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ENH: add new type MGF#53

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VinzentRisch merged 6 commits intomainfrom
mgf-type
Aug 18, 2025
Merged

ENH: add new type MGF#53
VinzentRisch merged 6 commits intomainfrom
mgf-type

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@fethalen
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@fethalen fethalen commented Aug 8, 2025

This pull request closes issue #52 by adding the semantic type MGF, the file format MGFFileFormat, and the directory format MGFDirFormat. Tests were added for both formats. The tests make use of the MGF parser in Pyteomics for validation.

@fethalen fethalen requested a review from VinzentRisch August 8, 2025 11:46
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Hey congratulations on your first PR! 🎉

For a working Semantic type there is one thing still missing though. The directory format has to be connected with the semantic type with plugin.register_semantic_type_to_format(). It also goes into plugin_setup with the other registrations.

To test the registration you can try to actually import an MGF file into an artifact with qiime tools import on the command line.

And also see some adjustments below:

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codecov bot commented Aug 11, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.67%. Comparing base (785917b) to head (d3b0aa5).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #53      +/-   ##
==========================================
+ Coverage   99.65%   99.67%   +0.01%     
==========================================
  Files           8        8              
  Lines         289      306      +17     
  Branches       38       39       +1     
==========================================
+ Hits          288      305      +17     
  Misses          1        1              

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@fethalen fethalen requested a review from VinzentRisch August 18, 2025 13:27
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Hey Looks great!!
Ready for merging!

@VinzentRisch VinzentRisch merged commit ef26195 into main Aug 18, 2025
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2 participants