gnu: python-modin: Update to 0.37.1.

* gnu/packages/python-science.scm (python-modin): Update to 0.37.1.
[arguments] <test-flags>: Rework options.
<phases>: Remove 'loosen-requirements; add 'versioneer, and
'fix-pytest-config; rework {check} phase to include some API tests
scenarios.
[propagated-inputs]: Remove python-cloudpickle and python-s3fs; add
python-fsspec, python-psutil, and python-typing-extensions.
[native-inputs]: Remove python-jinja2, python-lxml, python-matplotlib,
python-msgpack, python-openpyxl, python-psutil, python-pyarrow,
python-pytest-benchmark, python-pytest-cov, python-scipy,
python-sqlalchemy, python-tables, python-tqdm, python-xarray,
python-xlrd, and python-wheel; add python-s3fs, python-setuptools, and
python-versioneer.

Change-Id: I86feaa9f1cd110ed2c430e9816d34da165bccb74
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyopengl: Skip one test.

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

Change-Id: I9ed0fb8093f3429fd7bb2f0ad5e2f26220300736
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cleanlab: Fix build.

* gnu/packages/machine-learning.scm (python-cleanlab)[arguments]
<test-flags>: Skip one more test.
<phases>: Add 'relax-requirements.
[native-inputs]: Remove python-wheel; add python-matplotlib.

Change-Id: I10e9d8a2eadc2de6d26f6247dc5e2305a215bd91
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-arviz: Update to 0.22.0.

* gnu/packages/statistics.scm (python-arviz): Update to 0.22.0.
[arguments] <test-flags>: Run base tests only, deselect 10 tests.
<phases>: Remove 'remove-radon, and 'write-permission; add 'pre-check.
[propagated-inputs]: Remove python-dm-tree, python-setuptools, and
python-wheel.
[native-inputs]: Add python-setuptools.

Change-Id: If8ab6c9917cb19463ab07935709d9d2f10c2329a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-arboreto: Update to 0.1.6-0.79f916b.

* gnu/packages/bioinformatics.scm (python-arboreto): Update to
79f916b0ea25c00989331b8db243826049c3d66c commit.
[arguments] <tests?, test-backend> Enable.
<phases>: Add 'disable-failing-tests.
[propagated-inputs]: Remove python-lz4, python-pyarrow, and
python-tornado-6.
[native-inputs]: Remove python-wheel.

Change-Id: If380a31f7a27832c0e0fd1dda80d5dfd3e539345
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-naima: Update to 0.10.3.

* gnu/packages/astronomy.scm (python-naima): Update to 0.10.3.
[native-inputs]: Remove python-setuptools, python-setuptools-scm, and
python-wheel; add python-hatch-vcs and python-hatchling.
[propagated-inputs]: Add python-numpy.

Change-Id: I91676156429f90237190f15cd1a7429ff31b4026
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-xarray-einstats: Update to 0.9.1.

* gnu/packages/python-science.scm (python-xarray-einstats): Update to 0.9.1.
[propagated-inputs]: Add python-einops and python-numba.
[native-inputs]: Remove python-einops and python-numba.

Change-Id: Ic3e05114dc3d6343523aec222f527ef9653ed2d6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-spectral-cube: Update to 0.6.7.

* gnu/packages/astronomy.scm (python-spectral-cube): Update to 0.6.7.
[arguments] <tests?, test-flags>: Enable, skip 5 tests.
[propagated-inputs]: Remove python-aplpy, python-distributed,
python-fsspec, python-matplotlib, python-pvextractor-bootstrap, and
python-reproject.
[native-inputs]: Remove python-wheel; add python-pytest,
python-pytest-astropy, python-pytest-xdist, and python-setuptools.

Change-Id: Ib34388a456f50d4296218c521e0a2af34a395362
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-reproject: Update to 0.19.0.

* gnu/packages/astronomy.scm (python-reproject): Update to 0.19.0.
[arguments] <test-flags>: Read options from pyproject.toml, skip 3 shaky
tests.
[inputs]: Remove python-asdf, python-gwcs, python-pyvo, python-shapely, and
python-sunpy-minimal.
[propagated-inputs]: Remove python-cloudpickle; add python-dask-image,
python-pillow, and python-pyavm.
[native-inputs]: Add python-asdf, python-gwcs, python-pyvo,
python-shapely, and python-sunpy-minimal.

Change-Id: I50792fc53a1e9d661704da1fe080b01c29bf1fb5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-dask-image: Update to 2025.11.0.

* gnu/packages/python-science.scm (python-dask-image): Update to 2025.11.0.
[arguments] <test-flags>: All tests passed.
<phases>: Add 'fix-pytest-config; rework 'set-version to read from envar.
[propagated-inputs]: Remove python-tifffile-for-dask-image; add
python-tifffile.
[native-inputs]: Remove python-setuptools-scm; add
python-setuptools-scm-next.

* gnu/packages/python-xyz.scm (python-tifffile-for-dask-image): Delete variable.

Change-Id: I928c39c848f3a20d5eb51d10e4c8374891b8f0b0
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-xarray: Update to 2025.12.0.

* gnu/packages/python-science.scm (python-xarray): Update to 2025.12.0.
[arguments] <test-flags> Rework skipped tests, do not depend on MyPy
type checker.
[native-inputs]: Remove python-wheel; add python-pytest-asyncio.

Change-Id: I49e33b614926cde8bd5fad09ac278bc79e9d3cb1
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: catch2: Update to 2.13.10.

* gnu/packages/check.scm (catch2): Update to 2.13.10.

Change-Id: I77467d122e445d6df233adbbf32565caadb3446c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-numba: Update to 0.62.1.

* gnu/packages/python-xyz.scm (python-numba): Update to 0.62.1.
[arguments] <test-backend, tests-flags>: Rework the most of the skipped
tests as they passed a few times at least on AMD Ryzen 7 3800X CPU, skip
long running tests in the first place with "--exclude-tags" option.
<phases>: Add 'pre-check; use default 'check, set
'disable-proprietary-features after 'build phase.
[native-inputs]: Remove python-wheel.

Change-Id: I10e555f53b48d6404945faee373253bac4598e84
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-llvmlite: Update to 0.45.0.

* gnu/packages/llvm.scm (python-llvmlite): Update to 0.45.0.
[inputs]: Remove patches for llvm-15; add llvm-20.
[native-inputs]: Add cmake-minimal.

Change-Id: Icb1f55a64de6e580645e286dc6f7f10dfe985c01
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: pyscenic: Update to 0.12.1-2.06bafba4.

* gnu/packages/bioinformatics.scm (pyscenic): Update to
06bafba412792f6efa5a552a23bb221cc3bdea1b commit.
[native-inputs]: Remove python-wheel; add python-setuptools.

Change-Id: I42b8c3701484f617c14d67f3bfa2408b83e50d6e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-tables: Update to 3.10.2-0.aad9079.

* gnu/packages/python-xyz.scm (python-tables): Update to
aad9079c80ce3ae7f385d00af760d171dcc10535 commit.
[source]: Switch to git-fetch providing comparability with python-numexpr.
<snippet>: Delete "hdf5-blosc" git submodule.
[phases]{pre-build}: Substitute "hdf5-blosc" source path.
[inputs]: Add hdf5-blosc.

Change-Id: I7624af17709e150cea4f316cc4fd7f1786c3df1c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-annoy: Add python-h5py.

* gnu/packages/python-xyz.scm (python-annoy)[arguments]<test-flags>:
Skip 3 tests requiring network access.
[native-inputs]: Add python-h5py.

Change-Id: I6cd3343d43b0f91ddf6c117844afa6ba1e662068
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: cpat: Update to 3.0.5.

* gnu/packages/bioinformatics.scm (cpat): Update to 3.0.5.
[source]: Switch to git-fetch providing test data.
<snippet>: Remove as no longer required.
[phases]{check}: Rework test steps, run cpat directly with correct
inputs.
[native-inputs]: Remove python-wheel.

Change-Id: I813cdf4aff2e75b855fc75237d9103f34aff45f2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-linetools: Skip 2 tests.

* gnu/packages/astronomy.scm (python-linetools)[arguments]<test-flags>:
Skip 2 incompatible with NumPy 2 tests.

Change-Id: Ib89bca6ebd2cd600b6f29fee643436c6f996b487
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

* gnu/packages/astronomy.scm (python-kanon)[propagated-inputs]: Remove
python-numpy; add python-numpy-1.

Change-Id: I3ded448d4f6fb6e7d34eaf24064816f3415e45a9
Signed-off-by: Rutherther <rutherther@ditigal.xyz>