous_x_fullrange"
|
|
"test_coord_trans_backtransforms"
|
|
"test_coord_trans_se_false"
|
|
"test_datetime_scale_limits"
|
|
"test_dir_v_ncol"
|
|
"test_discrete_x"
|
|
"test_discrete_x_fullrange"
|
|
"test_facet_grid_drop_false"
|
|
"test_facet_grid_expression"
|
|
"test_facet_grid_space_ratios"
|
|
"test_facet_wrap"
|
|
"test_facet_wrap_expression"
|
|
"test_facet_wrap_label_both"
|
|
"test_label_context_wrap2vars"
|
|
"test_labeller_cols_both_grid"
|
|
"test_labeller_cols_both_wrap"
|
|
"test_labeller_towords"
|
|
"test_missing_data_discrete_scale"
|
|
"test_ribbon_facetting"
|
|
"test_stack_non_linear_scale"
|
|
"test_uneven_num_of_lines"
|
|
|
|
;; Missing optional modules
|
|
"test_non_linear_smooth"
|
|
"test_non_linear_smooth_no_ci")
|
|
" and not " 'prefix)))
|
|
#:phases
|
|
'(modify-phases %standard-phases
|
|
(add-before 'check 'pre-check
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
;; The data files are referenced by the tests but they are not
|
|
;; installed.
|
|
(copy-recursively "plotnine/data"
|
|
(string-append (site-packages inputs outputs)
|
|
"/plotnine/data"))
|
|
;; Matplotlib needs to be able to write its configuration file
|
|
;; somewhere.
|
|
(setenv "MPLCONFIGDIR" "/tmp")
|
|
(setenv "TZ" "UTC")
|
|
(setenv "TZDIR"
|
|
(search-input-directory inputs "share/zoneinfo")))))))
|
|
(propagated-inputs
|
|
(list python-adjusttext
|
|
python-matplotlib
|
|
python-mizani
|
|
python-numpy
|
|
python-patsy
|
|
python-scipy
|
|
python-statsmodels))
|
|
(native-inputs
|
|
(list python-geopandas
|
|
python-mock
|
|
python-pandas
|
|
python-pytest python-pytest-cov
|
|
tzdata-for-tests))
|
|
(home-page "https://github.com/has2k1/plotnine")
|
|
(synopsis "Grammar of Graphics for Python")
|
|
(description
|
|
"Plotnine is a Python implementation of the Grammar of Graphics.
|
|
It is a powerful graphics concept for creating plots and visualizations in a
|
|
structured and declarative manner. It is inspired by the R package ggplot2
|
|
and aims to provide a similar API and functionality in Python.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-pyvista
|
|
(package
|
|
(name "python-pyvista")
|
|
(version "0.42.3")
|
|
(source
|
|
;; The PyPI tarball does not contain the tests.
|
|
;; (However, we don't yet actually run the tests.)
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/pyvista/pyvista")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "1qxq0y0hc72hb60w3qq48fma8l6ffz7bdm75ymn1020bvfqrm1s4"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-imageio
|
|
python-matplotlib
|
|
python-meshio
|
|
python-numpy
|
|
python-pillow
|
|
python-pooch
|
|
python-scooby
|
|
vtk))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
;; Disable tests for now because they require several modules
|
|
;; currently unpackaged in Guix.
|
|
(delete 'check)
|
|
;; Disable the sanity check, which fails with the following error:
|
|
;;
|
|
;; ...checking requirements: ERROR: pyvista==0.42.3 DistributionNotFound(Requirement.parse('vtk'), {'pyvista'})
|
|
(delete 'sanity-check))))
|
|
(home-page "https://docs.pyvista.org/")
|
|
(synopsis "3D plotting and mesh analysis through VTK")
|
|
(description
|
|
"PyVista is...
|
|
|
|
@itemize
|
|
@item @emph{Pythonic VTK}: a high-level API to the Visualization
|
|
Toolkit (VTK);
|
|
@item mesh data structures and filtering methods for spatial datasets;
|
|
@item 3D plotting made simple and built for large/complex data geometries.
|
|
@end itemize
|
|
|
|
This package provides a Pythonic, well-documented interface exposing VTK's
|
|
powerful visualization backend to facilitate rapid prototyping, analysis, and
|
|
visual integration of spatially referenced datasets.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-simplespectral
|
|
(package
|
|
(name "python-simplespectral")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "SimpleSpectral" version))
|
|
(sha256
|
|
(base32 "0qh3xwdv9cwcqdamvglrhm586p4yaq1hd291py1fvykhk2a2d4w6"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
(list python-numpy python-scipy))
|
|
(home-page "https://github.com/xmikos/simplespectral")
|
|
(synopsis "FFT module for Python")
|
|
(description
|
|
"This package provides a simplified @code{scipy.signal.spectral} module
|
|
to do spectral analysis in Python.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-traittypes
|
|
(package
|
|
(name "python-traittypes")
|
|
(version "0.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "traittypes" version))
|
|
(sha256
|
|
(base32 "1mlv93irdrgxrhnhq3ksi9585d55bpi4mv9dha4p8gkkjiia4vxy"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
;; This one test fails because it doesn't raise an expected
|
|
;; exception.
|
|
(invoke "pytest" "-vv" "-k" "not test_bad_values")))))))
|
|
(propagated-inputs (list python-traitlets))
|
|
(native-inputs
|
|
(list python-numpy
|
|
python-pandas
|
|
python-nose
|
|
python-pytest
|
|
python-xarray))
|
|
(home-page "https://github.com/jupyter-widgets/traittypes")
|
|
(synopsis "Trait types for NumPy, SciPy and friends")
|
|
(description "The goal of this package is to provide a reference
|
|
implementation of trait types for common data structures used in the scipy
|
|
stack such as numpy arrays or pandas and xarray data structures. These are
|
|
out of the scope of the main traitlets project but are a common requirement to
|
|
build applications with traitlets in combination with the scipy stack.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-aplus
|
|
(package
|
|
(name "python-aplus")
|
|
(version "0.11.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "aplus" version))
|
|
(sha256
|
|
(base32 "1rznc26nlp641rn8gpdngfp79a3fji38yavqakxi35mx2da04msg"))))
|
|
(build-system python-build-system)
|
|
(home-page "https://github.com/xogeny/aplus")
|
|
(synopsis "Promises/A+ for Python")
|
|
(description "This package is an implementation of the Promises/A+
|
|
specification and test suite in Python.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-climin
|
|
(package
|
|
(name "python-climin")
|
|
(version "0.1a1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "climin" version))
|
|
(sha256
|
|
(base32
|
|
"1wpjisd5zzi5yvjff02hnxn84822k8sdxvvd33lil2x79wdb36rv"))))
|
|
(build-system python-build-system)
|
|
(native-inputs (list python-nose))
|
|
(propagated-inputs (list python-numpydoc python-numpy python-scipy))
|
|
(home-page "https://github.com/BRML/climin")
|
|
(synopsis "Optimization for machine learning")
|
|
(description
|
|
"@command{climin} is a Python package for optimization,
|
|
heavily biased to machine learning scenarios. It works on top of
|
|
@command{numpy} and (partially) @command{gnumpy}.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-paramz
|
|
(package
|
|
(name "python-paramz")
|
|
(version "0.9.5")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "paramz" version))
|
|
(sha256
|
|
(base32
|
|
"16hbh97kj6b1c2gw22rqnr3w3nqkszh9gj8vgx738gq81wf225q9"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs (list python-decorator python-numpy python-scipy
|
|
python-six))
|
|
(home-page "https://github.com/sods/paramz")
|
|
(synopsis "The Parameterization Framework")
|
|
(description
|
|
"@command{paramz} is a lightweight parameterization framework
|
|
for parameterized model creation and handling. Its features include:
|
|
|
|
@itemize
|
|
@item Easy model creation with parameters.
|
|
@item Fast optimized access of parameters for optimization routines.
|
|
@item Memory efficient storage of parameters (only one copy in memory).
|
|
@item Renaming of parameters.
|
|
@item Intuitive printing of models and parameters.
|
|
@item Gradient saving directly inside parameters.
|
|
@item Gradient checking of parameters.
|
|
@item Optimization of parameters.
|
|
@item Jupyter notebook integration.
|
|
@item Efficient storage of models, for reloading.
|
|
@item Efficient caching.
|
|
@end itemize")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-gpy
|
|
(package
|
|
(name "python-gpy")
|
|
(version "1.10.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "GPy" version))
|
|
(sha256
|
|
(base32
|
|
"1yx65ajrmqp02ykclhlb0n8s3bx5r0xj075swwwigiqaippr7dx2"))
|
|
(snippet
|
|
#~(begin (use-modules (guix build utils))
|
|
(substitute* "GPy/models/state_space_main.py"
|
|
(("collections\\.Iterable") "collections.abc.Iterable"))))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases (modify-phases %standard-phases
|
|
(add-before 'check 'remove-plotting-tests
|
|
;; These fail
|
|
(lambda _
|
|
(delete-file "GPy/testing/plotting_tests.py"))))))
|
|
(native-inputs (list python-cython python-nose python-climin))
|
|
(propagated-inputs (list python-numpy python-paramz python-scipy
|
|
python-six))
|
|
(home-page "https://sheffieldml.github.io/GPy/")
|
|
(synopsis "The Gaussian Process Toolbox")
|
|
(description
|
|
"@command{GPy} is a Gaussian Process (GP) framework written in
|
|
Python, from the Sheffield machine learning group. GPy implements a range of
|
|
machine learning algorithms based on GPs.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-pyfma
|
|
(package
|
|
(name "python-pyfma")
|
|
(version "0.1.6")
|
|
(source (origin
|
|
(method git-fetch) ;for tests
|
|
(uri (git-reference
|
|
(url "https://github.com/nschloe/pyfma")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"12i68jj9n1qj9phjnj6f0kmfhlsd3fqjlk9p6d4gs008azw5m8yn"))))
|
|
(build-system pyproject-build-system)
|
|
(propagated-inputs (list python-numpy))
|
|
(native-inputs (list pybind11 python-pytest))
|
|
(home-page "https://github.com/nschloe/pyfma")
|
|
(synopsis "Fused multiply-add for Python")
|
|
(description "@code{pyfma} provides an implementation of fused
|
|
multiply-add which computes @code{(x*y) + z} with a single rounding.
|
|
This is useful for dot products, matrix multiplications, polynomial
|
|
evaluations (e.g., with Horner's rule), Newton's method for evaluating
|
|
functions, convolutions, artificial neural networks etc.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-pydicom
|
|
(package
|
|
(name "python-pydicom")
|
|
(version "2.3.0")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/pydicom/pydicom")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"18l26s53yf5j9yh2zwq83n74qq4f2iq0cfblamsw4y9k35l1c108"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(chdir "pydicom/tests")
|
|
(invoke "python3" "-m" "pytest" "-k" ;skip tests using web data
|
|
(string-append
|
|
"not test_jpeg_ls_pixel_data.py"
|
|
" and not test_gdcm_pixel_data.py"
|
|
" and not test_pillow_pixel_data.py"
|
|
" and not test_rle_pixel_data.py"
|
|
" and not Test_JPEG_LS_Lossless_transfer_syntax"
|
|
" and not test_numpy_pixel_data.py"
|
|
" and not test_data_manager.py"
|
|
" and not test_handler_util.py"
|
|
" and not test_overlay_np.py"
|
|
" and not test_encoders_pydicom.py"
|
|
" and not test_encaps.py"
|
|
" and not test_reading_ds_with_known_tags_with_UN_VR"
|
|
" and not TestDatasetOverlayArray"
|
|
" and not TestReader"
|
|
" and not test_filewriter.py"))))))))
|
|
(native-inputs (list python-pytest))
|
|
(inputs (list gdcm libjpeg-turbo))
|
|
(propagated-inputs (list python-numpy python-pillow))
|
|
(home-page "https://github.com/pydicom/pydicom")
|
|
(synopsis "Python library for reading and writing DICOM data")
|
|
(description "@code{python-pydicom} is a Python library for reading and
|
|
writing DICOM medical imaging data. It lets developers read, modify and write
|
|
DICOM data in a pythonic way.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-deepdish
|
|
(package
|
|
(name "python-deepdish")
|
|
(version "0.3.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "deepdish" version))
|
|
(sha256
|
|
(base32
|
|
"1wqzwh3y0mjdyba5kfbvlamn561d3afz50zi712c7klkysz3mzva"))))
|
|
(arguments
|
|
(list #:phases #~(modify-phases %standard-phases
|
|
(add-after 'unpack 'dont-vendor-six
|
|
(lambda _
|
|
(delete-file "deepdish/six.py")
|
|
(substitute* "deepdish/io/hdf5io.py"
|
|
(("from deepdish import six") "import six"))
|
|
(substitute* "deepdish/io/ls.py"
|
|
(("from deepdish import io, six, __version__")
|
|
"from deepdish import io, __version__
|
|
import six
|
|
")))))))
|
|
(build-system python-build-system)
|
|
(native-inputs (list python-pandas))
|
|
(propagated-inputs (list python-numpy python-scipy python-six
|
|
python-tables))
|
|
(home-page "https://github.com/uchicago-cs/deepdish")
|
|
(synopsis "Python library for HDF5 file saving and loading")
|
|
(description
|
|
"Deepdish is a Python library to load and save HDF5 files.
|
|
The primary feature of deepdish is its ability to save and load all kinds of
|
|
data as HDF5. It can save any Python data structure, offering the same ease
|
|
of use as pickling or @code{numpy.save}, but with the language
|
|
interoperability offered by HDF5.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-simple-pid
|
|
(package
|
|
(name "python-simple-pid")
|
|
(version "1.0.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "simple-pid" version))
|
|
(sha256
|
|
(base32
|
|
"094mz6rmfq1h0gpns5vlxb7xf9297hlkhndw7g9k95ziqfkv7mk0"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "python" "-m" "unittest" "discover" "tests/")))))))
|
|
(home-page "https://github.com/m-lundberg/simple-pid")
|
|
(synopsis "Easy to use PID controller")
|
|
(description "This package provides a simple and easy-to-use @acronym{PID,
|
|
proportional-integral-derivative} controller.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-opt-einsum
|
|
(package
|
|
(name "python-opt-einsum")
|
|
(version "3.3.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "opt_einsum" version))
|
|
(sha256
|
|
(base32
|
|
"0jb5lia0q742d1713jk33vlj41y61sf52j6pgk7pvhxvfxglgxjr"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "pytest" "-vv")))))))
|
|
(propagated-inputs (list python-numpy))
|
|
(native-inputs (list python-pytest python-pytest-cov python-pytest-pep8))
|
|
(home-page "https://github.com/dgasmith/opt_einsum")
|
|
(synopsis "Optimizing numpys einsum function")
|
|
(description
|
|
"Optimized einsum can significantly reduce the overall execution time of
|
|
einsum-like expressions by optimizing the expression's contraction order and
|
|
dispatching many operations to canonical BLAS, cuBLAS, or other specialized
|
|
routines. Optimized einsum is agnostic to the backend and can handle NumPy,
|
|
Dask, PyTorch, Tensorflow, CuPy, Sparse, Theano, JAX, and Autograd arrays as
|
|
well as potentially any library which conforms to a standard API. See the
|
|
documentation for more information.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-vaex-core
|
|
(package
|
|
(name "python-vaex-core")
|
|
(version "4.13.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "vaex-core" version))
|
|
(sha256
|
|
(base32 "0ni862x5njhfsldjy49xmasd34plrs7yrmkyss6z1b6sgkbw9fsb"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Remove bundled libraries
|
|
'(for-each delete-file-recursively
|
|
(list "vendor/boost"
|
|
"vendor/pcre"
|
|
"vendor/pybind11")))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:tests? #false ;require vaex.server and others, which require vaex-core.
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "pytest" "-vv" )))))))
|
|
(inputs
|
|
(list boost pcre pybind11-2.3))
|
|
(propagated-inputs
|
|
(list python-aplus
|
|
python-blake3
|
|
python-click ;XXX for dask
|
|
python-cloudpickle
|
|
python-dask
|
|
python-filelock
|
|
python-frozendict
|
|
python-future
|
|
python-nest-asyncio
|
|
python-numpy
|
|
python-pandas
|
|
python-progressbar2
|
|
python-pyarrow
|
|
python-pydantic
|
|
python-pyyaml
|
|
python-requests
|
|
python-rich
|
|
python-six
|
|
python-tabulate))
|
|
(native-inputs
|
|
(list python-pytest python-cython))
|
|
(home-page "https://www.github.com/maartenbreddels/vaex")
|
|
(synopsis "Core of Vaex library for exploring tabular datasets")
|
|
(description "Vaex is a high performance Python library for lazy
|
|
Out-of-Core DataFrames (similar to Pandas), to visualize and explore big
|
|
tabular datasets. This package provides the core modules of Vaex.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-salib
|
|
(package
|
|
(name "python-salib")
|
|
(version "1.4.7")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/SALib/SALib")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"18xfyzircsx2q2lmfc9lxb6xvkxicnc83qzghd7df1jsprr5ymch"))))
|
|
(build-system pyproject-build-system)
|
|
(propagated-inputs (list python-matplotlib
|
|
python-multiprocess
|
|
python-numpy
|
|
python-pandas
|
|
python-scipy))
|
|
(native-inputs (list python-hatchling python-pytest python-pytest-cov))
|
|
(home-page "https://salib.readthedocs.io/en/latest/")
|
|
(synopsis "Tools for global sensitivity analysis")
|
|
(description "SALib provides tools for global sensitivity analysis. It
|
|
contains Sobol', Morris, FAST, DGSM, PAWN, HDMR, Moment Independent and
|
|
fractional factorial methods.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-pylems
|
|
(package
|
|
(name "python-pylems")
|
|
(version "0.6.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "PyLEMS" version))
|
|
(sha256
|
|
(base32
|
|
"074azbyivjbwi61fs5p8z9n6d8nk8xw6fmln1www13z1dccb3740"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs (list python-lxml))
|
|
(home-page "https://github.com/LEMS/pylems")
|
|
(synopsis
|
|
"Python support for the Low Entropy Model Specification language (LEMS)")
|
|
(description
|
|
"A LEMS simulator written in Python which can be used to run
|
|
NeuroML2 models.")
|
|
(license license:lgpl3)))
|
|
|
|
(define-public python-libneuroml
|
|
(package
|
|
(name "python-libneuroml")
|
|
(version "0.4.1")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/NeuralEnsemble/libNeuroML.git")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0mrm4rd6x1sm6hkvhk20mkqp9q53sl3lbvq6hqzyymkw1iqq6bhy"))))
|
|
(build-system pyproject-build-system)
|
|
(propagated-inputs (list python-lxml python-six))
|
|
(native-inputs (list python-pytest python-numpy python-tables))
|
|
(home-page "https://libneuroml.readthedocs.org/en/latest/")
|
|
(synopsis
|
|
"Python library for working with NeuroML descriptions of neuronal models")
|
|
(description
|
|
"This package provides a Python library for working with NeuroML descriptions of
|
|
neuronal models")
|
|
(license license:bsd-3)))
|
|
|
|
;;;
|
|
;;; Avoid adding new packages to the end of this file. To reduce the chances
|
|
;;; of a merge conflict, place them above by existing packages with similar
|
|
;;; functionality or similar names.
|
|
;;;
|