Introduces the `obikpartition` crate containing the `KmerPartition` struct to manage open layers in sequential order. The `open` constructor eagerly initializes layers under a specified directory, while the `find` method returns the index of the first layer containing a given k-mer. Dependencies are strictly scoped to `obilayeredmap` and `obikseq`, with unit tests validating layer ingestion and single-kmer lookup behavior. Batch lookups and further migration are deferred to a subsequent phase.
The `Layer` enum is transformed into a lifecycle-aware state machine with an `Empty` variant representing an unconstructed directory. Read and query operations now explicitly panic when invoked on this state, enforcing explicit progression through `create()` before use. Iterator methods are updated to handle the new variant exhaustively, and module visibility constants are adjusted to support the refactored structure.
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 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.
Eric Coissac