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Author SHA1 Message Date
Ricardo Wurmus
b460f89d93
gnu: tadbit: Add missing input. 
* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib.

Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
c085139bc9
gnu: python-captum: Update to 0.7.0. 
* gnu/packages/machine-learning.scm (python-captum): Update to 0.7.0.
[propagated-inputs]: Add python-tqdm.

Change-Id: I8917b6e294fe08077a3af4423deefa9769ba9384
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
efd98a9c45
gnu: python-poliastro: Make compatible with latest matplotlib. 
* gnu/packages/astronomy.scm (python-poliastro)[arguments]: Add phase
'matplotlib-compatibility; disable test_porkchop_plotting.

Change-Id: Ie70673c69d4bdfa424e324d2848e9567360b03ef
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
2c94760dcb
gnu: python-cleanlab: Disable test_aux_inputs, enable other tests. 
* gnu/packages/machine-learning.scm (python-cleanlab)[arguments]: Remove
'disable-bad-tests phase and ignore test files in #:test-flags instead;
disable test_aux_inputs test, but re-enable tests from
test_multilabel_classification.py.
[native-inputs]: Add python-pytest-lazy-fixture.

Change-Id: I77a16768ff61215e918c98bccd3efa216fb30d7f
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
447876fa0d
gnu: python-scanpy: Update to 1.9.6. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.6.
[arguments]: Update test flags.
[native-inputs]: Add python-hatchling, python-hatch-vcs, and
python-pytest-nunit.

Change-Id: I6d4dcd267a076c5697ed103650841f520dc9917f
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
6a2f1863e7
gnu: Add python-pytest-nunit. 
* gnu/packages/check.scm (python-pytest-nunit): New variable.

Change-Id: Ic67c973460f09b15bf683f70040a3f5e4381108d
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
c647bd42a3
gnu: python-seaborn: Update to 0.13.1. 
* gnu/packages/python-xyz.scm (python-seaborn): Update to 0.13.1.
[propagated-inputs]: Add python-ipykernel, python-mypy, python-nbconvert,
python-numpydoc, python-pyyaml, and python-statsmodels.
[native-inputs]: Add python-flake8, python-pre-commit, python-pytest-cov, and
python-pytest-xdist; remove python-pypa-build.

Change-Id: Id1ed6cfaf7e0950e99c06900fd68fb1ab884bee0
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
82b7c3077f
gnu: python-matplotlib: Update to 3.8.2. 
* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.8.2.
[build-system]: Use pyproject-build-system.
[arguments]: Enable more tests; simplify custom 'check phase.
[propagated-inputs]: Remove gobject-introspection, python-cairocffi,
python-certifi, python-pygobject, python-pytz, python-six, and
python-wxpython; add python-contourpy and python-importlib-resources.
[native-inputs]: Add pybind11.

Change-Id: Ie34826882fdcc20fac3b09130bcd0f4ad4f76b07
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
c7646437a2
gnu: Add python-contourpy. 
* gnu/packages/python-xyz.scm (python-contourpy): New variable.

Change-Id: Icbbe4a358242095fae36639c5c039c029eea4ee3
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
037cb397c1
gnu: python-kiwisolver: Update to 1.4.5. 
* gnu/packages/maths.scm (python-kiwisolver): Update to 1.4.5.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Add python-typing-extension.
[native-inputs]: Add python-cppy, python-pytest, and python-setuptools-scm.

Change-Id: Iea75440dc58fa342dcf4a2a381b6dcc17e71e618
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
9ea9346168
gnu: Add python-cppy. 
* gnu/packages/python-xyz.scm (python-cppy): New variable.

Change-Id: I584fcddc3430960098d65f1916278a7473249a87
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
fa5d8c839a
gnu: python-umap-learn: Update to 0.5.5. 
* gnu/packages/machine-learning.scm (python-umap-learn): Update to 0.5.5.
[build-system]: Use pyproject-build-system.
[arguments]: Remove 'numpy-compatibility and custom 'check phases.

Change-Id: I2123f66519730d43e454d9536e8cb7b6c4569d56
 2024-01-16 12:44:35 +01:00
Ricardo Wurmus
ca1749c243
gnu: python-pynndescent: Update to 0.5.11. 
* gnu/packages/machine-learning.scm (python-pynndescent): Update to 0.5.11.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
[propagated-inputs]: Add python-importlib-metadata.

Change-Id: I14f15ea98157ed15b360971c30fe00c5f00af4a7
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
247c427302
gnu: python-scikit-learn: Update to 1.3.2. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.3.2.
[build-system]: Use pyproject-build-system.
[arguments]: Move test flags to #:test-flags.
[native-inputs]: Replace python-cython with python-cython-0.29.35.

Change-Id: Iac6107dae752c42d9f57448a66eed0526974d57e
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
e759380796
gnu: python-matplotx: Disable test_png test. 
* gnu/packages/python-xyz.scm (python-matplotx)[arguments]: Disable test_png
test.

Change-Id: I19a954786d828a1b717c9c4021ad7f5c6172366c
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
2057f778a4
gnu: python-pypng: Update to 0.20220715.0. 
* gnu/packages/python-xyz.scm (python-pypng): Update to 0.20220715.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add 'pre-check phase.
[native-inputs]: Add python-pytest.

Change-Id: Ic47c653f94a688048383eba216f01d7987625680
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
e2c76bdd83
gnu: python-scikit-image: Update to 0.22.0. 
* gnu/packages/python-science.scm (python-scikit-image): Update to 0.22.0.
[source]: Fetch from git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; remove custom 'build phase; simplify 'check
phase; enable all tests.
[propagated-inputs]: Add python-lazy-loader.
[native-inputs]: Add meson-python, python-numpydoc, python-packaging, and
python-wheel.

Change-Id: I00ede026a7941eae36157106f753a21fb64099c3
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
32edfc4a85
gnu: python-imageio: Update to 2.33.1. 
* gnu/packages/python-xyz.scm (python-imageio): Update to 2.33.1.
[propagated-inputs]: Remove python-psutil; add python-tifffile.
[native-inputs]: Add python-black, python-flake8, python-fsspec, and
python-pytest-cov.

Change-Id: I5c64d939f5ee94ac9ec8fdbd7b51cd978b7df0fb
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
6fbbffd6ef
gnu: python-lazy-loader: Update to 0.3. 
* gnu/packages/python-xyz.scm (python-lazy-loader): Update to 0.3.
[native-inputs]: Add python-pre-commit.

Change-Id: Id4f8b61e6e60dd6da04beb8c1e4d064dc34d994c
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
299455fef2
gnu: python-tifffile: Update to 2023.12.9. 
* gnu/packages/python-xyz.scm (python-tifffile): Update to 2023.12.9.
[propagated-inputs]: Remove python-imagecodecs.
[native-inputs]: Add python-pytest.

Change-Id: I2567bef390e286ed4399cc67b80a9df503f53c0a
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
accd091fff
gnu: python-scipy: Update to 1.11.4. 
* gnu/packages/python-science.scm (python-scipy): Update to 1.11.4.
[arguments]: Use mesonpy backend.
[inputs]: Replace pybind11 with pybind11-2.10.
[native-inputs]: Add python-click, python-doit, python-pooch, and
python-pydevtool; replace python-cython with python-cython-0.29.35.

Change-Id: I4b26e1b6382899bba24f84461f154e97765e08f5
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
22c5d2d835
gnu: meson-python: Update to 0.15.0. 
* gnu/packages/build-tools.scm (meson-python): Update to 0.15.0.
[arguments]: Add phase 'delete-directory.
[propagated-inputs]: Add python-cython, python-pyproject-metadata-0.7, and
python-typing-extensions.
[native-inputs]: Add python-pytest-cov.

Change-Id: I412af929c9e0485aa2a15e316d247f58e6f3477b
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
08f48f2939
gnu: Add python-pydevtool. 
* gnu/packages/python-xyz.scm (python-pydevtool): New variable.

Change-Id: I325b81fa6421094a5a64084c06e66b8fa136e270
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
1c91d45724
gnu: Add python-pyproject-metadata-0.7. 
* gnu/packages/python-xyz.scm (python-pyproject-metadata-0.7): New variable.

Change-Id: I7c47c911fa2a33c0b5711b0009f31b3e32c1c1d7
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
1fb5d95e75
gnu: python-doit: Update to 0.36.0. 
* gnu/packages/python-xyz.scm (python-doit): Update to 0.36.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable test_execute test.
[propagated-inputs]: Remove python-pyinotify; add python-importlib-metadata.
[description]: Add missing spaces between two sentences.

Change-Id: I1d046201c9bef63477f8fb0a2f8494bffbbbc711
 2024-01-16 12:44:34 +01:00
Ricardo Wurmus
1d91698478
gnu: Add pybind11-2.10. 
* gnu/packages/python-xyz.scm (pybind11-2.10): New variable.

Change-Id: Ia7915af3baca36b0677d3f762046585abc473f56
 2024-01-16 12:44:33 +01:00
Ricardo Wurmus
ce451cdcb8
gnu: Add python-cython-0.29.35. 
* gnu/packages/python-xyz.scm (python-cython-0.29.35): New variable.

Change-Id: I09ec851a2051e885f6417524bbeeb81b743bef0b
 2024-01-16 12:44:33 +01:00
Ricardo Wurmus
33d0a549e9
gnu: Add python-pydoc-markdown. 
* gnu/packages/python-xyz.scm (python-pydoc-markdown): New variable.

Change-Id: I03e45c2b87f626f7a8113d785c72c14a301d79be
 2024-01-16 12:36:08 +01:00
Ricardo Wurmus
b05fe5c763
gnu: python-yapf: Update to 0.32.0. 
* gnu/packages/python-xyz.scm (python-yapf): Update to 0.32.0.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-pytest.
[propagated-inputs]: Add python-importlib-metadata, python-platformdirs, and
python-tomli.

Change-Id: I30fa0b9d643f6585624da87d5c1a1edbb59425c4
 2024-01-16 12:21:07 +01:00
Ricardo Wurmus
1fcf3d2a0c
gnu: Add python-docspec-python. 
* gnu/packages/python-xyz.scm (python-docspec-python): New variable.

Change-Id: Ic607d0a34a8601dd464251edd8c8509314b7489c
 2024-01-16 11:56:34 +01:00
Ricardo Wurmus
8721b9c1fb
gnu: Add python-nr-util. 
* gnu/packages/python-xyz.scm (python-nr-util): New variable.

Change-Id: I26dda5e5bc03334fb476e3f1fd2fa6aaf93a91c3
 2024-01-16 11:37:07 +01:00
Artyom V. Poptsov
21f5d20d68
gnu: go-github-com-arceliar-ironwood: Update to v0.0.0-20231127131626-465b82dfb5bd. 
* gnu/packages/golang.scm (go-github-com-arceliar-ironwood): Update to
  v0.0.0-20231127131626-465b82dfb5bd.

Change-Id: Ia94d7c88e54d33f7bb7b5054a757d7ef203d47c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-15 23:18:58 +00:00
Artyom V. Poptsov
5358b308a1
gnu: yggdrasil: Update to 0.5.4. 
* gnu/packages/networking.scm (yggdrasil): Update to 0.5.4.

Change-Id: I4f386e1b69627b0c5a6095c42274b8a8bff8bfd9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-15 23:18:35 +00:00
Troy Figiel
eb0f35e16d
gnu: hypercorn: Reformat with guix style. 
* gnu/packages/python-web.scm (hypercorn): Reformat with guix style.
 2024-01-15 22:43:58 +00:00
Troy Figiel
68763a00a3
gnu: hypercorn: Adjust inputs. 
* gnu/packages/python-web.scm (hypercorn)[propagated-inputs]: Add
python-exceptiongroup and python-tomli. Remove python-toml and
python-typing-extensions.
[native-inputs]: Remove python-mock.
 2024-01-15 22:43:35 +00:00
Ricardo Wurmus
287dee537b
gnu: Remove python-tslearn. 
This package now lives in the guix-science channel.

* gnu/packages/machine-learning.scm (python-tslearn): Remove variable.

Change-Id: I655df3417d258cb1231746626817fde9628e9569
 2024-01-15 23:35:25 +01:00
Ricardo Wurmus
ddde736722
gnu: Add python-docspec. 
* gnu/packages/python-xyz.scm (python-docspec): New variable.

Change-Id: I3103bde3483273a335156b38de742f493fd366f1
 2024-01-15 23:06:15 +01:00
Ricardo Wurmus
12ae026e51
gnu: Add python-databind-json. 
* gnu/packages/python-xyz.scm (python-databind-json): New variable.

Change-Id: Iaab64e28ba6772c14704ff67cffab21a2f555460
 2024-01-15 23:06:15 +01:00
Ricardo Wurmus
97692be948
gnu: Add python-databind-core. 
* gnu/packages/python-xyz.scm (python-databind-core): New variable.

Change-Id: I45bf0ec5ef123ea20c50e2ca3caf930bfba45eea
 2024-01-15 23:06:15 +01:00
Ricardo Wurmus
6b81503bae
gnu: Add python-typeapi. 
* gnu/packages/python-xyz.scm (python-typeapi): New variable.

Change-Id: Id89f3152bcd593d677c4fcb7c98d586cd50e820b
 2024-01-15 23:06:15 +01:00
Ricardo Wurmus
7dfe41aa71
gnu: Add python-nr-stream. 
* gnu/packages/python-xyz.scm (python-nr-stream): New variable.

Change-Id: I59489156e4675a64a31b1cb7f62b7c845c005ce8
 2024-01-15 23:06:15 +01:00
Ricardo Wurmus
aa51d1d25f
gnu: Add python-nr-date. 
* gnu/packages/python-xyz.scm (python-nr-date): New variable.

Change-Id: I4251aef073df29ccada70f1398bce38cfb8962ba
 2024-01-15 23:06:15 +01:00
Ricardo Wurmus
7a2d128779
gnu: Add python-namex. 
* gnu/packages/python-xyz.scm (python-namex): New variable.

Change-Id: I02d4ed5e426f0b432c27086aa90628ae54759ca2
 2024-01-15 23:06:15 +01:00
Troy Figiel
19db1551dc
gnu: python-requests-kerberos: Enable tests. 
* gnu/packages/python-web.scm (python-requests-kerberos): Enable tests.
[source]: Replace the PyPI release by the Github release.
[build-system]: Swap to pyproject-build-system.
[native-inputs]: Add python-pytest and python-pytest-mock.

Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Iea750cf722293c4054a6c6e43787806f8f2fd5e2
 2024-01-15 21:47:27 +00:00
Troy Figiel
da3764b75c
gnu: python-requests-kerberos: Fix build. 
* gnu/packages/python-web.scm (python-requests-kerberos)[propagated-inputs]:
Add python-gssapi.

Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I65d1fac0339a119e7a4912d5db150b4adb7586ad
 2024-01-15 21:43:20 +00:00
Sharlatan Hellseher
7061f0b1d0
gnu: python-pyspnego: Propagate python-krb5. 
* gnu/packages/python-xyz.scm (python-pyspnego)[propagated-inputs]: Add
python-krb5.

Change-Id: I2c8ccbd66394cb90ea047f7327d05ecbfe2ec22d
 2024-01-15 21:29:49 +00:00
Troy Figiel
bba2fa646d
gnu: Add python-krb5. 
* gnu/packages/python-xyz.scm (python-krb5): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-01-15 21:15:09 +00:00
Sharlatan Hellseher
1e3f1f9f92
gnu: Remove python-activepapers. 
<https://issues.guix.gnu.org/68425>

This package fails to build and has been not maintained since 2017.

* gnu/packages/python-xyz.scm (python-activepapers): Remove variable.

Reported-by: Troy Figiel <troy@troyfigiel.com>
Change-Id: Id1e968cd4e06919a80ad05e5c8d3fb207426fdde
 2024-01-15 20:56:22 +00:00
Ludovic Courtès
162d6a2fdd
gnu: hpcguix-web: Add explicit dependency on Guile-GnuTLS. 
This is necessary in hpcguix-web 0.4.1 to connect to
https://disarchive.guix.gnu.org.

* gnu/packages/web.scm (hpcguix-web)[arguments]: In ‘wrap-program’ phase,
add guile-gnutls to the wrapper’s search path.
[inputs]: Add GUILE-GNUTLS.

Change-Id: Ic4d6f65adeb763a404fc24c7e1c87fd7d26550c7
 2024-01-15 08:57:01 +01:00
Tanguy Le Carrour
f6afaf58b0
gnu: fish-foreign-env: Update to 0.20230823. 
* gnu/packages/shells.scm (fish-foreign-env): Update to 0.20230823.
[arguments]: Do no substitute in file that no longer exists.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Change-Id: I04138c1d3e8c174b2197e5ca60aaca4caa5453cc
 2024-01-14 23:00:04 +01:00