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build-system/pyproject: Use python-sans-pip-wrapper as default-python.

Browse source 
Also adds python-setuptools and python-wheel to relevant packages,
either to native-inputs or to propagated inputs if the pkg_resources
Python module is loaded at runtime.

* guix/build-system/pyproject.scm (default-python): Default to
python-sans-pip-wrapper.

Change-Id: I2d986c2225114f54459dd6bb360913106e52cdf4
This commit is contained in:
Lars-Dominik Braun 2023-05-11 08:33:02 +02:00 • committed by Sharlatan Hellseher
parent ca945f7c35
commit fdc0fefd46
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GPG key ID: 76D727BFF62CD2B5
36 changed files with 555 additions and 226 deletions
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13
gnu/packages/admin.scm
View file

@ -5080,10 +5080,17 @@ elogind's uaccess feature.")
;; XXX Guix's America/Los_Angeles time zone is somehow broken.
(add-before 'check 'hack-time-zone
(lambda _
(setenv "TZ" "PST8PDT"))))))
(native-inputs (list python-pytest))
(setenv "TZ" "PST8PDT")
(substitute* (find-files "tests" "^test.*\\.py$")
(("America/Los_Angeles") "PST8PDT")))))))
(native-inputs
(list python-pytest
python-setuptools
python-wheel))
(propagated-inputs
(list python-pygments python-ruamel.yaml python-xmltodict))
(list python-pygments
python-ruamel.yaml
python-xmltodict))
(home-page "https://github.com/kellyjonbrazil/jc")
(synopsis "Convert the output of command-line tools to JSON")
(description "@code{jc} JSONifies the output of many CLI tools and

90
gnu/packages/bioinformatics.scm
View file

@ -2023,8 +2023,13 @@ intended to behave exactly the same as the original BWK awk.")
(base32
"1pm1szyxabhn8jismrj9cjhf88ajgcmm39f0cgf36iagw5qakprl"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-biopython python-six))
(native-inputs (list python-pytest))
(native-inputs
(list python-pytest))
(propagated-inputs
(list python-biopython
python-setuptools
python-six
python-wheel))
(home-page "https://github.com/chapmanb/bcbb/tree/master/gff")
(synopsis "Read and write GFF files with Biopython integration")
(description
@ -2148,7 +2153,7 @@ from bokeh.util.dataclasses import entries\n"))
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
@ -2479,7 +2484,11 @@ biological activities from omics data within a unified framework.")
python-scikit-learn
python-scipy
python-seaborn))
(native-inputs (list python-cython python-setuptools-scm))
(native-inputs
(list python-cython
python-setuptools
python-setuptools-scm
python-wheel))
(home-page "https://github.com/lilab-bcb/demuxEM")
(synopsis "Analyze cell-hashing/nucleus-hashing data")
(description
@ -2578,6 +2587,7 @@ datasets with fuzzy k-means and locally linear adjustments.")
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
@ -2649,7 +2659,7 @@ varies in similar way among cells which are nearby in the given metric.")
"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/")
@ -2749,6 +2759,7 @@ framework enables the use of any LR method with any resources.")
(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
@ -2983,7 +2994,8 @@ three prime UTR.")
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
@ -3042,7 +3054,7 @@ weight.astype(\"str\") + '\\n')")))))))
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
@ -3073,6 +3085,7 @@ similarities between cells and then identifying communities in this graph.")
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")
@ -3152,6 +3165,8 @@ phylogenetic markers, and can also scale to very large phylogenies comprising
python-cython
kentutils ; for bedGraphToBigWig
python-six
python-setuptools
python-wheel
;; For the test suite.
python-pytest
python-psutil))
@ -3597,6 +3612,7 @@ alignments and perform the following operations:
(build-system pyproject-build-system)
(arguments (list #:tests? #false)) ;there are none
(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
@ -3778,6 +3794,7 @@ sequencing.")
(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
@ -4839,7 +4856,8 @@ off-target reads for a capture method that targets CpG-rich region.")
(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
@ -5065,6 +5083,8 @@ subgroups.")
(native-inputs
(list python-cython
python-pytest
python-setuptools
python-wheel
;; Dependencies below are are for tests only.
samtools
bcftools))
@ -5158,6 +5178,8 @@ UCSC genome browser.")
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
("python-setuptools" ,python-setuptools)
("python-wheel" ,python-wheel)
("test-data"
,(origin
(method url-fetch)
@ -5485,7 +5507,8 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(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/")
@ -5837,6 +5860,7 @@ gkm-SVM.")
(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
@ -5962,9 +5986,12 @@ Note that this package has been deprecated in favor of @code{pyfaidx}.")
python-mypy-extensions
python-rdflib
python-requests
python-ruamel.yaml))
python-ruamel.yaml
python-setuptools ; For pkg_resources.
python-typing-extensions))
(native-inputs
(list python-black python-pytest python-pytest-runner python-pytest-xdist))
(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
@ -6048,6 +6075,7 @@ resources for bioinformatics.")
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
@ -6213,6 +6241,7 @@ documents.")
python-requests
python-ruamel.yaml
python-schema-salad
python-setuptools ; For pkg_resources.
python-shellescape
python-spython
python-typing-extensions
@ -6226,7 +6255,7 @@ documents.")
python-pytest-cov
python-pytest-mock
python-pytest-runner
python-pytest-xdist))
python-wheel))
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis "Common Workflow Language reference implementation")
@ -6280,7 +6309,8 @@ CWL descriptions.")
(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
@ -7100,7 +7130,8 @@ multiple DJU methods.")
(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
@ -7198,7 +7229,7 @@ analysis tool Scanpy (Genome Biology, 2018).")
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
@ -7219,6 +7250,7 @@ exploration.")
(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
@ -7242,6 +7274,7 @@ Illumina paired-end data (for CASAVA 1.8+).")
(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
@ -10974,7 +11007,9 @@ complexity samples.")
(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.
@ -11316,7 +11351,7 @@ bioinformatics file formats, sequence alignment, and more.")
(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
@ -14553,10 +14588,12 @@ replacement for strverscmp.")
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
@ -16380,9 +16417,10 @@ using the same syntax.")
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,
@ -16498,9 +16536,10 @@ API services.")
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
@ -18795,6 +18834,7 @@ implementation differs in these ways:
python-patsy
python-scikit-learn
python-scipy
python-setuptools ; For pkg_resources.
python-seaborn
python-session-info
python-sinfo
@ -19188,7 +19228,9 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
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
@ -19310,7 +19352,7 @@ includes operations like compartment, insulation or peak calling.")
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
@ -20173,6 +20215,7 @@ polymorphisms) and indels with respect to a reference genome and more.")
;; R packages
r-dnacopy))
(inputs (list r-minimal)) ;for tests
(native-inputs (list python-setuptools python-wheel))
(home-page "https://cnvkit.readthedocs.org/")
(synopsis "Copy number variant detection from targeted DNA sequencing")
(description
@ -22474,7 +22517,9 @@ coordinates between different assemblies.")
(list python-pytest
lsof
inetutils
openssl))
openssl
python-setuptools
python-wheel))
(inputs (list time))
(propagated-inputs
(list python-apsw
@ -22979,6 +23024,7 @@ feature is fast retrieval of range queries into numpy arrays.")
(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")

3
gnu/packages/bootloaders.scm
View file

@ -76,6 +76,7 @@
#:use-module (gnu packages version-control)
#: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)
@ -787,6 +788,8 @@ tree binary files. These are board description files used by Linux and BSD.")
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/")

9
gnu/packages/check.scm
View file

@ -1041,7 +1041,7 @@ report generation engine.")
(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
@ -2174,7 +2174,8 @@ timeout has been exceeded.")
;; 'hypothesis' plugin is not in the environment (due to
;; <http://issues.guix.gnu.org/25235>), 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
@ -2499,7 +2500,7 @@ executed.")
(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")
@ -2992,7 +2993,9 @@ a Pytest test execution.")
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

12
gnu/packages/databases.scm
View file

@ -3229,6 +3229,7 @@ protocol with Cython for performance.")
(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
@ -3670,7 +3671,8 @@ on localhost.")
(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
@ -3905,7 +3907,7 @@ text search extension.")
(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")
@ -3978,7 +3980,7 @@ PickleShare.")
"10yfbasi4mq63g0svyl1h49ylwn9znjylq78id16dzxzk9q9ipdx"))))
(build-system pyproject-build-system)
(native-inputs
(list unzip))
(list unzip python-setuptools python-wheel))
(inputs (list sqlite-next)) ;SQLite 3.45.1 required.
(arguments
(list
@ -4333,7 +4335,7 @@ for Python. The design goals are:
;; 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")
@ -4457,6 +4459,8 @@ reasonable substitute.")
python-pytest
python-pytest-asyncio
python-pytest-timeout
python-setuptools
python-wheel
redis))
(propagated-inputs
(list python-async-timeout))

5
gnu/packages/digest.scm
View file

@ -116,7 +116,10 @@ platforms (both big and little endian).")
"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

11
gnu/packages/engineering.scm
View file

@ -2669,9 +2669,14 @@ specification can be downloaded at @url{http://3mf.io/specification/}.")
(substitute* "pyvisa/shell.py"
(("from .thirdparty import prettytable")
"import prettytable")))))))
(native-inputs (list python-pytest))
(propagated-inputs (list python-dataclasses python-prettytable
python-typing-extensions))
(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/")
(synopsis "Python binding for the VISA library")
(description "PyVISA is a Python package for support of the

19
gnu/packages/fontutils.scm
View file

@ -532,7 +532,11 @@ converts any cubic curves to quadratic. The most useful function is probably
(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
@ -679,7 +683,8 @@ process. FontParts is the successor of RoboFab.")
"--ignore=tests/builder/interpolation_test.py")))
(native-inputs
(list python-setuptools-scm
python-setuptools
python-wheel
;; For tests.
python-pytest
python-xmldiff))
@ -859,6 +864,7 @@ suite of the @code{psautohint} package.")
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")
@ -1782,8 +1788,13 @@ with @samp{nameIDs}.")
(base32 "0yx4i8q5rfyqhr2fj70a7z1bp1jv7bdlr64ww9z4nv9ycbda4x9j"))))
(build-system pyproject-build-system)
(native-inputs
(list python-pytest python-setuptools-scm))
(propagated-inputs (list python-attrs python-fonttools))
(list python-pytest
python-setuptools
python-setuptools-scm
python-wheel))
(propagated-inputs
(list python-attrs
python-fonttools))
(home-page "https://github.com/fonttools/ufoLib2")
(synopsis "Unified Font Object (UFO) font processing library")
(description "The ufoLib2 Python library is meant to be a thin

10
gnu/packages/geo.scm
View file

@ -359,7 +359,9 @@ subdivisions.")
python-numpy
python-pytest
python-scikit-build
python-setuptools-scm))
python-setuptools
python-setuptools-scm
python-wheel))
(inputs (list h3))
(home-page "https://uber.github.io/h3-py")
(synopsis "Python bindings for H3")
@ -1012,7 +1014,7 @@ pyproj, Rtree, and Shapely.")
(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
@ -1141,7 +1143,7 @@ during conversion.")
python-pandas
python-requests
python-shapely))
(native-inputs (list python-hatchling python-pytest))
(native-inputs (list python-hatchling python-pytest python-setuptools python-wheel))
(home-page "https://github.com/gboeing/osmnx")
(synopsis
"Retrieve, model, analyze, and visualize OpenStreetMap street networks")
@ -2109,7 +2111,7 @@ from multiple records.")
(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")

13
gnu/packages/graph.scm
View file

@ -250,8 +250,12 @@ more.")
var (format #f "[~s]~%"
(string-append igraph "/lib")))))))))))
(inputs (list igraph))
(propagated-inputs (list python-texttable))
(native-inputs (list python-pytest))
(propagated-inputs
(list python-texttable))
(native-inputs
(list python-pytest
python-setuptools
python-wheel))
(home-page "https://igraph.org/python/")
(synopsis "Python bindings for the igraph network analysis library"))))
@ -419,11 +423,12 @@ algorithm for community detection in large networks.")
(("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

4
gnu/packages/graphviz.scm
View file

@ -160,7 +160,9 @@ interfaces for other technical domains.")
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

17
gnu/packages/license.scm
View file

@ -191,12 +191,17 @@ belonging to various licenses.")
(add-before 'check 'chdir
(lambda _
(chdir "/tmp"))))))
(native-inputs (list python-poetry-core python-pytest))
(inputs (list python-binaryornot
python-boolean.py
python-debian
python-jinja2
python-license-expression))
(native-inputs
(list python-poetry-core
python-pytest
python-wheel))
(inputs
(list python-binaryornot
python-boolean.py
python-debian
python-jinja2
python-license-expression
python-setuptools)) ; For pkg_resources.
(home-page "https://reuse.software/")
(synopsis "Provide and verify copyright and licensing information")
(description

28
gnu/packages/machine-learning.scm
View file

@ -1047,7 +1047,7 @@ and not test_wmt22_references")
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")
@ -1088,7 +1088,7 @@ unsupervised text tokenizer.")
(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
@ -1109,7 +1109,7 @@ compatibility.")
(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
@ -1967,6 +1967,8 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
python-pandas
python-pytest
python-pytest-cov
python-setuptools
python-wheel
tensorflow))
(home-page "https://github.com/scikit-learn-contrib/imbalanced-learn")
(synopsis "Toolbox for imbalanced dataset in machine learning")
@ -2147,7 +2149,9 @@ standard feature selection algorithms.")
(list python-pytest
python-pytest-lazy-fixture
python-pytorch
python-torchvision))
python-torchvision
python-setuptools
python-wheel))
(home-page "https://cleanlab.ai")
(synopsis "Automatically find and fix dataset issues")
(description
@ -2179,7 +2183,7 @@ data by providing clean labels during training.")
python-scipy
python-tqdm))
(native-inputs
(list python-pytest))))
(list python-pytest python-setuptools python-wheel))))
(define-public python-cma
(package
@ -2220,7 +2224,7 @@ and a few related numerical optimization tools.")
(base32 "17bk60mhkglz6s7wz6xcyhw1h4mvghc1iid0805dra7jdyafwrfn"))
(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")
@ -2386,13 +2390,15 @@ interactive learning.")
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
@ -3962,7 +3968,8 @@ These include a barrier, broadcast, and allreduce.")
;; 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
@ -5123,6 +5130,7 @@ as torchvision, torchtext, and others.")
(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
@ -5391,7 +5399,7 @@ implementations and an easy-to-use API to create custom metrics. It offers:
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
@ -5994,7 +6002,7 @@ fi"
;; 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

5
gnu/packages/monitoring.scm
View file

@ -326,7 +326,10 @@ solution (server-side)")))
(string-append #$output "/share/doc/"
#$name "/html")))))))
(native-inputs
(list python-pytest python-sphinx))
(list python-pytest
python-setuptools
python-sphinx
python-wheel))
(inputs
(list ncurses python-requests))
(home-page "https://github.com/unioslo/zabbix-cli")

9
gnu/packages/package-management.scm
View file

@ -1090,7 +1090,11 @@ and not test_conda_root_outside_root_environment"))
(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
@ -1098,7 +1102,8 @@ and not test_conda_root_outside_root_environment"))
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

9
gnu/packages/potassco.scm
View file

@ -589,7 +589,7 @@ are already predefined, but more can be added as logic programs.")
(setenv "CLORM_NOCLINGO" "1")
(delete-file "tests/test_mypy_query.py"))))))
(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,
@ -651,6 +651,7 @@ the most probable model as well as finding all models and their probabilities.")
"1q6hlh4b5hsa4n5agvmfa9rhsxfd2g6kpl4b9kfccwbmf6dh51k6"))))
(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
@ -678,8 +679,10 @@ logic programs based on clingo.")
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

4
gnu/packages/protobuf.scm
View file

@ -395,7 +395,9 @@ any memory-restricted system.")
(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

3
gnu/packages/python-build.scm
View file

@ -219,7 +219,7 @@ Python file, so it can be easily copied into your project.")
(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
@ -650,6 +650,7 @@ specified by PEP 517, @code{flit_core.buildapi}.")
;; 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

43
gnu/packages/python-check.scm
View file

@ -792,8 +792,13 @@ files and/or directories.")
;; Requiring git available.
" and not test_generate_diff_basic"))))
(native-inputs
(list python-numpy python-pytest python-setuptools-scm))
(home-page "https://github.com/scientific-python/pytest-doctestplus")
(list python-numpy
python-pytest
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
"This package contains a plugin for the Pytest framework that provides
@ -842,7 +847,9 @@ for interactively selecting and running Pytest tests.")
(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
@ -947,7 +954,10 @@ were inadvertently left open at the end of a unit test.")
"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")
@ -1042,6 +1052,7 @@ framework and makes it easy to undo any monkey patching. The fixtures are:
#:test-flags #~(list "-m" "mpl_image_compare")))
(native-inputs
(list python-pytest
python-setuptools
python-setuptools-scm
python-wheel))
(propagated-inputs
@ -2075,7 +2086,11 @@ the implementation of that name.")
(("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")
@ -2532,7 +2547,7 @@ most situations.")
(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
@ -2780,7 +2795,9 @@ which make writing and running functional and integration tests easier.")
(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
@ -2933,8 +2950,12 @@ parametrize. This plugin allows you to use all four.")
(sha256
(base32 "1ncpd74hmsz4sadvjg99fnfscxpgh3mc2siini0dhxzwgwdkk5i7"))))
(build-system pyproject-build-system)
(native-inputs
(list python-pytest
python-pytest-asyncio
python-setuptools
python-wheel))
(propagated-inputs (list python-httpx))
(native-inputs (list python-pytest python-pytest-asyncio))
(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
@ -3011,7 +3032,11 @@ running acceptance tests on headless servers.")
;; 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")

28
gnu/packages/python-compression.scm
View file

@ -114,7 +114,9 @@ This Python package wraps the Blosc library.")
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
@ -251,7 +253,9 @@ following algorithms are available:
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
@ -311,6 +315,7 @@ Jump conversion filter by CFFI for Python.")
(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
@ -332,7 +337,9 @@ library.")
(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 "Compression/decompression library")
(description "The @code{inflate64} package provides @code{Deflater} and
@ -361,7 +368,7 @@ compression algorithm.")
(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
@ -407,7 +414,9 @@ headers compressed with QPACK.")
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
@ -468,9 +477,8 @@ several possible methods.")
python-pyzstd
python-texttable))
(native-inputs
(list python-setuptools
python-setuptools-scm
python-coverage
(list python-coverage
python-setuptools
python-coveralls
python-libarchive-c
python-py-cpuinfo
@ -479,7 +487,9 @@ several possible methods.")
python-pytest-benchmark
python-pytest-cov
python-pytest-remotedata
python-pytest-timeout))
python-pytest-timeout
python-setuptools-scm
python-wheel))
(home-page "https://github.com/miurahr/py7zr")
(synopsis "7-zip in Python")
(description "This package provides py7zr, which implements 7-zip

25
gnu/packages/python-crypto.scm
View file

@ -302,7 +302,9 @@ do what is needed for client/server Kerberos authentication based on
(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
@ -530,11 +532,13 @@ is used by the Requests library to verify HTTPS requests.")
(build-system pyproject-build-system)
(arguments (list #:tests? #f)) ; No tests included.
(native-inputs
(list python-flit-core))
(list python-flit-core
python-setuptools
python-wheel))
(home-page "https://github.com/pyca/cryptography")
(synopsis "Test vectors for the cryptography package")
(description
"This package contains test vectors for the cryptography package.")
"This package contains test vectors for the cryptography package.")
;; Distributed under either BSD-3 or ASL2.0
(license (list license:bsd-3 license:asl2.0))))
@ -574,7 +578,10 @@ is used by the Requests library to verify HTTPS requests.")
python-iso8601
python-pretend
python-pytest ;for subtests
python-pytest-benchmark))
python-pytest-benchmark
python-pytest-subtests
python-setuptools
python-wheel))
(inputs (list python-cryptography-rust))
(propagated-inputs (list python-cffi))
(home-page "https://github.com/pyca/cryptography")
@ -1093,7 +1100,7 @@ provides drop-in compatibility with PyCrypto.")))
;; 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
@ -1280,7 +1287,11 @@ derivation function.")
(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/")
@ -1511,6 +1522,8 @@ items and collections, editing items, locking and unlocking collections
python-pytest
python-pytest-cov
python-service-identity
python-setuptools
python-wheel
python-zipp))
(propagated-inputs
(list python-cryptography

22
gnu/packages/python-science.scm
View file

@ -370,9 +370,12 @@ routines such as routines for numerical integration and optimization.")
(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
@ -591,7 +594,7 @@ swarm algorithm.")
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
@ -1852,7 +1855,7 @@ multiple deep learning frameworks.")
(string-append "not test_datetime_conversion_warning"
" and not test_timedelta_conversion_warning"))))
(native-inputs
(list python-setuptools-scm python-pytest))
(list python-setuptools python-setuptools-scm python-pytest python-wheel))
(propagated-inputs
(list python-numpy python-packaging python-pandas))
(home-page "https://github.com/pydata/xarray")
@ -2019,7 +2022,9 @@ parentdir_prefix = pytensor-
(native-inputs (list python-cython
python-pytest
python-pytest-mock
python-versioneer))
python-versioneer
python-setuptools
python-wheel))
(propagated-inputs (list python-cons
python-etuples
python-filelock
@ -2882,7 +2887,9 @@ aggregated sum and more.")
python-pandas
python-pytest
python-pytest-cov
python-setuptools
python-setuptools-scm
python-wheel
tzdata-for-tests))
(home-page "https://github.com/has2k1/plotnine")
(synopsis "Grammar of Graphics for Python")
@ -3666,7 +3673,12 @@ compagnies.")
"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-setuptools
python-tables
python-wheel))
(home-page "https://libneuroml.readthedocs.org/en/latest/")
(synopsis
"Python library for working with NeuroML descriptions of neuronal models")

63
gnu/packages/python-web.scm
View file

@ -444,7 +444,12 @@ by calling @code{FrozenList.freeze}.")
(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
@ -765,7 +770,9 @@ WSGI. This package includes libraries for implementing ASGI servers.")
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)
@ -806,7 +813,9 @@ that is then compared to a @code{csrftoken} hidden form field or a
(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")
@ -970,7 +979,9 @@ Model} (SAM) templates into AWS CloudFormation templates.")
python-pytest-benchmark
python-requests
python-sqlalchemy
python-webtest))
python-webtest
python-setuptools
python-wheel))
(propagated-inputs
(list python-aiohttp
python-botocore
@ -1310,7 +1321,9 @@ over a different origin than that of the web application.")
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
@ -1706,7 +1719,7 @@ for use in Python programs that implement HTTP/2.")
(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
@ -2165,7 +2178,9 @@ is Python’s.")
python-pytest-socket
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
@ -2195,7 +2210,7 @@ service.")
(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
@ -2400,7 +2415,7 @@ for clients and servers.")
"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")
@ -2578,7 +2593,7 @@ set out in RFC 7540 Section 5.3 (Stream Priority).")
(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/")
@ -4503,7 +4518,7 @@ presume or force a developer to use a particular tool or library.")
"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
@ -4526,6 +4541,7 @@ headers required for a compressed response and compresses the response data.")
(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
@ -4961,7 +4977,7 @@ Betamax that may possibly end up in the main package.")
"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
@ -4988,7 +5004,9 @@ apps.")
(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
@ -5654,9 +5672,9 @@ package from WTForms. The package has been renamed to
(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")
@ -5929,6 +5947,7 @@ with oauthlib.")
python-stem
python-validators
python-waitress))
(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
@ -6026,7 +6045,7 @@ ecosystem.")
;; Pretend to be a CI system to skip flaky tests.
(setenv "CI" "true"))))))
(native-inputs
(list python-pytest))
(list python-pytest python-setuptools python-wheel))
(propagated-inputs
(list python-idna))
(home-page "https://github.com/python-hyper/hyperlink")
@ -6810,7 +6829,9 @@ and serve updated contents upon changes to the directory.")
python-pytest-httpbin
python-pytest-trio
python-uvicorn
python-trustme))
python-setuptools
python-trustme
python-wheel))
(propagated-inputs
(list python-anyio
python-certifi
@ -6844,7 +6865,7 @@ Some things HTTP Core does do:
(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
@ -6889,7 +6910,9 @@ Some things HTTP Core does do:
python-trio
python-trio-typing
python-trustme
python-uvicorn))
python-uvicorn
python-setuptools
python-wheel))
(propagated-inputs
(list python-charset-normalizer
python-brotli
@ -7121,7 +7144,7 @@ major web browsers.")
"/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.")

273
gnu/packages/python-xyz.scm
View file

@ -514,7 +514,8 @@ similar XML files, in the same way the @command{diff} utility does it.")
(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
@ -977,6 +978,7 @@ and variables you'll need already imported and created.
(substitute* "setup.py"
((".\\*\"") "\"")))))))
(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
@ -995,7 +997,8 @@ scipy and numpy of negative binomial maximum likelihood estimation.")
"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
@ -1073,6 +1076,7 @@ features of the Python's built-in dict.")
(build-system pyproject-build-system)
(arguments (list #:tests? #false)) ;there are none
(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
@ -1234,6 +1238,7 @@ HoloViews, and Datashader.")
"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
@ -1256,7 +1261,8 @@ names for 256 color terminal setups.")
(base32 "0kyy9qhvrb5m9h8xmri7c88i0k1g5qc7017anw39gx44an7mn33y"))))
(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")
@ -1697,7 +1703,8 @@ Specification v2.0 (PEP 249).")
(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
@ -1804,6 +1811,7 @@ different units.")
"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.")
@ -1998,6 +2006,8 @@ generator MkDocs.")
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")
@ -2165,7 +2175,7 @@ threads.")
(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
@ -2650,7 +2660,7 @@ utilities such as ping(1).")
python-click-plugins
python-cligj
python-numpy
python-setuptools
python-setuptools ; For pkg_resources.
python-snuggs))
(native-inputs (list gdal
python-boto3
@ -2659,7 +2669,8 @@ utilities such as ping(1).")
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
@ -2686,7 +2697,7 @@ with Numpy and SciPy.")
;; Cython extensions have to be built before running the tests.
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(native-inputs
(list python-cython python-matplotlib python-pytest))
(list python-cython python-matplotlib python-pytest python-setuptools python-wheel))
(inputs
(list geos))
(propagated-inputs
@ -2972,7 +2983,9 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of
(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")
@ -3314,7 +3327,7 @@ and lookups.")
(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")
@ -3436,7 +3449,8 @@ inter-process communication.")
(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
@ -3720,7 +3734,8 @@ your Python package version as a calendar version.")
;; 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
@ -3733,7 +3748,8 @@ your Python package version as a calendar version.")
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
@ -3868,6 +3884,7 @@ a library.")
(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
@ -4078,6 +4095,7 @@ for additional processing.")
;; 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
@ -4311,6 +4329,8 @@ of @code{xmlfile}.")
python-pytest
python-pytest-rerunfailures
python-pytest-xdist
python-setuptools
python-wheel
unzip
(origin
(method url-fetch)
@ -4673,7 +4693,9 @@ Python.")
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
@ -4902,7 +4924,7 @@ commands.")
(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
@ -4983,7 +5005,8 @@ syntax.")
(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
@ -5134,7 +5157,9 @@ PDF, PNG, EPS and SVG).")
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
@ -5242,14 +5267,16 @@ and is not compatible with JSON.")
python-pytest-astropy
python-pytest-cov
python-setuptools-scm
python-tomli))
python-tomli
python-setuptools
python-wheel))
(home-page "https://extension-helpers.readthedocs.io")
(synopsis "Astropy ecosystem utilities for building and installing packages")
(description
"The extension-helpers package includes convenience helpers to assist with
building Python packages with compiled C/Cython extensions. It is developed by
the Astropy project but is intended to be general and usable by any Python
package.")
"The extension-helpers package includes convenience helpers to assist
with building Python packages with compiled C/Cython extensions. It is
developed by the Astropy project but is intended to be general and usable by
any Python package.")
(license license:bsd-3)))
(define-public python-extras
@ -5737,12 +5764,14 @@ clickgen is using @code{anicursorgen} and @code{xcursorgen} under the hood.")
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")
@ -5787,7 +5816,7 @@ well-tested and interoperable CLIs for handling GeoJSON.")
"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
@ -5915,7 +5944,8 @@ and convert DDL to BigQuery JSON schema.")
(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
@ -6118,7 +6148,9 @@ memory usage and transliteration quality.")
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
@ -6366,7 +6398,7 @@ work on your part.")
(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
@ -6388,7 +6420,7 @@ for linkify-it-py projects.")
"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
@ -6413,7 +6445,7 @@ recognition library with full Unicode support. It has features like:
"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
@ -7091,8 +7123,8 @@ via commands such as @command{rst2man}, as well as supporting Python code.")
(list behave
python-pyparsing
python-pytest
python-pytest-cov
python-pytest-xdist))
python-setuptools
python-wheel))
(propagated-inputs
(list python-lxml python-typing-extensions))
(home-page "https://github.com/python-openxml/python-docx/")
@ -7235,7 +7267,7 @@ with Python.")
;; basic tests.
'(list "--ignore-glob=tests/*/*")))
(native-inputs
(list python-pytest))
(list python-pytest python-setuptools python-wheel))
(home-page "https://pygments.org/")
(synopsis "Syntax highlighting")
(description
@ -7290,6 +7322,7 @@ working with Valve's VDF text format.")
(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
@ -9015,7 +9048,7 @@ readable format.")
(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.")
@ -9228,7 +9261,9 @@ semantic version parser for Node.js.")
(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.")
@ -10223,7 +10258,7 @@ and therefore easier to read and write.")
;; NOTE: Any value works, the variable just has to be present.
(setenv "SKIP_ONLINE" "1"))))))
(native-inputs
(list python-pytest))
(list python-pytest python-setuptools python-wheel))
(inputs
(list bash-minimal))
(home-page "https://github.com/pypa/distlib")
@ -10963,10 +10998,10 @@ from FFMPEG, reliably terminating the process when done.")
(delete-file "tests/test_freeimage.py"))))))
(inputs (list freeimage))
(propagated-inputs
(list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
(list python-imageio-ffmpeg python-numpy python-pillow python-tifffile python-setuptools))
(native-inputs
(list python-black python-flake8 python-fsspec python-pytest
python-pytest-cov))
python-pytest-cov python-wheel))
(home-page "https://imageio.github.io/")
(synopsis "Library for reading and writing a wide range of image data")
(description
@ -12183,7 +12218,9 @@ releases.")
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.")
@ -12631,6 +12668,7 @@ container data structures in Python).")
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
@ -12668,7 +12706,9 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
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
@ -12744,7 +12784,9 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
;; and causes deprecation warnings. Using the bootstrap variant
;; avoids that.
python-pytest-bootstrap
python-pytest-timeout))
python-pytest-timeout
python-setuptools
python-wheel))
(home-page "https://ipython.org")
(synopsis "IPython Kernel for Jupyter")
(description "This package provides the IPython kernel for Jupyter.")
@ -12763,7 +12805,7 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
;; 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)
@ -12833,7 +12875,9 @@ callback signature using a prototype function.")
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
@ -14266,6 +14310,7 @@ falling into the Python interpreter.")
"{ 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
@ -14326,7 +14371,9 @@ low-level X clients. It is written entirely in Python.")
(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")
@ -14762,7 +14809,8 @@ plugin for flake8 to check PEP-8 naming conventions.")
"0yvs59ymz5gdix34a95wxlxvk9bnvjgrzsnmnc3ws7whpfv3yasm"))))
(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
@ -15595,7 +15643,8 @@ the @code{sendfile(2)} system call.")
;; 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")
@ -16386,7 +16435,8 @@ asyncio.")
"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.")
@ -16873,7 +16923,7 @@ domains support.")
(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
@ -17531,7 +17581,9 @@ significantly better performance.")
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
@ -17614,7 +17666,7 @@ systems, as a command line tool, and as a Python library.")
(delete-file-recursively "bleach/_vendor/html5lib")))))
(build-system pyproject-build-system)
(propagated-inputs (list python-html5lib python-tinycss2))
(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.")
@ -18150,7 +18202,7 @@ simulation, statistical modeling, machine learning and much more.")
(base32
"1r9ixxnish9j3dq4h0z0cwlkr4f5lgi6d8mhbzw59hbbjlmp2qhd"))))
(native-inputs
(list python-pytest))
(list python-pytest python-setuptools python-wheel))
(build-system pyproject-build-system)
(arguments
(list #:test-flags
@ -18364,7 +18416,7 @@ This allows one to make simple text-mode user interfaces on Unix-like systems")
(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
@ -18431,7 +18483,8 @@ config files.")
(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
@ -18450,10 +18503,10 @@ consistent API regardless of how the configuration was created.")
(base32
"1l866g1dcf2ljf8fl7ggpxk1rggry0lya4d5b264gradi1qp81p7"))))
(build-system pyproject-build-system)
(native-inputs
(list python-mock python-pytest))
(propagated-inputs
(list python-pyyaml))
(native-inputs
(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.")
@ -19600,6 +19653,7 @@ in pure Python.")
(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")
@ -20118,7 +20172,8 @@ synchronously (wait until ready).")
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
@ -20195,7 +20250,8 @@ ISO 8859, etc.).")
(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
@ -20383,7 +20439,9 @@ checking library.")
python-pytest
python-pytest-cov
python-pytest-dependency
python-tomli))
python-tomli
python-setuptools
python-wheel))
(arguments
`(#:phases
(modify-phases %standard-phases
@ -21517,7 +21575,9 @@ def get_requires_for_build_sdist(config_settings=None):
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
@ -23789,7 +23849,8 @@ JPEG2000 and GIF files in pure Python.")
(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
@ -23873,6 +23934,7 @@ efficient as possible on all supported Python versions.")
"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
@ -23935,7 +23997,9 @@ Mustache templating language renderer.")
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
@ -24856,6 +24920,7 @@ point is the point of maximum curvature.")
python-jinja2
python-pluggy
python-pygments
python-setuptools ; For pkg_resources.
python-tomli))
(native-inputs
(list python-flake8
@ -25070,7 +25135,8 @@ while only declaring the test-specific fields.")
;; 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
@ -25601,7 +25667,9 @@ manipulation, or @code{stdout}.")
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
@ -25663,7 +25731,9 @@ datatypes to and from native Python datatypes.")
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
@ -25682,7 +25752,7 @@ Swagger.")
(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
@ -25692,7 +25762,8 @@ Swagger.")
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
@ -26412,7 +26483,9 @@ particularly convenient for use in tests.")
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")
@ -26536,7 +26609,9 @@ queue.")
(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
@ -26726,7 +26801,7 @@ files, and Makefiles.")
(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
@ -26748,7 +26823,7 @@ functions by partial application of operators.")
(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.
@ -27227,7 +27302,7 @@ working with iterables.")
"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
@ -28392,7 +28467,8 @@ tool).")
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
@ -28518,6 +28594,7 @@ N-dimensional arrays for Python.")
python-pandas
python-scipy
python-scikit-learn
python-setuptools ; For pkg_resources.
python-zarr))
(native-inputs
(list python-awkward
@ -28564,7 +28641,7 @@ object-oriented library such as @code{scikit-learn}.")
(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
@ -28616,6 +28693,7 @@ preload_resources\
(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
@ -28928,7 +29006,8 @@ append on old values. Partd excels at shuffling operations.")
(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
@ -29239,6 +29318,7 @@ RFC 8265 and RFC 8266.")
(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
@ -29543,7 +29623,8 @@ programs that do multiple things at the same time with parallelized I/O.")
(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))
@ -30809,7 +30890,7 @@ scripts to load entry points more quickly.")
(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")
@ -31085,7 +31166,9 @@ but portable.")
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
@ -32486,7 +32569,7 @@ placement and scaling of SVG figures and adding markers, such as labels.")
;; 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
@ -32761,7 +32844,8 @@ It adds a simple and readable way to print stuff during development.")
(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
@ -33662,7 +33746,9 @@ older versions of Python and so are packaged here.")
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")
@ -36317,6 +36403,7 @@ Python, with static types.")
"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.")
@ -36349,6 +36436,7 @@ Python, with static types.")
(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.")
@ -36366,6 +36454,7 @@ Python, with static types.")
"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
@ -36782,7 +36871,9 @@ than trying to just split strings.")
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
@ -37034,7 +37125,7 @@ objects.")
(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
@ -37148,7 +37239,10 @@ object, which can be useful if you want to force your objects into a table.")
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
@ -37177,7 +37271,9 @@ other.")
(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
@ -37629,7 +37725,7 @@ versa. Extended WKB/WKT are also supported.")
(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
@ -38070,7 +38166,10 @@ path.")
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
@ -38163,8 +38262,9 @@ markdown-compliant strings.")
(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
@ -38183,6 +38283,7 @@ read all zbar supported codes.")
"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

6
gnu/packages/qt.scm
View file

@ -4002,9 +4002,9 @@ Python.")
(list python-wrapper python-setuptools python-setuptools-scm-next))
(propagated-inputs
(list python-tomli
python-packaging))
;; no test.
(arguments (list #:tests? #f))
python-packaging
python-setuptools
python-wheel))
(home-page "https://www.riverbankcomputing.com/software/sip/intro")
(synopsis "Python binding creator for C and C++ libraries")
(description

2
gnu/packages/rpc.scm
View file

@ -254,7 +254,7 @@ type information of gRPC.")
(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")

4
gnu/packages/serialization.scm
View file

@ -746,7 +746,9 @@ RPC system. Think JSON, except binary. Or think Protocol Buffers, except faste
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")

4
gnu/packages/sphinx.scm
View file

@ -453,7 +453,9 @@ supported with @code{sphinx-issues}.")
(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

14
gnu/packages/statistics.scm
View file

@ -2191,7 +2191,7 @@ and fast file reading.")
;; 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")
@ -2236,6 +2236,7 @@ and Vega-Lite examples.")
python-jsonschema
python-numpy
python-pandas
python-setuptools
python-toolz
python-typing-extensions))
(native-inputs (list python-black
@ -2323,7 +2324,8 @@ correlated samples from Markov Chain Monte Carlo (MCMC).")
(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")
@ -2374,7 +2376,9 @@ machine learning, computer vision, and high-dimensional statistics.")
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
@ -2670,7 +2674,9 @@ sampler for Markov chain Monte Carlo (MCMC).")
python-pytest
python-pytest-randomly
python-pytest-xdist
python-setuptools-scm))
python-setuptools-scm
python-setuptools
python-wheel))
(home-page
(string-append "https://www.statsmodels.org/v" version "/"))
(synopsis "Statistical modeling and econometrics in Python")

5
gnu/packages/terminals.scm
View file

@ -115,6 +115,7 @@
#: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-check)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
@ -255,8 +256,8 @@ managers.")
(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

3
gnu/packages/time.scm
View file

@ -285,6 +285,7 @@ datetime module, available in Python 2.3+.")
"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
@ -368,7 +369,7 @@ Python datetime objects.")
;; 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")

4
gnu/packages/tor.scm
View file

@ -50,6 +50,7 @@
#: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)
@ -447,7 +448,8 @@ Potential client and exit connections are scrubbed of sensitive information.")
"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

4
gnu/packages/tree-sitter.scm
View file

@ -32,6 +32,7 @@
#: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)
@ -89,7 +90,8 @@
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

2
gnu/packages/video.scm
View file

@ -6181,7 +6181,7 @@ video from a Wayland session.")
"1z9j3r9pm4rdynlmhgsgnwnnaqw5274yfy4kyillgd77msnpbhaw"))))
(build-system pyproject-build-system)
(native-inputs
(list gettext-minimal pkg-config))
(list gettext-minimal pkg-config python-setuptools python-wheel))
(inputs
(list bash-minimal
python-pygobject

8
gnu/packages/vim.scm
View file

@ -72,6 +72,7 @@
#: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)
@ -1030,7 +1031,12 @@ through its msgpack-rpc API.")
(base32
"00kxlb3f1k7iaxzpsr07scavmnyg8c1jmicmr13mfk2lcdac6g2b"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-psutil python-pynvim))
(native-inputs
(list python-wheel))
(propagated-inputs
(list python-psutil
python-pynvim
python-setuptools))
(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

7
guix/build-system/pyproject.scm
View file

@ -52,7 +52,12 @@
"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"))