3369 lines
133 KiB
Scheme
3369 lines
133 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
|
||
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
|
||
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
|
||
;;; Copyright © 2016, 2022-2024 Efraim Flashner <efraim@flashner.co.il>
|
||
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
|
||
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
|
||
;;; Copyright © 2019, 2021, 2022, 2023, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
|
||
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
|
||
;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
|
||
;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net>
|
||
;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
|
||
;;; Copyright © 2021 Roel Janssen <roel@gnu.org>
|
||
;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
|
||
;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
|
||
;;; Copyright © 2021, 2023 Felix Gruber <felgru@posteo.net>
|
||
;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes@gmail.com>
|
||
;;; Copyright © 2022 Guillaume Le Vaillant <glv@posteo.net>
|
||
;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
|
||
;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
|
||
;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
|
||
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
|
||
;;; Copyright © 2022 jgart <jgart@dismail.de>
|
||
;;; Copyright © 2023, 2024 Troy Figiel <troy@troyfigiel.com>
|
||
;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
|
||
;;; Copyright © 2024 Marco Baggio <marco.baggio@mdc-berlin.de>
|
||
;;;
|
||
;;; This file is part of GNU Guix.
|
||
;;;
|
||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||
;;; under the terms of the GNU General Public License as published by
|
||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||
;;; your option) any later version.
|
||
;;;
|
||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||
;;; GNU General Public License for more details.
|
||
;;;
|
||
;;; You should have received a copy of the GNU General Public License
|
||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||
|
||
(define-module (gnu packages python-science)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages base)
|
||
#:use-module (gnu packages bioinformatics)
|
||
#:use-module (gnu packages boost)
|
||
#:use-module (gnu packages build-tools)
|
||
#:use-module (gnu packages check)
|
||
#:use-module (gnu packages chemistry)
|
||
#:use-module (gnu packages cmake)
|
||
#:use-module (gnu packages cpp)
|
||
#:use-module (gnu packages crates-io)
|
||
#:use-module (gnu packages crypto)
|
||
#:use-module (gnu packages databases)
|
||
#:use-module (gnu packages digest)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages geo)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages image-processing)
|
||
#:use-module (gnu packages machine-learning)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages mpi)
|
||
#:use-module (gnu packages pcre)
|
||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages python)
|
||
#:use-module (gnu packages python-build)
|
||
#:use-module (gnu packages python-crypto)
|
||
#:use-module (gnu packages python-check)
|
||
#:use-module (gnu packages python-web)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages rust-apps)
|
||
#:use-module (gnu packages simulation)
|
||
#:use-module (gnu packages sphinx)
|
||
#:use-module (gnu packages statistics)
|
||
#:use-module (gnu packages time)
|
||
#:use-module (gnu packages xdisorg)
|
||
#:use-module (gnu packages xml)
|
||
#:use-module (gnu packages xorg)
|
||
#:use-module (guix packages)
|
||
#:use-module (guix gexp)
|
||
#:use-module (guix download)
|
||
#:use-module (guix git-download)
|
||
#:use-module (guix utils)
|
||
#:use-module (guix build-system cargo)
|
||
#:use-module (guix build-system python)
|
||
#:use-module (guix build-system pyproject))
|
||
|
||
(define-public python-cvxpy
|
||
(package
|
||
(name "python-cvxpy")
|
||
(version "1.4.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "cvxpy" version))
|
||
(sha256
|
||
(base32 "0lyri9j5gyg6m1bvfy1a4q2sqdy3w45lp0bxiq9as8srq347ic5i"))))
|
||
(build-system pyproject-build-system)
|
||
;; It's odd but cvxpy appears to need pybind11 at runtime according to its
|
||
;; specification. Moving pybind11 to native-inputs would break downstream
|
||
;; packages using cvxpy.
|
||
(propagated-inputs (list pybind11
|
||
python-clarabel
|
||
python-ecos
|
||
python-numpy
|
||
python-osqp
|
||
python-scipy
|
||
python-scs))
|
||
(native-inputs (list python-pytest python-setuptools))
|
||
(home-page "https://github.com/cvxpy/cvxpy")
|
||
(synopsis "DSL for modeling convex optimization problems")
|
||
(description
|
||
"This package provides a domain-specific language for modeling convex
|
||
optimization problems in Python.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-ecos
|
||
(package
|
||
(name "python-ecos")
|
||
(version "2.0.13")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/embotech/ecos-python")
|
||
(commit (string-append "v" version))
|
||
(recursive? #true)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "16ljq8maflfkgbw16rldg6cy14vgz2pb3b2iga60i7yzkq2ikmyw"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy python-scipy))
|
||
(native-inputs (list python-pytest python-setuptools python-wheel))
|
||
(home-page "https://github.com/embotech/ecos")
|
||
(synopsis "Embedded Cone Solver")
|
||
(description
|
||
"This is the Python package for ECOS: Embedded Cone Solver. ECOS is
|
||
numerical software for solving convex second-order cone programs (SOCPs).")
|
||
(license license:gpl3)))
|
||
|
||
(define-public python-formulaic
|
||
(package
|
||
(name "python-formulaic")
|
||
(version "1.0.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "formulaic" version))
|
||
(sha256
|
||
(base32 "18gvd3f2x358jj0df8vx5fhhnvzw047rsrs03vmvqnxaly97kpb4"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-astor
|
||
python-cached-property
|
||
python-interface-meta
|
||
python-numpy
|
||
python-pandas
|
||
python-scipy
|
||
python-typing-extensions
|
||
python-wrapt))
|
||
(native-inputs (list python-hatchling python-hatch-vcs python-pytest))
|
||
(home-page "https://github.com/matthewwardrop/formulaic")
|
||
(synopsis "Implementation of Wilkinson formulas")
|
||
(description "Formulaic is a high-performance implementation of Wilkinson
|
||
formulas for Python.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-osqp
|
||
(package
|
||
(name "python-osqp")
|
||
(version "0.6.5")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/osqp/osqp-python")
|
||
(commit (string-append "v" version))
|
||
(recursive? #true)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0s1nbzkfsi2h4ji3v0k14pfcrvinakrwy4xdbz320lbaq3yb0b65"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; Some of these test failures are explained by
|
||
;; https://github.com/osqp/osqp-python/issues/121.
|
||
;; These tests require the module "vec_emosqp", which we don't have.
|
||
'(list "--ignore=src/osqp/tests/codegen_vectors_test.py"
|
||
;; These tests need "mat_emosqp".
|
||
"--ignore=src/osqp/tests/codegen_matrices_test.py"
|
||
;; These fail with accuracy differences
|
||
"--ignore=src/osqp/tests/update_matrices_test.py"
|
||
"--ignore=src/osqp/tests/feasibility_test.py"
|
||
"--ignore=src/osqp/tests/polishing_test.py"
|
||
;; This requires the nonfree MKL.
|
||
"--ignore=src/osqp/tests/mkl_pardiso_test.py")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
;; It looks like the upgrade to scipy 1.12.0 only broke the test
|
||
;; suite, not the features of this library. See
|
||
;; https://github.com/osqp/osqp-python/issues/121.
|
||
(add-after 'unpack 'relax-requirements
|
||
(lambda _
|
||
(substitute* "requirements.txt"
|
||
(("scipy.*1.12.0") "scipy <= 1.12.0"))))
|
||
(add-before 'build 'set-version
|
||
(lambda _
|
||
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
|
||
(propagated-inputs (list python-numpy python-qdldl python-scipy))
|
||
;; We need setuptools-scm only for the version number. Without it the
|
||
;; version number will be "0.0.0" and downstream packages will complain.
|
||
(native-inputs (list cmake-minimal python-pytest python-setuptools-scm))
|
||
(home-page "https://osqp.org/")
|
||
(synopsis "OSQP: operator splitting QP solver")
|
||
(description "The OSQP (Operator Splitting Quadratic Program) solver is a
|
||
numerical optimization package.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-qdldl
|
||
(package
|
||
(name "python-qdldl")
|
||
(version "0.1.7.post2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "qdldl" version))
|
||
(sha256
|
||
(base32 "1lspam0k8gnw1yglqxvdv350fq00nkgdfmkizmx7bk0hxjjkj5ab"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs (list cmake-minimal pybind11))
|
||
(propagated-inputs (list python-numpy python-scipy))
|
||
(home-page "https://github.com/oxfordcontrol/qdldl-python/")
|
||
(synopsis "QDLDL LDL factorization routine")
|
||
(description "This package provides a Python interface to the QDLDL LDL
|
||
factorization routine for quasi-definite linear system.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-scipy
|
||
(package
|
||
(name "python-scipy")
|
||
(version "1.12.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "scipy" version))
|
||
(sha256
|
||
(base32 "18rn15wg3lp58z204fbjjhy0h79c53yg3c4qqs9h3liniamspxab"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
;; Step out of the source directory to avoid interference.
|
||
(with-directory-excursion "/tmp"
|
||
(invoke "python" "-c"
|
||
(string-append
|
||
"import scipy; scipy.test('fast', parallel="
|
||
(number->string (parallel-job-count))
|
||
", verbose=2)"))))))
|
||
(add-after 'check 'install-doc
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; FIXME: Documentation cannot be built because it requires
|
||
;; a newer version of pydata-sphinx-theme, which currently
|
||
;; cannot build without internet access:
|
||
;; <https://github.com/pydata/pydata-sphinx-theme/issues/628>.
|
||
;; Keep the phase for easy testing.
|
||
(let ((sphinx-build (false-if-exception
|
||
(search-input-file input "bin/sphinx-build"))))
|
||
(if sphinx-build
|
||
(let* ((doc (assoc-ref outputs "doc"))
|
||
(data (string-append doc "/share"))
|
||
(docdir (string-append
|
||
data "/doc/"
|
||
#$(package-name this-package) "-"
|
||
#$(package-version this-package)))
|
||
(html (string-append docdir "/html")))
|
||
(with-directory-excursion "doc"
|
||
;; Build doc.
|
||
(invoke "make" "html"
|
||
;; Building the documentation takes a very long time.
|
||
;; Parallelize it.
|
||
(string-append "SPHINXOPTS=-j"
|
||
(number->string (parallel-job-count))))
|
||
;; Install doc.
|
||
(mkdir-p html)
|
||
(copy-recursively "build/html" html)))
|
||
(format #t "sphinx-build not found, skipping~%"))))))))
|
||
(propagated-inputs
|
||
(append
|
||
(if (supported-package? python-jupytext) ; Depends on pandoc.
|
||
(list python-jupytext)
|
||
'())
|
||
(list python-matplotlib
|
||
python-mpmath
|
||
python-mypy
|
||
python-numpy
|
||
python-numpydoc
|
||
python-pydata-sphinx-theme
|
||
python-pydevtool
|
||
python-pythran
|
||
python-rich-click
|
||
python-sphinx
|
||
python-threadpoolctl
|
||
python-typing-extensions)))
|
||
(inputs (list openblas pybind11-2.10))
|
||
(native-inputs
|
||
(list gfortran
|
||
;; XXX: Adding gfortran shadows GCC headers, causing a compilation
|
||
;; failure. Somehow also providing GCC works around it ...
|
||
gcc
|
||
meson-python
|
||
pkg-config
|
||
python-click
|
||
python-cython-0.29.35
|
||
python-doit
|
||
python-hypothesis
|
||
python-pooch
|
||
python-pycodestyle
|
||
python-pydevtool
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-pytest-timeout
|
||
python-pytest-xdist))
|
||
(home-page "https://scipy.org/")
|
||
(synopsis "The Scipy library provides efficient numerical routines")
|
||
(description "The SciPy library is one of the core packages that make up
|
||
the SciPy stack. It provides many user-friendly and efficient numerical
|
||
routines such as routines for numerical integration and optimization.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-scikit-allel
|
||
(package
|
||
(name "python-scikit-allel")
|
||
(version "1.3.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "scikit-allel" version))
|
||
(sha256
|
||
(base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "-k"
|
||
(string-append
|
||
;; AttributeError: 'Dataset' object has no attribute 'asstr'
|
||
"not test_vcf_to_hdf5"
|
||
" and not test_vcf_to_hdf5_exclude"
|
||
" and not test_vcf_to_hdf5_rename"
|
||
" and not test_vcf_to_hdf5_group"
|
||
" and not test_vcf_to_hdf5_ann"
|
||
;; Does not work with recent hmmlearn
|
||
" and not test_roh_mhmm_0pct"
|
||
" and not test_roh_mhmm_100pct"))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-before 'check 'build-ext
|
||
(lambda _
|
||
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
||
(propagated-inputs
|
||
(list python-dask
|
||
python-numpy))
|
||
(native-inputs
|
||
(list python-cython
|
||
;; The following are all needed for the tests
|
||
htslib
|
||
python-h5py
|
||
python-hmmlearn
|
||
python-numexpr
|
||
python-pytest
|
||
python-scipy
|
||
python-setuptools-scm
|
||
python-zarr))
|
||
(home-page "https://github.com/cggh/scikit-allel")
|
||
(synopsis "Explore and analyze genetic variation data")
|
||
(description
|
||
"This package provides utilities for exploratory analysis of large scale
|
||
genetic variation data.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-scikit-build-core
|
||
(package
|
||
(name "python-scikit-build-core")
|
||
(version "0.9.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "scikit_build_core" version))
|
||
(sha256
|
||
(base32 "146k3w3kcamyyqassmsmp6h4f5lb3cdqnbjjcbf0jm1s8wz1279l"))))
|
||
(build-system pyproject-build-system)
|
||
;; Tests are aborted with the admonition: "setup.py install is
|
||
;; deprecated. Use build and pip and other standards-based tools."
|
||
(arguments (list #:tests? #false))
|
||
(propagated-inputs (list python-exceptiongroup
|
||
python-importlib-metadata
|
||
python-importlib-resources
|
||
python-packaging
|
||
python-pathspec
|
||
python-tomli
|
||
python-typing-extensions))
|
||
(native-inputs (list pybind11
|
||
python-pypa-build
|
||
python-cattrs
|
||
python-fastjsonschema
|
||
python-hatch-fancy-pypi-readme
|
||
python-hatch-vcs
|
||
python-hatchling
|
||
python-numpy
|
||
python-pip
|
||
python-pytest
|
||
python-rich
|
||
python-setuptools
|
||
python-setuptools-scm
|
||
python-virtualenv
|
||
python-wheel))
|
||
(home-page "https://github.com/scikit-build/scikit-build-core")
|
||
(synopsis "Build backend for CMake based projects")
|
||
(description "Scikit-build-core is a build backend for Python that uses
|
||
CMake to build extension modules. It has a simple yet powerful static
|
||
configuration system in pyproject.toml, and supports almost unlimited
|
||
flexibility via CMake. It was initially developed to support the demanding
|
||
needs of scientific users, but can build any sort of package that uses
|
||
CMake.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-scikit-fem
|
||
(package
|
||
(name "python-scikit-fem")
|
||
(version "9.0.1")
|
||
(source (origin
|
||
(method git-fetch) ; no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/kinnala/scikit-fem")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1r1c88rbaa7vjfnljbzx8paf36yzpy33bragl99ykn6i2srmjrd4"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-meshio python-numpy python-scipy))
|
||
(native-inputs
|
||
(list python-autograd
|
||
python-pyamg
|
||
python-pytest
|
||
python-shapely))
|
||
(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.
|
||
Its main purpose is the transformation of bilinear forms into sparse matrices
|
||
and linear forms into vectors.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-scikit-fuzzy
|
||
(package
|
||
(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 "0.23.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/scikit-image/scikit-image")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1bc8i57sjk44vd9k1ilr6fpvfq1zbq9yfi22lz22k26mzrlisym3"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
;; Disable flaky test
|
||
#:test-flags #~(list "-k" "not test_ellipse_parameter_stability")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-before 'build 'change-home-dir
|
||
(lambda _
|
||
;; Change from /homeless-shelter to /tmp for write permission.
|
||
(setenv "HOME" "/tmp")))
|
||
(replace 'check
|
||
(lambda* (#:key tests? test-flags #:allow-other-keys)
|
||
(when tests?
|
||
(with-directory-excursion "/tmp"
|
||
(apply invoke "pytest" "-v" "--doctest-modules"
|
||
(append test-flags (list #$output))))))))))
|
||
;; 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-lazy-loader
|
||
python-matplotlib
|
||
python-networkx
|
||
python-numpy
|
||
python-pillow
|
||
python-pythran
|
||
python-pywavelets
|
||
python-scipy
|
||
python-tifffile))
|
||
(native-inputs
|
||
(list meson-python
|
||
python-cython
|
||
python-numpydoc
|
||
python-packaging
|
||
python-pytest
|
||
python-pytest-localserver
|
||
python-wheel))
|
||
(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-opt
|
||
(package
|
||
(name "python-scikit-opt")
|
||
(version "0.6.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "scikit-opt" version))
|
||
(sha256
|
||
(base32 "0ycqizgsj7q57asc1bphzhf1fx9zqn0vx5rli7q541bas64hfqiy"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy python-pytorch python-scipy))
|
||
(home-page "https://github.com/guofei9987/scikit-opt")
|
||
(synopsis "Swarm intelligence algorithms in Python")
|
||
(description
|
||
"Scikit-opt (or sko) is a Python module implementing @dfn{swarm
|
||
intelligence} algorithms: genetic algorithm, particle swarm optimization,
|
||
simulated annealing, ant colony algorithm, immune algorithm, artificial fish
|
||
swarm algorithm.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-scikit-optimize
|
||
(package
|
||
(name "python-scikit-optimize")
|
||
(version "0.9.0")
|
||
(source (origin
|
||
(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"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Since scikit-learn 1.3 max_features no longer supports
|
||
;; 'auto', which is identical to 'sqrt'
|
||
'(substitute* '("skopt/learning/forest.py"
|
||
"skopt/learning/tests/test_forest.py")
|
||
(("max_features=['\"]auto['\"]")
|
||
"max_features='sqrt'")))))
|
||
(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-scikit-survival
|
||
(let ((revision "1")
|
||
;; We need a later commit for support of a more recent sklearn and
|
||
;; numpy 2.
|
||
(commit "bceb53ebb8306f959c70fae2be9d552f33dd3f21"))
|
||
(package
|
||
(name "python-scikit-survival")
|
||
(version (git-version "0.22.2" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/sebp/scikit-survival")
|
||
(commit commit)
|
||
;; This package contains a copy of Eigen. It would be good to
|
||
;; figure out how to use our own Eigen package.
|
||
(recursive? #true)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1m3z64nv4sgay0mdrrw4q4z5ylx63a9w2x43w1r4g8kpg7z9rdfc"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-before 'build 'set-version
|
||
(lambda _
|
||
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
|
||
#$(version-major+minor version)))))))
|
||
(propagated-inputs
|
||
(list python-ecos
|
||
python-importlib-resources
|
||
python-joblib
|
||
python-numexpr
|
||
python-numpy
|
||
python-osqp
|
||
python-pandas
|
||
python-scikit-learn
|
||
python-scipy))
|
||
(native-inputs
|
||
(list python-black
|
||
python-pypa-build
|
||
python-coverage
|
||
python-cython-3
|
||
python-packaging
|
||
python-pytest
|
||
python-setuptools-scm
|
||
python-tomli
|
||
python-tox))
|
||
(home-page "https://github.com/sebp/scikit-survival")
|
||
(synopsis "Survival analysis built on top of scikit-learn")
|
||
(description "Scikit-survival is a Python module for survival analysis
|
||
built on top of scikit-learn. It allows doing survival analysis while
|
||
utilizing the power of scikit-learn, e.g., for pre-processing or doing
|
||
cross-validation.")
|
||
(license license:gpl3+))))
|
||
|
||
(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
|
||
(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 "4.0.10")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ; no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/mikedh/trimesh")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0ry04qaw0pb3hkxv4gmna87jwk97aqangd21wbr2dr4xshmkbyyb"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
#~(list "-k" (string-append
|
||
;; XXX: When more optional modules are available review
|
||
;; disabled tests once again.
|
||
;;
|
||
;; Disable tests requiring optional, not packed modules.
|
||
"not test_material_round"
|
||
" and not test_bezier_example"
|
||
" and not test_discrete"
|
||
" and not test_dxf"
|
||
" and not test_layer"
|
||
" and not test_multi_nodupe"
|
||
" and not test_obj_roundtrip"
|
||
" and not test_roundtrip"
|
||
" and not test_scene"
|
||
" and not test_slice_onplane"
|
||
" and not test_svg"
|
||
" and not test_svg"))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'fix-build
|
||
(lambda _
|
||
(substitute* "trimesh/resources/templates/blender_boolean.py.tmpl"
|
||
(("\\$MESH_PRE")
|
||
"'$MESH_PRE'")))))))
|
||
(native-inputs
|
||
(list python-coveralls
|
||
python-pyinstrument
|
||
python-pytest
|
||
python-pytest-cov))
|
||
(propagated-inputs
|
||
(list python-chardet
|
||
python-colorlog
|
||
python-httpx
|
||
python-jsonschema
|
||
python-lxml
|
||
python-networkx
|
||
python-numpy
|
||
python-pillow
|
||
;; python-pycollada ; not packed yet, optional
|
||
;; python-pyglet ; not packed yet, optional
|
||
python-requests
|
||
python-rtree
|
||
python-scipy
|
||
python-setuptools
|
||
python-shapely
|
||
;; python-svg-path ; not packed yet, optional
|
||
python-sympy
|
||
python-xxhash))
|
||
(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-pyamg
|
||
(package
|
||
(name "python-pyamg")
|
||
(version "5.0.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pyamg" version))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Delete autogenerated files, regenerate in a phase.
|
||
#~(begin
|
||
(for-each
|
||
(lambda (file)
|
||
(delete-file (string-append "pyamg/amg_core/" file)))
|
||
'("air_bind.cpp"
|
||
"evolution_strength_bind.cpp"
|
||
"graph_bind.cpp"
|
||
"krylov_bind.cpp"
|
||
"linalg_bind.cpp"
|
||
"relaxation_bind.cpp"
|
||
"ruge_stuben_bind.cpp"
|
||
"smoothed_aggregation_bind.cpp"
|
||
"tests/bind_examples_bind.cpp"))))
|
||
(sha256
|
||
(base32
|
||
"0l3dliwynxyjvbgpmi2k8jqvkkw6fc00c8w69h6swhrkfh0ql12z"))))
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; Test installed package in order to find C++ modules.
|
||
#~(list "--pyargs" "pyamg.tests")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
;; Regenerate the autogenerated files.
|
||
(add-after 'unpack 'amg-core-bind-them
|
||
(lambda _
|
||
;; bindthem.py heavily depends on location to produce *_bind.cpp
|
||
;; file, make it available in tests as well.
|
||
(copy-file "pyamg/amg_core/bindthem.py"
|
||
"pyamg/amg_core/tests/bindthem.py")
|
||
(with-directory-excursion "pyamg/amg_core"
|
||
(substitute* "bindthem.py"
|
||
(("/usr/bin/env python3") (which "python3")))
|
||
(invoke "sh" "generate.sh"))
|
||
(with-directory-excursion "pyamg/amg_core/tests"
|
||
(invoke "python" "bindthem.py" "bind_examples.h")))))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs
|
||
(list pybind11
|
||
python-cppheaderparser
|
||
python-pytest
|
||
python-pyyaml
|
||
python-setuptools-scm))
|
||
(propagated-inputs (list python-numpy python-scipy))
|
||
(home-page "https://github.com/pyamg/pyamg")
|
||
(synopsis "Algebraic Multigrid Solvers in Python")
|
||
(description "PyAMG is a Python library of Algebraic Multigrid
|
||
(AMG) solvers. It features implementations of:
|
||
@itemize
|
||
@item Ruge-Stuben (RS) or Classical AMG
|
||
@item AMG based on Smoothed Aggregation (SA)
|
||
@item Adaptive Smoothed Aggregation (αSA)
|
||
@item Compatible Relaxation (CR)
|
||
@item Krylov methods such as CG, GMRES, FGMRES, BiCGStab, MINRES, etc.
|
||
@end itemize")
|
||
(license license:expat)))
|
||
|
||
(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-1
|
||
(package
|
||
(name "python-pandas")
|
||
(version "1.5.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pandas" version))
|
||
(sha256
|
||
(base32 "1cdhngylzh352wx5s3sjyznn7a6kmjqcfg97hgqm5h3yb9zgv8vl"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "--pyargs" "pandas"
|
||
"-n" (number->string (parallel-job-count))
|
||
"-m" "not slow and not network and not db"
|
||
"-k"
|
||
(string-append
|
||
;; TODO: Missing input
|
||
"not TestS3"
|
||
" and not s3"
|
||
;; No module named 'pandas.io.sas._sas'
|
||
" and not test_read_expands_user_home_dir"
|
||
" and not test_read_non_existent"
|
||
;; Unknown failures
|
||
" and not test_switch_options"
|
||
;; Crashes
|
||
" and not test_bytes_exceed_2gb"
|
||
;; get_subplotspec() returns None; possibly related to
|
||
;; https://github.com/pandas-dev/pandas/issues/54577
|
||
" and not test_plain_axes"
|
||
;; This test fails when run with pytest-xdist
|
||
;; (see https://github.com/pandas-dev/pandas/issues/39096).
|
||
" and not test_memory_usage"))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-build-system
|
||
(lambda _
|
||
(substitute* "pyproject.toml"
|
||
;; Not all data files are distributed with the tarball.
|
||
(("--strict-data-files ") "")
|
||
;; Unknown property "asyncio_mode"
|
||
(("asyncio_mode = \"strict\"") ""))))
|
||
(add-after 'unpack 'patch-which
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(substitute* "pandas/io/clipboard/__init__.py"
|
||
(("^WHICH_CMD = .*")
|
||
(string-append "WHICH_CMD = \""
|
||
(search-input-file inputs "/bin/which")
|
||
"\"\n")))))
|
||
(add-before 'check 'prepare-x
|
||
(lambda _
|
||
(system "Xvfb &")
|
||
(setenv "DISPLAY" ":0")
|
||
;; xsel needs to write a log file.
|
||
(setenv "HOME" "/tmp")))
|
||
;; The compiled libraries are only in the output at this point,
|
||
;; but they are needed to run tests.
|
||
;; FIXME: This should be handled by the pyargs pytest argument,
|
||
;; but is not for some reason.
|
||
(add-before 'check 'pre-check
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(copy-recursively
|
||
(string-append (site-packages inputs outputs)
|
||
"/pandas/_libs")
|
||
"pandas/_libs"))))))
|
||
(propagated-inputs
|
||
(list python-jinja2
|
||
python-matplotlib
|
||
python-numpy
|
||
python-openpyxl
|
||
python-pytz
|
||
python-dateutil
|
||
python-xlrd
|
||
python-xlsxwriter))
|
||
(inputs
|
||
(list which xclip xsel))
|
||
(native-inputs
|
||
(list python-cython-0.29.35
|
||
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-pandas-2
|
||
(package
|
||
(name "python-pandas")
|
||
(version "2.1.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pandas-dev/pandas")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1v9j38bvw739csdfl98ga6fqjdm61q3p5a2l7h364kg925nbc9r1"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
#~(list "--pyargs" "pandas"
|
||
;; "--exitfirst"
|
||
;; FIXME "-n" (number->string (parallel-job-count))
|
||
"-m" "not slow and not network and not db"
|
||
"-k" (string-append
|
||
"not test_git_version"
|
||
" and not test_show_versions_console"
|
||
;; Not testing ~ expansion.
|
||
" and not test_expand_user"
|
||
" and not test_get_handle_with_path"
|
||
;; 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]
|
||
" and 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"
|
||
" and not test_parsing_tzlocal_deprecated"))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'version-set-by-guix
|
||
(lambda _
|
||
(with-output-to-file "_version.py"
|
||
(lambda _
|
||
(display
|
||
(string-append "__version__ = \""
|
||
#$(package-version this-package)
|
||
"\""))))))
|
||
(add-before 'check 'prepare-x
|
||
(lambda _
|
||
(system "Xvfb &")
|
||
(setenv "DISPLAY" ":0")
|
||
(setenv "HOME" ".")
|
||
;; Skip tests that require lots of resources.
|
||
(setenv "PANDAS_CI" "1")))
|
||
(add-after 'unpack 'patch-which
|
||
(lambda _
|
||
(substitute* "pandas/io/clipboard/__init__.py"
|
||
(("^WHICH_CMD = .*")
|
||
(string-append "WHICH_CMD = \""
|
||
#$(this-package-input "which")
|
||
"/bin/which\"\n")))))
|
||
;; The compiled libraries are only in the output at this point,
|
||
;; but they are needed to run tests.
|
||
;; FIXME: This should be handled by the pyargs pytest argument,
|
||
;; but is not for some reason.
|
||
(add-before 'check 'pre-check
|
||
(lambda _
|
||
(copy-recursively
|
||
(string-append #$output
|
||
"/lib/python3.10/site-packages/pandas/_libs")
|
||
"pandas/_libs"))))))
|
||
(propagated-inputs
|
||
(list python-dateutil
|
||
python-jinja2
|
||
python-matplotlib
|
||
python-numpy
|
||
python-openpyxl
|
||
python-pytz
|
||
python-tzdata
|
||
python-xlrd
|
||
python-xlsxwriter))
|
||
(inputs
|
||
(list which xclip xsel))
|
||
(native-inputs
|
||
(list meson-python/newer
|
||
python-beautifulsoup4
|
||
python-cython-0.29.35
|
||
python-html5lib
|
||
python-lxml
|
||
python-matplotlib
|
||
python-openpyxl
|
||
python-pytest-asyncio
|
||
python-pytest-next
|
||
python-pytest-localserver
|
||
python-pytest-mock
|
||
python-pytest-xdist
|
||
python-versioneer
|
||
;; 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-pandas python-pandas-2)
|
||
|
||
(define-public python-pandas-stubs
|
||
(package
|
||
(name "python-pandas-stubs")
|
||
;; The versioning follows that of Pandas and uses the date of the
|
||
;; python-pandas-stubs release.
|
||
(version "2.1.1.230928")
|
||
(source
|
||
(origin
|
||
;; No tests in the PyPI tarball.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pandas-dev/pandas-stubs")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "13b6wcwf9ybxf492w1l8qqf2bcgch21xds5r88pfkmrvqhxwfpyr"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags #~(list "-k"
|
||
(string-append
|
||
;; The python-pyarrow package in Guix is built
|
||
;; with ORC integration, but these tests fail with
|
||
;; an abort in ORC because a timezone file is not
|
||
;; in the expected location:
|
||
;; https://github.com/apache/arrow/issues/40633
|
||
"not test_orc"
|
||
" and not test_orc_path"
|
||
" and not test_orc_buffer"
|
||
" and not test_orc_columns"
|
||
" and not test_orc_bytes"
|
||
" and not test_all_read_without_lxml_dtype_backend"
|
||
|
||
;; Apparently "numpy.bool_" is not the same as the
|
||
;; expected "bool".
|
||
" and not test_timedelta_cmp"
|
||
" and not test_timedelta_cmp_rhs"
|
||
" and not test_timestamp_cmp"
|
||
" and not test_timestamp_eq_ne_rhs"))
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
;; We cannot yet upgrade numpy to 1.26 because numba needs numpy
|
||
;; >1.24.
|
||
(add-after 'unpack 'relax-requirements
|
||
(lambda _
|
||
(substitute* "pyproject.toml"
|
||
(("numpy = \\{ version = \">=1.26.0\", python = \"<3.13\" \\}")
|
||
"numpy = { version = \">=1.23.0\", python = \"<3.13\" }"))))
|
||
(add-before 'check 'prepare-x
|
||
(lambda _
|
||
(system "Xvfb &")
|
||
(setenv "DISPLAY" ":0")
|
||
;; xsel needs to write a log file.
|
||
(setenv "HOME" (getcwd)))))))
|
||
(propagated-inputs (list python-types-pytz))
|
||
;; Add python-fastparquet to native inputs once it has been packaged. Its
|
||
;; tests will be skipped for now.
|
||
(native-inputs (list python-lxml
|
||
python-matplotlib
|
||
python-odfpy
|
||
python-pandas
|
||
python-poetry-core
|
||
python-pyarrow
|
||
python-pyreadstat
|
||
python-pytest
|
||
python-scipy
|
||
python-sqlalchemy
|
||
python-tables
|
||
python-tabulate
|
||
python-xarray
|
||
;; Needed to test clipboard support.
|
||
which
|
||
xclip
|
||
xorg-server-for-tests
|
||
xsel))
|
||
(home-page "https://pandas.pydata.org")
|
||
(synopsis "Type annotations for pandas")
|
||
(description
|
||
"This package contains public type stubs for @code{python-pandas},
|
||
following the convention of providing stubs in a separate package, as
|
||
specified in @acronym{PEP, Python Enhancement Proposal} 561. The stubs cover
|
||
the most typical use cases of @code{python-pandas}. In general, these stubs
|
||
are narrower than what is possibly allowed by @code{python-pandas}, but follow
|
||
a convention of suggesting best recommended practices for using
|
||
@code{python-pandas}.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-pandarallel
|
||
(package
|
||
(name "python-pandarallel")
|
||
(version "1.6.5")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ; no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/nalepae/pandarallel/")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0r2wlxlwp4wia0vm15k4cp421mwa20k4k5g2ml01inprj8bl1p0p"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags #~(list "-n" (number->string (parallel-job-count)))))
|
||
(propagated-inputs
|
||
(list python-dill
|
||
python-pandas
|
||
python-psutil))
|
||
(native-inputs
|
||
(list python-mkdocs-material
|
||
python-numpy
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-pytest-xdist))
|
||
(home-page "https://nalepae.github.io/pandarallel/")
|
||
(synopsis "Tool to parallelize Pandas operations across CPUs")
|
||
(description
|
||
"@code{pandarallel} allows any Pandas user to take advantage of their
|
||
multi-core computer, while Pandas uses only one core. @code{pandarallel} also
|
||
offers nice progress bars (available on Notebook and terminal) to get an rough
|
||
idea of the remaining amount of computation to be done.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-pandera
|
||
(package
|
||
(name "python-pandera")
|
||
(version "0.18.0")
|
||
(source
|
||
(origin
|
||
;; No tests in the PyPI tarball.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/unionai-oss/pandera")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "14b5aij5zjkwvsimg0v00qvp59mhhq7ljim4qghcn432vkg9gh47"))
|
||
(modules '((guix build utils)))
|
||
;; These tests require PySpark and Modin. We need to remove the entire
|
||
;; directory, since the conftest.py in these directories contain
|
||
;; imports. (See: https://github.com/pytest-dev/pytest/issues/7452)
|
||
(snippet '(begin
|
||
(delete-file-recursively "tests/pyspark")
|
||
(delete-file-recursively "tests/modin")))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags '(list "-k"
|
||
(string-append
|
||
;; Mypy functionality is experimental and relying
|
||
;; on pandas-stubs can lead to false
|
||
;; positives. These tests currently fail.
|
||
"not test_python_std_list_dict_generics"
|
||
" and not test_python_std_list_dict_empty_and_none"
|
||
" and not test_pandas_modules_importable"
|
||
" and not test_check_groups"))))
|
||
;; Pandera comes with a lot of extras. We test as many as possible, but do
|
||
;; not include all of them in the propagated-inputs. Currently, we have to
|
||
;; skip the pyspark and io tests due to missing packages python-pyspark
|
||
;; and python-frictionless.
|
||
(propagated-inputs (list python-hypothesis ;strategies extra
|
||
python-multimethod
|
||
python-numpy
|
||
python-packaging
|
||
python-pandas
|
||
python-pandas-stubs ;mypy extra
|
||
python-pydantic
|
||
python-scipy ;hypotheses extra
|
||
python-typeguard-4
|
||
python-typing-inspect
|
||
python-wrapt))
|
||
(native-inputs (list python-dask ;dask extra
|
||
python-fastapi ;fastapi extra
|
||
python-geopandas ;geopandas extra
|
||
python-pyarrow ;needed to run fastapi tests
|
||
python-pytest
|
||
python-pytest-asyncio
|
||
python-sphinx
|
||
python-uvicorn)) ;needed to run fastapi tests
|
||
(home-page "https://github.com/unionai-oss/pandera")
|
||
(synopsis "Perform data validation on dataframe-like objects")
|
||
(description
|
||
"@code{python-pandera} provides a flexible and expressive API for
|
||
performing data validation on dataframe-like objects to make data processing
|
||
pipelines more readable and robust. Dataframes contain information that
|
||
@code{python-pandera} explicitly validates at runtime. This is useful in
|
||
production-critical data pipelines or reproducible research settings. With
|
||
@code{python-pandera}, you can:
|
||
|
||
@itemize
|
||
@item Define a schema once and use it to validate different dataframe types.
|
||
@item Check the types and properties of columns.
|
||
@item Perform more complex statistical validation like hypothesis testing.
|
||
@item Seamlessly integrate with existing data pipelines via function decorators.
|
||
@item Define dataframe models with the class-based API with pydantic-style syntax.
|
||
@item Synthesize data from schema objects for property-based testing.
|
||
@item Lazily validate dataframes so that all validation rules are executed.
|
||
@item Integrate with a rich ecosystem of tools like @code{python-pydantic},
|
||
@code{python-fastapi} and @code{python-mypy}.
|
||
@end itemize")
|
||
(license license:expat)))
|
||
|
||
(define-public python-pyjanitor
|
||
(package
|
||
(name "python-pyjanitor")
|
||
(version "0.27.0")
|
||
(source
|
||
(origin
|
||
;; The build requires the mkdocs directory for the description in
|
||
;; setup.py. This is not included in the PyPI tarball.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/pyjanitor-devs/pyjanitor")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "04vsg189msv8frx4zhpcg61djl7wsfvibmz0zmiih4rvkgly2cdr"))))
|
||
(build-system pyproject-build-system)
|
||
;; Pyjanitor has an extensive test suite. For quick debugging, the tests
|
||
;; marked turtle can be skipped using "-m" "not turtle".
|
||
(arguments
|
||
(list
|
||
#:test-flags '(list
|
||
"-n" (number->string (parallel-job-count))
|
||
;; Tries to connect to the internet.
|
||
"-k" (string-append "not test_is_connected"
|
||
;; Test files are not included
|
||
" and not test_read_commandline_bad_cmd"
|
||
;; This fails due to differences in accuracy
|
||
" and not test_jitter_results")
|
||
;; Test files are not included
|
||
"--ignore=tests/io/test_read_csvs.py"
|
||
;; PySpark has not been packaged yet.
|
||
"--ignore=tests/spark/functions/test_clean_names_spark.py"
|
||
"--ignore=tests/spark/functions/test_update_where_spark.py")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
;; Pandas 2.1.1 does not offer the BME frequency.
|
||
(add-after 'unpack 'pandas-compat
|
||
(lambda _
|
||
(substitute* '("tests/functions/test_select_rows.py"
|
||
"tests/functions/test_select_columns.py")
|
||
(("freq=\"BME\"") "freq=\"BM\""))))
|
||
(add-before 'check 'set-env-ci
|
||
(lambda _
|
||
;; Some tests are skipped if the JANITOR_CI_MACHINE
|
||
;; variable is not set.
|
||
(setenv "JANITOR_CI_MACHINE" "1"))))))
|
||
(propagated-inputs (list python-multipledispatch
|
||
python-natsort
|
||
python-pandas-flavor
|
||
python-scipy
|
||
;; Optional imports.
|
||
python-biopython ;biology submodule
|
||
python-unyt)) ;engineering submodule
|
||
(native-inputs (list python-pytest
|
||
python-pytest-xdist
|
||
;; Optional imports. We do not propagate them due to
|
||
;; their size.
|
||
python-numba ;speedup of joins
|
||
rdkit)) ;chemistry submodule
|
||
(home-page "https://github.com/pyjanitor-devs/pyjanitor")
|
||
(synopsis "Tools for cleaning and transforming pandas DataFrames")
|
||
(description
|
||
"@code{pyjanitor} provides a set of data cleaning routines for
|
||
@code{pandas} DataFrames. These routines extend the method chaining API
|
||
defined by @code{pandas} for a subset of its methods. Originally, this
|
||
package was a port of the R package by the same name and it is inspired by the
|
||
ease-of-use and expressiveness of the @code{dplyr} package.")
|
||
(license license:expat)))
|
||
|
||
(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 "0.13.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pyts" version))
|
||
(sha256
|
||
(base32
|
||
"00pdzfkl0b4vhfdm8zas7b904jm2hhivdwv3wcmpik7l2p1yr85c"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs
|
||
(list python-joblib 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-fastcluster
|
||
(package
|
||
(name "python-fastcluster")
|
||
(version "1.2.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "fastcluster" version))
|
||
(sha256
|
||
(base32 "19labbgnq85p4r4jbli2p045lgh57larhi2g2anagfxnlzpqdf5a"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy))
|
||
(native-inputs (list python-scipy))
|
||
(home-page "https://danifold.net/fastcluster.html")
|
||
(synopsis "Fast hierarchical clustering routines for R and Python")
|
||
(description "The fastcluster package implements seven common hierarchical
|
||
clustering schemes efficiently. The package is made with two interfaces to
|
||
standard software: R and Python.")
|
||
(license license:bsd-2)))
|
||
|
||
(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 "2023.12.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "xarray" version))
|
||
(sha256
|
||
(base32
|
||
"0cyldwchcrmbm1y7l1ry70kk8zdh7frxci3c6iwf4iyyj34dnra5"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; This needs a more recent version of python-hypothesis
|
||
'(list "--ignore=xarray/tests/test_strategies.py"
|
||
;; These are known to fail with Pandas 2
|
||
"-k"
|
||
(string-append "not test_datetime_conversion_warning"
|
||
" and not test_timedelta_conversion_warning"))))
|
||
(native-inputs
|
||
(list python-setuptools-scm python-pytest))
|
||
(propagated-inputs
|
||
(list python-numpy python-packaging 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-dataclasses
|
||
(package
|
||
(name "python-xarray-dataclasses")
|
||
(version "1.7.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/astropenguin/xarray-dataclasses/")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "043lc1hadr5y0y16g682viiafy0hfsa7q18lqmndpyvnmcgm893z"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy python-typing-extensions
|
||
python-xarray))
|
||
(native-inputs (list python-pytest python-poetry-core))
|
||
(home-page "https://github.com/astropenguin/xarray-dataclasses/")
|
||
(synopsis "xarray data creation made easy by dataclass")
|
||
(description "@code{xarray-dataclasses} is a Python package that makes it
|
||
easy to create @code{xarray}'s @code{DataArray} and @code{Datase} objects that
|
||
are \"typed\" (i.e. fixed dimensions, data type, coordinates, attributes, and
|
||
name) using the Python's @code{dataclass}.")
|
||
(license license:expat)))
|
||
|
||
;; Note that this package will be folded into xarray eventually. See
|
||
;; https://github.com/pydata/xarray/issues/8572 for details.
|
||
(define-public python-xarray-datatree
|
||
(package
|
||
(name "python-xarray-datatree")
|
||
(version "0.0.14")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "xarray-datatree" version))
|
||
(sha256
|
||
(base32 "1x1s25s6dp1f2hck9qw8vl8hgkyy23rcwag2a9vd3w0dbgrrl5i6"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-packaging python-xarray))
|
||
;; We need setuptools-scm to correctly record the version string.
|
||
(native-inputs (list python-pytest python-setuptools-scm python-zarr))
|
||
(home-page "https://github.com/xarray-contrib/datatree")
|
||
(synopsis "Hierarchical tree-like data structures for xarray")
|
||
(description "Datatree is a prototype implementation of a tree-like
|
||
hierarchical data structure for @code{xarray}. Datatree is in the process of
|
||
being merged upstream into @code{xarray}.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-xarray-einstats
|
||
(package
|
||
(name "python-xarray-einstats")
|
||
(version "0.7.0")
|
||
(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
|
||
"14c424swpdginaz4pm3nmkizxy34x19q6xq3d4spx9s9031f6n3a"))))
|
||
(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-xarray-schema
|
||
(package
|
||
(name "python-xarray-schema")
|
||
(version "0.0.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "xarray-schema" version))
|
||
(sha256
|
||
(base32 "08194629696z98dkc74i6c9zmy1jicvd2ajb75q0lsf0i427cv4w"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy python-xarray))
|
||
(native-inputs (list python-pytest python-setuptools-scm))
|
||
(home-page "https://github.com/carbonplan/xarray-schema")
|
||
(synopsis "Schema validation for Xarray objects")
|
||
(description "This package implements schema validation for Xarray
|
||
objects.")
|
||
(license license:expat)))
|
||
|
||
(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-scs
|
||
(package
|
||
(name "python-scs")
|
||
(version "3.2.4")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/bodono/scs-python")
|
||
(commit "3.2.4")
|
||
(recursive? #true)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "06wd8m3ri0gaddl7qq6243g25zjlnh3da915b73jnrfh7sg1nqsj"))))
|
||
(build-system pyproject-build-system)
|
||
(inputs (list meson-python openblas))
|
||
(propagated-inputs (list python-numpy python-scipy))
|
||
(native-inputs
|
||
(list pkg-config
|
||
python-meson-python
|
||
python-pytest))
|
||
(home-page "https://github.com/bodono/scs-python")
|
||
(synopsis "Splitting conic solver")
|
||
(description "This package provides a Python interface for the
|
||
SCS (Splitting conic solver) library.")
|
||
(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-unyt
|
||
(package
|
||
(name "python-unyt")
|
||
(version "3.0.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "unyt" version))
|
||
(sha256
|
||
(base32 "00900bw24rxgcgwgxp9xlx0l5im96r1n5hn0r3mxvbdgc3lyyq48"))))
|
||
(build-system pyproject-build-system)
|
||
;; Astropy is an optional import, but we do not include it as it creates a
|
||
;; module cycle: astronomy->python-science->astronomy.
|
||
(propagated-inputs (list python-h5py ; optional import
|
||
python-matplotlib ; optional import
|
||
python-numpy
|
||
python-sympy))
|
||
;; Pint is optional, but we do not propagate it due to its size.
|
||
(native-inputs (list python-pint python-pytest python-setuptools-scm))
|
||
(home-page "https://unyt.readthedocs.io")
|
||
(synopsis "Library for working with data that has physical units")
|
||
(description
|
||
"@code{unyt} is a Python library working with data that has physical
|
||
units. It defines the @code{unyt.array.unyt_array} and
|
||
@code{unyt.array.unyt_quantity} classess (subclasses of NumPy’s ndarray class)
|
||
for handling arrays and scalars with units,respectively")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-upsetplot
|
||
(package
|
||
(name "python-upsetplot")
|
||
(version "0.9.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "UpSetPlot" version))
|
||
(sha256
|
||
(base32
|
||
"14l5gcj88cclkj1mf74bcy1pxq1hgsiy27fa3vxrsk32ik1nmdwm"))))
|
||
(build-system pyproject-build-system)
|
||
(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 "0.5.4")
|
||
(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
|
||
"1j3qkgvyc31604ddl952h4hwza7schg8kwkycmxvpvx7xjj7nn68"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; This one fails due to minor differences in accuracy
|
||
'(list "-k" "not test_logistic_regression")
|
||
#: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]*") ""))))
|
||
(add-after 'unpack 'sklearn-compatibility
|
||
(lambda _
|
||
(substitute* "pingouin/regression.py"
|
||
(("kwargs\\[\"penalty\"\\] = \"none\"")
|
||
"kwargs[\"penalty\"] = None")))))))
|
||
(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-dask-expr
|
||
(package
|
||
(name "python-dask-expr")
|
||
(version "1.0.14")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/dask/dask-expr")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0c2q8w8wl5d2hycbjp9vavkl5f36kaz390wxlis2d8d43jnqhf0d"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:tests? #false ;need python-distributed, which needs dask-expr.
|
||
#: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 = dask_expr/_version.py
|
||
versionfile_build = dask_expr/_version.py
|
||
tag_prefix =
|
||
parentdir_prefix = dask_expr-
|
||
")))
|
||
(invoke "versioneer" "install")
|
||
(substitute* "setup.py"
|
||
(("versioneer.get_version\\(\\)")
|
||
(string-append "\"" #$version "\""))))))))
|
||
(propagated-inputs (list python-pandas python-pyarrow))
|
||
(native-inputs
|
||
;; We use python-dask/bootstrap so that python-dask can propagate this
|
||
;; package without creating a mutually recursive dependency.
|
||
(list python-dask/bootstrap
|
||
python-pytest
|
||
python-versioneer))
|
||
(home-page "https://github.com/dask/dask-expr")
|
||
(synopsis "Dask DataFrames with query optimization")
|
||
(description "This is a rewrite of Dask DataFrame that includes query
|
||
optimization and generally improved organization.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-distributed
|
||
(package
|
||
(name "python-distributed")
|
||
(version "2024.4.2")
|
||
(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
|
||
"0sy9mqa8qlxsagbz8xn304csrlxhxj4b6k84yrjxdcmkp9pkx166"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
'(list "-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_messages_are_ordered_bsend"
|
||
"test_messages_are_ordered_raw"
|
||
"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_preload_manager_sequence"
|
||
"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_tell_workers_when_peers_have_left"
|
||
"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 ")
|
||
|
||
;; This seems to want to use 64GB of memory.
|
||
" and not test_computation_object_code_dask_compute"
|
||
|
||
;; 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"
|
||
" and not test_task_groups_update_start_stop"
|
||
" and not test_web_preload"
|
||
" and not test_web_preload_worker"))
|
||
#: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")
|
||
;; Disable job queueing
|
||
(setenv "DASK_DISTRIBUTED__SCHEDULER__WORKER_SATURATION" "inf")
|
||
;; Do not use dask-expr
|
||
(setenv "DASK_DATAFRAME__QUERY_PLANNING" "False")
|
||
;; 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-dask-expr
|
||
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-flaky
|
||
python-importlib-metadata
|
||
python-pytest
|
||
python-pytest-timeout
|
||
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")
|
||
(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
|
||
;; XXX: Check for any new failing tests during next update cycle.
|
||
;; 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_custom_shape"
|
||
"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"
|
||
|
||
;; This triggers an unexpected but harmless
|
||
;; warning.
|
||
"test_save_method"
|
||
|
||
;; 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
|
||
python-setuptools-scm
|
||
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 pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
;; This one test fails because it doesn't raise an expected exception.
|
||
#:test-flags #~(list "-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-clarabel
|
||
(package
|
||
(name "python-clarabel")
|
||
(version "0.7.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "clarabel" version))
|
||
(sha256
|
||
(base32 "15k32ynvh45n9q905bxwamh5w5cia9bxzmwz69wbribmyhsv22m3"))
|
||
(patches
|
||
(search-patches "python-clarabel-blas.patch"))))
|
||
(build-system cargo-build-system)
|
||
(arguments
|
||
(list
|
||
#:imported-modules `(,@%cargo-build-system-modules
|
||
,@%pyproject-build-system-modules)
|
||
#:modules '((guix build cargo-build-system)
|
||
((guix build pyproject-build-system) #:prefix py:)
|
||
(guix build utils))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'prepare-python-module 'build-python-module
|
||
(assoc-ref py:%standard-phases 'build))
|
||
(add-after 'build-python-module 'install-python-module
|
||
(assoc-ref py:%standard-phases 'install)))
|
||
#:cargo-inputs
|
||
`(("rust-amd" ,rust-amd-0.2)
|
||
("rust-blas" ,rust-blas-0.22)
|
||
("rust-cfg-if" ,rust-cfg-if-1)
|
||
("rust-derive-builder" ,rust-derive-builder-0.11)
|
||
("rust-enum-dispatch" ,rust-enum-dispatch-0.3) ;0.3.8
|
||
("rust-itertools" ,rust-itertools-0.11)
|
||
("rust-lapack" ,rust-lapack-0.19)
|
||
("rust-lazy-static" ,rust-lazy-static-1) ;1.4
|
||
("rust-libc" ,rust-libc-0.2)
|
||
("rust-num-derive" ,rust-num-derive-0.2)
|
||
("rust-num-traits" ,rust-num-traits-0.2)
|
||
("rust-pyo3" ,rust-pyo3-0.20)
|
||
("rust-serde" ,rust-serde-1)
|
||
("rust-serde-json" ,rust-serde-json-1)
|
||
("rust-thiserror" ,rust-thiserror-1))
|
||
#:features '(list "python")
|
||
#:install-source? #false))
|
||
(inputs
|
||
(list maturin))
|
||
(native-inputs
|
||
(list python-wrapper))
|
||
(propagated-inputs (list python-numpy python-scipy))
|
||
(home-page "https://github.com/oxfordcontrol/Clarabel.rs")
|
||
(synopsis "Interior-point solver for convex conic optimisation problems")
|
||
(description "Clarabel.rs is a Rust implementation of an interior point
|
||
numerical solver for convex optimization problems using a novel homogeneous
|
||
embedding.")
|
||
(license license:asl2.0)))
|
||
|
||
(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 "0.9.6")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/sods/paramz")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1ywc2jzj40m6wmq227j3snxvp4434s0m1xk1abg6v6mr87pv2sa9"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-decorator python-numpy python-scipy
|
||
python-six))
|
||
(native-inputs (list python-nose))
|
||
(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 "1.13.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "GPy" version))
|
||
(sha256
|
||
(base32
|
||
"05d1ry4jpp0srsrmp3qd6s0p2bjc4c0z99450pzdr79vagbfvlk4"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'compatibility
|
||
(lambda _
|
||
;; This file uses Python 2 statements
|
||
(delete-file "GPy/testing/mpi_test__.py")
|
||
(substitute* "setup.py"
|
||
(("scipy>=1.3.0,<1.12.0")
|
||
"scipy>=1.3.0,<=1.13.0"))
|
||
;; Use numpy.exp because scipy.ext no longer exists
|
||
(substitute* "GPy/kern/src/sde_standard_periodic.py"
|
||
(("sp\\.exp") "np.exp"))
|
||
(substitute* "GPy/kern/src/sde_stationary.py"
|
||
(("sp\\.poly1d") "np.poly1d")
|
||
(("sp\\.roots") "np.roots")))))))
|
||
(native-inputs
|
||
(list python-cython python-matplotlib python-pods python-pytest))
|
||
(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-pods
|
||
(package
|
||
(name "python-pods")
|
||
(version "0.1.14")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pods" version))
|
||
(sha256
|
||
(base32 "157xxs12qbnz1g6agy0a4dqhsa4msbqryrxpg5w3r3pb8gxdl4dh"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments (list #:tests? #f)) ;no test suite
|
||
(propagated-inputs (list python-pandas python-pyyaml python-scipy
|
||
python-tables))
|
||
(home-page "https://github.com/lawrennd/ods")
|
||
(synopsis "Python software for Open Data Science")
|
||
(description "This package provides utilities and tools for open data
|
||
science including tools for accessing data sets in Python.")
|
||
(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 "2.4.4")
|
||
(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
|
||
"0ksyyc1hbhyqy289a2frn84ss29fb7czirx3dkxx56f4ia33b4c8"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; Skip tests that require networking.
|
||
#~(list "-k" (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 can read, modify and write DICOM
|
||
data.")
|
||
(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
|
||
;; XXX: The project may no longer be compatible with the version of
|
||
;; numpy packed in Guix.
|
||
;; See: https://github.com/uchicago-cs/deepdish/issues/50.
|
||
;;
|
||
;; However, there is a maintained fork that appears to be a good
|
||
;; replacement: https://github.com/portugueslab/flammkuchen.
|
||
;;
|
||
;; Disable few failing tests to pass the build.
|
||
(list #:test-flags
|
||
#~(list "-k" (string-append "not test_pad"
|
||
" and not test_pad_repeat_border"
|
||
" and not test_pad_repeat_border_corner"
|
||
" and not test_pad_to_size"))
|
||
#: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 pyproject-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-supersmoother
|
||
(package
|
||
(name "python-supersmoother")
|
||
(version "0.4")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ; no package in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/jakevdp/supersmoother")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1lkj8l2mpki6x2pxcwlrplx63lhi8h9v2rzxgjfb0cppsfr8m1wp"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy))
|
||
(native-inputs (list python-scipy))
|
||
(home-page "http://github.com/jakevdp/supersmoother")
|
||
(synopsis "Python implementation of Friedman's Supersmoother")
|
||
(description
|
||
"This package provides an efficient implementation of
|
||
@url{https://www.slac.stanford.edu/pubs/slacpubs/3250/slac-pub-3477.pdf,
|
||
Friedman's SuperSmoother} based in Python. It makes use of numpy for fast
|
||
numerical computation.")
|
||
(license license:bsd-2)))
|
||
|
||
(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-pynetdicom
|
||
(package
|
||
(name "python-pynetdicom")
|
||
(version "2.0.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "pynetdicom" version))
|
||
(sha256
|
||
(base32
|
||
"0farmgviaarb3f4xn751card3v0lza57vwgl5azxxq65p7li44i3"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; Tests takes about 10-15min to complete.
|
||
;; Skip tests that require networking.
|
||
#~(list "-k" (string-append
|
||
" not TestFindSCP"
|
||
" and not TestQRGetServiceClass"
|
||
" and not TestQRMoveServiceClass"
|
||
" and not TestStoreSCP"
|
||
" and not test_ae.py"
|
||
" and not test_echoscp.py"
|
||
" and not test_qrscp_echo.py"
|
||
" and not test_storescp.py"
|
||
" and not test_pr_level_patient"
|
||
" and not test_pr_level_series"
|
||
" and not test_scp_cancelled"))))
|
||
(native-inputs (list python-pyfakefs python-pytest))
|
||
(propagated-inputs (list python-pydicom python-sqlalchemy))
|
||
(home-page "https://github.com/pydicom/pynetdicom")
|
||
(synopsis "Python implementation of the DICOM networking protocol")
|
||
(description
|
||
"@code{pynetdicom} is a Python package that implements the DICOM
|
||
networking protocol. It allows the easy creation of DICOM
|
||
@acronym{SCUs,Service Class Users} and @acronym{SCPs,Service Class
|
||
Providers}.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-pynrrd
|
||
(package
|
||
(name "python-pynrrd")
|
||
(version "1.0.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mhe/pynrrd")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"09gdyi4kbi3512ydgqxkgr4j7b9a95qh83fk2n9s41bns4id9xj7"))))
|
||
(build-system python-build-system)
|
||
(propagated-inputs
|
||
(list python-nptyping python-numpy python-typing-extensions))
|
||
(home-page "https://github.com/mhe/pynrrd")
|
||
(synopsis "Python module for reading and writing NRRD files")
|
||
(description
|
||
"@code{pynrrd} is a Python module for reading and writing @acronym{NRRD,
|
||
Nearly Raw Raster Data} files (format designed to support scientific
|
||
visualization and image processing involving N-dimensional raster data) into
|
||
and from numpy arrays.")
|
||
(license license:expat)))
|
||
|
||
(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.
|
||
;;;
|