Implement yaml parsing

[K20shores]

Currently, there is a JSON parsing class (include/open_atmos/mechanism_configuration/json_parser.hpp; src/json_parser.cpp) that is used to read mechanism configuration files, which uses the nlohmann::json library. There is also a stubbed-out version of a equivalent YAML parser that has yet to be implemented (include/open_atmos/mechanism_configuration/yaml_parser.hpp; src/yaml_parser.cpp).

As we've learned, yaml-cpp can parse json as well as yaml. Replace the existing json and to-be-implemented yaml parsers with a single json/yaml parser that reads both types of files.

Acceptance criteria

• nlohmann::json is removed
• all parsing is done with yaml-cpp
• Existing tests that parse json still work
• New tests are added that parse corresponding yaml examples

Ideas

• Something similar was done in micm, this PR could act as a guide
• Instead of separating the unit tests into yaml and json folders, put all tests for both config types into a single test file
  • For example, all tests here could be duplicated and include a read of yaml data: https://github.com/open-atmos/MechanismConfiguration/blob/main/test/unit/json/test_parse_arrhenius.cpp
  • Do the same for all of them
• Ensure all of these are taken care of
  • Parse species
  • Parse aerosol phases
  • Parse arrhenius reactions
  • Parse troe reactions
  • Parse branched reactions
  • Parse tunnelling reactions
  • Parse surface reacdtions
  • Parse photolysis reactions
  • Parse emissions reaction
  • Parse first order loss reactions
  • Parse condensed phase photolysis reactions
  • Parse condensed phase arrhenius reactions
  • Parse aqueous equilibrium reactions
  • Parse henry's law phase transfer
  • Parse wet deposition
  • Parse simpol phase transfer
• use this (chatgpt generated) python scrip to convert any existing json samples to yaml

import json
import yaml

def json_to_yaml(json_file_path, yaml_file_path):
    """
    Reads a JSON file and exports its contents to a YAML file.

    :param json_file_path: Path to the JSON file to read.
    :param yaml_file_path: Path to the YAML file to write.
    """
    try:
        # Open and read the JSON file
        with open(json_file_path, 'r') as json_file:
            data = json.load(json_file)

        # Write the data to a YAML file
        with open(yaml_file_path, 'w') as yaml_file:
            yaml.dump(data, yaml_file, default_flow_style=False)

        print(f"Successfully converted {json_file_path} to {yaml_file_path}")

    except FileNotFoundError:
        print(f"Error: The file {json_file_path} does not exist.")
    except json.JSONDecodeError:
        print(f"Error: Failed to decode JSON from the file {json_file_path}.")
    except Exception as e:
        print(f"An unexpected error occurred: {e}")

# Example usage
if __name__ == "__main__":
    # Replace with your file paths
    input_json_file = "input.json"
    output_yaml_file = "output.yaml"

    json_to_yaml(input_json_file, output_yaml_file)