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>

gnu: python-matplotlib: Update to 3.10.8.

* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.10.8.
[source]: Fetch from git and delete patches.
[#:configure-flags]: New argument.
[#:test-flags]: Consolidate all test arguments here, adding "-n" and
"--pyargs". Update skipped tests regexps.
[#:phases] {fix-and-disable-failing-tests}: Rename to...
{patch-commands}: ... this, and streamline phase.
{patch-dlopen}: Update patched file name.
{configure-environment}: Streamline.
{chdir}: New phase.
[native-inputs]: Add meson-python.
* gnu/packages/patches/python-matplotlib-fix-legend-loc-best-test.patch:
Delete file.
* gnu/local.mk (dist_patch_DATA): De-register it.

Change-Id: Ib002aae96559efa625d2059c783536f77f4170a5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-httptools: Update to 0.7.1.

* gnu/packages/python-web.scm (python-httptools): Update to 0.7.1.

Change-Id: Iae65ddeff91abec3029403998469ae53547f295b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

* gnu/packages/python-xyz.scm (python-numpy-2): Deprecated in favor of
python-numpy.
(python-omero-py, python-numexpr) [propagated-inputs]: Remove
python-numpy-2; add python-numpy.

* gnu/packages/algebra.scm (kissfft)
[native-inputs]: Remove python-numpy-2; add python-numpy.

* gnu/packages/image.scm (vigra):
[inputs]: Remove python-numpy-2; add python-numpy.

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

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

* gnu/packages/maths.scm (python-blis):
[native-inputs]: Remove python-numpy-2; add python-numpy.

Change-Id: Ie6041de76a227246ec63b0efa04d293dcc22b40b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-numpy: Set NumPy 2 as default.

* gnu/packages/python-xyz.scm (python-numpy): Move definition from
python-numpy-2 here.
(python-numpy-1): New variable, inherit from python-numpy.

Change-Id: I78bf7cae09b5bea59b536fe4ba14649a3398539c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-cython-next.

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

Change-Id: I9bc2e1881edb4113f5919d39a6481067da986045
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cython: Update to 3.1.7.

* gnu/packages/python-xyz.scm (python-cython): Update to 3.1.7.

Change-Id: I0771e680017223c0ef0fee01fc30edda0e274ebb
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>