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-rw-r--r--gnu/packages/python-science.scm1176
1 files changed, 661 insertions, 515 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index b71f693538..65f385d494 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -7,7 +7,7 @@
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2022 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2019, 2021, 2022, 2023, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019-2025 Maxim Cournoyer <maxim@guixotic.coop>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020-2025 Vinicius Monego <monego@posteo.net>
@@ -35,6 +35,8 @@
;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
;;; Copyright © 2025 Mark Walker <mark.damon.walker@gmail.com>
;;; Copyright © 2025 Nguyễn Gia Phong <mcsinyx@disroot.org>
+;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
+;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -63,7 +65,6 @@
#: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)
@@ -82,6 +83,7 @@
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
+ #:use-module (gnu packages python-compression)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-graphics)
#:use-module (gnu packages python-web)
@@ -253,28 +255,36 @@ possibility to differentiate functions that contain matrix functions as
(define-public python-anndata
(package
(name "python-anndata")
- (version "0.11.1")
+ (version "0.12.1")
(source
(origin
;; The tarball from PyPi doesn't include tests.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/theislab/anndata")
- (commit version)))
+ (url "https://github.com/theislab/anndata")
+ (commit version)))
(file-name (git-file-name name version))
(sha256
- (base32
- "0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw"))))
+ (base32 "1pwqy1pxsiqf13kfshcbqah1a92x4044s6jyr94488ngpqkr275z"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
- #~(list "-k" #$(string-append
- ;; This one test seemingly freezes
- "not test_read_lazy_h5_cluster"
- ;; Fails with a numpy deprecation warning
- ;; but not an actual failure
- " and not test_read_write_X"))
+ #~(list "--numprocesses" (number->string (parallel-job-count))
+ ;; XXX: AttributeError: module 'pyarrow.lib' has no attribute
+ ;; 'PyExtensionType
+ "--ignore=tests/test_awkward.py"
+ "-k" (string-join
+ ;; TypeError: read_text() takes from 1 to 2 positional
+ ;; arguments but 4 were given
+ (list "not test_read_csv"
+ ;; TypeError: _fix_co_filename() argument 2 must be
+ ;; str, not PosixPath
+ "test_hints"
+ ;; Failed: DID NOT WARN. No warnings of type (<class
+ ;; 'FutureWarning'>,) were emitted.
+ "test_readloom_deprecations")
+ " and not "))
#:phases
#~(modify-phases %standard-phases
;; Doctests require scanpy from (gnu packages bioinformatics)
@@ -293,15 +303,14 @@ possibility to differentiate functions that contain matrix functions as
(setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs
(list python-array-api-compat
- python-exceptiongroup ;only for Python <3.11
python-h5py
python-importlib-metadata
+ python-legacy-api-wrap
python-natsort
- python-numcodecs
python-packaging
python-pandas
- python-scipy
python-scikit-learn
+ python-scipy
python-setuptools ; For pkg_resources.
python-zarr))
(native-inputs
@@ -309,17 +318,14 @@ possibility to differentiate functions that contain matrix functions as
python-boltons
python-dask
python-distributed
- python-hatchling
python-hatch-vcs
+ python-hatchling
python-joblib
python-loompy
python-matplotlib
python-pytest
python-pytest-mock
- python-pytest-doctestplus
python-pytest-xdist
- python-toml
- python-flit
python-setuptools-scm))
(home-page "https://github.com/theislab/anndata")
(synopsis "Annotated data for data analysis pipelines")
@@ -330,22 +336,49 @@ reduces the code overhead typically encountered when using a mostly
object-oriented library such as @code{scikit-learn}.")
(license license:bsd-3)))
-(define-public python-aplus
+(define-public python-anndata-0.11
(package
- (name "python-aplus")
- (version "0.11.0")
+ (inherit python-anndata)
+ (name "python-anndata")
+ (version "0.11.4")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "aplus" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/theislab/anndata")
+ (commit version)))
+ (file-name (git-file-name name 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)))
+ (base32 "05i805k5kvmwp5k0qw9vxvpgjwys284nq529mfn7vwlryz9d247m"))))))
+
+;; XXX: See: <https://codeberg.org/guix/guix/issues/3093>.
+(define-public python-aplus
+ ;; PyPI release lacks the latest version, Git has no tags.
+ (let ((commit "1ab8ebec987fb7213766784aad02cbf4410d9036")
+ (revision "0"))
+ (package
+ (name "python-aplus")
+ (version (git-version "0.11.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/xogeny/aplus")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "02jcfj7dywvs0sd60c85pxwh0mwsj9p1q27445pba6j489x3dffj"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f)) ;they depend on Nose test runner
+ (native-inputs
+ (list python-setuptools))
+ (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.
@@ -384,16 +417,22 @@ supersedes the RTED algorithm for computing the tree edit distance.")
(define-public python-asap3
(package
(name "python-asap3")
- (version "3.13.7")
+ (version "3.13.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asap3" version))
(sha256
- (base32 "0z6m9ybiy4fdnzlkfkvyxich18iwlwlgj1jd99fylyfwf8l160am"))))
+ (base32 "0r4sx93v2ck4m9ykzj9zaar2l9wk4nrb3d3rlik1nqimk6pnnbm2"))))
(build-system pyproject-build-system)
- (propagated-inputs (list python-ase))
- (native-inputs (list python-setuptools python-wheel which))
+ (arguments
+ (list #:tests? #f)) ;TODO: collecting ... ERROR: Wrong command line.
+ (native-inputs
+ (list python-setuptools
+ which)) ;for build
+ (propagated-inputs
+ (list python-ase
+ python-numpy))
(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
@@ -538,26 +577,10 @@ written in C.")
(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))
+ (cons maturin (cargo-inputs 'python-clarabel)))
(native-inputs
(list python-wrapper))
(propagated-inputs (list python-numpy python-scipy))
@@ -801,10 +824,9 @@ parentdir_prefix = dask-
(list python-importlib-metadata
python-pytest
python-pytest-rerunfailures
- python-pytest-runner
python-pytest-xdist
python-versioneer
- python-wheel))
+ python-setuptools))
(home-page "https://github.com/dask/dask/")
(synopsis "Parallel computing with task scheduling")
(description
@@ -893,19 +915,19 @@ optimization and generally improved organization.")
(build-system pyproject-build-system)
(arguments
(list
+ ;; tests: 2152 passed, 177 skipped, 6 deselected, 4037 warnings
#:test-flags
- ;; Flake8 attribute errors.
- '(list "--ignore=dask_image/ndfilters/_threshold.py"
- "--ignore=dask_image/ndfourier/_utils.py"
- "--ignore=dask_image/ndinterp/__init__.py"
- "--ignore=dask_image/ndmeasure/__init__.py"
- "--ignore=dask_image/ndmeasure/_utils/_find_objects.py"
- "--ignore=dask_image/ndmeasure/_utils/_label.py"
- "--ignore=tests/test_dask_image/test_ndfilters/test__conv.py"
- "--ignore=tests/test_dask_image/test_ndfourier/test_core.py"
- "--ignore=tests/test_dask_image/test_ndinterp/test_spline_filter.py"
- "--ignore=tests/test_dask_image/test_ndmeasure/test_core.py"
- "--ignore=tests/test_dask_image/test_ndmeasure/test_find_objects.py")
+ #~(list "-k" (string-join
+ ;; KeyError: 'float32
+ (list "not test_spline_filter_output_dtype[None-float32_1]"
+ "test_spline_filter_output_dtype[-1-float32_1]"
+ ;; AttributeError: 'str' object has no attribute
+ ;; 'start'
+ "test_find_objects"
+ "test_3d_find_objects"
+ ;; assert False
+ "test_find_objects_with_empty_chunks")
+ " and not "))
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'set-version
@@ -914,23 +936,18 @@ optimization and generally improved organization.")
(("^version_file.*") "")
(("dynamic = \\[\"version\"\\]")
(string-append "version = \"" #$version "\""))))))))
- (propagated-inputs (list python-dask
- python-numpy
- python-pandas-2
- python-pims
- python-scipy
- python-tifffile))
(native-inputs
- (list python-coverage
- python-flake8
- python-pytest
- python-pytest-cov
- python-pytest-flake8
+ (list python-pytest
python-pytest-timeout
python-setuptools
- python-setuptools-scm
- python-twine
- python-wheel))
+ python-setuptools-scm))
+ (propagated-inputs
+ (list python-dask
+ python-numpy
+ python-pandas
+ python-pims
+ python-scipy
+ python-tifffile-for-dask-image))
(home-page "https://github.com/dask/dask-image")
(synopsis "Distributed image processing")
(description "This is a package for image processing with Dask arrays.
@@ -942,8 +959,7 @@ Features:
@item Includes a few N-D Fourier filters.
@item Provides some functions for working with N-D label images.
@item Supports a few N-D morphological operators.
-@end itemize
-")
+@end itemize")
(license license:bsd-3)))
(define-public python-decaylanguage
@@ -1368,6 +1384,7 @@ that is 20-25x faster than @code{numpy.histogram2d}.")
(sha256
(base32 "19labbgnq85p4r4jbli2p045lgh57larhi2g2anagfxnlzpqdf5a"))))
(build-system pyproject-build-system)
+ (arguments (list #:test-backend #~'unittest))
(propagated-inputs (list python-numpy))
(native-inputs (list python-scipy python-setuptools python-wheel))
(home-page "https://danifold.net/fastcluster.html")
@@ -1497,7 +1514,7 @@ trickery (i.e. combining characters) to plot overlaying histograms.")
(define-public python-imagehash
(package
(name "python-imagehash")
- (version "4.3.1")
+ (version "4.3.2")
(source
(origin
(method git-fetch) ;no tests in PyPI
@@ -1509,8 +1526,21 @@ trickery (i.e. combining characters) to plot overlaying histograms.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1lw9lxzrzy9s5v3xc35vmh97hlyavnla087fp19k77va6v8vbjjf"))))
+ (base32 "1rz1fpwhcx0cbln189bcs61wlwgngcjcn77jvm0yji5s7lshhipy"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Upstream plans to remove Python 2 compatibility:
+ ;; https://github.com/JohannesBuchner/imagehash/pull/223
+ (add-after 'unpack 'remove-six
+ (lambda _
+ (substitute* (find-files "." ".py$")
+ (("import six") "")
+ (("six\\.assertRaisesRegex\\(self, ")
+ "self.assertRaisesRegex(")
+ (("six\\.exec_") "")))))))
(native-inputs
(list python-pytest
python-setuptools
@@ -1540,6 +1570,32 @@ Features:
@end itemize")
(license license:bsd-2)))
+(define-public python-legendkit
+ (package
+ (name "python-legendkit")
+ (version "0.3.6")
+ (source
+ (origin
+ (method git-fetch) ;no tests in PyPI archive
+ (uri (git-reference
+ (url "https://github.com/Marsilea-viz/legendkit")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "03xdhh95w4zydwa4ahp3gyfa6i60c9s5arfcj366knckb1bnpnn9"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-hatchling
+ python-pytest))
+ (propagated-inputs
+ (list python-matplotlib))
+ (home-page "https://github.com/Marsilea-viz/legendki")
+ (synopsis "Legend creation and manipulation for matplotlib")
+ (description
+ "This package implements a functionality to create and manipulate plot
+legends for @code{matplotlib}.")
+ (license license:expat)))
+
(define-public python-libneuroml
(package
(name "python-libneuroml")
@@ -1572,6 +1628,39 @@ Features:
neuronal models")
(license license:bsd-3)))
+(define-public python-marsilea
+ (package
+ (name "python-marsilea")
+ (version "0.5.4")
+ (source
+ (origin
+ (method git-fetch) ;no tests in PyPI archive
+ (uri (git-reference
+ (url "https://github.com/Marsilea-viz/marsilea")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "09pyfx0gn46ypsp991d3n4a4xx6zlbpss078lw6yywnhl834v2i0"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-hatchling
+ python-pytest))
+ (propagated-inputs
+ (list python-legendkit
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-platformdirs
+ python-scipy
+ python-seaborn))
+ (home-page "https://github.com/Marsilea-viz/marsilea")
+ (synopsis "Declarative creation of composable visualizations")
+ (description
+ "Marsilea is a Python library for creating composable visualizations in a
+declarative way. It is built on top of Matplotlib and provides a high-level
+API for you to puzzle different visualizations together like logo.")
+ (license license:expat)))
+
(define-public python-meshzoo
(package
(name "python-meshzoo")
@@ -1865,7 +1954,11 @@ between dataframe libraries.
(sha256
(base32 "1lpgsagmgxzsas7g8yiv6wmyss8q57w92h70fn11rnpadsvx16xz"))))
(build-system pyproject-build-system)
- (arguments (list #:test-flags #~(list "-c" "/dev/null"))) ;avoid coverage
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-c" "/dev/null" ;avoid coverage
+ "-k" "not test_iter_indices_matmul"))) ; flaky
(native-inputs
(list python-cython
python-numpy
@@ -2404,19 +2497,19 @@ or as a TikZ file for use in LaTeX documents;
(define-public python-qdldl
(package
(name "python-qdldl")
- (version "0.1.7.post2")
+ (version "0.1.7.post5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "qdldl" version))
(sha256
- (base32 "1lspam0k8gnw1yglqxvdv350fq00nkgdfmkizmx7bk0hxjjkj5ab"))))
+ (base32 "0vi8dgrw32qj03z2dd3zqd0d625pibq3xmlgmidfsnwvqkhrj4qb"))))
(build-system pyproject-build-system)
(native-inputs
(list cmake-minimal
pybind11
- python-setuptools
- python-wheel))
+ python-pytest
+ python-setuptools))
(propagated-inputs (list python-numpy python-scipy))
(home-page "https://github.com/oxfordcontrol/qdldl-python/")
(synopsis "QDLDL LDL factorization routine")
@@ -2650,7 +2743,7 @@ CMake.")
(define-public python-scikit-fem
(package
(name "python-scikit-fem")
- (version "10.0.2")
+ (version "11.0.0")
(source
(origin
(method git-fetch) ; no tests in PyPI
@@ -2659,7 +2752,7 @@ CMake.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "10kvzm4fmazsrddd83m0903wan67fkj13vdp6w1iw6wm6a0b5h28"))))
+ (base32 "13zh57raz2qcdfhsvpdlyiba5q0s0lh5b3gmsmh4cfrncrkdh6mh"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -2673,11 +2766,11 @@ CMake.")
;; python-jax ; not packed yet
python-pytest
python-shapely
- python-setuptools
- python-wheel))
+ python-setuptools))
(propagated-inputs
(list python-meshio
python-numpy
+ python-matplotlib
python-scipy))
(home-page "https://scikit-fem.readthedocs.io/en/latest/")
(synopsis "Library for performing finite element assembly")
@@ -2785,6 +2878,39 @@ logic, also known as grey logic.")
"Scikit-image is a collection of algorithms for image processing.")
(license license:bsd-3)))
+;; TODO: Port simplified test steps to python-scikit on the next refresh round.
+(define-public python-scikit-image-next
+ (package
+ (inherit python-scikit-image)
+ (name "python-scikit-image")
+ (version "0.25.2")
+ (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 "1cr3ki47z9g8kylnff1nrmv5fr3lrgmibl41q0v98pldghnslxdv"))))
+ (arguments
+ (list
+ ;; tests: 8489 passed, 128 skipped
+ #:test-flags
+ #~(list "--ignore=benchmarks"
+ "--pyargs" "skimage")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'remove-local-skimage
+ (lambda _
+ ;; This would otherwise interfere with finding the installed
+ ;; skimage when running tests.
+ (delete-file-recursively "skimage")))
+ (add-before 'check 'post-check
+ (lambda _
+ (for-each delete-file-recursively
+ (find-files #$output "__pycache__" #:directories? #t)))))))))
+
(define-public python-scikit-misc
(package
(name "python-scikit-misc")
@@ -2845,8 +2971,13 @@ and scientific computing.")
(sha256
(base32 "0ycqizgsj7q57asc1bphzhf1fx9zqn0vx5rli7q541bas64hfqiy"))))
(build-system pyproject-build-system)
- (propagated-inputs (list python-numpy python-pytorch python-scipy))
- (native-inputs (list python-setuptools))
+ (native-inputs
+ (list python-pytest
+ python-setuptools))
+ (propagated-inputs
+ (list python-numpy
+ python-pytorch
+ python-scipy))
(home-page "https://github.com/guofei9987/scikit-opt")
(synopsis "Swarm intelligence algorithms in Python")
(description
@@ -2857,19 +2988,57 @@ swarm algorithm.")
(license license:expat)))
(define-public python-scikit-optimize
+ ;; XXX: The project might be not maintained, see
+ ;; <https://github.com/holgern/scikit-optimize/issues/6>.
(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"))))
+ (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)
+ (arguments
+ (list
+ ;; tests: 398 passed, 1 skipped, 179 warnings
+ #:test-flags
+ #~(list "--numprocesses" (number->string (parallel-job-count))
+ "-k" (string-join
+ ;; XXX: As the project is not actively maintained, review
+ ;; failing test when a fresh release is available.
+ (list "not test_acq_optimizer"
+ "test_acq_optimizer_with_time_api"
+ "test_categorical_init_vals"
+ "test_consistent_x_iter_dimensions"
+ "test_early_stopping_delta_x"
+ "test_early_stopping_delta_x_empty_result_object"
+ "test_early_stopping_delta_y"
+ "test_early_stopping_delta_y_with_x0"
+ "test_exhaust_initial_calls"
+ "test_fixed_random_states"
+ "test_init_points_and_models"
+ "test_init_vals"
+ "test_init_vals_and_models"
+ "test_minimizer_api"
+ "test_minimizer_api_random_only"
+ "test_minimizer_space_constraint"
+ "test_minimizer_with_space"
+ "test_mixed_spaces"
+ "test_optimizer_base_estimator_string_smoke"
+ "test_optimizer_base_estimator_string_smoke_njobs"
+ "test_per_second_api"
+ "test_repeated_x"
+ "test_tree_based_minimize")
+ " and not "))))
+ (native-inputs
+ (list python-pytest
+ python-pytest-xdist
+ python-setuptools))
(propagated-inputs
(list python-joblib
python-matplotlib
@@ -2877,14 +3046,13 @@ swarm algorithm.")
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.")
+ (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
@@ -2936,25 +3104,25 @@ the following purposes in mind:
(license license:bsd-3)))
(define-public python-scikit-survival
- (let ((revision "1")
+ (let ((revision "0")
;; We need a later commit for support of a more recent sklearn and
- ;; numpy 2.
- (commit "bceb53ebb8306f959c70fae2be9d552f33dd3f21"))
+ ;; NumPy 2.
+ (commit "bc4a8914e8337c3be1b98371a3c26382696215a9"))
(package
(name "python-scikit-survival")
- (version (git-version "0.22.2" revision commit))
+ (version (git-version "0.25.0" 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)))
+ (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"))))
+ (base32 "001w73sz55vszp18h25dha74r34bbfzl02yh4d6zbli9zvr36hy4"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -2966,7 +3134,6 @@ the following purposes in mind:
#$(version-major+minor version)))))))
(propagated-inputs
(list python-ecos
- python-importlib-resources
python-joblib
python-numexpr
python-numpy
@@ -2975,16 +3142,11 @@ the following purposes in mind:
python-scikit-learn
python-scipy))
(native-inputs
- (list python-black
- python-pypa-build
- python-coverage
- python-cython-3
+ (list python-cython
python-packaging
python-pytest
python-setuptools
- python-setuptools-scm
- python-tomli
- python-tox))
+ python-setuptools-scm))
(home-page "https://github.com/sebp/scikit-survival")
(synopsis "Survival analysis built on top of scikit-learn")
(description "Scikit-survival is a Python module for survival analysis
@@ -3008,6 +3170,15 @@ cross-validation.")
(list
#:phases
#~(modify-phases %standard-phases
+ #$@(if (target-x86-32?)
+ #~((add-after 'unpack 'apply-i686-patch
+ (lambda _
+ (let ((patch-file
+ #$(local-file
+ (search-patch "python-scipy-i686.patch"))))
+ (invoke "patch" "--force" "-p1" "-i"
+ patch-file)))))
+ #~())
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
@@ -3017,53 +3188,7 @@ cross-validation.")
(string-append
"import scipy; scipy.test('fast', parallel="
(number->string (parallel-job-count))
- ", verbose=2)"))))))
- (add-after 'check 'install-doc
- (lambda* (#:key outputs #:allow-other-keys)
- ;; FIXME: Documentation cannot be built because it requires
- ;; a newer version of pydata-sphinx-theme, which currently
- ;; cannot build without internet access:
- ;; <https://github.com/pydata/pydata-sphinx-theme/issues/628>.
- ;; Keep the phase for easy testing.
- (let ((sphinx-build (false-if-exception
- (search-input-file input "bin/sphinx-build"))))
- (if sphinx-build
- (let* ((doc (assoc-ref outputs "doc"))
- (data (string-append doc "/share"))
- (docdir (string-append
- data "/doc/"
- #$(package-name this-package) "-"
- #$(package-version this-package)))
- (html (string-append docdir "/html")))
- (with-directory-excursion "doc"
- ;; Build doc.
- (invoke "make" "html"
- ;; Building the documentation takes a very long time.
- ;; Parallelize it.
- (string-append "SPHINXOPTS=-j"
- (number->string (parallel-job-count))))
- ;; Install doc.
- (mkdir-p html)
- (copy-recursively "build/html" html)))
- (format #t "sphinx-build not found, skipping~%"))))))))
- (propagated-inputs
- (append
- (if (supported-package? python-jupytext) ; Depends on pandoc.
- (list python-jupytext)
- '())
- (list python-matplotlib
- python-mpmath
- python-mypy
- python-numpy
- python-numpydoc
- python-pydata-sphinx-theme
- python-pydevtool
- python-pythran
- python-rich-click
- python-sphinx
- python-threadpoolctl
- python-typing-extensions)))
- (inputs (list openblas pybind11-2.10))
+ ", verbose=2)")))))))))
(native-inputs
(list gfortran
;; XXX: Adding gfortran shadows GCC headers, causing a compilation
@@ -3072,16 +3197,25 @@ cross-validation.")
meson-python
pkg-config
python-click
- python-cython-0.29.35
+ python-cython-0
python-doit
- python-hypothesis
+ python-mpmath
+ python-numpydoc
python-pooch
python-pycodestyle
python-pydevtool
python-pytest
- python-pytest-cov
python-pytest-timeout
- python-pytest-xdist))
+ python-pytest-xdist
+ python-pythran
+ python-rich-click
+ python-threadpoolctl
+ python-typing-extensions))
+ (inputs
+ (list openblas
+ pybind11-2.10))
+ (propagated-inputs
+ (list python-numpy))
(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
@@ -3293,7 +3427,7 @@ Snakemake and its storage plugins.")
python-pytest
python-pytest-cov
python-setuptools
- python-setuptools-scm-next
+ python-setuptools-scm
python-wheel))
(home-page "https://github.com/pydata/sparse/")
(synopsis "Library for multi-dimensional sparse arrays")
@@ -3504,108 +3638,6 @@ library.")
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")
@@ -3662,6 +3694,9 @@ doing practical, real world data analysis in Python.")
;; It requires a fresh python-tzdata, including new
;; timezones.
"test_repr"
+ ;; Fails with Pytest@8.4.1, fixed on main branch.
+ ;; See: <https://github.com/pandas-dev/pandas/issues/61557>.
+ "test_groupby_raises_category_on_category"
;; These tests should be skipped on 32bit systems:
;; Cannot cast array data from dtype('int64') to dtype('int32')
#$@(if (not (target-64bit?))
@@ -3869,76 +3904,72 @@ idea of the remaining amount of computation to be done.")
(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")
+ (version "0.26.1")
(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))
+ (method url-fetch)
+ (uri (pypi-uri "pandera" version))
(sha256
- (base32 "14b5aij5zjkwvsimg0v00qvp59mhhq7ljim4qghcn432vkg9gh47"))))
+ (base32 "10px2wy3rb8gg2jyry8962yrd0m3jq88wgjcpyrk23bp55j5m9c1"))))
(build-system pyproject-build-system)
(arguments
(list
+ ;; tests: 3093 passed, 48 skipped, 21 xfailed, 8232 warnings
#:test-flags
- #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
+ ;; With higher threads count tests randomly fail during collection.
+ #~(list "--numprocesses" (number->string (min 4 (parallel-job-count)))
+ ;; TODO: Ignore tests for not packaged python-ibis-framework,
+ ;; python-polars, and python-pyspark.
+ "--ignore=tests/ibis"
+ "--ignore=tests/polars"
"--ignore=tests/pyspark"
"-k" (string-join
- ;; Failed: DID NOT RAISE <class 'pandera.errors.SchemaError'>
- (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', (<class
- ;; 'pandas.core.series.Series'>, <class 'NoneType'>,
- ;; <class 'int'>), [])
- "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")
+ ;; Network access is required.
+ (list "not test_items_endpoint"
+ "test_transactions_endpoint"
+ "test_upload_file_endpoint"
+ ;; AssertionError: assert dtype('bool') == 'object'
+ "test_index_dtypes[dask-Index-True-bool]"
+ "test_index_dtypes[dask-Index-False-bool]"
+ ;; TypeError: __class__ assignment: 'GeoDataFrame'
+ ;; object layout differs from 'DataFrame'
+ "test_schema_model[data0-True]"
+ "test_schema_from_dataframe[data1-True]"
+ "test_schema_no_geometry")
" 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))
+ (native-inputs
+ (list python-joblib
+ python-pytest
+ python-pytest-asyncio
+ python-pytest-xdist
+ python-setuptools
+ python-setuptools-scm
+ python-uvicorn))
+ (inputs
+ ;; [optional]
+ ;; 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.
+ (list python-dask
+ python-distributed
+ python-geopandas
+ python-hypothesis
+ ;; python-ibis-framework ;missing from Guix
+ python-modin
+ python-numpy
+ python-pandas
+ ;; python-polars ;missing from Guix
+ ;; python-pyspark ;missing from Guix
+ ;; python-ray ;missing from Guix
+ python-scipy
+ python-shapely))
+ (propagated-inputs
+ (list python-packaging
+ python-pydantic-2
+ python-typeguard
+ python-typing-extensions
+ python-typing-inspect))
(home-page "https://github.com/unionai-oss/pandera")
(synopsis "Perform data validation on dataframe-like objects")
(description
@@ -3982,19 +4013,25 @@ production-critical data pipelines or reproducible research settings. With
;; 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")
+ ;; tests: 1042 passed, 2 skipped, 2 deselected, 45 xfailed, 6 xpassed,
+ ;; 735 warnings
+ #:test-flags
+ ;; The tests take quite long, so consider adding the "-n" line and
+ ;; adding python-pytest-xdist to the native-inputs when testing.
+ ;; However, the tests are not deterministic when ran with -n, so
+ ;; disable again before committing.
+ #~(list ;; "-n" (number->string (parallel-job-count))
+ ;; 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"
+ ;; 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"))
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'set-env-ci
@@ -4002,20 +4039,22 @@ production-critical data pipelines or reproducible research settings. With
;; Some tests are skipped if the JANITOR_CI_MACHINE
;; variable is not set.
(setenv "JANITOR_CI_MACHINE" "1"))))))
+ ;; TODO: Remove python-requests and inject its target data to make the
+ ;; package behaviour reproducible.
(propagated-inputs (list python-multipledispatch
python-natsort
python-pandas-flavor
+ python-requests
python-scipy
;; Optional imports.
python-biopython ;biology submodule
python-unyt)) ;engineering submodule
(native-inputs (list python-pytest
- python-pytest-xdist
+ ;;python-pytest-xdist ;only for -n when testing
+ python-setuptools
;; 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")
@@ -4083,6 +4122,10 @@ y, z)}.")
(build-system pyproject-build-system)
(arguments
(list
+ ;; FIXME: find more reliable tests file(s), all tests from
+ ;; test_typing.py fail with error: ModuleNotFoundError: No module named
+ ;; 'distutils.msvccompiler'.
+ #:tests? #f
#:test-flags
'(list (string-append "--numprocesses=" (number->string
(parallel-job-count)))
@@ -4171,6 +4214,8 @@ changed, it made sense to abstract away the nuisance of having to re-learn
them.")
(license license:bsd-3)))
+;; XXX: Not maintained since 2019. The project was archived by the owner on
+;; Nov 2, 2020. It is now read-only.
(define-public python-fbpca
(package
(name "python-fbpca")
@@ -4181,7 +4226,10 @@ them.")
(sha256
(base32
"1lbjqhqsdmqk86lb86q3ywf7561zmdny1dfvgwqkyrkr4ij7f1hm"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags #~(list "fbpca.py")))
+ (native-inputs (list python-pytest python-setuptools))
(propagated-inputs
(list python-numpy python-scipy))
(home-page "https://fbpca.readthedocs.io/")
@@ -4296,6 +4344,61 @@ units. It defines the @code{unyt.array.unyt_array} and
for handling arrays and scalars with units,respectively")
(license license:bsd-3)))
+(define-public python-uproot
+ (package
+ (name "python-uproot")
+ (version "5.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "uproot" version))
+ (sha256
+ (base32 "024k5kjwcd2nw5hfxhpl0x9p5aq0qrg0nlh9v24vr39rcqadh52a"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list
+ ;; conftest.py is not required and it imports modules we do not use.
+ "--noconftest"
+ ;; There is no easy way to skip tests that require the network, so
+ ;; just run a handful of tests that pass.
+ "tests/test_0351_write_TList.py"
+ "tests/test_0352_write_THashList.py"
+ "tests/test_0439_check_awkward_before_numpy.py"
+ "tests/test_0976_path_object_split.py"
+ "tests/test_1198_coalesce.py"
+ "tests/test_1264_write_NumPy_array_of_strings.py"
+ "tests/test_1318_dont_compare_big_endian_in_awkward.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-version
+ (lambda _
+ ;; Version is determined dynamically from .git.
+ (substitute* "pyproject.toml"
+ (("\\[project\\]")
+ (string-append "[project]" "\n" "version = \""
+ #$version "\""))
+ (("\"version\"") "")))))))
+ (native-inputs
+ (list python-hatch-vcs
+ python-pytest
+ python-pytest-timeout
+ python-setuptools))
+ (propagated-inputs
+ (list python-awkward
+ python-cramjam
+ python-fsspec
+ python-numpy
+ python-packaging
+ python-xxhash))
+ (home-page "https://uproot.readthedocs.io")
+ (synopsis "ROOT I/O in Python using NumPy")
+ (description
+ "Uproot is a Python library for reading and writing ROOT files. It uses
+NumPy and does not depend on C++ ROOT.")
+ (license license:bsd-3)))
+
(define-public python-upsetplot
(package
(name "python-upsetplot")
@@ -4949,9 +5052,9 @@ and more
(chdir "packages/python/plotly"))))))
(native-inputs
(list python-ipywidgets
+ python-nbformat
python-pytest
python-setuptools
- python-wheel
python-xarray))
(propagated-inputs
(list python-ipython
@@ -5094,16 +5197,127 @@ and aims to provide a similar API and functionality in Python.")
(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))))
+ (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)
+ (arguments
+ (list
+ ;; tests: 5891 passed, 623 skipped, 355 deselected, 3 xfailed, 167 warnings
+ #:test-flags
+ ;; TODO: Find out what's going on with skipped tests.
+ #~(list "--ignore=tests/plotting/test_charts.py"
+ "--ignore=tests/examples/test_download_files.py"
+ "--ignore=tests/examples/test_downloads.py"
+ "--ignore=tests/plotting/test_texture.py"
+ "-k" (string-join
+ (list "not test_actor_texture"
+ "test_add_multiple"
+ "test_add_timer_event"
+ "test_avsucd_reader"
+ "test_binarymarchingcubesreader"
+ "test_bmpreader"
+ "test_box_axes"
+ "test_byureader"
+ "test_cast_to_numpy_raises"
+ "test_compute_boundary_mesh_quality"
+ "test_connectivity_"
+ "test_dataset_loader_cubemap"
+ "test_dataset_loader_dicom"
+ "test_dataset_loader_from_nested_files_and_directory"
+ "test_dataset_loader_from_nested_multiblock"
+ "test_dataset_loader_one_file"
+ "test_dataset_loader_two_files_both_loadable"
+ "test_dataset_loader_two_files_one_loadable"
+ "test_dcmreader"
+ "test_demreader"
+ "test_ensight_multi_block_io"
+ "test_ensightreader_arrays"
+ "test_ensightreader_time_sets"
+ "test_ensightreader_timepoints"
+ "test_facetreader"
+ "test_fluentcffreader"
+ "test_gambitreader"
+ "test_gaussian_cubes_reader"
+ "test_gesignareader"
+ "test_gif_reader"
+ "test_hdf_reader"
+ "test_hdr_reader"
+ "test_init_cmap"
+ "test_interpolate"
+ "test_jpegreader"
+ "test_legend_"
+ "test_load_dataset_no_reader"
+ "test_load_theme"
+ "test_meta_image_reader"
+ "test_multiblockplot3dreader"
+ "test_nifti_reader"
+ "test_nrrd_reader"
+ "test_objreader"
+ "test_only_screenshots_flag"
+ "test_openfoam_case_type"
+ "test_openfoam_cell_to_point_default"
+ "test_openfoam_patch_arrays"
+ "test_openfoam_skip_zero_time"
+ "test_openfoamreader_active_time"
+ "test_openfoamreader_arrays_time"
+ "test_openfoamreader_read_data_time_point"
+ "test_openfoamreader_read_data_time_value"
+ "test_particle_reader"
+ "test_partition"
+ "test_pdbreader"
+ "test_plot3dmetareader"
+ "test_plot_return_img_with_cpos"
+ "test_plot_return_img_without_cpos"
+ "test_png_reader"
+ "test_pnm_reader"
+ "test_prostar_reader"
+ "test_protein_ribbon"
+ "test_pvdreader"
+ "test_pvdreader_no_part_group"
+ "test_pvdreader_no_time_group"
+ "test_read_cgns"
+ "test_repr"
+ "test_save_before_close_callback"
+ "test_slc_reader"
+ "test_stlreader"
+ "test_tecplotreader"
+ "test_tiff_reader"
+ "test_timer"
+ "test_translate_direction_collinear"
+ "test_user_logo"
+ "test_xdmf_reader")
+ " and not "))
+ #: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 _
+ (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") ""))))
+ ;; test phase writes files to $HOME
+ (add-before 'check 'redirect-HOME
+ (lambda _
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs
+ (list python-ipython
+ python-pytest
+ python-scipy
+ python-tqdm
+ python-trimesh))
(propagated-inputs
(list python-imageio
python-matplotlib
@@ -5113,127 +5327,6 @@ and aims to provide a similar API and functionality in Python.")
python-pooch
python-scooby
vtk))
- ;; packages needed for testing
- (native-inputs (list python-pytest
- python-scipy
- python-ipython
- python-trimesh
- python-tqdm))
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- ;; vtk check fails in sanity-check, comment out
- (add-after 'unpack 'patch-pyproject
- (lambda _
- (substitute* "pyproject.toml"
- (("'vtk<9\\.4\\.0'," all) (string-append "#" all)))))
- (add-after 'unpack 'fix-failing-tests
- (lambda _
- (rename-file "tests/plotting/test_charts.py" "tests/plotting/_test_charts.py")
- (rename-file "tests/examples/test_download_files.py" "tests/examples/_test_download_files.py")
- (rename-file "tests/examples/test_downloads.py" "tests/examples/_test_downloads.py")
- (rename-file "tests/plotting/test_texture.py" "tests/plotting/_test_texture.py")
- (substitute* "tests/plotting/test_plotting.py"
- (("\"\"\"Determine if using mesa.\"\"\"" all)
- (string-append all "\n return False")))
- (substitute* "tests/test_meshio.py"
- (("cow = .*$" 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
@@ -5251,6 +5344,54 @@ powerful visualization backend to facilitate rapid prototyping, analysis, and
visual integration of spatially referenced datasets.")
(license license:expat)))
+(define-public python-pyvistaqt
+ (package
+ (name "python-pyvistaqt")
+ (version "0.11.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyvista/pyvistaqt")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "04f9cd98k463pdrpi8jby411x9mc0ih62gl0nv0h9w3r7pwl61yl"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-pytest
+ (lambda _
+ (substitute* "tests/conftest.py"
+ (("pytest.skip")
+ "pytest.mark.skipif"))))
+ (add-before 'check 'before-check
+ (lambda _
+ ;; Testing requires write access.
+ (setenv "HOME" "/tmp")
+ ;; Testing requires a running xorg server.
+ (system "Xvfb :99 -screen 0 1024x768x24 &")
+ (setenv "DISPLAY" ":99.0"))))))
+ (propagated-inputs (list python-pyvista python-qtpy))
+ (native-inputs (list python-ipython
+ python-matplotlib
+ python-numpy
+ python-pytest
+ python-pytest-cov
+ python-pytest-qt
+ python-setuptools
+ python-sphinx-gallery
+ xorg-server))
+ (home-page "https://github.com/pyvista/pyvistaqt")
+ (synopsis "Qt support for PyVista")
+ (description
+ "@code{pyvistaqt} is a helper module for @code{pyvista} to enable you to
+plot using Qt by placing a vtk-widget into a background renderer. This can be
+quite useful when you desire to update your plot in real-time.")
+ (license license:expat)))
+
(define-public python-simplespectral
(package
(name "python-simplespectral")
@@ -5431,34 +5572,37 @@ 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
+ ;; 0.4 was release in 2017, there a lot of changes on master branch
+ ;; providing tests fixtures.
+ (let ((commit "0a81544ac6bb33bdb08deeba69e97a4ceebcebcf")
+ (revision "0"))
+ (package
+ (name "python-supersmoother")
+ (version (git-version "0.4" revision commit))
+ (source
+ (origin
+ (method git-fetch) ; no package in PyPI
+ (uri (git-reference
+ (url "https://github.com/jakevdp/supersmoother")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1r79nssw4a44zizvqg8y685nv3asdfj440s227phfww6kz33s3la"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest
+ python-scipy
+ python-setuptools))
+ (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)))
+ (license license:bsd-2))))
(define-public python-pylems
(package
@@ -5547,18 +5691,20 @@ compagnies.")
(define-public python-pyqtgraph
(package
(name "python-pyqtgraph")
- (version "0.13.3")
+ (version "0.13.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyqtgraph" version))
(sha256
- (base32 "1kiazyc8mqyx0479qdcvdclzq0g1hpp93dyq8444w1f72628s42q"))))
+ (base32 "1qyr461hcvhgy02slfkgrbip2xwa8zz6dvmi1476v6f66lclzy34"))))
(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")
+ (list #:test-flags
+ ;; The test_reload test fails. It suggests to disable assert
+ ;; rewriting in Pytest, but it still doesn't pass.
+ #~(list "-k" "not test_reload"
+ "-n" (number->string (parallel-job-count)))
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'set-qpa
generated by cgit v1.2.3 (git 2.50.1) at 2025-10-15 23:49:16 +0000