Adds Taylor Series rate constant type

[mattldawson]

Adds a new rate constant type to the V1 configuration. This type is needed to support GECKO-A mechanisms. I have asked for references for this equation, but haven't got them yet. If they arrive in time, I can add them to this PR, otherwise I can submit a follow-up PR. The rate constant is calculated as an Arrhenius reactions multiplied by a variable order Taylor series based on temperature.

[Copilot]

Pull Request Overview

This PR introduces a new Taylor Series rate constant type in the V1 configuration to support GECKO-A mechanisms by combining an Arrhenius term with a variable‐order Taylor series.

• Added the TaylorSeries struct and integrated its parser
• Created schema, unit tests, and CMake updates for validation
• Updated documentation to describe the new reaction format

Reviewed Changes

Copilot reviewed 20 out of 23 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
test/unit/v1/v1_unit_configs/reactions/taylor_series/valid.yaml, valid.json	Add valid Taylor series configuration tests
test/unit/v1/v1_unit_configs/reactions/taylor_series/unknown_species.yaml, .json	Add tests for unknown species error
test/unit/v1/v1_unit_configs/reactions/taylor_series/mutually_exclusive.yaml, .json	Add tests for C vs. Ea mutual exclusivity
test/unit/v1/v1_unit_configs/reactions/taylor_series/missing_phase.yaml, .json	Add tests for missing phase error
test/unit/v1/v1_unit_configs/reactions/taylor_series/bad_reaction_component.yaml, .json	Add tests for invalid reaction component keys
test/unit/v1/reactions/test_parse_taylor_series.cpp	Implement parser unit tests for Taylor series
test/unit/v1/reactions/CMakeLists.txt	Register Taylor series test target
src/v1/reactions/taylor_series_parser.cpp	Implement the TaylorSeriesParser logic
src/v1/reactions/CMakeLists.txt	Include parser source in build
src/v1/mechanism_parsers.cpp	Register TaylorSeriesParser in mechanism parser
include/mechanism_configuration/v1/validation.hpp	Define schema keys for TAYLOR_SERIES and keys
include/mechanism_configuration/v1/reaction_types.hpp	Define the TaylorSeries reaction type
include/mechanism_configuration/v1/reaction_parsers.hpp	Declare the TaylorSeriesParser interface
docs/source/reactions/taylor_series.rst	Add documentation for Taylor series reactions
docs/source/reactions/index.rst	Add taylor_series entry to reactions index

Comments suppressed due to low confidence (3)

test/unit/v1/reactions/test_parse_taylor_series.cpp:76

• Add a unit test for a reaction that specifies only Ea (without C) to verify that the parser correctly converts Ea into C using the Boltzmann constant.

}

docs/source/reactions/taylor_series.rst:45

• The YAML example shows reactants and products as mappings (e.g., spec1:), but the parser expects a sequence of objects with species name and optional coefficient. Update the example to match the actual list-based format.

            reactants:

docs/source/reactions/taylor_series.rst:44

• The example includes a time unit field which is not parsed by the TaylorSeries parser. Either remove it from the sample or document its handling explicitly.

            time unit: MIN

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.95%. Comparing base (58f3ff1) to head (0b1fe53).

Additional details and impacted files

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  Lines          23       23           
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  Hits           20       20           
  Misses          3        3           

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[boulderdaze]

Looks good! I just noticed that some files don't have any content in them but everything looks good.