gnu: python-pyjanitor: Update to 0.32.5.

* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.32.5.
[arguments] <test-flags>: Rework ignored/skipped tests.
[propagated-inputs]: Remove python-requests.
[native-inputs]: Add python-openpyxl and python-requests.
[synopsys]: pandas->Pandas.

Change-Id: I12f3f1f6ab84d63882325103e8c729d44656c97c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pandas-flavor: Update to 0.8.1.

* gnu/packages/python-science.scm (python-pandas-flavor): Update to 0.8.1.
[phases]{fix-pytest-config}: New phase.
[propagated-inputs]: Remove python-lazy-loader and python-packaging.
[native-inputs]: Add python-setuptools and python-setuptools-scm.

Change-Id: I1f1325350f77ed61146f32da5bdc81aad1daec27
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-misc: Don't propagate python-numpydoc.

* gnu/packages/python-science.scm (python-scikit-misc)
[propagated-inputs]: Remove python-numpydoc.
[native-inputs]: Add python-numpydoc.

Change-Id: I9f3d3550789dd2943f496d90f59a063ac7df5e97
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pynetdicom: Don't propagate python-numpydoc.

* gnu/packages/python-science.scm (python-pynetdicom)
[propagated-inputs]: Remove python-numpydoc.
[native-inputs]: Add python-numpydoc.

Change-Id: Ib0bc20a289972af1d346f38213413c6930218ef0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ruffus: Switch to pyproject.

* gnu/packages/python-science.scm (python-ruffus):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Improve style.  Improve 'check phase.
[native-inputs]: Add python-setuptools.

Change-Id: If6607ce5db313c97d5aaff062ac8bfa4b55d5dee
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-geosketch: Update to 1.3.

* gnu/packages/python-science.scm (python-geosketch): Update to 1.3.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests>: Ignore them.
[native-inputs]: Add python-setuptools.

Change-Id: Ib86bb1a690585d925f3cd7ba801e89e04273d8e1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyvista: Ignore failing test.

* gnu/packages/python-science.scm (python-pyvista)[arguments]
<#:test-flags>: Ignore failing test.

Change-Id: I0dba730e92c7fd7e9d7d6273bba3b5e7646278c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyts: Update to 0.13.0-0.4f3d97b.

* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0-0.4f3d97b.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-wheel.
[description]: Improve it.

Change-Id: I64947107888826ad3db8cf1e2e4d3790c6a3e070
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-qutip: Update to 5.2.2.

* gnu/packages/python-science.scm (python-qutip): Update to 5.2.2.
[arguments] <test-flags>: Rework skipped/ignored tests.
<phases>: Use default 'check; add 'remove-local-source.
[propagated-inputs]: Add python-cvxopt, python-cvxpy, python-mpi4py,
python-mpmath, and python-tqdm.
[native-inputs]: Remove python-numpy, python-packaging, python-scipy,
and python-wheel; add python-pytest-rerunfailures.

Change-Id: I1ee08658e6a7c6ef2c6b42b9d121113dedad04f7
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-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-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: Remove python-statannot.

A message from upstream: "This repository is not maintained anymore. I
recommend using the forked package trevismd/statannotations, which has a
cleaner API and further extends the functionalities of statannot."

* gnu/packages/python-science.scm (python-statannot): Delete variable.

Fixes: guix/guix#5355
Change-Id: Ib3347ff2077f62d4e97c0f9dc437b419d260c4b5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pandas-stubs: Update to 2.3.3.251219.

* gnu/packages/python-science.scm (python-pandas-stubs): Update to 2.3.3.251219.
[arguments]: Drop all but 2 skipped tests.
[propagated-inputs]: Add python-numpy.
[native-inputs]: Remove python-tables, which, xclip,
xorg-server-for-tests, and xsel; add python-beautifulsoup4,
python-fsspec, python-html5lib, python-jinja2, python-loguru,
python-mypy, python-numexpr, python-openpyxl, python-typing-extensions,
python-xlrd, python-xlsxwriter, and tzdata-for-tests.

Change-Id: I7b7b85c1ce9b1e575069a79321db4ff515372942
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-narwhals: Update to 2.15.0.

* gnu/packages/python-science.scm (python-narwhals): Update to 2.15.0.
[propagated-inputs]: Add python-duckdb, python-packaging, and python-rich.
[native-inputs]: Remove python-duckdb.

Change-Id: I0af82e4cbe2b3c2b3ae3803b77cde5f6c921a1a6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-narwhals-minimal.

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

Change-Id: I972010ea88c649d41227c51256b739a022a350df
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-libneuroml: Update to 0.6.7.

* gnu/packages/python-science.scm (python-libneuroml): Update to 0.6.7.
[native-inputs]: Remove python-wheel.

Change-Id: I7ef49953a922116bd2c1aeb12ea548d0dd8afb18
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

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

Change-Id: I8236576e39b7e6f8b981126cbf67fc55f35db83c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>