gnu: python-nanobind: Update to 2.10.2.

* gnu/packages/python-xyz.scm (python-nanobind): Update to 2.10.2.
[native-inputs]: Add python-numpy, python-pathspec, and python-scipy.
[synopsis]: Fix lint warning: "synopsis should start with an upper-case
letter or digit".

Change-Id: I26dd624d3a9ead7af7744769cc59f05bb56de56d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pytools: Add missing propagated inputs, enable tests.

* gnu/packages/opencl.scm (python-pytools):
[arguments] <tests?>: Enable.
[propagated-inputs]: Remove python-appdirs and python-numpy; add
python-platformdirs, python-siphash24, and python-typing-extensions.
[native-inputs]: Add python-pytest.

Change-Id: Ib4635f375306b1ea9415bd0eca79013d0521b9cc
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-siphash24.

* gnu/packages/python-xyz.scm (python-siphash24): New variable.

Change-Id: I297103197b867e9be3a60caf53a8536f5c32aa63
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add c-siphash.

* gnu/packages/c.scm (c-siphash): New variable.

Change-Id: Icc2cbe8cb408ea345d3921b4fce74e5761f79b87
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add c-stdaux.

* gnu/packages/c.scm (c-stdaux): New variable.

Change-Id: Iddb4f0f77e5b4c9be03d8029272d47e2dddf7bf1
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pymol: Use python-numpy@1.

* gnu/packages/chemistry.scm (python-pymol):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.

Change-Id: Icfb0eb4116ecb7b9d34fe13bc8bd81d85a4a64ec
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: openmm: Remove shaky tests.

The package could not finish build in CI because of some not
deterministic tests, see:
<https://ci.guix.gnu.org/build/16867177/details>. This change removes
some of them.

* gnu/packages/machine-learning.scm (openmm):
[phases]{remove-shaky-tests}: New phase.

Change-Id: I508b23db8b6f0d5a567561b190897bc90cb8faf3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pymc: Update to 5.27.0.

* gnu/packages/statistics.scm (python-pymc): Update to 5.27.0.
[arguments] <phases>: Remove 'relax-requirements.

Change-Id: I8e7cb8d2a035b922c998e79b7a07f55fe41b9979
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pytensor: Update to 2.36.3.

* gnu/packages/python-science.scm (python-pytensor): Update to 2.36.3.
[arguments] <test-flags>: Add option to skip/disable benchmark tests and
rework skipped tests.
[native-inputs]: Add python-pytest-benchmark and python-pytest-xdist.

Change-Id: I9c3c42c21091524741ccef55e4698b59e818512d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fastparquet: Update to 2025.12.0.

* gnu/packages/databases.scm (python-fastparquet): Update to 2025.12.0.
[arguments] <phases>: Remove 'relax-requirements,'pretend-version, and
'build-cython-extensions; add 'remove-dependencies-on-git, 'set-version
and 'remove-local-source.
[native-inputs]: Remove python-wheel.

Change-Id: I808357310fbd78c1465d638788a3040ba2b8a452
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pygam: Update to 0.12.0.

* gnu/packages/bioinformatics.scm (python-pygam): Update to 0.12.0.
[arguments] <test-flags>: Skip one test.
<phases>: Remove 'patch-pyproject.
[propagated-inputs]: Remove python-black, python-flake8, python-ipython,
and python-poetry-core.
[native-inputs]: Remove python-pytest-cov; add python-matplotlib and
python-setuptools.

Change-Id: I5b3b95deb2bbe455582d4c74fe672c62b9aa8ff4
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyemd: Use python-numpy@1.

* gnu/packages/python-xyz.scm (python-pyemd):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: I7cad3d609f1eec432d3e77945ffd2b2dc30b4900
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pot: Update to 0.9.6.post1.

* gnu/packages/machine-learning.scm (python-pot): Update to 0.9.6.post1.
[arguments]: Drop all.
[propagated-inputs]: Add python-cvxopt and python-matplotlib.
[native-inputs]: Remove python-pytest-cov.

Change-Id: I763bf521a30f1bd4067089133421239af160173c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pingouin: Fix tests.

* gnu/packages/python-science.scm (python-pingouin):
[arguments] <test-flags>: Rework skipped tests.
<phases>: Add 'relax-requirements.
[native-inputs]: Remove python-pytest-cov; add python-setuptools.

Change-Id: If45e91fabbd479819731041c09dd6e1e561774d6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-phenograph: Fix tests.

* gnu/packages/bioinformatics.scm (python-phenograph):
[arguments] <test-flags>: Skip 3 more tests.
<phases>: Remove 'disable-leiden-test, and move logic to <#:test-flags>.
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: Id7a7cb67adb13749bde59ad93d5c1125f2903065
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-survival: Fix indentation.

* gnu/packages/python-science.scm (python-scikit-survival): Fix indentation.

Change-Id: Iff0ab38a0b484938613df08ffb0fbd83da489289
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-survival: Update to 0.26.0.

* gnu/packages/python-science.scm (python-scikit-survival): Update to 0.26.0.
[native-inputs]: Add python-pytest-xdist.

Change-Id: If92ba627c894cb65976b7687062e738656b06e96
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-dask-expr.

* gnu/packages/python-science.scm (python-dask/bootstrap)
(python-dask-expr): Delete variables.

Fixes: guix/guix#4766
Change-Id: I8243329353fe41b0ffff35fd4383a9a09047cd52
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: openmm: Update to 8.4.0.

* gnu/packages/machine-learning.scm (openmm): Update to 8.4.0.

Change-Id: If91f5557966b7982b3504800d7761cc9b79b3af2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove fanc.

* gnu/packages/bioinformatics.scm (fanc): Delete variable.

Change-Id: I6ecb68155c021a67ff548bb2bd3bb6052676dc3a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>