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Use annotators to compute features at graph construction and after actions#97

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cmalinmayor merged 20 commits into2-feature-infrastructurefrom
use-annotators-to-compute-features
Oct 27, 2025
Merged

Use annotators to compute features at graph construction and after actions#97
cmalinmayor merged 20 commits into2-feature-infrastructurefrom
use-annotators-to-compute-features

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@cmalinmayor cmalinmayor commented Oct 24, 2025

List of features included:

  • Split actions into BaseAction and ActionGroup types
  • Disable computing features by default in annotators
  • Use AnnotatorRegistry instead of AnnotatorManager - syncing code goes into Tracks
  • Pass through all Actions to all Annotators to update accordingly
  • UpdateNodeAttrs can't modify any of the computed attributes or time
  • Move track_id bookkeeping into the TrackAnnotator
  • Allow import_from_geff to compute features other than area.

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codecov Bot commented Oct 24, 2025

Codecov Report

❌ Patch coverage is 94.22492% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.70%. Comparing base (a4613aa) to head (dff965c).
⚠️ Report is 22 commits behind head on 2-feature-infrastructure.

Files with missing lines Patch % Lines
src/funtracks/annotators/_annotator_registry.py 91.30% 4 Missing ⚠️
src/funtracks/annotators/_regionprops_annotator.py 82.60% 4 Missing ⚠️
src/funtracks/import_export/import_from_geff.py 80.00% 3 Missing ⚠️
src/funtracks/annotators/_edge_annotator.py 92.00% 2 Missing ⚠️
src/funtracks/annotators/_track_annotator.py 96.72% 2 Missing ⚠️
src/funtracks/annotators/_graph_annotator.py 93.33% 1 Missing ⚠️
src/funtracks/data_model/solution_tracks.py 95.23% 1 Missing ⚠️
src/funtracks/data_model/tracks_controller.py 87.50% 1 Missing ⚠️
src/funtracks/import_export/export_to_geff.py 66.66% 1 Missing ⚠️
Additional details and impacted files
@@                     Coverage Diff                      @@
##           2-feature-infrastructure      #97      +/-   ##
============================================================
+ Coverage                     90.59%   90.70%   +0.10%     
============================================================
  Files                            39       39              
  Lines                          1659     1656       -3     
============================================================
- Hits                           1503     1502       -1     
+ Misses                          156      154       -2     

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@cmalinmayor cmalinmayor marked this pull request as ready for review October 24, 2025 16:44
Comment thread src/funtracks/actions/add_delete_node.py Outdated
Comment thread src/funtracks/actions/add_delete_node.py Outdated
Comment thread src/funtracks/actions/update_node_attrs.py Outdated
Comment thread src/funtracks/actions/update_track_id.py Outdated
]

@classmethod
def get_managed_features(cls, tracks: Tracks) -> dict[str, Feature]:
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Still don't like that this returns the default string keys. Can we really just do the Features?

Comment thread src/funtracks/annotators/_annotator_registry.py
Comment thread src/funtracks/annotators/_annotator_registry.py Outdated
Comment thread src/funtracks/annotators/_regionprops_annotator.py Outdated
Comment thread src/funtracks/import_export/import_from_geff.py Outdated
Comment thread src/funtracks/actions/add_delete_node.py Outdated
@cmalinmayor cmalinmayor merged commit ad118e8 into 2-feature-infrastructure Oct 27, 2025
15 checks passed
@cmalinmayor cmalinmayor deleted the use-annotators-to-compute-features branch October 27, 2025 21:21
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