Establishes foundational infrastructure across multiple crates by introducing unified persistent bit matrix storage with columnar, packed, and implicit variants, alongside De Bruijn graph node encoding and unitig iteration logic. Adds a macro-driven parallel pipeline scheduler featuring NUMA-aware runners, bounded channels, and memory budgets to enforce concurrency limits. Implements streaming nucleotide parsers with pooled page buffers for FASTA, FASTQ, and Genbank formats, complemented by system resource monitoring, progress tracking, and stage profiling utilities. Collectively, these changes provide the core data models, execution frameworks, and I/O pipelines required for downstream k-mer indexing and analysis workloads.
Introduces a counting semaphore-based throttling mechanism to limit concurrent file I/O and pipeline processing. Replaces custom path wrappers with standardized `Throttled` types across `obikmer` and `obikpartitionner`, ensuring RAII-based resource cleanup and explicit backpressure. Additionally, documents how to redirect Cargo build artifacts to local scratch storage on HPC filesystems to prevent compilation slowdowns.
- Replace WorkerPool-based pipelines with typed `Pipe` abstraction in obipipeline
- Introduce Pipe/PipeIter for composable, sourceless/sink-less pipelines
- Update partition and superkmer commands to use new Pipe API via make_pipe!
- Remove Arc<Mutex<...>> patterns; simplify state management
- Fix macOS available_memory() returning 0 by falling back to half total memory in dereplicate()
- Remove unused `format: "zstd"` field from partition.meta
- Replace crossbeam-channel-based threading model
- Introduce obipipeline crate with Stage::Transform/Flat support
- Replace single input + format detection by multiple inputs via PathIter
- Implement pipeline stages: open_chunks → normalize → build_superkmers (flat) + write_batch
- Add SharedFlatFn for 1→N transformations with delta tracking in scheduler loop
- Introduce `obipipline` crate with multi-threaded data pipeline architecture
- Implement core types: SourceFn, SharedFun (Arc), SinkFN with biased scheduler and crossbeam channels
- Add macros: `make_source!`, `transform!/fallible`/sink!, and high-level DSL macro
- Replace old wrapper/error modules with unified scheduler module (renamed types, improved error variants)
- Update workspace: add `obipipeline` member to Cargo.toml and lockfile
- Document pipeline in docmd/implementation with full architecture, error handling & example
- Refactor sandbox_pipeline.rs to use new DSL instead of manual channel wiring
Eric Coissac