gnu: python-vector: Update to 1.7.0.

* gnu/packages/python-science.scm (python-vector): Update to 1.7.0.
[propagated-inputs]: Add python-awkward, python-numba, and python-sympy.
[native-inputs]: Remove python-awkward and python-sympy; add python-notebook,
python-optree, and python-papermill.

Change-Id: I760c26d69b5a5e4530e80d8e57af65db2fdf319f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-xarray-datatree.

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

Fixes: guix/guix#5348
Change-Id: I7150cbe534f900286fb575f5883d9fe0980aa975
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-multiscale-spatial-image: Update to 2.0.3.

* gnu/packages/python-science.scm (python-multiscale-spatial-image): Update to 2.0.3.
[propagated-inputs]: Remove quasiquote and ((unquote insight-toolkit) "python"); add
python-dask, python-numpy, python-dateutil, python-spatial-image,
python-xarray, python-xarray-dataclass, and python-zarr.
[native-inputs]: Remove python-fsspec, python-ipfsspec, python-jsonschema,
python-nbmake, python-pooch, python-pytest, python-pytest-mypy,
python-urllib3, and python-zarr.

Change-Id: I22f93379f92da785f851c17d149745ea9124a999
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-xarray-dataclass.

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

Change-Id: Id4293a97741704c434b6847b7b1ede8d35dd1edd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

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

Change-Id: I8c4e2bd6538411df0f33d05b80fe178690fcc4d8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-tdda: Skip one more test.

* gnu/packages/python-science.scm (python-tdda):
[arguments] <test-flags>: Skip one more test.
[native-inputs]: Remove python-wheel.

Change-Id: I1bcb5223627945d580d64e911cd73cf2da06287a
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: 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: 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-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: 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: python-fbpca: Fix tests.

* gnu/packages/python-science.scm (python-fbpca)[arguments]
<test-flags>: Skip one test.

Change-Id: I98ea94a1986e465ad41e6d0099ad4a1f45506c8e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pandera: Update to 0.27.1.

* gnu/packages/python-science.scm (python-pandera): Update to 0.27.1.
[arguments] <test-flags>: Rework skipped tests.

Change-Id: I7a21aa0e343cdf726e9d2c677bfccb0041dac39a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-anndata-minimal.

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

Change-Id: I9503ac08d0fa630d748574bb121690144a80bfea
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-anndata: Update to 0.12.7.

* gnu/packages/python-science.scm (python-anndata): Update to 0.12.7.
[arguments] <test-flags>: Skip CUDA dependent tests.
[phases]{set-version}: Remove setting zip timestamp logic.
[propagated-inputs]: Remove python-importlib-metadata,
python-scikit-learn, and python-setuptools; add python-numpy.
[native-inputs]: Add hdf5, python-openpyxl, python-pyarrow,
python-pytest-randomly, and python-scikit-learn.

Change-Id: I8e68cf85d435a13db995ea966ed5ff9edac3d672
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pythran: Clean up artifacts.

* gnu/packages/python-science.scm (python-pythran): Adjust style and
remove unused parts.
[source] <url>: Use a direct URL string.
[arguments] <test-flags, phase:pre-check>: Drop them as not used.
[native-inputs]: Remove openblas, python-pytest, python-pytest-xdist,
and python-wheel.
[home-page]: Move above [synopsis].

Change-Id: I7708981548ce68351c00fbf4e8f8e806a18f798a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-asap3: Update to 3.13.10.

* gnu/packages/python-science.scm (python-asap3): Update to 3.13.10.
[arguments] <tests?>: Enable.
[native-inputs]: Add python-pytest.

Change-Id: I166dfaf5f07f23d2d835d70f460cfa5f3f31ddb9
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ase: Update to 3.26.0.

* gnu/packages/python-science.scm (python-ase): Update to 3.26.0.
[arguments] <test-flags>: Run tests in parallel up to 8 threads.
[native-inputs]: Remove python-wheel.

Change-Id: Ib2e5c9751f6c3358bb35084076f79586473da88f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>