gnu: python-pygsp: Update to 0.6.0.

* gnu/packages/graph.scm (python-pygsp): Update to 0.6.0.
[source] <pypi-uri>: Fix name.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'disable-doctets.
[propagated-inputs]: Remove python-scikit-image.
[native-inputs]: Remove python-coverage, python-coveralls, and
python-flake8; add python-matplotlib, python-pyunlocbox,
python-scikit-image, and python-setuptools.

Change-Id: Ic2ef43e47967897e2d7df7e628a8d02ff7684360
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pyunlocbox.

* gnu/packages/graph.scm (python-pyunlocbox): New variable.

Change-Id: I0281d2e1cfa4ad61a64e168f2c70344afd96ad3a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-verde: Update to 1.8.1.

* gnu/packages/geo.scm (python-verde): Update to 1.8.1.
[arguments] <test-flag>: Skip one more test.
[propagated-inputs]: Add python-pykdtree and python-numba.
[native-inputs]: Remove python-wheel; add python-matplotlib and
python-pytest-mpl.

Change-Id: Iaeefd5f40cb553fd0c76556663279f75aa7917ad
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-metacells: Simplify.

* gnu/packages/bioinformatics.scm (python-metacells):
[arguments] <phases>: Merge 'set-numba-cache-dir and 'build-extension
into 'pre-check and just remove local source to prevent rebuilding
expansions for tests, it saves some compute time with the same output.
[native-inputs]: Add pybind11.

Change-Id: I95e6706813cc5d3167593440c714c5091303cb00
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-crosshair: Update to 0.0.101.

* gnu/packages/python-check.scm (python-crosshair): Update to 0.0.101.
[arguments] <test-flags>: Rework skipped tests, pass more.
<phases>: Remove 'fix-dependencies; add 'relax-requirements.
[native-inputs]: Remove python-wheel.
[propagated-inputs]: Add python-pygls.

Change-Id: I5b9c84d165c09ce62d364dbbd2da7108dc2eda1c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pygls.

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

Change-Id: Ifb4bf0277f87fec87161f57ec09b8916ee5de077
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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>