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Fix chemkin file duplicate flags #1856

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Fix chemkin file duplicate flags #1856

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Commits on Aug 17, 2023

  1. Fix chemkin duplicate reaction detection. 

    Hopefully fixes #1823 and #1336

This whole procedure is probably a bit slow and could 
probably be optimized, or done less often. 
If it matters (don't do it before profiling).
    @rwest
    rwest committed Aug 17, 2023
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  2. Tweak logging message for writing chemkin surface files

    @rwest
    rwest committed Aug 17, 2023
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  3. Don't UNMARK duplicate reactions so aggressively. 

    There's a model from Klippenstein/Glarborg, with three
duplicate reactions, two PDep and one not.
The previous implementation would notice that because 
one is PDep and one is not, it would REMOVE the DUPLICATE
flag, even though there's a THIRD reaction that means 
the DUPLICATE flag should remain.

Now we just log a warning and leave the flag alone.
    @rwest
    rwest committed Aug 17, 2023
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  4. Fix unit tests for: Don't UNMARK duplicate reactions so aggressively. 

    The new code doesn't remove duplicate reaction marks, so 
this test is marked as a work in progress.

Unless we decide the current behavior is ideal, in which case
we can change the expected outcomes and make this pass.
    @rwest
    rwest committed Aug 17, 2023
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  5. Update unit test for new pytest framework

    @rwest
    rwest committed Aug 17, 2023
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