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>

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

* gnu/packages/astronomy.scm (python-zodipy)[arguments] <phases>:
Remove 'relax-requirements.

Change-Id: I9b4ba21b06764f34212fd3fc019073f699cd36b9
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jacobi: Fix tests.

* gnu/packages/python-science.scm (python-jacobi)[arguments]<phases>:
Add 'fix-pytest-config.

Change-Id: Ia8b4c30d2d8d6cfe9bae79342614747c90ae6735
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-statmorph: Adjust inputs.

* gnu/packages/astronomy.scm (python-statmorph)[propagated-inputs]:
Remove python-scikit-image-next; add python-scikit-image.

Change-Id: I5aea37615dafdf495741f28dff42714ba3630762
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-image-next: Deprecate by python-scikit-image.

* gnu/packages/python-science.scm (python-scikit-image-next): Deprecate
in favor of python-scikit-image.

Change-Id: I006f4a302eabab82abd9c853f1b6a3d352f546ef
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-image: Update to 0.25.2.

* gnu/packages/python-science.scm (python-scikit-image): Update to 0.25.2.
[arguments] <test-flags>: Ignore benchmark tests.
<phases>: Remove 'change-home-dir, 'pre-check, 'post-check; add
'remove-local-source.
[propagated-inputs]: Remove python-cloudpickle, python-dask,
python-matplotlib, python-pythran, and python-pywavelets; add
python-packaging.
[native-inputs]: Remove python-numpydoc, python-packaging, and
python-wheel; add python-pythran.

Change-Id: Ifbfbb3e2d28dc8784f600a4cd1a0f0c7129fddb5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fits-schema: Update to 0.5.6-0.ccffe04.

* gnu/packages/astronomy.scm (python-fits-schema): Update to
ccffe04a8a47f2bd0f69014caaf73d9679b89a87 commit.
[source]: Switch to git-fetch providing compatibility with NumPy 2.
[arguments] <phases>: Remove 'fix-setup.cfg; add 'set-version.
[native-inputs]: Add python-setuptools-scm.

Change-Id: Ib826726400fef943c69e08a2528269495e1cb481
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

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

Change-Id: Iece347ed1b15d5e30e5989f1a2f8afe70c42ccef
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

* gnu/packages/astronomy.scm (python-jwst): [arguments]<phases>: Remove
'relax-requirements.

Change-Id: I67a1fcf9a9ac399267f2dd651874e4eff16f2e04
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

* gnu/packages/astronomy.scm (python-gwcs)[arguments]<phases>: Remove
'relax-requirements.

Change-Id: Ie7fe77594d220af84f40f18475f66addaf02f90d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fgivenx: Update to 2.4.2-0.cf51dbf.

* gnu/packages/python-science.scm (python-fgivenx): Update
towcf51dbf8b7efdd8d84f055740a069a5b882dcf77.
[source]: Switch to git-fetch providing comparability with recent
matblotlib version.
[arguments]: Drop all.
[home-page]: Fix URL https://github.com/fgivenx/fgivenx responding with
404, new one is taken from PyPI page.

Change-Id: Ia255f4b44967ee32e9b4a18cc15b80aa4cf0b09e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: genetic: Use python-pynbody@2.

* gnu/packages/astronomy.scm (genetic)[native-inputs]: Remove
python-pynbody-1; add python-pynbody.

Change-Id: I8996778f953adfe1deae811b6564139f276972de
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-esutil: Fix build with gcc-14.

* gnu/packages/astronomy.scm (python-esutil)[arguments] <phases>: Add
relax-gcc-14-strictness.
[native-inputs]: Remove python-numpy and python-wheel.

Change-Id: I2e896fdc6250cd19e93a12017836da8c33de0be8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>