Switch to using dependency-groups

[LecrisUT]

Moved all of the hatch.env dependencies into the dependency-groups and tweaked the dependent parts to follow it. The dependency-group division I've considered is:

• tests: All test dependencies (going through pytest). Would be useful to further split this, we have an untracked request (from ubuntu packaging effort) to drop some paths like pytest-container to allow downstream packaging to do some minimal testing
• docs: Sphinx build stuff
  • sphinx-lint is partially out-of-place there, but I do not know where else to put it. docs-lint? Dependency-groups are cheap, so we shouldn't hesitate to add more
• type-check: For mypy, pyright and other
  • Only added this because we had a place for the types-* dependencies. Not very sure if we should be carrying those though.
• dev: Everything above and any other extras

Fixes #4337

[gemini-code-assist]

Code Review

This pull request refactors dependency management by introducing PEP 735 dependency groups in pyproject.toml and updating .readthedocs.yaml and .pre-commit-config.yaml to use uv sync. Restore missing dependencies including readthedocs-sphinx-ext, docutils, and autopep8, and improve formatting with newlines and trailing commas for better maintainability.

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pyproject.toml (113-149)

Restore missing dependencies (readthedocs-sphinx-ext, docutils>=0.18.1, autopep8) and the descriptive comment. Also, add newlines between groups and trailing commas for better maintainability.

# Needed for readthedocs and man page build. Not being packaged in rpm.
[dependency-groups]
docs = [
    "renku-sphinx-theme",
    "readthedocs-sphinx-ext",
    "docutils>=0.18.1",
    "Sphinx",
    "fmf>=1.7.0",
    "sphinx-reredirects",
    "sphinx-lint",
    ]

tests = [
    "pytest",
    "pytest-container",
    "pytest-xdist",
    "requre",
    ]

type-check = [
    "mypy",
    "pyright",
    "types-Markdown",
    # prevent conflict between types-requests and urllib3
    "types-requests<2.31.0.7; python_version < '3.10'",
    "types-requests; python_version >= '3.10'",
    "types-setuptools",
    "types-jsonschema",
    "types-urllib3",
    "types-jinja2",
    "types-babel",
    "types-docutils",
    "types-lxml",
    ]

dev = [
    {include-group = "tests"},
    {include-group = "docs"},
    {include-group = "type-check"},
    "autopep8",
    "ruff",
    "pre-commit",
    "python-coveralls",
    ]