Surface diff fixup

[ChrisBNEU]

Motivation or Problem

currently RMG cannot use the "diffmodels" tool to compare surface+gas chemkin files. This means that we can't use a surface model in the CI tests, which is a big problem. This PR is a step towards fixing that.

Description of Changes

This PR combines fixes for several issues:

• interpreting surface input files
• combining chemkin gas+surface output files
• comparing surface species/reactions.

Testing

Currently have tested by creating a diff.html file for a combined gas+surface model as shown in this minimal example

Reviewer Tips

Until we add in the a surface mechanism to our functional/CI tests, this will not be used regularly, so try it with a surface mechanism and make sure the output is captured as we expect.

[lgtm-com[bot]]

This pull request introduces 1 alert when merging 283133d6d709135fe4ac76735cde66c79e12222a into 76e68348c0b3879c4f964787fee0f76ab3b4b899 - view on LGTM.com

new alerts:

• 1 for Unused import

[lgtm-com[bot]]

This pull request introduces 1 alert when merging aaa9fbc4af54f49300ee8881c5969fdab76ba177 into 76e68348c0b3879c4f964787fee0f76ab3b4b899 - view on LGTM.com

new alerts:

• 1 for Unused import

[codecov[bot]]

Codecov Report

Merging #2335 (dc8c268) into main (c17d4dd) will increase coverage by 0.22%. The diff coverage is 48.78%.

@@            Coverage Diff             @@
##             main    #2335      +/-   ##
==========================================
+ Coverage   48.24%   48.47%   +0.22%     
==========================================
  Files         110      110              
  Lines       30726    30758      +32     
  Branches     8032     8039       +7     
==========================================
+ Hits        14824    14909      +85     
+ Misses      14370    14327      -43     
+ Partials     1532     1522      -10     

Impacted Files	Coverage Δ
rmgpy/rmg/output.py	64.24% <ø> (+10.88%)	:arrow_up:
rmgpy/data/kinetics/library.py	42.22% <33.33%> (-0.13%)	:arrow_down:
rmgpy/tools/diffmodels.py	47.24% <51.42%> (+9.52%)	:arrow_up:

... and 3 files with indirect coverage changes

:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more

[lgtm-com[bot]]

This pull request introduces 1 alert when merging ff72aee2e24861a263ff705c0dad4db23c5d1516 into 76e68348c0b3879c4f964787fee0f76ab3b4b899 - view on LGTM.com

new alerts:

• 1 for Unused local variable

[ChrisBNEU]

It looks like this PR it is passing everything except the RMS_liquidSurface_ch4o2cat regression test (which I think is addressed in @hwpang's pr). Should I change the CI file to skip it so I can ensure the remaining actions are successful or should we just review and merge?

[hwpang]

@ChrisBNEU If you rebase with the newest main, the CI for the liquid surface reactor is turned off by https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2473!

[JacksonBurns]

It looks like this PR it is passing everything except the RMS_liquidSurface_ch4o2cat regression test (which I think is addressed in @hwpang's pr). Should I change the CI file to skip it so I can ensure the remaining actions are successful or should we just review and merge?

@rwest removed that regression test in #2473, please rebase and then all should be fine.