My work: documentation system setup (issue #61)

[sumit08kumar]

Describe your changes

This PR implements the foundational Sphinx documentation system for neural-lam, as requested in Issue #61.

Key Changes:

• Sphinx Configuration: Set up docs/conf.py with 8 extensions (autodoc, napoleon, intersphinx, myst-parser, etc.) and sphinx-book-theme.
• API Reference: Created .rst stubs for 8 core modules to auto-generate documentation from Python docstrings.
• User Guide Migration: Transformed the monolithic README into a structured navigation tree (getting_started.md, user_guide/data.md, user_guide/graphs.md, training.md, evaluation.md, contributing.md).
• CI/CD Pipeline: Added .github/workflows/docs.yml to validate documentation on every PR (warnings become errors).
• RTD Deployment: Configured .readthedocs.yaml with CPU-only PyTorch for automated staging and production deployment.

Motivation and Context:
Currently, code documentation is buried in docstrings and the README has grown too large to navigate easily. This PR provides a searchable, versioned, and hyperlinked documentation website similar to PyTorch Geometric, making the project more accessible to researchers.

Dependencies:
Added docs dependency group to pyproject.toml including:
sphinx, sphinx-book-theme, myst-parser, sphinx-autodoc-typehints, sphinx-copybutton.

Issue Link

Closes #61

Type of change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
• 📖 Documentation (Addition or improvements to documentation)

Checklist before requesting a review

• My branch is up-to-date with the target branch - if not update your fork with the changes from the target branch (use pull with --rebase option if possible).
• I have performed a self-review of my code
• For any new/modified functions/classes I have added docstrings that clearly describe its purpose, expected inputs and returned values
• I have placed in-line comments to clarify the intent of any hard-to-understand passages of my code
• I have updated the README to cover introduced code changes
• I have added tests that prove my fix is effective or that my feature works
• I have given the PR a name that clearly describes the change, written in imperative form (context).
• I have requested a reviewer and an assignee (assignee is responsible for merging). This applies only if you have write access to the repo, otherwise feel free to tag a maintainer to add a reviewer and assignee.

Checklist for reviewers

Each PR comes with its own improvements and flaws. The reviewer should check the following:

• the code is readable
• the code is well tested
• the code is documented (including return types and parameters)
• the code is easy to maintain
• the build passes without warnings

Author checklist after completed review

• I have added a line to the CHANGELOG describing this change, in a section
  reflecting type of change (add section where missing):
  • added: when you have added new functionality
  • changed: when default behaviour of the code has been changed
  • fixes: when your contribution fixes a bug
  • maintenance: when your contribution is relates to repo maintenance, e.g. CI/CD or documentation
    maintenance: implemented Sphinx documentation system with RTD and CI/CD validation

Checklist for assignee

• PR is up to date with the base branch
• the tests pass
• (if the PR is not just maintenance/bugfix) the PR is assigned to the next milestone. If it is not, propose it for a future milestone.
• author has added an entry to the changelog (and designated the change as added, changed, fixed or maintenance)
• Once the PR is ready to be merged, squash commits and merge the PR.

[sadamov]

please contribute directly in this PR instead #252 #272