Nicolas Graves
c4bc6cf49f
gnu: Remove python-cookies.
...
This is a leaf package in python, broken and undevelopped for 10 years.
* gnu/packages/python-web.scm (python-cookies): Delete variable.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:29 +02:00
Nicolas Graves
d7817735b2
gnu: python-port-for: Update to 0.7.4.
...
* gnu/packages/python-web.scm (python-port-for): Update to 0.7.4.
[build-system]: Switch to pyproject.
[native-inputs]: Remove python-mock. Add python-setuptools,
python-wheel.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:29 +02:00
Nicolas Graves
8021ffb34c
gnu: python-rq-scheduler: Update to 0.14.
...
* gnu/packages/databases.scm (python-rq-scheduler): Update to 0.14.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore failing tests. They fail because of
mcron's requirements to be run with root when -u flag is used.
{phases}: Remove 'check phase replacement.
[native-inputs]: Add python-crontab, python-freezegun, python-pytest,
python-setuptools, python-wheel. Remove which.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:29 +02:00
Nicolas Graves
180a69e23a
gnu: python-stone: Update to 3.3.9.
...
* gnu/packages/python-xyz.scm (python-stone): Update to 3.3.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject.
[arguments]: Remove field.
[propagated-inputs]: Add python-jinja2, python-packaging.
[native-inputs]: Add python-setuptools, python-wheel. Remove
python-coverage, python-mock.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:29 +02:00
Nicolas Graves
4fe1a73ab8
gnu: python-crontab: Update to 3.2.0.
...
* gnu/packages/python-xyz.scm (python-crontab): Update to 3.2.0.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore test.
{phases}: Remove phase 'disable-failing-tests. Add phase
default-to-mcron.
[inputs]: Add mcron.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:29 +02:00
Nicolas Graves
b717b894a0
gnu: python-rq: Update to 2.3.1.
...
* gnu/packages/databases.scm (python-rq): Update to 2.3.1.
[build-system]: Switch to pyproject.
[arguments]{phases}: Delete 'check phase replacement. Improve style.
[native-inputs]: Add python-hatchling.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
22416fb20d
gnu: python-furl: Update to 2.1.4.
...
* gnu/packages/python-web.scm (python-furl): Update to 2.1.4.
[build-system]: Swtich to pyproject.
[arguments]{test-flags}: Ignore failing tests.
[propagated-inputs]: Sort.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
6363f5002c
gnu: python-pgpy: Fix tests.
...
* gnu/packages/python-crypto.scm (python-pgpy): Fix tests.
[build-system]: Switch to pyproject.
[arguments]{phases}: Remove argument.
{test-flags}: Ignore failing tests.
[native-inputs]: Add python-setuptools.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
9938b7cc49
gnu: python-duniterpy: Update to 1.2.1.
...
* gnu/packages/finance.scm (python-duniterpy): Update to 1.2.1.
[source]: Switch to git-fetch to get tests.
[arguments]: Remove field.
[native-inputs]: Replace python-poetry-core by
python-poetry-core-next. Add python-pytest.
[propagated-inputs]: Remove python-attrs.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
f29a7770d3
gnu: Add python-poetry-core-next.
...
* gnu/packages/python-build.scm (python-poetry-core-next): New variable.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
e58d654373
gnu: python-pysnptools: Fix build and enable tests.
...
* gnu/packages/bioinformatics.scm (python-pysnptools): Fix build and enable
tests.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Add 'patch-data-path and 'loosen-requirements phases.
(pysnptools-examples-files): Add origin.
(bgen-sample-files): Add origin.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
db14ce5c4d
gnu: python-bed-reader: Fix build and enable tests.
...
* gnu/packages/bioinformatics.scm (python-bed-reader): Fix build and enable tests.
[source]{snippet}: Delete bundled website-related javascript.
{patches}: Use the store-cached instead of pooch-cached samples.
[arguments]{tests?}: Enable them.
{cargo-test-flags}: Skip doc tests. Skip failing tests.
{cargo-inputs}: Improve style.
{cargo-development-inputs}: Improve style.
{phases}: Add phases 'set-data-path, 'patch-data-path to use
store-cached samples for library and tests. Rewrite phase
'prepare-python-module to rely more on the existing info in
pyproject.toml. Rewrite phase 'check-python entirely, and
marginaly rewrite phase 'install-python-library to match 'check-python
phase style.
{modules}: Adapt accordingly.
{propagated-inputs}: Remove python-pooch. Add python-scipy.
(bed-sample-files): Add origin, used in python-bed-reader.
* gnu/packages/patches/python-bed-reader-use-store-samples.patch: Add
patch.
* gnu/local.mk: Record patch.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
e8e46bbeb5
gnu: python-qasync: Ignore failing test.
...
* gnu/packages/python-xyz.scm (python-qasync)[arguments]{test-flags}:
Ignore failing tests.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
c42f6d6a18
gnu: python-pgmpy: Update to 1.0.0.
...
* gnu/packages/statistics.scm (python-pgmpy): Update to 1.0.0.
[arguments]{test-flags}: Ignore failing tests.
[native-inputs]: Add python-pyro-ppl, python-setuptools, python-wheel,
python-xgboost.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
984a35fbde
gnu: python-botorch: Update to 0.13.0.
...
* gnu/packages/machine-learning.scm (python-botorch): Update to
0.13.0.
[native-inputs]: Add python-pyre-extensions.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
81265ddfa7
gnu: python-gpytorch: Update to 1.14.
...
* gnu/packages/machine-learning.scm (python-gpytorch): Update to 1.14.
[arguments]{test-flags}: Ignore additional failing test.
[propagated-inputs]: Add python-jaxtyping.
[native-inputs]: Add python-setuptools, python-wheel.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:28 +02:00
Nicolas Graves
691ef2ca0f
gnu: python-botorch: Add missing native-inputs.
...
* gnu/packages/machine-learning.scm (python-botorch)[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
fd9b448bed
gnu: python-gpytorch: Remove uneeded inputs.
...
* gnu/packages/machine-learning.scm (python-gpytorch): Remove uneeded
inputs.
[arguments]{test-flags}: Ignore costly examples tests.
[native-inputs]: Remove python-coverage, python-flake8,
python-flake8-print, python-twine.
Change-Id: Id3b9537d9f3306cc4a8e0eed19aabd5732854813
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:27 +02:00
Nicolas Graves
c326653ea5
gnu: python-linear-operator: Update to 0.6.
...
* gnu/packages/machine-learning.scm (python-linear-operator): Update
to 0.6.
[propagated-inputs]: Remove python-typeguard. Add python-mpmath.
[native-inputs]: Remove python-flake8, python-flake8-print,
python-twine. Add python-typeguard, python-wheel.
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16 11:46:27 +02:00
Nicolas Graves
c1b3887d56
gnu: python-lcapy: Add missing native-inputs.
...
* gnu/packages/engineering.scm (python-lcapy)[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
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
