Codecov Report

Attention: Patch coverage is 68.73156% with 106 lines in your changes are missing coverage. Please review.

Project coverage is 72.76%. Comparing base (d49d6f5) to head (c9c2f93).
Report is 10 commits behind head on main.

@@            Coverage Diff             @@
##             main    #1262      +/-   ##
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- Coverage   72.78%   72.76%   -0.02%     
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  Files         375      378       +3     
  Lines       56679    56986     +307     
  Branches    20607    20691      +84     
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+ Hits        41255    41468     +213     
- Misses      12400    12463      +63     
- Partials     3024     3055      +31     

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@speth @bryanwweber I made a file lxcatml2yaml.py, which is used similarly to ctml2yaml. Do you know how to make a list in yaml compact?
Ex.

• [1.0, 2.0, 3.0] instead of
• 1.0
• 2.0
• 3.0

Do you know how to make a list in yaml compact?

This is what's know as "flow" style in YAML. Here's how it's done in ck2yaml for both lists and maps:

I tried run and debug in vs code. from . import utilities causes an issue, so I can only insert print() to investigate. It would be nice if we can just run a particular test in a test file.

I tried run and debug in vs code. from . import utilities causes an issue, so I can only insert print() to investigate. It would be nice if we can just run a particular test in a test file.

From the command line, it is definitely possible to run a single test. After executing scons build, a command like the following should work:

LD_LIBRARY_PATH=build/lib pytest -raP --verbose test/python/test_reaction.py -k 'add_rxn'

where the -k option is a filter based on test names. On macOS, you would need to replace LD_LIBRARY_PATH with DYLD_LIBRARY_PATH.

You can also add the --pdb option to have it drop you into a debug terminal after any assertion failure.

Almost finish. I will add the test for lxcatml2yaml.

@speth @ischoegl I have made some significant progress on this PR, and I think it is ready to be reviewed. The branch is not synchronized. Not sure why.

@BangShiuh thank you for the reminder. Could you rebase to the most recent main so the merge conflict is resolved?

@ischoegl I did it already but the PR information here is not up-to-date. Should I reopen a PR to fix this issue?

@ischoegl I did it already but the PR information here is not up-to-date. Should I reopen a PR to fix this issue?

I had an issue like this just the other day (apparently a glitch in GH). You may be able to fix it by introducing a minor change in one of the commits (example: edit a docstring) and force-push again.

@speth I have fixed most of the issues. The flag m_ROP_ok = false is still odd. test_jacobian fails if m_ROP_ok = false only implemented at each rate. I managed to make the tests passed by not removing m_ROP_ok = false at the original place.

@speth I have addressed most of the issues. The new commit "fix setContext check for reactants" might be the fix.

Many plasma physicists around here are computing close to fully-ionized plasma ; where the electron density cannot be considered negligible compared to the total concentration. @BangShiuh @speth if you're making this assumption ensure a warning or an error is raised if electron density is (for instance) >0.1% of total density.

R = ct.Reaction(
            equation=equation,
            rate=ct.ElectronCollisionPlasmaRate(energy_levels=energy_levels,
                                                cross_sections=cross_sections))

My fix works for a yaml reaction initiation, but fails for the initiation without kin object.

@speth take a look and let me know if this fix for the third body issue is fine.