Fix species identification in reaction wells when generating flux diagrams #145
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e.g., if the concentrations were fed incorrectly
To properly count species in cases where a species label is contained within another species label, e.g., 'NO' and 'NO2'. This is avoided when using RMG labels like 'S(1243)', but is not avoided when generating flux diagrams for non-RMG generated Cantera models
To create edges only between a list of selected nodes if desired
Also refactored `report_flux_ratio`
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #145 +/- ##
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+ Coverage 73.46% 74.91% +1.44%
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Files 22 24 +2
Lines 2891 3317 +426
Branches 762 853 +91
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+ Hits 2124 2485 +361
- Misses 552 601 +49
- Partials 215 231 +16
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Properly count species in cases where a species label is contained within another species label, e.g.,
NOandNO2. This is avoided when using RMG labels likeS(1243), but is not avoided when generating flux diagrams for non-RMG generated Cantera models.Tests added.
Also added additional features to the flux diagram generator, such as
allowed_speciesto only show specific species of interest, and whether to report the actual flux or the relative flux on the arrows.