gnu: python-milc: Add missing inputs.

* gnu/packages/python-xyz.scm (python-milc)[native-inputs]: Add
python-setuptools and python-wheel.

Change-Id: I8711c8fff3f8cae5a875f0cf74ae049e3719ca80

gnu: python-rdflib: Update to 7.1.1.

* gnu/packages/rdf.scm (python-rdflib): Update to 7.1.1.
[arguments]: Use #:test-flags; remove custom build phases.
[native-inputs]: Add python-pytest-cov.
[propagated-inputs]: Add python-lxml, python-networkx, and python-orjson;
remove python-html5lib.

Change-Id: If1a10cb359be8e838963edf72c7d1a5ee08b396a

gnu: python-islenska: Update to 1.0.3.

* gnu/packages/python-xyz.scm (python-islenska): Update to 1.0.3.

Change-Id: I053a53c7c215064d9dba3a2e91b20e6bc4225d2a

gnu: set-xorg-configuration: Update code comment.

* gnu/services/xorg.scm (set-xorg-configuration): Update the comment
about platforms with rust support.

Change-Id: I6237ee9d26b5a74fb0d0b6680d3ff827d2a67418

gnu: desktop-services-for-system: Update code comment.

* gnu/services/desktop.scm (desktop-services-for-system): Update the
comment about platforms with rust support.

Change-Id: Ibefa826494e29498870f392c0fec87d606d386ec

gnu: python-stsci-imagestats: Fix build.

* gnu/packages/astronomy.scm (python-stsci-imagestats)[native-inputs]: Add
python-setuptools, python-wheel.

Change-Id: I3a788e066cdbba59983b1cdb0e81c7dc5733d7a5

gnu: python-lsp-server: Update to 1.12.0, fixing build.

* gnu/packages/python-xyz.scm (python-lsp-server): Update to 1.12.0.
[source]: Update URI.
[arguments]: Via #:test-flags, reinstate test_pydocstyle_lint test and skip
the test_jedi_completion_with_fuzzy_enabled one.  Ignore conftest.py.
[native-inputs]: Remove python-coverage and python-pytest-cov.  Add
python-setuptools-scm.

Change-Id: I48eed0b0ecd3ca6ac187292620d75aba9090307f

gnu: python-yapf: Update to 0.43.0.

* gnu/packages/python-xyz.scm (python-yapf): Update to 0.43.0.
[native-inputs]: Remove python-importlib-metadata.

Change-Id: I0d168d157d9daae664c19282d4a5b60a27dd9dc3

gnu: python-rope: Fix build.

* gnu/packages/python-xyz.scm (python-rope)
[native-inputs]: Add python-pip.

Change-Id: I20d2c77b9f343c6012af9e7b33fe73fed78ddc18

gnu: c-blosc: Update home page URL.

* gnu/packages/compression.scm (c-blosc) [home-page]: Update URL.

Change-Id: I72bb93a9d166294da991201b29f16a8f41f1f44e

gnu: python-nptyping: Update to 2.5.0.

This reinstates commit 843bec9a15eb3f3293ddfeefde97bde461ced7ee, with
necessary changes for the test suite to pass.

* gnu/packages/python-check.scm (python-nptyping): Update to 2.5.0.
[arguments]: Add #:test-flags.
[native-inputs]: Add python-feedparser, python-pandas, python-pytest

Change-Id: I352cb042cfa11de43993ec3bdcbc0b3008750755

gnu: python-pytest-cython: Add python-wheel to native inputs.

* gnu/packages/python-check.scm (python-pytest-cython)
[native-inputs]: Add python-wheel.

Change-Id: I7557ccc6ef8fbb30cd3c7e89049a0089a8df94d6

gnu: python-pytest-cython: Remove extraneous python-nox native input.

* gnu/packages/python-check.scm (python-pytest-cython)
[native-inputs]: Remove python-nox.

Change-Id: I585b17d63e52e62fd7c633354b74e4ae6233f722

gnu: python-tox: Update to 4.8.0 and disable tests.

* gnu/packages/python-check.scm (python-tox): Update to 4.8.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Delete #:phases.  Add #:test-flags.
[propagated-inputs]: Remove python-py, python-six and python-toml.  Add
python-cachetools, python-chardet, python-colorama, python-platformdirs,
python-pyproject-api and python-tomli.
[native-inputs]: Remove python-pathlib2, python-pytest-freezegun,
python-pytest-timeout, python-setuptools-scm.  Add python-distlib,
python-hatchling, python-hatch-vcs, python-psutil, python-pytest-mock,
python-pytest-xdist and python-re-assert.

Change-Id: I7c58649ac4c0fcb72e5009a7a2a06570e28d3eff

gnu: python-pandas-stubs: Update to 2.2.3.241126.

* gnu/packages/python-science.scm (python-pandas-stubs): Update to
2.2.3.241126.
[arguments]: Ignore tests/test_io.py in #:test-flags.
[native-inputs]: Replace python-sqlalchemy with python-sqlalchemy-2.

Change-Id: If27b3a5b687ca230a209e8a8087a89802414912e

gnu: python-tables: Update to 3.10.1.

* gnu/packages/python-xyz.scm (python-tables): Update to 3.10.1.
[source]: Update snippet.
[arguments]: Delete FIXME, which no longer applies to reworked definition.
Delete use-gcc phase.  Delete build phase override.  Add set-LD_LIBRARY_PATH
phase.  Honor TESTS? in check phase.
[propagated-inputs]: Add python-blosc2 and python-typing-extensions.
[inputs]: Add c-blosc2.

Change-Id: Idfed15a617e51c8ec1593d9a35afdcfa132e0740

gnu: Add python-blosc2.

* gnu/packages/python-compression.scm (python-blosc2): New variable.

Change-Id: Id83074efd08b03c09e4c620d3a92a57c0d6340d0

gnu: Add python-ndindex.

Adapted from <https://raw.githubusercontent.com/Blosc/python-blosc2/refs/heads/main/.guix/modules/python-blosc2-package.scm>.

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

Co-authored-by: Ivan Vilata i Balaguer <ivan@selidor.net>
Change-Id: I38fbcbd8859c2ddbfdd39e8d84a63b20deef75c4

gnu: Add c-blosc2.

Adapted from
https://raw.githubusercontent.com/Blosc/c-blosc2/refs/heads/main/.guix/modules/c-blosc2-package.scm.

* gnu/packages/compression.scm (c-blosc2): New variable.

Change-Id: Ic0f11487e8d920dd31dfb009485c204fa1b575f7
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Co-authored-by: Ivan Vilata i Balaguer <ivan@selidor.net>

gnu: python-sphinx-prompt: Update to 1.9.0.

* gnu/packages/sphinx.scm (python-sphinx-prompt): Update to 1.9.0.
[source]: Switch to PyPI URL.
[build-system]: Switch to pyproject-build-system.
[arguments]: Delete #:phases.  Add #:tests?.
[native-inputs]: Remove python-pytest and python-sphinx.  Add
python-poetry-core.
[propagated-inputs]: Add python-certify, python-docutils, python-idna,
python-pygments, python-sphinx and python-urllib3.

Change-Id: Iaa70e214594730d6eee983bfbd80cb05a35ebab7