diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 700 |
1 files changed, 534 insertions, 166 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index f5baea60b5..a0123dac21 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -3,13 +3,13 @@ ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> -;;; Copyright © 2016, 2022, 2023 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2022-2024 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org> ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> -;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net> +;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2021 Greg Hogan <code@greghogan.com> ;;; Copyright © 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com> @@ -22,7 +22,7 @@ ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net> ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org> ;;; Copyright © 2022 jgart <jgart@dismail.de> -;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com> +;;; Copyright © 2023, 2024 Troy Figiel <troy@troyfigiel.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -47,9 +47,11 @@ #: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 cpp) #:use-module (gnu packages crypto) #:use-module (gnu packages databases) + #:use-module (gnu packages digest) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages image) @@ -84,13 +86,13 @@ (define-public python-scipy (package (name "python-scipy") - (version "1.11.4") + (version "1.12.0") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 - (base32 "1amfxpnni0cagwjpb0i1kdgnh4sh484ryn4gfkgbjcspgy7bg8lh")))) + (base32 "18rn15wg3lp58z204fbjjhy0h79c53yg3c4qqs9h3liniamspxab")))) (build-system pyproject-build-system) (arguments (list @@ -135,7 +137,22 @@ (copy-recursively "build/html" html))) (format #t "sphinx-build not found, skipping~%")))))))) (propagated-inputs - (list python-numpy python-matplotlib python-pyparsing python-pythran)) + (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 @@ -147,11 +164,14 @@ python-click python-cython-0.29.35 python-doit + python-hypothesis python-pooch + python-pycodestyle python-pydevtool python-pytest - python-pytest-xdist - python-threadpoolctl)) + 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 @@ -213,7 +233,7 @@ genetic variation data.") (define-public python-scikit-fem (package (name "python-scikit-fem") - (version "8.1.0") + (version "9.0.1") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference @@ -222,13 +242,14 @@ genetic variation data.") (file-name (git-file-name name version)) (sha256 (base32 - "1zpn0wpsvls5nkrav5a43z77yg9nc09dpyy9ri0dpmpm2ndh2mhs")))) + "1r1c88rbaa7vjfnljbzx8paf36yzpy33bragl99ykn6i2srmjrd4")))) (build-system pyproject-build-system) - (arguments - ;; Examples below require python-autograd and python-pyamg. - (list #:test-flags #~(list "-k" "not TestEx32 and not TestEx45"))) (propagated-inputs (list python-meshio python-numpy python-scipy)) - (native-inputs (list python-pytest)) + (native-inputs + (list python-autograd + python-pyamg + python-pytest + python-shapely)) (home-page "https://scikit-fem.readthedocs.io/en/latest/") (synopsis "Library for performing finite element assembly") (description @@ -375,11 +396,6 @@ implements several methods for sequential model-based optimization. (build-system pyproject-build-system) (arguments '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* "setup.py" - (("pandas>=1.5.2") - "pandas")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -397,31 +413,68 @@ of regular expressions from text data and automatic test generation.") (define-public python-trimesh (package (name "python-trimesh") - (version "3.23.5") + (version "4.0.10") (source (origin - (method url-fetch) - (uri (pypi-uri "trimesh" version)) + (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 "08967axlnmfv98n05dhrkynyrmcc814hl8184gzzmcy4rjg6dzdx")))) - (build-system python-build-system) - (propagated-inputs - (list python-numpy)) + (base32 "0ry04qaw0pb3hkxv4gmna87jwk97aqangd21wbr2dr4xshmkbyyb")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-k" (string-append + ;; XXX: When more optional modules are available review + ;; disabled tests once again. + ;; + ;; Disable tests requiring optional, not packed modules. + "not test_material_round" + " and not test_bezier_example" + " and not test_discrete" + " and not test_dxf" + " and not test_layer" + " and not test_multi_nodupe" + " and not test_obj_roundtrip" + " and not test_roundtrip" + " and not test_scene" + " and not test_slice_onplane" + " and not test_svg" + " and not test_svg")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-build + (lambda _ + (substitute* "trimesh/resources/templates/blender_boolean.py.tmpl" + (("\\$MESH_PRE") + "'$MESH_PRE'"))))))) (native-inputs (list python-coveralls python-pyinstrument python-pytest python-pytest-cov)) - (arguments - `(;; TODO: Get tests to work. - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-build - (lambda _ - (substitute* "trimesh/resources/templates/blender_boolean.py.tmpl" - (("\\$MESH_PRE") - "'$MESH_PRE'"))))))) + (propagated-inputs + (list python-chardet + python-colorlog + python-httpx + python-jsonschema + python-lxml + python-networkx + python-numpy + python-pillow + ;; python-pycollada ; not packed yet, optional + ;; python-pyglet ; not packed yet, optional + python-requests + python-rtree + python-scipy + python-setuptools + python-shapely + ;; python-svg-path ; not packed yet, optional + python-sympy + python-xxhash)) (home-page "https://github.com/mikedh/trimesh") (synopsis "Python library for loading and using triangular meshes") (description @@ -457,6 +510,73 @@ volume computations for simple domains like regular polygons, disks, spheres, cubes, etc.") (license license:gpl3+))) +(define-public python-pyamg + (package + (name "python-pyamg") + (version "5.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyamg" version)) + (modules '((guix build utils))) + (snippet + ;; Delete autogenerated files, regenerate in a phase. + #~(begin + (for-each + (lambda (file) + (delete-file (string-append "pyamg/amg_core/" file))) + '("air_bind.cpp" + "evolution_strength_bind.cpp" + "graph_bind.cpp" + "krylov_bind.cpp" + "linalg_bind.cpp" + "relaxation_bind.cpp" + "ruge_stuben_bind.cpp" + "smoothed_aggregation_bind.cpp" + "tests/bind_examples_bind.cpp")))) + (sha256 + (base32 + "0l3dliwynxyjvbgpmi2k8jqvkkw6fc00c8w69h6swhrkfh0ql12z")))) + (arguments + (list + #:test-flags + ;; Test installed package in order to find C++ modules. + #~(list "--pyargs" "pyamg.tests") + #:phases + #~(modify-phases %standard-phases + ;; Regenerate the autogenerated files. + (add-after 'unpack 'amg-core-bind-them + (lambda _ + ;; bindthem.py heavily depends on location to produce *_bind.cpp + ;; file, make it available in tests as well. + (copy-file "pyamg/amg_core/bindthem.py" + "pyamg/amg_core/tests/bindthem.py") + (with-directory-excursion "pyamg/amg_core" + (substitute* "bindthem.py" + (("/usr/bin/env python3") (which "python3"))) + (invoke "sh" "generate.sh")) + (with-directory-excursion "pyamg/amg_core/tests" + (invoke "python" "bindthem.py" "bind_examples.h"))))))) + (build-system pyproject-build-system) + (native-inputs + (list pybind11 + python-cppheaderparser + python-pytest + python-pyyaml + python-setuptools-scm)) + (propagated-inputs (list python-numpy python-scipy)) + (home-page "https://github.com/pyamg/pyamg") + (synopsis "Algebraic Multigrid Solvers in Python") + (description "PyAMG is a Python library of Algebraic Multigrid +(AMG) solvers. It features implementations of: +@itemize +@item Ruge-Stuben (RS) or Classical AMG +@item AMG based on Smoothed Aggregation (SA) +@item Adaptive Smoothed Aggregation (αSA) +@item Compatible Relaxation (CR) +@item Krylov methods such as CG, GMRES, FGMRES, BiCGStab, MINRES, etc. +@end itemize") + (license license:expat))) + (define-public python-tspex (package (name "python-tspex") @@ -575,6 +695,211 @@ 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-stubs + (package + (name "python-pandas-stubs") + ;; The versioning follows that of Pandas and uses the date of the + ;; python-pandas-stubs release. This is the latest version of + ;; python-pandas-stubs for python-pandas 1.5.3. + (version "1.5.3.230321") + (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 "1blwlq5053pxnmx721zdd6v8njiybz4azribx2ygq33jcpmknda6")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags #~(list "-k" + (string-append + ;; The python-pyarrow package in Guix is not built + ;; with ORC integration, causing these tests to + ;; fail. + "not test_orc" + " and not test_orc_path" + " and not test_orc_buffer" + " and not test_orc_columns" + " and not test_orc_bytes")) + #:phases '(modify-phases %standard-phases + (add-before 'check 'prepare-x + (lambda _ + (system "Xvfb &") + (setenv "DISPLAY" ":0") + ;; xsel needs to write a log file. + (setenv "HOME" + (getcwd))))))) + (propagated-inputs (list python-types-pytz)) + ;; Add python-fastparquet to native inputs once it has been packaged. Its + ;; tests will be skipped for now. + (native-inputs (list python-lxml + python-matplotlib + python-odfpy + python-pandas + python-poetry-core + python-pyarrow + python-pyreadstat + python-pytest + python-scipy + python-sqlalchemy + python-tables + python-tabulate + python-xarray + ;; Needed to test clipboard support. + which + xclip + xorg-server-for-tests + xsel)) + (home-page "https://pandas.pydata.org") + (synopsis "Type annotations for pandas") + (description + "This package contains public type stubs for @code{python-pandas}, +following the convention of providing stubs in a separate package, as +specified in @acronym{PEP, Python Enhancement Proposal} 561. The stubs cover +the most typical use cases of @code{python-pandas}. In general, these stubs +are narrower than what is possibly allowed by @code{python-pandas}, but follow +a convention of suggesting best recommended practices for using +@code{python-pandas}.") + (license license:bsd-3))) + +(define-public python-pandera + (package + (name "python-pandera") + (version "0.17.2") + (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 "1mnqk583z90k1n0z3lfa4rd0ng40v7hqfk7phz5gjmxlzfjbxa1x")) + (modules '((guix build utils))) + ;; These tests require PySpark and Modin. We need to remove the entire + ;; directory, since the conftest.py in these directories contain + ;; imports. (See: https://github.com/pytest-dev/pytest/issues/7452) + (snippet '(begin + (delete-file-recursively "tests/pyspark") + (delete-file-recursively "tests/modin"))))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags '(list "-k" + (string-append + ;; Mypy functionality is experimental and relying + ;; on pandas-stubs can lead to false + ;; positives. These tests currently fail. + "not test_python_std_list_dict_generics" + " and not test_python_std_list_dict_empty_and_none" + " and not test_pandas_modules_importable")))) + ;; Pandera comes with a lot of extras. We test as many as possible, but do + ;; not include all of them in the propagated-inputs. Currently, we have to + ;; skip the pyspark and io tests due to missing packages python-pyspark + ;; and python-frictionless. + (propagated-inputs (list python-hypothesis ;strategies extra + python-multimethod + python-numpy + python-packaging + python-pandas + python-pandas-stubs ;mypy extra + python-pydantic + python-scipy ;hypotheses extra + python-typeguard-4 + python-typing-inspect + python-wrapt)) + (native-inputs (list python-dask ;dask extra + python-fastapi ;fastapi extra + python-geopandas ;geopandas extra + python-pyarrow ;needed to run fastapi tests + python-pytest + python-pytest-asyncio + python-sphinx + python-uvicorn)) ;needed to run fastapi tests + (home-page "https://github.com/unionai-oss/pandera") + (synopsis "Perform data validation on dataframe-like objects") + (description + "@code{python-pandera} provides a flexible and expressive API for +performing data validation on dataframe-like objects to make data processing +pipelines more readable and robust. Dataframes contain information that +@code{python-pandera} explicitly validates at runtime. This is useful in +production-critical data pipelines or reproducible research settings. With +@code{python-pandera}, you can: + +@itemize +@item Define a schema once and use it to validate different dataframe types. +@item Check the types and properties of columns. +@item Perform more complex statistical validation like hypothesis testing. +@item Seamlessly integrate with existing data pipelines via function decorators. +@item Define dataframe models with the class-based API with pydantic-style syntax. +@item Synthesize data from schema objects for property-based testing. +@item Lazily validate dataframes so that all validation rules are executed. +@item Integrate with a rich ecosystem of tools like @code{python-pydantic}, +@code{python-fastapi} and @code{python-mypy}. +@end itemize") + (license license:expat))) + +(define-public python-pyjanitor + (package + (name "python-pyjanitor") + (version "0.26.0") + (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 "1f8xbl1k9l2z56bapp7v6bd3016zrk48igcaz6hb553r6yfl7vfx")))) + (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" "not test_is_connected" + ;; 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 + rdkit)) ;chemistry submodule + (home-page "https://github.com/pyjanitor-devs/pyjanitor") + (synopsis "Tools for cleaning and transforming pandas DataFrames") + (description + "@code{pyjanitor} provides a set of data cleaning routines for +@code{pandas} DataFrames. These routines extend the method chaining API +defined by @code{pandas} for a subset of its methods. Originally, this +package was a port of the R package by the same name and it is inspired by the +ease-of-use and expressiveness of the @code{dplyr} package.") + (license license:expat))) + (define-public python-pythran (package (name "python-pythran") @@ -635,34 +960,16 @@ Python module with the same interface, but (hopefully) faster.") (define-public python-pyts (package (name "python-pyts") - (version "0.12.0") + (version "0.13.0") (source (origin (method url-fetch) (uri (pypi-uri "pyts" version)) (sha256 (base32 - "1cb5jwp8g52a3hxay6mxbfzk16ly6yj6rphq8cwbwk1k2jdf11dg")))) - (build-system python-build-system) - (arguments - (list - #:phases - '(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-v" - ;; XXX: This test fails for unknown reasons - ;; Expected: - ;; (40, 9086) - ;; Got: - ;; (40, 9088) - "-k" - "not pyts.multivariate.transformation.weasel_muse.WEASELMUSE"))))))) + "00pdzfkl0b4vhfdm8zas7b904jm2hhivdwv3wcmpik7l2p1yr85c")))) + (build-system pyproject-build-system) (propagated-inputs - (list python-joblib - python-matplotlib - python-numba - python-numpy + (list python-joblib python-numba python-numpy python-scikit-learn python-scipy)) (native-inputs @@ -861,7 +1168,7 @@ and visualization with these data structures.") (define-public python-xarray-einstats (package (name "python-xarray-einstats") - (version "0.5.1") + (version "0.7.0") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference @@ -870,7 +1177,7 @@ and visualization with these data structures.") (file-name (git-file-name name version)) (sha256 (base32 - "1gg7p2lq7zxic64nbr6a8ynizs8rjzb29fnqib7hw3lmp13wsfm0")))) + "14c424swpdginaz4pm3nmkizxy34x19q6xq3d4spx9s9031f6n3a")))) (build-system pyproject-build-system) (native-inputs (list python-einops python-flit-core python-numba python-pytest)) @@ -1040,6 +1347,34 @@ automated with the minimum of fuss and the least effort.") annotations on an existing boxplots and barplots generated by seaborn.") (license license:expat))) +(define-public python-unyt + (package + (name "python-unyt") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "unyt" version)) + (sha256 + (base32 "00900bw24rxgcgwgxp9xlx0l5im96r1n5hn0r3mxvbdgc3lyyq48")))) + (build-system pyproject-build-system) + ;; Astropy is an optional import, but we do not include it as it creates a + ;; module cycle: astronomy->python-science->astronomy. + (propagated-inputs (list python-h5py ; optional import + python-matplotlib ; optional import + python-numpy + python-sympy)) + ;; Pint is optional, but we do not propagate it due to its size. + (native-inputs (list python-pint python-pytest)) + (home-page "https://unyt.readthedocs.io") + (synopsis "Library for working with data that has physical units") + (description + "@code{unyt} is a Python library working with data that has physical +units. It defines the @code{unyt.array.unyt_array} and +@code{unyt.array.unyt_quantity} classess (subclasses of NumPy’s ndarray class) +for handling arrays and scalars with units,respectively") + (license license:bsd-3))) + (define-public python-upsetplot (package (name "python-upsetplot") @@ -1607,91 +1942,90 @@ aggregated sum and more.") (define-public python-plotnine (package (name "python-plotnine") - ;; XXX Version 0.12.x exists, but we can't build it because we're still at - ;; matplotlib 3.5. We'd need at least 3.6. (version "0.10.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/has2k1/plotnine") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0lg53wcm00lj8zbb4q9yj4a0n0fqaqq7c7vj18bda0k56gg0fpwl")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/has2k1/plotnine") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0lg53wcm00lj8zbb4q9yj4a0n0fqaqq7c7vj18bda0k56gg0fpwl")))) (build-system pyproject-build-system) (arguments (list #:test-flags + ;; XXX: Check for any new failing tests during next update cycle. ;; These all fail because the images are considered to be too different, ;; though they really do look fine. - '(list "-k" (string-append - "not TestThemes" - (string-join - (list - ;; Image tests - "test_adjust_text" - "test_annotation_logticks_coord_flip_discrete" - "test_annotation_logticks_faceting" - "test_arrow" - "test_aslabeller_dict_0tag" - "test_caption_simple" - "test_continuous_x" - "test_continuous_x_fullrange" - "test_coord_trans_backtransforms" - "test_coord_trans_se_false" - "test_datetime_scale_limits" - "test_dir_v_ncol" - "test_discrete_x" - "test_discrete_x_fullrange" - "test_facet_grid_drop_false" - "test_facet_grid_expression" - "test_facet_grid_space_ratios" - "test_facet_wrap" - "test_facet_wrap_expression" - "test_facet_wrap_label_both" - "test_label_context_wrap2vars" - "test_labeller_cols_both_grid" - "test_labeller_cols_both_wrap" - "test_labeller_towords" - "test_missing_data_discrete_scale" - "test_ribbon_facetting" - "test_stack_non_linear_scale" - "test_uneven_num_of_lines" - - ;; Missing optional modules - "test_non_linear_smooth" - "test_non_linear_smooth_no_ci") - " and not " 'prefix))) - #:phases - '(modify-phases %standard-phases - (add-before 'check 'pre-check - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; The data files are referenced by the tests but they are not - ;; installed. - (copy-recursively "plotnine/data" - (string-append (site-packages inputs outputs) - "/plotnine/data")) - ;; Matplotlib needs to be able to write its configuration file - ;; somewhere. - (setenv "MPLCONFIGDIR" "/tmp") - (setenv "TZ" "UTC") - (setenv "TZDIR" - (search-input-directory inputs "share/zoneinfo"))))))) - (propagated-inputs - (list python-adjusttext - python-matplotlib - python-mizani - python-numpy - python-patsy - python-scipy - python-statsmodels)) - (native-inputs - (list python-geopandas - python-mock - python-pandas - python-pytest python-pytest-cov - tzdata-for-tests)) + '(list "-k" + (string-append "not TestThemes" + (string-join (list + ;; Image tests + "test_adjust_text" + "test_annotation_logticks_coord_flip_discrete" + "test_annotation_logticks_faceting" + "test_arrow" + "test_aslabeller_dict_0tag" + "test_caption_simple" + "test_continuous_x" + "test_continuous_x_fullrange" + "test_coord_trans_backtransforms" + "test_coord_trans_se_false" + "test_custom_shape" + "test_datetime_scale_limits" + "test_dir_v_ncol" + "test_discrete_x" + "test_discrete_x_fullrange" + "test_facet_grid_drop_false" + "test_facet_grid_expression" + "test_facet_grid_space_ratios" + "test_facet_wrap" + "test_facet_wrap_expression" + "test_facet_wrap_label_both" + "test_label_context_wrap2vars" + "test_labeller_cols_both_grid" + "test_labeller_cols_both_wrap" + "test_labeller_towords" + "test_missing_data_discrete_scale" + "test_ribbon_facetting" + "test_stack_non_linear_scale" + "test_uneven_num_of_lines" + + ;; Missing optional modules + "test_non_linear_smooth" + "test_non_linear_smooth_no_ci") + " and not " + 'prefix))) + #:phases '(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; The data files are referenced by the tests but they are not + ;; installed. + (copy-recursively "plotnine/data" + (string-append (site-packages inputs + outputs) + "/plotnine/data")) + ;; Matplotlib needs to be able to write its configuration file + ;; somewhere. + (setenv "MPLCONFIGDIR" "/tmp") + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs "share/zoneinfo"))))))) + (propagated-inputs (list python-adjusttext + python-matplotlib + python-mizani + python-numpy + python-patsy + python-scipy + python-statsmodels)) + (native-inputs (list python-geopandas + python-mock + python-pandas + python-pytest + python-pytest-cov + tzdata-for-tests)) (home-page "https://github.com/has2k1/plotnine") (synopsis "Grammar of Graphics for Python") (description @@ -1941,7 +2275,7 @@ functions, convolutions, artificial neural networks etc.") (define-public python-pydicom (package (name "python-pydicom") - (version "2.3.0") + (version "2.4.4") (source (origin (method git-fetch) (uri (git-reference @@ -1950,41 +2284,36 @@ functions, convolutions, artificial neural networks etc.") (file-name (git-file-name name version)) (sha256 (base32 - "18l26s53yf5j9yh2zwq83n74qq4f2iq0cfblamsw4y9k35l1c108")))) - (build-system python-build-system) + "0ksyyc1hbhyqy289a2frn84ss29fb7czirx3dkxx56f4ia33b4c8")))) + (build-system pyproject-build-system) (arguments (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (chdir "pydicom/tests") - (invoke "python3" "-m" "pytest" "-k" ;skip tests using web data - (string-append - "not test_jpeg_ls_pixel_data.py" - " and not test_gdcm_pixel_data.py" - " and not test_pillow_pixel_data.py" - " and not test_rle_pixel_data.py" - " and not Test_JPEG_LS_Lossless_transfer_syntax" - " and not test_numpy_pixel_data.py" - " and not test_data_manager.py" - " and not test_handler_util.py" - " and not test_overlay_np.py" - " and not test_encoders_pydicom.py" - " and not test_encaps.py" - " and not test_reading_ds_with_known_tags_with_UN_VR" - " and not TestDatasetOverlayArray" - " and not TestReader" - " and not test_filewriter.py")))))))) + #:test-flags + ;; Skip tests that require networking. + #~(list "-k" (string-append + "not test_jpeg_ls_pixel_data.py" + " and not test_gdcm_pixel_data.py" + " and not test_pillow_pixel_data.py" + " and not test_rle_pixel_data.py" + " and not Test_JPEG_LS_Lossless_transfer_syntax" + " and not test_numpy_pixel_data.py" + " and not test_data_manager.py" + " and not test_handler_util.py" + " and not test_overlay_np.py" + " and not test_encoders_pydicom.py" + " and not test_encaps.py" + " and not test_reading_ds_with_known_tags_with_UN_VR" + " and not TestDatasetOverlayArray" + " and not TestReader" + " and not test_filewriter.py")))) (native-inputs (list python-pytest)) (inputs (list gdcm libjpeg-turbo)) (propagated-inputs (list python-numpy python-pillow)) (home-page "https://github.com/pydicom/pydicom") (synopsis "Python library for reading and writing DICOM data") (description "@code{python-pydicom} is a Python library for reading and -writing DICOM medical imaging data. It lets developers read, modify and write -DICOM data in a pythonic way.") +writing DICOM medical imaging data. It can read, modify and write DICOM +data.") (license license:expat))) (define-public python-deepdish @@ -2196,6 +2525,45 @@ fractional factorial methods.") NeuroML2 models.") (license license:lgpl3))) +(define-public python-pynetdicom + (package + (name "python-pynetdicom") + (version "2.0.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "pynetdicom" version)) + (sha256 + (base32 + "0farmgviaarb3f4xn751card3v0lza57vwgl5azxxq65p7li44i3")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; Tests takes about 10-15min to complete. + ;; Skip tests that require networking. + #~(list "-k" (string-append + " not TestFindSCP" + " and not TestQRGetServiceClass" + " and not TestQRMoveServiceClass" + " and not TestStoreSCP" + " and not test_ae.py" + " and not test_echoscp.py" + " and not test_qrscp_echo.py" + " and not test_storescp.py" + " and not test_pr_level_patient" + " and not test_pr_level_series" + " and not test_scp_cancelled")))) + (native-inputs (list python-pyfakefs python-pytest)) + (propagated-inputs (list python-pydicom python-sqlalchemy)) + (home-page "https://github.com/pydicom/pynetdicom") + (synopsis "Python implementation of the DICOM networking protocol") + (description + "@code{pynetdicom} is a Python package that implements the DICOM +networking protocol. It allows the easy creation of DICOM +@acronym{SCUs,Service Class Users} and @acronym{SCPs,Service Class +Providers}.") + (license license:expat))) + (define-public python-libneuroml (package (name "python-libneuroml") |