refactor: rename obikindex to obikindexer

DevDocMD/implementation/partition_layer_cache.md

@@ -16,6 +16,22 @@ tier / Index tier, each depending only downward) are unchanged; only the
 crate-vs-module packaging changed. See [obikindex::layer](layer_tier.md)
 for the current module doc.
 
+**Superseded, second event, same day (2026-08-21):** `obikpartitionner`
+and `obikderep`, the two algorithm crates, are also gone — but unlike
+`obikpartition`/`obilayeredmap` above, they were **not** folded into
+`obikindex`. They were first (mistakenly) merged into `obikindex` as an
+`algorithms` submodule, then corrected into a new sibling crate,
+**`obikindexer`**, holding `obikindexer::algorithms::{partitionner,
+dereplicator}` and depending on `obikindex` — never the reverse, same
+dependency direction `obikpartitionner`/`obikderep` already had. Read
+`obikpartitionner::X` as `obikindexer::algorithms::partitionner::X` and
+`obikderep::X` as `obikindexer::algorithms::dereplicator::X` throughout
+what follows. The distinction the mistake surfaced, worth keeping: data
+crates (`obikindex`, holding the `index`/`partition`/`layer` model) merge
+naturally into one crate as submodules; algorithm crates that operate on
+that model from outside stay separate, so the dependency only ever runs
+one way.
+
 Status (2026-08-20, latest pass): (1) done — `obilayeredmap::Layer`
 exists, `Mat` is gone. (1b) done — `Layer::Empty`, the first non-ready
 state, added (panics on every read method). (2a) done — the

src/Cargo.lock

@@ -1539,11 +1539,9 @@ dependencies = [
  "obicompactvec",
  "obidebruinj",
  "obikentropy",
- "obikrope",
  "obikseq",
  "obipipeline",
  "obiread",
- "obiskbuilder",
  "obiskio",
  "obisys",
  "obitaxonomy",
@@ -1551,12 +1549,37 @@ dependencies = [
  "rayon",
  "serde",
  "serde_json",
- "sysinfo",
  "tempfile",
  "tracing",
  "tracing-subscriber",
 ]
 
+[[package]]
+name = "obikindexer"
+version = "0.1.0"
+dependencies = [
+ "cacheline-ef",
+ "epserde",
+ "memmap2",
+ "niffler",
+ "obicompactvec",
+ "obikindex",
+ "obikrope",
+ "obikseq",
+ "obipipeline",
+ "obiread",
+ "obiskbuilder",
+ "obiskio",
+ "obisys",
+ "ptr_hash",
+ "rayon",
+ "serde",
+ "serde_json",
+ "sysinfo",
+ "tempfile",
+ "tracing",
+]
+
 [[package]]
 name = "obikmer"
 version = "1.2.2"
@@ -1568,6 +1591,7 @@ dependencies = [
  "obidebruinj",
  "obifastwrite",
  "obikindex",
+ "obikindexer",
  "obikphylo",
  "obikrope",
  "obikseq",
@@ -1595,6 +1619,7 @@ dependencies = [
  "ndarray",
  "obicompactvec",
  "obikindex",
+ "obikindexer",
  "obikseq",
  "obipipeline",
  "obiread",

src/Cargo.toml

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

src/obikindex/Cargo.toml

@@ -12,8 +12,6 @@ obicompactvec    = { path = "../obicompactvec" }
 obidebruinj      = { path = "../obidebruinj" }
 obipipeline      = { path = "../obipipeline" }
 obikentropy      = { path = "../obikentropy" }
-obiread          = { path = "../obiread" }
-obiskbuilder     = { path = "../obiskbuilder" }
 cacheline-ef     = "1.1"
 epserde          = "0.8"
 ptr_hash         = "1.1"
@@ -27,12 +25,11 @@ serde_json       = "1"
 indicatif        = "0.18"
 tracing          = "0.1.44"
 bitvec           = "1"
-sysinfo          = "0.39"
 hwlocality       = { version = "1.0.0-alpha.11", features = ["vendored"], optional = true }
 
 [dev-dependencies]
+obiread  = { path = "../obiread" }
 obikseq  = { path = "../obikseq", features = ["test-utils"] }
-obikrope = { path = "../obikrope" }
 tempfile = "3"
 tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
 anyhow   = "1"

src/obikindex/src/algorithms/mod.rs

@@ -1,9 +0,0 @@
-//! Indexing-pipeline algorithms: code that operates on a
-//! [`crate::index::KmerIndex`] to build or transform its content, as
-//! opposed to the `index`/`partition`/`layer` modules, which are the data
-//! model itself. Each algorithm is its own submodule: [`partitionner`]
-//! (routing raw super-kmers into partitions, then counting), [`dereplicator`]
-//! (deduplicating a partition's raw super-kmers before counting).
-
-pub mod dereplicator;
-pub mod partitionner;

src/obikindex/src/index/kmer_index.rs

@@ -159,10 +159,10 @@ impl KmerIndex {
     /// Path of partition `i`'s raw directory (`partitions/part_{i:05}`) —
     /// delegates to `crate::partition`, the Partition tier's own naming
     /// primitive (mirrors `layer_dir` delegating to `crate::layer`).
-    /// `crate::algorithms::partitionner::PartitionRouter` reaches this same
+    /// `obikindexer::algorithms::partitionner::PartitionRouter` reaches this
-    /// directory only indirectly, through this method — it depends on
+    /// same directory only indirectly, through this method — `obikindexer`
-    /// `KmerIndex`, not the other way around, even though both now live in
+    /// depends on `KmerIndex`, not the other way around — see
-    /// this crate — see `DevDocMD/implementation/partition_layer_cache.md`.
+    /// `DevDocMD/implementation/partition_layer_cache.md`.
     pub fn partition_dir(&self, i: usize) -> PathBuf {
         crate::partition::partition_dir(&self.root_path, i)
     }
@@ -232,7 +232,7 @@ impl KmerIndex {
 
     /// Write `spectrums/{label}.json` from an already-computed kmer
     /// spectrum (`f0`/`f1`/abundance histogram). Takes plain values rather
-    /// than `crate::algorithms::partitionner::KmerSpectrum` — `KmerIndex`
+    /// than `obikindexer::algorithms::partitionner::KmerSpectrum` — `KmerIndex`
     /// is the data model, `PartitionRouter` the algorithm that depends on
     /// it (see `DevDocMD/implementation/partition_layer_cache.md`), not
     /// the other way around, and this is the only field of that type it

src/obikindex/src/layer/typed_layer.rs

@@ -46,9 +46,9 @@ const SK_EXT: &str = "skmer.zst";
 
 /// Path of a layer's raw, not-yet-dereplicated superkmer file — written by
 /// whichever algorithm routes superkmers into this layer (today:
-/// `crate::algorithms::partitionner::PartitionRouter`), read by whichever
+/// `obikindexer::algorithms::partitionner::PartitionRouter`), read by whichever
 /// algorithm dereplicates it (today:
-/// `crate::algorithms::dereplicator::Dereplicator`). Naming this once
+/// `obikindexer::algorithms::dereplicator::Dereplicator`). Naming this once
 /// here, rather than in either algorithm submodule, is what lets the two
 /// agree on the filename without depending on each other directly — see
 /// `DevDocMD/implementation/partition_layer_cache.md`.
@@ -57,9 +57,9 @@ pub fn raw_superkmers_path(layer_dir: &Path) -> PathBuf {
 }
 
 /// Path of a layer's dereplicated superkmer file — written by
-/// `crate::algorithms::dereplicator::Dereplicator`, read by whichever
+/// `obikindexer::algorithms::dereplicator::Dereplicator`, read by whichever
 /// algorithm counts kmer abundances from it (today:
-/// `crate::algorithms::partitionner::PartitionRouter::count_kmer`) and,
+/// `obikindexer::algorithms::partitionner::PartitionRouter::count_kmer`) and,
 /// later, by `obikindex::build_index_layer` to build the real layer.
 pub fn dereplicated_superkmers_path(layer_dir: &Path) -> PathBuf {
     layer_dir.join(format!("dereplicated.{SK_EXT}"))

src/obikindex/src/lib.rs

@@ -3,11 +3,11 @@
 //! section for the authoritative naming/scope discussion. Each tier is a
 //! submodule: [`layer`] (was the `obilayeredmap` crate), [`partition`]
 //! (was the `obikpartition` crate), [`index`] (this crate's original
-//! content). [`algorithms`] (was the `obikpartitionner` and `obikderep`
+//! content). Indexing-pipeline algorithms that build or transform an
-//! crates) sits alongside the model: code that builds or transforms an
+//! index's content (the former `obikpartitionner`/`obikderep` crates) live
-//! index's content rather than defining its shape.
+//! in the separate `obikindexer` crate, which depends on this one, not the
+//! other way around.
 
-pub mod algorithms;
 pub mod index;
 pub mod layer;
 pub mod partition;

src/obikindexer/Cargo.toml

@@ -0,0 +1,29 @@
+[package]
+name = "obikindexer"
+version = "0.1.0"
+edition = "2024"
+
+[dependencies]
+obikindex        = { path = "../obikindex" }
+obikseq          = { path = "../obikseq" }
+obiskio          = { path = "../obiskio" }
+obisys           = { path = "../obisys" }
+obicompactvec    = { path = "../obicompactvec" }
+obipipeline      = { path = "../obipipeline" }
+obiread          = { path = "../obiread" }
+obiskbuilder     = { path = "../obiskbuilder" }
+cacheline-ef     = "1.1"
+epserde          = "0.8"
+ptr_hash         = "1.1"
+niffler          = "3.0.0"
+memmap2          = "0.9.10"
+rayon            = "1"
+serde            = { version = "1", features = ["derive"] }
+serde_json       = "1"
+tracing          = "0.1.44"
+sysinfo          = "0.39"
+
+[dev-dependencies]
+obikseq  = { path = "../obikseq", features = ["test-utils"] }
+obikrope = { path = "../obikrope" }
+tempfile = "3"

src/obikindexer/src/algorithms/dereplicator/dereplicate.rs

@@ -14,12 +14,12 @@ use niffler::send::compression::Format;
 use niffler::Level;
 use obikseq::superkmer::SuperKmer;
 use obikseq::Sequence;
-use crate::layer::{dereplicated_superkmers_path, raw_superkmers_path};
+use obikindex::layer::{dereplicated_superkmers_path, raw_superkmers_path};
 use obiskio::{SKFileMeta, SKFileReader, SKFileWriter, SKResult};
 
 /// Scratch-file extension for this algorithm's own intermediate split
 /// buckets — never read by anything outside [`dereplicate_partition`],
-/// unlike `raw`/`dereplicated` (see `crate::layer::{raw_superkmers_path,
+/// unlike `raw`/`dereplicated` (see `obikindex::layer::{raw_superkmers_path,
 /// dereplicated_superkmers_path}`, the actual cross-module contract).
 const TEMP_EXT: &str = "skmer.zst";
 

src/obikindexer/src/algorithms/dereplicator/mod.rs

@@ -15,7 +15,7 @@ use obisys::Progress;
 use rayon::prelude::*;
 use sysinfo::System;
 
-use crate::index::KmerIndex;
+use obikindex::KmerIndex;
 
 use dereplicate::{dereplicate_partition, optimal_buckets};
 
@@ -84,7 +84,7 @@ impl<'a> Dereplicator<'a> {
             .map(|i| {
                 let dir = self.index.layer_dir(i, 0);
                 let result = if dir.exists() {
-                    let raw_path = crate::layer::raw_superkmers_path(&dir);
+                    let raw_path = obikindex::layer::raw_superkmers_path(&dir);
                     let n_buckets = optimal_buckets(&raw_path, available_per_thread);
                     dereplicate_partition(&dir, level, n_buckets)
                 } else {

src/obikindexer/src/algorithms/mod.rs

@@ -0,0 +1,9 @@
+//! Indexing-pipeline algorithms: code that operates on an
+//! [`obikindex::KmerIndex`] to build or transform its content — `obikindex`
+//! itself is the `index`/`partition`/`layer` data model, not this. Each
+//! algorithm is its own submodule: [`partitionner`] (routing raw super-kmers
+//! into partitions, then counting), [`dereplicator`] (deduplicating a
+//! partition's raw super-kmers before counting).
+
+pub mod dereplicator;
+pub mod partitionner;

src/obikindexer/src/algorithms/partitionner/mod.rs

@@ -6,7 +6,7 @@
 //!
 //! Submodules: [`router`] (`PartitionRouter`, `KmerSpectrum`, the
 //! routing/counting lifecycle API — partition/layer path naming itself
-//! lives on `crate::index::KmerIndex`, not here), [`count`] (unique-kmer
+//! lives on `obikindex::KmerIndex`, not here), [`count`] (unique-kmer
 //! enumeration, MPHF, abundance counting), `kmer_sort` (external sort
 //! support for `count`).
 

src/obikindexer/src/algorithms/partitionner/router.rs

@@ -6,9 +6,9 @@ use std::sync::atomic::{AtomicU32, AtomicU64, Ordering};
 use std::sync::Arc;
 use std::time::Instant;
 
-use crate::index::KmerIndex;
+use obikindex::KmerIndex;
 use obikseq::RoutableSuperKmer;
-use crate::layer::Layer;
+use obikindex::layer::Layer;
 use obiskio::SKResult;
 use obisys::{progress_bar, Progress};
 use rayon::prelude::*;
@@ -80,7 +80,7 @@ impl Drop for GuardedIter {
 ///
 /// Holds `&mut KmerIndex` — this is an algorithm operating on an index, not
 /// a data structure of its own; it owns no path-naming knowledge (every
-/// path comes from `index.index_dir`/`crate::layer::layer_dir`/
+/// path comes from `index.index_dir`/`obikindex::layer::layer_dir`/
 /// `Layer::create`), only the transient routing/dereplication/counting
 /// state a run needs.
 ///
@@ -291,7 +291,7 @@ impl<'a> PartitionRouter<'a> {
             .into_par_iter()
             .map(|i| {
                 let dir = self.layer0_dir(i);
-                let dedup_path = crate::layer::dereplicated_superkmers_path(&dir);
+                let dedup_path = obikindex::layer::dereplicated_superkmers_path(&dir);
                 if !dedup_path.exists() {
                     pb.inc(1);
                     return Ok(());
@@ -343,9 +343,9 @@ impl<'a> PartitionRouter<'a> {
     /// Directory of partition `i`'s layer 0 — every raw/dereplicated
     /// superkmer file and provisional `mphf1.bin`/`counts1.bin` this router
     /// produces lives here, alongside where `build_index_layer`
-    /// (`crate::index`) will later turn it into the real layer 0.
+    /// (`obikindex`) will later turn it into the real layer 0.
     fn layer0_dir(&self, i: usize) -> PathBuf {
-        crate::layer::layer_dir(&self.index.index_dir(i), 0)
+        obikindex::layer::layer_dir(&self.index.index_dir(i), 0)
     }
 
     fn check_not_closed(&self) -> SKResult<()> {
@@ -360,7 +360,7 @@ impl<'a> PartitionRouter<'a> {
         if self.writers[partition].is_none() {
             let dir = self.layer0_dir(partition);
             Layer::create(&dir).map_err(|e| io::Error::other(e.to_string()))?;
-            let file_path = crate::layer::raw_superkmers_path(&dir);
+            let file_path = obikindex::layer::raw_superkmers_path(&dir);
             let writer = SKFileWriter::create_with(file_path, Format::Zstd, self.level)?;
             self.writers[partition] = Some(writer);
         }

src/obikindexer/src/algorithms/partitionner/tests.rs

@@ -2,8 +2,8 @@ use std::collections::HashMap;
 use std::fs;
 
 use crate::algorithms::dereplicator::Dereplicator;
-use crate::{IndexConfig, KmerIndex};
+use obikindex::{IndexConfig, KmerIndex};
-use crate::layer::IndexMode;
+use obikindex::layer::IndexMode;
 use obikrope::Rope;
 use obikseq::SuperKmer;
 use obiskbuilder::build_superkmers;
@@ -69,7 +69,7 @@ fn pipeline_counts(seqs: &[&[u8]]) -> (u64, u64) {
     Dereplicator::new(&index).run(None::<fn(obisys::Progress)>).unwrap();
 
     let part_dir = index.layer_dir(0, 0);
-    let dedup_path = crate::layer::dereplicated_superkmers_path(&part_dir);
+    let dedup_path = obikindex::layer::dereplicated_superkmers_path(&part_dir);
     if !dedup_path.exists() {
         return (0, 0);
     }

src/obikindexer/src/lib.rs

@@ -0,0 +1,13 @@
+//! Indexing-pipeline algorithms: code that builds or transforms an
+//! `obikindex::KmerIndex`'s content, as opposed to `obikindex` itself,
+//! which is the `Index { Partition { Layer } }` data model. Kept as a
+//! separate crate — not a module of `obikindex` — so the dependency runs
+//! one way only (algorithms depend on the data model, never the reverse)
+//! and `obikindex` doesn't grow every algorithm's own dependencies.
+//!
+//! [`algorithms`] holds each algorithm as its own submodule: `partitionner`
+//! (routing raw super-kmers into partitions, then counting), `dereplicator`
+//! (deduplicating a partition's raw super-kmers before counting). A future
+//! `extensions` module will sit alongside it.
+
+pub mod algorithms;

src/obikmer/Cargo.toml

@@ -18,6 +18,7 @@ obikrope      = { path = "../obikrope" }
 obisys        = { path = "../obisys" }
 obiskio       = { path = "../obiskio" }
 obikindex     = { path = "../obikindex", default-features = false }
+obikindexer   = { path = "../obikindexer" }
 obikphylo     = { path = "../obikphylo" }
 obitaxonomy   = { path = "../obitaxonomy" }
 clap          = { version = "4", features = ["derive"] }

src/obikmer/src/cmd/index/mod.rs

@@ -2,8 +2,8 @@ use std::path::PathBuf;
 use std::time::Instant;
 
 use clap::Args;
-use obikindex::algorithms::dereplicator::Dereplicator;
+use obikindexer::algorithms::dereplicator::Dereplicator;
-use obikindex::algorithms::partitionner::PartitionRouter;
+use obikindexer::algorithms::partitionner::PartitionRouter;
 use obikindex::{validate_label, GenomeInfo, IndexConfig, IndexState, KmerIndex};
 use obikindex::layer::IndexMode;
 

src/obikphylo/Cargo.toml

@@ -19,5 +19,6 @@ tracing          = "0.1.44"
 
 [dev-dependencies]
 obiread     = { path = "../obiread" }
+obikindexer = { path = "../obikindexer" }
 tempfile = "3"
 tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }

src/obikphylo/src/siblings/tests.rs

@@ -6,8 +6,8 @@ use obikindex::layer::MphfLayer;
 use obisys::Reporter;
 use tempfile::tempdir;
 
-use obikindex::algorithms::dereplicator::Dereplicator;
+use obikindexer::algorithms::dereplicator::Dereplicator;
-use obikindex::algorithms::partitionner::PartitionRouter;
+use obikindexer::algorithms::partitionner::PartitionRouter;
 use obikindex::{GenomeInfo, IndexConfig, KmerIndex, MergeMode};
 
 use super::alignment::SnpAlignmentExt;