Allow v1 mechanism configuration to be organized across multiple yaml files

[boulderdaze]

Adds support for organizing v1 configurations across multiple files to address the request described in #255.
You can have a main file that specifies where to find each component file, as shown below.

# structure
examples/v1/config/yaml/
├── gas_phase.yaml
├── main.yaml
├── species.yaml
├── stratosphere.yaml
└── troposphere.yaml

# main.yaml
version: "1.1.0"
name: troposophere and stratosphere configs
species:
  files:
    - species.yaml
phases:
  files:
    - gas_phase.yaml
reactions:
  files:
    - troposophere.yaml
    - stratosphere.yaml

# species.yaml
- name: A
- name: B
  ...

# gas_phase.yaml
- name: gas
  species:
    - A
    - B

# stratosphere.yaml
- type: ARRHENIUS
  gas phase: gas
  ...

[Copilot]

Pull request overview

Adds support for organizing v1 mechanism configurations across multiple files (file-list format) and introduces unit/integration tests plus example multi-file configs to validate the behavior.

Changes:

• Extend the v1 parser to detect “inline” vs “file-list” entity formats and load/merge entities from multiple files for v1.1.x configs.
• Add unit tests and fixture configs for multi-file parsing and error cases.
• Add example v1 JSON/YAML multi-file configurations and an integration test to parse them.

Reviewed changes

Copilot reviewed 47 out of 47 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
src/v1/parser.cpp	Implements entity format detection and file-list config loading/merging logic.
include/mechanism_configuration/v1/parser.hpp	Exposes new helper/API for parsing file-list configs.
test/unit/v1/CMakeLists.txt	Adds the new file_configs unit-test subdirectory.
test/unit/v1/file_configs/CMakeLists.txt	Adds a unit test target and a copy target for file-config fixtures.
test/unit/v1/file_configs/test/test_parse_from_file_configs.cpp	Adds unit tests for file-list parsing and several error scenarios.
test/unit/v1/file_configs/configs/two_species_sets/main.json	Fixture: species split across multiple files, reactions split across files.
test/unit/v1/file_configs/configs/two_species_sets/species_set_1.json	Fixture: first species subset.
test/unit/v1/file_configs/configs/two_species_sets/species_set_2.json	Fixture: second species subset.
test/unit/v1/file_configs/configs/two_species_sets/gas_phase.json	Fixture: phase definition used by two-species-sets case.
test/unit/v1/file_configs/configs/two_species_sets/troposophere.json	Fixture: first reaction file for two-species-sets.
test/unit/v1/file_configs/configs/two_species_sets/stratosphere.json	Fixture: second reaction file for two-species-sets.
test/unit/v1/file_configs/configs/two_phases_sets/main.json	Fixture: phases split across multiple files.
test/unit/v1/file_configs/configs/two_phases_sets/species.json	Fixture: shared species for two-phases-sets case.
test/unit/v1/file_configs/configs/two_phases_sets/gas_phase_1.json	Fixture: first phase file.
test/unit/v1/file_configs/configs/two_phases_sets/gas_phase_2.json	Fixture: second phase file.
test/unit/v1/file_configs/configs/two_phases_sets/troposophere.json	Fixture: photolysis reactions file.
test/unit/v1/file_configs/configs/two_phases_sets/stratosphere.json	Fixture: arrhenius reactions file.
test/unit/v1/file_configs/configs/missing_species_set/main.json	Fixture: missing required top-level species key.
test/unit/v1/file_configs/configs/missing_species_set/gas_phase.json	Fixture: phase file for missing-species-set case.
test/unit/v1/file_configs/configs/missing_species_set/troposophere.json	Fixture: reaction file for missing-species-set case.
test/unit/v1/file_configs/configs/missing_species_set/stratosphere.json	Fixture: reaction file for missing-species-set case.
test/unit/v1/file_configs/configs/missing_phase_set/main.json	Fixture: phases present but missing files key.
test/unit/v1/file_configs/configs/missing_phase_set/species.json	Fixture: species file for missing-phase-set case.
test/unit/v1/file_configs/configs/missing_phase_set/troposophere.json	Fixture: reaction file for missing-phase-set case.
test/unit/v1/file_configs/configs/missing_phase_set/stratosphere.json	Fixture: reaction file for missing-phase-set case.
test/unit/v1/file_configs/configs/missing_reaction_set/main.json	Fixture: reactions file list is empty.
test/unit/v1/file_configs/configs/missing_reaction_set/species.json	Fixture: species file for missing-reaction-set case.
test/unit/v1/file_configs/configs/missing_reaction_set/gas_phase.json	Fixture: phase file for missing-reaction-set case.
test/unit/v1/file_configs/configs/version_mismatch/main.json	Fixture: version minor mismatch for file-list format.
test/unit/v1/file_configs/configs/duplicate_species_set/main.json	Fixture: duplicate species across multiple included files (currently not asserted by a test).
test/unit/v1/file_configs/configs/duplicate_species_set/species_set_1.json	Fixture: duplicate species set 1.
test/unit/v1/file_configs/configs/duplicate_species_set/species_set_2.json	Fixture: duplicate species set 2.
test/unit/v1/file_configs/configs/duplicate_species_set/gas_phase.json	Fixture: phase for duplicate-species-set case.
test/unit/v1/file_configs/configs/duplicate_species_set/troposophere.json	Fixture: reaction file for duplicate-species-set case.
test/unit/v1/file_configs/configs/duplicate_species_set/stratosphere.json	Fixture: reaction file for duplicate-species-set case.
test/integration/CMakeLists.txt	Adds a new integration test target for reading the example file-list configs.
test/integration/test_v1_read_from_file_configs.cpp	Integration test that parses the example JSON/YAML file-list configs.
examples/v1/config/json/main.json	Example v1 JSON main config using file lists.
examples/v1/config/json/species.json	Example v1 JSON species file.
examples/v1/config/json/gas_phase.json	Example v1 JSON phases file.
examples/v1/config/json/troposophere.json	Example v1 JSON reactions file (part 1).
examples/v1/config/json/stratosphere.json	Example v1 JSON reactions file (part 2).
examples/v1/config/yaml/main.yaml	Example v1 YAML main config using file lists.
examples/v1/config/yaml/species.yaml	Example v1 YAML species file.
examples/v1/config/yaml/gas_phase.yaml	Example v1 YAML phases file.
examples/v1/config/yaml/troposophere.yaml	Example v1 YAML reactions file (part 1).
examples/v1/config/yaml/stratosphere.yaml	Example v1 YAML reactions file (part 2).

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[Copilot]

Pull request overview

Copilot reviewed 47 out of 47 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

src/v1/parser.cpp:197

• ParseFromNode no longer performs schema/version validation and will call .as<std::string>() on required keys unconditionally (e.g., object[version]), which can throw if callers pass an invalid/partial YAML node. Since ParseFromNode is a public API (and is used by tests), consider restoring ValidateSchema/version checks inside ParseFromNode or making this method private/internal so callers cannot accidentally bypass validation.

    ParserResult<types::Mechanism> Parser::ParseFromNode(const YAML::Node& object)
    {
      ParserResult<types::Mechanism> result;
      std::unique_ptr<types::Mechanism> mechanism = std::make_unique<types::Mechanism>();

      mechanism->version = Version(object[validation::version].as<std::string>());

      if (object[validation::name])
      {
        std::string name = object[validation::name].as<std::string>();
        mechanism->name = name;
      }

      auto species_parsing = ParseSpecies(object[validation::species]);
      result.errors.insert(result.errors.end(), species_parsing.first.begin(), species_parsing.first.end());
      mechanism->species = species_parsing.second;

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[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 70.00%. Comparing base (f1ebd17) to head (ba03bdb).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #256   +/-   ##
=======================================
  Coverage   70.00%   70.00%           
=======================================
  Files           5        5           
  Lines          10       10           
=======================================
  Hits            7        7           
  Misses          3        3           

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[K20shores]

Neat. I'd also like this documented in our docs. Please address that either in this PR or a follow up PR

[boulderdaze]

Neat. I'd also like this documented in our docs. Please address that either in this PR or a follow up PR

Added