Push ooxwzorvsqvy #26

2026-06-13T09:59:01Z

coissac commented

2026-06-13 09:59:01 +00:00

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coissac added 6 commits 2026-06-13 09:59:01 +00:00

refactor: migrate pipeline stages and improve graph processing 8b563d0804

Refactored neighbor resolution to explicitly track unvisited indices for degree-1 nodes, updated display formatting, and added timing and debug logging to the degree computation routine. Migrated pipeline stages from eager vector returns to explicit flat implementations, enabling backpressure-aware streaming, configurable batch processing, incremental yielding, and progress tracking via a delta channel.

refactor: replace explicit collect with Unitig::from_nucleotides 5f98d2ef96

Introduce a thread-local buffer to materialize nucleotide iterators into contiguous slices. Update `try_for_each_unitig` across the debruijn, index, merge, and rebuild layers to directly instantiate `Unitig` via `from_nucleotides()` instead of explicitly collecting iterators. This eliminates intermediate allocations and aligns test code with the new approach.

refactor: replace mutex with channels for parallel debruijn processing 1f336fe496

Add `rayon` and `crossbeam-channel` dependencies to support concurrent execution. Replace the synchronous, mutex-protected closure pattern with a channel-based producer-consumer approach using `std::thread::scope`. This decouples unitig iteration from processing, eliminating lock contention and `Mutex` overhead while enabling parallel workloads.

refactor: pass Unitig objects directly instead of raw byte slices fb8c6e427c

Refactored `try_for_each_unitig` and related pipelines across `obidebruinj` and `obikpartitionner` to accept `Unitig` instances directly. This eliminates manual `Unitig::from_nucleotides()` conversions, simplifies the data flow, and reduces unnecessary allocation overhead.

feat: add CPU-aware parallel worker pool for partition merging bc14346f5f

Introduce CpuSample to measure process-level CPU efficiency and wall-clock time. Use crossbeam-channel to distribute partition merging tasks to a dynamic worker pool that scales based on CPU utilization, capped at half the available cores. Update diagnostics to track pool usage.

style: apply consistent formatting and whitespace normalization fddf630772

Applies consistent formatting, whitespace normalization, and indentation standardization to `debruijn.rs` and `merge.rs`. Reorganizes imports and downgrades a unitig traversal log from `info!` to `debug!`. No functional logic or runtime behavior is altered.

coissac merged commit fb5b53dca9 into main

2026-06-13 09:59:07 +00:00

coissac deleted branch push-ooxwzorvsqvy

2026-06-13 09:59:08 +00:00

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Reference: OBIKmers/obikmer#26