gnu: python-pycollada: Update to 0.9.2.

* gnu/packages/python-xyz.scm (python-pycollada): Update to 0.9.2.
[native-inputs]: Remove python-wheel.

Change-Id: I3cc70c7eeda9e4c54a0457ba430e4c6cbe1697f3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-console: Move to jupyter.

* gnu/packages/python-xyz.scm (python-jupyter-console): Move from here ...
* gnu/packages/jupyter.scm: ... to here.

Change-Id: I687d44df58fab4d62a3eac92f2dab1eebdc89921
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-console: Update to 6.6.3.

* gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.6.3.
[arguments] <test-flags>: Skip one test.
<phases>: Add 'pre-check.
[propagated-inputs]: Add python-ipython, python-jupyter-core,
python-pyzmq, and python-traitlets.
[native-inputs]: Remove python-setuptools; add python-flaky and
python-hatchling.

Change-Id: Ia7d12b313cfcc890a5173813b92d97872ece742b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-jupyter-console-minimal.

Variable is not public and not in use by any other packages.

* gnu/packages/python-xyz.scm (python-jupyter-console-minimal): Delete variable.

Fixes: guix/guix#4881
Change-Id: I3b13ec6522f8c7c61a39e8f2262b652fbcb4210b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-client: Move to jupyter.

* gnu/packages/python-xyz.scm (python-jupyter-client,
python-jupyter-client-bootstrap): Move from here ...
* gnu/packages/jupyter.scm: ... to here.

Change-Id: I036632e68c808877de14da7f91863be50cdafd61
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-client: Simplfy bootstrapping.

* gnu/packages/python-xyz.scm (python-jupyter-client): Take over
definition of python-jupyter-client-bootsrap with adjustments.
[arguments] <phases>: Remove 'hide-zmq-deprecation-warnings, and
'set-tool-file-name, it uses Python's "subprocess.Popen" now; add
'fix-pytest-config, and 'pre-check'; use default 'check.
(python-jupyter-client-bootsrap): Inherit from python-jupyter-client

Change-Id: I2cf3aceb4d33995853cd36e79034a5867e51444e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-core: Move to jupyter.

* gnu/packages/python-xyz.scm (python-jupyter-core): Move from here ...
* gnu/packages/jupyter.scm: ... to here.

Change-Id: Id577b47b0a6c9a8754e6dc4f07e5ac8ba4ea106d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-ipython-minimal.

* gnu/packages/python-xyz.scm (python-ipython-minimal): New variable.

Change-Id: Ib68f3a7f2d45064aa83c7d034011ce4b43391ab6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ipython: Update to 9.8.0.

* gnu/packages/python-xyz.scm (python-ipython): Update to 9.8.0.
[arguments] <test-backend, test-flags>: Move custom {check} options
here.
<phases>: Remove 'make-docs-reproducible, resolved upstream; add
'pre-check and use default 'check.
[inputs]: Remove readline and which.
[propagated-inputs]: Remove python-colorama and python-exceptiongroup;
add python-ipython-pygments-lexers.
[native-inputs]: Remove python-pickleshare, python-pytest-asyncio-0.21,
and python-wheel; add python-pytest-asyncio and python-trio.

Change-Id: I3f96109e70772cb07b6a24bb83058473f182e3ed
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-contourpy: Update to 1.3.3.

* gnu/packages/python-xyz.scm (python-contourpy): Update to 1.3.3.

Change-Id: Id764c632d375f6e68782adf5385f227eefaebefd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jmespath: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-jmespath):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Remove python-setuptools-67; add  python-setuptools.

Change-Id: I7c140b87eb9da476cfffc090663e5960b2c57de8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-hnswlib: Update to 0.8.0.

* gnu/packages/python-xyz.scm (python-hnswlib): Update to 0.8.0.

Change-Id: I494260ebd9230c729ca4dca0cc7ef5c2685bf19a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-seaborn: Skip 3 tests.

* gnu/packages/python-xyz.scm (python-seaborn)[arguments] <test-flags>:
Skip 3 tests.

Change-Id: I32ea08c88eadddf1afcbcab51f813ea5a79f8481
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-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-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: python-xmp-toolkit: Update to 2.1.0.

* gnu/packages/python-xyz.scm (python-xmp-toolkit): Update to 2.1.0.
[source]: Remove patch as applied upstream.
[arguments] <test-flags>: Run all tests.
<phases>: Remove 'configure-environment; add 'patch-source.
[native-inputs]: Remove python-setuptools and python-wheel; add
python-flit-core.

* gnu/packages/patches/python-xmp-toolkit-add-missing-error-codes.patch:
Delete file.
* gnu/local.mk (dist_patch_DATA): Deregister patch.

Change-Id: I3443ecd6ad2bd423544d06d1e6e0de7079ed6296
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pydantic-extra-types.

* gnu/packages/python-xyz.scm (python-pydantic-extra-types): New variable.

Change-Id: I6603d0f0a5cbef6b4b9aede144623604ad5fbf37
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-annotated-doc.

* gnu/packages/python-xyz.scm (python-annotated-doc): New variable.

Change-Id: Iff2bb3c690d9260d543e268210286c2591e67c84
Signed-off-by: Rutherther <rutherther@ditigal.xyz>