refactor(docs): move the documentation into docs/source

Author: harryswift01

.gitignore

@@ -63,8 +63,8 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
-docs/autosummary/
+docs/build/
+docs/source/autosummary/
 
 # PyBuilder
 target/

README.md

@@ -14,8 +14,8 @@ CodeEntropy
 CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
 
 <p align="center">
-    <img src="docs/_static/logos/biosim-codeentropy_logo_light.png#gh-dark-mode-only" alt="CodeEntropy logo" width="300"/>
-    <img src="docs/_static/logos/biosim-codeentropy_logo_dark.png#gh-light-mode-only" alt="CodeEntropy logo" width="300"/>
+    <img src="docs/source/_static/logos/biosim-codeentropy_logo_light.png#gh-dark-mode-only" alt="CodeEntropy logo" width="300"/>
+    <img src="docs/source/_static/logos/biosim-codeentropy_logo_dark.png#gh-light-mode-only" alt="CodeEntropy logo" width="300"/>
 </p>
 
 See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information.

docs/Makefile

@@ -5,8 +5,8 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 SPHINXPROJ    = CodeEntropy
-SOURCEDIR     = .
-BUILDDIR      = _build
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/_static/custom.css docs/source/_static/custom.cssdocs/_static/custom.css renamed to docs/source/_static/custom.css

@@ -191,19 +191,18 @@ Run the same checks locally with `uv <https://docs.astral.sh/uv/>`_::
 Building Documentation
 ----------------------
 
-Build documentation locally::
+Install the documentation dependencies and build the documentation locally::
 
+    pip install -e ".[docs]"
     cd docs
     make html
 
 The generated HTML files will be in ``docs/build/html/``.
 
 Open ``index.html`` in your browser to preview.
 
-Documentation sources are located in:
-
-- ``docs/user_guide/``
-- ``docs/developer_guide/``
+The documentation sources are in ``docs/source/``, and the API reference is generated
+from the source code by sphinx-autoapi.
 
 Contributing Code
 -----------------