Fix issues for undeclared third-bodies and implicit third-body reactions

[ischoegl]

Changes proposed in this pull request

Fix a series of bugs and edge cases that involve undeclared third-body colliders and/or implicitly defined third-body reactions.

• Add skip-undeclared-third-bodies to serialization (see #1403)
• Prevent segfault if an implicitly defined third-body reaction contains an invalid collider (see #1587)
• Prevent silent skipping of invalid reactions in Python API for creation of Solution from scratch
• Fix samples/python/kinetics/extract_submechanism.py sample, where reaction list included invalid reactions
• Address several edge cases where Reaction objects are created from reactant/product Composition, where several invalid combinations were not caught (also, implicit third-bodies were not implemented correctly).
• Deprecate Reaction.reactants/products setter in Python, as they allow for undefined behavior

If applicable, fill in the issue number this pull request is fixing

Closes #1403 Closes #1587

If applicable, provide an example illustrating new features this pull request is introducing

Checklist

• [x] The pull request includes a clear description of this code change
• [x] Commit messages have short titles and reference relevant issues
• [x] Build passes (scons build & scons test) and unit tests address code coverage
• [x] Style & formatting of contributed code follows contributing guidelines
• [x] The pull request is ready for review

[codecov[bot]]

Codecov Report

Merging #1588 (884565b) into main (e00c23f) will decrease coverage by 0.01%. The diff coverage is 60.71%.

@@            Coverage Diff             @@
##             main    #1588      +/-   ##
==========================================
- Coverage   70.60%   70.60%   -0.01%     
==========================================
  Files         379      379              
  Lines       59144    59164      +20     
  Branches    21252    21263      +11     
==========================================
+ Hits        41760    41770      +10     
- Misses      14311    14320       +9     
- Partials     3073     3074       +1     

Files Changed	Coverage Δ
include/cantera/kinetics/Kinetics.h	32.66% <ø> (ø)
interfaces/cython/cantera/reaction.pyx	81.74% <42.85%> (-0.48%)	:arrow_down:
src/kinetics/Reaction.cpp	77.83% <61.11%> (-0.67%)	:arrow_down:
src/kinetics/BulkKinetics.cpp	93.65% <100.00%> (+0.01%)	:arrow_up:
src/kinetics/Kinetics.cpp	74.03% <100.00%> (+0.11%)	:arrow_up:

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[ischoegl]

Thanks for the comments, @speth!

[...] I think this mostly makes sense, with one caveat.

Namely, I think that attempting to add a reaction like 2 H + CO2 <=> H2 + CO2 to a phase that doesn't contain CO2 using the Solution "from parts" constructor should not be treated as an error. The traditional behavior of the Solution constructor has been to automatically skip unknown third bodies, and it shouldn't matter whether or not that the unknown species is the only valid third body for a reaction.

The traditional treatment of this was to not detect explicit 3rd body colliders, which means that these species show up in product/reactant maps and thus these reactions were not included.

In part, this behavior is because we don't currently provide a way for the user to specify that unknown 3rd bodies should be skipped when using this constructor. But more importantly, it's because when constructing a mechanism directly from an input file, it's much more likely that an unknown species is typo that should be detected as an error, whereas when working with Reaction objects, I think it's more likely that an unknown species is intentionally not part of the phase definition, and it's easier to have Cantera skip it than make the user do the additional filtering.

~I converted the errors to warnings. For example, the extract_submechanism.py now gives a warning, but runs through without modifications:~ ... Edit: the reaction is now skipped silently

path/to/extract_submechanism.py:58: UserWarning: Skipping three-body reaction(s) with undeclared species:
- H + O2 + AR <=> HO2 + AR    <three-body-Arrhenius>

[ischoegl]

Nevermind. I removed the Skipping three-body reaction(s) with undeclared species warning as it addresses a very minor issue that nevertheless opened a can of worms in CI testing (the run-examples runner fails if any warnings are issued).