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Author SHA1 Message Date
Nicolas Graves
a2b0677470 gnu: python-pyro4: Update to 4.82. 
* gnu/packages/python-xyz.scm (python-pyro4): Update to 4.82.
[build-system]: Switch to pyproject-build-system.
[arguments]{tests?}: Remove to enable tests.
{test-flags}: Skip missing tests.
{phases}: Add 'check phase replacement.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:27 +02:00
Nicolas Graves
88866dd4aa gnu: python-serpent: Update to 1.41. 
* gnu/packages/python-xyz.scm (python-serpent): Update to 1.41.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:27 +02:00
Nicolas Graves
a081c80b2f gnu: python-attr: Update to 0.3.2. 
* gnu/packages/python-xyz.scm (python-attr): Update to 0.3.2.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:27 +02:00
Nicolas Graves
e4750cbff9 gnu: python-property-cached: Fix build. 
* gnu/packages/python-xyz.scm (python-property-cached): Fix build.
* gnu/packages/patches/python-property-cached-asyncio-3_11.patch: Add
patch.
* gnu/local.mk: Record patch.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:27 +02:00
Nicolas Graves
1c27ceac65 gnu: Remove pybind11-2.3. 
This package is now a leaf package that fails to build.

* gnu/packages/python-xyz.scm (pybind11-2.3): Delete variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:27 +02:00
Nicolas Graves
ac5a45243a gnu: python-vaex-core: Update to 4.17.1. 
* gnu/packages/python-science.scm (python-vaex-core): Update to 4.17.1.
* gnu/packages/patches/python-vaex-core-fix-tsl-use.patch: Add patch.
* gnu/local.mk: Record patch.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:27 +02:00
Nicolas Graves
58ca499bff gnu: python-pytensor: Update to 2.28.3. 
* gnu/packages/python-science.scm (python-pytensor): Update to 2.28.3.
[arguments]{test-flags}: Use field.
{phases}: Remove 'check phase replacement. Simplify 'versioneer. Add
phase 'pre-check.

Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I8f324863438356ebc1ad3d62e86b5b17c416cd02
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
2d30f21fb9 gnu: Add string-view-lite. 
* gnu/packages/cpp.scm (string-view-lite): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
5300ed2893 gnu: python-pytorch-geometric: Skip failing tests. 
* gnu/packages/machine-learning.scm (python-pytorch-geometric):
[arguments]{test-flags}: Skip test_type_repr failing test.

Change-Id: I8ec82761a107ed6021c655250f8ab5b1187980c8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
e01edc1146 gnu: mageck: Add missing native-inputs. 
* gnu/packages/bioinformatics.scm (mageck)[native-inputs]: Add
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
ec22768c11 gnu: autokey: Add missing native-inputs. 
* gnu/packages/python-xyz.scm (autokey)[native-inputs]: Add
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
89a891a7e1 gnu: scregseg: Add missing native-inputs. 
* gnu/packages/bioinformatics.scm (scregseg)[native-inputs]: Add
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
576ffc088a gnu: labelme: Add missing native-inputs. 
* gnu/packages/image-processing.scm (labelme)[native-inputs]: Add
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
8cd6103d8d gnu: Add clipper2. 
* gnu/packages/cpp.scm (clipper2): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Sharlatan Hellseher
bc4c4b0a88 gnu: python-numdifftools: Skip some tests. 
* gnu/packages/python-science.scm (python-numdifftools) [arguments]
<test-flags>: Skip 7 tests failing with a NumPy 1.26.2.

Change-Id: I5dc5865d0ac1ba47e79aac57d4e1768ecdb590be
 2025-04-16 11:46:26 +02:00
Nicolas Graves
36949b911d gnu: python-mechanize: Update to 0.4.10. 
* gnu/packages/python-xyz.scm (python-mechanize): Update to 0.4.10.
[build-system]: Switch to pyproject-build-system.
[arguments]{tests?}: Disable them.
{phases}: Add 'configure-tests phase to setup GUIX_PYTHONPATH.
[native-inputs]: Add python-html5-parser, python-html5lib,
python-lxml, python-service-identity, python-setuptools, python-six,
python-twisted, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
f8cedfb8c0 gnu: openmolar: Fix build. 
* gnu/packages/medical.scm (openmolar): Fix build.
[build-system]: Switch to pyproject-build-system.
[arguments]{use-setuptools?}: Drop it.
{phases}: Add phase 'set-acceptable-version.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:26 +02:00
Nicolas Graves
0f30a646cd gnu: libei: Update to 1.4.0. 
* gnu/packages/freedesktop.scm (libei): Update to 1.4.0.
[native-inputs]: Add dbus, python-pyaml. Remove python-black.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
5cbb9d2166 gnu: python-cu2qu: Fix tests. 
* gnu/packages/fontutils.scm (python-cu2qu): Fix tests.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test (most likely due to
lagging behing python-fonttools package).
[native-inputs]: Add python-setuptools, python-wheel.
* gnu/packages/python-xyz.scm (python-fonttools-minimal): Add comment.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
356e356ee7 gnu: conan: Update to 2.7.1. 
* gnu/packages/package-management.scm (conan): Update to 2.7.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Use field. Ignore failing tests (old versions
of cmake, performance tests, docker/premake/scons requirements.
{phases}: Refresh phases. Replace 'check phase by a 'configure-tests
phase and the native 'check phase.
[propagated-inputs]: Replace python-urllib3 by python-urllib3-next.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
2be1c0e507 gnu: veusz: Update to 3.6.2. 
* gnu/packages/maths.scm (veusz): Update to 3.6.2.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style, use gexps.
{phases}: Remove phase 'fix-sip-dir. Add phase
'fix-pyqt5-include-dir. Refresh phase 'wrap-executable.
[native-inputs]: Add python-astropy, python-setuptools,
python-wheel. Remove python-sip-4.
[inputs]: Add qtwayland-5.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
f806aa80aa gnu: python-patch-ng: Update to 1.18.1. 
* gnu/packages/python-xyz.scm (python-patch-ng): Update to 1.18.1.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
b0c6e6017e gnu: cpplint: Update to 2.0.0. 
* gnu/packages/cpp.scm (cpplint): Update to 2.0.0.
[arguments]{phases}: Add phase 'patch-build-system.
[native-inputs]: Add python-parameterized, python-pytest-timeout.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
29661328c7 gnu: umi-tools: Update to 1.1.6. 
* gnu/packages/bioinformatics.scm (umi-tools): Update to 1.1.6.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[inputs]: Add python-pybktree, python-scipy.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
5676350d87 gnu: Add python-pybktree. 
* gnu/packages/backup.scm (python-pybktree): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
8088bd7604 gnu: python-sip: Update to 6.10.0. 
* gnu/packages/qt.scm (python-sip): Update to 6.10.0.
[source]: Add snippet to relax python-setuptools requirement.
[native-inputs]: Remove python-wrapper. Add python-wheel. Sort inputs.
[propagated-inputs]: Remove python-tomli, python-wheel. Sort inputs.

* gnu/packages/backup.scm (vorta)[native-inputs]: Add
python-setuptools, python-wheel.

* gnu/packages/python-xyz.scm (python-echo)[native-inputs]: Add
python-setuptools, python-wheel.

* gnu/packages/patches/python-sip-include-dirs.patch: Refresh patch.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
ce93d3697d gnu: python-rstr: Update to 3.2.2. Enable tests. 
* gnu/packages/python-xyz.scm (python-rstr): Update to 3.2.2.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]{phases}: Add phase 'pretend-version.
[native-inputs]: Add python-pytest, python-setuptools,
python-setuptools-scm, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:25 +02:00
Nicolas Graves
a5d3be8a89 gnu: taxtastic: Update to 0.11.1. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.11.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test.
{phases}: Improve style with gexp. Update phase
'prepare-directory. Improve phase 'check with test-flags inclusion.
[native-inputs]: Add python-setuptools, python-wheel.
[propagated-inputs]: Sort inputs. Replace python-psycopg2 by both
python-psycopg and python-psycopg2-binary. Add python-sqlparse.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
5139f5e47f gnu: Remove python-pyfasta. 
This package is archived and deprecated in favor or python-pyfaidx for
7 years.

* gnu/packages/bioinformatics.scm (python-pyfasta): Delete variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
4d8be83440 gnu: seqmagick: Update to 0.8.6-0.dee6ab9. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.6-0.dee6ab9.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
0b875355d5 gnu: rseqc: Switch to pyproject-build-system. 
* gnu/packages/bioinformatics.scm (rseqc):
[build-system]: Switch to pyproject-build-system.
[inputs]: Sort inputs. Add python-pyparsing, python-setuptools,
python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
71e787161c gnu: python-locust: Update to 2.33.2. 
* gnu/packages/benchmark.scm (python-locust): Update to 2.33.2.
[arguments]{test-flags}: Add additional missing test.
{phases}: Add phase 'pretend-version. Adapt phase fix-version.
[native-inputs]: Remove python-poetry-core,
python-poetry-dynamic-versioning. Add python-hatchling,
python-hatch-vcs.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
e8cdc2d6fb gnu: python-pyquery: Update to 2.0.1. 
* gnu/packages/python-xyz.scm (python-pyquery): Update to 2.0.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore a test that requires network access.
[native-inputs]: Add python-pytest, python-pytest-cov,
python-requests, python-setuptools, python-webob, python-webtest,
python-wheel.
[propagated-inputs]: Sort inputs.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
0e5db833b3 gnu: Remove python-anyjson. 
This package is a leaf package in Guix, is stale for 13 years, and its
upstream repository is not even up anymore.

* gnu/packages/python-xyz.scm (python-anyjson): Delete variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
ae23597c2e gnu: Remove python-parameterizedtestcase. 
This package is a leaf package in Guix, has been abandonned for 11
years (aside from a License change).

* gnu/packages/python-check.scm (python-parameterizedtestcase): Delete variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
31a494c658 gnu: python-pyvcf: Use the fork python-pyvcf3. 
* gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of
'deprecated-package'.
(python-pyvcf3): New variable.
(python-nanosv): Replace python-pyvcf by python-pyvcf3.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
55d4ab9a08 gnu: python-jsonargparse: Update to 4.37.0. 
* gnu/packages/python-xyz.scm (python-jsonargparse): Update to 4.37.0.
[arguments]{test-flags}: Remove uneeded test-flags.
[propagated-inputs]: Remove python-contextvars,
python-docstring-parser, python-pyyaml, python-typeshed-client.
[native-inputs]: Add python-pypa-build. Remove python-coverage,
python-pycodestyle, python-tox, python-types-requests.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:24 +02:00
Nicolas Graves
7780df4ee7 gnu: python-databricks-cli: Update to 0.18.0. 
* gnu/packages/python-web.scm (python-databricks-cli): Update to
0.18.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style, use gexps.
[native-inputs]: Add python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:23 +02:00
Nicolas Graves
f6d9a7cc79 gnu: python-cchardet: Update to 2.2.0a2. 
* gnu/packages/freedesktop.scm (python-cchardet): Update to 2.2.0a2.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:23 +02:00
Nicolas Graves
e1b1759832 gnu: python-zeroc-ice: Update to 3.7.10.1. 
* gnu/packages/python-xyz.scm (python-zeroc-ice): Update to 3.7.10.1.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
0ba4394718 gnu: python-css-parser: Update to 1.0.10. 
* gnu/packages/python-web.scm (python-css-parser): Update to 1.0.10.

Change-Id: I2775f4f7871582d066ed5d4bb1831bb666f730aa
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
cb42767a79 gnu: abjad-ext-rmakers: Adjust inputs. 
* gnu/packages/music.scm (abjad-ext-rmakers): [native-inputs]: Add
python-pytest-cov.

Change-Id: I33dd4f77533172acfbf5fb56ed0c7787845be60c
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
b86e8f8ce1 gnu: python-uqbar: Update to 0.7.2. 
* gnu/packages/graphviz.scm (python-uqbar): Update to 0.7.2.
[arguments] <test-flags>: Run all tests; provide "--pyargs" option.
[propagated-inputs]: Remove python-sphinx-5 and python-sphinx-rtd-theme;
add python-sphinx.
[native-inputs]: Remove python-flake8, python-isort, and python-mypy;
add python-defusedxml and python-typing-extensions.

Change-Id: I530799178e6d99ec097325b05c65770d3af8f732
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
1a3482af80 gnu: python-ont-fast5-api: Update to 4.1.3. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.1.3.

Change-Id: I8dc6f2a911624b62fbf419b28cfad840200a207c
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
a56bfbb4e9 gnu: python-js2py: Update to 0.74. 
* gnu/packages/python-web.scm (python-js2py): Update to 0.74.
[build-system]: Swap to pyproject-build-system.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.
[propagated-inputs]: Remove python-six; add python-numpy.

Change-Id: I0b2a31241fd2c075c8555a921b805e254436de6a
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
1e46fbd812 gnu: python-iced: Update to 0.5.13. 
* gnu/packages/bioinformatics.scm (python-iced): Update to 0.5.13.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: I2251b0ba37dab29bf82a2db73be1e05fee11c34e
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
2e3f8619a3 gnu: labelme: Update to 5.2.1, fix build. 
* gnu/packages/image-processing.scm (labelme): Update to 5.2.1, improve
package style.
[source] <uri>: Remove trailing ".git" from URL.
[build-system]: Swap to pyproject-build-system.
[arguments]: Use G-expressions.
<test-flags>: Utilize it.
<phases>: Use default 'check, remove 'loosen-requirements
[propagated-inputs]: Add python-natsort.
[description]: Fix indentation.

Change-Id: I9552637358ea7b6335d99f49a63cbedbe4984302
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
b58bf70620 gnu: python-docrepr: Disable tests. 
* gnu/packages/documentation.scm: Add (guix build-system pyproject)
and (gnu packages python-build).
(python-docrepr) [build-system]: Swap to pyproject-build-system.
[arguments] <test?>: Disable them as all fail.
<phases>: Use default 'check.
[native-inputs]: Remove python-pytest and python-pytest-asyncio; add
python-setuptools and python-wheel.

Change-Id: I27fc1b56cb44efc2c261896c1429200ce83cc080
 2025-04-16 11:46:23 +02:00
Sharlatan Hellseher
5737570c2a gnu: python-fastparquet: Update to 2024.11.0, fix build. 
* gnu/packages/databases.scm (python-fastparquet): Update to 2024.11.0.
[native-inputs]: Remove python-pytest-runner; add python-pytest, python-setuptools,
and python-wheel.

Change-Id: I4a798972077cd1646e48cea28b4bc369a7a68fd1
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
3fd29e131b gnu: python-crosshair: Update to 0.0.84, fix build. 
* gnu/packages/check.scm (python-crosshair): Update to 0.0.84.
[phases] {fix-dependencies}: Adjust version check for z3-solver.
[propagated-inputs]: Add python-importlib-metadata, python-packaging,
and python-typing-extensions.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I31a1ee4dbd57aa6c3382006c7f02772ff205277f
 2025-04-16 11:46:22 +02:00