remove duplication in dependency groups

[pacrob]

What was wrong?

• Extra dependencies were across dev, docs, and test groups, and most duplicated.
• We were using [project.optional-dependencies] for our dev dependencies instead of the recommended [dependency-groups] - See https://pydevtools.com/handbook/explanation/what-are-optional-dependencies-and-dependency-groups/

How was it fixed?

• Use [dependency-groups]
• Update how groups are included in tox.ini and .readthedocs.yaml due to switching from [project.optional-dependencies] to [dependency-groups].
• Keep separate groups, but remove duplication
• Also bumped towncrier version for py313 support from them.

To-Do

• Clean up commit history
• Add or update documentation related to these changes
• Add entry to the release notes

Cute Animal Picture

[seetadev]

@pacrob : Thanks a lot for this PR, Paul — this is a solid cleanup and very much appreciated 🙏

The move from [project.optional-dependencies] to [dependency-groups] is definitely the right direction. Reducing duplication across dev / docs / test while still keeping logical separation is fantastic and will enable better and easier maintenance.

Wish to share some of the improvements, which will be helpful to us:

• The identification and removal of duplicated deps across groups — this has been a bit of friction for contributors and CI alike.
• Updating tox.ini and .readthedocs.yaml in lockstep with the change — this avoids the usual “half-migrated” state that can be painful later.
• The addition for py313 support is great 👍
• The commits (extras → groups, RTD fixes, uv handling) are neat :)

From my side, I don’t see any conceptual blockers. I’m 👍 on merging this.

Happy to help review or co-author the documentation update if that’s useful.

Thanks again for taking this on — changes like this quietly improve the project significantly over time.

[seetadev]

@pacrob : The one CI/CD failure is unrelated to this PR and related to pub-sub test cases. I'll open up a discussion page and ask @Winter-Soren, @acul71 and @sumanjeet0012 to fix it up in a separate PR: wish to share the logs:

=========================== short test summary info ===========================
FAILED tests/core/pubsub/test_dummyaccount_demo.py::test_simple_seven_nodes_tree_topography
===== 1 failed, 1746 passed, 12 skipped, 3 warnings in 1026.55s (0:17:06) =====
py3.11-core: exit 1 (1029.58 seconds) D:\a\py-libp2p\py-libp2p> pytest -n auto --timeout=1200 tests/core pid=7736
py3.11-core: FAIL code 1 (1085.89=setup[37.14]+cmd[0.17,19.00,1029.58] seconds)
evaluation failed :( (1090.05 seconds)
Error: Process completed with exit code 1.