From patchwork Wed Aug 2 10:37:57 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Lars-Dominik Braun X-Patchwork-Id: 52456 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 7141327BBE9; Wed, 2 Aug 2023 11:39:37 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 844B527BBE2 for ; Wed, 2 Aug 2023 11:39:14 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qR9Fx-0005qX-68; Wed, 02 Aug 2023 06:39:05 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qR9Fu-0005nc-ID for guix-patches@gnu.org; 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Wed, 2 Aug 2023 12:38:01 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=6xq.net; s=MBO0001; t=1690972681; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=HBTjh7Wetr85kInxMwwdrX/TQR1C20rOwFUXle07Scc=; b=qxnq/Fq8McHUFGtAjZEyn5Fsy8Fahhg0drdxfUy4zhEg6+e158o0kwef3+o/NfXAfpjrji YfO2Jta2K/98vhLQZ7ch12qw7bb9GOgH12epACIp7JVWBOyU4HmygR29Cv+BnVYMQblx3+ e+PMazScEDcTSB7qe2MQZrj0+WvhvFA90tZb+Pp51VJbh5VnkT/+3riPVe2XchwrNTzc6p s8Jjq2jVyNyrKrrLGfMsZGdbMuJIGKTQ/nTod9hER5IMNuYW5Fk10pjuo9x4OXQrMjqckX x7bptRqUeb8NuBwrRLpAmC9fC5a0bNtNjmy3kYavZRF92o+Rxr1D8Oh7Xn76gQ== Date: Wed, 2 Aug 2023 12:37:57 +0200 From: Lars-Dominik Braun Message-ID: MIME-Version: 1.0 Content-Disposition: inline X-Rspamd-Queue-Id: 4RG7jP2t11z9slv Received-SPF: pass client-ip=80.241.56.152; envelope-from=lars@6xq.net; helo=mout-p-102.mailbox.org X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches Hi, the attached patches contain various Python build system improvements including an original TOML parser (which may be used by other build systems and importers in the future too) and fixes for #62781 and #63044. I’m also pushing the patches to the pyproject-toml branch. As always, a world rebuild is required. Cheers, Lars Lars-Dominik Braun (8): build-system/pyproject: Use python-sans-pip-wrapper as default-python. build-system/python: Ignore symlinks when changing mtime. gnu: criu: Change file mtimes to fix build. gnu: sssd: Change file mtimes to fix build. guix: toml: Add TOML parser. build-system/pyproject: Use TOML parser. gnu: python-pytest-xdist: Disable failing test. guix: pyproject-build-system: Default configure-flags to empty dictionary. Makefile.am | 2 + gnu/packages/admin.scm | 2 +- gnu/packages/astronomy.scm | 81 +++-- gnu/packages/bioinformatics.scm | 79 +++-- gnu/packages/bootloaders.scm | 3 + gnu/packages/build-tools.scm | 10 +- gnu/packages/check.scm | 14 +- gnu/packages/databases.scm | 12 +- gnu/packages/digest.scm | 2 +- gnu/packages/engineering.scm | 2 +- gnu/packages/fontutils.scm | 9 +- gnu/packages/geo.scm | 10 +- gnu/packages/graph.scm | 7 +- gnu/packages/graphviz.scm | 4 +- gnu/packages/license.scm | 5 +- gnu/packages/machine-learning.scm | 32 +- gnu/packages/maths.scm | 4 +- gnu/packages/monitoring.scm | 2 +- gnu/packages/package-management.scm | 6 +- gnu/packages/potassco.scm | 10 +- gnu/packages/protobuf.scm | 4 +- gnu/packages/python-build.scm | 33 +- gnu/packages/python-check.scm | 30 +- gnu/packages/python-compression.scm | 20 +- gnu/packages/python-crypto.scm | 15 +- gnu/packages/python-science.scm | 24 +- gnu/packages/python-web.scm | 57 ++- gnu/packages/python-xyz.scm | 260 +++++++++----- gnu/packages/qt.scm | 3 +- gnu/packages/rpc.scm | 2 +- gnu/packages/serialization.scm | 4 +- gnu/packages/sphinx.scm | 4 +- gnu/packages/sssd.scm | 9 +- gnu/packages/statistics.scm | 14 +- gnu/packages/terminals.scm | 5 +- gnu/packages/time.scm | 3 +- gnu/packages/tor.scm | 4 +- gnu/packages/tree-sitter.scm | 4 +- gnu/packages/video.scm | 2 +- gnu/packages/vim.scm | 4 +- gnu/packages/virtualization.scm | 20 +- guix/build-system/pyproject.scm | 12 +- guix/build/pyproject-build-system.scm | 56 +-- guix/build/python-build-system.scm | 4 +- guix/build/toml.scm | 478 ++++++++++++++++++++++++++ tests/toml.scm | 442 ++++++++++++++++++++++++ 46 files changed, 1503 insertions(+), 306 deletions(-) create mode 100644 guix/build/toml.scm create mode 100644 tests/toml.scm base-commit: 5aceacac65784bd2e1fd12304f965ae6026de49d diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index fa697b79fb..75b8c9f2f1 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4848,7 +4848,7 @@ (define-public jc (lambda _ (substitute* (find-files "tests" "^test.*\\.py$") (("America/Los_Angeles") "PST8PDT"))))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-pygments python-ruamel.yaml python-xmltodict)) (home-page "https://github.com/kellyjonbrazil/jc") diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 5b9434fb33..8fc727e0d6 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -521,7 +521,8 @@ (define-public python-astroml (propagated-inputs (list python-astropy python-matplotlib python-numpy python-scikit-learn python-scipy)) (native-inputs (list python-pytest-astropy-header python-pytest-cov - python-pytest-doctestplus python-pytest-remotedata)) + python-pytest-doctestplus python-pytest-remotedata + python-setuptools python-wheel)) (home-page "https://astroml.org") (synopsis "Tools for machine learning and data mining in astronomy") (description "This package provides tools for machine learning and data @@ -613,7 +614,8 @@ (define-public python-gatspy ;; XXX: we don't have supersmoother " and not test_supersmoother.py")))) (propagated-inputs (list python-astroml python-numpy python-scipy)) - (native-inputs (list python-pytest python-nose python-setuptools-scm)) + (native-inputs (list python-pytest python-nose python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/astroml/gatspy") (synopsis "General tools for astronomical time series in Python") (description "This package provides general tools for astronomical time @@ -1470,7 +1472,9 @@ (define-public python-astropy-healpix (list python-extension-helpers python-hypothesis python-pytest-astropy - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (propagated-inputs (list python-astropy python-numpy)) (home-page "https://github.com/astropy/astropy-healpix") @@ -1553,7 +1557,9 @@ (define-public python-astroscrappy python-pytest-astropy python-scikit-image python-scipy - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (propagated-inputs (list python-astropy python-numpy)) (home-page "https://github.com/astropy/astroscrappy") (synopsis "Speedy Cosmic Ray Annihilation Package in Python") @@ -1651,7 +1657,9 @@ (define-public python-cdflib python-pytest python-pytest-cov python-pytest-remotedata - python-xarray)) + python-xarray + python-setuptools + python-wheel)) (home-page "https://github.com/MAVENSDC/cdflib") (synopsis "Python library to deal with NASA's CDF astronmical data format") (description "This package provides a Python @acronym{CDF, Computable @@ -1741,7 +1749,9 @@ (define-public python-czml3 (list python-astropy python-pytest python-pytest-cov - python-pytest-mypy)) + python-pytest-mypy + python-setuptools + python-wheel)) (home-page "https://github.com/poliastro/czml3") (synopsis "Python library to write CZML") (description @@ -1818,9 +1828,10 @@ (define-public python-drizzle ;; Cython extensions have to be built before running ;; the tests. (invoke "python" "setup.py" "build_ext" "--inplace")))))) - (propagated-inputs (list python-astropy python-numpy)) + (propagated-inputs (list python-astropy python-numpy python-setuptools)) (native-inputs (list python-coverage python-flake8 python-pytest - python-pytest-cov python-setuptools-scm)) + python-pytest-cov python-setuptools-scm + python-wheel)) (home-page "https://github.com/spacetelescope/drizzle") (synopsis "Astronomical tool for combining dithered images into a single image") @@ -1871,7 +1882,8 @@ (define-public python-hvpy (arguments (list #:tests? #f)) ; Requires HTTP(S) access to api.beta.helioviewer.org (propagated-inputs (list python-pydantic python-requests)) - (native-inputs (list python-pytest python-pytest-astropy)) + (native-inputs (list python-pytest python-pytest-astropy python-setuptools + python-wheel)) (home-page "https://helioviewer.org/") (synopsis "Helioviewer Python API Wrapper") (description "@code{hvpy} is a Python API wrapper around the formal @@ -1892,7 +1904,9 @@ (define-public python-mpl-animators (native-inputs (list python-pytest python-pytest-mpl - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (propagated-inputs (list python-astropy python-matplotlib @@ -2039,7 +2053,9 @@ (define-public python-poppy python-pytest python-pytest-astropy python-sphinx - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://poppy-optics.readthedocs.io/") (synopsis "Physical Optics Propagation in Python") (description @@ -2069,7 +2085,8 @@ (define-public python-pyvo (base32 "17acv1yhz1jrsx9f35nr1vg276ibaivh4i243qkmp6abzvfyg907")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest-astropy python-requests-mock python-setuptools-scm)) + (list python-pytest-astropy python-requests-mock python-setuptools-scm + python-setuptools python-wheel)) (propagated-inputs (list python-astropy python-mimeparse python-pillow python-requests)) (home-page "https://github.com/astropy/pyvo") @@ -2405,8 +2422,9 @@ (define-public python-stsci-image ;; the tests. (invoke "python" "setup.py" "build_ext" "--inplace")))))) - (propagated-inputs (list python-numpy python-scipy)) - (native-inputs (list python-pytest python-setuptools-scm)) + (propagated-inputs (list python-numpy python-scipy python-setuptools)) + (native-inputs (list python-pytest python-setuptools-scm + python-wheel)) (home-page "https://github.com/spacetelescope/stsci.image") (synopsis "Image array manipulation functions") (description @@ -2456,7 +2474,8 @@ (define-public python-stsci-stimage #:tests? #f)) (propagated-inputs (list python-numpy)) (native-inputs (list python-codecov python-pytest python-pytest-cov - python-setuptools-scm)) + python-setuptools python-setuptools-scm + python-wheel)) (home-page "https://stscistimage.readthedocs.io/en/latest/") (synopsis "STScI image processing") (description "This package provides an astronomical Python package with @@ -2486,7 +2505,9 @@ (define-public python-stcal python-pytest-cov python-pytest-doctestplus python-pytest-openfiles - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://github.com/spacetelescope/stcal") (synopsis "STScI tools and algorithms used in calibration pipelines") (description "STScI tools and algorithms used in calibration pipelines.") @@ -3296,7 +3317,9 @@ (define-public python-pynbody (native-inputs (list python-cython python-pandas - python-pytest)) + python-pytest + python-setuptools + python-wheel)) (propagated-inputs (list python-h5py python-matplotlib @@ -3328,9 +3351,10 @@ (define-public python-pysynphot (setenv "PYSYN_CDBS" (string-append #$output "/crds"))))))) (native-inputs (list python-pytest python-pytest-remotedata - python-setuptools-scm)) + python-setuptools-scm python-wheel)) (propagated-inputs (list python-astropy python-beautifulsoup4 python-numpy - python-pytest-astropy-header python-six)) + python-pytest-astropy-header python-six + python-setuptools)) (home-page "https://github.com/spacetelescope/pysynphot") (synopsis "Python Synthetic Photometry Utilities") (description @@ -3396,7 +3420,7 @@ (define-public python-synphot #:tests? #f)) (propagated-inputs (list python-astropy python-numpy python-scipy)) (native-inputs (list python-pytest python-pytest-astropy - python-setuptools-scm)) + python-setuptools-scm python-setuptools python-wheel)) (home-page "https://github.com/spacetelescope/synphot_refactor") (synopsis "Synthetic photometry using Astropy") (description @@ -3467,7 +3491,9 @@ (define-public python-asdf python-pytest-openfiles python-pytest-remotedata python-semantic-version - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (propagated-inputs (list python-asdf-standard python-asdf-transform-schemas @@ -3514,7 +3540,9 @@ (define-public python-asdf-standard python-pypa-build python-pytest python-packaging - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (propagated-inputs (list python-importlib-resources)) (home-page "https://asdf-standard.readthedocs.io/") (synopsis "ASDF standard schemas") @@ -3542,7 +3570,7 @@ (define python-asdf-transform-schemas (arguments ;; Dependency cycle with python-asdf (list #:tests? #f)) - (native-inputs (list python-setuptools-scm)) + (native-inputs (list python-setuptools-scm python-setuptools python-wheel)) (propagated-inputs (list python-asdf-standard python-importlib-resources)) (home-page "https://github.com/asdf-format/asdf-transform-schemas") (synopsis "ASDF schemas for transforms") @@ -3661,7 +3689,7 @@ (define python-asdf-unit-schemas (arguments ;; Dependency cycle with python-asdf (list #:tests? #f)) - (native-inputs (list python-setuptools-scm)) + (native-inputs (list python-setuptools-scm python-setuptools python-wheel)) (propagated-inputs (list python-asdf-standard python-importlib-resources)) (home-page "https://asdf-unit-schemas.readthedocs.io/") (synopsis "ASDF serialization schemas for the units defined by @code{astropy.units}") @@ -3903,9 +3931,10 @@ (define-public python-wiimatch (base32 "0x6p5z6a2cqinckwlpinjxagvmswl149s1jn6ihmdxk4k0h8rrz0")))) (build-system pyproject-build-system) - (propagated-inputs (list python-numpy python-scipy)) + (propagated-inputs (list python-numpy python-scipy python-setuptools)) (native-inputs (list python-codecov python-pytest python-pytest-cov - python-pytest-doctestplus python-setuptools-scm)) + python-pytest-doctestplus python-setuptools-scm + python-wheel)) (home-page "https://github.com/spacetelescope/wiimatch") (synopsis "Optimal matching of weighted N-dimensional image intensity data") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d1448e390f..e6ba3e561a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1401,7 +1401,8 @@ (define-public python-bcbio-gff (base32 "1pm1szyxabhn8jismrj9cjhf88ajgcmm39f0cgf36iagw5qakprl")))) (build-system pyproject-build-system) - (propagated-inputs (list python-biopython python-six)) + (propagated-inputs (list python-biopython python-six python-setuptools + python-wheel)) (native-inputs (list python-pytest)) (home-page "https://github.com/chapmanb/bcbb/tree/master/gff") (synopsis "Read and write GFF files with Biopython integration") @@ -1526,7 +1527,7 @@ (define-public python-bulkvis python-tornado-6 python-tqdm python-umap-learn)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/LooseLab/bulkVis") (synopsis "Interactive visualization of bulk RNA-seq data") (description @@ -1765,7 +1766,8 @@ (define-public python-demuxem python-scikit-learn python-scipy python-seaborn)) - (native-inputs (list python-cython python-setuptools-scm)) + (native-inputs (list python-cython python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/lilab-bcb/demuxEM") (synopsis "Analyze cell-hashing/nucleus-hashing data") (description @@ -1838,6 +1840,7 @@ (define-public python-hclust2 python-numpy python-pandas python-scipy)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/SegataLab/hclust2/") (synopsis "Plotting heat-maps for publications") (description @@ -1857,7 +1860,7 @@ (define-public python-htsget "111q4pzkav26aa3hkgh948wqlyrq7dq6sjml9z63n3blw8s6b0c4")))) (build-system pyproject-build-system) (native-inputs - (list python-setuptools-scm)) + (list python-setuptools-scm python-setuptools python-wheel)) (propagated-inputs (list python-humanize python-requests python-six)) (home-page "https://pypi.org/project/htsget/") @@ -1935,6 +1938,7 @@ (define-public python-logomaker (build-system pyproject-build-system) (propagated-inputs (list python-matplotlib python-numpy python-pandas)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://logomaker.readthedocs.io") (synopsis "Package for making Sequence Logos") (description "Logomaker is a Python package for generating @@ -1968,7 +1972,8 @@ (define-public python-pegasusio python-pillow python-scipy python-zarr)) - (native-inputs (list python-cython python-setuptools-scm)) + (native-inputs (list python-cython python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/lilab-bcb/pegasusio") (synopsis "Read or write single-cell genomics data") (description @@ -2027,7 +2032,7 @@ (define-public python-phenograph python-scikit-learn python-scipy)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/dpeerlab/PhenoGraph.git") (synopsis "Graph-based clustering for high-dimensional single-cell data") (description @@ -2058,6 +2063,7 @@ (define-public python-phylophlan python-numpy python-pandas python-seaborn)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/biobakery/phylophlan") (synopsis "Phylogenetic analysis of microbial isolates and genomes from metagenomes") @@ -2137,6 +2143,8 @@ (define-public python-pybedtools python-cython kentutils ; for bedGraphToBigWig python-six + python-setuptools + python-wheel ;; For the test suite. python-pytest python-psutil)) @@ -2330,6 +2338,7 @@ (define-public python-readpaf "15m6ffks4zwpp1ycwk6n02py6mw2yh7qr0vhpc178b91gldr97ia")))) (build-system pyproject-build-system) (propagated-inputs (list python-pandas)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/alexomics/read-paf") (synopsis "Minimap2 PAF file reader") (description @@ -2442,6 +2451,7 @@ (define-public python-biopython (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-numpy)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://biopython.org/") (synopsis "Tools for biological computation in Python") (description @@ -3494,7 +3504,8 @@ (define-public python-bx-python (inputs (list zlib)) (native-inputs - (list python-cython python-lzo python-pytest)) + (list python-cython python-lzo python-pytest python-setuptools + python-wheel)) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description @@ -3656,6 +3667,8 @@ (define-public python-pysam (native-inputs (list python-cython python-pytest + python-setuptools + python-wheel ;; Dependencies below are are for tests only. samtools bcftools)) @@ -3734,6 +3747,8 @@ (define-public python-plastid (native-inputs `(("python-cython" ,python-cython) ("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools) + ("python-wheel" ,python-wheel) ("test-data" ,(origin (method url-fetch) @@ -4061,7 +4076,8 @@ (define-public python-dnaio (arguments (list #:tests? #false)) ;there are none (native-inputs - (list python-cython python-pytest python-setuptools-scm)) + (list python-cython python-pytest python-setuptools-scm + python-setuptools python-wheel)) (propagated-inputs (list python-xopen)) (home-page "https://github.com/marcelm/dnaio/") @@ -4239,6 +4255,7 @@ (define-public python-pybigwig (list python-numpy)) (inputs (list libbigwig zlib curl)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/dpryan79/pyBigWig") (synopsis "Access bigWig files in Python using libBigWig") (description @@ -4277,9 +4294,11 @@ (define-public python-schema-salad python-rdflib-jsonld python-requests python-ruamel.yaml + python-setuptools ; For pkg_resources. python-typing-extensions)) (native-inputs - (list python-black python-pytest python-pytest-runner)) + (list python-black python-pytest python-pytest-runner + python-wheel)) (home-page "https://github.com/common-workflow-language/schema_salad") (synopsis "Schema Annotations for Linked Avro Data (SALAD)") (description @@ -4380,6 +4399,7 @@ (define-public python-scrublet python-scikit-learn python-scipy python-umap-learn)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/swolock/scrublet") (synopsis "Tool to indentify and remove doublets in single-cell data") (description "This package provides a tool for identifying and removing @@ -4456,6 +4476,7 @@ (define-public cwltool python-requests python-ruamel.yaml python-schema-salad + python-setuptools ; For pkg_resources. python-shellescape python-typing-extensions ;; Not listed as needed but still necessary: @@ -4467,7 +4488,8 @@ (define-public cwltool python-pytest python-pytest-cov python-pytest-mock - python-pytest-runner)) + python-pytest-runner + python-wheel)) (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis "Common Workflow Language reference implementation") @@ -4521,7 +4543,8 @@ (define-public python-dendropy (substitute* "tests/test_datamodel_taxon.py" (("collections.Iterable") "collections.abc.Iterable"))))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-wheel)) + (propagated-inputs (list python-setuptools)) (home-page "https://dendropy.org/") (synopsis "Library for phylogenetics and phylogenetic computing") (description @@ -5115,7 +5138,8 @@ (define-public python-bamnostic (base32 "0cjpzyqz6r4lmiwry2gcxdczwpkhl3lyyjg4s8addln17691ysxk")))) (build-system pyproject-build-system) - (propagated-inputs (list python-pytest)) + (propagated-inputs (list python-pytest python-setuptools)) + (native-inputs (list python-wheel)) (home-page "https://github.com/betteridiot/bamnostic/") (synopsis "Tool for binary alignment map, random access and parsing") (description @@ -5213,7 +5237,7 @@ (define-public python-ete3 python-pyqt python-scipy)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "http://etetoolkit.org") (synopsis "Python environment for phylogenetic tree exploration") (description @@ -5234,6 +5258,7 @@ (define-public python-illumina-utils (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none (propagated-inputs (list python-matplotlib python-numpy python-levenshtein)) + (native-inputs (list python-setuptools python-wheel python-pip)) (home-page "https://github.com/meren/illumina-utils") (synopsis "Library and scripts to work with Illumina paired-end data") (description @@ -5255,6 +5280,7 @@ (define-public python-pyani (propagated-inputs (list python-biopython python-matplotlib python-pandas python-scipy python-seaborn)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://widdowquinn.github.io/pyani/") (synopsis "Calculate genome-scale average nucleotide identity") (description @@ -8607,7 +8633,9 @@ (define-public python-screed (build-system pyproject-build-system) (native-inputs (list python-pytest-cov - python-pytest-runner)) + python-pytest-runner + python-setuptools + python-wheel)) (home-page "https://github.com/dib-lab/screed/") (synopsis "Short read sequence database utilities") (description "Screed parses FASTA and FASTQ files and generates databases. @@ -8949,7 +8977,7 @@ (define-public seqmagick (inputs (list python-biopython python-pygtrie)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description @@ -11672,10 +11700,12 @@ (define-public multiqc python-requests python-rich python-rich-click + python-setuptools ; For pkg_resources. python-simplejson python-spectra)) (native-inputs `(("python-pytest" ,python-pytest) + ("python-wheel" ,python-wheel) ("tests" ,(let ((commit "c3e7400affe3f3ca996973805797af61b93070ba")) (origin @@ -13301,9 +13331,10 @@ (define-public python-goatools python-pydot python-requests python-scipy + python-setuptools python-statsmodels python-xlsxwriter)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-wheel)) (home-page "https://github.com/tanghaibao/goatools") (synopsis "Python scripts to find enrichment of GO terms") (description "Python scripts to find enrichment of GO terms. In addition, @@ -13419,9 +13450,10 @@ (define-public python-mgatk python-pysam python-regex python-ruamel.yaml + python-setuptools snakemake)) (native-inputs - (list python-pytest)) + (list python-pytest python-wheel)) (home-page "https://github.com/caleblareau/mgatk") (synopsis "Mitochondrial genome analysis toolkit.") (description "This package is a Python-based command line interface for @@ -15658,6 +15690,7 @@ (define-public python-scanpy python-patsy python-scikit-learn python-scipy + python-setuptools ; For pkg_resources. python-seaborn python-session-info python-sinfo @@ -16008,7 +16041,9 @@ (define-public python-pyfaidx python-mock python-numpy python-pytest - python-pytest-cov)) + python-pytest-cov + python-wheel)) + (propagated-inputs (list python-setuptools)) (home-page "http://mattshirley.com") (synopsis "Random access to fasta subsequences") (description @@ -16174,7 +16209,7 @@ (define-public python-hicmatrix python-scipy python-tables)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/deeptools/HiCMatrix/") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (description @@ -17038,6 +17073,7 @@ (define-public cnvkit python-scipy ;; R packages r-dnacopy)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://cnvkit.readthedocs.org/") (synopsis "Copy number variant detection from targeted DNA sequencing") (description @@ -19146,7 +19182,9 @@ (define-public python-cgatcore (list python-pytest lsof inetutils - openssl)) + openssl + python-setuptools + python-wheel)) (inputs (list time)) (propagated-inputs (list python-apsw @@ -19647,6 +19685,7 @@ (define-public python-dna-features-viewer (list python-biopython python-matplotlib python-packaging)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences") diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 069d02b52c..ec8cddbd16 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -69,6 +69,7 @@ (define-module (gnu packages bootloaders) #:use-module (gnu packages valgrind) #:use-module (gnu packages virtualization) #:use-module (gnu packages xorg) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (guix build-system gnu) @@ -676,6 +677,8 @@ (define u-boot pkg-config ;for 'make menuconfig' python python-pyelftools + python-setuptools + python-wheel swig (list util-linux "lib"))) (home-page "https://www.denx.de/wiki/U-Boot/") diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 71dc9eb54b..691fe67605 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -833,7 +833,7 @@ (define-public python-gixy (base32 "0gymjcnvjx9snyrzdbmjnk93ibb161q72xam29vnl3yyac4r1330")))) (build-system pyproject-build-system) - (native-inputs (list python-nose)) + (native-inputs (list python-nose python-setuptools python-wheel)) (propagated-inputs (list python-cached-property python-configargparse python-jinja2 python-six @@ -1705,7 +1705,8 @@ (define-public python-pytest-forked ;; 'hypothesis' plugin is not in the environment (due to ;; ), which would cause the test suite ;; to fail (see: https://github.com/pytest-dev/pytest-forked/issues/54). - (list python-pytest-bootstrap python-setuptools-scm)) + (list python-pytest-bootstrap python-setuptools + python-setuptools-scm python-wheel)) (home-page "https://github.com/pytest-dev/pytest-forked") (synopsis "Pytest plugin to run tests in isolated forked subprocesses") (description "This package provides a Pytest plugin which enables running @@ -2030,7 +2031,7 @@ (define-public python-pytest-asyncio (lambda _ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$(package-version this-package))))))) - (native-inputs (list python-setuptools-scm)) + (native-inputs (list python-setuptools-scm python-setuptools python-wheel)) (propagated-inputs (list python-pytest)) (home-page "https://github.com/pytest-dev/pytest-asyncio") (synopsis "Pytest support for asyncio") @@ -2467,7 +2468,9 @@ (define-public python-pytest-mypy-plugins python-mypy python-pytest python-pyyaml + python-setuptools python-regex)) + (native-inputs (list python-wheel)) (home-page "https://github.com/TypedDjango/pytest-mypy-plugins") (synopsis "Pytest plugin for writing tests for mypy plugins") (description "This package provides a pytest plugin for writing tests for diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 762d8bd402..bdaa84f00a 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3062,6 +3062,7 @@ (define-public python-aiomysql (build-system pyproject-build-system) (arguments '(#:tests? #f)) ;test suite requires docker (propagated-inputs (list python-pymysql)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/aio-libs/aiomysql") (synopsis "MySQL driver for Python") (description "@code{aiomysql} is a driver for accessing a MySQL database @@ -3452,7 +3453,8 @@ (define-public python-sqlalchemy (build-system pyproject-build-system) (native-inputs (list python-cython ; for C extensions - python-pytest python-mock python-pytest-xdist)) ; for tests + python-pytest python-mock python-pytest-xdist ; for tests + python-setuptools python-wheel)) (propagated-inputs (list python-greenlet)) (arguments @@ -3646,7 +3648,7 @@ (define-public python-sqlite-utils (propagated-inputs (list python-click python-click-default-group python-dateutil python-sqlite-fts4 python-tabulate)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/simonw/sqlite-utils") (synopsis "CLI tool and Python utility functions for manipulating SQLite databases") @@ -3719,7 +3721,7 @@ (define-public python-apsw "02sgja00azvd08wi2wm105apmhp2644s7aw9b1zdg3dkcwjnsiad")))) (build-system pyproject-build-system) (native-inputs - (list python-cython unzip)) + (list python-cython unzip python-setuptools python-wheel)) (inputs (list sqlite-next)) ;SQLite 3.40 required. (arguments (list @@ -4039,7 +4041,7 @@ (define-public python-hiredis ;; The fix was forwarded upstream, see: ;; https://github.com/redis/hiredis-py/pull/160. (delete-file "tests/__init__.py")))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (inputs (list hiredis)) (home-page "https://github.com/redis/hiredis-py") (synopsis "Python extension that wraps protocol parsing code in hiredis") @@ -4131,6 +4133,8 @@ (define-public python-redis (list python-pytest python-pytest-asyncio python-pytest-timeout + python-setuptools + python-wheel redis)) (propagated-inputs (list python-async-timeout)) diff --git a/gnu/packages/digest.scm b/gnu/packages/digest.scm index 481771804b..e478f43b77 100644 --- a/gnu/packages/digest.scm +++ b/gnu/packages/digest.scm @@ -123,7 +123,7 @@ (define-public python-xxhash "1hdxcscry59gh0znlm71ya23mm9rfmvz8lvvlplzxzf63pib28dc")))) (build-system pyproject-build-system) ;; Needed to embed the correct version string - (native-inputs (list python-setuptools-scm)) + (native-inputs (list python-setuptools-scm python-setuptools python-wheel)) (home-page "https://github.com/ifduyue/python-xxhash") (synopsis "Python binding for xxHash") (description "This package provides Python bindings for the xxHash hash diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 88f541d2e9..11b85508ec 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -2530,7 +2530,7 @@ (define-public python-pyvisa (substitute* "pyvisa/shell.py" (("from .thirdparty import prettytable") "import prettytable"))))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-dataclasses python-prettytable python-typing-extensions)) (home-page "https://pyvisa.readthedocs.io/en/latest/") diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 153602b4b4..7b0123b6cb 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -491,7 +491,8 @@ (define-public python-ufo2ft (sha256 (base32 "1rg2997af8blvswlwif0kpz2vxrlh555gzqslz6yv9y7i7v8lphl")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest python-setuptools-scm)) + (native-inputs (list python-pytest python-setuptools-scm + python-setuptools python-wheel)) (propagated-inputs (list python-booleanoperations python-cffsubr @@ -638,7 +639,8 @@ (define-public python-glyphslib "--ignore=tests/builder/interpolation_test.py"))) (native-inputs (list python-setuptools-scm - + python-setuptools + python-wheel ;; For tests. python-pytest python-xmldiff)) @@ -809,6 +811,7 @@ (define-public psautohint python-pytest-cov python-pytest-xdist python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/adobe-type-tools/psautohint") (synopsis "Adobe's PostScript autohinter") @@ -1693,7 +1696,7 @@ (define-public python-ufolib2 (base32 "0yx4i8q5rfyqhr2fj70a7z1bp1jv7bdlr64ww9z4nv9ycbda4x9j")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest python-setuptools-scm)) + (list python-pytest python-setuptools-scm python-setuptools python-wheel)) (propagated-inputs (list python-attrs python-fonttools)) (home-page "https://github.com/fonttools/ufoLib2") (synopsis "Unified Font Object (UFO) font processing library") diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index cce4f2518d..78d683d9e4 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -351,7 +351,9 @@ (define-public python-h3 python-numpy python-pytest python-scikit-build - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (inputs (list h3)) (home-page "https://uber.github.io/h3-py") (synopsis "Python bindings for H3") @@ -959,7 +961,7 @@ (define-public python-geopandas (list python-fiona python-packaging python-pandas python-pyproj python-shapely)) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://geopandas.org") (synopsis "Geographic pandas extensions") (description "The goal of GeoPandas is to make working with @@ -1014,7 +1016,7 @@ (define-public python-osmnx python-rtree python-shapely)) (native-inputs - (list python-numpy python-pytest)) + (list python-numpy python-pytest python-setuptools python-wheel)) (home-page "https://github.com/gboeing/osmnx") (synopsis "Retrieve, model, analyze, and visualize OpenStreetMap street networks") @@ -1801,7 +1803,7 @@ (define-public python-rtree (string-append "\"" libspatialindex "/lib/libspatialindex_c.so\""))))))))) (native-inputs - (list python-numpy python-pytest python-wheel)) + (list python-numpy python-pytest python-setuptools python-wheel)) (inputs (list libspatialindex)) (home-page "https://github.com/Toblerity/rtree") diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 5510828edf..013ef1a193 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -185,7 +185,7 @@ (define-public python-igraph (string-append igraph "/lib"))))))))))) (inputs (list igraph)) (propagated-inputs (list python-texttable)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://igraph.org/python/") (synopsis "Python bindings for the igraph network analysis library")))) @@ -353,11 +353,12 @@ (define-public python-vtraag-louvain (("self.use_pkgconfig = False") "self.use_pkgconfig = True"))))))) (inputs (list igraph)) - (propagated-inputs (list python-igraph)) + (propagated-inputs (list python-igraph python-setuptools)) (native-inputs (list pkg-config python-ddt - python-setuptools-scm)) + python-setuptools-scm + python-wheel)) (home-page "https://github.com/vtraag/louvain") (synopsis "Community detection in large networks") (description diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index b91c365e3c..9ba62f9e07 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -156,7 +156,9 @@ (define-public python-graphviz python-mock python-pytest python-pytest-cov - python-pytest-mock)) + python-pytest-mock + python-setuptools + python-wheel)) (home-page "https://github.com/xflr6/graphviz") (synopsis "Simple Python interface for Graphviz") (description diff --git a/gnu/packages/license.scm b/gnu/packages/license.scm index ca8375d19d..3a10bf3293 100644 --- a/gnu/packages/license.scm +++ b/gnu/packages/license.scm @@ -179,13 +179,14 @@ (define-public reuse (base32 "0ij2mpdnawjabnsy291157wzci9050dfclwib95phg7pnmd6xsw0")))) (build-system pyproject-build-system) (native-inputs - (list python-poetry-core python-pytest)) + (list python-poetry-core python-pytest python-wheel)) (inputs (list python-binaryornot python-boolean.py python-debian python-jinja2 - python-license-expression)) + python-license-expression + python-setuptools)) ; For pkg_resources. (home-page "https://reuse.software/") (synopsis "Provide and verify copyright and licensing information") (description diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 3923573d57..0532083b02 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -745,7 +745,7 @@ (define-public python-sacrebleu python-portalocker python-regex python-tabulate)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/mjpost/sacrebleu") (synopsis "Compute shareable, comparable, and reproducible BLEU, chrF, and TER scores") @@ -786,7 +786,7 @@ (define-public python-spacy-legacy (build-system pyproject-build-system) ;; This package depends on spacy, which depends on this package. (arguments (list #:tests? #false)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://spacy.io") (synopsis "Legacy registered functions for spaCy backwards compatibility") (description @@ -807,7 +807,7 @@ (define-public python-spacy-loggers (build-system pyproject-build-system) ;; This package depends on spacy, which depends on this package. (arguments (list #:tests? #false)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/explosion/spacy-loggers") (synopsis "Logging utilities for SpaCy") (description "This package provides logging utilities for the SpaCy @@ -1548,7 +1548,7 @@ (define-public python-tslearn python-scikit-learn tensorflow python-wheel)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/tslearn-team/tslearn") (synopsis "Machine learning toolkit for time series data") (description "This is a Python library for time series data mining. @@ -1594,7 +1594,9 @@ (define-public python-imbalanced-learn python-mypy python-pandas python-pytest - python-pytest-cov)) + python-pytest-cov + python-setuptools + python-wheel)) (home-page "https://github.com/scikit-learn-contrib/imbalanced-learn") (synopsis "Toolbox for imbalanced dataset in machine learning") (description "This is a Python package offering a number of re-sampling @@ -1737,7 +1739,9 @@ (define-public python-cleanlab (native-inputs (list python-pytest python-pytorch - python-torchvision)) + python-torchvision + python-setuptools + python-wheel)) (home-page "https://cleanlab.ai") (synopsis "Automatically find and fix dataset issues") (description @@ -1769,7 +1773,7 @@ (define-public python-cleanlab-1 python-scipy python-tqdm)) (native-inputs - (list python-pytest)))) + (list python-pytest python-setuptools python-wheel)))) (define-public python-cma (package @@ -1810,7 +1814,7 @@ (define-public python-cmaes (base32 "1f3143w8ii6i93bdh65iazrq1lryccd805ndnqww5l8h7qnnzpkm")) (file-name (git-file-name name version)))) (build-system pyproject-build-system) - (native-inputs (list python-hypothesis)) + (native-inputs (list python-hypothesis python-setuptools python-wheel)) (propagated-inputs (list python-numpy)) (home-page "https://github.com/CyberAgentAILab/cmaes") (synopsis "CMA-ES implementation for Python") @@ -1981,13 +1985,15 @@ (define-public python-hyperopt python-networkx python-numpy python-scipy + python-setuptools ; For pkg_resources. python-six python-tqdm)) (native-inputs (list python-black python-nose python-pymongo - python-pytest)) + python-pytest + python-wheel)) (home-page "https://hyperopt.github.io/hyperopt/") (synopsis "Library for hyperparameter optimization") (description "Hyperopt is a Python library for serial and parallel @@ -3537,7 +3543,8 @@ (define-public python-tensorly ;; nor is examples/plot_quantum.py " and not test_file_is_generated")))) (propagated-inputs (list python-jsmin python-numpy python-scipy)) - (native-inputs (list python-pytest python-pytest-cov python-sphinx)) + (native-inputs (list python-pytest python-pytest-cov python-sphinx + python-setuptools python-wheel)) (home-page "https://github.com/tensorly/tensorly") (synopsis "Tensor learning in Python") (description @@ -3966,6 +3973,7 @@ (define-public python-readchar (lambda _ (delete-file "readchar/_win_read.py")))))) (propagated-inputs (list python-setuptools)) + (native-inputs (list python-wheel)) (home-page "https://github.com/magmax/python-readchar") (synopsis "Library to easily read single chars and key strokes") (description "This package provides a Python library to easily read single @@ -4199,7 +4207,7 @@ (define-public python-torchvision python-pillow-simd python-pytorch)) (native-inputs - (list which python-pytest)) + (list which python-pytest python-setuptools python-wheel)) (home-page "https://pytorch.org/vision/stable/index.html") (synopsis "Datasets, transforms and models specific to computer vision") (description @@ -4747,7 +4755,7 @@ (define-public python-brian2 ;; Required by codegen. python-setuptools python-sympy)) - (native-inputs (list python-pytest python-pytest-xdist)) + (native-inputs (list python-pytest python-pytest-xdist python-wheel)) (home-page "https://briansimulator.org/") (synopsis "Clock-driven simulator for spiking neural networks") (description diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0d74a2a55c..112e3ee071 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -161,6 +161,7 @@ (define-module (gnu packages maths) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) @@ -4823,7 +4824,8 @@ (define-public python-blis (invoke "python" "setup.py" "build_ext" "--inplace" "-j" (number->string (parallel-job-count)))))))) (propagated-inputs (list python-numpy)) - (native-inputs (list python-cython python-pytest)) + (native-inputs (list python-cython python-pytest + python-setuptools python-wheel)) (home-page "https://github.com/explosion/cython-blis") (synopsis "Blis as a self-contained C-extension for Python") (description diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index 3238f11fb4..b979feff06 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -326,7 +326,7 @@ (define-public zabbix-cli (string-append #$output "/share/doc/" #$name "/html"))))))) (native-inputs - (list python-pytest python-sphinx)) + (list python-pytest python-sphinx python-setuptools python-wheel)) (inputs (list ncurses python-requests)) (home-page "https://github.com/unioslo/zabbix-cli") diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index dacd4433d2..4aedbd613c 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -963,7 +963,8 @@ (define-public python-anaconda-client (add-before 'check 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - (list python-clyent python-nbformat python-pyyaml python-requests)) + (list python-clyent python-nbformat python-pyyaml python-requests + python-setuptools)) (native-inputs (list python-coverage python-dateutil @@ -971,7 +972,8 @@ (define-public python-anaconda-client python-mock python-pillow python-pytest - python-pytz)) + python-pytz + python-wheel)) (home-page "https://github.com/Anaconda-Platform/anaconda-client") (synopsis "Anaconda Cloud command line client library") (description diff --git a/gnu/packages/potassco.scm b/gnu/packages/potassco.scm index e6d7caa1ef..217521f37b 100644 --- a/gnu/packages/potassco.scm +++ b/gnu/packages/potassco.scm @@ -341,7 +341,8 @@ (define-public python-clorm (("self\\.assertTrue\\(os_called\\)" all) (string-append "# " all)))))))) (propagated-inputs (list python-clingo)) - (native-inputs (list python-typing-extensions)) + (native-inputs (list python-typing-extensions + python-setuptools python-wheel)) (home-page "https://potassco.org") (synopsis "Object relational mapping to clingo") (description "@acronym{Clorm, Clingo ORM} provides an @acronym{ORM, @@ -366,6 +367,7 @@ (define-public python-telingo "0g3khxfdzc2hc7dkiyyqhb399h6h21m5wkp6wy8w71n0m32fiy53")))) (build-system pyproject-build-system) (propagated-inputs (list python-clingo)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://potassco.org/") (synopsis "Solve dynamic temporal logic programs") (description "This package provides a system to solve dynamic temporal @@ -393,8 +395,10 @@ (define-public python-clingraph python-imageio python-jinja2 python-jsonschema - python-networkx)) - (native-inputs (list dot2tex graphviz python-pylint python-pytest)) + python-networkx + python-setuptools)) + (native-inputs (list dot2tex graphviz python-pylint python-pytest + python-wheel)) (home-page "https://github.com/potassco/clingraph") (synopsis "Visualizer for graphs defined as logic programs") (description diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index 8cd805799e..d026809093 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -381,7 +381,9 @@ (define-public python-mypy-protobuf (list python-grpc-stubs python-grpcio-tools python-pytest - python-typing-extensions)) + python-typing-extensions + python-setuptools + python-wheel)) (propagated-inputs (list protobuf python-protobuf diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm index 154c97e9e4..faaffbcea5 100644 --- a/gnu/packages/python-build.scm +++ b/gnu/packages/python-build.scm @@ -206,7 +206,7 @@ (define-public python-trove-classifiers (build-system pyproject-build-system) (arguments (list #:build-backend "setuptools.build_meta" #:tests? #f)) ;keep dependencies to a minimum - (native-inputs (list python-wheel)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/pypa/trove-classifiers") (synopsis "Canonical source for classifiers on PyPI") (description "This package is the canonical source for classifiers use on @@ -588,6 +588,7 @@ (define-public python-flit-scm ;; builder instead. #:build-backend "setuptools.build_meta")) (propagated-inputs (list python-flit-core python-setuptools-scm python-tomli)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://gitlab.com/WillDaSilva/flit_scm") (synopsis "PEP 518 build backend combining flit_core and setuptools_scm") (description "This package provides a PEP 518 build backend that uses diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 87e15b4560..92289cb164 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -586,7 +586,9 @@ (define-public python-pytest-doctestplus " and not test_remote_data_requires" " and not test_remote_data_ignore_warnings")))) (native-inputs - (list python-numpy python-pytest python-setuptools-scm)) + (list python-numpy python-pytest python-setuptools python-setuptools-scm + python-wheel)) + (propagated-inputs (list python-setuptools)) ;; for pkg_resources (home-page "https://github.com/astropy/pytest-doctestplus") (synopsis "Pytest plugin with advanced doctest features") (description @@ -636,7 +638,9 @@ (define-public python-pytest-filter-subpackage (list python-pytest python-pytest-cov python-pytest-doctestplus - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://github.com/astropy/pytest-filter-subpackage") (synopsis "Pytest plugin for filtering based on sub-packages") (description @@ -749,7 +753,8 @@ (define-public python-pytest-remotedata "not test_default_behavior" " and not test_strict_with_decorator")))) (native-inputs - (list python-pytest python-setuptools-scm)) + (list python-pytest python-setuptools python-setuptools-scm + python-wheel)) (propagated-inputs (list python-packaging)) (home-page "https://github.com/astropy/pytest-remotedata") @@ -843,7 +848,9 @@ (define-public python-pytest-mpl (list #:test-flags #~(list "-m" "mpl_image_compare"))) (native-inputs - (list python-pytest)) + (list python-pytest + python-setuptools + python-wheel)) (propagated-inputs (list python-jinja2 python-matplotlib @@ -1770,7 +1777,8 @@ (define-public python-memory-profiler (("def test_memory_profiler") "def __off_test_memory_profiler"))))))) (native-inputs - (list python-pytest python-pytest-fixture-config python-safety)) + (list python-pytest python-pytest-fixture-config python-safety + python-setuptools python-wheel)) (propagated-inputs (list python-psutil)) (home-page "https://github.com/pythonprofilers/memory_profiler") (synopsis "Memory profiler for Python") @@ -2178,7 +2186,7 @@ (define-public python-aioresponses (native-inputs (list python-pbr python-ddt python-pytest)) (propagated-inputs - (list python-aiohttp)) + (list python-aiohttp python-setuptools)) (home-page "https://github.com/pnuckowski/aioresponses") (synopsis "Mock out requests made by ClientSession from aiohttp package") (description @@ -2390,7 +2398,9 @@ (define-public python-nox (native-inputs (list python-jinja2 python-pytest - python-tox)) + python-tox + python-setuptools + python-wheel)) (home-page "https://nox.thea.codes/") (synopsis "Flexible test automation") (description @@ -2544,7 +2554,8 @@ (define-public python-pytest-httpx (base32 "1ncpd74hmsz4sadvjg99fnfscxpgh3mc2siini0dhxzwgwdkk5i7")))) (build-system pyproject-build-system) (propagated-inputs (list python-httpx)) - (native-inputs (list python-pytest python-pytest-asyncio)) + (native-inputs (list python-pytest python-pytest-asyncio python-setuptools + python-wheel)) (home-page "https://colin-b.github.io/pytest_httpx/") (synopsis "Pytest plugin to mock httpx") (description "This package provides a pytest fixture to mock httpx @@ -2621,7 +2632,8 @@ (define-public python-vulture ;; skip test that uses python-pint ;; pint has many dependencies "not test_whitelists_with_python"))))))) - (native-inputs (list python-pytest python-pytest-cov)) + (native-inputs (list python-pytest python-pytest-cov + python-setuptools python-wheel)) (propagated-inputs (list python-toml)) (home-page "https://github.com/jendrikseipp/vulture") (synopsis "Find dead Python code") diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 000d42524d..9d8ea8b156 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -64,7 +64,9 @@ (define-public python-multivolumefile python-hypothesis python-pyannotate python-pytest - python-pytest-cov)) + python-pytest-cov + python-setuptools + python-wheel)) (home-page "https://github.com/miurahr/multivolume") (synopsis "Treat multiple files as one") (description "MultiVolumefile is a Python library that provides a @@ -89,7 +91,9 @@ (define-public python-pybcj python-hypothesis python-pytest python-pytest-cov - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://codeberg.org/miurahr/pybcj") (synopsis "BCJ filter library") (description "In data compression, BCJ, short for Branch-Call-Jump, refers @@ -149,6 +153,7 @@ (define-public python-brotlicffi (setenv "USE_SHARED_BROTLI" "1")))))) (propagated-inputs (list python-cffi)) (inputs (list brotli)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/python-hyper/brotlicffi") (synopsis "Python CFFI bindings to the Brotli library") (description "This package provides Python CFFI bindings to the Brotli @@ -170,7 +175,9 @@ (define-public python-inflate64 (native-inputs (list python-pyannotate python-pytest - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://pypi.org/project/inflate64/") (synopsis "deflate64 compression/decompression library") (description "The @code{inflate64} package provides @code{Deflater} and @@ -199,7 +206,7 @@ (define-public python-isal (add-after 'unpack 'use-dynamic-linking (lambda _ (setenv "PYTHON_ISAL_LINK_DYNAMIC" "1")))))) (inputs (list isa-l)) - (native-inputs (list python-cython)) + (native-inputs (list python-cython python-setuptools python-wheel)) (home-page "https://github.com/pycompression/python-isal") (synopsis "Python bindings for the ISA-L compression library") (description @@ -225,7 +232,9 @@ (define-public python-pyppmd python-pytest-benchmark python-pytest-cov python-pytest-timeout - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://github.com/miurahr/pyppmd") (synopsis "PPMd compression/decompression library") (description "Pyppmd provides classes and functions for compressing and @@ -287,6 +296,7 @@ (define-public python-py7zr python-texttable)) (native-inputs (list python-setuptools + python-wheel python-setuptools-scm python-coverage python-coveralls diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 44babe5c8c..fb4cc63097 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -298,7 +298,9 @@ (define-public python-keyring (native-inputs (list python-toml python-pytest - python-setuptools-scm)) + python-setuptools + python-setuptools-scm + python-wheel)) (propagated-inputs (list python-importlib-metadata python-jaraco-classes @@ -530,7 +532,9 @@ (define-public python-cryptography python-pretend python-pytest ;for subtests python-pytest-benchmark - python-pytest-subtests)) + python-pytest-subtests + python-setuptools + python-wheel)) (inputs (list python-cryptography-rust)) (propagated-inputs (list python-cffi)) (home-page "https://github.com/pyca/cryptography") @@ -1038,7 +1042,7 @@ (define-public python-m2crypto ;; certificates. #:tests? #f)) (inputs (list openssl)) - (native-inputs (list swig)) + (native-inputs (list swig python-setuptools python-wheel)) (home-page "https://gitlab.com/m2crypto/m2crypto") (synopsis "Python crypto and TLS toolkit") (description "@code{M2Crypto} is a complete Python wrapper for OpenSSL @@ -1218,7 +1222,8 @@ (define-public python-service-identity (base32 "0d4x84crbz0a17d8gi90z6zlxwm9pslc65rx0cdw2797ra360v3f")))) (build-system pyproject-build-system) - (native-inputs (list python-idna python-pytest)) + (native-inputs (list python-idna python-pytest python-setuptools + python-wheel)) (propagated-inputs (list python-attrs python-cryptography python-pyasn1 python-pyasn1-modules python-six)) (home-page "https://service-identity.readthedocs.io/") @@ -1449,6 +1454,8 @@ (define-public python-trustme python-pytest python-pytest-cov python-service-identity + python-setuptools + python-wheel python-zipp)) (propagated-inputs (list python-cryptography diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 86ba4209fd..538a3c2f0e 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -191,9 +191,12 @@ (define-public python-scikit-allel (invoke "python" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs (list python-dask - python-numpy)) + python-numpy + python-click)) (native-inputs (list python-cython + python-setuptools + python-wheel ;; The following are all needed for the tests htslib python-h5py @@ -340,7 +343,7 @@ (define-public python-scikit-optimize python-scikit-learn python-scipy)) (native-inputs - (list python-pytest)) + (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 @@ -743,7 +746,7 @@ (define-public python-xarray "1339fz5gxkizq02h6vn19546x9p4c3nd9ipzpcg39h7gwhg26yi6")))) (build-system pyproject-build-system) (native-inputs - (list python-setuptools-scm python-pytest)) + (list python-setuptools python-setuptools-scm python-pytest python-wheel)) (propagated-inputs (list python-numpy python-pandas)) (home-page "https://github.com/pydata/xarray") @@ -840,7 +843,8 @@ (define-public python-pytensor "--ignore" "tests/tensor/" "--ignore" "tests/sandbox/" "--ignore" "tests/sparse/sandbox/"))))))) - (native-inputs (list python-cython python-pytest python-versioneer)) + (native-inputs (list python-cython python-pytest python-versioneer + python-setuptools python-wheel)) (propagated-inputs (list python-cons python-etuples python-filelock @@ -1585,7 +1589,9 @@ (define-public python-plotnine python-mock python-pandas python-pytest python-pytest-cov - tzdata-for-tests)) + tzdata-for-tests + python-setuptools + python-wheel)) (home-page "https://github.com/has2k1/plotnine") (synopsis "Grammar of Graphics for Python") (description @@ -2035,7 +2041,8 @@ (define-public python-libneuroml "0mrm4rd6x1sm6hkvhk20mkqp9q53sl3lbvq6hqzyymkw1iqq6bhy")))) (build-system pyproject-build-system) (propagated-inputs (list python-lxml python-six)) - (native-inputs (list python-pytest python-numpy python-tables)) + (native-inputs (list python-pytest python-numpy python-tables + python-setuptools python-wheel)) (home-page "https://libneuroml.readthedocs.org/en/latest/") (synopsis "Python library for working with NeuroML descriptions of neuronal models") diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 17c9563cfd..1389a15934 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -304,7 +304,8 @@ (define-public python-aiosignal (build-system pyproject-build-system) (arguments (list #:test-flags #~(list "tests"))) (propagated-inputs (list python-frozenlist)) - (native-inputs (list python-pytest python-pytest-asyncio python-pytest-cov)) + (native-inputs (list python-pytest python-pytest-asyncio python-pytest-cov + python-setuptools python-wheel)) (home-page "https://github.com/aio-libs/aiosignal") (synopsis "Callback manager for Python @code{asyncio} projects") (description "This Python module provides @code{Signal}, an abstraction to @@ -601,7 +602,9 @@ (define-public python-asgi-csrf python-httpx python-pytest python-pytest-asyncio - python-starlette)) + python-starlette + python-setuptools + python-wheel)) (home-page "https://github.com/simonw/asgi-csrf") (synopsis "ASGI middleware for protecting against CSRF attacks") (description "This Asynchronous Server Gateway Interface (ASGI) @@ -642,7 +645,9 @@ (define-public python-asgi-lifespan (native-inputs (list python-pytest python-pytest-asyncio python-pytest-trio - python-starlette)) + python-starlette + python-setuptools + python-wheel)) (propagated-inputs (list python-sniffio)) (home-page "https://github.com/florimondmanca/asgi-lifespan") (synopsis "Programmatic startup/shutdown of ASGI apps") @@ -764,7 +769,9 @@ (define-public python-aws-xray-sdk python-pytest-benchmark python-requests python-sqlalchemy - python-webtest)) + python-webtest + python-setuptools + python-wheel)) (propagated-inputs (list python-aiohttp python-botocore @@ -1101,7 +1108,9 @@ (define-public python-httplib2 python-pytest-randomly python-pytest-timeout python-pytest-xdist - python-six)) + python-six + python-setuptools + python-wheel)) (home-page "https://github.com/httplib2/httplib2") (synopsis "Comprehensive HTTP client library") (description @@ -1419,7 +1428,7 @@ (define-public python-h11 (base32 "17b97c56y31hi0n0x0cb5a87x4xr9jijf2y06pzj0977k6zgn6cg")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/python-hyper/h11") (synopsis "Pure-Python, bring-your-own-I/O implementation of HTTP/1.1") (description @@ -1825,7 +1834,9 @@ (define-public python-omnipath python-pytest-mock python-requests-mock python-setuptools-scm - python-tox)) + python-tox + python-setuptools + python-wheel)) (home-page "https://omnipathdb.org/") (synopsis "Python client for the OmniPath web service") (description "This package provides a Python client for the OmniPath web @@ -1855,7 +1866,7 @@ (define-public python-openai (propagated-inputs (list python-aiohttp python-requests python-tqdm python-typing-extensions)) (native-inputs (list python-black python-pytest python-pytest-asyncio - python-pytest-mock)) + python-pytest-mock python-setuptools python-wheel)) (home-page "https://github.com/openai/openai-python") (synopsis "Python client library for the OpenAI API") (description "This package provides a Python client library for the @@ -2060,7 +2071,7 @@ (define-public python-cssutils "and not encutils " "and not website.logging"))))))) (native-inputs - (list python-pytest python-jaraco-test)) + (list python-pytest python-jaraco-test python-setuptools python-wheel)) (home-page "https://github.com/jaraco/cssutils") (synopsis "CSS Cascading Style Sheets library for Python") @@ -2243,7 +2254,7 @@ (define-public python-wsproto (base32 "0rahm1j9danv1l6i6as80acwv16ycihxkhrvwjiqh9drxhk5ymmd")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-h11)) (home-page "https://github.com/python-hyper/wsproto/") @@ -3728,7 +3739,7 @@ (define-public python-flask-compress "178jzz6jxlxllcjqamzh5q7ahfh90m5cl1il9vmjs3xhz65z35pf")))) (build-system pyproject-build-system) (propagated-inputs (list python-brotli python-flask)) - (native-inputs (list python-setuptools-scm)) + (native-inputs (list python-setuptools-scm python-setuptools python-wheel)) (home-page "https://github.com/colour-science/flask-compress") (synopsis "Compress responses in a Flask app") (description @@ -3751,6 +3762,7 @@ (define-public python-flask-seasurf (arguments (list #:tests? #false)) ;there are none (propagated-inputs (list python-flask)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/maxcountryman/flask-seasurf/") (synopsis "CSRF extension for Flask") (description "SeaSurf is a Flask extension for preventing cross-site @@ -4182,7 +4194,7 @@ (define-public python-flask-jwt "flask_jwt/__init__.py") (("access_token.decode\\('utf-8'\\)") "access_token"))))))) (propagated-inputs (list python-flask python-pyjwt)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/mattupstate/flask-jwt") (synopsis "JWT token authentication for Flask apps") (description "This package implements JWT token authentication for Flask @@ -4209,7 +4221,9 @@ (define-public python-flask-restful (native-inputs (list python-blinker python-mock - python-pytest)) + python-pytest + python-setuptools + python-wheel)) (home-page "https://www.github.com/flask-restful/flask-restful/") (synopsis "Flask module for creating REST APIs") (description @@ -4870,9 +4884,9 @@ (define-public python-paste (delete-file "tests/test_proxy.py") #t)))) (build-system pyproject-build-system) (native-inputs - (list python-pytest python-nose)) + (list python-pytest python-wheel)) (propagated-inputs - (list python-six)) + (list python-six python-setuptools)) (home-page "https://pythonpaste.readthedocs.io/") (synopsis "Python web development tools, focusing on WSGI") @@ -5148,6 +5162,7 @@ (define-public whoogle-search python-wcwidth python-werkzeug python-dotenv)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/benbusby/whoogle-search") (synopsis "Self-hosted, ad-free, privacy-respecting metasearch engine") (description @@ -5989,7 +6004,9 @@ (define-public python-httpcore python-pytest-httpbin python-pytest-trio python-uvicorn - python-trustme)) + python-setuptools + python-trustme + python-wheel)) (propagated-inputs (list python-anyio python-certifi @@ -6023,7 +6040,7 @@ (define-public python-httpcore-bootstrap (package/inherit python-httpcore (name "python-httpcore-bootstrap") (arguments (list #:tests? #f)) - (native-inputs '())))) + (native-inputs (list python-setuptools python-wheel))))) (define-public python-httpx (package @@ -6067,7 +6084,9 @@ (define-public python-httpx python-trio python-trio-typing python-trustme - python-uvicorn)) + python-uvicorn + python-setuptools + python-wheel)) (propagated-inputs (list python-charset-normalizer python-brotli @@ -6299,7 +6318,7 @@ (define-public python-rapidjson "/include/rapidjson" "'")) (("if not os.path.isdir.*") "if False:"))))))) (native-inputs - (list rapidjson python-pytest python-pytz)) + (list rapidjson python-pytest python-pytz python-setuptools python-wheel)) (home-page "https://github.com/python-rapidjson/python-rapidjson") (synopsis "Python wrapper around rapidjson") (description "This package provides a python wrapper around rapidjson.") diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b8e8097c7b..eee0e5f744 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -307,7 +307,8 @@ (define-public python-janus (base32 "04hnrdcf03g1s0x3sr72sh9gnszz6kyfsl9dg8a4n0zvvhn6z5yz")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest python-pytest-cov python-pytest-asyncio)) + (list python-pytest python-pytest-cov python-pytest-asyncio + python-setuptools python-wheel)) (propagated-inputs (list python-typing-extensions)) (home-page "https://github.com/aio-libs/janus/") (synopsis @@ -579,6 +580,7 @@ (define-public python-fit-nbinom "12v8l5i35vjbpvh5i4lw29ys6vpr3z7pysyrx33hxaq09zr015mx")))) (build-system pyproject-build-system) (propagated-inputs (list python-numpy python-scipy)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/joachimwolff/fit_nbinom") (synopsis "Negative binomial maximum likelihood estimator") (description "This package provides an implementation in Python using @@ -597,7 +599,8 @@ (define-public python-docrep "0523jrzjj29kxpdllmfhrfj9kysi9mphp2m7ippjkn5b07i1g2pd")))) (build-system pyproject-build-system) (propagated-inputs (list python-six)) - (native-inputs (list python-pytest python-pytest-runner)) + (native-inputs (list python-pytest python-pytest-runner + python-setuptools python-wheel)) (home-page "https://github.com/Chilipp/docrep") (synopsis "Python package for docstring repetition") (description "Docrep is the documentation repetition module. This module @@ -655,6 +658,7 @@ (define-public python-adjusttext "05zf0xn7ab40dan213fwbp1z4rybih8dphf9mzb2ddmbafxq41mv")))) (build-system pyproject-build-system) (propagated-inputs (list python-matplotlib python-numpy)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/Phlya/adjustText") (synopsis "Adjust text position in matplotlib plots to minimize overlaps") (description @@ -772,6 +776,7 @@ (define-public python-colored "196ins0m7f90xz5dw764dlx060ziqbcydqzzq40b4ir5858baf3r")))) (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;the tests are not run automatically + (native-inputs (list python-setuptools python-wheel)) (home-page "https://gitlab.com/dslackw/colored") (synopsis "Simple library for color and formatting to terminal") (description "This is a very simple Python library for color and @@ -794,7 +799,8 @@ (define-public python-colorful (base32 "1fcz5v8b318a3dsdha4c874jsf3wmcw3f25bv2csixclyzacli98")))) (build-system pyproject-build-system) (native-inputs - (list python-coverage python-flake8 python-pytest)) + (list python-coverage python-flake8 python-pytest python-setuptools + python-wheel)) (propagated-inputs (list python-colorama)) (home-page "http://github.com/timofurrer/colorful") @@ -1101,7 +1107,8 @@ (define-public python-pdoc (base32 "0gxkw607nrd67ck4w8jri9vfrm5g60qvp8b134m8zkiphbxjnx0l")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest python-jinja2 python-pygments)) + (native-inputs (list python-pytest python-jinja2 python-pygments + python-setuptools python-wheel)) (arguments (list ;; Some tests fail, presumably because of slight version mismatches of @@ -1202,6 +1209,7 @@ (define-public python-plotext "1gpy1z2i4vq1mcrhysxahz4339pbl9rzk58rf5m5gf5ym9xji6ii")))) (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/piccolomo/plotext") (synopsis "Plots in the terminal") (description "Plotext lets you plot directly to the terminal.") @@ -1331,6 +1339,8 @@ (define-public python-skranger python-matplotlib python-pandas python-poetry-core + python-setuptools + python-wheel python-pytest)) (home-page "https://github.com/crflynn/skranger") (synopsis "Python bindings for C++ ranger random forests") @@ -1399,7 +1409,7 @@ (define-public python-tenacity (build-system pyproject-build-system) (native-inputs (list python-setuptools-scm python-tornado-6 python-typeguard - python-pytest)) + python-pytest python-setuptools python-wheel)) (home-page "https://github.com/jd/tenacity") (synopsis "Retrying library for python") (description "Tenacity is a general-purpose python library to simplify the @@ -1527,7 +1537,7 @@ (define-public python-glymur ;; which is patched above. (delete-file "tests/test_config.py")))))) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (inputs (list openjpeg ; glymur/lib/openjp2.py libtiff)) ; glymur/lib/tiff.py @@ -1796,7 +1806,7 @@ (define-public python-rasterio python-click-plugins python-cligj python-numpy - python-setuptools + python-setuptools ; For pkg_resources. python-snuggs)) (native-inputs (list gdal python-boto3 @@ -1805,7 +1815,8 @@ (define-public python-rasterio python-packaging python-pytest python-pytest-cov - python-shapely)) + python-shapely + python-wheel)) (home-page "https://github.com/rasterio/rasterio") (synopsis "Fast and direct raster I/O for use with Numpy and SciPy") (description "This package implements fast and direct raster I/O for use @@ -1833,7 +1844,7 @@ (define-public python-shapely (invoke "python" "setup.py" "build_ext" "--inplace")))))) (native-inputs (list python-cython python-matplotlib python-pytest - python-pytest-cov)) + python-pytest-cov python-setuptools python-wheel)) (inputs (list geos)) (propagated-inputs @@ -2119,7 +2130,9 @@ (define-public python-h5netcdf (native-inputs (list python-netcdf4 python-pytest - python-setuptools-scm)) + python-setuptools + python-setuptools-scm + python-wheel)) (propagated-inputs (list python-h5py python-packaging)) (home-page "https://h5netcdf.org") @@ -2414,7 +2427,7 @@ (define-public python-license-expression (base32 "0lvshl2fhwa568d3y3vmx45hdp8gk5w9yl3b2q5d66r5vqn1sfwl")))) (build-system pyproject-build-system) (native-inputs - (list python-setuptools-scm python-pytest)) + (list python-setuptools-scm python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-boolean.py)) (home-page "https://github.com/nexB/license-expression") @@ -2537,7 +2550,8 @@ (define-public python-filelock-3.5 (base32 "058av1r760ws7z6qffsjpqa39fmdxw0s1wnyr7p50y3zclg6cyqk")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest python-setuptools-scm)) + (native-inputs (list python-pytest python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/tox-dev/py-filelock") (synopsis "Platform independent file lock") (description "@code{filelock} contains a single module implementing @@ -2798,7 +2812,8 @@ (define-public python-can ;; These tests fail with "OSError: [Errno 19] No such device". "-k" "not BasicTestUdpMulticastBusIPv"))) (propagated-inputs - (list python-msgpack python-typing-extensions python-wrapt)) + (list python-msgpack python-typing-extensions python-wrapt + python-setuptools)) (native-inputs (list ;; python-canalystii ; Not packed yet python-codecov @@ -2811,7 +2826,8 @@ (define-public python-can python-pytest python-pytest-cov python-pytest-runner - python-pytest-timeout)) + python-pytest-timeout + python-wheel)) (home-page "https://github.com/hardbyte/python-can") (synopsis "Controller Area Network (CAN) interface module for Python") (description "This package defines the @code{can} module, which provides @@ -2912,6 +2928,7 @@ (define-public python-optparse-pretty (base32 "1920wbh2b7a8qn7zx2iiqbcdaax335l81a73x9pp8h11yzs2jdmh")))) (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;There are none + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/gvalkov/optparse-pretty") (synopsis "Compact help formatter for optparse") (description @@ -3156,6 +3173,7 @@ (define-public python-fastprogress ;; XXX: Fails with: "In procedure utime: No such file ;; or directory". (delete 'ensure-no-mtimes-pre-1980)))) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/fastai/fastprogress") (synopsis "Progress bar for Jupyter Notebook and console") (description @@ -3389,6 +3407,8 @@ (define-public python-omero-py python-pytest python-pytest-rerunfailures python-pytest-xdist + python-setuptools + python-wheel unzip (origin (method url-fetch) @@ -3679,7 +3699,9 @@ (define-public python-jsonargparse python-pytest-subtests python-responses python-tox - python-types-requests)) + python-types-requests + python-setuptools + python-wheel)) (home-page "https://github.com/omni-us/jsonargparse/") (synopsis "Implement minimal boilerplate CLIs derived from type hints") (description @@ -3884,7 +3906,7 @@ (define-public python-palettable (base32 "1a4h0jpsr3wjciqg9a5kslxv65d3qqgmqgkpai4cl77wlpcxfk89")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://jiffyclub.github.io/palettable/") (synopsis "Color palettes for Python") (description "Palettable (formerly brewer2mpl) is a library of color @@ -3965,7 +3987,8 @@ (define-public python-parsley (string-append "not test_sending_empty_netstring" " and not test_sending_one_netstring" " and not test_sending_two_netstrings")))) - (native-inputs (list python-pytest python-twisted)) + (native-inputs (list python-pytest python-twisted python-setuptools + python-wheel)) (home-page "https://launchpad.net/parsley") (synopsis "Parsing and pattern matching Python library") (description @@ -4069,7 +4092,9 @@ (define-public python-portalocker python-pytest-cov python-pytest-mypy python-pytest-timeout - python-redis)) + python-redis + python-setuptools + python-wheel)) (home-page "https://github.com/WoLpH/portalocker") (synopsis "Python library for file locking") (description "Portalocker is a library to provide an easy API to file @@ -4159,7 +4184,9 @@ (define-public python-extension-helpers python-pytest python-pytest-astropy python-pytest-cov - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://extension-helpers.readthedocs.io") (synopsis "Astropy ecosystem utilities for building and installing packages") (description @@ -4633,12 +4660,14 @@ (define-public python-clickhouse-connect python-orjson python-pandas python-pytz + python-setuptools ; For pkg_resources. python-sqlalchemy python-urllib3 python-zstandard)) (native-inputs (list python-cython - python-pytest)) + python-pytest + python-wheel)) (home-page "https://github.com/ClickHouse/clickhouse-connect") (synopsis "ClickHouse database core driver for Python, Pandas, and Superset") @@ -4683,7 +4712,7 @@ (define-public python-cloup "05c6cjpnf9s72gyn5dckxbmd8rf2kgdzfsl7pqzrnc1lcdl13zmv")))) (build-system pyproject-build-system) (propagated-inputs (list python-click)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/janLuke/cloup") (synopsis "Extension library for python-click") (description @@ -4787,7 +4816,8 @@ (define-public python-jsonschema (when tests? (setenv "JSON_SCHEMA_TEST_SUITE" "json") (invoke "trial" "jsonschema"))))))) - (native-inputs (list python-setuptools-scm python-twisted)) + (native-inputs (list python-setuptools-scm python-twisted + python-setuptools python-wheel)) (propagated-inputs (list python-attrs python-importlib-metadata @@ -4990,7 +5020,9 @@ (define-public python-pyjwt python-cryptography python-pytest python-sphinx - python-sphinx-rtd-theme)) + python-sphinx-rtd-theme + python-setuptools + python-wheel)) (home-page "https://github.com/progrium/pyjwt") (synopsis "JSON Web Token implementation in Python") (description @@ -5237,7 +5269,7 @@ (define-public python-uc-micro-py (base32 "17f55gi55rg47nm88fn3f8851ph03dgykdp011lxr3j6hk18lyfv")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/tsutsu3/uc.micro-py") (synopsis "Unicode data files for linkify-it-py projects") (description "This package contains a micro subset of Unicode data files @@ -5259,7 +5291,7 @@ (define-public python-linkify-it-py "0fg0a1lc8xbb62y9krxcp708ll58dxcwm8i7rrwpkd5sh2229f6x")))) (build-system pyproject-build-system) (propagated-inputs (list python-uc-micro-py)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/tsutsu3/linkify-it-py") (synopsis "Links recognition library with full Unicode support") (description "This is Python port of @@ -5284,7 +5316,7 @@ (define-public python-makefun "19a8dga8rnmjn5gy1cy1wdi28swbkdkypwbqikbxil6ynqcg3c20")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest python-setuptools-scm)) + (list python-pytest python-setuptools python-setuptools-scm python-wheel)) (home-page "https://github.com/smarie/python-makefun") (synopsis "Library to dynamically create python functions") (description "@code{makefun} helps create functions dynamically with a @@ -5867,7 +5899,9 @@ (define-public python-docx python-flake8 python-mock python-pyparsing - python-pytest)) + python-pytest + python-setuptools + python-wheel)) (propagated-inputs (list python-lxml)) (home-page "https://github.com/python-openxml/python-docx/") @@ -6025,6 +6059,7 @@ (define-public python-pygtrie (base32 "1qm4xdmzd4q5pc9h5gjdpr5m7lg06k8dvqnjn7d07d3fhani8d90")))) (build-system pyproject-build-system) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/mina86/pygtrie") (synopsis "Pure Python trie data structure implementation") (description @@ -7447,7 +7482,7 @@ (define-public python-pygit2 (base32 "1v34xdvh6i5cn5srwicvp0i2kvv8fzsv0v9p72ng081nsczmhgvr")))) (build-system pyproject-build-system) (propagated-inputs (list python-cffi libgit2)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/libgit2/pygit2") (synopsis "Python bindings for libgit2") (description "Pygit2 is a set of Python bindings to the libgit2 shared library.") @@ -7685,7 +7720,9 @@ (define-public python-norns (base32 "1r1lcq59v6l75wkbp7mypanr69a6fv6m58v6dw3v6b4vwz5nqg0z")))) (build-system pyproject-build-system) - (propagated-inputs (list python-appdirs python-nose python-pyyaml)) + (propagated-inputs (list python-appdirs python-nose python-pyyaml + python-setuptools)) + (native-inputs (list python-wheel)) (home-page "https://github.com/simonvh/norns") (synopsis "Simple YAML-based config module") (description "This package provides a simple YAML-based config module.") @@ -9006,9 +9043,10 @@ (define-public python-imageio (delete-file "tests/test_freeimage.py")))))) (inputs (list freeimage)) (propagated-inputs - (list python-imageio-ffmpeg python-numpy python-pillow python-psutil)) + (list python-imageio-ffmpeg python-numpy python-pillow python-psutil + python-setuptools)) (native-inputs - (list python-pytest)) + (list python-pytest python-wheel)) (home-page "https://imageio.github.io/") (synopsis "Library for reading and writing a wide range of image data") (description @@ -10083,7 +10121,9 @@ (define-public python-jaraco-test python-pytest-cov python-pytest-enabler python-pytest-flake8 - python-pytest-mypy)) + python-pytest-mypy + python-setuptools + python-wheel)) (home-page "https://github.com/jaraco/jaraco.test") (synopsis "Testing support by jaraco") (description "This package provides testing support by jaraco.") @@ -10441,6 +10481,7 @@ (define-public python-jupyter-client-bootstrap python-pyzmq python-tornado-6 python-traitlets)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://jupyter.org/") (synopsis "Jupyter protocol implementation and client libraries") (description @@ -10478,7 +10519,9 @@ (define-public python-jupyter-client python-pytest-timeout python-async-generator python-ipython - python-ipykernel-bootstrap)) + python-ipykernel-bootstrap + python-setuptools + python-wheel)) (properties (alist-delete 'hidden? (package-properties base)))))) (define-public python-ipykernel @@ -10559,6 +10602,8 @@ (define-public python-ipykernel ;; avoids that. python-pytest-bootstrap python-pytest-timeout + python-setuptools + python-wheel tini)) (home-page "https://ipython.org") (synopsis "IPython Kernel for Jupyter") @@ -10578,7 +10623,7 @@ (define-public python-ipykernel-bootstrap ;; left out here to break the cycle. #:phases #~(modify-phases %standard-phases (delete 'sanity-check)))) - (native-inputs '()) + (native-inputs (list python-setuptools python-wheel)) (propagated-inputs (modify-inputs (package-propagated-inputs parent) (replace "python-jupyter-client" python-jupyter-client-bootstrap) @@ -10648,7 +10693,9 @@ (define-public python-pubmed-parser python-unidecode)) (native-inputs (list python-pytest - python-pytest-cov)) + python-pytest-cov + python-setuptools + python-wheel)) (home-page "https://github.com/titipata/pubmed_parser") (synopsis "Parser for Pubmed Open-Access Subset and MEDLINE XML repository") (description @@ -11875,6 +11922,7 @@ (define-public python-qnorm "{ name = \"Maarten van der Sande\", email = \"maartenvandersande@hotmail.com\"}") (("license = \"MIT\"") "license = { file = \"LICENSE\"}"))))))) (propagated-inputs (list python-numba python-numpy python-pandas)) + (native-inputs (list python-setuptools python-wheel python-toml)) (home-page "https://github.com/Maarten-vd-Sande/qnorm") (synopsis "Quantile normalization") (description "This tool implements quantile normalization. It properly @@ -11935,7 +11983,9 @@ (define-public python-singledispatch (build-system pyproject-build-system) (native-inputs (list python-pytest - python-six)) ; required for conversion, not at run-time + python-setuptools + python-six ; required for conversion, not at run-time + python-wheel)) (home-page "https://docs.python.org/3/library/functools.html#functools.singledispatch") (synopsis "Backport of singledispatch feature from Python 3.4") @@ -12363,7 +12413,8 @@ (define-public python-pyproject-metadata "00zahgw9zjfqwf0218bj5k732aibnn68cq1p8f0wmbirb7fy5k31")))) (build-system pyproject-build-system) (propagated-inputs (list python-packaging)) - (native-inputs (list python-pypa-build python-pytest python-tomli)) + (native-inputs (list python-pypa-build python-pytest python-setuptools + python-tomli python-wheel)) (home-page "https://github.com/FFY00/python-pyproject-metadata") (synopsis "Dataclass for PEP 621 metadata") (description "This project does not implement the parsing of @@ -13134,7 +13185,8 @@ (define-public python-pyftpdlib ;; Using Pytest instead of the Makefile causes the command line tests to ;; fail on unknown Pytest arguments. (arguments (list #:test-flags #~(list "-k" "not TestCommandLineParser"))) - (native-inputs (list python-psutil python-pytest)) + (native-inputs (list python-psutil python-pytest python-setuptools + python-wheel)) (propagated-inputs (list python-pyopenssl python-pysendfile)) (home-page "https://github.com/giampaolo/pyftpdlib/") (synopsis "Asynchronous and scalable Python FTP server library") @@ -13881,7 +13933,8 @@ (define-public python-snuggs "0yv1wayrw9g6k0c2f721kha7wsv0s1fdlxpf5x7f34iqzq9z272h")))) (build-system pyproject-build-system) (propagated-inputs (list python-numpy python-pyparsing)) - (native-inputs (list python-hypothesis python-pytest)) + (native-inputs (list python-hypothesis python-pytest python-setuptools + python-wheel)) (home-page "https://github.com/mapbox/snuggs") (synopsis "Snuggs are S-expressions for Numpy") (description "Snuggs are S-expressions for Numpy.") @@ -14326,7 +14379,7 @@ (define-public python-path-bootstrap (build-system pyproject-build-system) (arguments (list #:tests? #f)) - (native-inputs (list python-setuptools-scm)) + (native-inputs (list python-setuptools python-setuptools-scm python-wheel)) (home-page "https://github.com/jaraco/path") (synopsis "Object-oriented file system path manipulation library") (description "@code{path} (formerly @code{path.py}) implements path @@ -14932,7 +14985,9 @@ (define-public python-fastjsonschema python-pylint python-pytest python-pytest-benchmark - python-pytest-cache)) + python-pytest-cache + python-setuptools + python-wheel)) (home-page "https://github.com/horejsek/python-fastjsonschema") (synopsis @@ -15015,7 +15070,7 @@ (define-public python-bleach (delete-file-recursively "bleach/_vendor/html5lib"))))) (build-system pyproject-build-system) (propagated-inputs (list python-html5lib python-tinycss2 python-webencodings)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/mozilla/bleach") (synopsis "Whitelist-based HTML-sanitizing tool") (description "Bleach is an easy whitelist-based HTML-sanitizing tool.") @@ -15551,7 +15606,7 @@ (define-public python-chardet (base32 "1r9ixxnish9j3dq4h0z0cwlkr4f5lgi6d8mhbzw59hbbjlmp2qhd")))) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (build-system pyproject-build-system) (arguments (list #:test-flags @@ -15752,7 +15807,7 @@ (define-public python-confection (build-system pyproject-build-system) (propagated-inputs (list python-pydantic python-srsly python-typing-extensions)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/explosion/confection") (synopsis "Config system for Python") (description "Confection is a lightweight library that offers a @@ -15816,7 +15871,8 @@ (define-public python-omegaconf (propagated-inputs (list java-antlr4-runtime-python python-pydevd python-pyyaml)) - (native-inputs (list icedtea antlr4 python-pytest python-pytest-mock)) + (native-inputs (list icedtea antlr4 python-pytest python-pytest-mock + python-setuptools python-wheel)) (home-page "https://github.com/omry/omegaconf") (synopsis "Flexible configuration system") (description "OmegaConf is a hierarchical configuration system and @@ -15836,7 +15892,7 @@ (define-public python-configargparse "17vky4ihicbf7nggg30xs7h3g5rxzwgch8vilnnrvdaacszkq2qv")))) (build-system pyproject-build-system) (native-inputs - (list python-mock python-pytest)) + (list python-mock python-pytest python-setuptools python-wheel)) (synopsis "Replacement for argparse") (description "A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.") @@ -16951,6 +17007,7 @@ (define-public python-xdg (base32 "14hwk9j5zjc8rvirw95mrb07zdnpjaxjx2mj3rnq8pnlyaa809r4")))) (build-system pyproject-build-system) + (arguments (list #:tests? #f)) ; No tests in PyPi tarball. (native-inputs (list python-poetry-core)) (home-page "https://github.com/srstevenson/xdg-base-dirs") @@ -17433,7 +17490,8 @@ (define-public python-cesium python-scikit-learn python-scipy python-toolz)) - (native-inputs (list python-cython python-pytest python-setuptools-scm)) + (native-inputs (list python-cython python-pytest python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://pypi.org/project/cesium/") (synopsis "Library for time-series feature extraction and processing") (description @@ -17510,7 +17568,8 @@ (define-public python-pyqtgraph (lambda _ (setenv "QT_QPA_PLATFORM" "offscreen")))))) (native-inputs - (list python-pytest python-pytest-cov python-pytest-xdist)) + (list python-pytest python-pytest-cov python-pytest-xdist + python-setuptools python-wheel)) (inputs (list qtbase-5)) (propagated-inputs @@ -17699,7 +17758,9 @@ (define-public python-codespell python-pytest python-pytest-cov python-pytest-dependency - python-tomli)) + python-tomli + python-setuptools + python-wheel)) (arguments `(#:phases (modify-phases %standard-phases @@ -18823,7 +18884,9 @@ (define-public python-inflect python-pytest-flake8 python-pytest-mypy ;; For the version number - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://github.com/jaraco/inflect") (synopsis "Correctly generate plurals, singular nouns, ordinals, indefinite articles") (description @@ -20873,7 +20936,8 @@ (define-public python-xopen (propagated-inputs (list pigz python-isal python-typing-extensions)) (native-inputs - (list python-pytest python-pytest-timeout python-setuptools-scm)) + (list python-pytest python-pytest-timeout python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/marcelm/xopen/") (synopsis "Open compressed files transparently") (description "This module provides an @code{xopen} function that works @@ -20957,6 +21021,7 @@ (define-public python-chevron "1gqfh00ics2k1sm5g46l3bi8cl5fc5d1cwzh1ylvcxvdvypklqc7")))) (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/noahmorrison/chevron") (synopsis "Mustache templating language renderer") (description "This package provides a Python implementation of the @@ -21009,7 +21074,9 @@ (define-public python-duckdb python-pyarrow python-pytest python-pytest-runner - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://www.duckdb.org") (synopsis "DuckDB embedded database") (description "DuckDB is an in-process SQL OLAP database management @@ -21868,6 +21935,7 @@ (define-public python-diff-cover python-jinja2 python-pluggy python-pygments + python-setuptools ; For pkg_resources. python-tomli)) (native-inputs (list python-flake8 @@ -22082,7 +22150,8 @@ (define-public python-gtts ;; Disable tests that require internet. (list #:test-flags '(list "-k" "not net"))) (native-inputs - (list python-pytest python-testfixtures python-click python-requests)) + (list python-pytest python-testfixtures python-click python-requests + python-setuptools python-wheel)) (home-page "https://github.com/pndurette/gTTS") (synopsis "Google Translate text-to-speech interface") (description @@ -22574,7 +22643,9 @@ (define-public python-marshmallow python-mypy python-pytest python-pytz - python-simplejson)) + python-simplejson + python-setuptools + python-wheel)) (home-page "https://github.com/marshmallow-code/marshmallow") (synopsis "Convert complex datatypes to and from native Python datatypes") (description "@code{marshmallow} provides a library for converting complex @@ -22636,7 +22707,9 @@ (define-public python-apispec python-marshmallow python-mypy python-pytest - python-pyyaml)) + python-pyyaml + python-setuptools + python-wheel)) (home-page "https://github.com/marshmallow-code/apispec") (synopsis "Swagger/OpenAPI specification generator") (description "@code{python-apispec} is a pluggable API specification @@ -22655,7 +22728,7 @@ (define-public python-apispec-webframeworks (base32 "1wyw30402xq2a8icrsjmy9v43jyvawcjd85ccb2zicqlg4k5pcqd")))) (build-system pyproject-build-system) - (propagated-inputs (list python-apispec)) + (propagated-inputs (list python-apispec python-setuptools)) (native-inputs (list python-bottle python-flake8 @@ -22665,7 +22738,8 @@ (define-public python-apispec-webframeworks python-pytest python-pyyaml python-tornado - python-tox)) + python-tox + python-wheel)) (home-page "https://github.com/marshmallow-code/apispec-webframeworks") (synopsis "Web framework plugins for apispec") (description "This package provides plugins for using @code{apispec} with @@ -23354,7 +23428,9 @@ (define-public python-tempora python-pytest-mypy python-setuptools-scm python-types-freezegun - python-types-pytz)) + python-types-pytz + python-setuptools + python-wheel)) (propagated-inputs (list python-jaraco-functools python-pytz)) (home-page "https://github.com/jaraco/tempora") (synopsis "Python date and time objects and routines") @@ -23530,7 +23606,9 @@ (define-public python-zict (list python-pytest python-pytest-asyncio python-pytest-repeat - python-pytest-timeout)) + python-pytest-timeout + python-setuptools + python-wheel)) (home-page "https://zict.readthedocs.io/en/latest/") (synopsis "Composable mutable mapping tools") (description "This package provides abstract @code{MutableMapping} classes @@ -23716,7 +23794,7 @@ (define-public python-whatever (base32 "1q7ajgqjfivxqsqgnhp4lc4p6jxyh4zprcsdbpd6dw54inaf0av5")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/Suor/whatever") (synopsis "Make anonymous functions by partial application of operators") (description "@code{whatever} provides an easy way to make anonymous @@ -23738,7 +23816,7 @@ (define-public python-funcy (file-name (git-file-name name version)))) (build-system pyproject-build-system) (native-inputs - (list python-pytest python-whatever)) + (list python-pytest python-whatever python-setuptools python-wheel)) (home-page "https://github.com/Suor/funcy") (synopsis "Functional tools") (description "@code{funcy} is a library that provides functional tools. @@ -24126,7 +24204,7 @@ (define-public python-pybloom-live "040i6bjqvl33j30v865shsk30s3h7f16pqwiaj5kig857dfmqm4r")))) (build-system pyproject-build-system) (propagated-inputs (list python-bitarray python-xxhash)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/joseph-fox/python-bloomfilter") (synopsis "Bloom filter") (description "This package provides a scalable Bloom filter implemented in @@ -25063,7 +25141,8 @@ (define-public python-numcodecs python-msgpack python-typing-extensions)) (native-inputs - (list python-cython python-pytest python-setuptools-scm)) + (list python-cython python-pytest python-setuptools-scm + python-setuptools python-wheel)) (home-page "https://github.com/zarr-developers/numcodecs") (synopsis "Buffer compression and transformation codecs") (description @@ -25169,6 +25248,7 @@ (define-public python-anndata python-pandas python-scipy python-scikit-learn + python-setuptools ; For pkg_resources. python-zarr)) (native-inputs (list python-boltons @@ -25206,7 +25286,7 @@ (define-public python-dill (with-directory-excursion "/tmp" (invoke "nosetests" "-v")))))))) (native-inputs - (list python-nose)) + (list python-nose python-setuptools python-wheel)) (home-page "https://pypi.org/project/dill/") (synopsis "Serialize all of Python") (description "Dill extends Python's @code{pickle} module for serializing @@ -25258,6 +25338,7 @@ (define-public python-multiprocess (invoke "python" "-m" "multiprocess.tests"))))))) (propagated-inputs (list python-dill)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://pypi.org/project/multiprocess/") (synopsis "Multiprocessing and multithreading in Python") (description @@ -25619,7 +25700,8 @@ (define-public python-fsspec (propagated-inputs (list python-aiohttp python-libarchive-c python-requests python-tqdm)) (native-inputs - (list python-pytest python-pytest-mock python-numpy)) + (list python-pytest python-pytest-mock python-numpy python-setuptools + python-wheel)) (home-page "https://github.com/intake/filesystem_spec") (synopsis "File-system specification") (description "The purpose of this package is to produce a template or @@ -25845,6 +25927,7 @@ (define-public python-absl-py (base32 "0ga3b0m8lfsv1m3260p83lhis52yvz3d42q8gip4gfj823849hnj")))) (build-system pyproject-build-system) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/abseil/abseil-py") (synopsis "Abseil Python common libraries") (description @@ -26149,7 +26232,8 @@ (define-public python-trio-typing (sha256 (base32 "15wa66cs165wawh4pi808ac43n67b8jqddi5ppdcbkj5gfi68hpi")))) (build-system pyproject-build-system) - (native-inputs (list python-attrs python-pytest)) + (native-inputs (list python-attrs python-pytest python-setuptools + python-wheel)) (propagated-inputs (list python-mypy python-mypy-extensions python-trio python-typing-extensions)) @@ -27291,7 +27375,7 @@ (define-public python-funcparserlib (when tests? (invoke "python" "-m" "unittest" "discover" "-v"))))))) ;; ModuleNotFoundError: No module named 'poetry' - (native-inputs (list python-poetry-core)) + (native-inputs (list python-poetry-core python-six)) (home-page "https://github.com/vlasovskikh/funcparserlib") (synopsis "Recursive descent parsing library based on functional combinators") @@ -27575,7 +27659,9 @@ (define-public python-watchgod python-pytest-cov python-pytest-mock python-pytest-sugar - python-pytest-toolbox)) + python-pytest-toolbox + python-setuptools + python-wheel)) (home-page "https://github.com/samuelcolvin/watchgod") (synopsis "Simple, modern file watching and code reload in Python") (description @@ -28838,7 +28924,7 @@ (define-public python-blessed ;; Avoid python-pytest-coverage #:test-flags '(list "-c /dev/null"))) (propagated-inputs (list python-six python-wcwidth)) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/jquast/blessed") (synopsis "Wrapper around terminal capabilities") (description @@ -29105,7 +29191,8 @@ (define-public python-dateparser (list python-dateutil python-pytz python-regex python-ruamel.yaml python-tzlocal)) (native-inputs - (list python-flake8 python-pytest python-parameterized tzdata-for-tests)) + (list python-flake8 python-pytest python-parameterized tzdata-for-tests + python-setuptools python-wheel)) (arguments `(#:phases (modify-phases %standard-phases @@ -29802,7 +29889,9 @@ (define-public python-loguru python-sphinx python-sphinx-autobuild python-sphinx-rtd-theme - python-tox)) + python-tox + python-setuptools + python-wheel)) (home-page "https://github.com/Delgan/loguru") (synopsis "Python logging made (stupidly) simple") (description "Python logging made (stupidly) simple") @@ -31896,6 +31985,7 @@ (define-public python-types-requests "0cas3cjkhrvsz2rmqnhqiihy9j79wxi9xbih8jk0p9r48c2q3iyy")))) (build-system pyproject-build-system) (propagated-inputs (list python-types-urllib3)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/python/typeshed") (synopsis "Typing stubs for requests") (description "This package provides typing stubs for requests.") @@ -31928,6 +32018,7 @@ (define-public python-types-urllib3 (base32 "0zcipjdnbnc8ymk8mh9n5mypa0qr03rqj98lbmahldcdrrap6md1")))) (build-system pyproject-build-system) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/python/typeshed") (synopsis "Typing stubs for urllib3") (description "This package provides typing stubs for urllib3.") @@ -31945,6 +32036,7 @@ (define-public python-typeshed-client "1vdwp1jjg27b22qxgm49v21nb8vm1iki3bfsm0fnq2rsz5alfwz2")))) (build-system pyproject-build-system) (propagated-inputs (list python-importlib-resources)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/JelleZijlstra/typeshed_client") (synopsis "Library for accessing stubs in typeshed") (description @@ -32349,7 +32441,9 @@ (define-public python-srsly python-pytest-timeout python-mock python-numpy - python-psutil)) + python-psutil + python-setuptools + python-wheel)) (home-page "https://github.com/explosion/srsly") (synopsis "Serialization utilities for Python") (description "This package bundles some of the best Python serialization @@ -32578,7 +32672,7 @@ (define-public python-iteround (base32 "1irw4sqrsgpc0ibxdv1hlx0d0jr1fqs48bj6mpfylzqkag9ywlfj")))) (build-system pyproject-build-system) (native-inputs - (list python-pytest)) + (list python-pytest python-setuptools python-wheel)) (home-page "https://github.com/cgdeboer/iteround") (synopsis "Sum-safe rounding for Iterables") (description "Iteround is a standard library sum-safe rounding library for @@ -32692,7 +32786,10 @@ (define-public python-deepdiff python-mock python-numpy python-pytest - python-pyyaml)) + python-pyyaml + python-setuptools + python-wheel + python-toml)) (home-page "https://github.com/seperman/deepdiff") (synopsis "Deep difference and search of any Python object/data") (description @@ -32721,7 +32818,9 @@ (define-public python-deepmerge (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) (native-inputs (list python-setuptools-scm - python-pytest)) + python-pytest + python-setuptools + python-wheel)) (home-page "https://deepmerge.readthedocs.io/en/latest/") (synopsis "Merge nested data structures") (description @@ -33146,7 +33245,7 @@ (define-public python-cogapp (base32 "1c0xx3p3lzrlyqhmccyq9c50f8v9pqk2992gb4nl50h2yy1m3s8v")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (home-page "https://nedbatchelder.com/code/cog") (synopsis "Content generation tool that leverages Python") (description "Cog is a file generation tool. It allows using pieces of @@ -33556,7 +33655,10 @@ (define-public staticsite python-ruamel.yaml python-slugify python-tornado - tzdata-for-tests)) + tzdata-for-tests + python-setuptools + python-wheel + python-toml)) (home-page "https://github.com/spanezz/staticsite") (synopsis "Static site generator") (description "Statistic is a static site generator based on Markdown and @@ -33632,8 +33734,9 @@ (define-public python-zbarlight (base32 "1v5c9bim8af6g8kgxp2dhm96n5vkr8sqi56w0bdh1xy49v03lw3g")))) (build-system pyproject-build-system) - (propagated-inputs (list python-pillow)) + (propagated-inputs (list python-pillow python-setuptools)) (inputs (list zbar)) + (native-inputs (list python-wheel)) (home-page "https://github.com/Polyconseil/zbarlight") (synopsis "Simple Python wrapper for the zbar barcode library") (description "Zbarlight is a simple wrapper for the zbar library. It can @@ -33652,6 +33755,7 @@ (define-public python-zeroc-ice "0bqkrjxp2fbz34x3wxkxji39kxinypzg8q2994sibiay29mpipxb")))) (build-system pyproject-build-system) (inputs (list openssl)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://zeroc.com") (synopsis "RPC framework") (description diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index e8654eee44..08bc47fded 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -3220,7 +3220,8 @@ (define-public python-sip (native-inputs (list python-wrapper)) (propagated-inputs - (list python-toml python-packaging python-ply)) + (list python-toml python-packaging python-ply python-setuptools + python-wheel)) (home-page "https://www.riverbankcomputing.com/software/sip/intro") (synopsis "Python binding creator for C and C++ libraries") (description diff --git a/gnu/packages/rpc.scm b/gnu/packages/rpc.scm index a88c79f8b9..83c951c337 100644 --- a/gnu/packages/rpc.scm +++ b/gnu/packages/rpc.scm @@ -253,7 +253,7 @@ (define-public python-grpcio (inputs (list abseil-cpp-20211102.0 c-ares grpc-for-python-grpcio openssl re2 zlib)) (native-inputs - (list python-cython)) + (list python-cython python-setuptools python-wheel)) (propagated-inputs (list python-six)) (home-page "https://grpc.io") diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 9c114aaf39..6d6c4386c9 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -656,7 +656,9 @@ (define-public python-msgspec python-mypy python-pytest python-setuptools-scm - python-versioneer)) + python-versioneer + python-setuptools + python-wheel)) (propagated-inputs (list python-pyyaml python-tomli python-tomli-w)) (home-page "https://jcristharif.com/msgspec/") (synopsis "Fast serialization/validation library") diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 173accd768..5d70da8fec 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -371,7 +371,9 @@ (define-public python-sphinx-panels (propagated-inputs (list python-docutils-0.15 python-sphinx-4)) (native-inputs (list python-pytest - python-pytest-regressions)) + python-pytest-regressions + python-setuptools + python-wheel)) (home-page "https://github.com/executablebooks/sphinx-panels") (synopsis "Sphinx extension for creating panels in a grid layout") (description diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dc620b13a1..9b314c3773 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2049,7 +2049,7 @@ (define-public python-vega-datasets ;; Remove dataset with unclear license. (lambda _ (delete-file "vega_datasets/_data/la-riots.csv")))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-pandas)) (home-page "https://github.com/altair-viz/vega_datasets") (synopsis "Example datasets used by Vega-related projects") @@ -2082,6 +2082,7 @@ (define-public python-altair python-jsonschema python-numpy python-pandas + python-setuptools python-toolz python-typing-extensions)) (native-inputs (list python-black @@ -2115,7 +2116,8 @@ (define-public python-hdmedians (lambda _ ;; Cython extensions have to be built before running the tests. (invoke "python" "setup.py" "build_ext" "--inplace")))))) - (propagated-inputs (list python-cython python-numpy)) + (propagated-inputs (list python-cython python-numpy python-setuptools + python-wheel)) (native-inputs (list python-nose)) (home-page "http://github.com/daleroberts/hdmedians") (synopsis "High-dimensional medians") @@ -2165,7 +2167,9 @@ (define-public python-arviz python-scipy python-typing-extensions python-xarray - python-xarray-einstats)) + python-xarray-einstats + python-setuptools + python-wheel)) (home-page "https://github.com/arviz-devs/arviz") (synopsis "Exploratory analysis of Bayesian models") (description @@ -2307,7 +2311,9 @@ (define-public python-statsmodels python-pytest python-pytest-randomly python-pytest-xdist - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page "https://statsmodels.sourceforge.net/") (synopsis "Statistical modeling and econometrics in Python") (description diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 081ef19af1..a336b33d34 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -99,6 +99,7 @@ (define-module (gnu packages terminals) #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) @@ -244,8 +245,8 @@ (define-public asciinema (substitute* "tests/pty_test.py" (("python3") (search-input-file inputs "/bin/python3")))))))) (native-inputs - ;; For tests. - (list python-pytest)) + (list python-pytest ; For tests. + python-setuptools python-wheel)) (home-page "https://asciinema.org") (synopsis "Terminal session recorder") (description diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index 5c8f65a1e6..33b0457af2 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -245,6 +245,7 @@ (define-public python-dateutils "1wg3f3imjq3snvjccv64h5498pqv9xz664xhni7bsh8mnay91p83")))) (build-system pyproject-build-system) (propagated-inputs (list python-dateutil python-pytz)) + (native-inputs (list python-setuptools python-wheel)) (home-page "https://github.com/jmcantrell/python-dateutils") (synopsis "Various utilities for working with date and datetime objects") (description @@ -328,7 +329,7 @@ (define-public python-timezonefinder ;; It's optional, remove this constrain where python-pytz is updated. #:test-flags #~(list "-k" "not test_with_pytz"))) (native-inputs - (list python-poetry-core python-pytest)) + (list python-poetry-core python-pytest python-setuptools)) (propagated-inputs (list python-cffi python-h3-3 python-numba python-numpy python-pytz)) (home-page "https://timezonefinder.michelfe.it/gui") diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 8ae2118188..ec4fb58f38 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -50,6 +50,7 @@ (define-module (gnu packages tor) #:use-module (gnu packages glib) #: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-web) @@ -446,7 +447,8 @@ (define-public tractor "1542g6alycwlmvndxcijzn4d5lgycmxxb78gqd8qwgm9kw0fnr3q")))) (build-system pyproject-build-system) (native-inputs - (list (list glib "bin"))) ; for glib-compile-schemas. + (list python-setuptools python-wheel + (list glib "bin"))) ; for glib-compile-schemas. (inputs (list python-fire python-psutil diff --git a/gnu/packages/tree-sitter.scm b/gnu/packages/tree-sitter.scm index 117c2acb0c..f4e897fbc5 100644 --- a/gnu/packages/tree-sitter.scm +++ b/gnu/packages/tree-sitter.scm @@ -29,6 +29,7 @@ (define-module (gnu packages tree-sitter) #:use-module (gnu packages graphviz) #:use-module (gnu packages icu4c) #:use-module (gnu packages node) + #:use-module (gnu packages python-build) #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) #:use-module (guix build-system pyproject) @@ -86,7 +87,8 @@ (define-public python-tree-sitter name))))))))) (inputs (list tree-sitter)) (native-inputs - (list tree-sitter-python tree-sitter-javascript)) + (list tree-sitter-python tree-sitter-javascript + python-setuptools python-wheel)) (home-page "https://github.com/tree-sitter/py-tree-sitter") (synopsis "Python bindings to the Tree-sitter parsing library") (description "This package provides Python bindings to the diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 801c2602e4..ea3dd7c793 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -5051,7 +5051,7 @@ (define-public gaupol "1z9j3r9pm4rdynlmhgsgnwnnaqw5274yfy4kyillgd77msnpbhaw")))) (build-system pyproject-build-system) (native-inputs - (list gettext-minimal pkg-config)) + (list gettext-minimal pkg-config python-setuptools python-wheel)) (inputs (list python-pygobject gtk+ diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index d58b022123..a0c738e768 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -65,6 +65,7 @@ (define-module (gnu packages vim) #: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-xyz) #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) @@ -935,7 +936,8 @@ (define-public python-neovim-remote (base32 "00kxlb3f1k7iaxzpsr07scavmnyg8c1jmicmr13mfk2lcdac6g2b")))) (build-system pyproject-build-system) - (propagated-inputs (list python-psutil python-pynvim)) + (propagated-inputs (list python-psutil python-pynvim python-setuptools)) + (native-inputs (list python-wheel)) (home-page "https://github.com/mhinz/neovim-remote") (synopsis "Control nvim processes using `nvr` commandline tool") (description "This package provide a `nvr` command, which can open File in diff --git a/guix/build-system/pyproject.scm b/guix/build-system/pyproject.scm index 2a2c3af3f3..94b9d79692 100644 --- a/guix/build-system/pyproject.scm +++ b/guix/build-system/pyproject.scm @@ -52,7 +52,12 @@ (define (default-python) "Return the default Python package." ;; Lazily resolve the binding to avoid a circular dependency. (let ((python (resolve-interface '(gnu packages python)))) - (module-ref python 'python-toolchain))) + ;; We are using python-sans-pip-wrapper, because it does not contain + ;; setuptools. This allows us to skip the dependency on setuptools for + ;; packages which don’t need it. And it allows us to more easily swap + ;; out setuptools if a different version is required. + ;; Using python-toolchain here might cause dependency cycles. + (module-ref python 'python-sans-pip-wrapper))) (define sanity-check.py (search-auxiliary-file "python/sanity-check.py"))