Extracts directory bookkeeping and construction methods into a new IndexBuilder trait, separating maintenance operations from scientific computation logic. Migrates relevant methods to the new trait, updates module imports across obikindex, and narrows the crate's public API surface. Adds an end-to-end CLI smoke test to verify multi-index merge workflows.
Moves pipeline state bookkeeping, including sentinel file marking and spectrum persistence, into the algorithms' run and close methods. Introduces a crate-private extension trait to satisfy Rust's orphan rule while implementing construction-only operations on KmerIndex. Updates helper function visibility for cross-crate access and removes the now-empty index_layer module.
This commit renames the `Layer` type to `KmerLayer` throughout the `obikindex` and `obikphylo` crates. All imports, struct fields, function signatures, pattern matches, and instantiation calls have been updated accordingly. The change is a purely structural refactor that tightens type constraints without altering runtime behavior or data models.
Introduce a dedicated LayerBuilder struct to orchestrate parallel layer 0 construction across partitions. The fluent API supports configurable abundance thresholds and intermediate artifact retention. Parallel execution is delegated to a NUMA-aware PartitionRunner scheduler, while progress reporting and stage timing are shifted to the command layer. A new mark_indexed method cleanly separates state tracking from orchestration by generating a completion sentinel.
The layer API has been updated to rename `index` and `index_batch` to `hash` and `hash_batch`, aligning with raw MPHF slot hashing behavior. New public methods have been added to directly expose kmer hashing and iteration, enforcing strict state validation on empty layers. All other modifications are consistent code formatting adjustments without functional changes.
The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.
Move partition dereplication logic into a dedicated `obikderep` crate that implements a two-phase hash-split/merge strategy with Rayon for parallel processing. Centralize superkmer file path construction in `obilayeredmap` and update dependent crates to use the new pipeline and shared path helpers. Adjust test suites to explicitly invoke the dereplication step.
Invert dependencies by moving partition path primitives to a dedicated module and updating the index crate accordingly. Reshape the partition router to accept a mutable index reference, enabling chainable configuration and resolving lifetime issues with explicit drops. Shift orchestration logic from the index crate to the CLI, replacing monolithic scatter calls with discrete dereplication and counting steps. Introduce a generic progress callback API to decouple rate calculation from UI rendering, and correct file I/O paths to route layer-0 artifacts under the partition index directory.
Renames `Layer<D>` to `TypedLayer<D>` to establish a distinct typed abstraction. Introduces a new heterogeneous `Layer` enum that unifies count and presence storage with runtime dispatch, delegating operations to the underlying typed variants. Updates cache, index, and phylo consumers to align with the renamed type and new extension traits, preserving full test suite stability while preparing the foundation for multi-partition caching.
Consolidates partition logic, metadata storage, and layer management directly into KmerIndex. Renames obikpartitionner to obikpartition, retaining only PartitionRouter for superkmer routing. Removes intermediate .partition() accessors in favor of direct methods on the index and updates PartitionCache::build to accept &KmerIndex directly. Derives n_partitions from config.n_bits and consolidates k-mer/minimizer sizes into IndexMeta.config. Fixes a regression where PartitionRouter::open incorrectly defaulted to closed.
Update all dependent crates and internal imports to reference the renamed module. Expose configuration parameters and genome metadata through new public accessor methods in the index API, and update documentation comments to align with the new package name.
Update Cargo manifests, dependency paths, and Rust imports across the workspace to reflect the `obikpartitionner` to `obikpartition` rename. Synchronize architecture and implementation documentation with the new module structure. Fix minor syntax issues in test assertions to ensure compilation compatibility. No behavioral or API changes are introduced.
Rename the KmerPartition type to KmerPartitions across obikindex, obikpartitionner, and obikphylo/siblings to reflect an updated data model. Update the Mat enum in siblings/cache.rs to add a SparsePresence variant and simplify opening logic by delegating sparse versus dense detection to PersistentBitMatrix. Apply consistent code formatting, import reordering, and multi-line refactoring throughout the affected modules.
Replaced scattered direct metadata loading with centralized instance methods on `KmerPartition` to guarantee consistent error mapping and legacy recovery. Introduced `StorageKind`, `LayerContent`, and `EvidenceKind` enums alongside lightweight disk-probe methods that inspect file presence without opening heavy data structures. Updated callers across the index, partitioner, and phylo modules to use the new partition API, and added unit tests validating the introspection behavior.
Introduce a design specification outlining performance bottlenecks in layer data access and an agreed-upon implementation direction for caching. Refactor the codebase to centralize index and layer directory path resolution within the partition object, replacing manual string joining and external helper functions with dedicated accessor methods.
Standardizes layer directory path resolution across obikindex, obikpartitionner, and obikphylo by replacing inline string formatting and join calls with the centralized obilayeredmap::layer_dir utility. This refactoring removes redundant path construction logic while preserving existing iteration bounds, control flow, and public APIs.
Replace manual directory formatting and inline matrix opening with the newly introduced `layer_dir` and `open_data` helpers from the `obilayeredmap` crate. This standardizes filesystem access, encapsulates layer naming conventions, and simplifies error handling without altering computational behavior or test suites.
Bumps core dependencies including ndarray, rand, hashbrown, niffler, ureq, sysinfo, indicatif, lru, and remove_dir_all. Adapts source code to accommodate breaking changes by migrating RNG initialization, adjusting HTTP response handling, and replacing the fs4 crate with standard library file locking. Adds a planning document for query benchmarking and sparse index regression tests.
Restructure the project by moving the standalone compare_sparse utility into an example directory, removing Sankoff parameter configurations and benchmark scripts, updating version control ignores, and expanding the test suite with diagnostic checks and performance benchmarks.
Introduce runtime dimension tracking, matrix shape validation, and per-layer diagnostics across multiple modules to improve execution observability. Extract intermediate computation results into local variables, standardize collection patterns in partial methods, and replace naive iteration with optimized pairwise counting. All modifications are strictly additive or structural; public APIs, data models, and core logic remain unchanged.
Introduce a `Sparse` variant for `PersistentBitMatrix` with full method dispatch and implementations of `ColumnWeights` and `BitPartials` traits. Refactor distance matrix computations in layered stores to eagerly collect results before reduction, enabling reliable dimension tracking. Add comprehensive debug logging across phylo commands and distance modules to report matrix shapes and flag out-of-bounds indices during CSV iteration.
The index packing API now accepts a `sparse` parameter to generate `PersistentSparseBitMatrix` files alongside existing dense matrices. The sibling cache automatically detects this format via an `is_multi.prsb` marker file and routes queries identically to the dense variant. A new `--sparse` CLI flag exposes the option, with tests verifying end-to-end pipeline correctness and storage equivalence.
Documents a proposed redesign for cross-partition batch resolution, shifting trigger logic to per-destination accumulator thresholds and introducing entropy-based pruning criteria. Adds an `n_layers_per_partition` method to the index, exposing partition metadata with consistent error handling and clarified documentation regarding build-time structural properties.
Shifts sibling annex construction from slot-indexed enumeration to iteration-order traversal by correcting cumulative k-mer offset tracking in batch enumeration. Replaces coarse per-partition parallelism with chunked work distribution to prevent thread starvation on skewed partitions. Decouples custom progress messages from ETA updates to eliminate display clobbering during high-frequency callbacks. Adds regression tests validating batch offset correctness, partial batch handling, and iterator-order consistency across layer builds.
Relocate the `siblings` and `cardcomp` modules from `obikindex` to a dedicated `obikphylo` workspace member. Convert inherent methods on `KmerIndex` into extension traits, update import paths across `obikmer`, and add supporting accessor methods to `obikseq` and `obilayeredmap`. This restructuring reduces the public API surface of `obikindex` while organizing phylogenetic iteration, caching, and distance calculation logic under a dedicated crate.
Transitions the index from MPHF slot-based to physical iteration-order indexing, aligning with the unitig layout. Introduces a streaming-only pipeline for k-mer iteration that adheres to memory constraints by avoiding full in-memory collections. Updates layer and sibling iterators to own an Arc clone of the file reader, making them Send + 'static and safe for concurrent use without borrowing the parent. Exposes batch and k-mer iterator types publicly while simplifying signature syntax with modern lifetime elision.
Transition the minorant flag from a derived value to a stored field within the family mask, resolving a performance regression where on-the-fly reconstruction consumed significant query time. This change introduces O(1) k-mer reconstruction APIs, shifts minorant computation to the index build phase, and enables direct annex-based statistics. Supporting updates include adopting shared ownership for partition caches and refactoring batch processing pipelines.
Refactor `scan_layer_families` across the siblings module to accept a closure callback instead of returning an intermediate collection. This eliminates eager materialization and per-layer buffering by streaming results directly into genome-specific buffers or tally matrices. The update introduces bounded batch processing and scratch buffer reuse to cap peak auxiliary memory, while preserving existing computational behavior, control flow, and error semantics.
The sibling calculation modules now process layer directories sequentially instead of in parallel. This eliminates concurrent processing overhead and prevents interleaved cache sweeps, improving disk I/O and page-cache locality for partition-grouped data access. Progress bar updates and result accumulation have been adapted to the sequential control flow, while core filtering logic and output structures remain unchanged.
Introduces a dedicated `family_scan` submodule to consolidate per-layer family traversal logic. Centralizes path validation, minorant filtering, and conditional matrix instantiation into a shared `scan_layer_families` function. Updates sibling-annex consumers to leverage the new abstraction, reducing inline scanning code. Adds a test fixture to verify numerical consistency across consumer methods for co-occurrence and base-pair metrics.
Extracts directory cleanup, partition initialization, and finalization into dedicated helper methods within KmerIndex. This centralizes force-flag handling and reduces boilerplate across merge, rebuild, and select workflows. Additionally updates the CLI progress bar template to display an ETA indicator following elapsed time.
Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
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 new predicate module in obikindex that implements genome metadata predicate parsing, evaluation, and group classification using three-valued logic. Extends the IndexMeta API with methods for single-predicate filtering and group quorum filtering. Updates obikmer command modules to delegate filter construction and matching to the centralized index API, removing local definitions and simplifying call sites.
Replaced the legacy Sankoff parsimony pipeline with a new cardinality-composition decomposition that constructs row-normalized transition probability matrices symmetrized via geometric mean. This ensures reversibility, reduces free parameters from 240 to 120, and guarantees a zero diagonal. Tallies are now explicitly restricted to variable families to align with +ASC-corrected alignment populations. Additionally, fixed `--exclude-genome` handling to re-scan surviving sequences and drop newly monomorphic columns, preventing silent data corruption in downstream tree inference tools.
Implements a calibrated 16-state Sankoff substitution cost matrix and CLI pipeline for evolutionary distance computation, including empirical calibration via saturation-filtered SNP counts. Refactors the sibling scanning stage to use batched transforms for improved synchronization efficiency. Introduces an OS-level advisory directory lock across all index-modifying commands to prevent concurrent write corruption. Updates dependencies and exposes new Sankoff utilities in the public API.
Re-enables the `numa` feature in CI workflows to prevent container/cgroup deadlocks while preserving validation correctness. Fixes concurrent test race conditions by replacing thread-local parameter storage with process-wide atomics and mutex locks. Integrates `tracing-subscriber` for structured logging and adds thread-ID tracking to debug worker lifecycles. Additionally bumps the crate version, updates `.gitignore`, documents experimental evolutionary distance pipelines, and refactors hardcoded test constants.
Introduce `obisys::effective_parallelism()` to read Linux cgroup v1/v2 CPU quotas from sysfs, preventing thread pool oversubscription in containerized environments. Replace direct `std::thread::available_parallelism()` calls across `obikindex` and `obikmer` with this centralized function. Bump `obikmer` version to 1.1.41.
Introduces a `SnpAlignment` struct and helper methods to construct per-genome SNP pseudo-alignments from sibling k-mer data, filtering monomorphic families and encoding bases as IUPAC ambiguity codes. Exposes the type at the crate root for simplified imports. Adds a `--snp` CLI flag to compute and export these alignments as an IUPAC-coded FASTA file. Updates theory documentation to propose a multi-genome framing approach for joint phylogenetic inference, resolving pairwise correspondence ambiguities through positional homology and partial coverage thresholds. Bumps crate version to 1.1.40.
Exposes RawSnpDistanceOutput and implements KmerIndex::raw_snp_distance() to compute pairwise single-copy locus counts under a paralogy-aware rule. The implementation leverages ndarray for parallel matrix aggregation, producing raw p-distance matrices for sanity-checking. A --raw-snp-distance CLI flag is added to export results as CSV, mapping zero-eligible pairs to NA.
Replaces the explicit `SiblingInfo` struct and 3-bit minorant flags with a derived 4-bit presence mask (`FamilyMask`) that tracks observed bases per family. This eliminates redundant file I/O overhead by introducing a `PartitionCache` for batch lookups, simplifies serialization, and updates all downstream builders, stats computation, and tests to operate on the new bitmask representation. Adjusts CLI output to report deduplicated family sizes instead of histograms, ignores generated CSV files, and updates documentation to reflect the fixed canonical reference and new theory.
Add the `obipipeline` crate and replace sequential scatter/gather logic with a concurrent pipeline using `Flat` and `Transform` stages. Introduce `SiblingAnnexStats` API to compute distributions, and add CLI flags to `distance.rs` for constructing the annex and exporting statistics as CSV.
Introduce the siblingannex module in obicompactvec to store per-slot minorant flags and sibling counts in a memory-mapped annex file. Add a scatter-gather pipeline in obikindex to compute these values across index layers and write them to .psib files. Implement central_canonical_neighbors in obikseq for generating strand-aware k-mer variants around the middle base. Expose rolling statistics in obiskbuilder and update dependency graphs accordingly.
Implement the Mash distance metric across the CLI, index, and compact vector traits. This includes adding a `Mash` variant to the `DistanceMetric` enum and `MetricArg` CLI argument, implementing the conversion from Jaccard distances using the standard mutation-rate estimator formula, and updating documentation with supported metrics and algorithmic references. Additionally, add an `entropy` method to rolling statistics for computing order-specific entropy.
Shifts the NUMA-aware runner from a flat, round-robin model to a per-node architecture using dedicated `NodeActivation` channels. Replaces absolute deltas with relative scaling based on the previous growth step's worker count, decoupling growth from node count to fix slow ramp-up and enforce per-node fairness. Updates architecture documentation to reflect these changes and focus tuning questions on `INITIAL`/`GROWTH_DIVISOR` parameters for I/O-bound validation.
Replaces the monolithic CPU scaling threshold with separate CPU and I/O spawn thresholds. Introduces an `IoSample` struct with platform-specific byte reading and a relative throughput growth heuristic. Adds a 0.1s wall-clock guard to `CpuSample` to suppress artificial efficiency spikes, and updates `maybe_activate` to trigger worker scaling when either resource indicates headroom. Bumps `obikmer` to v1.1.33 and updates architecture documentation.
Updates the release workflow to run macOS builds inside a Docker container with explicit registry authentication and adjusted artifact paths. Bumps the obikmer crate version to 1.1.29 and adds *.log to .gitignore. Simplifies NUMA worker spawning by lowering the activation threshold from 0.95 to 0.2, replacing complex stateful tracking with a direct efficiency check, and downgrading progress logging to debug level. Includes general code formatting improvements for readability.
Refactor the release workflow to use a structured container object with authenticated pulls for macOS ARM64 builds. Replace single-worker activation with dynamic upfront provisioning based on node and worker counts. Implement an absolute efficiency gain threshold for scaling checks and add early termination to improve adaptive scaling stability. Bump obikmer crate version to 1.1.27.
Eric Coissac