Sphinx based docs with CI action to build and hosted on gh-pages (#119)

* started rtd

* testing docs action

* update pip

* corrected python version

* added s to docs

* publish every time

* added static folder

* skipping ci for non code files

* changed to rerad the docs theme

* started install section

* added more sections

* added api class

* docs ci using conda

* added -y for freecad

* trying py 3.12

* mimic working conda ci

* using rst so no markdown convertion needed

* added github edit link

* removed path prints

* added readme link, badge

* format

.github/workflows/ci.yml

@@ -5,6 +5,12 @@ on:
       branches:
         - dev
         - main
+      paths-ignore:
+        - "**.md"
+        - "**.txt"
+        - "**.cff"
+        - 'docs/**'
+        - '.gitignore'
     push:
       branches:
         - main

.github/workflows/documentation.yml

@@ -0,0 +1,50 @@
+name: documentation
+
+on:
+  pull_request:
+    branches:
+      - dev
+      - main
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  testing:
+    name: Documentation
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+      - name: checkout actions
+        uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+
+      - name: install dependencies
+        run: conda install -c conda-forge freecad -y
+
+      - name: install package
+        run: |
+          pip install --upgrade pip
+          pip install .[docs]
+      - name: Sphinx build
+        run: |
+          sphinx-build docs _build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

.github/workflows/python-publish.yml

@@ -1,4 +1,4 @@
-name: Upload Python Package
+name: PyPI Python Package
 
 on:
   release:

.gitignore

@@ -173,6 +173,9 @@ Warning_Solids_definition.txt
 
 .vscode
 **/__pycache__
+
+# documentation
+_build
 docs/source/_build/**
 docs/build/**
 docs/source/_autosummary/*

README.md

@@ -1,6 +1,10 @@
 [![CI testing](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/ci.yml)
-
 [![Upload Python Package](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/python-publish.yml/badge.svg)](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/python-publish.yml)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
+[![documentation](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/documentation.yml/badge.svg)](https://github.com/GEOUNED-org/GEOUNED/actions/workflows/documentation.yml)
+
+:book: [Documentation](https://GEOUNED-org.github.io/GEOUNED/python_api.html)
+
 
 # GEOUNED
 A tool to convert from CAD to CSG & CSG to CAD for Monte Carlo transport codes (MCNP & OpenMC).

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     = .
+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)

docs/conf.py

@@ -0,0 +1,67 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../../src"))
+
+# -- Project information -----------------------------------------------------
+
+project = "GEOUNED"
+copyright = "2024, UNED"
+author = "Juan-Pablo Catalan and Patrick Sauvan"
+
+# The full version, including alpha/beta/rc tags
+release = "1.0.1"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.viewcode",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+html_context = {
+    "display_github": True,
+}
+# html_favicon = "favicon.ico"

docs/developer_guide.rst

@@ -0,0 +1,4 @@
+Developer guide
+===============
+
+TOOD

docs/index.rst

@@ -0,0 +1,20 @@
+.. GEOUNED documentation master file, created by
+   sphinx-quickstart on Tue Apr 30 09:47:11 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+GEOUNED
+=======
+
+GEOUNED converts CAD to Constructive Solid Geometry (CSG) formats for use in
+Monte Carlo transport codes.
+Supported codes include OpenMC, PHITS, Serpent and MCNP.
+
+.. toctree::
+   :maxdepth: 2
+
+   install
+   usage
+   python_api
+   methodology
+   developer_guide

docs/install.rst

@@ -0,0 +1,172 @@
+Install
+=======
+
+There are several options for installing GEOUNED package.
+The installation selected has implications for how you run GEOUNED Python scripts.
+Currently the Mamba / Conda install is the recommended method.
+The main difficulty in installing GEOUNED is integration between the main dependnacy (FreeCAD) and the users system Python.
+Mamba / Conda provides the a connection between the FreeCAD Python library and your system Python.
+Users have had success installing FreeCAD and making use of the FreeCAD Python as well so these installation methods are listed for completeness.
+
+
+Linux
+-----
+
+Mamba
+~~~~~
+
+First we need to install a Mamba distribution. There are a few options but here we opt for Miniforge3 as it includes Mamba.
+
+You can follow the install instructions for `Miniforge3 here <https://github.com/conda-forge/miniforge>`_ or follows the commands below.
+Download 
+
+.. code-block:: sh
+
+    curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+    bash Miniforge3-$(uname)-$(uname -m).sh
+
+Install Miniforge3
+
+.. code-block:: sh
+
+    bash Miniforge3-Linux-x86_64.sh
+
+
+Activate the base environment in your current terminal
+
+.. code-block:: sh
+
+    mamba activate
+
+
+It is recommended to create a new environment
+
+.. code-block:: sh
+
+    mamba create --name new_new python=3.11
+
+
+Activate the new environment
+
+.. code-block:: sh
+
+    mamba activate new_new
+
+We have aspirations to create a conda-forge package which will combine these final two steps, but for now FreeCAD and GEOUNED can be installed in two commands.
+Install FreeCAD which is the main dependency
+
+.. code-block:: sh
+
+    mamba install -c conda-forge freecad
+
+
+Install GEOUNED with pip
+
+.. code-block:: sh
+
+    pip install git+https://github.com/GEOUNED-code/GEOUNED.git
+
+Then you will be able to run import GEOUNED from within Python
+
+.. code-block:: python
+
+    import geouned
+
+Conda
+~~~~~
+
+First we need to install a Conda distribution. There are a few options but we here we opt for [MiniConda3](https://docs.anaconda.com/free/miniconda/) as it downloads quicker than the fuller [AnaConda](https://www.anaconda.com/download).
+
+You can follow the install instructions for [MiniConda3 here](https://docs.anaconda.com/free/miniconda/) or follow the commands below.
+Download.
+
+.. code-block:: sh
+
+    mkdir -p ~/miniconda3
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
+
+Install MiniConda3
+
+.. code-block:: sh
+
+    bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
+
+
+Activate the base environment in your current terminal
+
+.. code-block:: sh
+
+    ~/miniconda3/bin/conda init bash
+
+
+It is recommended to create a new environment
+
+.. code-block:: sh
+
+    conda create --name new_new python=3.11
+
+
+Activate the new environment
+
+.. code-block:: sh
+
+    conda activate new_new
+
+We have aspirations to create a conda-forge package which will combine these final two steps, but for now FreeCAD and GEOUNED can be installed in two commands.
+Install FreeCAD which is the main dependency
+
+.. code-block:: sh
+
+    conda install -c conda-forge freecad
+
+
+Install GEOUNED with pip
+
+.. code-block:: sh
+
+    pip install git+https://github.com/GEOUNED-code/GEOUNED.git
+
+Then you will be able to run import GEOUNED from within Python
+
+.. code-block:: python
+
+    import geouned
+
+Apt-get
+~~~~~~~
+
+Snap
+~~~~
+
+AppImage
+~~~~~~~~
+
+Mac
+---
+
+
+Mamba
+~~~~~
+
+Conda
+~~~~~
+
+Brew
+~~~~
+
+
+Windows
+-------
+
+Mamba
+~~~~~
+
+Conda
+~~~~~
+
+Portable FreeCAD installer
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Windows Subsystem for Linux (WSL)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+