gnu: python-anndata: Add test dependency python-filelock.

It was found this build issue while building dependents of python-zarr.

* gnu/packages/python-science.scm (python-anndata):
[native-inputs]: Add python-filelock; missing for tests.

Change-Id: Ia83b631bc321f43e7a51fa558753f6189530bd76
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add python-durationpy.

* gnu/packages/python-xyz.scm (python-durationpy): New variable.

Change-Id: Ibb3ee965a1f121dc0301f3fdaaea2a432cad5010
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: aerich: Update to 0.9.2.

As it's a final program all propagated inputs moved to inputs.

* gnu/packages/databases.scm (aerich): Update to 0.9.2.
[arguments] <test-flags>: Skip one tests searching for "uvx".
[inputs]: Add python-anyio, python-asyncclick, python-dictdiffer,
python-tortoise-orm, python-aiomysql, python-asyncmy, python-asyncpg,
python-psycopg, and python-tomli-w.
[propagated-inputs]: Remove python-asyncclick, python-asyncmy,
python-asyncpg, python-dictdiffer, python-pydantic, python-tomli-w, and
python-tortoise-orm.
[native-inputs]: Remove python-poetry-core; add python-pdm-backend,
python-pydantic-2, python-pydantic-settings, and python-tortoise-vector.

Change-Id: I9bcb13f0fc9f70428b5f794893d1a4bddf611a5d

gnu: Add python-tortoise-vector.

* gnu/packages/databases.scm (python-tortoise-vector): New variable.

Change-Id: Ib6646bc813fe04ba6e55b2b78dff373d2b52268e

gnu: python-asyncclick: Update to 8.3.0.3.

Upstream has resolved all issues:
- <https://github.com/python-trio/asyncclick/issues/39>
- <https://github.com/python-trio/asyncclick/issues/42>

* gnu/packages/python-xyz.scm (python-asyncclick): Update to 8.3.0.3.
[arguments]: Drop all.
[native-inputs]: Remove python-anyio; add less.
[propagated-inputs]: Add python-anyio.

Change-Id: I689ddbe231760a21986080b0dbcebdf6c56f1039

gnu: Remove python-dbus-next.

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

Fixes: guix/guix#2725
Change-Id: Ifc65d8e1c5efaa40e1e43f0b457878302a93dc43

gnu: Add zola.

* gnu/packages/rust-apps.scm (zola): New variable.
* gnu/packages/rust-crates.scm (zola): Map cargo inputs.

Change-Id: I9b7fb89af687f4a58c8ff77effc5695773363165
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: python: Graft secure package.

* gnu/packages/python.scm (python/fixed): Add new variable.
(python): Graft python/fixed.

Change-Id: I8b1537a64be1984c52170ba3f2fbdca5737290e8

gnu: python-3.10: Update to 3.10.19.

* gnu/packages/python.scm (python-3.10): Update to 3.10.19.

Change-Id: Ib38ee006d8deaed8029000b5202547b001cb8f6c

gnu: btop: Update to 1.4.5.

* gnu/packages/admin.scm (btop): Update to 1.4.5.

Change-Id: Idbe210521579f83188f52ac929d313c7accbc753

gnu: thermald: Update to 2.5.10.

* gnu/packages/admin.scm (thermald): Update to 2.5.10.
[home-page]: Set URI to "https://github.com/intel/thermal_daemon" as the
original URI is permanently redirected.

Change-Id: I2fa1ff116de64c2c8e9476fe7f529a5c1542ba41

gnu: python-dask-image: Fix tests.

* gnu/packages/python-science.scm (python-dask-image)[arguments]
<test-flags>: Rework skipped tests and enable more tests.
[propagated-inputs]: Remove python-tifffile; add
python-tifffile-for-dask-image.
[description]: Remove new line in the end.

* gnu/packages/python-xyz.scm (python-tifffile-for-dask-image): New variable.

Change-Id: I8539569aab1134d049ec8e8c0041191ce61e2eb7

gnu: python-icontract: Fix tests.

* gnu/packages/python-check.scm (python-icontract)[arguments] <phases>:
Add 'relax-requirements.
[native-inputs]: Remove python-wheel; add python-deal,
python-dpcontracts, and python-pytest.

Change-Id: Ie2d418673f15f7db3128c5a0b81a320765fc5df7

gnu: Add python-deal.

* gnu/packages/python-check.scm (python-deal): New variable.

Change-Id: I2d3e96329715471a559fe154c0dbdd7d666e908b

gnu: Add python-dpcontracts.

* gnu/packages/python-check.scm (python-dpcontracts): New variable.

Change-Id: Iaaf6aedfd1e4f1f853fe70cc821edcaa805b9dbd

gnu: python-typeshed-client: Update to 2.8.2.

* gnu/packages/python-xyz.scm (python-typeshed-client): Update to 2.8.2.
[source]: Switch to git-fetch providing test data.
[arguments] <test-backend>: Use custom.
[propagated-inputs]: Add python-typing-extensions.
[native-inputs]: Remove python-wheel.

Change-Id: Icfbb809b45e0ca9e4b29237f0f622d77928f9730

gnu: python-lfdfiles: Update to 2025.9.17.

* gnu/packages/python-xyz.scm (python-lfdfiles): Update to 2025.9.17.
[source, propagated-inputs]: Improve style.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I728400b74276b036d021c25b6c25c92709f7776c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-tifffile: Update to 2025.10.4.

* gnu/packages/python-xyz.scm (python-tifffile): Update to 2025.10.4.
[build-system]: Switch to pyproject-build-system.
[arguments, description]: Improve style.
[native-inputs]: Add python-setuptools.  Remove python-pytest, as
tests are not run.

Change-Id: Ica27197142bf7f80a7078cae1581b65a73a9b4b2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-roifile: Update to 2025.5.10.

* gnu/packages/python-xyz.scm (python-roifile): Update to 2025.5.10.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
[native-inputs]: Add python-setuptools.

Change-Id: I35e052527647cc13ae345be3a2d99b7445bc3257
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-imagecodecs: Update to 2025.8.2.

Warning: In phase 'create-configuration, I've disabled 3 modules that
fail compilation with gcc@14, although they should theorically
compile: apng, lzo, tiff.  IMO it's a bit out of the scope for a
already heavy patch to try and fix C compilation errors. I added a
FIXME comment though.

* gnu/packages/python-xyz.scm (python-imagecodecs): Update to 2025.8.2.
[source]<snippet>: Remove code unbundling 3rd party modules.  Almost
all of those are not bundled in the sense that they are extracted and
patched from upstream sources, and using those upstream sources
directly won't help.
[build-system]: Switch to pyproject-build-system.
[arguments]: Use gexps.
<#:tests?>: Enable them.
<#:test-flags>: Ignore flaky test.
<#:phases>: Re-factor phase 'create-configuration. Add phase
'fix-sanity-check and 'configure-tests.
[inputs]: Add lcms, libheif, lzfse, python-blosc2.
[propagated-inputs]: Add python-matplotlib, python-tifffile.
[native-inputs]: Add python-pytest, python-setuptools.
[synopsis]: Improve style.

Change-Id: I1c13eea510136891c667741f73fbf1d3f4231551
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>