Doxygen updates from develop

.github/scripts/build-gh-pages.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+
+set -e
+
+#Run with sudo if not root user
+SUDO=""
+if [ $(id -u) -ne 0 ]; then
+    SUDO="sudo"
+fi
+
+echo "Installing apt packages"
+$SUDO apt-get update >/dev/null
+$SUDO apt-get install -y wget git cmake graphviz >/dev/null
+
+echo "Installing Doxygen"
+wget -q https://www.doxygen.nl/files/doxygen-1.12.0.linux.bin.tar.gz
+tar -xzf doxygen-1.12.0.linux.bin.tar.gz >/dev/null
+export PATH="$PWD/doxygen-1.12.0/bin:$PATH"
+
+#List of branches to build docs for
+#TODO: Remove doxygen branch once tested
+BRANCHES="master develop"
+
+build-docs() (
+    git checkout $1
+
+    #The CMake Doxygen stuff is weird, and doesn't 
+    #properly clean up and/or overwrite old outputs.
+    #So to make sure we get the correct doc configs,
+    #we need to delete everything
+    #We put the docs themselves into a hidden directory
+    #so they don't get included in this glob
+    rm -rf ./*
+
+    cmake ../ -DBUILD_DOCS=ON -DDOCS_ONLY=ON \
+        -DFENIX_DOCS_MAN=OFF -DFENIX_BRANCH=$1 \
+        -DFENIX_DOCS_OUTPUT=$PWD/.docs
+    make docs
+)
+
+git clone https://www.github.com/sandialabs/Fenix.git
+mkdir Fenix/build
+cd Fenix/build
+
+for branch in $BRANCHES; do
+    echo "Building docs for $branch"
+
+    #TODO: Fail if any branch fails to build,
+    #  once the develop and master branches have doxygen
+    #  merged in
+    build-docs $branch || true
+
+    echo
+    echo
+done
+
+if [ -n "$GITHUB_ENV" ]; then
+    echo "DOCS_DIR=$PWD/.docs" >> $GITHUB_ENV
+fi

.github/workflows/docs.yml

@@ -0,0 +1,39 @@
+name: Publish GH Pages
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+#Only one of this workflow runs at a time
+concurrency:
+  group: docs
+  cancel-in-progress: true
+
+jobs:
+  build-pages:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build pages
+        run: /bin/bash .github/scripts/build-gh-pages.sh
+
+      - name: Upload documentation artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ${{ env.DOCS_DIR }}
+
+  deploy-docs:
+    needs: build-pages
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+
+    steps:
+      - name: Deploy documentation to GH Pages
+        uses: actions/deploy-pages@v4
+

CMakeLists.txt

@@ -16,37 +16,42 @@ set(FENIX_VERSION_MAJOR 1)
 set(FENIX_VERSION_MINOR 0)
 
 option(BUILD_EXAMPLES    "Builds example programs from the examples directory" OFF)
-option(BUILD_TESTING     "Builds tests and test modes of files" ON)
-
+option(BUILD_TESTING     "Builds tests and test modes of files"                ON)
+option(BUILD_DOCS        "Builds documentation if is doxygen found"            ON)
+option(DOCS_ONLY         "Only build documentation"                            OFF)
 
 #Solves an issue with some system environments putting their MPI headers before
 #the headers CMake includes. Forces non-system MPI headers when incorrect headers
 #detected in include path.
 option(FENIX_SYSTEM_INC_FIX    "Attempts to force overriding any system MPI headers" ON)
 option(FENIX_PROPAGATE_INC_FIX "Attempt overriding system MPI headers in linking projects" ON)
 
-find_package(MPI REQUIRED)
 
-if(${FENIX_SYSTEM_INC_FIX})
-  include(cmake/systemMPIOverride.cmake)
-endif()
+if(NOT DOCS_ONLY)
+    find_package(MPI REQUIRED)
 
+    if(${FENIX_SYSTEM_INC_FIX})
+      include(cmake/systemMPIOverride.cmake)
+    endif()
 
-add_subdirectory(src)
+    add_subdirectory(src)
 
+    include(CTest)
+    list(APPEND MPIEXEC_PREFLAGS "--with-ft;mpi")
 
-include(CTest)
-list(APPEND MPIEXEC_PREFLAGS "--with-ft;mpi")
+    if(BUILD_EXAMPLES)
+        add_subdirectory(examples)
+    endif()
 
-if(BUILD_EXAMPLES)
-    add_subdirectory(examples)
-endif()
+    if(BUILD_TESTING)
+        add_subdirectory(test)
+    endif()
 
-
-if(BUILD_TESTING)
-    add_subdirectory(test)
 endif()
 
+if(BUILD_DOCS)
+    add_subdirectory(doc)
+endif()
 
 configure_file(
     ${CMAKE_CURRENT_SOURCE_DIR}/include/fenix-config.h.in

doc/CMakeLists.txt

@@ -0,0 +1,39 @@
+find_package(Doxygen)
+
+set(FENIX_DOCS_OUTPUT ${CMAKE_CURRENT_BINARY_DIR} CACHE PATH "Documentation output directory")
+set(FENIX_DOCS_MAN "YES" CACHE BOOL "Option to disable man page generation for CI builds")
+set(FENIX_BRANCH "local" CACHE BOOL "Git branch being documented, or local if not building for Github Pages")
+
+if(NOT DOXYGEN_FOUND)
+    message(STATUS "Doxygen not found, `make docs` disabled")
+    return()
+endif()
+
+list(APPEND DOXYGEN_EXAMPLE_PATH markdown)
+list(APPEND DOXYGEN_IMAGE_PATH images)
+
+set(DOXYGEN_USE_MDFILE_AS_MAINPAGE markdown/Introduction.md)
+set(DOXYGEN_LAYOUT_FILE DoxygenLayout.xml)
+set(DOXYGEN_OUTPUT_DIRECTORY ${FENIX_DOCS_OUTPUT})
+
+set(DOXYGEN_GENERATE_MAN ${FENIX_DOCS_MAN})
+
+set(DOXYGEN_QUIET YES)
+set(DOXYGEN_WARN_IF_UNDOCUMENTED NO)
+set(DOXYGEN_WARN_IF_DOC_ERROR YES)
+set(DOXYGEN_WARN_NO_PARAMDOC YES)
+set(DOXYGEN_SHOW_INCLUDE_FILES NO)
+set(DOXYGEN_WARN_IF_UNDOC_ENUM_VAL NO)
+
+list(APPEND DOXYGEN_ALIASES "returnstatus=@return FENIX_SUCCESS if successful, any [return code](@ref ReturnCodes) otherwise.")
+list(APPEND DOXYGEN_ALIASES "unimplemented=@qualifier UNIMPLEMENTED @brief @htmlonly <span class=\\\"mlabel\\\"> @endhtmlonly UNIMPLEMENTED @htmlonly </span> @endhtmlonly")
+
+add_subdirectory(html)
+
+doxygen_add_docs(docs
+    markdown/Introduction.md fake_init.h ../include ../src
+    ALL
+    COMMENT "Generate Fenix documentation")
+message(STATUS "Run `make docs` to build documentation")
+
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/man DESTINATION ${CMAKE_INSTALL_PREFIX})