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b58bf70620d373bebfa4ebc72949f863de7a515e
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146102 Commits

Author SHA1 Message Date
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
Sharlatan Hellseher
aae586b0e0 gnu: Remove python-asynctest. 
No updates since 2019, fails to build and has no users in Guix.  See
<https://github.com/Martiusweb/asynctest/issues/163> there is a standard
'unittest.IsolatedAsyncioTestCase' drop-in replacement.

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

Change-Id: If63cfd698a74f86c6895db04e0d7cd02728ae757
 2025-04-16 11:46:20 +02:00
Sharlatan Hellseher
9c3f7ebb9c gnu: python-asyncua: Fix build. 
python-asynctest has not been updated for 6y and fails to build, but
it's optional in tests. This change removes it from native inputs.

* gnu/packages/engineering.scm (python-asyncua): Update to 1.1.5.
[source]: Mention about the third party submodule on recursive option.
[native-inputs]: Remove python-asynctest and python-pytest-runner; add
python-pytest.

Change-Id: I9d268c43ebe97fcaacc5125e1038f6ff371d39b2
 2025-04-16 11:46:20 +02:00
Sharlatan Hellseher
2999dea81b gnu: python-asn1tools: Update to 0.167.0 and fix build. 
* gnu/packages/python-xyz.scm (python-asn1tools): Update to 0.167.0, fix
build.
[build-system]: Swap to pyproject-build-system.
[arguments] <test-flags>: Skip 7 failing tests.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: I36d12d9bfe2fd6d62a75dd0d30de42a782c4a746
 2025-04-16 11:46:20 +02:00
Sharlatan Hellseher
5101eb697e gnu: nikola: Skip one test. 
* gnu/packages/python-xyz.scm (nikola) [arguments] <test-flags>: Skip
one test.

Change-Id: I10d4edf07b7c7b4e19020773215da5eae27cd0f4
 2025-04-16 11:46:20 +02:00
Sharlatan Hellseher
633e0ca804 gnu: gita: Improve package style. 
* gnu/packages/version-control.scm (gita): Use G-expressions, refresh
style.
[native-inputs]: Remove git; add git-minimal/pinned.

Change-Id: I61707538f5248e14207aa2ca0931286741697ed8
 2025-04-16 11:46:20 +02:00
Sharlatan Hellseher
799383555a gnu: gita: Fix indentation. 
* gnu/packages/version-control.scm (gita): Fix indentation.

Change-Id: Ib918212b2f6659897c00a4c452776cf0e5d36c35
 2025-04-16 11:46:19 +02:00
Sharlatan Hellseher
ec5a9784c9 gnu: gita: Update to 0.16.7.2. 
* gnu/packages/version-control.scm (gita): Update to 0.16.7.2.
[build-system]: Swap to pyproject-build-system.
[arguments] <test-flags>: Ignore one test file.
<phases>: Use default 'check, add 'pre-check.
[phases] {install-shell-completions}: Fix path to completion files.
[propagated-inputs]: Remove python-pyyaml; add python-argcomplete.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I3b53b804c4b436613c5463911716f1a832064517
 2025-04-16 11:46:19 +02:00
Sharlatan Hellseher
8618fd5283 gnu: Remove python-nose-randomly. 
Deprecated: "This repository was archived by the owner on Feb 8,
2019. It is now read-only."; fails to build, has no user in Guix.

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

Change-Id: I1866da62f092fefc7f6167fa8f80ad33402bfb40
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
8a0e82f26d gnu: python-biopython-1.73: Make compatible with Python 3.11. 
* gnu/packages/bioinformatics.scm (python-biopython-1.73)[arguments]: Add
phases 'python3.11-compatibility, 'numpy-compatibility, 'set-home,
'build-extensions, and 'patch-tests.

Change-Id: Iac6b0638dd5699a7b11862bff9cce1e7b2fee49b
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
ca3d1683d7 gnu: python-biopython: Update to 1.85. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.85.
[arguments]: Add phase 'numpy-compatibility; replace 'check phase.

Change-Id: I4e3ef0d9a357155e36ef61052af4d90f4fa95d5e
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
177935dc70 gnu: cpp-httplib: Update to 0.20.0. 
* gnu/packages/cpp.scm (cpp-httplib): Update to 0.20.0.

Change-Id: I279c00feb30d11b636c122b6ba42ef7bb852012e
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
842cca0056 gnu: mididings: Update to 0-2.bc71ea9. 
This also makes mididings compatible with Python 3.11.

* gnu/packages/music.scm (mididings): Update to 0-2.bc71ea9.
[build-system]: Use meson-build-system.
[inputs]: Add python.

Change-Id: I3a68cd4f5f8e9cf3c89cc7bb178e03ec9d045494
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
7628b065f0 gnu: guitarix: Make compatible with Python 3.11. 
* gnu/packages/audio.scm (guitarix)[arguments]: Add phase
'python3.11-compatibility.

Change-Id: I09d5517f0d2cbe0b4b888f812cc8109f6a5f1f08
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
589a74c25a gnu: mypaint: Make compatible with Python 3.11. 
* gnu/packages/image.scm (mypaint)[arguments]: Add phase
'python3.11-compatibility.

Change-Id: I4e103ad169148127c388a40b999b1a0ae4868f4e
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
96d6060e7c gnu: blueman: Use G-expressions. 
* gnu/packages/networking.scm (blueman)[arguments]: Use G-expressions to avoid
ASSOC-REF.

Change-Id: I38a6e0487fdf1597b89bd395c712b9da672daef1
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
f4579a4fdb gnu: blueman: Update to 2.4.4. 
* gnu/packages/networking.scm (blueman): Update to 2.4.4.

Change-Id: I1e86739e1410e12deea05c726a13bbfa5f8858e0
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
c683efc2ef gnu: aubio: Use JACK 2. 
* gnu/packages/audio.scm (aubio)[inputs]: Replace jack-1 with jack-2.

Change-Id: I5f3ecdaef3852b6d21caea3135ddb1764d712e48
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
5d9eb70354 gnu: aubio: Make compatible with Python 3.11. 
* gnu/packages/audio.scm (aubio)[arguments]: Use G-expression; add phase
'python3.11-compatibility.

Change-Id: I6739a18db4c1642dfca9299a821292a254726695
 2025-04-16 11:46:19 +02:00
Ricardo Wurmus
93878712a2 gnu: Add python-pyemd. 
* gnu/packages/python-xyz.scm (python-pyemd): New variable.

Change-Id: Ibdbbebd22616aa1a83ad721d3a96caa75ab7e1b1
 2025-04-16 11:46:18 +02:00
Ricardo Wurmus
b744e8a144 gnu: python-funsor: Disable one test. 
* gnu/packages/machine-learning.scm (python-funsor)[arguments]: Disable
test_function_of_numeric_array.

Change-Id: I76f38abb3db01f8732e0b60dfa65690d1b98db4a
 2025-04-16 11:46:18 +02:00