gnu: python-xmp-toolkit: Update to 2.1.0.

* gnu/packages/python-xyz.scm (python-xmp-toolkit): Update to 2.1.0.
[source]: Remove patch as applied upstream.
[arguments] <test-flags>: Run all tests.
<phases>: Remove 'configure-environment; add 'patch-source.
[native-inputs]: Remove python-setuptools and python-wheel; add
python-flit-core.

* gnu/packages/patches/python-xmp-toolkit-add-missing-error-codes.patch:
Delete file.
* gnu/local.mk (dist_patch_DATA): Deregister patch.

Change-Id: I3443ecd6ad2bd423544d06d1e6e0de7079ed6296
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-astropy-6: Skip some tests.

* gnu/packages/astronomy.scm (python-astropy-6)[arguments]: Substitute
from python-astropy and skip 4 more tests.

Change-Id: I14cd880c8428fd6ca90fb6f322e0fea08e8b5457
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fastapi: Update to 0.124.0.

* gnu/packages/python-web.scm (python-fastapi): Update to 0.124.0.
[arguments] <test-flags>: Rework them, do not run tests on documentation
and toturials.
<phases>: Remove 'relax-requirements.
[propagated-inputs]: Add python-annotated-doc and
python-pydantic-extra-types.
[native-inputs]: Add python-anyio, python-types-orjson, and
python-types-ujson.

Change-Id: I699102d132838e3a8ac120063c6fdb89b25db89f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pydantic-extra-types.

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

Change-Id: I6603d0f0a5cbef6b4b9aede144623604ad5fbf37
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-annotated-doc.

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

Change-Id: Iff2bb3c690d9260d543e268210286c2591e67c84
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-cron-converter.

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

Change-Id: I961bdbcbdc106ee9cd358471894497598251dfbd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-ulid.

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

Change-Id: I251d3fb5c481879aab0de664232d612a9231a4cb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-casa-formats-io: Fix tests.

* gnu/packages/astronomy.scm (python-casa-formats-io):
[arguments] <test-flags>: Skip one test, run tests against installed
module.
<phases>: Remove 'build-extensions; add 'remove-local-source.
[native-inputs]: Remove python-pytest-cov and python-wheel, add
python-setuptools-scm.

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

gnu: python-pydantic-settings: Update to 2.12.0.

* gnu/packages/python-xyz.scm (python-pydantic-settings): Update to 2.12.0.
[arguments] <test-flags>: Simplify.
<phases>: Remove 'relax-requirements.
[propagated-inputs]: Add python-typing-inspection, python-pyyaml, and
python-tomli.

Change-Id: I4163761c01d60f121e580b460f948f447c95f256
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-netcdf4: Update to 1.7.2.

* gnu/packages/python-xyz.scm (python-netcdf4): Update to 1.7.2.
[source]: Switch to git-fetch.
[phases]{set-configure-flags}: Add "-g -O2" options and set JPEG_DIR.
[propagated-inputs]: Add python-certifi.
[native-inputs]: Remove python-wheel; add python-packaging,
python-pytest, python-setuptools-scm, and python-typing-extensions.

Change-Id: I7e50f12623f3fc0afc42679a7dbc71286a0a3be1
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: netcdf: Update to 4.9.2.

* gnu/packages/maths.scm (netcdf): Update to 4.9.2.
[arguments] <configure-flags>: Remove not required GCC 1.14 workaround
options, silent "--enable-doxygen" for now; provide "--with-plugin-dir"
<phases>: Add 'fix-tests.
[inputs]: Remove unzip; add bzip2 and zstd.
[native-inputs]: Add unzip.

Change-Id: Ib82e80328d9b0d991e40c99e031a8612c915177f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-blosc2: Update to 3.12.2.

* gnu/packages/python-compression.scm (python-blosc2): Update to 3.12.2.
[propagated-inputs]: Add python-platformdirs and python-requests.
[native-inputs]: Remove python-scikit-build; add python-psutil, python-pytorch, and
python-scikit-build-core.

Change-Id: I31a5c34c77f9b6fd104aa74d4805717c58df9c22
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: c-blosc2: Update to 2.22.0.

* gnu/packages/compression.scm (c-blosc2): Update to 2.22.0.

Change-Id: I4043f73d1857261444fd7b33e8db3b6416398da6
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-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>