Automated doxygen documenation to github pages

.github/workflows/doc.yml

@@ -1,13 +1,33 @@
-name: CI
+name: Doxygen Build and Deploy
 
-on: [push, pull_request]
+on:
+  push:
+    branches: [doxygen]
+  pull_request:
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
+    permissions:
+      contents: write
+
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
     - name: Build the testing docker image
       run: docker build -t partmc-doc -f Dockerfile.doc .
+    - name: Run container to generate docs
+      run: docker run --name partmc-doc-container partmc-doc
+    - name: Create docs directory
+      run: mkdir -p doc
+    - name: Copy docs from container to local workspace
+      run: docker cp partmc-doc-container:/partmc/doc/html ./doc/html
+    - name: Deploy to GitHub Pages
+      if: github.event_name == 'push'
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+         branch: gh-pages
+         folder: doc/html
+    - name: Clean up container
+      run: docker rm partmc-doc-container

README.md

@@ -3,15 +3,14 @@
 
 PartMC: Particle-resolved Monte Carlo code for atmospheric aerosol simulation
 
-[![Latest version](https://img.shields.io/github/tag/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc/blob/master/ChangeLog.md) [![Docker build status](https://img.shields.io/docker/automated/compdyn/partmc.svg)](https://hub.docker.com/r/compdyn/partmc/builds/) [![Github Actions Status](https://github.com/compdyn/partmc/workflows/CI/badge.svg?branch=master)](https://github.com/compdyn/partmc/actions/workflows/main.yml) [![License](https://img.shields.io/github/license/compdyn/partmc.svg)](https://github.com/compdyn/partmc/blob/master/COPYING) [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992) [![Coverage Status](https://codecov.io/gh/compdyn/partmc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/compdyn/partmc)    
-
+[![Latest version](https://img.shields.io/github/tag/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc/blob/master/ChangeLog.md) [![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://compdyn.github.io/partmc/) [![Docker build status](https://img.shields.io/docker/automated/compdyn/partmc.svg)](https://hub.docker.com/r/compdyn/partmc/builds/) [![Github Actions Status](https://github.com/compdyn/partmc/workflows/CI/badge.svg?branch=master)](https://github.com/compdyn/partmc/actions/workflows/main.yml) [![License](https://img.shields.io/github/license/compdyn/partmc.svg)](https://github.com/compdyn/partmc/blob/master/COPYING) [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992) [![Coverage Status](https://codecov.io/gh/compdyn/partmc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/compdyn/partmc)    
 
 Version 2.8.0  
 Released 2024-02-23
 
-**Source:** <https://github.com/compdyn/partmc>
+**Repository:** <https://github.com/compdyn/partmc>
 
-**Homepage:** <http://lagrange.mechse.illinois.edu/partmc/>
+**Documentation:** <https://compdyn.github.io/partmc/>
 
 **Cite as:** M. West, N. Riemer, J. Curtis, M. Michelotti, and J. Tian (2024) PartMC, [![version](https://img.shields.io/github/release/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc), [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
 

doc/Doxyfile

@@ -844,7 +844,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../src
+INPUT                  = ../README.md ../src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -895,6 +895,7 @@ FILE_PATTERNS          = *.c \
                          *.php3 \
                          *.inc \
                          *.m \
+                         *.md \
                          *.mm \
                          *.dox \
                          *.py \
@@ -1023,7 +1024,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = ../README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing