;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2018, 2020-2025 Ricardo Wurmus ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2016, 2021-2025 Efraim Flashner ;;; Copyright © 2016-2020, 2022 Marius Bakke ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2018, 2022 Leo Famulari ;;; Copyright © 2019, 2021, 2022, 2023, 2024 Maxim Cournoyer ;;; Copyright © 2019 Giacomo Leidi ;;; Copyright © 2020 Pierre Langlois ;;; Copyright © 2020-2025 Vinicius Monego ;;; Copyright © 2021 Greg Hogan ;;; Copyright © 2021 Roel Janssen ;;; Copyright © 2021 Paul Garlick ;;; Copyright © 2021 Arun Isaac ;;; Copyright © 2021 Vagrant Cascadian ;;; Copyright © 2021, 2023 Felix Gruber ;;; Copyright © 2022 Malte Frank Gerdes ;;; Copyright © 2021, 2022 Guillaume Le Vaillant ;;; Copyright © 2022 Paul A. Patience ;;; Copyright © 2022 Wiktor Żelazny ;;; Copyright © 2022 Eric Bavier ;;; Copyright © 2022 kiasoc5 ;;; Copyright © 2022, 2024 Antero Mejr ;;; Copyright © 2022 jgart ;;; Copyright © 2022 Sarah Morgensen ;;; Copyright © 2023, 2024 Troy Figiel ;;; Copyright © 2024-2025 Sharlatan Hellseher ;;; Copyright © 2024 Marco Baggio ;;; Copyright © 2024 Nicolas Graves ;;; Copyright © 2024 Rick Huijzer ;;; Copyright © 2025 Nicolas Graves ;;; Copyright © 2025 Mark Walker ;;; Copyright © 2025 Nguyễn Gia Phong ;;; ;;; 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 . (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 compression) #: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 graphviz) #: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 package-management) #: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-check) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-graphics) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages rust-apps) #:use-module (gnu packages simulation) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages statistics) #:use-module (gnu packages time) #:use-module (gnu packages version-control) #: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 cmake) #:use-module (guix build-system python) #:use-module (guix build-system pyproject)) (define-public pyre (package (name "pyre") (version "1.12.5") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/pyre/pyre") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0crmssga481q2ggwcmj40nj5n9975wri14p609jdr9hwg4vdyvj2")))) (build-system cmake-build-system) (arguments (list #:imported-modules (append %cmake-build-system-modules %python-build-system-modules) #:modules '((guix build cmake-build-system) ((guix build python-build-system) #:prefix python:) (guix build utils)) #:configure-flags #~(list (string-append "-DPYRE_VERSION=" #$version) (string-append "-DPYRE_DEST_PACKAGES=" (python:site-packages %build-inputs %outputs))) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'enable-bytecode-determinism (assoc-ref python:%standard-phases 'enable-bytecode-determinism)) ;; Move the check phase after the Python 'pyre' module ;; is installed and made available. (delete 'check) (add-after 'install 'add-to-pythonpath (lambda* (#:key inputs outputs #:allow-other-keys) (python:add-installed-pythonpath inputs outputs))) (add-after 'add-to-pythonpath 'wrap (assoc-ref python:%standard-phases 'wrap)) (add-after 'add-to-pythonpath 'check (lambda* (#:key tests? parallel-tests? #:allow-other-keys) (when tests? (setenv "CTEST_OUTPUT_ON_FAILURE" "1") (let ((ignored-tests (list ;; The MPI tests are failing for unknown reasons (see: ;; https://github.com/pyre/pyre/issues/126). "tests.mpi" ;; These tests have a cleanup phase that fails ;; non-deterministically (see: ;; https://github.com/pyre/pyre/issues/125). "tests.pyre.lib.viz.flow" ;; This test expects a TCP port 22 to be listening. "tests.pyre.pkg.ipc.tcp.py" ;; These postgres tests require a running postgresql ;; daemon; they are also skipped in upstream CI. "tests.postgres.ext" ;; This test fails due to pre-1980 timestamps, not ;; supported by ZIP. "tests.pyre.pkg.filesystem.zip_open.py" ;; This one trips on the patched python3 shebang. "tests.pyre.pkg.filesystem.local_open.py"))) (invoke "ctest" "-j" (if parallel-tests? (number->string (parallel-job-count)) "1") "-E" (string-join ignored-tests "|"))))))))) (native-inputs (list openssh-sans-x python python-numpy pybind11 zip)) (inputs (list gsl hdf5 openmpi postgresql)) (propagated-inputs (list python-pyyaml)) ;for the Python bindings (home-page "http://pyre.orthologue.com/") (synopsis "Framework for building Scientific applications") (description "This package provides a framework for building scientific applications. It aims to bring state of the art software design practices to scientific computing, with the goal of providing a strong skeleton on which to build scientific codes by steering the implementation towards usability and maintainability.") (license license:bsd-3))) (define-public python-adjusttext (package (name "python-adjusttext") (version "1.3.0") (source (origin (method url-fetch) (uri (pypi-uri "adjusttext" version)) (sha256 (base32 "18dw5kqxan4m8kvw3w1lm0p69gj95i7rcgmcfs485x1s8pa5rdsa")))) (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none (native-inputs (list python-setuptools python-wheel)) (propagated-inputs (list python-matplotlib python-numpy python-scipy)) (home-page "https://github.com/Phlya/adjustText") (synopsis "Adjust text position in matplotlib plots to minimize overlaps") (description "Often when we want to label multiple points on a graph the text will start heavily overlapping with both other labels and data points. This can be a major problem requiring manual solution. However this can be largely automated by smart placing of the labels (difficult) or iterative adjustment of their positions to minimize overlaps (relatively easy). This library implements the latter option to help with matplotlib graphs.") (license license:expat))) (define-public python-algopy (package (name "python-algopy") (version "0.6.0") ; the higher versions requir NumPy 2+ stack (source (origin (method url-fetch) (uri (pypi-uri "algopy" version)) (sha256 (base32 "1vjrzzxa3gvyh2zvm1vwg0s6a7dv23rihgdvgyj1vqniyymp91nq")))) (build-system pyproject-build-system) (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-numpy python-scipy)) (home-page "https://pythonhosted.org/algopy") (synopsis "Algorithmic Differentation in Python") (description "AlgoPy provides a functionality to differentiate functions implemented as computer programs by using Algorithmic Differentiation (AD) techniques in the forward and reverse mode. The forward mode propagates univariate Taylor polynomials of arbitrary order. Hence it is also possible to use AlgoPy to evaluate higher-order derivative tensors. The reverse mode is also known as backpropagation and can be found in similar form in tools like PyTorch. Speciality of AlgoPy is the possibility to differentiate functions that contain matrix functions as +,-,*,/, dot, solve, qr, eigh, cholesky.") (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-apted ;; PyPI release lacks tests and there is no Git tag. (let ((commit "828b3e3f4c053f7d35f0b55b0d5597e8041719ac") (revision "0")) (package (name "python-apted") (version (git-version "1.0.3" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/JoaoFelipe/apted") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1vw1sbn41cysmhr4ib58cw3hzs1xjxwb1d8r1yhrqgjk5q6ckjw7")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--deselect=apted/tests/test_chained.py::test_factory" "--deselect=apted/tests/test_correctness.py::test_factory" "--deselect=apted/tests/test_per_edit_operation_correctness.py::test_factory"))) (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/JoaoFelipe/apted") (synopsis "Algorithm for the tree edit distance") (description "This is a Python implementation of the APTED algorithm,which supersedes the RTED algorithm for computing the tree edit distance.") (license license:expat)))) (define-public python-asap3 (package (name "python-asap3") (version "3.13.7") (source (origin (method url-fetch) (uri (pypi-uri "asap3" version)) (sha256 (base32 "0z6m9ybiy4fdnzlkfkvyxich18iwlwlgj1jd99fylyfwf8l160am")))) (build-system pyproject-build-system) (propagated-inputs (list python-ase)) (native-inputs (list python-setuptools python-wheel which)) (home-page "https://wiki.fysik.dtu.dk/asap") (synopsis "ASAP - classical potentials for Molecular Dynamics with ASE.") (description "This package provides accelerated simulations and potentials of solids.") (license license:lgpl3))) (define-public python-ase (package (name "python-ase") (version "3.25.0") (source (origin (method url-fetch) (uri (pypi-uri "ase" version)) (sha256 (base32 "1hk2r5042cs9shqv49w0jvf65wkyq74s6vc5drfz1275kz5ghk1p")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list ;; DeprecationWarning. "--deselect" "ase/test/fio/test_espresso.py::test_pw_input_write_nested_flat" ;; UserWarning. "--deselect" "ase/test/fio/test_espresso.py::TestConstraints::test_fix_scaled"))) (propagated-inputs (list python-matplotlib python-numpy python-scipy)) (native-inputs (list python-pytest python-pytest-xdist python-setuptools python-wheel)) (inputs (list spglib)) (home-page "https://wiki.fysik.dtu.dk/ase/") (synopsis "Atomic Simulation Environment") (description "This package provides a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.") (license license:lgpl2.1+))) (define-public python-baycomp (package (name "python-baycomp") (version "1.0.3") (source (origin (method url-fetch) (uri (pypi-uri "baycomp" version)) (sha256 (base32 "1v6s4mfr6xzjbv9a2v89hywm6fbv5nii0qczvcfjanvdn7bmmcij")))) (build-system pyproject-build-system) (native-inputs (list python-pytest python-setuptools python-wheel)) (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-boost-histogram (package (name "python-boost-histogram") (version "1.5.2") (source (origin (method url-fetch) (uri (pypi-uri "boost_histogram" version)) (sha256 (base32 "0p2f90p5jwlwrjz3hq2fzaifkmny33g2mpi89nnhi3w41f1jxr2i")))) (build-system pyproject-build-system) ;; This package bundles files from Boost::Histogram and doesn't provide ;; a way to use a system library. (propagated-inputs (list python-numpy)) (native-inputs (list cmake-minimal pybind11 python-pytest python-pytest-benchmark python-scikit-build-core python-setuptools-scm)) (home-page "https://boost-histogram.readthedocs.io/en/latest/") (synopsis "Python bindings for the Boost::Histogram library") (description "This package provides Python bindings for the Boost::Histogram library, one of the fastest libraries for histogramming.") (license license:bsd-3))) (define-public python-bottleneck (package (name "python-bottleneck") (version "1.4.2") (source (origin (method url-fetch) (uri (pypi-uri "bottleneck" version)) (sha256 (base32 "1x29yj4yr12v646si63gkxj9b6lx1xk65536wqy4i9fyk4bqx3ps")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-before 'check 'rebuild-ext (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))))) (native-inputs (list python-pytest python-setuptools python-wheel)) (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-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 'build '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-cmocean (package (name "python-cmocean") (version "4.0.3") (source (origin (method url-fetch) (uri (pypi-uri "cmocean" version)) (sha256 (base32 "0z0d4ma6i228gwpgnkai8scs9bmzz41rirlnqpmb8hazzfcq71ip")))) (build-system pyproject-build-system) (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-matplotlib python-numpy python-packaging)) (home-page "https://github.com/matplotlib/cmocean") (synopsis "Colormaps for Oceanography") (description "This package contains colormaps for commonly-used oceanographic variables. Most of the colormaps started from @code{matplotlib} colormaps, but have now been adjusted using the viscm tool to be perceptually uniform.") (license license:expat))) (define-public python-corner (package (name "python-corner") (version "2.2.2") (source (origin (method git-fetch) ;no tests in PyPi archive (uri (git-reference (url "https://github.com/dfm/corner.py") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1i4dk4jxh0saysya2cnsfwlxwpldbdl174i9pwi4qj82av9jr2ii")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list ;; XXX: Disable tests which failed with mismatched images, check why. "-k" (string-append "not test_labels[png]" " and not test_title_quantiles[png]" " and not test_title_quantiles_default[png]" " and not test_title_quantiles_raises[png]" " and not test_bins[png]" " and not test_bins_log[png]" " and not test_titles1[png]" " and not test_titles2[png]" " and not test_pandas[png]" " and not test_tight[png]" " and not test_extended_overplotting[png]" " and not test_reverse_overplotting[png]" " and not test_arviz[png]" " and not test_range_fig_arg[png]")) #:phases #~(modify-phases %standard-phases (add-before 'build 'pretend-version ;; XXX: Make sure you're either building from a fully intact git ;; repository or PyPI tarballs. Most other sources (such as GitHub's ;; tarballs, a git checkout without the .git folder) don't contain ;; the necessary metadata and will not work. (lambda _ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) (propagated-inputs (list python-matplotlib)) (native-inputs (list python-arviz python-pytest python-scipy python-setuptools-scm)) (home-page "http://corner.readthedocs.io/") (synopsis "Make some beautiful corner plots") (description "This Python module uses @code{matplotlib} to visualize multidimensional samples using a scatterplot matrix. In these visualizations, each one- and two-dimensional projection of the sample is plotted to reveal covariances. corner was originally conceived to display the results of Markov Chain Monte Carlo simulations and the defaults are chosen with this application in mind but it can be used for displaying many qualitatively different samples.") (license license:bsd-2))) (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 python-wheel)) (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-dask-expr (package (name "python-dask-expr") (version "1.1.21") (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 "0m920db2asmqf4w2dncpnkccdhx4c9sfcsd96bh1jfdh8sw2wf6z")))) (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-setuptools python-versioneer python-wheel)) (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-decaylanguage (package (name "python-decaylanguage") (version "0.18.6") (source (origin (method url-fetch) (uri (pypi-uri "decaylanguage" version)) (sha256 (base32 "0kc9i9k51kg2zv8dwywpigiipxzmyxpzb101imjsvv1licip7b8v")))) (build-system pyproject-build-system) (arguments (list ;; This file fails to be collected with "DeprecationWarning: setDaemon() ;; is deprecated, set the daemon attribute instead". #:test-flags #~(list "--ignore" "tests/test_convert.py"))) (propagated-inputs (list python-attrs python-graphviz python-hepunits python-lark python-numpy python-pandas python-particle python-plumbum)) (native-inputs (list python-hatch-vcs python-hatchling python-pytest)) (home-page "https://decaylanguage.readthedocs.io/en/latest/") (synopsis "Language to describe, manipulate and convert particle decays") (description "DecayLanguage implements a language to describe and convert particle decays between digital representations, effectively making it possible to interoperate several fitting programs. Particular interest is given to programs dedicated to amplitude analyses.") (license license:bsd-3))) (define-public python-deepdish ;; XXX: The project may no longer be compatible with the version of NumPy ;; packed in Guix (now 1.24.4), use the latest commit containing fixes. ;; See: . ;; However, there is a maintained fork that appears to be a good ;; replacement: https://github.com/portugueslab/flammkuchen. (let ((commit "3f2dff7a03f1b31f6924b665ad5b8c299329c1cd") (revision "0")) (package (name "python-deepdish") (version (git-version "0.3.7" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/uchicago-cs/deepdish") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1n3r6z5zd18kdmzyg1gkm9lqi573szlxbls1ck5wjn4a14ar9fw3")))) (arguments ;; 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-pytest python-pandas python-setuptools python-wheel)) (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-distributed (package (name "python-distributed") (version "2024.12.1") (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 "1k0kmzd48mvaaizbf3b6lk84s0fw88x9v7hfgiddyyv6mf4x7h27")))) (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") ;; This disables FutureWarning that are caught as error, ;; related to the merge of python-dask-expr in python-dask. "-W" (string-append "ignore::FutureWarning") "-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_closed_exception" "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_transition_failure_triggers_log_event" "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 python-wheel)) (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-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-fast-histogram (package (name "python-fast-histogram") (version "0.14") (source (origin (method url-fetch) (uri (pypi-uri "fast_histogram" version)) (sha256 (base32 "1sk9xa85cgm4sylzblwv3qr2dmm0ic06zkwxqa2xlazjiawp629r")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-before 'check 'build-extensions (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))))) (native-inputs (list python-hypothesis python-pytest python-setuptools python-setuptools-scm python-wheel)) (propagated-inputs (list python-numpy)) (home-page "https://github.com/astrofrog/fast-histogram") (synopsis "Fast simple 1D and 2D histograms") (description "The fast-histogram mini-package aims to provide simple and fast histogram functions for regular bins that don't compromise on performance. It doesn't do anything complicated - it just implements a simple histogram algorithm in C and keeps it simple. The aim is to have functions that are fast but also robust and reliable. The result is a 1D histogram function here that is 7-15x faster than @code{numpy.histogram}, and a 2D histogram function that is 20-25x faster than @code{numpy.histogram2d}.") (license license:bsd-3))) (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 python-setuptools python-wheel)) (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-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-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-hepunits (package (name "python-hepunits") (version "2.3.5") (source (origin (method url-fetch) (uri (pypi-uri "hepunits" version)) (sha256 (base32 "1n1nf2rz2d86qzjmcwykbc16jzsqb45vs8lyksg98b3jd8nwsd4l")))) (build-system pyproject-build-system) (native-inputs (list python-hatch-vcs python-hatchling python-pytest)) (home-page "https://github.com/scikit-hep/hepunits") (synopsis "Units and constants in the HEP system of units") (description "@code{hepunits} collects the most commonly used units and constants in the HEP System of Units, as derived from the basic units originally defined by the CLHEP project.") (license license:bsd-3))) (define-public python-hist (package (name "python-hist") (version "2.8.1") (source (origin (method url-fetch) (uri (pypi-uri "hist" version)) (sha256 (base32 "17cd46c0ixq18fr2kgzam09w1sr4qkd9l6nsjdbl4vggw80ck9vx")))) (build-system pyproject-build-system) (propagated-inputs (list python-boost-histogram python-histoprint python-numpy python-typing-extensions)) (native-inputs (list python-hatch-vcs python-hatchling python-pytest python-pytest-mpl)) (home-page "https://hist.readthedocs.io/en/latest/") (synopsis "Hist classes and utilities") (description "Hist is an analyst-friendly front-end for @code{boost-histogram}.") (license license:bsd-3))) (define-public python-histoprint (package (name "python-histoprint") (version "2.6.0") (source (origin (method url-fetch) (uri (pypi-uri "histoprint" version)) (sha256 (base32 "07d2lk64gwhjvw4wccvwks3j4ig7g99q627jjxz4ans5a29p5pz1")))) (build-system pyproject-build-system) (propagated-inputs (list python-click python-numpy python-uhi)) (native-inputs (list python-awkward python-boost-histogram python-hatch-vcs python-hatchling python-pytest python-rich)) (home-page "https://github.com/scikit-hep/histoprint") (synopsis "Pretty print histograms to the console") (description "Histoprint uses a mix of terminal color codes and Unicode trickery (i.e. combining characters) to plot overlaying histograms.") (license license:expat))) (define-public python-imagehash (package (name "python-imagehash") (version "4.3.1") (source (origin (method git-fetch) ;no tests in PyPI (uri (git-reference ;; It's an effective and maintained fork of ;; project, which ;; has the latest release in 2016. (url "https://github.com/JohannesBuchner/imagehash") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1lw9lxzrzy9s5v3xc35vmh97hlyavnla087fp19k77va6v8vbjjf")))) (build-system pyproject-build-system) (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-numpy python-pillow python-pywavelets python-scipy)) (home-page "https://github.com/JohannesBuchner/imagehash") (synopsis "Perceptual Image Hashing library") (description "This package implements a functionality to tell whether two images look nearly identical. The image hash algorithms (average, perceptual, difference, wavelet) analyse the image structure on luminance (without color information). The color hash algorithm analyses the color distribution and black & gray fractions (without position information). Features: @itemize @item average hashing @item perceptual hashing @item difference hashing @item wavelet hashing @item HSV color hashing (colorhash) @item crop-resistant hashing @end itemize") (license license:bsd-2))) (define-public python-libneuroml (package (name "python-libneuroml") (version "0.6.5") (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 "04cfff9phm19x87p86xrkhd6wlpxvdwk3rf1c3qgyncfchws0sjh")))) (build-system pyproject-build-system) (native-inputs (list python-pytest python-numpy python-setuptools python-tables python-wheel)) (propagated-inputs (list python-lxml python-natsort python-networkx)) (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))) (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-modin (package (name "python-modin") (version "0.32.0") (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 "1vb3iffgspryb6nvwiwdnypb922vkn2yvyzc1y0wwxcb0c0fl78d")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--numprocesses" (number->string (min 8 (parallel-job-count))) ;; These four tests fail because an expected error is not raised. "-k" "not test_binary_bad_broadcast") #:phases '(modify-phases %standard-phases (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? test-flags #:allow-other-keys) (when tests? (setenv "MODIN_ENGINE" "dask") (apply invoke "python" "-m" "pytest" "modin/tests/numpy" test-flags) (setenv "MODIN_ENGINE" "python") (apply invoke "python" "-m" "pytest" "modin/tests/numpy" test-flags))))))) (propagated-inputs (list python-cloudpickle python-dask python-distributed python-numpy python-packaging python-pandas python-s3fs)) (native-inputs (list python-boto3 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 python-wheel)) (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-mpl-scatter-density (package (name "python-mpl-scatter-density") (version "0.8") (source (origin (method url-fetch) (uri (pypi-uri "mpl_scatter_density" version)) (sha256 (base32 "0cynk1rk6k2xklgv69difphrz6id77x3xb58kbs4mc4q7z6bvfid")))) (build-system pyproject-build-system) (arguments (list ;; See . #:test-flags #~(list "-k" "not test_default_dpi"))) (native-inputs (list python-pytest python-pytest-cov python-pytest-mpl python-setuptools python-setuptools-scm python-wheel)) (propagated-inputs (list python-fast-histogram python-matplotlib python-numpy)) (home-page "https://github.com/astrofrog/mpl-scatter-density") (synopsis "Matplotlib helpers to make density scatter plots") (description "This package provides functionality to make it easy to make scatter density maps, both for interactive and non-interactive use.") (license license:bsd-2))) (define-public python-mpsplines ;; No release on PyPI no git tag, use the latest commit. (let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2") (revision "0")) (package (name "python-mpsplines") (version (git-version "0.0.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/jararias/mpsplines") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1wqfvjp1d6xzb07qnq72h76f0mx7za9pasgw3qp3ciaycmlkvdr3")))) (build-system pyproject-build-system) (arguments (list #:tests? #f)) ; no tests provided (native-inputs (list python-setuptools python-wheel)) (propagated-inputs (list python-scipy python-numpy python-loguru)) (home-page "https://github.com/jararias/mpsplines") (synopsis "Mean preserving interpolation with splines") (description "Thi package implements a functionality for mean-preserving interpolation of 1D data (for example, time series) with splines.") (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-narwhals (package (name "python-narwhals") (version "1.44.0") (source (origin (method url-fetch) (uri (pypi-uri "narwhals" version)) (sha256 (base32 "07fk7b1via9a81ig38316l10avdbrjbdxz2n7ddj48bg9xnn3w4c")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--numprocesses" (number->string (parallel-job-count)) ;; Run a minimal portion of tests, the complete test suite ;; requires Polars, PySpark and SqlFrame packages. "--constructors=pandas" "-k" (string-join ;; XXX: ValueError: Minimum version of modin supported by Narwhals is ;; (0, 8, 2), found: (0,) (list "not test_allow_series" "test_cross_join_non_pandas" "test_eager_only_eager" "test_from_native_roundtrip_identity" "test_namespace_series_from_iterable" "test_series_only" "test_to_native_namespace") " and not ")))) (native-inputs (list python-pytest python-pytest-xdist python-duckdb python-pytest-env python-hatchling)) (propagated-inputs (list python-pandas python-dask python-modin python-pyarrow)) (home-page "https://narwhals-dev.github.io/narwhals/") (synopsis "Compatibility layer between dataframe libraries") (description "This package provides an extremely lightweight compatibility layer between dataframe libraries. @itemize @item full API support: cuDF, Modin, pandas, Polars, PyArrow @item lazy-only support: Dask, DuckDB, Ibis, PySpark, SQLFrame @end itemize") (license license:expat))) (define-public python-ndindex (package (name "python-ndindex") (version "1.7") ;newer versions require a newer numpy (source (origin (method url-fetch) (uri (pypi-uri "ndindex" version)) (sha256 (base32 "1lpgsagmgxzsas7g8yiv6wmyss8q57w92h70fn11rnpadsvx16xz")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "-c" "/dev/null"))) ;avoid coverage (native-inputs (list python-cython python-numpy python-pytest python-setuptools python-wheel)) (home-page "https://quansight-labs.github.io/ndindex/") (synopsis "Python library for manipulating indices of ndarrays") (description "This package provides a Python library for manipulating indices of @code{ndarrays}.") (license license:expat))) (define-public python-nibabel (package (name "python-nibabel") (version "5.3.2") (source (origin (method url-fetch) (uri (pypi-uri "nibabel" version)) (sha256 (base32 "16snprwgp7qzp51j3mx0zdn7brvx6r14ankldi24ny0w7d8adp0b")))) (build-system pyproject-build-system) (arguments (list ;; AttributeError: 'dict' object has no attribute 'add'. #:test-flags #~(list "-k" "not test_first and not test_second"))) (propagated-inputs (list python-importlib-resources python-numpy python-packaging python-typing-extensions)) (native-inputs (list python-hatch-vcs python-hatchling python-pytest python-pytest-httpserver python-pytest-xdist)) (home-page "https://nipy.org/nibabel/") (synopsis "Read and write access to common neuroimaging file formats") (description "@code{nibabel} is a library that provides read and write access to common neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD, ECAT and Philips PAR/REC. In addition, NiBabel also supports FreeSurfer’s MGH, geometry, annotation and morphometry files, and provides some limited support for DICOM.") (license license:expat))) ; and other non-copyleft licenses (define-public python-numdifftools (package (name "python-numdifftools") (version "0.9.41") (source (origin (method url-fetch) (uri (pypi-uri "numdifftools" version)) (sha256 (base32 "1d49wd5jqnl0500jyws0vb7nv4dy4bb5ml4z9qx1n8867k6hbxsf")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--pyargs" "numdifftools" "-k" (string-join ;; Tests failing with error: TypeError: a must be an array ;; of real numbers, see ;; . (list "not test_high_order_derivative" "test_low_order_derivative_on_example_functions" "test_sinx_div_x" "test_complex_hessian_issue_35" "numdifftools.fornberg.Taylor" "numdifftools.fornberg.derivative" "numdifftools.fornberg.taylor") " and not ")) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'relax-requirements (lambda _ (substitute* "setup.py" ;; We can run tests without deprecated pytest-runner. (("setup_requires.*") ""))))))) (native-inputs (list python-algopy python-line-profiler python-pytest python-setuptools python-setuptools-scm python-statsmodels python-wheel)) (propagated-inputs (list python-numpy python-scipy)) (home-page "https://github.com/pbrod/numdifftools") (synopsis "Solves automatic numerical differentiation problems") (description "This package implements a functionality to solve automatic numerical differentiation problems in one or more variables. Finite differences are used in an adaptive manner, coupled with a Richardson extrapolation methodology to provide a maximally accurate result. The user can configure many options like; changing the order of the method or the extrapolation, even allowing the user to specify whether complex-step, central, forward or backward differences are used.") (license license:bsd-3))) (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-setuptools python-sympy python-wheel)) (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-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-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 pyproject-build-system) (propagated-inputs (list python-numpy)) (native-inputs (list python-pytest python-pytest-cov python-setuptools python-wheel)) (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-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 python-setuptools python-wheel)) (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-particle (package (name "python-particle") (version "0.25.3") (source (origin (method url-fetch) (uri (pypi-uri "particle" version)) (sha256 (base32 "0as50k5hinxszsm6lnghnmx2cyjy77c0i2gvzf2q64g2x5b7xkvq")))) (build-system pyproject-build-system) (propagated-inputs (list python-attrs python-hepunits python-typing-extensions)) (native-inputs (list python-hatch-vcs python-hatchling python-pandas python-pytest python-pytest-benchmark python-tabulate)) (home-page "https://github.com/scikit-hep/particle") (synopsis "Extended PDG particle data and MC identification codes") (description "@code{Particle} provides a pythonic interface to the Particle Data Group (PDG) particle data tables and particle identification codes, with extended particle information and extra goodies.") (license license:bsd-3))) (define-public python-pint (package (name "python-pint") (version "0.24.4") (source (origin (method url-fetch) (uri (pypi-uri "pint" version)) (sha256 (base32 "100vp5jg2sqj5wxaflj1rqjv2pk4fd55l2h2sdn7m0vlnlwm89rm")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--ignore=pint/testsuite/benchmarks") #:phases #~(modify-phases %standard-phases (add-before 'check 'pre-check (lambda _ ;; PermissionError: [Errno 13] Permission denied: ;; '/homeless-shelter' (setenv "HOME" "/tmp")))))) (native-inputs (list python-pytest python-pytest-mpl python-pytest-subtests python-setuptools python-setuptools-scm python-wheel)) (propagated-inputs (list python-flexcache python-flexparser python-platformdirs python-typing-extensions)) (home-page "https://github.com/hgrecco/pint") (synopsis "Physical quantities module") (description "Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units.") (license license:bsd-3))) (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 python-setuptools-scm python-wheel)) (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-pyet (package (name "python-pyet") (version "1.3.1") (source (origin (method url-fetch) (uri (pypi-uri "pyet" version)) (sha256 (base32 "1dblsx0bv1g453hcx5vwij1zgankwgwvhwllqkn47k578h038xvy")))) (build-system pyproject-build-system) (native-inputs (list python-mock python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-pandas python-xarray)) (home-page "https://github.com/pyet-org/pyet") (synopsis "Python package for evapotranspiration calculation") (description "This package provides a Python library for calculating Evapotranspiration using various standard methods.") (license license:expat))) (define-public python-pynetdicom (package (name "python-pynetdicom") (version "2.1.1") (source (origin (method url-fetch) (uri (pypi-uri "pynetdicom" version)) (sha256 (base32 "1smzrnc93nmv8jz4np9knas74a46b1nhb3hjpf8n9vfpxypgnwcn")))) (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-codespell python-coverage python-poetry-core python-pytest python-pytest-cov python-pytest-xdist python-sphinx python-sphinx-rtd-theme)) (propagated-inputs (list python-mypy python-numpydoc python-pydicom python-pyfakefs 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-pyzx (package (name "python-pyzx") (version "0.9.0") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference (url "https://github.com/zxcalc/pyzx") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1bnmz08w1bmipir1wnn1k3fw64rply7891xns22qfj6yh0j1n6rj")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list ;; Ignore long running tests "--ignore=tests/long_test.py" "--ignore=tests/long_scalar_test.py") #:phases #~(modify-phases %standard-phases (add-before 'check 'pre-check (lambda* (#:key inputs outputs #:allow-other-keys) (setenv "HOME" "/tmp") ;; Matplotlib needs to be able to write its ;; configuration file somewhere. (setenv "MPLCONFIGDIR" "/tmp")))))) (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-ipywidgets python-lark python-numpy python-pyperclip python-tqdm)) (home-page "https://github.com/zxcalc/pyzx") (synopsis "Quantum circuit rewriting and optimisation using the ZX-calculus") (description "PyZX is a Python tool implementing the theory of ZX-calculus for the creation, visualisation, and automated rewriting of large-scale quantum circuits. PyZX currently allows you to: @itemize @item Read in quantum circuits in the file format of QASM, Quipper or Quantomatic; @item Rewrite circuits into a pseudo-normal form using the ZX-calculus; @item Extract new simplified circuits from these reduced graphs; @item Visualise the ZX-graphs and rewrites using either Matplotlib, Quantomatic or as a TikZ file for use in LaTeX documents; @item Output the optimised circuits in QASM, QC or QUIPPER format. @end itemize") (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 python-setuptools python-wheel)) (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-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-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-scikit-allel (package (name "python-scikit-allel") (version "1.3.13") (source (origin (method url-fetch) (uri (pypi-uri "scikit_allel" version)) (sha256 (base32 "0d9yadzhsjjqkh6rz273f53iwczk0c7pv9dajzcrmfnk036b8f4s")))) (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 htslib python-cython python-h5py python-hmmlearn python-numexpr python-numpy python-pytest python-setuptools python-setuptools-scm python-wheel 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 "0.11.2") (source (origin (method url-fetch) (uri (pypi-uri "scikit_build_core" version)) (sha256 (base32 "0baaava7jvc69r5j803vjxvf2cnx0f3gjhqalipp7l4d1cgwg3vp")))) (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-cattrs python-fastjsonschema python-hatch-fancy-pypi-readme python-hatch-vcs python-hatchling python-numpy python-pip python-pypa-build python-pytest python-pytest-subprocess 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 "10.0.2") (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 "10kvzm4fmazsrddd83m0903wan67fkj13vdp6w1iw6wm6a0b5h28")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list ;; Tests require Jax. "--ignore=tests/test_autodiff.py" "--ignore=tests/test_examples.py"))) (native-inputs (list python-autograd python-pyamg ;; python-jax ; not packed yet python-pytest python-shapely python-setuptools python-wheel)) (propagated-inputs (list python-meshio python-numpy python-scipy)) (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 "0.5.0") (source (origin (method url-fetch) (uri (pypi-uri "scikit_fuzzy" version)) (sha256 (base32 "0zsfyd8cpd2l82fwh3smxbwhb3bkqwlq17cbav53axma4c2k9r9f")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--pyargs" "skfuzzy"))) (native-inputs (list python-pytest python-setuptools python-wheel)) (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 #:test-flags ;; To make sure we test compiled and installed module. #~(list (string-append #$output "/lib/python" #$(version-major+minor (package-version python)) "/site-packages") "--pyargs" "skimage" ;; Disable flaky test "-k" (string-join (list "not test_ellipse_parameter_stability" ;; ValueError: Cannot call len() on object with unknown chunk size. "test_thresholds_dask_compatibility[threshold_triangle-41-43]") " and not ")) #:phases #~(modify-phases %standard-phases (add-before 'build 'change-home-dir (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. (setenv "HOME" "/tmp"))) (add-before 'check 'pre-check (lambda _ ;; To prevent loading tests twise. ;; 16277 passed, 240 skipped, 4 deselected (delete-file-recursively "skimage"))) (add-before 'check 'post-check (lambda _ (for-each delete-file-recursively (find-files #$output "__pycache__" #:directories? #t))))))) ;; 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-misc (package (name "python-scikit-misc") (version "0.5.1") (source (origin (method url-fetch) (uri (pypi-uri "scikit_misc" version)) (sha256 (base32 "18sj7qa3kk4pqh3rzg2c64lf03nciv9cf985yh1h2kpqqndgdhf5")))) (build-system pyproject-build-system) (arguments (list #:test-flags '(list "--pyargs" "skmisc") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'fix-version (lambda _ (call-with-output-file "skmisc/_version.py" (lambda (port) (display (string-append "__version__ = \"" #$version "\"") port))) (substitute* "meson.build" (("^ version: run_command.*") (string-append " version: '" #$version "',\n"))) (substitute* "pyproject.toml" (("dynamic = \\['version'\\]") (string-append "version = \"" #$version "\"")))))))) (propagated-inputs (list meson-python python-numpy python-numpydoc python-spin python-twine)) (native-inputs (list gfortran pkg-config python-cython-3 python-meson-python python-numpy python-pytest python-pytest-cov python-setuptools python-wheel)) (home-page "https://has2k1.github.io/scikit-misc/stable") (synopsis "Miscellaneous tools for scientific computing.") (description "This package provides miscellaneous tools for data analysis and scientific computing.") (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)) (native-inputs (list python-setuptools)) (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 "0.10.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/holgern/scikit-optimize") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0pc6avzxz8l32km5jvv3maih0a5x2akxybvxl2hdg04qz2l0kz8b")))) (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 python-setuptools python-wheel)) (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-surprise (package (name "python-scikit-surprise") (version "1.1.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/NicolasHug/Surprise") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "15ckx2i41vs21sa3yqyj12zr0h4zrcdf3lrwcy2c1cq2bjq7mnvz")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-before 'check 'set-home (lambda _ ;; Change from /homeless-shelter to /tmp for write ;; permission. (setenv "HOME" "/tmp")))))) (native-inputs (list python-cython-3 python-pandas python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-joblib python-numpy python-scikit-learn)) (home-page "https://surpriselib.com/") (synopsis "Recommender system library for Scikit-learn") (description "This package provides a Python library for building and analyzing recommender systems that deal with explicit rating data. It was designed with the following purposes in mind: @itemize @item Provide tools to handle downloaded or user-provided datasets. @item Provide ready-to-use prediction algorithms and similarity measures. @item Provide a base for creating custom algorithms. @item Provide tools to evaluate, analyse and compare algorithm performance. @item Provide documentation with precise details regarding library algorithms. @end itemize") (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 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-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: ;; . ;; 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-simple-pid (package (name "python-simple-pid") (version "2.0.1") (source (origin (method url-fetch) (uri (pypi-uri "simple_pid" version)) (sha256 (base32 "17p9bgka5yv5lbnbk374yjccrlizm572wv3xb479072lahf7cwap")))) (build-system pyproject-build-system) (native-inputs (list python-pytest python-setuptools python-wheel)) (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-snakemake-interface-common (package (name "python-snakemake-interface-common") (version "1.17.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/snakemake/snakemake-interface-common") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "19fyqs048zdvrmq5sdayzch850kwsyv2x6xn57cjjzcm4zpjrh9w")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "python3" "tests/tests.py"))))))) (native-inputs (list python-poetry-core python-pytest)) (propagated-inputs (list python-argparse-dataclass python-configargparse)) (home-page "https://github.com/snakemake/snakemake-interface-common") (synopsis "Common functions and classes for Snakemake and its plugins") (description "This package provides common functions and classes for Snakemake and its plugins.") (license license:expat))) (define-public python-snakemake-interface-executor-plugins (package (name "python-snakemake-interface-executor-plugins") (version "9.3.3") (source (origin (method git-fetch) (uri (git-reference (url (string-append "https://github.com/snakemake/" "snakemake-interface-executor-plugins")) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1kjjcgkk1rbavb687x5ayw35ayhsnhpg9262k317x911wqpsj2fm")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "python3" "tests/tests.py"))))))) (propagated-inputs (list python-argparse-dataclass python-snakemake-interface-common python-throttler)) (native-inputs (list python-poetry-core python-pytest)) (home-page (string-append "https://github.com/snakemake/" "python-snakemake-interface-executor-plugins")) (synopsis "Interface for Snakemake executor plugins") (description "This package provides a stable interface for interactions between Snakemake and its executor plugins.") (license license:expat))) (define-public python-snakemake-interface-report-plugins (package (name "python-snakemake-interface-report-plugins") (version "1.1.0") (source (origin (method git-fetch) (uri (git-reference (url (string-append "https://github.com/snakemake/" "snakemake-interface-report-plugins")) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0i6z9vk6nv2m3jsym0glrb7h9isdlfza2yq14vbqcslybdi9ykfa")))) (build-system pyproject-build-system) (arguments (list #:tests? #f ;circular dependency on snakemake #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "python3" "tests/tests.py"))))))) (propagated-inputs (list python-snakemake-interface-common python-pytest)) (native-inputs (list python-poetry-core)) (home-page (string-append "https://github.com/snakemake/" "python-snakemake-interface-report-plugins")) (synopsis "Interface for Snakemake report plugins") (description "This package provides a stable interface for interactions between Snakemake and its report plugins.") (license license:expat))) (define-public python-snakemake-interface-software-deployment-plugins (package (name "python-snakemake-interface-software-deployment-plugins") (version "0.6.1") (source (origin (method git-fetch) (uri (git-reference (url (string-append "https://github.com/snakemake/" "snakemake-interface-software-deployment-plugins")) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0b4kkznfyfck9f92pkimhyl13ljisfn67rsilm1a5inq2ywpmxba")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "python3" "tests/tests.py"))))))) (propagated-inputs (list python-argparse-dataclass python-snakemake-interface-common)) (native-inputs (list python-poetry-core)) (home-page (string-append "https://github.com/snakemake/" "snakemake-interface-software-deployment-plugins")) (synopsis "Interface for Snakemake software deployment plugins") (description "This package provides a stable interface for interactions between Snakemake and its software deployment plugins.") (license license:expat))) (define-public python-snakemake-interface-storage-plugins (package (name "python-snakemake-interface-storage-plugins") (version "3.3.0") (source (origin (method git-fetch) (uri (git-reference (url (string-append "https://github.com/snakemake/" "snakemake-interface-storage-plugins")) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "05n5xgwagb01nyzi8xfvp0nvdfl24lxidgksm7k86p68n1rijd5a")))) (build-system pyproject-build-system) (arguments (list #:tests? #f ;circular dependency on snakemake #:phases #~(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "python3" "tests/tests.py"))))))) (propagated-inputs (list python-reretry python-snakemake-interface-common python-throttler python-wrapt)) (native-inputs (list python-poetry-core python-pytest)) (home-page (string-append "https://github.com/snakemake/" "snakemake-interface-storage-plugins")) (synopsis "Interface for Snakemake storage plugins") (description "This package provides a stable interface for interactions between Snakemake and its storage plugins.") (license license:expat))) (define-public python-tdda (package (name "python-tdda") (version "2.2.17") (source (origin (method url-fetch) (uri (pypi-uri "tdda" version)) (sha256 (base32 "1l2ph60m20ii4ljgd81wccpp5p8p2m81irr97k7850s2l1qnikcw")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list ;; One test fails with error: AssertionError: False is not true : 5 ;; lines are different, starting at line 1 "--deselect=tdda/test_tdda.py::TestOne::test_ddiff_values_output") #:phases #~(modify-phases %standard-phases ;; "datetime.UTC" is not availalbe in Python 3.10 but in ;; 3.11 it's present ;; . (add-after 'unpack 'fix-Python3.11-datetime.UTC (lambda _ (substitute* (find-files "." "\\.py") (("datetime.UTC") "datetime.timezone.utc"))))))) (native-inputs (list python-numpy python-chardet python-pandas python-pyarrow python-pytest python-rich python-setuptools python-wheel)) (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 perform 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-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") #:phases '(modify-phases %standard-phases (add-after 'unpack 'numpy-compatibility (lambda _ (substitute* "traittypes/tests/test_traittypes.py" (("np\\.int") "int"))))))) (propagated-inputs (list python-traitlets)) (native-inputs (list python-numpy python-pandas python-nose python-pytest python-setuptools python-xarray python-wheel)) (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-trimesh (package (name "python-trimesh") (version "4.5.3") (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 "17fyapp8nffnnf95bmcvllvg41fjlpvlv6qndbm048hnyayixxld")))) (build-system pyproject-build-system) (arguments (list #:test-flags ;; XXX: When more optional modules are available review ;; disabled tests once again. ;; ;; Disable tests requiring optional, not packed modules. #~(list "-k" (string-join (list "not test_bezier_example" "test_discrete" "test_dxf" "test_ply_path_bezier" "test_ply_path_line" "test_ply_path_multi" "test_revolve" "test_screw" "test_simple_closed" "test_simple_extrude" "test_simple_open" "test_slice_onplane" "test_spline_3D" "test_svg" ;; Following tests require network: "test_fuze" "test_remote") " and not ")) #:phases #~(modify-phases %standard-phases ;; XXX: It struggles to load and fails with error: AttributeError: ;; module 'trimesh' has no attribute '__main__'. (delete 'sanity-check)))) (native-inputs (list python-coveralls python-pyinstrument python-pytest)) (propagated-inputs (list ;; python-cascadio ; not packed yet, optional python-chardet python-colorlog python-httpx python-jsonschema python-lxml ;; python-mapbox-earcut ; not packed yet, optional ;; python-manifold3d ; not packed yet, optional python-meshio python-networkx python-numpy ;; python-openctm ; not packed yet, optional python-pillow python-psutil python-pycollada python-pyglet python-requests python-rtree python-scikit-image python-scipy python-setuptools python-shapely ;; python-svg-path ; not packed yet, optional python-sympy ;; python-vhacdx ; not packed yet, optional ;; python-xatlas ; not packed yet, optional 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-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" ;; These fail with: td64 doesn't return NotImplemented, see numpy#17017 " and not test_nat_comparisons" ;; 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 python-setuptools python-wheel ;; 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 "2.2.3") (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 "00f6jnplwg7iffnxdm4hpfls0ncbarc23933xq1rm5nk5g8dcldx")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--pyargs" "pandas" ;; "--exitfirst" ;; XXX The tests won't even start on my 16 core laptop, but they ;; start with 4 processes. "--numprocesses" (number->string (min 4 (parallel-job-count))) "-m" "not slow and not network and not db" ;; All tests errored. "--ignore=pandas/tests/io/test_clipboard.py" "-k" (string-join (list "not test_git_version" "test_show_versions_console" ;; Not testing ~ expansion. "test_expand_user" "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] "test_wrong_url" ;; TODO: Missing input "TestS3" "s3" ;; This test fails when run with pytest-xdist ;; (see: https://github.com/pandas-dev/pandas/issues/39096). "test_memory_usage" "test_parsing_tzlocal_deprecated" ;; PyArrow is optional. "test_style_bar_with_pyarrow_NA_values" "test_very_negative_exponent" "test_usecols_no_header_pyarrow" "test_scientific_no_exponent[pyarrow-None]" "test_inspect_getmembers" ;; SciPy introduces cycle, optional. "test_savefig" ;; It requires a fresh python-tzdata, including new ;; timezones. "test_repr" ;; These tests should be skipped on 32bit systems: ;; Cannot cast array data from dtype('int64') to dtype('int32') #$@(if (not (target-64bit?)) #~("test_inf_bound_infinite_recursion" "test_reindex_behavior_with_interval_index" "test_repeating_interval_index_with_infs") #~())) " and not ")) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'version-set-by-guix (lambda _ (with-output-to-file "_version.py" (lambda _ (display (string-append "__version__ = \"" #$(package-version this-package) "\"")))))) (add-before 'check 'pre-check (lambda _ (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/python3.11/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 python-beautifulsoup4 python-cython-3 python-html5lib python-lxml python-matplotlib python-openpyxl python-pytest-asyncio python-pytest python-pytest-localserver python-pytest-mock python-pytest-xdist python-versioneer)) (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 "2.2.3.241126") (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 "0xbvin2l7h8vq9g24n4n2l49pdxbi15qghq7zkhh567p3pbmvsyb")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--ignore=tests/test_io.py" ;requires python-calamine "-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-2 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 python-setuptools python-wheel)) (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") ;; FIXME: The latest version requires hypothesis >= 6.92.7, which can't be ;; picked from python-hypothesis-next for some reason. (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")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "--numprocesses" (number->string (min 8 (parallel-job-count))) "--ignore=tests/pyspark" "-k" (string-join ;; Failed: DID NOT RAISE (list "not test_from_records_validates_the_schema" "test_init_pandas_dataframe_errors" "test_schema_dtype_crs_without_coerce" "test_schema_from_dataframe" "test_schema_model" "test_validate_coerce_on_init" ;; multimethod.DispatchError: ('str_length: 0 ;; methods found', (, , ;; ), []) "test_succeeding" "test_failing" "test_failing_with_none" ;; pandera.errors.SchemaError: Error while executing ;; check function: KeyError("foo") "test_check_groups" ;; [pandas_series.py-plugin_mypy.ini-expected_errors13] ;; - assert 1 == 2 "test_pandas_stubs_false_positives" ;; TypeError: type 'Series' is not subscriptable "test_pandas_modules_importable") " and not ")))) ;; 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-next ;strategies extra python-modin python-multimethod python-numpy python-packaging python-pandas python-pandas-stubs ;mypy extra python-pydantic-2 python-scipy ;hypotheses extra python-typeguard 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-pytest-xdist python-setuptools python-sphinx python-uvicorn ;needed to run fastapi tests python-wheel)) (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 "0.31.0") (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 "06y6fvydrsjqdpbd20icd194693x127qhb19fgw248jfjyg5ga44")))) (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") ;; Test files are not included "--ignore=tests/io/test_read_csvs.py" ;; Polars has not been packaged yet. "--ignore=tests/polars" ;; 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 (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 python-setuptools python-wheel 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-pymcubes (package (name "python-pymcubes") (version "0.1.6") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference (url "https://github.com/pmneila/PyMCubes") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1v2qhc4pwanx6a8k843mbh45yk77n3w63sy5lzk5c3q4pkvfj1b9")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-before 'check 'prepare-test-environment (lambda _ ;; FileNotFoundError: [Errno 2] No such file or directory: ;; 'output/test.obj' (mkdir "output") (invoke "python" "setup.py" "build_ext" "--inplace")))))) (native-inputs (list python-cython python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-pycollada python-numpy python-scipy)) (home-page "https://github.com/pmneila/PyMCubes") (synopsis "Marching cubes for Python") (description "@code{PyMCubes} is an implementation of the marching cubes algorithm to extract iso-surfaces from volumetric data. The volumetric data can be given as a three-dimensional @code{NumPy} array or as a Python function @code{f(x, y, z)}.") (license license:bsd-3))) (define-public python-pythran (package (name "python-pythran") (version "0.17.0") (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 "1rm9lfbz5qvah1m0rr5gaaahkf1gzwlw1ysvym2l2yh0clglav94")))) (build-system pyproject-build-system) (arguments (list #:test-flags '(list (string-append "--numprocesses=" (number->string (parallel-job-count))) ;; XXX There are lots of tests of the format ;; pythran/tests/test_*.py, but they cannot easily be selected. "pythran/tests/test_typing.py") #:phases #~(modify-phases %standard-phases (add-before 'check 'pre-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~%"))))))))) (native-inputs ;; For tests. (list openblas python-pytest python-pytest-xdist python-setuptools python-wheel)) (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 python-setuptools python-wheel)) (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-spin (package (name "python-spin") (version "0.8") (source (origin (method url-fetch) (uri (pypi-uri "spin" version)) (sha256 (base32 "0ff48nagfaai3j26g1db4zq2bwdv6kj5l7xhcs2l9kzg7qzrmhr7")))) (build-system pyproject-build-system) (propagated-inputs (list python-click python-colorama python-tomli)) (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/scientific-python/spin") (synopsis "Developer tool for scientific Python libraries") (description "@code{spin} is a simple interface for common development tasks. It comes with a few common build commands out the box, but can easily be customized per project. The impetus behind developing the tool was the mass migration of scientific Python libraries (SciPy, scikit-image, and NumPy, etc.) to Meson, after distutils was deprecated. When many of the build and installation commands changed, it made sense to abstract away the nuisance of having to re-learn them.") (license license:bsd-3))) (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-einops (package (name "python-einops") (version "0.8.1") (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 "07xd5a4sya3mr003f17hxykcbq3zf3mnr51qagv7fy55qcnbkn97")))) (build-system pyproject-build-system) (arguments (list #:test-flags ;; Skip optional dependency on Jupyter during tests. #~(list "--ignore=scripts/test_notebooks.py") #: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 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-uhi (package (name "python-uhi") (version "0.5.0") (source (origin (method url-fetch) (uri (pypi-uri "uhi" version)) (sha256 (base32 "0753b7yw0zi06g4azafnk3w8i3q6js9i6wwg3pya464gygrbnncm")))) (build-system pyproject-build-system) (propagated-inputs (list python-numpy)) (native-inputs (list python-boost-histogram python-fastjsonschema python-hatch-vcs python-hatchling python-pytest)) (home-page "https://github.com/scikit-hep/uhi") (synopsis "Universal Histogram Interface") (description "This is a package meant primarily for documenting histogram indexing and the PlottableHistogram Protocol and any future cross-library standards. It also contains the code for the PlottableHistogram Protocol, to be used in type checking libraries wanting to conform to the protocol. It is not usually a runtime dependency, but only a type checking, testing, and/or docs dependency in support of other libraries.") (license license:bsd-3))) (define-public python-unyt (package (name "python-unyt") (version "3.0.3") (source (origin (method url-fetch) (uri (pypi-uri "unyt" version)) (sha256 (base32 "0jrq2vhan2h280h6cw1sm5hys2nzmf19w4py64k3nrkc320z9mni")))) (build-system pyproject-build-system) (arguments ;; This is a Numpy DeprecationWarning, remove it on next update. (list #:test-flags ''("-k" "not test_h5_io"))) ;; Pint is optional, but we do not propagate it due to its size. (native-inputs (list python-pint python-pytest python-setuptools python-setuptools-scm python-wheel)) ;; 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)) (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} classes (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 python-setuptools python-wheel)) (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-vaex-core (package (name "python-vaex-core") (version "4.18.1") (source (origin (method git-fetch) (uri (git-reference (url "https://www.github.com/maartenbreddels/vaex") (commit (string-append "core-v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1sp096msbzgjlwi8c1ink2bp4pjff9pvikqz1y1li8d3in4gpgdr")) (patches (search-patches "python-vaex-core-fix-tsl-use.patch")) (modules '((guix build utils) (ice-9 ftw))) (snippet #~(begin ;; Delete everything except for vaex-core itself: (define (delete-except exception) (lambda (file) (unless (member file `("." ".." ,exception)) (delete-file-recursively file)))) (for-each (delete-except "packages") (scandir ".")) (with-directory-excursion "packages" (for-each (delete-except "vaex-core") (scandir "."))) (for-each (lambda (file) (unless (member file '("." "..")) (rename-file (string-append "packages/vaex-core/" file) file))) (scandir "packages/vaex-core")) (delete-file-recursively "packages") (delete-file-recursively "vendor"))))) (build-system pyproject-build-system) (arguments (list #:tests? #f ; require vaex.server and others, which require vaex-core. #:phases #~(modify-phases %standard-phases (add-after 'unpack 'relax-requirements (lambda _ (substitute* "setup.py" ;; "dask!=2022.4.0,<2024.9"; there is a note "fingerprinting ;; in no longer deterministic as of 2024.9.0" which may be ;; resolved in 2024.12.1. ((",<2024.9") ""))))))) (inputs (list boost pcre pybind11 string-view-lite tsl-hopscotch-map)) (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-2 python-pydantic-settings python-pyyaml python-requests python-rich python-six python-tabulate)) (native-inputs (list python-pytest python-cython-3 python-setuptools python-wheel)) (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-vector (package (name "python-vector") (version "1.6.2") (source (origin (method url-fetch) (uri (pypi-uri "vector" version)) (sha256 (base32 "1jhfgx54a6l1cz9as2wlwrph86f8s1882biaakx1cl31igdxjnbf")))) (build-system pyproject-build-system) (arguments (list ;; This file requires python-papermill (not yet packaged). #:test-flags #~(list "--ignore" "tests/test_notebooks.py"))) (propagated-inputs (list python-numpy python-packaging)) (native-inputs (list python-awkward python-hatch-vcs python-hatchling python-pytest python-sympy)) (home-page "https://github.com/scikit-hep/vector") (synopsis "Arrays of 2D, 3D, and Lorentz vectors") (description "Vector is a Python library for 2D and 3D spatial vectors, as well as 4D space-time vectors. It is especially intended for performing geometric calculations on arrays of vectors, rather than one vector at a time in a Python @code{for} loop.") (license license:bsd-3))) (define-public python-vedo (package (name "python-vedo") (version "2025.5.3") (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 "0hrqyvcxxbc1wz0cnafc8rvsi5mj19kck4b6pmddh25rlhdcr5qb")))) (build-system pyproject-build-system) (arguments (list ;; XXX: The whole test suite depends on the data from ;; providing samples which need to be ;; downloaded during tests, find the way how to enable it. #:tests? #f #:phases #~(modify-phases %standard-phases (add-after 'unpack 'relax-requirements ;; vtk does not provide Python metadata. ;; ;; ...checking requirements: ERROR: vedo==2025.5.3 ;; DistributionNotFound(Requirement.parse('vtk'), {'vedo'}) (lambda _ (substitute* "pyproject.toml" (("\"vtk\",") ""))))))) (native-inputs (list pkg-config python-pkgconfig python-setuptools python-wheel)) (propagated-inputs (list python-deprecated python-matplotlib python-numpy python-pygments 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-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" ;; These expect deprecation warnings that are not ;; emitted in our case. " and not test_drop_index_labels" " and not test_rename_multiindex")))) (native-inputs (list python-setuptools python-setuptools-scm python-pytest python-wheel)) (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 "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 python-setuptools-scm python-wheel 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 python-setuptools-scm python-wheel)) (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 "2.28.3") ; the minimal version supporting SciPy 1.12.0 (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 "1yz1yslms6kdmy4sgnvbnghhclcpkc80z3vaw9c2y3b3j1fs9b4v")))) (build-system pyproject-build-system) (arguments (list #:test-flags ;; XXX: Full test suite takes about 20-30min to complete in single ;; thread, attempt to run tests in parallel with pytest-xdist fails even ;; so upstream provides a support for that, try to figure out how to ;; improve it. ;; ;; Upstream implements a script, showing slow tests which may be used to ;; exclude even more hanging/slow ones, see ;; . ;; ;; Skip computationally intensive tests. #~(list "--ignore" "tests/scan/" "--ignore" "tests/tensor/" "--ignore" "tests/sandbox/" "--ignore" "tests/sparse/sandbox/" ;; Tests hang while running from these files. "--ignore" "tests/compile/test_compilelock.py" "--ignore" "tests/link/jax/test_tensor_basic.py" ;; XXX: Tests finish with error in these files, check why. "--ignore" "tests/compile/function/test_types.py" "--ignore" "tests/link/numba/test_basic.py" "--ignore" "tests/link/numba/test_blockwise.py" "--ignore" "tests/link/numba/test_elemwise.py" "-k" (string-join ;; Skip benchmark tests. (list "not test_elemwise_speed" "test_logsumexp_benchmark" "test_fused_elemwise_benchmark" "test_scan_multiple_output" "test_vector_taps_benchmark" "test_cython_performance" ;; Assertion fails in tests. "test_choose_signature" "test_fgraph_to_python_names") " and not ") ;; Tests collection selects pytensor, which does not contain ;; tests and fails to pass; manually provide a test directory ;; instead. "tests") #:phases #~(modify-phases %standard-phases ;; Replace version manually because pytensor uses ;; versioneer, which requires git metadata. (add-after 'unpack 'versioneer (lambda _ (invoke "versioneer" "install") (substitute* "setup.py" (("version=versioneer.get_version\\(),") (format #f "version=~s," #$version))))) (add-before 'check 'pre-check (lambda _ ;; It is required for most tests. (setenv "HOME" "/tmp") ;; Cython extensions have to be built before running the tests. (invoke "python" "setup.py" "build_ext" "--inplace")))))) (native-inputs (list python-cython python-pytest python-pytest-mock python-versioneer python-setuptools python-wheel)) (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-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) (native-inputs (list pkg-config python-pytest meson-python)) (inputs (list openblas)) (propagated-inputs (list python-numpy python-scipy)) (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-pandas-flavor (package (name "python-pandas-flavor") (version "0.7.0") (source (origin (method url-fetch) (uri (pypi-uri "pandas_flavor" version)) (sha256 (base32 "0zmgxnrxlvjgsr5f6yiwdn093kibb48zd16jkgy7l082d7wzjyv1")))) (build-system pyproject-build-system) (native-inputs (list python-pytest)) (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 "0.5.5") (source (origin (method git-fetch) ; no tests in PyPI tarball (uri (git-reference (url "https://github.com/raphaelvallat/pingouin") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0i3yzdlj08di3mzi69ci57jm5myl123hp8c5vn1g35k77m4zpgvd")))) (build-system pyproject-build-system) (arguments (list ;; _flapack.error: (liwork>=max(1,10*n)||liwork==-1) ;; failed for 10th keyword liwork: dsyevr:liwork=1 #:test-flags #~(list "-k" (string-append "not test_box_m" " and not test_linear_regression")))) (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-plotly (package (name "python-plotly") (version "5.20.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/plotly/plotly.py") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0i22sv8p3kl84nkldbv1253kld85rbwp2pdxivxn64wwflfpqvx6")))) (build-system pyproject-build-system) (arguments (list #:test-flags ;; 2658 passed, 18 skipped, 38 deselected, 574 warnings #~(list "-k" (string-join ;; python-polars is not packaged yet. (list "not test_build_df_from_vaex_and_polars" "test_build_df_with_hover_data_from_vaex_and_polars" ;; ValueError "test_bytesio" "test_ensure_orca_ping_and_proc" "test_kaleido_engine_to_image_returns_bytes" "test_kaleido_fulljson" "test_latex_fig_to_image[eps]" "test_mimetype_combination" "test_orca_version_number" "test_pdf_renderer_show_override" "test_png_renderer_mimetype" "test_problematic_environment_variables[eps]" "test_server_timeout_shutdown" "test_simple_to_image[eps]" "test_svg_renderer_show" "test_to_image_default[eps]" "test_topojson_fig_to_image[eps]" "test_validate_orca" "test_write_image_string[eps]" "test_write_image_string_bad_extension_override" "test_write_image_string_format_inference[eps]" "test_write_image_writeable[eps]" ;; XXX: check why these tests fail "test_dependencies_not_imported" "test_external_server_url" "test_invalid_figure_json" "test_lazy_imports" "test_legend_dots" "test_linestyle" "test_orca_executable_path" "test_sanitize_json[auto]" "test_sanitize_json[json]" "test_scraper" "test_write_image_string_bad_extension_failure") " and not ")) #:phases #~(modify-phases %standard-phases (add-before 'build 'skip-npm ;; npm is not packaged so build without it (lambda _ (setenv "SKIP_NPM" "T"))) (add-after 'unpack 'fix-version ;; TODO: Versioneer in Guix gets its release version from the ;; parent directory, but the plotly package is located inside a ;; depth 3 subdirectory. Try to use versioneer if possible. (lambda _ (substitute* "packages/python/plotly/setup.py" (("version=versioneer.get_version\\(),") (format #f "version=~s," #$version))) (substitute* "packages/python/plotly/plotly/version.py" (("__version__ = get_versions\\(\\)\\[\"version\"\\]") (format #f "__version__ = ~s" #$version))))) (add-after 'fix-version 'chdir (lambda _ (chdir "packages/python/plotly")))))) (native-inputs (list python-ipywidgets python-pytest python-setuptools python-wheel python-xarray)) (propagated-inputs (list python-ipython python-pandas python-pillow ;; python-polars python-requests python-retrying python-scikit-image python-statsmodels python-tenacity python-vaex-core)) (home-page "https://plotly.com/python/") (synopsis "Interactive plotting library for Python") (description "Plotly's Python graphing library makes interactive,publication-quality graphs online. Examples of how to make line plots, scatter plots, area charts, bar charts, error bars, box plots, histograms, heatmaps, subplots, multiple-axes, polar charts, and bubble charts.") (license license:expat))) (define-public python-plotnine (package (name "python-plotnine") (version "0.14.5") (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 "02ph0h312qn5a9ivh2qhv0x9sybccgbidzvb8im1hikwcqp8v2fw")))) (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. ;; See https://github.com/has2k1/plotnine/issues/627 `(list ,@(map (lambda (file) (string-append "--ignore=" file)) (list "tests/test_aes.py" "tests/test_annotation_logticks.py" "tests/test_coords.py" "tests/test_facet_labelling.py" "tests/test_facets.py" "tests/test_geom_bar_col_histogram.py" "tests/test_geom_bin_2d.py" "tests/test_geom_boxplot.py" "tests/test_geom_count.py" "tests/test_geom_density_2d.py" "tests/test_geom_density.py" "tests/test_geom_dotplot.py" "tests/test_geom_freqpoly.py" "tests/test_geom_map.py" "tests/test_geom_path_line_step.py" "tests/test_geom_point.py" "tests/test_geom_raster.py" "tests/test_geom_rect_tile.py" "tests/test_geom_ribbon_area.py" "tests/test_geom_sina.py" "tests/test_geom_smooth.py" "tests/test_geom_text_label.py" "tests/test_geom_violin.py" "tests/test_layout.py" "tests/test_position.py" "tests/test_qplot.py" "tests/test_scale_internals.py" "tests/test_scale_labelling.py" "tests/test_stat_ecdf.py" "tests/test_stat_function.py" "tests/test_stat_summary.py" "tests/test_theme.py")) "-k" (string-append "not " (string-join (list ;; This triggers an unexpected but harmless ;; warning. "test_save_method" ;; This test fails to set the locale. "test_no_after_scale_warning" ;; Missing optional modules "test_non_linear_smooth" "test_non_linear_smooth_no_ci") " and not " 'infix))) #:phases #~(modify-phases %standard-phases (add-before 'build 'pretend-version ;; The version string is usually derived via setuptools-scm, but ;; without the git metadata available, the version string is set to ;; '999'. (lambda _ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) (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")) (setenv "CI" "1") ;skip tests that are known to fail on CI. ;; 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 python-setuptools-scm python-wheel 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 "0.44.2") (source ;; The PyPI tarball does not contain 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 "0lnh4cvf6wld7hm293015d80ny0vnsk96ckfvc2crzd1b79ch1v5")))) (build-system pyproject-build-system) (propagated-inputs (list python-imageio python-matplotlib python-meshio python-numpy python-pillow python-pooch python-scooby vtk)) ;; packages needed for testing (native-inputs (list python-pytest python-scipy python-ipython python-trimesh python-tqdm)) (arguments '(#:phases (modify-phases %standard-phases ;; vtk check fails in sanity-check, comment out (add-after 'unpack 'patch-pyproject (lambda _ (substitute* "pyproject.toml" (("'vtk<9\\.4\\.0'," all) (string-append "#" all))))) (add-after 'unpack 'fix-failing-tests (lambda _ (rename-file "tests/plotting/test_charts.py" "tests/plotting/_test_charts.py") (rename-file "tests/examples/test_download_files.py" "tests/examples/_test_download_files.py") (rename-file "tests/examples/test_downloads.py" "tests/examples/_test_downloads.py") (rename-file "tests/plotting/test_texture.py" "tests/plotting/_test_texture.py") (substitute* "tests/plotting/test_plotting.py" (("\"\"\"Determine if using mesa.\"\"\"" all) (string-append all "\n return False"))) (substitute* "tests/test_meshio.py" (("cow = .*$" all) (string-append "#" all "\n")) ((", cow") "")) (substitute* "tests/core/test_dataset.py" (("test_partition") "_test_partition")) (substitute* "tests/core/test_composite.py" (("test_ensight_multi_block_io") "_test_ensight_multi_block_io")) (substitute* "tests/core/test_dataset_filters.py" (("test_connectivity_.*$" all) (string-append "_" all)) (("test_compute_boundary_mesh_quality") "_test_compute_boundary_mesh_quality")) (substitute* "tests/core/test_polydata_filters.py" (("test_protein_ribbon") "_test_protein_ribbon")) (substitute* "tests/core/test_validation.py" (("test_cast_to_numpy_raises") "_test_cast_to_numpy_raises")) (substitute* "tests/plotting/test_actor.py" (("test_actor_texture") "_test_actor_texture")) (substitute* "tests/plotting/test_lookup_table.py" (("test_init_cmap") "_test_init_cmap") (("test_repr") "_test_repr")) (substitute* "tests/plotting/test_plotter.py" (("test_add_multiple") "_test_add_multiple") (("test_plot_return_img_without_cpos") "_test_plot_return_img_without_cpos") (("test_plot_return_img_with_cpos") "_test_plot_return_img_with_cpos") (("test_only_screenshots_flag") "_test_only_screenshots_flag")) (substitute* "tests/plotting/test_plotting_utilities.py" (("test_gif_reader") "_test_gif_reader")) (substitute* "tests/plotting/test_render_window_interactor.py" (("test_timer") "_test_timer") (("test_add_timer_event") "_test_add_timer_event") (("test_interpolate") "_test_interpolate")) (substitute* "tests/plotting/test_renderer.py" (("test_legend_.*$" all) (string-append "_" all))) (substitute* "tests/plotting/test_theme.py" (("test_box_axes") "_test_box_axes") (("test_load_theme") "_test_load_theme") (("test_save_before_close_callback") "_test_save_before_close_callback") (("test_user_logo") "_test_user_logo")) (substitute* "tests/core/test_geometric_sources.py" (("test_translate_direction_collinear") "_test_translate_direction_collinear")) (substitute* "tests/examples/test_dataset_loader.py" (("test_dataset_loader_one_file") "_test_dataset_loader_one_file") (("test_dataset_loader_two_files_one_loadable") "_test_dataset_loader_two_files_one_loadable") (("test_dataset_loader_two_files_both_loadable") "_test_dataset_loader_two_files_both_loadable") (("test_dataset_loader_cubemap") "_test_dataset_loader_cubemap") (("test_dataset_loader_dicom") "_test_dataset_loader_dicom") (("test_dataset_loader_from_nested_files_and_directory") "_test_dataset_loader_from_nested_files_and_directory") (("test_dataset_loader_from_nested_multiblock") "_test_dataset_loader_from_nested_multiblock") (("test_load_dataset_no_reader") "_test_load_dataset_no_reader")) (substitute* "tests/core/test_reader.py" (("test_ensightreader_arrays") "_test_ensightreader_arrays") (("test_ensightreader_timepoints") "_test_ensightreader_timepoints") (("test_ensightreader_time_sets") "_test_ensightreader_time_sets") (("test_dcmreader") "_test_dcmreader") (("test_objreader") "_test_objreader") (("test_stlreader") "_test_stlreader") (("test_tecplotreader") "_test_tecplotreader") (("test_byureader") "_test_byureader") (("test_facetreader") "_test_facetreader") (("test_plot3dmetareader") "_test_plot3dmetareader") (("test_multiblockplot3dreader") "_test_multiblockplot3dreader") (("test_binarymarchingcubesreader") "_test_binarymarchingcubesreader") (("test_pvdreader") "_test_pvdreader") (("test_pvdreader_no_time_group") "_test_pvdreader_no_time_group") (("test_pvdreader_no_part_group") "_test_pvdreader_no_part_group") (("test_openfoamreader_arrays_time") "_test_openfoamreader_arrays_time") (("test_openfoamreader_active_time") "_test_openfoamreader_active_time") (("test_openfoamreader_read_data_time_value") "_test_openfoamreader_read_data_time_value") (("test_openfoamreader_read_data_time_point") "_test_openfoamreader_read_data_time_point") (("test_openfoam_skip_zero_time") "_test_openfoam_skip_zero_time") (("test_openfoam_cell_to_point_default") "_test_openfoam_cell_to_point_default") (("test_openfoam_patch_arrays") "_test_openfoam_patch_arrays") (("test_openfoam_case_type") "_test_openfoam_case_type") (("test_read_cgns") "_test_read_cgns") (("test_bmpreader") "_test_bmpreader") (("test_demreader") "_test_demreader") (("test_jpegreader") "_test_jpegreader") (("test_meta_image_reader") "_test_meta_image_reader") (("test_nifti_reader") "_test_nifti_reader") (("test_nrrd_reader") "_test_nrrd_reader") (("test_png_reader") "_test_png_reader") (("test_pnm_reader") "_test_pnm_reader") (("test_slc_reader") "_test_slc_reader") (("test_tiff_reader") "_test_tiff_reader") (("test_hdr_reader") "_test_hdr_reader") (("test_avsucd_reader") "_test_avsucd_reader") (("test_hdf_reader") "_test_hdf_reader") (("test_xdmf_reader") "_test_xdmf_reader") (("test_fluentcffreader") "_test_fluentcffreader") (("test_gambitreader") "_test_gambitreader") (("test_gaussian_cubes_reader") "_test_gaussian_cubes_reader") (("test_gesignareader") "_test_gesignareader") (("test_pdbreader") "_test_pdbreader") (("test_particle_reader") "_test_particle_reader") (("test_prostar_reader") "_test_prostar_reader")))) ;; test phase writes files to $HOME (add-before 'check 'redirect-HOME (lambda _ (setenv "HOME" "/tmp")))))) (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-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) (arguments (list #:test-flags #~(list "-k" ;; Two tests fail with error: TypeError: arrays to stack must be ;; passed as a "sequence" type such as list or tuple. (string-append "not test_raveled_index" " and not test_regular_expression_misc") "paramz/tests/array_core_tests.py" "paramz/tests/cacher_tests.py" "paramz/tests/examples_tests.py" "paramz/tests/index_operations_tests.py" "paramz/tests/init_tests.py" "paramz/tests/lists_and_dicts_tests.py" "paramz/tests/model_tests.py" "paramz/tests/observable_tests.py" "paramz/tests/parameterized_tests.py" "paramz/tests/pickle_tests.py" "paramz/tests/verbose_optimize_tests.py"))) (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-decorator python-numpy python-scipy python-six)) (home-page "https://github.com/sods/paramz") (synopsis "The Parameterization Framework") (description "@command{paramz} is a lightweight parameterization framework for parameterized model creation and handling. Its features include: @itemize @item Easy model creation with parameters. @item Fast optimized access of parameters for optimization routines. @item Memory efficient storage of parameters (only one copy in memory). @item Renaming of parameters. @item Intuitive printing of models and parameters. @item Gradient saving directly inside parameters. @item Gradient checking of parameters. @item Optimization of parameters. @item Jupyter notebook integration. @item Efficient storage of models, for reloading. @item Efficient caching. @end itemize") (license license:bsd-3))) (define-public python-pods (package (name "python-pods") (version "0.1.17") (source (origin (method url-fetch) (uri (pypi-uri "pods" version)) (sha256 (base32 "1z57jdwml2jzr2dq20p7pzx3ayhajgfd2d0xqjvgzx576hp2z1ac")))) (build-system pyproject-build-system) ;; Tests depend on Nose framework and try to download test data from ;; . (arguments (list #:tests? #f)) (native-inputs (list python-poetry-core)) (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 python-setuptools python-wheel)) (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 python-flit-core)) (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-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) (native-inputs (list python-pytest python-scipy python-setuptools python-wheel)) (propagated-inputs (list python-numpy)) (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-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-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-pynsee (package (name "python-pynsee") (version "0.1.8") (source (origin (method url-fetch) (uri (pypi-uri "pynsee" version)) (sha256 (base32 "1w084ynwdd9f4wpcnakqc0nxcbj9gr8vppv4rd258i3dp1qq4sw5")))) (build-system pyproject-build-system) (arguments (list #:tests? #f)) ; XXX: Tests require network access. (native-inputs (list python-setuptools python-wheel)) (propagated-inputs (list python-appdirs python-openpyxl python-pandas python-platformdirs python-pyarrow python-requests python-shapely python-tqdm python-unidecode python-urllib3 python-xlrd)) (home-page "https://pynsee.readthedocs.io") (synopsis "Tools to Easily Search and Download French Data From INSEE and IGN APIs") (description "This package provides tools to easily search and download French data from INSEE and IGN APIs. This data includes more than 150 000 macroeconomic series, a dozen datasets of local french data, numerous sources available on @url{insee.fr}, geographical limits of administrative areas taken from IGN as well as key metadata and SIRENE database containing data on all French compagnies.") (license license:expat))) (define-public python-pyqtgraph (package (name "python-pyqtgraph") (version "0.13.3") (source (origin (method url-fetch) (uri (pypi-uri "pyqtgraph" version)) (sha256 (base32 "1kiazyc8mqyx0479qdcvdclzq0g1hpp93dyq8444w1f72628s42q")))) (build-system pyproject-build-system) (arguments ;; This test fails. It suggests to disable assert rewriting in Pytest, ;; but it still doesn't pass. (list #:test-flags #~'("-k" "not test_reload") #:phases #~(modify-phases %standard-phases (add-before 'check 'set-qpa (lambda _ (setenv "QT_QPA_PLATFORM" "offscreen")))))) (native-inputs (list python-pytest python-pytest-cov python-pytest-xdist python-setuptools python-wheel)) (inputs (list qtbase-5)) (propagated-inputs (list python-h5py python-numpy python-pyopengl python-scipy python-pyqt)) (home-page "https://www.pyqtgraph.org") (synopsis "Scientific graphics and GUI library for Python") (description "PyQtGraph is a Pure-python graphics library for PyQt5, PyQt6, PySide2 and PySide6. It is intended for use in mathematics, scientific or engineering applications.") (license license:expat))) (define-public snakemake (package (name "snakemake") (version "8.29.2") (source (origin (method url-fetch) (uri (pypi-uri "snakemake" version)) (sha256 (base32 "1ilpmrjmnc529p4gw2x23ik1d8b5pm6k1dhq08dknvfjsf3vgyjr")))) (build-system pyproject-build-system) (arguments (list #:test-flags #~(list ;; XXX: Unclear why these tests fail. "--ignore=tests/test_report_href/test_script.py" "--ignore=tests/test_script_py/scripts/test_explicit_import.py" "--ignore=tests/test_output_index.py" ;; We don't care about testing old python@3.7 on Guix. "--ignore=tests/test_conda_python_3_7_script/test_script.py" ;; Those require additional snakemake plugins. "--ignore=tests/test_api.py" "--ignore=tests/test_executor_test_suite.py" ;; We don't care about lints. "--ignore=tests/test_linting.py" ;; These tests attempt to change S3 buckets on AWS and fail ;; because there are no AWS credentials. "--ignore=tests/test_tibanna" ;; It's a similar story with this test, which requires access ;; to the Google Storage service. "--ignore=tests/test_google_lifesciences") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'avoid-assets-download (lambda _ (substitute* "setup.py" (("^from assets import Assets") "") (("^Assets\\.deploy\\(\\)") "")))) ;; For cluster execution Snakemake will call Python. Since there is ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We ;; fix this by calling the snakemake wrapper instead. (add-after 'unpack 'call-wrapper-not-wrapped-snakemake (lambda _ (substitute* "snakemake/executors/__init__.py" (("self\\.get_python_executable\\(\\),") "") (("\"-m snakemake\"") (string-append "\"" #$output "/bin/snakemake" "\"")) ;; The snakemake command produced by format_job_exec contains ;; references to /gnu/store. Prior to patching above that's ;; just a reference to Python; after patching it's a reference ;; to the snakemake executable. ;; ;; In Tibanna execution mode Snakemake arranges for a certain ;; Docker image to be deployed to AWS. It then passes its own ;; command line to Tibanna. This is misguided because it only ;; ever works if the local Snakemake command was run inside ;; the same Docker image. In the case of using Guix this is ;; never correct, so we need to replace the store reference. (("tibanna_args.command = command") (string-append "tibanna_args.command = command.replace('" #$output "/bin/snakemake', 'python3 -m snakemake')"))))) (add-after 'unpack 'patch-version (lambda _ (substitute* "setup.py" (("version=versioneer.get_version\\(\\)") (format #f "version=~s" #$version))) (substitute* '("snakemake/_version.py" "versioneer.py") (("0\\+unknown") #$version)))) (add-before 'check 'pre-check (lambda* (#:key tests? #:allow-other-keys) (when tests? (setenv "HOME" "/tmp"))))))) (propagated-inputs (list python-appdirs python-conda-inject python-configargparse python-connection-pool python-dpath python-gitpython python-humanfriendly python-immutables python-jinja2 python-jsonschema python-nbformat python-packaging python-psutil python-pulp python-pyyaml python-requests python-reretry python-smart-open python-snakemake-interface-common python-snakemake-interface-executor-plugins python-snakemake-interface-report-plugins python-snakemake-interface-storage-plugins python-tabulate python-throttler python-wrapt python-yte)) (native-inputs (list python-docutils python-numpy python-pandas python-setuptools python-tomli python-wheel)) (home-page "https://snakemake.readthedocs.io") (synopsis "Python-based execution environment for make-like workflows") (description "Snakemake aims to reduce the complexity of creating workflows by providing a clean and modern domain specific specification language (DSL) in Python style, together with a fast and comfortable execution environment.") (license license:expat))) (define-public snakemake-5 (package (name "snakemake") (version "5.32.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/snakemake/snakemake") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm")))) (build-system pyproject-build-system) (arguments (list #:test-flags '(list ;; We have no TES support. "--ignore=tests/test_tes.py" ;; This test attempts to change S3 buckets on AWS and fails ;; because there are no AWS credentials. "--ignore=tests/test_tibanna.py" ;; It's a similar story with this test, which requires access ;; to the Google Storage service. "--ignore=tests/test_google_lifesciences.py" ;; Unclear failure. "-k" "not test_lint[long_run-positive]") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'tabulate-compatibility (lambda _ (substitute* "snakemake/dag.py" (("\"job\": rule,") "\"job\": rule.name,")))) (add-after 'unpack 'patch-version (lambda _ (substitute* "setup.py" (("version=versioneer.get_version\\(\\)") (format #f "version=~s" #$version))) (substitute* '("snakemake/_version.py" "versioneer.py") (("0\\+unknown") #$version)))) ;; For cluster execution Snakemake will call Python. Since there is ;; no suitable PYTHONPATH set, cluster execution will fail. We fix ;; this by calling the snakemake wrapper instead. (add-after 'unpack 'call-wrapper-not-wrapped-snakemake (lambda _ (substitute* "snakemake/executors/__init__.py" (("\\{sys.executable\\} -m snakemake") (string-append #$output "/bin/snakemake"))))) (add-before 'check 'pre-check (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-appdirs python-configargparse python-datrie python-docutils python-gitpython python-jinja2 python-jsonschema python-nbformat python-networkx python-psutil python-pulp python-pyyaml python-ratelimiter python-requests python-toposort python-wrapt)) (native-inputs (list git-minimal python-wrapper python-pytest python-pandas python-requests-mock python-setuptools python-wheel)) (home-page "https://snakemake.readthedocs.io") (synopsis "Python-based execution environment for make-like workflows") (description "Snakemake aims to reduce the complexity of creating workflows by providing a clean and modern domain specific specification language (DSL) in Python style, together with a fast and comfortable execution environment.") (license license:expat))) (define-public snakemake-6 (package (inherit snakemake-5) (name "snakemake") (version "6.15.5") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/snakemake/snakemake") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai")))) (build-system pyproject-build-system) (arguments (list #:test-flags '(list ;; This test attempts to change S3 buckets on AWS and fails ;; because there are no AWS credentials. "--ignore=tests/test_tibanna.py" ;; Unclear failure. "-k" "not test_lint[long_run-positive]") #:phases #~(modify-phases %standard-phases ;; For cluster execution Snakemake will call Python. Since there is ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We ;; fix this by calling the snakemake wrapper instead. ;; XXX: There is another instance of sys.executable on line 692, but ;; it is not clear how to patch it. (add-after 'unpack 'call-wrapper-not-wrapped-snakemake (lambda* (#:key outputs #:allow-other-keys) (substitute* "snakemake/executors/__init__.py" (("\\{sys.executable\\} -m snakemake") (string-append #$output "/bin/snakemake"))))) (add-after 'unpack 'tabulate-compatibility (lambda _ (substitute* "snakemake/dag.py" (("\"job\": rule,") "\"job\": rule.name,")))) (add-after 'unpack 'patch-version (lambda _ (substitute* "setup.py" (("version=versioneer.get_version\\(\\)") (format #f "version=~s" #$version))) (substitute* '("snakemake/_version.py" "versioneer.py") (("0\\+unknown") #$version)))) (add-before 'check 'pre-check (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-appdirs python-configargparse python-connection-pool python-datrie python-docutils python-filelock python-gitpython python-jinja2 python-jsonschema python-nbformat python-networkx python-psutil python-pulp python-pyyaml python-py-tes python-ratelimiter python-requests python-smart-open python-stopit python-tabulate python-toposort python-wrapt)) (native-inputs (list git-minimal python-wrapper python-pytest python-pandas python-requests-mock python-setuptools python-wheel)))) (define-public snakemake-7 (package (inherit snakemake-6) (name "snakemake") (version "7.32.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/snakemake/snakemake") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d")))) (build-system pyproject-build-system) (arguments (list #:test-flags ;; This test attempts to change S3 buckets on AWS and fails ;; because there are no AWS credentials. '(list "--ignore=tests/test_tibanna.py" ;; It's a similar story with this test, which requires access to ;; the Google Storage service. "--ignore=tests/test_google_lifesciences.py" "--ignore-glob=tests/test_conda_python_3_7_script/*" ;; We don't have a slurm installation in the build environment "--ignore=tests/test_slurm.py") #:phases #~(modify-phases %standard-phases ;; For cluster execution Snakemake will call Python. Since there is ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We ;; fix this by calling the snakemake wrapper instead. (add-after 'unpack 'call-wrapper-not-wrapped-snakemake (lambda* (#:key outputs #:allow-other-keys) (substitute* "snakemake/executors/__init__.py" (("self\\.get_python_executable\\(\\),") "") (("\"-m snakemake\"") (string-append "\"" #$output "/bin/snakemake" "\"")) ;; The snakemake command produced by format_job_exec contains ;; references to /gnu/store. Prior to patching above that's ;; just a reference to Python; after patching it's a reference ;; to the snakemake executable. ;; ;; In Tibanna execution mode Snakemake arranges for a certain ;; Docker image to be deployed to AWS. It then passes its own ;; command line to Tibanna. This is misguided because it only ;; ever works if the local Snakemake command was run inside ;; the same Docker image. In the case of using Guix this is ;; never correct, so we need to replace the store reference. (("tibanna_args.command = command") (string-append "tibanna_args.command = command.replace('" #$output "/bin/snakemake', 'python3 -m snakemake')"))))) (add-after 'unpack 'patch-version (lambda _ (substitute* "setup.py" (("version=versioneer.get_version\\(\\)") (format #f "version=~s" #$version))) (substitute* '("snakemake/_version.py" "versioneer.py") (("0\\+unknown") #$version)))) (add-before 'check 'pre-check (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-appdirs python-configargparse python-connection-pool python-datrie python-docutils python-filelock python-gitpython python-humanfriendly python-jinja2 python-jsonschema python-nbformat python-networkx python-psutil python-pulp python-pyyaml python-py-tes python-requests python-retry python-reretry python-smart-open python-stopit python-tabulate python-throttler python-toposort python-wrapt python-yte)) (native-inputs (list git-minimal python-wrapper python-pytest python-pandas python-requests-mock python-setuptools python-wheel)))) ;;; ;;; 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. ;;;