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lukas-paetow
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Serenity keeps MO information in binary .h5 files that can be found in a directory with the given molecular system name. My implementation assumes that the output file is still where it was left by Serenity, so that the molecule directory can be found relative to that path.

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codecov bot commented Oct 8, 2025

Codecov Report

❌ Patch coverage is 16.66667% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.89%. Comparing base (04b73bb) to head (7ac7442).
⚠️ Report is 9 commits behind head on master.

Files with missing lines Patch % Lines
cclib/parser/serenityparser.py 16.66% 15 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1675      +/-   ##
==========================================
- Coverage   82.02%   81.89%   -0.13%     
==========================================
  Files          75       75              
  Lines       15914    15943      +29     
==========================================
+ Hits        13053    13057       +4     
- Misses       2861     2886      +25     

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@shivupa
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shivupa commented Oct 10, 2025

For this PR could you check out the Turbomole parser and see how multiple files are handled. That might be a better way to handle this situation (a human readable outputfile and a binary file)

@lukas-paetow
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For this PR could you check out the Turbomole parser and see how multiple files are handled. That might be a better way to handle this situation (a human readable outputfile and a binary file)

Hi Shiv, I had some issues with the file wrapper when trying to parse binary files - I think the extract function should be avoided for binaries, since we don't want to read them line-wise (please correct me if I am wrong here) - if I am seeing it correctly, the turbomole parser sorts the files to deal with them using the parse function, which uses the extract function. Putting my code for the .h5 binaries into the after_parsing function was the easiest working solution. Should I consider a different function?

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