perturbation_space: skip None-keyed layers in _combine#1000
Merged
Conversation
sc.get.aggregate can leave a None-keyed layer on the AnnData it returns; PseudobulkSpace.compute strips it, but the _combine refactor in #994 added `key.endswith("_control_diff")` calls that crash on a stray None key (e.g. when callers hand-build the input). Filter to string keys before doing the string ops and the iteration that builds the new AnnData. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
sc.get.aggregatecan leave aNone-keyed layer on the returned AnnData.PseudobulkSpace.computealready strips it (added in fix ci #976), but the_combinerefactor in perturbation_space: cleanup, safer defaults, kill stale-state bugs #994 introducedkey.endswith("_control_diff")calls that crash on a strayNonekey — which is what the CI failure ontest_linear_operationswas hitting._combine.