[harryswift01]

Summary

This PR moves the CodeEntropy documentation to the shared CCPBioSim Sphinx theme (ccpbiosim-sphinx-theme) and generates the API reference with sphinx-autoapi.

Changes

• Replace Furo with ccpbiosim-sphinx-theme and set the theme in conf.py.
• Add a banner, quick start and section cards to the home page, with short labels in the navigation.
• Generate the API reference with sphinx-autoapi instead of sphinx-apidoc, so the files in docs/api/ and the autodoc mocks are no longer needed.
• Show constructor arguments from __init__ docstrings in the API reference.
• Remove nbsphinx, sphinx_copybutton, sphinx.ext.autodoc and sphinx.ext.autosummary, which are no longer needed or are loaded by other extensions.
• Move the documentation into docs/source to match the other CCPBioSim repositories, and update the Makefile, readthedocs.yml and README logo paths.
• Remove leftover files to match the Python template, and fix the build instructions in the developer guide.

Testing

• Built the docs with make -C docs html SPHINXOPTS="-W --keep-going" with no warnings.
• Checked the home page, API, Science and Getting Started pages, the "Edit on GitHub" links and the copy buttons.

Impact

• Docs only, no changes to the CodeEntropy package.
• The docs build no longer imports CodeEntropy, so MDAnalysis, rdkit and waterEntropy are not needed to build them.
• API page URLs change from api/... to reference/....

Checklist

• Tests added or updated
• Documentation updated
• If dependencies in pyproject.toml changed, the lower bounds were reviewed deliberately

[jimboid]

This is great work. Happy to see this merged in and spammed to other repos.