gnu: python-pandera: Update to 0.27.1.

* gnu/packages/python-science.scm (python-pandera): Update to 0.27.1.
[arguments] <test-flags>: Rework skipped tests.

Change-Id: I7a21aa0e343cdf726e9d2c677bfccb0041dac39a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-anndata-minimal.

* gnu/packages/python-science.scm (python-anndata-minimal): New variable.

Change-Id: I9503ac08d0fa630d748574bb121690144a80bfea
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-anndata: Update to 0.12.7.

* gnu/packages/python-science.scm (python-anndata): Update to 0.12.7.
[arguments] <test-flags>: Skip CUDA dependent tests.
[phases]{set-version}: Remove setting zip timestamp logic.
[propagated-inputs]: Remove python-importlib-metadata,
python-scikit-learn, and python-setuptools; add python-numpy.
[native-inputs]: Add hdf5, python-openpyxl, python-pyarrow,
python-pytest-randomly, and python-scikit-learn.

Change-Id: I8e68cf85d435a13db995ea966ed5ff9edac3d672
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pythran: Clean up artifacts.

* gnu/packages/python-science.scm (python-pythran): Adjust style and
remove unused parts.
[source] <url>: Use a direct URL string.
[arguments] <test-flags, phase:pre-check>: Drop them as not used.
[native-inputs]: Remove openblas, python-pytest, python-pytest-xdist,
and python-wheel.
[home-page]: Move above [synopsis].

Change-Id: I7708981548ce68351c00fbf4e8f8e806a18f798a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-asap3: Update to 3.13.10.

* gnu/packages/python-science.scm (python-asap3): Update to 3.13.10.
[arguments] <tests?>: Enable.
[native-inputs]: Add python-pytest.

Change-Id: I166dfaf5f07f23d2d835d70f460cfa5f3f31ddb9
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ase: Update to 3.26.0.

* gnu/packages/python-science.scm (python-ase): Update to 3.26.0.
[arguments] <test-flags>: Run tests in parallel up to 8 threads.
[native-inputs]: Remove python-wheel.

Change-Id: Ib2e5c9751f6c3358bb35084076f79586473da88f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-numdifftools: Update to 0.9.42.

* gnu/packages/python-science.scm (python-numdifftools): Update to 0.9.42.
[arguments] <test-flags>: Keep only exclusion markers.
<phases>: Remove 'relax-requirements; add 'fix-pytest-config.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Remove python-setuptools, python-setuptools-scm, and
python-wheel; add python-pdm-backend.

Change-Id: I87bdd34812df8771f53dd2ab8cfc4634ffb0b07d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-modin: Update to 0.37.1.

* gnu/packages/python-science.scm (python-modin): Update to 0.37.1.
[arguments] <test-flags>: Rework options.
<phases>: Remove 'loosen-requirements; add 'versioneer, and
'fix-pytest-config; rework {check} phase to include some API tests
scenarios.
[propagated-inputs]: Remove python-cloudpickle and python-s3fs; add
python-fsspec, python-psutil, and python-typing-extensions.
[native-inputs]: Remove python-jinja2, python-lxml, python-matplotlib,
python-msgpack, python-openpyxl, python-psutil, python-pyarrow,
python-pytest-benchmark, python-pytest-cov, python-scipy,
python-sqlalchemy, python-tables, python-tqdm, python-xarray,
python-xlrd, and python-wheel; add python-s3fs, python-setuptools, and
python-versioneer.

Change-Id: I86feaa9f1cd110ed2c430e9816d34da165bccb74
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-xarray-einstats: Update to 0.9.1.

* gnu/packages/python-science.scm (python-xarray-einstats): Update to 0.9.1.
[propagated-inputs]: Add python-einops and python-numba.
[native-inputs]: Remove python-einops and python-numba.

Change-Id: Ic3e05114dc3d6343523aec222f527ef9653ed2d6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-dask-image: Update to 2025.11.0.

* gnu/packages/python-science.scm (python-dask-image): Update to 2025.11.0.
[arguments] <test-flags>: All tests passed.
<phases>: Add 'fix-pytest-config; rework 'set-version to read from envar.
[propagated-inputs]: Remove python-tifffile-for-dask-image; add
python-tifffile.
[native-inputs]: Remove python-setuptools-scm; add
python-setuptools-scm-next.

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

Change-Id: I928c39c848f3a20d5eb51d10e4c8374891b8f0b0
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-xarray: Update to 2025.12.0.

* gnu/packages/python-science.scm (python-xarray): Update to 2025.12.0.
[arguments] <test-flags> Rework skipped tests, do not depend on MyPy
type checker.
[native-inputs]: Remove python-wheel; add python-pytest-asyncio.

Change-Id: I49e33b614926cde8bd5fad09ac278bc79e9d3cb1
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jacobi: Fix tests.

* gnu/packages/python-science.scm (python-jacobi)[arguments]<phases>:
Add 'fix-pytest-config.

Change-Id: Ia8b4c30d2d8d6cfe9bae79342614747c90ae6735
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-image-next: Deprecate by python-scikit-image.

* gnu/packages/python-science.scm (python-scikit-image-next): Deprecate
in favor of python-scikit-image.

Change-Id: I006f4a302eabab82abd9c853f1b6a3d352f546ef
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-image: Update to 0.25.2.

* gnu/packages/python-science.scm (python-scikit-image): Update to 0.25.2.
[arguments] <test-flags>: Ignore benchmark tests.
<phases>: Remove 'change-home-dir, 'pre-check, 'post-check; add
'remove-local-source.
[propagated-inputs]: Remove python-cloudpickle, python-dask,
python-matplotlib, python-pythran, and python-pywavelets; add
python-packaging.
[native-inputs]: Remove python-numpydoc, python-packaging, and
python-wheel; add python-pythran.

Change-Id: Ifbfbb3e2d28dc8784f600a4cd1a0f0c7129fddb5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fgivenx: Update to 2.4.2-0.cf51dbf.

* gnu/packages/python-science.scm (python-fgivenx): Update
towcf51dbf8b7efdd8d84f055740a069a5b882dcf77.
[source]: Switch to git-fetch providing comparability with recent
matblotlib version.
[arguments]: Drop all.
[home-page]: Fix URL https://github.com/fgivenx/fgivenx responding with
404, new one is taken from PyPI page.

Change-Id: Ia255f4b44967ee32e9b4a18cc15b80aa4cf0b09e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-algopy: Update to 0.7.2.

* gnu/packages/python-science.scm (python-algopy): Update to 0.7.2.
[native-inputs]: Remove python-wheel.

Change-Id: Ifac98dffd209bea3d50ef3ded0a0aee0a24faa8c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ndindex: Update to 1.10.1.

* gnu/packages/python-science.scm (python-ndindex): Update to 1.10.1.
[arguments] <test-flags>: Provide option to run tests again installed
module.
<phases>: Add 'remove-local-source.
[native-inputs]: Remove python-wheel; add python-sympy.

Change-Id: I2c7129b540c5fc4e25dac8945c38359cc6c71eac
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-distributed: Update to 2025.11.0.

* gnu/packages/python-science.scm (python-distributed): Update to 2025.11.0.
[arguments] <tests?, test-flags>: Disable for now.
<phases>: Remove 'versioneer, 'fix-references, and 'pre-check.
[propagated-inputs]: Remove python-cryptography, python-dask-expr, and
python-setuptools; add python-jinja2, python-locket, and
python-packaging.
[native-inputs]: Remove python-flaky, python-importlib-metadata,
python-pytest, python-pytest-timeout, python-versioneer, and
python-wheel; add python-setuptools and python-setuptools-scm-next.

Change-Id: I1c368ee626d4bc5dc206df06431d164cd8df3428
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pydantic-2: Deprecate by python-pydantic.

* gnu/packages/python-xyz.scm (python-pydantic-2): Deprecate variable.

* gnu/packages/astronomy.scm (python-czml3, python-edps, python-hvpy):
[propagated-inputs]: Remove python-pydantic-2; add python-pydantic.

* gnu/packages/cybersecurity.scm (gallia):
[inputs]: Remove python-pydantic-2; add python-pydantic.

* gnu/packages/databases.scm (python-prisma)[propagated-inputs]:
Remove python-pydantic-2; add python-pydantic.
(python-tortoise-orm, aerich)[native-inputs]: Remove python-pydantic-2;
add python-pydantic.

* gnu/packages/django.scm (python-django-ninja)[propagated-inputs]:
Remove python-pydantic-2; add python-pydantic.

* gnu/packages/finance.scm (python-schwifty)[native-inputs]: Remove
python-pydantic-2; add python-pydantic.

* gnu/packages/games.scm (tuxemon)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.

* gnu/packages/machine-learning.scm (python-spacy, python-thinc):
[propagated-inputs]: Remove python-pydantic-2; add python-pydantic.

* gnu/packages/maths.scm (python-libensemble)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.

* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:
Remove python-pydantic-2; add python-pydantic.

* gnu/packages/python-check.scm (python-inline-snapshot)[native-inputs]:
Remove python-pydantic-2; add python-pydantic.

* gnu/packages/python-science.scm (python-iminuit):[native-inputs]:
Remove python-pydantic-2; add python-pydantic.
(python-pandera, python-vaex-core)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.

* gnu/packages/python-web.scm: (python-cloudpathlib, python-huggingface-hub):
[native-inputs]: Remove python-pydantic-2; add python-pydantic.
(python-aws-sam-translator, python-weasel, python-openai,
python-fastapi, python-fastapi-csrf-protect,
python-fastapi-pagination-minimal, python-fastapi-pagination):
[propagated-inputs]: Remove python-pydantic-2; add python-pydantic.

* gnu/packages/python-xyz.scm: (python-safety-schemas,
python-pytoolconfig, python-pydantic-cli, python-pydantic-settings,
python-confection, python-safety)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.
(python-deepdiff, python-lief)[native-inputs]: Remove
python-pydantic-2; add python-pydantic.

Change-Id: I20842162ae8a6c0abd54e4ef1fc676f928541184
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-dask: Update to 2025.11.0.

* gnu/packages/python-science.scm (python-dask): Update to 2025.11.0.
[arguments] <test-flags>: Do not max out availalbe thread, keep them on
4 for stability; rework skipped/ignored tests.
<phases>: Remove 'versioneer, and 'patch-pyproject.
[propagated-inputs]: Remove python-dask-expr; add python-lz4 and
python-pyarrow.
[native-inputs]: Remove python-importlib-metadata and python-versioneer;
add python-pytest-asyncio, python-pytest-mock, python-pytest-timeout,
python-setuptools-scm-next, and tzdata-for-tests.

Change-Id: I8234ad1923a2a228c9c240bb34c9e1c9dfcbbd55
Signed-off-by: Rutherther <rutherther@ditigal.xyz>