Track optimized sage-core (fork master): sparse Mods + slim Peptide compat#62
Merged
Conversation
sage-core PR perf/lazy-peptide-modifications changes Peptide.modifications Vec<f32>->Mods (sparse) and proteins Vec->SmallVec. Adapt the 5 connector sites: construct via Mods::from_dense, expose via to_dense (Python API returns dense Vec<f32> unchanged), read residue mass via mass_at, filter via is_empty. proteins .iter()/.collect() work unchanged on SmallVec. NOTE: Cargo.toml sage-core deps temporarily pin branch=perf/lazy-peptide- modifications for compile verification; revert to master tracking once the sage PR merges.
The Sage build-memory work (sparse Mods + struct-slim + chunked E1 + the Bruker .d-reader fix) merged to the fork's master (872b533), so pin sage-core to master instead of the now-merged perf/lazy-peptide-modifications branch. qfdrust + connector compile clean against it (cargo check).
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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
Modswithto_dense/from_dense; slimmedPeptidewithBox<[..]>mods/proteins) —py_peptide,py_ion_series,py_database,py_scoring.sage-coregit dependency (connector + qfdrust) to the fork's master, where that optimization landed (872b533: sparse mods + struct-slim + chunked materialisation + a Bruker.dfile://→local-path reader fix). Was pinned to the now-mergedperf/lazy-peptide-modificationsbranch.The old lock was stale at the A+D commit (
2d1ab6a); this brings the connector current with the full landed work.Test plan
cargo check— qfdrust + connector compile against sage-core mastermaturin developbuilds the connector against sage-core master872b5339pytest sagepy/tests— 103 passed (incl.test_peptide,test_ion_series,test_sage_compat,test_enzyme,test_fdr)