Migrate from poetry to uv, sphinx to mkdocs

[amrit110]

This pull request makes a comprehensive migration from Poetry to uv for dependency management, updates the development and documentation workflows to use uv and MkDocs, and modernizes the documentation structure and build process. It removes legacy Sphinx and Poetry configurations, updates CI/CD pipelines, and provides clearer developer instructions.

The most important changes are:

Dependency Management and Development Workflow

• Migrated all development and CI workflows from Poetry to uv, including updating the documentation, contributing guides, and pre-commit hooks to reference uv commands and lock files instead of Poetry. (CONTRIBUTING.MD, docs/contributing.md, .pre-commit-config.yaml, .python-version) [1] [2] [3] [4]

Continuous Integration and Deployment

• Rewrote all GitHub Actions workflows (tests.yaml, smoke_tests.yaml, static_code_checks.yaml, publish_and_release.yml) to use uv for dependency installation, environment setup, and running scripts/tests, removing all Poetry-related steps and caches. [1] [2] [3] [4] [5] [6] [7]
• Added a new unified documentation workflow .github/workflows/docs.yml for building and deploying docs with uv and MkDocs, and removed legacy Sphinx-based workflows (docs_build.yml, docs_publish.yml). [1] [2] [3]

Documentation System Modernization

• Transitioned documentation from Sphinx to MkDocs, including removing Sphinx-specific files (docs/Makefile), updating the documentation structure, and adding new guides for building and serving docs locally with uv and MkDocs. (docs/README.md, docs/api.md, docs/examples/index.md) [1] [2] [3] [4]
• Updated documentation configuration references to point to mkdocs.yml and clarified the directory structure and build instructions.

General Cleanup

• Removed obsolete Sphinx and Poetry references and files throughout the repository to ensure consistency with the new uv-based workflow. [1] [2] [3]

These changes collectively modernize the project's developer experience, streamline CI/CD, and make documentation easier to build and maintain.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.95%. Comparing base (c5cb16e) to head (df107ae).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #474      +/-   ##
==========================================
- Coverage   79.65%   74.95%   -4.70%     
==========================================
  Files         166      166              
  Lines       10554    10554              
==========================================
- Hits         8407     7911     -496     
- Misses       2147     2643     +496     

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[emersodb]

It looks like there are still a number of places in the repository that reference the old poetry instructions. I'd suggest also updating them there to make sure we're consistent in guidance throughout, even in the research repositories folders etc.

[emersodb]

It looks like we also need to update the link https://docs.astral.sh/ruff faq/#how-does-ruff-compare-to-flake8 to https://docs.astral.sh/ruff/faq/#how-does-ruffs-linter-compare-to-flake8 in two places of the repository as they are broken with the previous link

[emersodb]

In CONTRIBUTING.md the note/alert renderings are broken for the note:

> [!NOTE]
> As a matter of convention choice, classes are documented through their `__init__` functions rather than at the "class" level.

and

> [!NOTE]
> The contents of the tests folder is not packed with the FL4Health library on release to PyPi

[emersodb]

It looks like the latex/math renderings are also broken. See :math:\mathbf{w}^t in the docs for fed_prox_client in the docs

[emersodb]

The code rendering for the docs is also broken. See the init function for the EmaMetric where we try to render a python code block.

[emersodb]

Overall a really needed migration from Poetry to UV. This will definitely help us a lot. A few minor comments and some other things that have broken with the move from Sphinx to mkdocs. I fixed some of them, but there are others that require a bit of looking into.

[emersodb]

It seems as though keras was removed here...

[amrit110]

Do you know if keras is actually used in the library? i don't see it being imported anywhere

[emersodb]

That's fair. It may not be. If the tests pass then we're probably good to remove it from the core. Might want to update the comment though that says it's being included in dev ("so keras is also in dev group")