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Author SHA1 Message Date
Ricardo Wurmus
6318f27f9c
gnu: python-scikit-survival: Add missing input. 
* gnu/packages/python-science.scm (python-scikit-survival)[native-inputs]: Add
python-setuptools.

Change-Id: I52e98c787cec226590f21c98e4287a41fb41f3d3
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
334707c78f
gnu: python-qdldl: Add missing input. 
* gnu/packages/python-science.scm (python-qdldl)[native-inputs]: Add
python-wheel.

Change-Id: I6bca560b20a9c259eae95c09edcf10ead685ec21
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
9afceff50e
gnu: python-osqp: Add missing inputs. 
* gnu/packages/python-science.scm (python-osqp)[native-inputs]: Add
python-setuptools and python-wheel.

Change-Id: Ief43d97442a98935dea1499c67e022e9beb5359e
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
0d80ffd4dc
gnu: python-scikit-learn-extra: Disable one test. 
* gnu/packages/machine-learning.scm (python-scikit-learn-extra)
[arguments]: Disable one test.

Change-Id: Idee17402250a55ca564724f00550ef36664982f6
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
48131cec81
gnu: python-scikit-fuzzy: Add missing inputs. 
* gnu/packages/python-science.scm (python-scikit-fuzzy)[native-inputs]: Add
python-setuptools and python-wheel.

Change-Id: Idbaf5fa622b3584f8fd348ec0783605936d3bf41
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
a3657b1a98
gnu: python-scikit-allel: Update to 1.3.13. 
* gnu/packages/python-science.scm (python-scikit-allel): Update to 1.3.13.
[propagated-inputs]: Remove python-click.
[native-inputs]: Remove python-scipy.

Change-Id: I3c29bd3d9f87d0866da747c344740bad71cae1c3
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
aed3995e60
gnu: python-resolvelib: Update to 1.1.0b1. 
* gnu/packages/python-xyz.scm (python-resolvelib): Update to 1.1.0b1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ida8eb599bcfc02e84fc95ac276fba4ba217a6511
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
c5b8e1429d
gnu: python-resampy: Update to 0.4.3. 
* gnu/packages/audio.scm (python-resampy): Update to 0.4.3.
[arguments]: Remove.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I79d0a460d4646c5fde3aec9314d9ccc6380002de
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
5d2d250333
gnu: python-pytest-tornado5: Add missing inputs. 
* gnu/packages/check.scm (python-pytest-tornado5)[native-inputs]: Add
python-setuptools and python-wheel.

Change-Id: I0b64ac5f3e50893cb3fab518c9779d2cd7b9c6a9
 2025-01-16 10:17:30 +01:00
Ricardo Wurmus
31eb69204f
gnu: Remove python-pathlib. 
This package is obsolete, the module it provides is part of the standard
library, and the package has no users.

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

Change-Id: I8c724ba7b62ad5602f6abdb4e5fdaf2806180ab5
 2025-01-16 10:17:29 +01:00
Ricardo Wurmus
8fba804af0
gnu: rust-jiter-0.2: Add missing input. 
* gnu/packages/crates-io.scm (rust-jiter-0.2)[native-inputs]: Add
python-minimal-wrapper.

Change-Id: Ieab1e0a1e3329528fc21a160669e7ea8376c0e5f
 2025-01-16 10:17:29 +01:00
Ricardo Wurmus
5a89243348
gnu: python-cachecontrol-0.11: Add missing inputs. 
* gnu/packages/python-web.scm (python-cachecontrol-0.11)[native-inputs]: Add
python-setuptools and python-wheel.

Change-Id: I02091636a09a92093af109b044614fe617a5dd4c
 2025-01-16 10:17:29 +01:00
Ricardo Wurmus
e83f4e980e
gnu: python-liana-py: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.4.0.
[arguments]: Adjust disabled tests.

Change-Id: I9245285e2d043b5e7cbce5fb95a30982cd981597
 2025-01-16 10:17:29 +01:00
Ricardo Wurmus
3b88afa1d9
gnu: python-mizani: Add missing input. 
* gnu/packages/python-xyz.scm (python-mizani)[native-inputs]: Add
python-wheel.

Change-Id: I9a1a7a4ee38db7a48e14069efb2b7b97dad32a80
 2025-01-16 10:17:29 +01:00
Ricardo Wurmus
a226723f23
gnu: python-decoupler-py: Add missing input. 
* gnu/packages/bioinformatics.scm (python-decoupler-py)[native-inputs]: Add
python-wheel.

Change-Id: I37b8162e0dde4513b3a6f94455315489d7d08499
 2025-01-16 10:17:29 +01:00
Ricardo Wurmus
03239c399c
gnu: python-cell2cell: Add missing input. 
* gnu/packages/bioinformatics.scm (python-cell2cell)[native-inputs]: Add
python-wheel.

Change-Id: I79015fa48c976489d4c1182cb4506aae139325ad
 2025-01-16 10:17:29 +01:00
Ricardo Wurmus
046f2594ab
gnu: python-gseapy: Add missing input. 
* gnu/packages/bioinformatics.scm (python-gseapy)[native-inputs]: Add
python-wheel.

Change-Id: I0ce3d3aeb5aa3fb1ab3f2aa524b066738cf9046a
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
06990f27c2
gnu: python-cattrs: Disable failing test. 
* gnu/packages/python-xyz.scm (python-cattrs)[arguments]: Disable one more
test.

Change-Id: I8296abaa2faa745404354cb26f0d08024e7960c8
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
72b411475a
gnu: python-mudata: Update to 0.3.1. 
* gnu/packages/bioinformatics.scm (python-mudata): Update to 0.3.1.
[arguments]: Add phase 'pretend-version.
[native-inputs]: Remove python-flit-core; add python-hatch-vcs and
python-hatchling.

Change-Id: I87b8dc6ec557e0ca69930d82db7d6e64727228e9
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
310a895029
gnu: python-locust: Disable some more tests. 
* gnu/packages/benchmark.scm (python-locust)[arguments]: Update list of
disabled tests.

Change-Id: I3d6d070a1cc771c006530454b0bb9506287bbe6b
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
d5d29afa84
gnu: python-locust: Update to 2.32.5. 
* gnu/packages/benchmark.scm (python-locust): Update to 2.32.5.
[source]: Get from git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Update list of disabled tests; remove custom 'check phase; add
phase 'fix-version.
[propagated-inputs]: Remove python-flask-basicauth and python-roundrobin; add
python-flask-login, python-setuptools, and python-tomli.
[native-inputs]: Add nss-certs-for-test, python-poetry-core,
and python-poetry-dynamic-versioning; remove python-mock and
python-setuptools-scm.

Change-Id: I5e7203d48eda9279531c9d3060d81d91974dee6e
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
9b67859ec7
gnu: python-flask-assets: Update to 2.1.0-1.62efd23. 
* gnu/packages/python-web.scm (python-flask-assets): Update to
2.1.0-1.62efd23.
[source]: Fetch from git repository.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add nss-certs-for-test, python-pytest, python-setuptools, and
python-wheel.

Change-Id: I8c3dedb39d4cc1e51d9c3ef9fe9298586f871736
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
a6adb438dd
gnu: python-webassets: Fix build. 
* gnu/packages/python-web.scm (python-webassets)[arguments]: Delete broken
tests; run tests with nosetests.
[propagated-inputs]: Add python-pyyaml.
[native-inputs]: Remove python-pytest.

Change-Id: Iee1a38b02770259d11e4c7f6eff5d25c6be52ff9
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
9f01de8663
gnu: Remove python-flask-basicauth. 
This project is abandoned and has test failures that indicate that it doesn't
actually work properly anymore.

* gnu/packages/python-web.scm (python-flask-basicauth): Remove variable.

Change-Id: I828bd5409d71d45c5549e74deba3edecbfac4572
 2025-01-16 10:17:28 +01:00
Ricardo Wurmus
a07a35714c
gnu: python-flask-login: Update to 0.6.3. 
* gnu/packages/python-web.scm (python-flask-login): Update to 0.6.3.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ie1dc0ffccc11172e21d0013d84c064b8c2793e5f
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
f50565b192
gnu: python-flask-htpasswd: Update to 0.5.0. 
* gnu/packages/python-web.scm (python-flask-htpasswd): Update to 0.5.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable tests.

Change-Id: I24ec759fcfbfef3b64f5ca730ed43bf48690288b
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
7578ea008f
gnu: python-scanpy: Update to 1.10.4. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.10.4.
[arguments]: Update list of disabled tests; rename phase 'discover-anndata to
'add-anndata-source.
[native-inputs]: Add python-pytest-mock.

Change-Id: I409678c67d15f3d3e4147be68c7a987c0e095d23
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
ec247999df
gnu: python-legacy-api-wrap: Update to 1.4.1. 
* gnu/packages/python-xyz.scm (python-legacy-api-wrap): Update to 1.4.1.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-coverage, python-hatch-vcs, python-hatchling, and
python-pytest.
[propagated-inputs]: Remove python-get-version, python-pytest,
python-pytest-black, python-pytest-cov, and python-setuptools.

Change-Id: I56ccdc6c9fd8b5e6bcbfcf9255f02949e8f1e705
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
228b5abbf7
gnu: python-omnipath: Update to 1.0.8-0.3d16134. 
* gnu/packages/python-web.scm (python-omnipath): Update to 1.0.8-0.3d16134.
[source]: Fetch from git repository.
[arguments]: Remove phase 'relax; update list of disabled tests; add phase
'pretend-version.
[native-inputs]: Add nss-certs-for-test.

Change-Id: I9e980702ac8e5662971a9c4bb88a5789758b48ed
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
856485da37
gnu: python-pypika-tortoise: Add missing input. 
* gnu/packages/databases.scm (python-pypika-tortoise)[native-inputs]: Add
python-setuptools.

Change-Id: Ibe96738292a0948cae2add596fe76ee349c9dfeb
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
bee4864de3
gnu: python-asgi-lifespan: Update to 2.1.0. 
* gnu/packages/python-web.scm (python-asgi-lifespan): Update to 2.1.0.
[arguments]: Update list of disabled tests; add phase 'compatibility.
[native-inputs]: Add python-httpx.

Change-Id: Ib4c01ec059920481eefbbe908ba2fdaa9cf3484d
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
b73e710d3f
gnu: python-fastapi-pagination-minimal: Update to 0.12.34. 
* gnu/packages/python-web.scm (python-fastapi-pagination-minimal): Update to
0.12.34.
[propagated-inputs]: Replace python-pydantic with python-pydantic-2.
[native-inputs]: Replace poetry with python-poetry-core.
(python-fastapi-pagination)[arguments]: Run unit tests; add phase
'patch-tests.
[propagated-inputs]: Replace python-pydantic with python-pydantic-2.
[native-inputs]: Add python-aiosqlite, python-asgi-lifespan, python-asyncpg,
python-faker, python-httpx, python-poetry-core, python-pytest,
python-pytest-asyncio, python-sqlalchemy, and python-typing-extensions.

Change-Id: Icab22aa811c70762296ef47723052702b33c6762
 2025-01-16 10:17:27 +01:00
Ricardo Wurmus
c4efd2eb39
gnu: python-anndata: Update to 0.11.1. 
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.11.1.
[arguments]: Update list of disabled tests; do not patch conftest.
[native-inputs]: Add python-pytest-mock.

Change-Id: I6f087bb19a71006fd9f9c2c92150fa4d038fa2a6
 2025-01-16 10:17:27 +01:00
Lars-Dominik Braun
55d4c898dd
guix: toml: Fix evaluation of empty inline tables. 
* guix/build/toml.scm (eval-toml-file): Add pattern for empty inline table.
* tests/toml.scm ("parse-toml: Empty inline table"): New testcase.

Change-Id: I69663af2a861716acfb801fad4474e029e102a1b
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
ccea7539d8
gnu: python-wrapt: Update to 1.17.0. 
* gnu/packages/python-xyz.scm (python-wrapt): Update to 1.17.0.
[arguments]: Enable tests.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: Ib2e973ec7b09454588bbbbdd5d8446afc53e835b
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
7372c6f807
gnu: python-pytorch-geometric: Disable one test. 
* gnu/packages/machine-learning.scm (python-pytorch-geometric)[arguments]:
Disable one more test.

Change-Id: Id69243e70c39b9307745b08156ed956f23d8daa4
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
826f248756
gnu: Remove python-starlette-for-fastapi-0.88. 
* gnu/packages/python-web.scm (python-starlette-for-fastapi-0.88): Delete
variable.

Change-Id: Idf8b453834dee2051cec8b7fc34f6681aa8480c6
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
ae74f998ac
gnu: python-fastapi: Relax requirements. 
* gnu/packages/python-web.scm (python-fastapi)[arguments]: Add phase
'relax-requirements.

Change-Id: I639d894eb1ee207cddcaa52344e48291c7a2a5c9
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
e22add61ea
gnu: python-starsessions: Disable one more test. 
* gnu/packages/python-web.scm (python-starsessions)[arguments]: Disable one
more test.

Change-Id: I9a10805eb73f829f12f2b41d1d25b6c41693c9ef
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
a9709de79a
gnu: python-starsessions: Update input. 
* gnu/packages/python-web.scm (python-starsessions)[propagated-inputs]:
Replace python-starlette-for-fastapi-0.88 with python-starlette.

Change-Id: I07d5bf85ae9980e862dad456d2cde7f1adc1a0ff
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
ebefdd0cd2
gnu: Remove python-fastapi-for-pytorch-lightning. 
* gnu/packages/python-web.scm (python-fastapi-for-pytorch-lightning): Remove
variable.

Change-Id: I5cc49baae28ee512698e2e4e25ed99b3655d653a
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
002eac5931
gnu: Rename python-starsessions-for-pytorch-lightning. 
* gnu/packages/python-web.scm (python-starsessions-for-pytorch-lightning):
Rename this variable...
(python-starsessions): ...to this.

Change-Id: I237b83f380ce0cd4aee5021f646e66700eeec746
 2025-01-16 10:17:26 +01:00
Ricardo Wurmus
10538d2d82
gnu: python-lightning-cloud: Update to 0.5.70. 
* gnu/packages/machine-learning.scm (python-lightning-cloud): Update to
0.5.70.
[propagated-inputs]: Add python-boto3 and python-protobuf; replace
python-fastapi-for-pytorch-lightning with python-fastapi.

Change-Id: I4c93a0120639af230fdaf53703c688ce3012e8e0
 2025-01-16 10:17:25 +01:00
Ricardo Wurmus
0c478474fc
gnu: python-pytorch-lightning: Update to 2.5.0.post0. 
* gnu/packages/machine-learning.scm (python-pytorch-lightning): Update to
2.5.0.post0.
[arguments]: Only run core tests.
[propagated-inputs]: Replace python-fastapi-for-pytorch-lightning with
python-fastapi; remove python-starsessions-for-pytorch-lightning.

Change-Id: I1bf392e19cc06194fdf662f07aeccbafc8d0ae4e
 2025-01-16 10:17:25 +01:00
Ricardo Wurmus
fe6af23778
gnu: python-path-bootstrap: Update to 17.1.0. 
* gnu/packages/python-xyz.scm (python-path-bootstrap): Update to 17.1.0.

Change-Id: I7a83d6cffb2b3818691eaae3a3c787da3c60ff72
 2025-01-16 10:17:25 +01:00
Ricardo Wurmus
0c0e55adb3
gnu: python-fastapi: Update to 0.115.6. 
* gnu/packages/python-web.scm (python-fastapi): Update to 0.115.6.
[arguments]: Update list of disabled tests.
[propagated-inputs]: Add python-fastapi-cli, python-pydantic-2,
and python-pydantic-settings; remove python-pydantic.
[native-inputs]: Delete python-databases, python-isort, python-jose,
python-mypy, python-hatchling, python-passlib, python-peewee,
python-types-orjson, and python-types-ujson.

Change-Id: Id2ea9e1376dbfb654a62e6b8218c49adeda68014
 2025-01-16 10:17:25 +01:00
Ricardo Wurmus
d13b2831b4
gnu: python-pydantic-settings: Update to 2.7.1. 
* gnu/packages/python-xyz.scm (python-pydantic-settings): Update to 2.7.1.
[arguments]: Ignore tests from test_docs.py.
[propagated-inputs]: Remove python-pyaml and python-tomli.

Change-Id: Ie43e098c1a7787923a3cc92313832089b835a986
 2025-01-16 10:17:25 +01:00
Ricardo Wurmus
0d9e4701e1
gnu: Add python-fastapi-cli. 
* gnu/packages/python-web.scm (python-fastapi-cli): New variable.

Change-Id: Id20edf30e9c4ba59bc010a96f219cafbcb7ea31e
 2025-01-16 10:17:25 +01:00
Ricardo Wurmus
dc33067999
gnu: python-pdm-backend: Update to 2.4.3. 
* gnu/packages/python-build.scm (python-pdm-backend): Update to 2.4.3.

Change-Id: If022f4e85ce7434167cd2eec485ba56e882e4543
 2025-01-16 10:17:25 +01:00
Ricardo Wurmus
3241d7331e
gnu: Add python-rich-toolkit. 
* gnu/packages/python-xyz.scm (python-rich-toolkit): New variable.

Change-Id: I1a5f0d9e8241fef0396aaed534b373d2670c48ad
 2025-01-16 10:17:25 +01:00