Add yaml writer test to compare yaml file generated by RMG and the ya…

[LekiaAnonim]

Motivation or Problem

Disparities were observed in the Ea, b, and A values for gas and surface reactions when comparing Cantera YAML files generated directly versus those converted from Chemkin files using the cantera.ck2yaml command. A script and corresponding tests have been written to facilitate this comparison.

Description of Changes

• Added a new test directory containing a script for comparing the two different YAML files.
• Created a test file for validating the comparison process.
• Added test data to the YAML files located in the yaml_writer_data directory.
  • The directly generated YAML file is located in /test/rmgpy/test_data/yaml_writer_data/cantera/.
  • The YAML file converted from Chemkin files is located in /test/rmgpy/test_data/yaml_writer_data/chemkin/.

Testing

A test script was written to compare species names, the number of species, reaction parameters, and the number of reactions in the YAML files generated by both methods.

Reviewer Tips

To review this PR, run the tests in /RMG-Py/test/rmgpy/yaml_writer/test_yaml.py. Note: You may need to adjust the file paths in test_yaml.py to match your local setup.

[Copilot]

Pull Request Overview

This PR adds a suite of tests and supporting utilities to compare YAML files generated by two different methods (direct Cantera generation versus Chemkin conversion) to ensure consistency in reaction and species data.

• Introduces new tests under test/rmgpy/yaml_writer/test_yaml.py for validating species counts, species names, phase-specific species counts, and reaction details.
• Implements helper classes (YamlAnalyst and CompareYaml) in test/rmgpy/yaml_writer/compare_yaml_outputs.py to load, analyze, and compare the YAML files.

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
test/rmgpy/yaml_writer/test_yaml.py	Adds test cases for comparing YAML outputs.
test/rmgpy/yaml_writer/compare_yaml_outputs.py	Introduces classes to load, parse, and compare YAML file content.

[Copilot]

Repeatedly calling self.load_yaml_file() within the loop may lead to unnecessary file reads. Consider loading the YAML content once and caching it to improve performance.

Suggested change

	for key, values in self.load_yaml_file().items():
	if key in [f"{phase['name']}-reactions" for phase in self.load_yaml_file()['phases']]:
	reactions_dict[key] = self.load_yaml_file()[key]
	elif key == 'gas_reactions':
	reactions_dict['gas_reactions'] = self.load_yaml_file()['gas_reactions']
	elif key == 'surface_reactions':
	reactions_dict['surface_reactions'] = self.load_yaml_file()['surface_reactions']
	yaml_content = self.load_yaml_file() # Cache the YAML content
	for key, values in yaml_content.items():
	if key in [f"{phase['name']}-reactions" for phase in yaml_content['phases']]:
	reactions_dict[key] = yaml_content[key]
	elif key == 'gas_reactions':
	reactions_dict['gas_reactions'] = yaml_content['gas_reactions']
	elif key == 'surface_reactions':
	reactions_dict['surface_reactions'] = yaml_content['surface_reactions']

[Copilot]

Assuming that the gas and surface phases always appear as the first two elements in the phases list can be brittle. Consider matching phases by name to ensure robustness if the order changes.

Suggested change

	phase_names1 = [phase['name'] for phase in self.yaml1.load_yaml_file()['phases']]
	phase_names2 = [phase['name'] for phase in self.yaml2.load_yaml_file()['phases']]
	all_phase_names = set(phase_names1).union(set(phase_names2))
	count_diff = {'gas': count_per_phase1[f"specie_count_{phase_names1[0]}"] - count_per_phase2[f"specie_count_{phase_names2[0]}"],
	'surface': count_per_phase1[f"specie_count_{phase_names1[1]}"] - count_per_phase2[f"specie_count_{phase_names2[1]}"]
	}
	phase_names1 = {phase['name']: idx for idx, phase in enumerate(self.yaml1.load_yaml_file()['phases'])}
	phase_names2 = {phase['name']: idx for idx, phase in enumerate(self.yaml2.load_yaml_file()['phases'])}
	count_diff = {}
	for phase_name in ['gas', 'surface']:
	if phase_name in phase_names1 and phase_name in phase_names2:
	count_diff[phase_name] = count_per_phase1[f"specie_count_{phase_name}"] - count_per_phase2[f"specie_count_{phase_name}"]
	else:
	count_diff[phase_name] = None # Handle missing phases gracefully