gnu: python-dask-image: Fix tests.

* gnu/packages/python-science.scm (python-dask-image)[arguments]
<test-flags>: Rework skipped tests and enable more tests.
[propagated-inputs]: Remove python-tifffile; add
python-tifffile-for-dask-image.
[description]: Remove new line in the end.

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

Change-Id: I8539569aab1134d049ec8e8c0041191ce61e2eb7

gnu: python-typeshed-client: Update to 2.8.2.

* gnu/packages/python-xyz.scm (python-typeshed-client): Update to 2.8.2.
[source]: Switch to git-fetch providing test data.
[arguments] <test-backend>: Use custom.
[propagated-inputs]: Add python-typing-extensions.
[native-inputs]: Remove python-wheel.

Change-Id: Icfbb809b45e0ca9e4b29237f0f622d77928f9730

gnu: python-lfdfiles: Update to 2025.9.17.

* gnu/packages/python-xyz.scm (python-lfdfiles): Update to 2025.9.17.
[source, propagated-inputs]: Improve style.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I728400b74276b036d021c25b6c25c92709f7776c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-tifffile: Update to 2025.10.4.

* gnu/packages/python-xyz.scm (python-tifffile): Update to 2025.10.4.
[build-system]: Switch to pyproject-build-system.
[arguments, description]: Improve style.
[native-inputs]: Add python-setuptools.  Remove python-pytest, as
tests are not run.

Change-Id: Ica27197142bf7f80a7078cae1581b65a73a9b4b2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-roifile: Update to 2025.5.10.

* gnu/packages/python-xyz.scm (python-roifile): Update to 2025.5.10.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
[native-inputs]: Add python-setuptools.

Change-Id: I35e052527647cc13ae345be3a2d99b7445bc3257
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-imagecodecs: Update to 2025.8.2.

Warning: In phase 'create-configuration, I've disabled 3 modules that
fail compilation with gcc@14, although they should theorically
compile: apng, lzo, tiff.  IMO it's a bit out of the scope for a
already heavy patch to try and fix C compilation errors. I added a
FIXME comment though.

* gnu/packages/python-xyz.scm (python-imagecodecs): Update to 2025.8.2.
[source]<snippet>: Remove code unbundling 3rd party modules.  Almost
all of those are not bundled in the sense that they are extracted and
patched from upstream sources, and using those upstream sources
directly won't help.
[build-system]: Switch to pyproject-build-system.
[arguments]: Use gexps.
<#:tests?>: Enable them.
<#:test-flags>: Ignore flaky test.
<#:phases>: Re-factor phase 'create-configuration. Add phase
'fix-sanity-check and 'configure-tests.
[inputs]: Add lcms, libheif, lzfse, python-blosc2.
[propagated-inputs]: Add python-matplotlib, python-tifffile.
[native-inputs]: Add python-pytest, python-setuptools.
[synopsis]: Improve style.

Change-Id: I1c13eea510136891c667741f73fbf1d3f4231551
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-executor: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-executor):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-mock, python-pytest, python-setuptools.
[decription]: Improve style.

Change-Id: Iaa0008971f89d92158170a066a742f883e9e1017
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-property-manager: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-property-manager):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.  Replace python-pytest-cov by
python-pytest.
[description]: Improve style.

Change-Id: Ib74ee7b09448964276016fa14fbc86126c51366f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pixelmatch: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-pixelmatch):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them for now, as I'm not able to
quickly diagnose the error.
[native-inputs]: Add python-poetry-core, python-pytest,
python-pytest-benchmark.
[description]: Improve style.

Change-Id: Ic63865d7d78ae49f06f953b460837f81daa9c361
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pikepdf: Update to 8.15.1.

* gnu/packages/python-xyz.scm (python-pikepdf): Update to 8.15.1.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Add phase 'set-version.
[native-inputs]: Add python-xmp-toolkit, python-setuptools.  Remove
python-coverage, python-pytest-cov.
[propagated-inputs]: Replace python-deprecation by python-deprecated.

Change-Id: Iae6014ce980a84461940f86866cd1000221c36cd
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add python-types-pyyaml.

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

Change-Id: I4420c567d2414a53aea2e54f5e2e121cef69155b
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Remove python-pyhull.

* gnu/packages/python-xyz.scm (python-pyhull): Delete variable.

Fixes: guix/guix#2886
Change-Id: I4ad2e4dd31c9606bdb4b95fb0feba643e43887b0

gnu: hatch: Move to package-management.

* gnu/packages/python-xyz.scm (hatch): Move from here ...
* gnu/packages/package-management.scm: ... to here.

Change-Id: I09eec61efc1f57d0e983ef5e366e89afad168364

gnu: hatch: Adjust inputs.

hatch is a final program which is not meant to be used as Python library,
this change move all propagated inputs to inputs.

* gnu/packages/python-xyz.scm (hatch)[propagated-inputs]: Move from here ...
[inputs]: ... to here.

Change-Id: I84feebbefd20db7656831becc8a62fff100e716d

gnu: hatch: Update to 1.9.7.

* gnu/packages/python-xyz.scm (hatch): Update to 1.9.7.
[source] <snippet>: Remove as no longer required.
[arguments] <test-flags>: Rework skipped tests and enable more.
[propagated-inputs]: Remove python-hatchling, python-pyperclip, and
python-virtualenv; add python-hatchling-for-hatch,
python-virtualenv-for-hatch, and python-zstandard.
[native-inputs]: Add nss-certs-for-test and python-hatch-vcs.

* gnu/packages/python-xyz.scm (python-virtualenv-for-hatch): New variable.
* gnu/packages/python-build.scm (python-hatchling-for-hatch): New variable.

Change-Id: Ib22be321c7afe79bb9d21029a1a0b1909508ed2f

gnu: python-rst.linker: Rename and update to 2.6.0.

* gnu/packages/python-xyz.scm (python-rst.linker): Rename to
python-rst-linker and update to 2.6.0.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Add phase 'set-version.
[native-inputs]: Add python-path, python-jaraco-vcs, python-pytest,
python-pytest-subprocess, python-setuptools-scm, python-setuptools.
[description]: Improve style.

Change-Id: I9dc2e2f9882ed3908766cf943a6d90611a165641
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add python-jaraco-versioning.

* gnu/packages/python-xyz.scm (python-jaraco-versioning): New variable.

Change-Id: I8d45cbdb7c498c9634a76ed3828037a49a989b71
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add python-jaraco-vcs.

* gnu/packages/python-xyz.scm (python-jaraco-vcs): New variable.

Change-Id: Ib029198d3e7dc629b221ac0133385850667b2d0b
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add python-jaraco-path.

* gnu/packages/python-xyz.scm (python-jaraco-path): New variable.

Change-Id: Iaf8bc8ff56fd361b73b664d95f8a358dc1edcc02
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-scp: Update to 0.15.0.

* gnu/packages/python-xyz.scm (python-scp): Update to 0.15.0.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.
[arguments, description, propagated-inputs]: Run guix style.

Change-Id: Ic79dd2d9a2b0f01c0596b0e6fde664174ab9ee2c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>