Rename obikpartition crate to obikpartitionner

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.

src/Cargo.lock

@@ -1600,7 +1600,7 @@ dependencies = [
  "indicatif",
  "ndarray",
  "obicompactvec",
- "obikpartition",
+ "obikpartitionner",
  "obikseq",
  "obilayeredmap",
  "obiread",
@@ -1626,7 +1626,7 @@ dependencies = [
  "obidebruinj",
  "obifastwrite",
  "obikindex",
- "obikpartition",
+ "obikpartitionner",
  "obikphylo",
  "obikrope",
  "obikseq",
@@ -1648,7 +1648,7 @@ dependencies = [
 ]
 
 [[package]]
-name = "obikpartition"
+name = "obikpartitionner"
 version = "0.1.0"
 dependencies = [
  "cacheline-ef",
@@ -1685,7 +1685,7 @@ dependencies = [
  "ndarray",
  "obicompactvec",
  "obikindex",
- "obikpartition",
+ "obikpartitionner",
  "obikseq",
  "obilayeredmap",
  "obipipeline",

src/Cargo.toml

@@ -1,5 +1,5 @@
 [workspace]
 resolver = "3"
-members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartition","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo"]
+members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo"]
 [profile.release]
 debug = 1

src/obicompactvec/src/bitmatrix/packed.rs

@@ -129,7 +129,7 @@ pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
     // A `matrix.pbmx` can already exist here even though columnar data is
     // still pending — e.g. copied verbatim from a merge's base source
     // before this layer was widened with more genome columns (see
-    // `obikpartition::merge_partition`). Only skip (re-)packing if the
+    // `obikpartitionner::merge_partition`). Only skip (re-)packing if the
     // existing file already reflects the current column count; otherwise
     // the columnar files are newer and must be (re-)packed, overwriting the
     // stale one — never silently discarded as "leftover cleanup".

src/obicompactvec/src/intmatrix.rs

@@ -232,7 +232,7 @@ pub fn pack_compact_int_matrix(dir: &Path) -> io::Result<()> {
     // A `matrix.pcmx` can already exist here even though columnar data is
     // still pending — e.g. copied verbatim from a merge's base source
     // before this layer was widened with more genome columns (see
-    // `obikpartition::merge_partition`). Only skip (re-)packing if the
+    // `obikpartitionner::merge_partition`). Only skip (re-)packing if the
     // existing file already reflects the current column count; otherwise
     // the columnar files are newer and must be (re-)packed, overwriting the
     // stale one — never silently discarded as "leftover cleanup".

src/obikindex/Cargo.toml

@@ -5,7 +5,7 @@ edition = "2024"
 
 [dependencies]
 obikseq          = { path = "../obikseq" }
-obikpartition = { path = "../obikpartition" }
+obikpartitionner = { path = "../obikpartitionner" }
 obitaxonomy      = { path = "../obitaxonomy" }
 obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }

src/obikindex/src/dump.rs

@@ -5,7 +5,7 @@ use rayon::prelude::*;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
-use obikpartition::KmerFilter;
+use obikpartitionner::KmerFilter;
 
 impl KmerIndex {
     /// Write a CSV table of all indexed kmers to `out`.

src/obikindex/src/index.rs

@@ -2,7 +2,7 @@ use std::collections::BTreeMap;
 use std::fs;
 use std::path::{Path, PathBuf};
 
-use obikpartition::{KmerPartitions, KmerSpectrum, PARTITIONS_SUBDIR};
+use obikpartitionner::{KmerPartitions, KmerSpectrum, PARTITIONS_SUBDIR};
 use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
 use tracing::info;
@@ -157,6 +157,33 @@ impl KmerIndex {
     pub fn minimizer_size(&self) -> usize {
         self.meta.config.minimizer_size
     }
+    pub fn n_bits(&self) -> usize {
+        self.meta.config.n_bits
+    }
+    pub fn with_counts(&self) -> bool {
+        self.meta.config.with_counts
+    }
+    pub fn evidence_mode(&self) -> &obilayeredmap::IndexMode {
+        &self.meta.config.evidence
+    }
+    /// Coarse evidence mode (`Exact`/`Approx`/`Hybrid`, no `b`/`z`
+    /// parameters) — see [`evidence_mode`](Self::evidence_mode) for the
+    /// full `IndexMode`. Same discriminant as `Layer::evidence_kind`, so a
+    /// layer's own evidence kind can be compared directly against the
+    /// index's.
+    pub fn evidence_kind(&self) -> obilayeredmap::EvidenceKind {
+        match self.meta.config.evidence {
+            obilayeredmap::IndexMode::Exact => obilayeredmap::EvidenceKind::Exact,
+            obilayeredmap::IndexMode::Approx { .. } => obilayeredmap::EvidenceKind::Approx,
+            obilayeredmap::IndexMode::Hybrid { .. } => obilayeredmap::EvidenceKind::Hybrid,
+        }
+    }
+    pub fn block_bits(&self) -> u8 {
+        self.meta.config.block_bits
+    }
+    pub fn genomes(&self) -> &[GenomeInfo] {
+        &self.meta.genomes
+    }
     pub fn n_partitions(&self) -> usize {
         self.partition.n_partitions()
     }

src/obikindex/src/merge.rs

@@ -13,7 +13,7 @@ use crate::index::KmerIndex;
 use crate::meta::{GenomeInfo, IndexMeta};
 use crate::state::{IndexState, SENTINEL_INDEXED};
 
-pub use obikpartition::MergeMode;
+pub use obikpartitionner::MergeMode;
 
 // ── per-partition diagnostic record ──────────────────────────────────────────
 
@@ -193,7 +193,7 @@ impl KmerIndex {
             let block_bits = dst.meta.config.block_bits;
 
             // Pre-build source list once (avoid rebuilding per partition)
-            let srcs: Vec<(&obikpartition::KmerPartitions, usize)> = remaining_sources
+            let srcs: Vec<(&obikpartitionner::KmerPartitions, usize)> = remaining_sources
                 .iter()
                 .map(|s| (&s.partition, s.meta.genomes.len()))
                 .collect();

src/obikindex/src/predicate.rs

@@ -1,6 +1,6 @@
 use std::collections::HashMap;
 
-use obikpartition::GroupQuorumFilter;
+use obikpartitionner::GroupQuorumFilter;
 use obitaxonomy::{TaxPath, TaxPattern};
 
 use crate::meta::{GenomeInfo, IndexMeta};

src/obikindex/src/rebuild.rs

@@ -1,6 +1,6 @@
 use std::path::Path;
 
-use obikpartition::{KmerFilter, MergeMode};
+use obikpartitionner::{KmerFilter, MergeMode};
 use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
 

src/obikindex/src/reindex.rs

@@ -1,4 +1,4 @@
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obilayeredmap::{IndexMode, layer::Layer};
 use obisys::{Reporter, Stage, progress_bar};
 use std::fs;

src/obikindex/src/select.rs

@@ -1,6 +1,6 @@
 use std::path::Path;
 
-use obikpartition::{KmerPartitions, OutputCol};
+use obikpartitionner::{KmerPartitions, OutputCol};
 use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
 

src/obikmer/Cargo.toml

@@ -15,7 +15,7 @@ obifastwrite  = { path = "../obifastwrite" }
 obidebruinj   = { path = "../obidebruinj" }
 obipipeline   = { path = "../obipipeline" }
 obikrope      = { path = "../obikrope" }
-obikpartition = { path = "../obikpartition" }
+obikpartitionner = { path = "../obikpartitionner" }
 obisys        = { path = "../obisys" }
 obiskio       = { path = "../obiskio" }
 obikindex     = { path = "../obikindex", default-features = false }

src/obikmer/src/cmd/filter/mod.rs

@@ -2,7 +2,7 @@ use std::path::PathBuf;
 
 use clap::Args;
 use obikindex::{KmerIndex, MergeMode};
-use obikpartition::filter::{MaxTotalCount, MinComplexity, MinTotalCount};
+use obikpartitionner::filter::{MaxTotalCount, MinComplexity, MinTotalCount};
 use obisys::Reporter;
 use tracing::info;
 

src/obikmer/src/cmd/predicate.rs

@@ -1,6 +1,6 @@
 use clap::Args;
 use obikindex::{GroupFilterParams, IndexMeta, MetaPred};
-use obikpartition::KmerFilter;
+use obikpartitionner::KmerFilter;
 
 /// CLI args for ingroup/outgroup filtering — embeddable in any command via `#[command(flatten)]`.
 #[derive(Args)]

src/obikmer/src/cmd/query/batch.rs

@@ -1,6 +1,6 @@
 use std::collections::HashMap;
 
-use obikpartition::KmerDesc;
+use obikpartitionner::KmerDesc;
 use obikseq::CanonicalKmer;
 use obiread::record::SeqRecord;
 use obiskbuilder::SuperKmerIter;

src/obikmer/src/cmd/query/chunk.rs

@@ -1,7 +1,7 @@
 use std::time::Instant;
 
 use obikindex::KmerIndex;
-use obikpartition::{KmerDesc, QueryHit, QueryStats};
+use obikpartitionner::{KmerDesc, QueryHit, QueryStats};
 use obikrope::Rope;
 use obikseq::CanonicalKmer;
 use obiread::record::parse_chunk;

src/obikmer/src/cmd/select/mod.rs

@@ -3,7 +3,7 @@ use std::path::PathBuf;
 
 use clap::{Args, ValueEnum};
 use obikindex::{IndexMeta, KmerIndex};
-use obikpartition::{AggOp, OutputCol};
+use obikpartitionner::{AggOp, OutputCol};
 use obisys::Reporter;
 use tracing::info;
 

src/obikmer/src/steps/scatter.rs

@@ -3,7 +3,7 @@ use std::sync::Arc;
 use std::sync::atomic::{AtomicU32, AtomicU64, Ordering};
 use std::time::Instant;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obipipeline::{ThrottleGuard, Throttled, throttle};
 use obiread::NucPage;
 use obisys::spinner;

src/obikpartitionner/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-name = "obikpartition"
+name = "obikpartitionner"
 version = "0.1.0"
 edition = "2024"
 

src/obikpartitionner/src/partition/kmer_partition.rs

@@ -197,7 +197,7 @@ impl KmerPartitions {
     }
 
     /// Partition `i`'s metadata (layer count, evidence mode) — the single
-    /// entry point for this, so that callers outside `obikpartition`
+    /// entry point for this, so that callers outside `obikpartitionner`
     /// never need to know it's a `meta.json` loaded via
     /// `obilayeredmap::meta::PartitionMeta`, nor handle its own recovery
     /// path for indexes built before that file existed (see

src/obikphylo/Cargo.toml

@@ -6,7 +6,7 @@ edition = "2024"
 [dependencies]
 obikindex        = { path = "../obikindex", default-features = false }
 obikseq          = { path = "../obikseq" }
-obikpartition = { path = "../obikpartition" }
+obikpartitionner = { path = "../obikpartitionner" }
 obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }

src/obikphylo/src/siblings/alignment.rs

@@ -1,6 +1,6 @@
 use std::sync::Arc;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obisys::progress_bar;
 
 use obikindex::KmerIndex;

src/obikphylo/src/siblings/build.rs

@@ -4,7 +4,7 @@ use std::sync::atomic::Ordering;
 
 use rayon::prelude::*;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obikseq::CanonicalKmer;
 use obilayeredmap::MphfLayer;
 use obilayeredmap::meta::IndexMode;

src/obikphylo/src/siblings/cache.rs

@@ -3,7 +3,7 @@ use rayon::prelude::*;
 use std::path::Path;
 
 use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obikseq::CanonicalKmer;
 use obilayeredmap::meta::IndexMode;
 use obilayeredmap::{Layer, OLMResult};

src/obikphylo/src/siblings/cardinality.rs

@@ -2,7 +2,7 @@ use std::sync::Arc;
 
 use ndarray::Array2;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obisys::progress_bar;
 
 use obikindex::KmerIndex;

src/obikphylo/src/siblings/distance.rs

@@ -2,7 +2,7 @@ use std::sync::Arc;
 
 use ndarray::Array2;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obisys::progress_bar;
 
 use obikindex::KmerIndex;

src/obikphylo/src/siblings/entropy.rs

@@ -13,7 +13,7 @@ use std::io::{BufWriter, Write};
 use std::path::{Path, PathBuf};
 use std::sync::Arc;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obisys::progress_bar;
 
 use obikindex::KmerIndex;

src/obikphylo/src/siblings/sankoff_bundle.rs

@@ -29,7 +29,7 @@ use std::sync::Arc;
 
 use ndarray::Array2;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obisys::progress_bar;
 
 use obikindex::KmerIndex;

src/obikphylo/src/siblings/stats.rs

@@ -2,7 +2,7 @@ use std::sync::Arc;
 
 use rayon::prelude::*;
 
-use obikpartition::KmerPartitions;
+use obikpartitionner::KmerPartitions;
 use obisys::progress_bar;
 
 use obikindex::KmerIndex;

src/obilayeredmap/src/layer.rs

@@ -33,7 +33,7 @@ pub trait LayerData: Sized {
 ///
 /// `obilayeredmap` operates within a single partition's index root; it has
 /// no notion of "partition" at all. Turning a partition number into that
-/// root is `obikpartition::KmerPartition::part_dir`'s job, one layer up
+/// root is `obikpartitionner::KmerPartition::part_dir`'s job, one layer up
 /// — callers here only ever name a layer *number*, never build the path
 /// themselves.
 pub fn layer_dir(root: &Path, i: usize) -> PathBuf {