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ReactionMechanismGenerator / T3

The Tandem Tool (T3) for automated chemical kinetic model development
https://reactionmechanismgenerator.github.io/T3/
MIT License
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Fix species identification in reaction wells when generating flux diagrams #145

Closed alongd closed 9 months ago

alongd commented 11 months ago

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. Tests added.

Also added additional features to the flux diagram generator, such as allowed_species to only show specific species of interest, and whether to report the actual flux or the relative flux on the arrows.

codecov-commenter commented 11 months ago

Codecov Report

Attention: 81 lines in your changes are missing coverage. Please review.

Comparison is base (2de3b76) 73.46% compared to head (8ac4929) 74.91%. Report is 84 commits behind head on main.

Files Patch % Lines
t3/utils/flux.py 81.42% 52 Missing and 13 partials :warning:
t3/utils/fix_cantera.py 90.66% 3 Missing and 4 partials :warning:
t3/simulate/rmg_constantTP.py 0.00% 5 Missing :warning:
t3/imports.py 40.00% 3 Missing :warning:
t3/runners/rmg_runner.py 0.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #145 +/- ## ========================================== + Coverage 73.46% 74.91% +1.44% ========================================== Files 22 24 +2 Lines 2891 3317 +426 Branches 762 853 +91 ========================================== + Hits 2124 2485 +361 - Misses 552 601 +49 - Partials 215 231 +16 ``` | [Flag](https://app.codecov.io/gh/ReactionMechanismGenerator/T3/pull/145/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/ReactionMechanismGenerator/T3/pull/145/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator) | `74.91% <81.46%> (?)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator#carryforward-flags-in-the-pull-request-comment) to find out more.

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