Introduce aerosol chemistry validation and parser support

[boulderdaze]

This PR:

• Adds aerosol representations and processes functions
• Adds check schema, validation function for aerosol
• Adds an integration test for the CAM cloud chemistry
• Makes reactions an optional key, since an aerosol configuration does not always require reactions. See the code and comments for details.
• Part of Add MIAM types to canonical Mechanism #271

Notes:

• I noticed that the emissions PR creates its own directory, which I think is a good approach for keeping things clean and organized. I considered doing the same for the aerosol model, but decided against it. Gas-phase chemistry and aerosol processes can be used together within a single chemistry system, and their configurations are often closely related.
• More unit tests will be added in a follow up PR.
• I restructured the Validate function into ValidateGasModel and introduced a separate ValidateAerosolModel.

Errors ValidateGasModel(const Mechanism& mechanism);
Errors ValidateAerosolModel(const Mechanism& mechanism);

During aerosol validation, the relationship between phases and species(eg. condensed phase and species, gas phase and species, solvent, molecular weight, density ) cannot be expressed in the current semantics::Input because the required relationship information is lost during flattening. It does not preserve which species belongs to which phase.

The intermediate type that I tried to introduced AerosolProcessRef also loses the structure by dropping the association between a specific species and its phase context.

The current aerosol validation cannot preserve the error locations for the reasons above. This will be addressed in #284

[codecov-commenter]

Codecov Report

❌ Patch coverage is 83.11688% with 91 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.65%. Comparing base (a8c7c0d) to head (8f0fe4e).

Files with missing lines	Patch %	Lines
src/v1/aerosol_type_schema.cpp	76.43%	41 Missing ⚠️
src/v1/aerosol_type_parsers.cpp	85.00%	27 Missing ⚠️
src/v1/parser.cpp	70.00%	12 Missing ⚠️
src/validate.cpp	95.00%	6 Missing ⚠️
src/v1/utils.cpp	80.95%	4 Missing ⚠️
src/errors.cpp	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #282      +/-   ##
==========================================
- Coverage   88.96%   87.65%   -1.32%     
==========================================
  Files          39       41       +2     
  Lines        1949     2478     +529     
==========================================
+ Hits         1734     2172     +438     
- Misses        215      306      +91     

Files with missing lines	Coverage Δ
include/mechanism_configuration/errors.hpp	57.14% <ø> (ø)
include/mechanism_configuration/mechanism.hpp	100.00% <ø> (ø)
src/v1/type_parsers.cpp	85.88% <100.00%> (+0.34%)	⬆️
src/v1/type_schema.cpp	83.09% <100.00%> (ø)
src/errors.cpp	34.21% <0.00%> (-0.93%)	⬇️
src/v1/utils.cpp	92.72% <80.95%> (-7.28%)	⬇️
src/validate.cpp	91.45% <95.00%> (+2.11%)	⬆️
src/v1/parser.cpp	84.22% <70.00%> (-2.82%)	⬇️
src/v1/aerosol_type_parsers.cpp	85.00% <85.00%> (ø)
src/v1/aerosol_type_schema.cpp	76.43% <76.43%> (ø)

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[K20shores]

We need to divorce the validation and parsing so that in-code mechanism can be validated. That means we need to update Validate to include aerosol validation

[K20shores]

A couple of comments, but nothing that should hold up a merge. There's only one comment that wouldn't be addressed by a future issue anyway. If you like the way things look now, I'm happy to accept it

[K20shores]

ValidateGasModel also includes line information because we have the semantic reference inputs, which I feel we should also add for aerosols

[boulderdaze]

The gas model can store them in a flat array without relationship information unlike aerosol.

[K20shores]

I'm not sure I follow what you mean here

[boulderdaze]

Its the discussion we had previously. Aerosol validation requires relationship information to determine which species/solvent belong to which phases, and so on, in order to perform the validation checks.
Gas-phase model can find this information in a flat array, which is implemented in semantic structs to locate where the errors are.

[boulderdaze]

Hi @smeechncar, @vweeks,
I pulled the emissions PR that has been recently merged and while working on resolving the conflicts, I noticed a few areas where for emissions implementation could be improved. Some of these are related to the changes by this aerosol PR. I'd appreciate your thoughts on whether these changes make sense.

• Improve Emissions handling consistency #291