Generate MEOS documentation with doxygen

.github/workflows/meos_generate_dev_docs.yml

@@ -28,18 +28,58 @@ jobs:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
     - uses: actions/checkout@v3
 
-    - name: Doxygen Action
+    - name: Generate documentation
       uses: mattnotmitt/doxygen-action@v1.9.5
       with:
         # Path to Doxyfile
         doxyfile-path: "./doxygen/Doxyfile_gha" # default is ./Doxyfile
         # Working directory
         working-directory: "." # default is .
 
-    - name: Deploy
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        # Default Doxyfile build documentation to html directory.
-        # Change the directory if changes in Doxyfile
-        publish_dir: ./html
+      # store the documentation files
+      - name: Upload output directory
+        uses: actions/upload-artifact@v2
+        with:
+          name: doc-files
+          path: |
+            docs/html/**
+          retention-days: 1
+
+  copy:
+    name: Deploy documentation
+    runs-on: ubuntu-latest
+    needs: build
+
+    steps:
+      # checkout the gh-pages branch
+      - uses: actions/checkout@v3
+        with:
+          ref: gh-pages
+
+      # download the doc files, most of which are generated above
+      - name: Download output directory
+        uses: actions/download-artifact@v2
+        with:
+          name: doc-files
+          path: docs-temp
+
+      # Rename the directory to master
+      - name: Rename the directory to master
+        if: ${{ github.ref == 'refs/heads/master' }}
+        run: |
+          rm -rf master
+          mv docs-temp master
+
+      # Rename the directory to master
+      - name: Rename the directory to develop
+        if: ${{ github.ref == 'refs/heads/develop' }}
+        run: |
+          rm -rf develop
+          mv docs-temp develop
+
+      # add, commit and push to gh-pages
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          message: 'Update docs'
+          branch: gh-pages

doxygen/Doxyfile_gha

@@ -2612,18 +2612,6 @@ DOT_GRAPH_MAX_NODES    = 100
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not seem
-# to support this out of the box.
-#
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_TRANSPARENT        = NO
-
 # Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
 # files in one run (i.e. multiple -o and -T options on the command line). This
 # makes dot run faster, but since only newer versions of dot (>1.8.10) support