ENH: update extract-annotations to generate per-contig feature table

[misialq]

Description

Closes #311.

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[Copilot]

Pull request overview

Enhances the EggNOG extract_annotations action to generate per-contig annotation counts and a function→contigs feature map in addition to the existing per-genome annotation counts.

Changes:

• Updated extract_annotations to return three outputs: per-genome counts table, function→contigs map, and per-contig counts table.
• Updated QIIME 2 plugin registration to expose the new outputs/types.
• Expanded unit tests and adjusted EggNOG test annotation fixture data to reflect per-contig behavior.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
q2_annotate/plugin_setup.py	Registers new outputs for extract_annotations, including FeatureMap[FunctionToContigs] and a per-contig FeatureTable[Frequency].
q2_annotate/eggnog/annotation.py	Refactors extraction to compute per-contig counts and build/merge function→contigs maps.
q2_annotate/eggnog/tests/test_annotation.py	Updates tests for new return signature and adds coverage for map merging.
q2_annotate/eggnog/tests/data/annotations/1e9ffc02-0847-4f2c-b1e2-3965a4a78b15.emapper.annotations	Adjusts fixture data to include a second contig for validating per-contig aggregation.

Comments suppressed due to low confidence (1)

q2_annotate/plugin_setup.py:1827

• The registered method description/name still says it "calculates its frequencies across all MAGs", but the method now also returns a per-contig feature table and a function→contigs feature map. Update the name/description (and/or output descriptions) to reflect the new behavior so users understand what the extra outputs represent.

    name="Extract annotation frequencies from all annotations.",
    description=(
        "This method extract a specific annotation from the table "
        "generated by EggNOG and calculates its frequencies across "
        "all MAGs."

---

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[codecov]

Codecov Report

❌ Patch coverage is 94.11765% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.50%. Comparing base (03def26) to head (c76890f).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
q2_annotate/eggnog/annotation.py	93.93%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #328      +/-   ##
==========================================
- Coverage   94.53%   94.50%   -0.03%     
==========================================
  Files          38       38              
  Lines        2854     2875      +21     
  Branches      435      437       +2     
==========================================
+ Hits         2698     2717      +19     
- Misses         78       79       +1     
- Partials       78       79       +1     

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[VinzentRisch]

Hello

I ran the code with some test data and it all looks good. I have some minor suggestions below:

[VinzentRisch]

Looks good :)

[misialq]

Thanks @VinzentRisch! 🙏