Add pytest for r_computematrix (salvage of #1369)#1433
Merged
Conversation
Salvaged from #1369: keeps only the computeMatrix test, which passes against the current Rust bindings. The alignmentSieve, bamCompare and bamCoverage tests from that PR were dropped because their Rust function signatures have since changed (and alignmentSieve2 is not yet wired up on 4.0.0). Co-Authored-By: Claude Fable 5 <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
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Salvages the compatible part of #1369 (stalled). Keeps only the
test_r_computeMatrix.pytest, which passes against the current Rust bindings.Dropped from #1369 (do not merge those as-is):
test_r_alignmentsieve.py—alignmentSieve2is not yet wired up on4.0.0(CLI entry point commented out; Python wrapper passes 15 args while the compiled binding requires 17). Also panics on empty blacklist path.test_r_bamCompare.py/test_r_bamCoverage.py— the Rust function signatures have since changed (e.g.bamCoveragenow requirescollapse;bamComparegainedsf1/sf2, split pseudocounts, etc.), so the positional calls no longer line up.Verified locally with
pixi run build && pixi run pytest test_r_computeMatrix.py— 2 passed.Original author: @gerikson. Partially supersedes #1369.
🤖 Generated with Claude Code