refactor: rename obikpartitionner crate to obikpartition

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.

src/Cargo.lock

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

src/Cargo.toml

@@ -1,5 +1,5 @@
 [workspace]
 resolver = "3"
-members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo"]
+members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartition","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
-    // `obikpartitionner::merge_partition`). Only skip (re-)packing if the
+    // `obikpartition::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
-    // `obikpartitionner::merge_partition`). Only skip (re-)packing if the
+    // `obikpartition::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" }
-obikpartitionner = { path = "../obikpartitionner" }
+obikpartition = { path = "../obikpartition" }
 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 obikpartitionner::KmerFilter;
+use obikpartition::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 obikpartitionner::{KmerPartitions, KmerSpectrum, PARTITIONS_SUBDIR};
+use obikpartition::{KmerPartitions, KmerSpectrum, PARTITIONS_SUBDIR};
 use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
 use tracing::info;

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 obikpartitionner::MergeMode;
+pub use obikpartition::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<(&obikpartitionner::KmerPartitions, usize)> = remaining_sources
+            let srcs: Vec<(&obikpartition::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 obikpartitionner::GroupQuorumFilter;
+use obikpartition::GroupQuorumFilter;
 use obitaxonomy::{TaxPath, TaxPattern};
 
 use crate::meta::{GenomeInfo, IndexMeta};

src/obikindex/src/rebuild.rs

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

src/obikindex/src/reindex.rs

@@ -1,4 +1,4 @@
-use obikpartitionner::KmerPartitions;
+use obikpartition::KmerPartitions;
 use obilayeredmap::{IndexMode, layer::Layer};
 use obisys::{Reporter, Stage, progress_bar};
 use std::fs;
@@ -71,11 +71,11 @@ impl KmerIndex {
 
 /// Process all layers of one partition's index directory.
 fn reindex_partition(
-    partition: &KmerPartitions
-   , i: usize
-   , target: &IndexMode
-   , block_bits: u,
-8) -> OKIResult<()> {
+    partition: &KmerPartitions,
+    i: usize,
+    target: &IndexMode,
+    block_bits: u8,
+) -> OKIResult<()> {
     if !partition.index_dir(i).exists() {
         return Ok(());
     }

src/obikindex/src/select.rs

@@ -1,6 +1,6 @@
 use std::path::Path;
 
-use obikpartitionner::{KmerPartitions, OutputCol};
+use obikpartition::{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" }
-obikpartitionner = { path = "../obikpartitionner" }
+obikpartition = { path = "../obikpartition" }
 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 obikpartitionner::filter::{MaxTotalCount, MinComplexity, MinTotalCount};
+use obikpartition::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 obikpartitionner::KmerFilter;
+use obikpartition::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 obikpartitionner::KmerDesc;
+use obikpartition::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 obikpartitionner::{KmerDesc, QueryHit, QueryStats};
+use obikpartition::{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 obikpartitionner::{AggOp, OutputCol};
+use obikpartition::{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 obikpartitionner::KmerPartitions;
+use obikpartition::KmerPartitions;
 use obipipeline::{ThrottleGuard, Throttled, throttle};
 use obiread::NucPage;
 use obisys::spinner;

src/obikpartition/Cargo.toml

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

src/obikpartition/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 `obikpartitionner`
+    /// entry point for this, so that callers outside `obikpartition`
     /// 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/obikpartition/src/tests/query_layer.rs

@@ -45,7 +45,7 @@ fn query_stats_default_is_zero() {
 fn query_partition_with_missing_index_dir_returns_default_stats() {
     let tmp = tempfile::tempdir().expect("tempdir");
     let partition =
-        KmerPartitions::create(tmp.path().join("idx"), 2, 21, 9, false.expect("create partition");
+        KmerPartitions::create(tmp.path().join("idx"), 2, 21, 9, false).expect("create partition");
 
     let mut kmers: HashMap<CanonicalKmer, Vec<KmerDesc>> = HashMap::new();
     // Any well-formed canonical k-mer works here — the call must return
@@ -66,7 +66,7 @@ fn query_partition_with_missing_index_dir_returns_default_stats() {
 fn query_partition_with_empty_kmers_is_a_noop() {
     let tmp = tempfile::tempdir().expect("tempdir");
     let partition =
-        KmerPartitions::create(tmp.path().join("idx"), 2, 21, 9, false.expect("create partition");
+        KmerPartitions::create(tmp.path().join("idx"), 2, 21, 9, false).expect("create partition");
 
     let kmers: HashMap<CanonicalKmer, Vec<KmerDesc>> = HashMap::new();
     let stats = partition

src/obikphylo/Cargo.toml

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

src/obikphylo/src/siblings/alignment.rs

@@ -1,6 +1,6 @@
 use std::sync::Arc;
 
-use obikpartitionner::KmerPartitions;
+use obikpartition::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 obikpartitionner::KmerPartitions;
+use obikpartition::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 obikpartitionner::KmerPartitions;
+use obikpartition::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 obikpartitionner::KmerPartitions;
+use obikpartition::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 obikpartitionner::KmerPartitions;
+use obikpartition::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 obikpartitionner::KmerPartitions;
+use obikpartition::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 obikpartitionner::KmerPartitions;
+use obikpartition::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 obikpartitionner::KmerPartitions;
+use obikpartition::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 `obikpartitionner::KmerPartition::part_dir`'s job, one layer up
+/// root is `obikpartition::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 {