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158,197 Commits 77 Branches 40 Tags
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141153 Commits

Author SHA1 Message Date
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
Sharlatan Hellseher
2e7ba7a88e gnu: python-quadpy: Deselect one failing test. 
* gnu/packages/maths.scm (python-quadpy) [arguments] <test-flags>:
Deselect one failing test.

Change-Id: I29ab3db45afb70928125773644b8704f9b731ada
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
f7cc9940e0 gnu: python-orthopy: Skip some tests, fix build. 
* gnu/packages/maths.scm (python-orthopy) [arguments] <test-flags>: Skip
5 failing tests.

Change-Id: Ic5e55d9a8a054eaba9f685e134a366dbfaa9bd8d
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
8afbc6f9ac gnu: python-peaks2utr: Update to 1.4.1 and fix build. 
* gnu/packages/bioinformatics.scm (python-peaks2utr): Update to 1.4.1.
[arguments] <test-flags>: Skip 2 more similar failing test.
<phases>: Add 'relax-requirements.

Change-Id: Ia26903116915c4ef031b4a6bdb5dae64d109a1f4
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
18a2ef9c62 gnu: python-gffutils: Update to 0.13 and fix build. 
* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.13.
[build-system]: Swap to pypproject-build-system.
[arguments] <phases>: Use default 'check, add 'set-HOME.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-nose; add python-pytest,
python-setuptools, and python-wheel.

Change-Id: I77b1ed5be8750bdd2f2cdff3135430207b80f6fc
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
a7885e4b3d gnu: python-parabam: Add a maintenance note. 
* gnu/packages/bioinformatics.scm (python-parabam): Add a maintenance
note on package build issue, reported upstream.

Change-Id: I447fa2354a2318b19d0eca5acf844a574e49db09
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
c01033e3fa gnu: python-astroml: Disable more tests. 
* gnu/packages/astronomy.scm (python-astroml) [arguments] <test-flags>:
Disable tests requiring NumPy, reported upstream.

Change-Id: I30693e2f3550ba8aab012b54d3d838508038c762
 2025-04-16 11:46:22 +02:00
Christopher Baines
51bd111732 gnu: python-pyopenssl: Skip TestDTLS::test_timeout. 
With the changes currently on the python-team branch, this seems to fail at
least on aarch64-linux, presumably due to faketime being used.

* gnu/packages/python-crypto.scm (python-pyopenssl)[arguments]: Skip
TestDTLS::test_timeout.

Change-Id: Ifca6dc323141219a01b9aff7baad8c712ac56b02
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
3f8bd3b983 gnu: python-autograd: Fix indentation. 
* gnu/packages/machine-learning.scm (python-autograd): Fix indentation.

Change-Id: I67b1c01d323e2458b49447969bb4164f71d1571b
 2025-04-16 11:46:22 +02:00
Sharlatan Hellseher
7b6f6e9604 gnu: python-autograd: Update to 1.7.0. 
* gnu/packages/machine-learning.scm (python-autograd): Update to 1.7.0.
[source]: Use the latest version tag.
[native-inputs]: Remove python-nose, python-setuptools, and
python-wheel; add python-hatchling.

Change-Id: I42cd6b9ce621c1509f459fb947b09d05635fb79b
 2025-04-16 11:46:22 +02:00
Nicolas Graves
ab3a8e1096 gnu: python-aiosmtpd: Update to 1.4.6. 
* gnu/packages/mail.scm (python-aiosmtpd): Update to 1.4.6.
[build-system]: Switch to pyproject.
[arguments]{phases}: Delete it.
{test-flags}: Switch a QA test.
[native-inputs]: Remove python-flufl-testing, python-node.  Add
python-pytest, python-pytest-asyncio, python-pytest-cov,
python-pytest-mock, python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:22 +02:00
Nicolas Graves
e156116942 gnu: python-netaddr: Update to 1.3.0. 
* gnu/packages/python-web.scm (python-netaddr): Update to 1.3.0.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-poetry-core, python-pytest,
python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:22 +02:00
Nicolas Graves
f4a21e1848 gnu: python-netaddr: Move to (gnu packages python-web). 
* gnu/packages/python-xyz.scm (python-netaddr): Move from here…
* gnu/packages/python-web.scm (python-netaddr): …to here.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
1fb50c3762 gnu: Standardize python-oslo.* package names. 
* gnu/packages/openstack.scm (python-oslo.concurrency,
python-oslo.config, python-oslo.context, python-oslo.i18n,
python-oslo.log, python-oslo.serialization, python-oslo.utils): Rename
packages.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
4528a0c866 gnu: python-debtcollector: Update to 3.0.0. 
* gnu/packages/openstack.scm (python-debtcollector): Update to 3.0.0.
[source]: Patch {origin} to remove unwanted native-inputs.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Remove python-six.
[native-inputs]: Add python-doc8, python-fixtures,
python-openstackdocstheme, python-reno, python-setuptools,
python-stestr and python-wheel. Remove python-subunit and
python-testrepository.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
0941987161 gnu: pwntools: Update to 4.4.0. 
* gnu/packages/cybersecurity.scm (pwntools): Update to 4.4.0.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
624f485fdb gnu: Add python-unix-ar. 
* gnu/packages/python-compression.scm (python-unix-ar): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
6b143b10eb gnu: Add python-colored-traceback. 
* gnu/packages/python-xyz.scm (python-colored-traceback): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
a759a6f342 gnu: python-pegasusio: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (python-pegasusio): Update to 0.9.1.
[propagated-inputs]: Add python-cython, python-setuptools. Remove
python-importlib-metadata.
[native-inputs]: Styling from guix style.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
c88c55d894 gnu: python-nptyping: Ignore failing test. 
* gnu/packages/python-check.scm (python-nptyping)[arguments]
{test-flags}: Ignore failing test.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
91677b47b2 gnu: python-ncls: Update to 0.0.68. 
* gnu/packages/python-xyz.scm (python-ncls): Update to 0.0.68.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-cython, python-pandas, python-pytest,
python-setuptools, python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
0edfbc0475 gnu: python-cell2cell: Update to 0.7.4. 
* gnu/packages/bioinformatics.scm (python-cell2cell): Update to 0.7.4.
[source]{origin}: Relax requirements in snippet.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
7bf4329019 gnu: crossmap: Add missing python-pyparsing native-input. 
* gnu/packages/bioinformatics.scm (python-pyparsing)[native-inputs]:
Add python-pyparsing.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:21 +02:00
Nicolas Graves
5b6622c4e9 gnu: python-bx-python: Update to 0.13.0. 
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.13.0.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:20 +02:00
Nicolas Graves
26826a0728 gnu: python-cesium: Move to (gnu packages astronomy). 
The dependencies of this package are already in (gnu packages astronomy).

* gnu/packages/python-xyz.scm (python-cesium): Move from here…
* gnu/packages/astronomy.scm (python-cesium): …to here.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:20 +02:00
Nicolas Graves
c83fe9e840 gnu: python-cleanlab: Update to 2.7.1. 
* gnu/packages/machine-learning.scm (python-cleanlab): Update to 2.7.1.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:20 +02:00
Nicolas Graves
591908f804 gnu: pairadise: Add missing native-inputs. 
* gnu/packages/bioinformatics.scm (pairadise)[native-inputs]: Add
python-setuptools and python-wheel.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:20 +02:00
Nicolas Graves
d8b3d0ec8e gnu: python-biom-format: Update to 2.1.16. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.16.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:20 +02:00