Sphinx documentation (#105)

* Sphinx documentation

* Clean up for singlehtml option

* add docs GitHub action

* add docs GitHub action

* add docs GitHub action

* add docs GitHub action

* add docs GitHub action

* add docs GitHub action

* add docs GitHub action

* change pythonpath

* remove old files

* remove old files

* remove old files

* remove redundant functions

* remove redundant functions

* .yml renive install

* .yml

* .yml

* .yml

* .yml

* .yml

* .yml debug

* .yml debug

* .yml debug

* .yml adjust build target path

* .yml reconfigure build path to carmm/docs

* remove redundant file

* .yml debug

* .yml point to main folder

* Move the build docs to the github repo

* fix .yml syntax

* revert

* create a docs artifact

* GitHub Pages now use gh-pages

* rerun all jobs

* add a github pages deployment in a .yml form using stored artifact

* add version to deploy-pages

* fix syntax .yml

* fix syntax .yml

* fix syntax .yml

* Deploy Github Pages workflow

* trigger sequence altered

* trigger sequence altered

* introduce dependancies

* test trigger on pull

* remove dependency for test

* dependency on docs.yml

* .yml debug

* .yml debug

* .yml debug

* .yml debug formatting

* combine deployment and building

* combine deployment and building

* adjust artifact name

* revert to separate docs build

* .nojekyll added to artifact

* use github-push-action

* use github-push-action

* fix .yml syntax

* fix .yml syntax

* fix .yml syntax

* fix .yml syntax

* attempt fix to trigger job

* update docs.yml

* Change the behaviour to update documentation on push to main

.github/workflows/docs.yml

@@ -0,0 +1,64 @@
+name: Sphinx
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build_docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Install Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
+
+    - name: Install Sphinx and necessary dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install sphinx sphinx-autodoc-typehints sphinx-rtd-theme
+
+    # Ensure the Python environment setup is consistent with the main.yml
+    - name: Setup Python environment
+      run: | 
+        echo "PYTHONPATH=/home/runner/work/carmm/carmm:$PYTHONPATH" >> $GITHUB_ENV
+
+    # Build the documentation dynamically from docstrings in the code
+    - name: Build Sphinx API documentation
+      run: |
+        sphinx-apidoc -o carmm/docs/source .
+
+    # Build a website based on the retrieved docstrings
+    - name: Build Sphinx HTML
+      run: |
+        sphinx-build -b html carmm/docs/source docs
+
+    # tell GitHub not to use the Jekyll builder explicitly
+    - name: Prevent using Jekyll to use static files properly
+      run: |
+        touch docs/.nojekyll 
+
+    # Publish built docs to gh-pages branch.
+    - name: Commit documentation changes
+      run: |
+        git clone https://github.com/logsdail/carmm.git --branch gh-pages --single-branch gh-pages
+        cp -r docs/* gh-pages/docs
+        cd gh-pages
+        git config --local user.email "action@github.com"
+        git config --local user.name "GitHub Action"
+        git add .
+        git commit -m "Update documentation" -a || true
+        # The above command will fail if no changes were present, so we ignore
+        # that.
+
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        branch: gh-pages
+        directory: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/linter.yml

@@ -6,8 +6,8 @@ name: linter-check
 on:
   push:
     # Only running on master in case there are direct merges
-    branches: [ master ]
-    #branches: [ master, ReactAims_documentation, harry_branch, cube_file_read, jack_molecules, ob ]
+    branches: [ main ]
+
   pull_request:
     # Run on all pull requests when updated.
 

.github/workflows/main.yml

@@ -6,7 +6,7 @@ name: ci-tests
 on:
   push:
     # Only running on master in case there are direct merges
-    branches: [ master ]
+    branches: [ main ]
     #branches: [ master, ReactAims_documentation, harry_branch, cube_file_read, jack_molecules, ob ]
   pull_request:
     # Run on all pull requests when updated.

carmm/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      = 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)

carmm/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=source
+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

carmm/docs/source/conf.py

@@ -0,0 +1,27 @@
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'CARMM'
+copyright = '2024, Logsdail Group'
+author = 'Logsdail Group'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx_autodoc_typehints', ]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

carmm/docs/source/index.rst

@@ -0,0 +1,20 @@
+.. CARMM documentation main file, created by
+   sphinx-quickstart on Thu Feb 29 16:57:31 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to CARMM's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`