gnu: python-astroml: Fix build.

* gnu/packages/astronomy.scm (python-astroml)[arguments]<test-flags>:
Skip 2 more tests.
[native-inputs]: Remove python-pytest-cov and python-wheel; add
python-pytest, python-pytest-astropy, and python-setuptools.

Change-Id: I38df8b11f652713d961d792d36efca25bfd8140b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-stwcs: Remove relax-requirements phase.

* gnu/packages/astronomy.scm (python-stwcs)[arguments]<phases>: Remove
'relax-requirements.

Change-Id: I7349cb56841adcf7e61c2d012d19d95f4b38bb5c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cloudpathlib: Fix tests.

* gnu/packages/python-web.scm (python-cloudpathlib)[native-inputs]:
Add python-psutil.

Change-Id: I2c13d89f7739f94ca5532188cafaba7d6b214f1d
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-dendropy: Update to 5.0.8.

* gnu/packages/bioinformatics.scm (python-dendropy): Update to 5.0.8.
[arguments] <phases>: Remove python-compatibility.
[propagated-inputs]: Remove python-setuptools.
[native-inputs]: Remove python-wheel; add python-setuptools.

Change-Id: Id8cec99a2c15081334c6584b2868bb2c729b5409
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-django-ninja: Update to 1.5.1.

* gnu/packages/django.scm (python-django-ninja): Update to 1.5.1.

Change-Id: I992bd64d06366faf315bf673708983eaacaa2689
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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>