gnu: Add python-lsprotocol.

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

Change-Id: Id12df328f4c8f51f9c45914fba8f4991857f7596
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fastcluster: Update to 1.3.0.

* gnu/packages/python-science.scm (python-fastcluster): Update to 1.3.0.
[arguments]: Drop all.
[native-inputs]: Remove python-wheel; add python-pytest.

Change-Id: Ib57e7067d7eff527f5d84f297d668cc0c7997a9c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cvxpy: Update to 1.7.5.

* gnu/packages/python-science.scm (python-cvxpy): Update to 1.7.5.
[arguments] <test-flags>: Skip some tests.
[propagated-inputs]: Remove pybind11; add python-cvxopt.
[native-inputs]: Remove python-wheel; add pybind11.

Change-Id: I83974c14d6422284c1f31fe8922cd9e7bc5a9253
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scs: Update to 3.2.10.

* gnu/packages/python-science.scm (python-scs): Update to 3.2.10.
[source]: Do not pull git submodules.
[phases]{substitute-git-submodules}: New phase.
[inputs]: Add lapack.
[native-inputs]: Add pythoncapi-compat and scs.

Change-Id: I44778c1969f074c80ca4ddf8350b6db5c2db136a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add scs.

* gnu/packages/maths.scm (scs): New variable.

Change-Id: Iea504b64a1da5cb4d446fe6461bbf4b2a47f4139
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-osqp: Update to 1.0.5.

* gnu/packages/python-science.scm (python-osqp): Update to 1.0.5.
[arguments] <test-flags>: Rework skipped tests.
[phases]{relax-requirements}: Remove phase.
{fix-osqp-source-location}: New phase.
[propagated-inputs]: Remove python-qdldl; add python-jinja2,
python-joblib, and python-setuptools.
[native-inputs]: Remove python-setuptools and python-wheel; add osqp,
pybind11, python-pytorch, python-scikit-build-core, and qdldl.

Change-Id: Ic6180f814a215d5bd772e4134f7ca291f1120081
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add osqp.

* gnu/packages/maths.scm (osqp): New variable.

Change-Id: If2eded2af7fa7060e793867f1128210e3b8f2ed1
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add qdldl.

* gnu/packages/maths.scm (qdldl): New variable.

Change-Id: Ic43b3a4e6af342748367e93f22f37efea4b923f6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-eventio-1.

* gnu/packages/astronomy.scm (python-eventio-1): Delete variable.

Fixes: guix/guix#5305
Change-Id: If753c3b722e748aafb52329e9fe8bab338617437
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: tangos: Update to 1.11.0.

* gnu/packages/astronomy.scm (tangos): Update to 1.11.0.

Change-Id: Iab7d48ccd5c29ad5ae4d37ebcad575af19ff2510
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-chaospy: Update to 4.3.21.

* gnu/packages/statistics.scm (python-chaospy): Update to 4.3.21.
[propagated-inputs]: Remove python-importlib-metadata.
[native-inputs]: Remove python-wheel.

Change-Id: I686c7fbaea1cf2e238c4a9eb3f1800489122b1c8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-numpoly: Update to 1.3.4.

* gnu/packages/python-science.scm (python-numpoly): Update to 1.3.4.
[arguments] <test-flags>: Skip one test.
[native-inputs]: Remove python-wheel; add python-cython.

Change-Id: I62142fd288ccfbc6506ed44d054b25af801a6b16
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyudev: Update to 0.24.4.

* gnu/packages/admin.scm (python-pyudev): Update to 0.24.4.
[source]: Switch to git-fetch for tests.
[build-system]: Switch to pyproject-build-system.
[arguments]: Use gexps.
<#:tests?>: Enable tests.
<#:test-flags>: Disable tests that need /sys/devices.
<#:phases>: Update 'patch-ctypes-udev phase.
[propagated-inputs]: Remove python-six.
[native-inputs]: Remove python-docutils, python-hypothesis, python-mock,
and python-sphinx; add python-setuptools.

Change-Id: I70834b09e280ef52c621b2a98455a8b7897f4367
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-plotly: Update to 5.24.1.

* gnu/packages/python-science.scm (python-plotly): Update to 5.24.1.
[arguments] <test-flags>: Rework skipped tests.
[propagated-inputs]: Remove python-ipython, python-pandas,
python-pillow, python-requests, python-retrying, python-scikit-image,
python-statsmodels, and python-vaex-core; add python-packaging.
[native-inputs]: Add python-geopandas, python-ipykernel,
python-ipython-minimal, python-matplotlib, python-numpy-1,
python-orjson, python-pandas, python-pillow, python-psutil,
python-pyshp, python-pytz, python-requests, python-retrying,
python-scikit-image, python-scipy, python-shapely, python-statsmodels,
python-tenacity, and python-vaex-core.

Change-Id: Ib9c80494d708627f4c0b30a18b4ddf53a33484ce
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-array-api-strict.

* gnu/packages/python-xyz.scm (python-array-api-strict): New variable.

Change-Id: Iab9649b967da898521316481ac466342afff2631
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ipywidgets: Update to 8.1.4.

* gnu/packages/python-xyz.scm (python-ipywidgets): Update to 8.1.4.
[build-system]: Switch pyproject-build-system.
[native-inputs]: Remove python-pytest-cov and python-setuptools-67; add
python-setuptools.

Change-Id: I09799c7cbcc5c59a04a792411977974c95d1688e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyterlab-widgets: Update to 3.0.12.

* gnu/packages/jupyter.scm (python-jupyterlab-widgets): Update to 3.0.12.

Change-Id: I934b1f4d3a9458821fbdcffb96ec663c7d315131
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-vaex-core: Update to 4.19.0.

* gnu/packages/python-science.scm (python-vaex-core): Update to 4.19.0.
[inputs]: Remove pybind11.
[propagated-inputs]: Remove python-click, python-progressbar2, python-pydantic-settings,
and python-requests; add python-diskcache, python-fsspec,
python-graphviz, python-h5py, python-httpx, python-psutil, and
python-s3fs.
[native-inputs]: Remove python-pytest and python-wheel; add pybind11.

Change-Id: Id9f65420d6be54e27ba850528c3fc3599696f320
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: htseq: Update to 2.0.9.

* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.9.
[propagated-inputs]: Remove python-matplotlib.
[native-inputs]: Remove python-wheel; add python-matplotlib.

Change-Id: I026cd0ecf01418b4c112b8d0f2f6c0ab709c38d7
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-coolbox: Update to 0.3.9.

* gnu/packages/bioinformatics.scm (python-coolbox): Update to 0.3.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?, test-flags>: Enable them.
<phases>: Delete 'sanity-check.
[inputs]: Remove pybind11.
[propagated-inputs]: Remove python-pybbi, python-pytest, and
python-termcolor.
[native-inputs]: Add pybind11, python-pytest, python-pypairix,
python-pybbi, python-setuptools, and samtools.

Change-Id: I356fa043a18e7901e50b15f2815f84178cf4e969
Signed-off-by: Rutherther <rutherther@ditigal.xyz>