Remove nlohman::json in favor of yaml-cpp since it parses both yaml and json

[mattldawson]

The current MICM configuration parser wraps the nlohman::json library. Modify the parser and the CMake build scripts to use yaml-cpp library instead, which will allow for mechanisms in JSON or YAML.

Acceptance Criteria

• nlohman::json library is no longer a dependency of MICM
• The MICM configuration parser usesyaml-cpp for parsing configuration files
• Include at least one test that reads a YAML configuration

Ideas

• Files that may need editing:
  • cmake/dependencies.cmake
  • CMakeLists.txt
    • In here we define a variable called MICM_ENABLE_JSON, maybe change that to MICM_ENABLE_CONFIG_READER or something similar
  • src/CMakeLists.txt
  • include/micm/configure/solver_config.hpp
  • test/unit/CMakeLists.txt
  • Many things in test/unit/configure
  • There may be others, but this is likely enough to start
• Possibly create a test in the configuration parser unit tests for a YAML configuration (the translation of an existing JSON configuration should be fairly easy in Python or an online converter

  micm/test/unit/configure/test_solver_config.cpp

  Lines 102 to 138 in 6b1c58a

  	TEST(SolverConfig, ReadAndParseSystemObject)
  	{
  	micm::SolverConfig solverConfig;
  	// Read and parse the configure files
  	EXPECT_NO_THROW(solverConfig.ReadAndParse("./unit_configs/small_mechanism/config.json"));
  	// Get solver parameters ('System', the collection of 'Process')
  	micm::SolverParameters solver_params = solverConfig.GetSolverParams();
  	// Check 'gas_phase' in 'System'
  	EXPECT_EQ(solver_params.system_.gas_phase_.species_.size(), 9);
  	// Check 'phases' in 'System'
  	EXPECT_EQ(solver_params.system_.phases_.size(), 0);
  	// Check 'name' and 'properties' in 'Species'
  	std::vector<std::pair<std::string, short>> species_name_and_num_properties = {
  	std::make_pair("Ar", 1), std::make_pair("CO2", 1), std::make_pair("H2O", 1),
  	std::make_pair("M", 0), std::make_pair("N2", 2), std::make_pair("O", 1),
  	std::make_pair("O1D", 1), std::make_pair("O2", 1), std::make_pair("O3", 1)
  	};
  	short idx = 0;
  	for (const auto& s : solver_params.system_.gas_phase_.species_)
  	{
  	EXPECT_EQ(s.name_, species_name_and_num_properties[idx].first);
  	EXPECT_EQ(s.properties_double_.size(), species_name_and_num_properties[idx].second);
  	idx++;
  	}
  	// check some specific properties
  	EXPECT_EQ(solver_params.system_.gas_phase_.species_[4].GetProperty<double>("absolute tolerance"), 1.0e-12);
  	EXPECT_EQ(solver_params.system_.gas_phase_.species_[4].GetProperty<double>("molecular weight [kg mol-1]"), 0.0280134);
  	EXPECT_EQ(solver_params.system_.gas_phase_.species_[4].GetProperty<std::string>("__custom string property"), "foo");
  	EXPECT_EQ(solver_params.system_.gas_phase_.species_[4].GetProperty<bool>("__custom bool property"), true);
  	EXPECT_EQ(solver_params.system_.gas_phase_.species_[4].GetProperty<int>("__custom int property"), 12);
  	}