Merge pull request #278 from IPPL-framework/documentation

Doxygen documentation

.github/workflows/main.yml

@@ -0,0 +1,37 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Doxygen Action
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches: [ master ]
+
+
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+    - uses: actions/checkout@v4
+
+    - name: Doxygen Action
+      uses: mattnotmitt/doxygen-action@v1.9.5
+      with:
+        # Path to Doxyfile
+        doxyfile-path: "doc/Doxyfile" # default is ./Doxyfile
+        # Working directory
+        working-directory: "." # default is .
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: doc/html

doc/Doxyfile

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "IPPL (Independent Parallel Particle Library)"
+PROJECT_NAME           = "IPPL (Independent Parallel Particle Layer)"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -416,7 +416,7 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = NO
+EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -684,7 +684,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            =
+LAYOUT_FILE            = DoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -771,7 +771,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../src/
+INPUT                  = ../src/ ../alpine/ ../README.md examples  extras
 
 # 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
@@ -844,27 +844,27 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           =
+EXAMPLE_PATH           = ../alpine/ ../examples/ #mainpage.md
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       =
+EXAMPLE_PATTERNS       = "*.cpp" "*.h" "*.hpp"
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands
 # irrespective of the value of the RECURSIVE tag.
 # The default value is: NO.
 
-EXAMPLE_RECURSIVE      = NO
+EXAMPLE_RECURSIVE      = YES
 
 # The IMAGE_PATH tag can be used to specify one or more files or directories
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =
+IMAGE_PATH             = images
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -920,7 +920,7 @@ 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
@@ -1471,7 +1471,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
@@ -1659,7 +1659,7 @@ PAPER_TYPE             = a4
 # If left blank no extra packages will be included.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-EXTRA_PACKAGES         =
+EXTRA_PACKAGES         = mathtools amsmath
 
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
 # generated LaTeX document. The header should contain everything until the first