46 implement yaml parsing (#52)

* removing nlohmann::json in favor of yaml-cpp * duplicating tests for json and yaml * finished troe parsing * starting to split the parsers out into multiple files * splitting all the parsers out * updating workflow files * responding to PR comment
open-atmos · Jan 16, 2025 · dae56fd · dae56fd
1 parent ced8006
commit dae56fd
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diff --git a/.github/workflows/mac.yml b/.github/workflows/mac.yml
@@ -1,14 +1,18 @@
 name: Mac
 
-on: [push, pull_request]
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
   cancel-in-progress: true
 
 jobs:
   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:
@@ -35,7 +39,6 @@ jobs:
           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:

diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -1,14 +1,18 @@
 name: Ubuntu
 
-on: [push, pull_request]
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 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:
@@ -34,7 +38,6 @@ jobs:
           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:

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -1,14 +1,18 @@
 name: Windows
 
-on: [push, pull_request]
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 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:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -22,24 +22,22 @@ message(STATUS "CMake build configuration for ${PROJECT_NAME} (${CMAKE_BUILD_TYP
 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)
-option(ENABLE_JSON "Include JSON support" ON)
-option(ENABLE_YAML "Include YAML support" ON)
+option(OPEN_ATMOS_ENABLE_TESTS "Build the tests" ON)
 
 ################################################################################
 # Dependencies
 
 include(cmake/dependencies.cmake)
 
 ################################################################################
-# micm targets and documentation
+# project source code
 
 add_subdirectory(src)
 
 ################################################################################
 # Tests
 
-if(PROJECT_IS_TOP_LEVEL AND ENABLE_TESTS)
+if(PROJECT_IS_TOP_LEVEL AND OPEN_ATMOS_ENABLE_TESTS)
   enable_testing()
   add_subdirectory(test)
 

diff --git a/cmake/dependencies.cmake b/cmake/dependencies.cmake
@@ -3,7 +3,7 @@ include(FetchContent)
 ################################################################################
 # google test
 
-if(PROJECT_IS_TOP_LEVEL AND ENABLE_TESTS)
+if(PROJECT_IS_TOP_LEVEL AND OPEN_ATMOS_ENABLE_TESTS)
   FetchContent_Declare(googletest
     GIT_REPOSITORY https://github.com/google/googletest.git
     GIT_TAG v1.14.0
@@ -15,24 +15,11 @@ if(PROJECT_IS_TOP_LEVEL AND ENABLE_TESTS)
   FetchContent_MakeAvailable(googletest)
 endif()
 
-################################################################################
-# nlohmann::json
-
-if(ENABLE_JSON)
-  FetchContent_Declare(json
-      GIT_REPOSITORY https://github.com/nlohmann/json.git
-      GIT_TAG v3.11.2
-  )
-  FetchContent_MakeAvailable(json)
-endif()
-
 ################################################################################
 # yaml-cpp
 
-if(ENABLE_YAML)
-  FetchContent_Declare(yaml
-      GIT_REPOSITORY https://github.com/jbeder/yaml-cpp.git
-      GIT_TAG 0.8.0
-  )
-  FetchContent_MakeAvailable(yaml)
-endif()
+FetchContent_Declare(yaml
+    GIT_REPOSITORY https://github.com/jbeder/yaml-cpp.git
+    GIT_TAG 0.8.0
+)
+FetchContent_MakeAvailable(yaml)
diff --git a/include/open_atmos/mechanism_configuration/json_parser.hpp b/include/open_atmos/mechanism_configuration/json_parser.hpp
diff --git a/...s/mechanism_configuration/yaml_parser.hpp → ..._atmos/mechanism_configuration/parser.hpp b/...s/mechanism_configuration/yaml_parser.hpp → ..._atmos/mechanism_configuration/parser.hpp
@@ -10,6 +10,7 @@
 #include <fstream>
 #include <iostream>
 #include <open_atmos/mechanism_configuration/parse_status.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/types.hpp>
 #include <string>
 #include <unordered_map>
@@ -20,7 +21,7 @@ namespace open_atmos
 {
   namespace mechanism_configuration
   {
-    class YamlParser
+    class Parser
     {
      public:
       /// @brief Reads a configuration from a YAML node

diff --git a/include/open_atmos/mechanism_configuration/parser_types.hpp b/include/open_atmos/mechanism_configuration/parser_types.hpp
@@ -0,0 +1,158 @@
+// Copyright (C) 2023-2024 National Center for Atmospheric Research, University of Illinois at Urbana-Champaign
+//
+// SPDX-License-Identifier: Apache-2.0
+
+#pragma once
+
+#include <yaml-cpp/yaml.h>
+
+#include <open_atmos/mechanism_configuration/parse_status.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
+#include <open_atmos/types.hpp>
+#include <vector>
+
+namespace open_atmos
+{
+  namespace mechanism_configuration
+  {
+    class CondensedPhaseArrheniusParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class TroeParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class BranchedParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class TunnelingParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class SurfaceParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class CondensedPhasePhotolysisParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class SimpolPhaseTransferParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class EmissionParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class PhotolysisParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class FirstOrderLossParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class AqueousEquilibriumParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class WetDepositionParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class HenrysLawParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+
+    class ArrheniusParser : public IReactionParser
+    {
+     public:
+      ConfigParseStatus parse(
+          const YAML::Node& object,
+          const std::vector<types::Species>& existing_species,
+          const std::vector<types::Phase>& existing_phases,
+          open_atmos::types::Reactions& reactions) override;
+    };
+  }  // namespace mechanism_configuration
+}  // namespace open_atmos