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Code Activity
158,119 Commits 73 Branches 40 Tags
71f392ca8d83df2bd4e415402b216bb274378dec
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146044 Commits

Author SHA1 Message Date
Ricardo Wurmus
71f392ca8d gnu: tensorflow: Fix build. 
* gnu/packages/machine-learning.scm (tensorflow)[arguments]: Rename phase
'python3.10-compatibility to 'python3.11-compatibility; update it to deal with
removals in Python 3.11; add phase 'numpy-compatibility.

Change-Id: I6c08b7b03cb01223fe9d62545f6687e9440b2011
 2025-04-16 11:46:18 +02:00
Ricardo Wurmus
a330b7acff gnu: Remove python-anyio/without-dataclasses. 
* gnu/packages/python-xyz.scm (python-anyio/without-dataclasses): Remove
variable.
* gnu/packages/jupyter.scm (python-jupyter-server)[propagated-inputs]: Replace
python-anyio/without-dataclasses with python-anyio.

Change-Id: I81433128fc3ed2f098bd84f1f89555e9dda62d6d
 2025-04-16 11:46:18 +02:00
Ricardo Wurmus
eb70b7c57f gnu: bedtools: Update to 2.31.1. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.31.1.

Change-Id: I9f104d68fbdc2040fee41f1565d48a40999bc219
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
fb347f8789 gnu: ams-lv2: Make compatible with Python 3.11. 
* gnu/packages/music.scm (ams-lv2)[arguments]: Add phase 'python3.11-compatibility.

Change-Id: Iaa2709495e24d586a7d9f75dda7e527ca920e127
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
cfb0fc85ef gnu: python-pecan: Update to 1.6.1. 
* gnu/packages/python-web.scm (python-pecan): Update to 1.6.1.
[build-system]: Use pyproject-build-system.
[native-inputs]: Remove uwsgi.
[arguments]: Remove 'relax-requirements phase and custom 'check phase.

Change-Id: I94a09a56fa2f353d8df3a96cb38a5bd73d5b0c0b
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
309373b9a9 gnu: python-dask-image: Update to 2024.5.3. 
* gnu/packages/python-xyz.scm (python-dask-image): Update to 2024.5.3.
[arguments]: Add phase 'set-version.
[native-inputs]: Add python-coverage, python-flake8, python-pytest-cov,
python-pytest-timeout, python-setuptools, python-setuptools-scm, python-twine,
and python-wheel.

Change-Id: I2297cb6942f7c97a330847bda8e0c33c84266322
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
6cdede88e9 gnu: python-duckdb: Disable one more test. 
* gnu/packages/python-xyz.scm (python-duckdb)[arguments]: Disable wrap
coverage test.

Change-Id: I625bc37c979d7c0fa3a2e67d35267993ae791b9e
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
6fa27ee0f4 gnu: python-pysam: Update to 0.23.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.23.0.
[arguments]: Use #:test-flags instead of custom 'check phase; add 'pre-check
phase.

Change-Id: I92c715d5dfd5cbdbcf6dd61fc5e472f6c6ca977d
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
80bdd80e52 gnu: htscodecs: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.1.

Change-Id: If5b4af407a8b639891d0b444056e81724cebac8c
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
cd8d613e0e gnu: bcftools: Update to 1.21. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.21.

Change-Id: I4a2a6c106f804a68c16074a6ce8ae449c299724e
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
89408dc096 gnu: htslib: Update to 1.21. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.21.
(htslib-1.19): New variable.

Change-Id: If2a53871e69c606d3aebe820ee75bcc945d939b0
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
6309ac44c6 gnu: python-ratelimiter: Update to 1.2.0.post1. 
* gnu/packages/python-xyz.scm (python-ratelimiter): Update to 1.2.0.post1.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'pytest-compatibility.
[native-inputs]: Add python-pytest, python-pytest-asyncio, python-setuptools,
and python-wheel.

Change-Id: I9f7665feb4cf31e38185be7e0cd5ffe7691e26f7
 2025-04-16 11:46:17 +02:00
Ricardo Wurmus
7ff7963cd9 gnu: snakemake-6: Disable one more test. 
* gnu/packages/python-xyz.scm (snakemake)[arguments]: Disable test_lint test;
replace custom 'check phase with 'pre-check phase.

Change-Id: I9631383ab6160ee8a234145515bbf198b54b1e57
 2025-04-16 11:46:16 +02:00
Ricardo Wurmus
62853330ed gnu: snakemake: Disable one more test. 
* gnu/packages/python-xyz.scm (snakemake)[arguments]: Disable test_lint test.

Change-Id: I00d3e1e900c5d4dacb660d253a2a1839c7c7826a
 2025-04-16 11:46:16 +02:00
Ricardo Wurmus
ce8db9583b gnu: python-yte: Update to 1.7.0. 
* gnu/packages/python-xyz.scm (python-yte): Update to 1.7.0.
[build-system]: Use pyproject-build-system.
[arguments]: Replace 'check phase.
[propagated-inputs]: Add python-dpath.
[native-inputs]: Add python-numpy, python-poetry-core, and python-pytest.

Change-Id: If1d4e8e0289d9a36205353ad2c9bb345076e4ff7
 2025-04-16 11:46:16 +02:00
Ricardo Wurmus
f7ac711df5 gnu: python-dpath: Update to 2.2.0. 
* gnu/packages/python-xyz.scm (python-dpath): Update to 2.2.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.
[native-inputs]: Remove python-mock and python-nose; add python-nose2,
python-setuptools, and python-wheel.

Change-Id: I30ca919712b03f868d3e9fed4802817e4602dcda
 2025-04-16 11:46:16 +02:00
Ricardo Wurmus
1dc317fbbd gnu: snakemake-7: Update to 7.32.4. 
* gnu/packages/python-xyz.scm (snakemake-7): Update to 7.32.4.
[arguments]: Use #:test-flags instead of a custom 'check phase; remove
'tabulate-compatibility phase; add 'pre-check phase.
[propagated-inputs]: Add python-humanfriendly, python-reretry, and
python-throttler; remove python-ratelimiter.

Change-Id: Iea7f17559b19098ca5a589d164355f3918f4bb3e
 2025-04-16 11:46:16 +02:00
Ricardo Wurmus
bcf4ab7511 gnu: python-toposort: Update to 1.10. 
* gnu/packages/python-xyz.scm (python-toposort): Update to 1.10.
[build-system]: Use pyproject-build-system.
[arguments]: Replace 'check phase.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ifde522ecba6331634c911856892c3b25098fbd88
 2025-04-16 11:46:16 +02:00
Ricardo Wurmus
9ebcce5a92 gnu: Add python-reretry. 
* gnu/packages/python-xyz.scm (python-reretry): New variable.

Change-Id: Ic54bdb5eee422b12d2c0e475abb6c4f142cad1e3
 2025-04-16 11:46:16 +02:00
Ricardo Wurmus
7af8a3ad8d gnu: Add python-throttler. 
* gnu/packages/python-xyz.scm (python-throttler): New variable.

Change-Id: I04a07281d4ba77d880d7c8176b1a3269713b9b63
 2025-04-16 11:46:16 +02:00
Sharlatan Hellseher
158323faa6 gnu: zbar: Update to 0.23.93. 
* gnu/packages/aidc.scm (zbar): Update to 0.23.93.

Change-Id: Id681057d67cfbd26d1b95a9450b2c9cace2545f6
 2025-04-16 11:46:16 +02:00
Sharlatan Hellseher
d722e9ef15 gnu: python-glue-astronomy: Avoid deprecation failure in tests. 
* gnu/packages/astronomy.scm (python-glue-astronomy) [arguments]
<test-flags>: Skip one failing test.

Change-Id: I4dd3d3e1d56b75cf8e6479bdeacf2c391d206e9c
 2025-04-16 11:46:16 +02:00
Sharlatan Hellseher
bd5df72ce9 gnu: python-sanic: Scip more tests, simplify. 
* gnu/packages/python-web.scm (python-sanic) [arguments] <test-flags>:
Ignore all benchmark and typing tests. Skip more failing tests.
<phases>: Use default 'check.
[native-inputs]: Remove python-bandit, python-chardet, python-coverage,
python-cryptography, python-docutils, python-mypy, python-pygments,
python-pytest-benchmark, python-pytest-sanic, python-slotscheck,
python-towncrier, python-tox, and python-types-ujson; add
python-pytest-asyncio.

Change-Id: I8804114656fd76639939ba2fa50fb95d65b823ab
 2025-04-16 11:46:16 +02:00
Sharlatan Hellseher
09ebf09185 gnu: python-debug: Use G-Expressions. 
* gnu/packages/python.scm (python-debug): Use G-Expressions, fix build.

Change-Id: I940ec4fddcea03a258659ca044b0dad4948c4ed5
 2025-04-16 11:46:15 +02:00
Sharlatan Hellseher
907ae7b07d gnu: python-uvloop: Fix build. 
* gnu/packages/python-web.scm (python-uvloop): Fix unquote-splicing
error as seen in <https://ci.guix.gnu.org/build/9605318/log/raw>.

Change-Id: I26bba8d29913e01e037c678d943607a7c00f5647
 2025-04-16 11:46:15 +02:00
Sharlatan Hellseher
18e9141d01 gnu: python-uvloop: Fix indentation. 
* gnu/packages/python-web.scm (python-uvloop): Fix indentation.

Change-Id: I72f6674c870317ebec48933e2bb5744bae6e0387
 2025-04-16 11:46:15 +02:00
Sharlatan Hellseher
43bd9c7f77 gnu: python-asyncpg: Update to 0.30.0. 
* gnu/packages/databases.scm (python-asyncpg): Update to 0.30.0. Fix build.
[build-system]: Swap to pyproject-build-system
[propagated-inputs]: Remove python-typing-extensions; add
python-async-timeout.
[native-inputs]: Add python-distro, python-setuptools, and python-wheel.

Change-Id: Icb586671370ac2f6d30577383b257003eda6a4d5
 2025-04-16 11:46:15 +02:00
Sharlatan Hellseher
a5b507230c gnu: python-cftime: Fix tests. 
* gnu/packages/python-xyz.scm (python-cftime) [arguments] <phases>:
Remove 'remove-unwanted-dev-dependencies, add ''remove-unwanted-pytest-options.
[native-inputs]: Remove python-sphinx.

Change-Id: Ib196a6a3781da4067d287f62f5f92b72eb024de3
 2025-04-16 11:46:15 +02:00
Nicolas Graves
de961c303b gnu: Remove python-pytest-pep8. 
This package is outdated.

* gnu/packages/check.scm (python-pytest-pep8): Delete variable.
(python-pytest-flakes)[native-inputs]: Remove python-pytest-pep8.
* gnu/packages/machine-learning.scm (python-keras,
python-keras-applications)[native-inputs]: Remove python-pytest-pep8.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:15 +02:00
Nicolas Graves
ae7d115436 gnu: Remove python-pep8. 
* gnu/packages/python-xyz.scm (python-pep8): Delete variable.
(python-cliapp, python-ttystatus)[native-inputs]: Remove python-pep8.
* gnu/packages/radio.scm (chirp)[native-inputs]: Remove python-pep8.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:15 +02:00
Nicolas Graves
a41f421b66 gnu: python-unyt: Avoid deprecation failure in tests. 
* gnu/packages/python-science.scm (python-unyt)[arguments]
{test-flags}: Ignore failing test.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:15 +02:00
Nicolas Graves
fcc266cf25 gnu: python-h2: Fix test-flags. 
* gnu/packages/python-web.scm (python-h2)[arguments]{test-flags}:
Fix quoting.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-04-16 11:46:15 +02:00
Nicolas Graves
24ad03da5a gnu: python-anndata: Ignore failing test. 
* gnu/packages/python-xyz.scm (python-anndata)[arguments]{test-flags}:
Ignore test_read_write_X test.
 2025-04-16 11:46:15 +02:00
Nicolas Graves
e78dfd6b7b gnu: python-ipympl: Update to 0.9.2. 
* gnu/packages/jupyter.scm (python-ipympl): Update to 0.9.2.
[native-inputs]: Add python-hatchling.
 2025-04-16 11:46:15 +02:00
Nicolas Graves
6838baeffc gnu: Remove python-dictpath. 
* gnu/packages/python-xyz.scm (python-dictpath): Remove variable.
* gnu/packages/python-web.scm (python-openapi-core)[propagated-inputs]:
Remove unecessary python-dictpath.
 2025-04-16 11:46:15 +02:00
Nicolas Graves
885b745e15 gnu: behave: Remove python-nose native-input. 
* gnu/packages/check.scm (behave)[native-inputs]: Remove python-nose.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
2fbc7fb085 gnu: python-pyparsing: Update to 3.2.1. 
* gnu/packages/python-build.scm (python-pyparsing): Update to 3.2.1.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-flit-core.
(python-pyparsing-2.4.7)[native-inputs]: Add python-setuptools,
python-wheel.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
20c8141746 gnu: python-vcrpy: Update to 7.0.0. 
* gnu/packages/python-check.scm (python-vcrpy): Update to 7.0.0.
[native-inputs]: Remove python-flask, python-ipaddress, python-mock.
Add python-aiohttp, python-boto3, python-httpx, python-pytest-aiohttp,
python-pytest-asyncio, python-requests, python-tornado,
python-werkzeug.
[propagated-inputs]: Remove python-six.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
0165b28b86 gnu: Remove python-rednose. 
This package is broken with the latest python version, and is easy to
remove.

* gnu/packages/check.scm (python-rednose): Delete variable.
* gnu/packages/python-xyz.scm (python-sure) and
* gnu/packages/web.scm (python-httpretty):
[arguments]: Add 'remove-rednose-dependency in {phases}.
[native-inputs]: Remove python-rednose.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
31eb603647 gnu: python-pytest-runner: Update to 6.0.1. 
* gnu/packages/check.scm (python-pytest-runner): Update to 6.0.1.
[arguments]: Remove {phases}.
[native-inputs]: Remove python-pip, python-pypa-build. Add
python-pytest-checkdocs, python-pytest-enabler,
python-types-setuptools.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
5a13bc717a gnu: sdkmanager: Update python-urllib3. 
* gnu/packages/android.scm (sdkmanager)[inputs]: Switch to
python-urllib3-next.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
fb00a1ec45 gnu: python-peachpy: Update to 0.2.0-3.349e8f8. 
* gnu/packages/python-xyz.scm (python-peachpy): Update to
0.2.0-3.349e8f8.
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove {phases}. Add {test-target} to ignore a failing
test.
[native-inputs]: Remove python-nose, python-rednose. Add
python-pytest, python-wheel.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
8195252da9 gnu: python-pykdtree: Update to 1.3.9. 
* gnu/packages/python-xyz.scm (python-pykdtree): Update to 1.3.9.
[native-inputs]: Remove python-nose. Add python-cython, python-pytest,
python-setuptools, python-wheel.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
b160f49b59 gnu: python-multiprocessing-on-dill: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-multiprocessing-on-dill): Use pyproject-build-system.
[arguments]: Remove field.
[native-inputs]: Remove uneeded python-check-manifest. Add python-pytest.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
090f572edf gnu: python-cftime: Update to 1.6.4. 
* gnu/packages/python-xyz.scm (python-cftime): Update to 1.6.4.
[arguments]{phases}: Add phase 'remove-unwanted-dev-dependencies.
[native-inputs]: Remove python-check-manifest, python-pytest-cov. Add
python-setuptools.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
6783699f74 gnu: python-beartype: Update to 0.19.0. 
* gnu/packages/python-check.scm (python-beartype): Update to 0.19.0.
[arguments]: Remove former test-flags.
[native-inputs]: Remove python-setuptools, python-wheel. Add
python-hatchling, python-numpy and python-pygments.
 2025-04-16 11:46:14 +02:00
Nicolas Graves
7e8f8c0d3d gnu: python-pillow-heif: Update test-flags. 
* gnu/packages/python-xyz.scm (python-pillow-heif)[arguments]{test-flags}:
Update them.
[native-inputs]: Remove uneeded python-pylint.
 2025-04-16 11:46:13 +02:00
Nicolas Graves
a35f661489 gnu: python-uvicorn: Rename python-watchgod native-input. 
* gnu/packages/python-web.scm (python-uvicorn)[native-inputs]: Rename
python-watchgod to python-watchfiles. Add python-a2wsgi.
 2025-04-16 11:46:13 +02:00
Nicolas Graves
1e099d3e47 gnu: python-watchgod: Rename package to python-watchfiles. 
* gnu/packages/python-xyz.scm (python-watchgod): Define in terms of
'deprecated-package'.
[version]: Update to 1.0.4.
[build-system]: Switch to cargo-build-system.
[arguments]: Likewise.
[native-inputs]: Add maturin, python-dirty-equals,
python-pytest-timeout, python-wrapper. Remove python-pygments,
python-pytest-sygar, python-setuptools and python-wheel.
(python-watchfiles): New variable, formerly known as
"python-watchgod".
 2025-04-16 11:46:13 +02:00
Nicolas Graves
b18cac33b4 gnu: Add rust-notify-7. 
* gnu/packages/crates-io.scm (rust-notify-7): New variable.
(rust-notify-6): Inherit from rust-notify-7.
 2025-04-16 11:46:13 +02:00