Add benchmarking test framework and improve featurization performance - #48
Merged
Conversation
# Conflicts: # tests/featurization/test_real_world_data.py
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #48 +/- ##
=======================================
Coverage ? 93.38%
=======================================
Files ? 15
Lines ? 1376
Branches ? 0
=======================================
Hits ? 1285
Misses ? 91
Partials ? 0 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
d33bs
marked this pull request as ready for review
August 5, 2026 22:29
MikeLippincott
approved these changes
Aug 6, 2026
MikeLippincott
left a comment
Member
There was a problem hiding this comment.
LGTM I left some minor concerns
Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>
Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>
Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>
Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>
Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>
Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>
Member
Author
|
Thanks @MikeLippincott ! |
d33bs
added a commit
to d33bs/ZedProfiler
that referenced
this pull request
Aug 7, 2026
Integrate the benchmarking framework and featurization performance refactor from upstream (PR WayScience#48) with the per-shard CLI and Metadata_Imaging_ImageID propagation work on this branch. The two lines of work touched disjoint regions and merged cleanly, but the upstream BenchmarkImageSet mock lacked the image_id attribute that the cli featurization functions now read. Add image_id to BenchmarkImageSet (mirroring ImageSetLoader's fallback to image_set_name) and regenerate the six accuracy-lock signatures in test_benchmark_contracts.py, which now include the Metadata_Imaging_ImageID column.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description
This PR adds a benchmarking test-based framework and improves feature extraction performance generally. I focused on making relatively boring or safe changes which don't interfere with the static output we already have achieved in this project. Below is a table of what we're seeing.
Synthetic data:
Real-world (small CP tutorial) data:
What kind of change(s) are included?
Checklist
Please ensure that all boxes are checked before indicating that this pull request is ready for review.
📚 Documentation preview 📚: https://zedprofiler--48.org.readthedocs.build/en/48/