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

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

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

gnu: python-pypika-tortoise: Add missing input.

* gnu/packages/databases.scm (python-pypika-tortoise)[native-inputs]: Add
python-setuptools.

Change-Id: Ibe96738292a0948cae2add596fe76ee349c9dfeb

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

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

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

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

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

gnu: python-pytorch-geometric: Disable one test.

* gnu/packages/machine-learning.scm (python-pytorch-geometric)[arguments]:
Disable one more test.

Change-Id: Id69243e70c39b9307745b08156ed956f23d8daa4

gnu: Remove python-starlette-for-fastapi-0.88.

* gnu/packages/python-web.scm (python-starlette-for-fastapi-0.88): Delete
variable.

Change-Id: Idf8b453834dee2051cec8b7fc34f6681aa8480c6

gnu: python-fastapi: Relax requirements.

* gnu/packages/python-web.scm (python-fastapi)[arguments]: Add phase
'relax-requirements.

Change-Id: I639d894eb1ee207cddcaa52344e48291c7a2a5c9

gnu: python-starsessions: Disable one more test.

* gnu/packages/python-web.scm (python-starsessions)[arguments]: Disable one
more test.

Change-Id: I9a10805eb73f829f12f2b41d1d25b6c41693c9ef

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

gnu: Remove python-fastapi-for-pytorch-lightning.

* gnu/packages/python-web.scm (python-fastapi-for-pytorch-lightning): Remove
variable.

Change-Id: I5cc49baae28ee512698e2e4e25ed99b3655d653a

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

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

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

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

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