🐛 Fix handling of None return_predictions in NucleusInstanceSegmentor CLI#1089
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Anannya30 wants to merge 5 commits into
Open
🐛 Fix handling of None return_predictions in NucleusInstanceSegmentor CLI#1089Anannya30 wants to merge 5 commits into
None return_predictions in NucleusInstanceSegmentor CLI#1089Anannya30 wants to merge 5 commits into
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When CLI passes return_predictions=None, any() crashes on line 1972. Added 'or (False,)' to safely default to (False,) when None is passed. Fixes nucleus instance segmentor AnnotationStore output via CLI.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #1089 +/- ##
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Coverage 99.88% 99.88%
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Files 85 85
Lines 11656 11657 +1
Branches 1531 1531
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+ Hits 11643 11644 +1
Misses 7 7
Partials 6 6 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Member
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Thank you @Anannya30 . Please could you add a test to catch this error? Also as the bug is in CLI, this should be fixed in |
* 🔥 Remove `albumentations` dependencies * 🔥 Remove `albumentations` dependencies * ✅ Add tests for coverage * ✅ Add tests for coverage * 🐛 Fix deepsource error
…_cli_default_return_predictions to catch this regression.
Author
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Hi @shaneahmed, thank you for the review! I have made both changes you requested:
Please review and let me know. |
shaneahmed
changed the title
None return_predictions in NucleusInstanceSegmentor CLI
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Problem :-
When running nucleus-instance-segmentor via CLI with AnnotationStore
output, it crashes with:
any(rp_ is True for rp_ in None)
TypeError: 'NoneType' is not iterable
This happens because CLI passes return_predictions=None but line 1972
expects a tuple.
Fix :-
Added
or (False,)fallback:return_predictions = kwargs.get("return_predictions") or (False,)
Testing :-
Verified fix works by running hovernet_fast-pannuke on a real WSI
region and successfully generating AnnotationStore output.