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Matthew-WhitlockMatthew-Whitlock
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Initial doxygen setup
Documentation Organize, setup versioned docs Deploy docs to Github pages Update doxygen header Use Doxygen 1.12.0 for github pages builds Improved Process Recovery docs writeup 'make doc' -> 'make docs'
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‎.github/scripts/build-gh-pages.sh

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

‎.github/workflows/docs.yml

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

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

‎doc/CMakeLists.txt

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

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