Parser stub

.github/workflows/gh-pages.yml

@@ -20,6 +20,10 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3
 
+      - name: Install dependencies
+        run: |
+          pip install -r docs/requirements.txt
+
       - name: Debugging information
         run: |
           echo "github.ref:" ${{github.ref}}
@@ -42,10 +46,6 @@ jobs:
           ( git branch gh-pages remotes/origin/gh-pages && git clone . --branch=gh-pages _gh-pages/ ) || mkdir _gh-pages
           rm -rf _gh-pages/.git/
 
-      - name: Install dependencies
-        run: |
-          pip install -r docs/requirements.txt
-
       - name: Build documentation
         run: |
           cd docs

.github/workflows/mac.yml

@@ -0,0 +1,86 @@
+name: Mac
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  xcode_macos_12:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-12
+    strategy:
+      matrix:
+        # all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-12-Readme.md#xcode
+        xcode: ['13.1', '14.1']
+        build_type: [Debug, Release]
+    env:
+      DEVELOPER_DIR: /Applications/Xcode_${{ matrix.xcode }}.app/Contents/Developer
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+
+  xcode_macos_13:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-13
+    strategy:
+      matrix:
+        # all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-13-Readme.md#xcode
+        xcode: ['14.1', '15.0']
+        build_type: [Debug, Release]
+    env:
+      DEVELOPER_DIR: /Applications/Xcode_${{ matrix.xcode }}.app/Contents/Developer
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+
+  macos_lateset:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        compiler:
+          - { cpp: g++-11, c: gcc-11}
+          - { cpp: g++-12, c: gcc-12}
+          - { cpp: clang++, c: clang}
+        build_type: [Debug, Release]
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10

.github/workflows/ubuntu.yml

@@ -0,0 +1,56 @@
+name: Ubuntu
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gcc:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        build_type: [Debug, Release]
+    env:
+      CC: gcc
+      CXX: g++
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+
+  clang:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        build_type: [Debug, Release]
+    env:
+      CC: clang
+      CXX: clang++
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --verbose
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10

.github/workflows/windows.yml

@@ -0,0 +1,31 @@
+name: Windows
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  msvc2022:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        build_type: [Release]
+        architecture: [Win32, x64]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Run CMake
+      run: cmake -S . -B build -A ${{ matrix.architecture }}
+      if: matrix.build_type == 'Release'
+    - name: Run CMake
+      run: cmake -S . -B build -A ${{ matrix.architecture }}
+      if: matrix.build_type == 'Debug'
+    - name: Build
+      run: cmake --build build --config ${{ matrix.build_type }} --parallel 10
+    - name: Run tests
+      run: |
+        cd build
+        ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose

.gitignore

@@ -1,2 +1,3 @@
 .DS_Store
 docs/build
+build

CMakeLists.txt

@@ -0,0 +1,51 @@
+################################################################################
+# Preamble
+cmake_minimum_required(VERSION 3.21)
+
+project(
+  mechanism_configuration
+  VERSION 1.0.0
+  LANGUAGES CXX
+)
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING
+      "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel."
+      FORCE)
+endif()
+
+message(STATUS "CMake build configuration for ${PROJECT_NAME} (${CMAKE_BUILD_TYPE}) ${PROJECT_VERSION}")
+
+################################################################################
+# Projet wide setup options
+
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
+set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake")
+
+option(ENABLE_TESTS "Build the tests" ON)
+
+################################################################################
+# Dependencies
+
+include(cmake/dependencies.cmake)
+
+################################################################################
+# micm targets and documentation
+
+add_subdirectory(src)
+
+################################################################################
+# Tests
+
+if(PROJECT_IS_TOP_LEVEL AND ENABLE_TESTS)
+  enable_testing()
+  add_subdirectory(test)
+endif()
+
+################################################################################
+# Packaging
+
+# only include packaging if we are the top level project being built
+if(PROJECT_IS_TOP_LEVEL)
+  add_subdirectory(packaging)
+endif()

README.md

@@ -4,9 +4,12 @@ An attempt at defining a model-independent configuration schema for atmospheric
 
 [![GitHub Releases](https://img.shields.io/github/release/open-atmos/MechanismConfiguration.svg)](https://github.com/open-atmos/MechanismConfiguration/releases)
 [![License](https://img.shields.io/github/license/open-atmos/MechanismConfiguration.svg)](https://github.com/open-atmos/MechanismConfiguration/blob/master/LICENSE)
-[![Builds](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/gh-pages.yml/badge.svg)](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/gh-pages.yml)
+[![Docs build](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/gh-pages.yml/badge.svg)](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/gh-pages.yml)
+[![Windows](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/windows.yml/badge.svg)](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/windows.yml)
+[![Mac](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/mac.yml/badge.svg)](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/mac.yml)
+[![Ubuntu](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/open-atmos/MechanismConfiguration/actions/workflows/ubuntu.yml)
 
-Copyright (C) 2017–2023 Barcelona Supercomputing Center, University of Illinois at Urbana–Champaign, and National Center for Atmospheric Research
+Copyright (C) 2017–2024 Barcelona Supercomputing Center, University of Illinois at Urbana–Champaign, and National Center for Atmospheric Research
 
 The configuration documentation can be found [here](https://open-atmos.github.io/MechanismConfiguration/).
 

cmake/cmake_uninstall.cmake.in

@@ -0,0 +1,37 @@
+# https://gitlab.kitware.com/cmake/community/-/wikis/FAQ#can-i-do-make-uninstall-with-cmake
+
+if(NOT EXISTS "@CMAKE_BINARY_DIR@/install_manifest.txt")
+  message(FATAL_ERROR "Cannot find install manifest: @CMAKE_BINARY_DIR@/install_manifest.txt")
+endif()
+
+file(READ "@CMAKE_BINARY_DIR@/install_manifest.txt" files)
+string(REGEX REPLACE "\n" ";" files "${files}")
+foreach(file ${files})
+  message(STATUS "Uninstalling $ENV{DESTDIR}${file}")
+  if(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+    exec_program(
+      "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
+      OUTPUT_VARIABLE rm_out
+      RETURN_VALUE rm_retval
+      )
+    if(NOT "${rm_retval}" STREQUAL 0)
+      message(FATAL_ERROR "Problem when removing $ENV{DESTDIR}${file}")
+    endif()
+  else(IS_SYMLINK "$ENV{DESTDIR}${file}" OR EXISTS "$ENV{DESTDIR}${file}")
+    message(STATUS "File $ENV{DESTDIR}${file} does not exist.")
+  endif()
+endforeach()
+
+set(uninstall_dirs "@INSTALL_PREFIX@;@cmake_config_install_location@")
+
+foreach(dir IN LISTS uninstall_dirs)
+  message(STATUS "Uninstalling ${dir}")
+  exec_program(
+    "@CMAKE_COMMAND@" ARGS "-E remove_directory ${dir}"
+    OUTPUT_VARIABLE rm_out
+    RETURN_VALUE rm_retval
+    )
+  if(NOT "${rm_retval}" STREQUAL 0)
+    message(FATAL_ERROR "Problem when removing ${dir}")
+  endif()
+endforeach()

cmake/dependencies.cmake

@@ -0,0 +1,25 @@
+include(FetchContent)
+
+################################################################################
+# google test
+
+if(PROJECT_IS_TOP_LEVEL AND ENABLE_TESTS)
+  FetchContent_Declare(googletest
+    GIT_REPOSITORY https://github.com/google/googletest.git
+    GIT_TAG v1.14.0
+  )
+
+  set(INSTALL_GTEST OFF CACHE BOOL "" FORCE)
+  set(BUILD_GMOCK OFF CACHE BOOL "" FORCE)
+
+  FetchContent_MakeAvailable(googletest)
+endif()
+
+################################################################################
+# nlohmann::json
+
+FetchContent_Declare(json
+    GIT_REPOSITORY https://github.com/nlohmann/json.git
+    GIT_TAG v3.11.2
+)
+FetchContent_MakeAvailable(json)

cmake/mechanism_configurationConfig.cmake.in

@@ -0,0 +1,5 @@
+@PACKAGE_INIT@
+
+include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@_Exports.cmake")
+
+check_required_components("@PROJECT_NAME@")

cmake/test_util.cmake

@@ -0,0 +1,38 @@
+################################################################################
+# build and add a standard test
+
+function(create_standard_test)
+  set(prefix TEST)
+  set(optionalValues SKIP_MEMCHECK)
+  set(singleValues NAME WORKING_DIRECTORY)
+  set(multiValues SOURCES LIBRARIES)
+
+  include(CMakeParseArguments)
+  cmake_parse_arguments(${prefix} "${optionalValues}" "${singleValues}" "${multiValues}" ${ARGN})
+
+  add_executable(test_${TEST_NAME} ${TEST_SOURCES})
+
+  target_link_libraries(test_${TEST_NAME} PUBLIC open_atmos::mechanism_configuration GTest::gtest_main)
+
+  # link additional libraries
+  foreach(library ${TEST_LIBRARIES})
+    target_link_libraries(test_${TEST_NAME} PUBLIC ${library})
+  endforeach()
+
+  if(NOT DEFINED TEST_WORKING_DIRECTORY)
+    set(TEST_WORKING_DIRECTORY "${CMAKE_BINARY_DIR}")
+  endif()
+
+  add_open_atmos_test(${TEST_NAME} test_${TEST_NAME} "" ${TEST_WORKING_DIRECTORY})
+endfunction(create_standard_test)
+
+################################################################################
+# Add a test
+
+function(add_open_atmos_test test_name test_binary test_args working_dir)
+  add_test(NAME ${test_name}
+            COMMAND ${test_binary} ${test_args}
+            WORKING_DIRECTORY ${working_dir})
+endfunction(add_open_atmos_test)
+
+################################################################################

docs/requirements.txt

@@ -1,4 +1,5 @@
 pydata-sphinx-theme
+setuptools
 sphinx
 sphinx-design
 sphinx-tabs