Fix yaml duplicate reaction check

[speth]

Changes proposed in this pull request

• Run duplicate reaction check for YAML input files (Fixes Duplicate reactions not being caught in ck2yaml #865)
• Improve error messages associated with duplicate reactions and other reaction errors by showing YAML input file context, e.g.

***********************************************************************
InputFileError thrown by Kinetics::checkDuplicates:
Error on lines 1531 and 1816 of ./dup.yaml:
Undeclared duplicate reactions detected:
Reaction 325: NNH + O2 <=> HO2 + N2
Reaction 206: NNH + O2 <=> HO2 + N2

|  Line |
|  1526 | - equation: NNH + M <=> N2 + H + M  # Reaction 205
|  1527 |   type: three-body
|  1528 |   rate-constant: {A: 1.3e+14, b: -0.11, Ea: 4980.0}
|  1529 |   efficiencies: {H2: 2.0, H2O: 6.0, CH4: 2.0, CO: 1.5, CO2: 2.0, C2H6: 3.0,
|  1530 |     AR: 0.7}
>  1531 > - equation: NNH + O2 <=> HO2 + N2  # Reaction 206
            ^
|  1532 |   rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0}
|  1533 | - equation: NNH + O <=> OH + N2  # Reaction 207
|  1534 |   rate-constant: {A: 2.5e+13, b: 0.0, Ea: 0.0}
...
|  1811 |   rate-constant: {A: 2.41e+13, b: 0.0, Ea: 0.0}
|  1812 | - equation: HO2 + C3H7 <=> O2 + C3H8  # Reaction 323
|  1813 |   rate-constant: {A: 2.55e+10, b: 0.255, Ea: -943.0}
|  1814 | - equation: HO2 + C3H7 => OH + C2H5 + CH2O  # Reaction 324
|  1815 |   rate-constant: {A: 2.41e+13, b: 0.0, Ea: 0.0}
>  1816 > - equation: NNH + O2 <=> HO2 + N2  # Reaction 206 (again)
            ^
|  1817 |   rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0}
|  1818 | - equation: CH3 + C3H7 <=> 2 C2H5  # Reaction 325
|  1819 |   rate-constant: {A: 1.927e+13, b: -0.32, Ea: 0.0}
***********************************************************************

• Replace the incomplete duplicate reaction check in ck2yaml.py with the full one done in the C++ Kinetics class, and parse the output of that error to provide line numbers of the duplicate reactions in the original input file, e.g.:

Wrote YAML mechanism file to './duplicate-reactions.yaml'.
Mechanism contains 4 species and 7 reactions.
Validating mechanism...FAILED.
Undeclared duplicate reaction C2 + H2 <=> C2H + H
found on lines 30 and 31 of  the kinetics input file.

• A little bit of refactoring of AnyValue and AnyMap to make this a bit easier.

Checklist

• There is a clear use-case for this code change
• The commit message has a short title & references relevant issues
• Build passes (scons build & scons test) and unit tests address code coverage
• The pull request is ready for review

[codecov]

Codecov Report

Merging #866 into master will decrease coverage by 0.00%.
The diff coverage is 84.05%.

@@            Coverage Diff             @@
##           master     #866      +/-   ##
==========================================
- Coverage   70.49%   70.49%   -0.01%     
==========================================
  Files         375      375              
  Lines       45649    45671      +22     
==========================================
+ Hits        32182    32197      +15     
- Misses      13467    13474       +7     

Impacted Files	Coverage Δ
src/thermo/ThermoFactory.cpp	83.81% <ø> (ø)
src/base/AnyMap.cpp	83.83% <80.39%> (-0.01%)	⬇️
src/kinetics/Kinetics.cpp	83.85% <88.88%> (-0.36%)	⬇️
include/cantera/base/AnyMap.h	100.00% <100.00%> (ø)
src/kinetics/KineticsFactory.cpp	96.38% <100.00%> (-1.12%)	⬇️
src/kinetics/Reaction.cpp	87.12% <0.00%> (-0.38%)	⬇️

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[bryanwweber]

Thanks for fixing this @speth! Just a few small things I noticed.

[bryanwweber]

Thanks, looks good now! I have a question below which is partly for my understanding, but may be worth adding a comment in the code for future us as well, depending on the answer.

[bryanwweber]

Why is this check necessary? From my quick test, adding a third duplicate reaction still only shows two of them. Are there other error conditions that can reach this function?

[speth]

Right, the error from Kinetics::checkDuplicates should only ever indicate two reactions. What I'm trying to hedge against is (a) the possibility there's some case where that error message doesn't have the expected format, or (b) some future change breaks this attempt at parsing the error message. If either of those happens, I'd rather output the original message from Kinetics::checkDuplicates than some error message generated caused by reactions not having the the expected number of entries.

[speth]

I added some comments to show_duplicate_reactions which will hopefully make some of this clear to our future selves. 😂