gnu: python-trimesh: Enable tests.

* gnu/packages/python-science.scm (python-trimesh): Enable tests and
apply new package style.
[source]: Use git checkout which has working test suit.
[arguments] <#:test-flags>: Disable tests requiring optional Python
modules.
[propagated-inputs]: Add python-chardet, python-colorlog python-httpx
python-jsonschema python-lxml python-networkx python-pillow
python-requests python-rtree python-scipy python-setuptools
python-shapely python-sympy and python-xxhash.

Change-Id: I1aa363053c2d736bc44b8f9071c637256cc2d952

gnu: python-trimesh: Update to 4.0.10.

* gnu/packages/python-science.scm (python-trimesh): Update to 4.0.10.
[build-system]: Swap to pyproject-build-system.

Change-Id: I757b4c27db9969d42021434883a057debbbc83fd

gnu: python-xarray-einstats: Update to 0.7.0.

* gnu/packages/python-science.scm (python-xarray-einstats): Update to 0.7.0.

Change-Id: Iddd1fca8c37f05a928d20b90f9f95814f31435b2

gnu: python-pyts: Update to 0.13.0.

* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; enable all tests.
[propagated-inputs]: Remove python-matplotlib.

Change-Id: Iafcc047d8bb14e1eef514fd92aa53f8fda38eab0

gnu: python-pydicom: Update to 2.4.4.

* gnu/packages/python-science.scm (python-pydicom): Update to 2.4.4.

Change-Id: I996115fb3bdf0bd61d2b2dcdb2500b31ce104597

gnu: python-pydicom: Simplify package style.

* gnu/packages/python-science.scm (python-pydicom)[build-system]: Swap
to pyproject-build-system.
[description]: Simplify wording, indent.

Change-Id: I7ef413ea2da6cbb83eb33424c559f7ac5ed549cb

gnu: python-pynetdicom: Simplify package style.

* gnu/package/python-science.scm (python-pynetdicom)[build-system]: Swap
to pyproject-build-system.
[description]: Simplify wording, indent.

Change-Id: If4e80d06edb0080685d0695f30abc2f9db669f45

gnu: Add python-pynetdicom.

* gnu/packages/python-science.scm (python-pynetdicom): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-scipy: Update to 1.12.0.

* gnu/packages/python-science.scm (python-scipy): Update to 1.12.0.
[propagated-inputs]: Add python-jupytext, python-mpmath, python-mypy,
python-numpydoc, python-pydata-sphinx-theme, python-pydevtool,
python-rich-click, python-sphinx, python-threadpoolctl, and
python-typing-extensions; remove python-pyparsing.
[native-inputs]: Add python-hypothesis, python-pycodestyle, python-pytest-cov,
and python-pytest-xdist; remove python-threadpoolctl.

Change-Id: I81a4831e3d94c58416f7d35ec47de90370b88210

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

* gnu/packages/python-science.scm (python-tdda)[arguments]<#:phases>: Remove relax-requirements phase.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-scikit-fem: Update to 9.0.1.

* gnu/packages/python-science.scm (python-scikit-fem): Update to 9.0.1.
[arguments]<#:test-flags>: Drop it to activate all tests.
[native-inputs]: Add python-autograd, python-pyamg, and python-shapely.

Change-Id: Ic4706196026bd5756b4db8230b15efacdca7d463

gnu: Add python-pyamg.

* gnu/packages/python-science.scm (python-pyamg): New variable.

Change-Id: Ibf39fecd14d4e6fd72078b217737e5e5cbbf2321
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pandera: Fix build.

* gnu/packages/python-science.scm (python-pandera): Fix build.
[source]: Delete tests/modin directory.
[native-inputs]: Remove python-modin.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pandas-stubs: Update to 1.5.3.230321.

* gnu/packages/python-science.scm (python-pandas-stubs): Update to
1.5.3.230321.
[arguments]<#:test-flags>: Ignore tests that require a version of
python-pyarrow with ORC integration.
[native-inputs]: Add python-odfpy.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-plotnine: Reformat with guix style.

* gnu/packages/python-science.scm (python-plotnine): Reformat with guix style.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-plotnine: Fix build.

* gnu/packages/python-science.scm (python-plotnine): Fix build.
[arguments]<#:test-flags>: Add test_custom_shape to ignored tests.

Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add python-pandera.

* gnu/packages/python-science.scm (python-pandera): New variable.

gnu: Add python-pandas-stubs.

* gnu/packages/python-science.scm (python-pandas-stubs): New variable.

gnu: python-deepdish: Fix build.

* gnu/packages/python-science.scm (python-deepdish): Fix build.
[build-system]: Swap to pyproject-build-system.
[arguments]<#:test-flags>: Silent failing tests.

Change-Id: I4c4df66fc80434aaf5b95a7a62b83e0c1c02a4c6

gnu: python-xarray: Update to 2023.12.0.

* gnu/packages/python-science.scm (python-xarray): Update to 2023.12.0.
[arguments]: Ignore one test file.
[propagated-inputs]: Add python-packaging.

Change-Id: I6b70f59670f7bc8b56787fe3436579db8ac113bb