Add in-code option for Python mechanisms

[mattldawson]

Adds the option to define chemical mechanisms directly in Python, without parsing JSON/YAML files. Also, updates a few minor inconsistencies in existing struct data member names and types.

The python test of the parser now includes validation of each component, and a test of an in-code mechanism equivalent to what is in the JSON/YAML test configuration files.

Let me know if there are ways to improve the Python API for creating the structs. I'm not sure if it's the most "Python" way of doing something like this.

[Copilot]

Pull Request Overview

This PR introduces an in‐code option for specifying chemical mechanisms in Python and updates the data model for reaction components.

• Changed tests to validate coefficients for species using a ReactionComponent instead of a plain string.
• Updated parser code in henrys_law and condensed_phase photolysis to construct ReactionComponent objects.
• Adjusted YAML configuration to reflect the new fields and structure.

Reviewed Changes

Copilot reviewed 10 out of 12 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test/unit/v1/test_parse_simpol_phase_transfer.cpp	Added coefficient checks for gas and aerosol species.
test/unit/v1/test_parse_henrys_law.cpp	Updated tests to confirm ReactionComponent fields for species.
test/unit/v1/test_parse_condensed_phase_photolysis.cpp	Updated scaling factor reference for photolysis reactions.
src/v1/henrys_law_parser.cpp	Refactored to build ReactionComponent objects for gas, aerosol, and water species.
src/v1/condensed_phase_photolysis_parser.cpp	Changed the scaling factor field to match the updated struct.
include/mechanism_configuration/v1/types.hpp	Modified member types: using ReactionComponent for species and renaming scaling_factor.
examples/v1/full_configuration.yaml	Revised reaction configuration keys and values to align with new schema.

Files not reviewed (2)

• Dockerfile: Language not supported
• examples/v1/full_configuration.json: Language not supported

Comments suppressed due to low confidence (2)

src/v1/henrys_law_parser.cpp:90

• The coefficient for gas_component is not explicitly set and relies on default initialization; please verify that ReactionComponent defaults its coefficient to 1 to satisfy the test expectations.

gas_component.species_name = gas_phase_species;

examples/v1/full_configuration.yaml:249

• Double-check that the updated ARRHENIUS reaction configuration—specifically the ordering and the inclusion of both species name and coefficient in the reactants—matches the expected schema in the parser.

- species name: A

[Copilot]

The coefficient for aerosol_component is not explicitly initialized; consider explicitly setting it to 1 to ensure consistency with the tests.

Suggested change

	aerosol_component.species_name = aerosol_phase_species;
	aerosol_component.species_name = aerosol_phase_species;
	aerosol_component.coefficient = 1; // Explicitly set coefficient to 1 for consistency

[Copilot]

The coefficient for aerosol_phase_water_component is also not explicitly set; explicitly assigning the default value can help prevent potential inconsistencies in reaction behavior.

Suggested change

	types::ReactionComponent aerosol_phase_water_component;
	types::ReactionComponent aerosol_phase_water_component;
	aerosol_phase_water_component.coefficient = 0.0; // Explicitly set default coefficient

[boulderdaze]

I like Kyle's suggestion. The code looks good to me, nothing to mention particularly. I'll review once more when all the tests pass.

[Copilot]

Pull Request Overview

This PR adds an in‑code option for defining chemical mechanisms directly in Python and updates several reaction component definitions to use a structured ReactionComponent instead of a simple string. Key changes include:

• Adding coefficient checks for reaction components in tests.
• Converting gas_phase_species and aerosol_phase_species from strings to ReactionComponent structures in both tests and parsers.
• Updating Python bindings and examples to reflect renamings and new struct representations.

Reviewed Changes

Copilot reviewed 13 out of 17 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
test/unit/v1/test_parse_simpol_phase_transfer.cpp	Added coefficient validations for simpol phase transfer reaction components.
test/unit/v1/test_parse_henrys_law.cpp	Updated gas and aerosol phase species checks to use ReactionComponent.
test/unit/v1/test_parse_condensed_phase_photolysis.cpp	Adjusted scaling factor field name to match the new field.
src/v1/henrys_law_parser.cpp	Changed assignment to construct a ReactionComponent for gas and aerosol phases.
src/v1/condensed_phase_photolysis_parser.cpp	Renamed scaling factor field to match updated struct.
mechanism_configuration/wrapper.cpp	Updated Pybind11 bindings, including renaming unknown_properties to other_properties and reorganizing the module structure.
include/mechanism_configuration/v1/types.hpp	Modified ReactionComponent fields and replaced fields with the new struct format.
examples/v1/full_configuration.yaml	Updated example configurations to align with new reaction and arrhenius definitions.

Files not reviewed (4)

• CMakeLists.txt: Language not supported
• Dockerfile: Language not supported
• examples/v1/full_configuration.json: Language not supported
• mechanism_configuration/CMakeLists.txt: Language not supported

Comments suppressed due to low confidence (2)

python/tests/test_parser.py:1

• The complete removal of test_parser.py may result in reduced coverage of the Python parser functionality. Please ensure that alternative tests are in place to validate the new in‑code mechanism feature.

import pytest

mechanism_configuration/wrapper.cpp:194

• [nitpick] The Python binding has renamed unknown_properties to other_properties. Consider updating the documentation/comments to clarify this naming choice, ensuring consistency for API users.

.def_readwrite("other_properties", &Species::unknown_properties)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.95%. Comparing base (ec956c2) to head (30e17c3).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #90   +/-   ##
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  Coverage   86.95%   86.95%           
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  Files           3        3           
  Lines          23       23           
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  Hits           20       20           
  Misses          3        3           

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