Sphinx Documentation

.github/workflows/ci.yml

@@ -14,7 +14,6 @@ permissions:
 
 env:
   UV_VERSION: "0.8"
-  UV_LINK_MODE: "copy"
 
 jobs:
   build:

.github/workflows/sphinx.yml

@@ -0,0 +1,43 @@
+name: "Sphinx: Render docs"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  UV_VERSION: "0.8"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
+    - name: Build HTML
+      uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: docs
+        build-command: make html
+        pre-build-command: |
+          python -m pip install -U pip
+          python -m pip install "uv==${{ env.UV_VERSION }}"
+          uv --version
+          uv venv
+          uv pip install -e ".[docs]"
+          df -h
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: html-docs
+        path: docs/source/build/html/
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/main'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/source/build/html

.gitignore

@@ -4,3 +4,16 @@ dist/*
 .DS_Store
 __pycache__/
 *.pyc
+
+models/
+
+# Sphinx build artifacts
+docs/_build/
+docs/build/
+docs/source/_build/
+docs/source/build/
+
+# Autosummary/autogenerated pages
+docs/source/_autosummary/
+docs/source/_generated/
+docs/source/_api/

README.md

@@ -9,7 +9,7 @@ Batched optimisation algorithms for neural network potential–driven molecular
 - IO methods for RDkit molecules and ASE atoms objects.
 
 ## Installation
-Pre-requisities: Python 3.11, PyTorch and PyTorch Geometric compatible with your envirnment
+Pre-requisities: Python 3.11, PyTorch and PyTorch Geometric compatible with your environment.
 
 ```bash
 # For example
@@ -136,9 +136,7 @@ class MyCalculator(Calculator):
         return energies, forces
 
     def to_atomic_data():
-        pass
-
-    def from_atomic_data():
+        # writing this in a batched format is crucial for GPU acceleration
         pass
 ```
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = source/_build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/api.rst

@@ -0,0 +1,12 @@
+.. rst
+
+API reference
+=============
+
+The public API is documented below. Expand entries to see available classes and functions.
+
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   neural_optimiser

docs/source/conf.py

@@ -0,0 +1,99 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import sys
+from datetime import date
+
+# Make the src/ directory importable so autodoc can find neural_optimiser
+sys.path.insert(0, os.path.abspath("../../src"))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "neural-optimiser"
+author = "Ewan Wallace"
+copyright = f"{date.today().year}, {author}"
+
+# Dynamic versioning
+release = "0.0.0"
+try:
+    from importlib.metadata import PackageNotFoundError, version  # py3.8+
+
+    try:
+        release = version("neural-optimiser")
+    except PackageNotFoundError:
+        try:
+            from neural_optimiser import __version__  # noqa: F401
+
+            release = __version__
+        except Exception:
+            pass
+except Exception:
+    pass
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.extlinks",
+    "myst_parser",
+]
+
+extlinks = {
+    "pyg": ("https://pytorch-geometric.readthedocs.io/en/latest/generated/%s.html", "%s"),
+}
+
+# Support .rst and .md sources
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = ["_static"]
+
+# Autodoc/autosummary
+autosummary_generate = True
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "inherited-members": True,
+    "show-inheritance": True,
+}
+autodoc_typehints = "description"
+
+# Napoleon (Google/Numpy style docstrings)
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_attr_annotations = True
+
+# Intersphinx links
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", {}),
+    "numpy": ("https://numpy.org/doc/stable/", {}),
+    "torch": ("https://pytorch.org/docs/stable/", {}),
+}
+
+# MyST config
+myst_enable_extensions = [
+    "colon_fence",
+    "deflist",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "tasklist",
+]

docs/source/index.rst

@@ -0,0 +1,20 @@
+.. neural-optimiser documentation master file, created by
+   sphinx-quickstart on Thu Oct 23 06:10:35 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+neural-optimiser documentation
+==============================
+
+Overview
+--------
+
+.. mdinclude:: ../../README.md
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 2
+
+   api

pyproject.toml

@@ -19,6 +19,7 @@ dependencies = [
     "numpy",
     "loguru",
     "universal-pathlib",
+    "sphinx",
 ]
 
 [project.optional-dependencies]
@@ -27,6 +28,13 @@ dev = [
     "pre-commit",
 ]
 
+docs = [
+    "sphinx>=3.0.0",
+    "furo==2021.11.16",
+    "myst-parser",
+    "sphinx-autodoc-typehints"
+]
+
 [tool.uv.sources]
 torch = { index = "pytorch-cu128" }
 torch-cluster = { index = "pyg-cu128" }