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-numexpr: Update to 2.14.1.

* gnu/packages/python-xyz.scm (python-numexpr): Update to 2.14.1.

Change-Id: I35da8bea473838fdf0858f6ea3b80bf628b496f9
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-scikit-learn: Update to 1.7.2.

* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.7.2.
[arguments] <test-flags>: Limit parallel tests up to 8 thread; all tests
passed, don't skip any.
[native-inputs]: Add pkg-config.

Change-Id: I4ef534538ba83feb6d8e2bfb91f766e5dfd157e8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-nbval: Reduce closure size.

* gnu/packages/python-check.scm (python-nbval):
[arguments] <test-flags>: Skip some more tests to reduce closure size.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-pytest-cov, python-sympy, and
python-wheel.

Change-Id: I3e3e4378a837d62c553ff432aecf45d266589aee
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: Add python-pydantic-1.

* gnu/packages/python-xyz.scm (python-pydantic-1): New variable.

Change-Id: Ifc4b64d7c1b34a083c35a0cad6be8da4d7e6c20b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pydantic: Update to 2.12.5.

* gnu/packages/python-xyz.scm (python-pydantic): Update to 2.12.5.
[propagated-inputs]: Add python-annotated-types, python-pydantic-core, and
python-typing-inspection.
[native-inputs]: Remove python-setuptools and python-wheel; add tzdata-for-tests,
python-dirty-equals, python-faker, python-hatch-fancy-pypi-readme,
python-hatchling, python-jsonschema, python-pytest-benchmark,
python-pytest-examples, and python-pytest-run-parallel.

Change-Id: Ic844bac49a97736c1f2e2e01f7b732c0e2c36ea0
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pydantic-core: Update to 2.41.5.

* gnu/packages/python-xyz.scm (python-pydantic-core): Update to
2.41.5. Enable tests.
[build-system]: Switch to pyproject-build-system.
[arguments] <modules>: Adjust for pyproject-build-system.
<phases>: Add 'prepare-cargo-build-system, and 'patch-pyproject.toml.
[native-inputs]: Add python-dirty-equals, python-pytest,
python-pytest-benchmark, python-pytest-mock, python-pytest-timeout,
python-typing-inspetion, python-tzdata, rust, and `(,rust "cargo")).

* gnu/packages/rust-crates.scm: (rust-cc-1.0.101, rust-jiter-0.11.1,
rust-lexical-parse-float-1.0.5, rust-lexical-parse-integer-1.0.5,
rust-lexical-util-1.0.6, rust-libc-0.2.155, rust-portable-atomic-1.6.0,
rust-proc-macro2-1.0.86, rust-pyo3-0.26.0,
rust-pyo3-build-config-0.26.0, rust-pyo3-ffi-0.26.0,
rust-pyo3-macros-0.26.0, rust-pyo3-macros-backend-0.26.0,
rust-quote-1.0.36, rust-rustversion-1.0.17, rust-speedate-0.17.0,
rust-syn-2.0.82): New variables.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs):
{python-pydantic-core}: Refresh the list.

Change-Id: Id861b1bdebad583c9d34a708ee229c61d7c2a799
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pytest-run-parallel.

* gnu/packages/python-check.scm (python-pytest-run-parallel): New variable.

Change-Id: I680f2dcc11e3457a3b05ebe65852a7cfd6c2df53
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-typing-inspection.

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

Change-Id: I1823a5683846b7c3620ed42c157bda437f7451f0
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>

gnu: python-setuptools-scm-next: Undeprecate.

This particular version is required for Dask update, I try to avoid
updating python-setuptools-scm to prevent triggering 8k+ rebuilds.

* gnu/packages/python-build.scm (python-setuptools-scm-next):
Undeprecate variable and set to 9.2.2 version.

Change-Id: I0e7f879bcf4f58ad9741ff4c7efb039c350f0014
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-blosc: Adjust inputs.

* gnu/packages/python-compression.scm (python-blosc):
[propagated-inputs]: Remove python-scikit-build.
[native-inputs]: Remove python-numpy; add python-numpy-1 and
python-scikit-build.

Change-Id: I30da797eea3b92909ba707af41cde90062d974bf
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-h5py: Update to 3.15.1.

* gnu/packages/python-xyz.scm (python-h5py): Update to 3.15.1.
[arguments] <test-flags>: Skip test recruiting the build with MPI
support.
<phases>: Remove 'relax-gcc-14-strictness; do not delete/implement custom
'check, use default.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-ipython, python-pytest-mpi, and
python-wheel.

Change-Id: Iee3bdaa9f3950404791e770ee600da1650842496
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pytest-regressions: Move to python-check.

* gnu/packages/check.scm (python-pytest-regressions): Move from here ...
* gnu/packages/python-check.scm: ... to here.

Change-Id: I829667aa3cadd8a762194e1948c88b72e6a4eeda
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pytest-regressions: Update to 2.8.3.

* gnu/packages/check.scm (python-pytest-regressions): Update to 2.8.3.
[arguments] <test-flags>: Remove requirements of expensive inputs.
[native-inputs]: Remove python-numpy, python-pandas, and python-pytest; add
python-pytest-bootstrap.

Change-Id: I482521782c8cd21c8a86ed69c11a8efa538326e4
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scipy: Update to 1.16.3.

* gnu/packages/python-science.scm (python-scipy): Update to 1.16.3.
[arguments] <test-flags>: Use Pytest directly, as seen in project's
GitHub Actions.
<phases>: Remove 'apply-i686-patch; add 'relax-requirements,
'hide-gfortran; rework custom 'check to run Pytest directly.
[native-inputs]: Remove gcc, python-cython-0; add python-cython, and
python-hypothesis.
[inputs]: Remove pybind11-2.10; add boost, pybind11, qhull, and xsimd.

* gnu/packages/patches/python-scipy-i686.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Deregister patch.

Change-Id: Ibc38577b9b0c915e54ca3b3096727c9c2f82e19c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-msgpack: Update to 1.1.2.

* gnu/packages/python-xyz.scm (python-msgpack): Update to 1.1.2.

Change-Id: Ic69b1b9f8fc9d6da32c00584e86de42af167ec0c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pandas: Update to 2.3.3.

* gnu/packages/python-science.scm (python-pandas-2): Update to 2.3.3 and
rename to python-pandas.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'pre-check, and 'patch-which; use custom 'check.
[inputs]: Remove which, it's implemanted with Python's `shutil.which()'.
[propagated-inputs]: Remove python-jinja2, python-matplotlib,
python-openpyxl, python-xlrd, and python-xlsxwriter.
[native-inputs]: Remove python-beautifulsoup4, python-cython,
python-html5lib, python-matplotlib, python-openpyxl,
python-pytest-localserver, and python-pytest-mock; add meson and
tzdata-for-tests.
(python-pandas-2): Deprecate variable in favor of python-pandas.

Change-Id: Ib4aefbbc33f46f793430ac396cbe5e6c4107ec2f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>