Extract indexing stage into LayerBuilder with NUMA-aware scheduling

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.

DevDocMD/implementation/partition_layer_cache.md

@@ -53,8 +53,11 @@ detail, session ended (budget) before implementation — see "(5) design
 agreed" below; **read it before touching `KmerPartition`/`Layer`
 signatures**, the shape is fully specified. (6) done — `Counter`, a third
 algorithm, extracted from `PartitionRouter` the same way `Dereplicator`
-was in (4); (5) itself still not implemented, still first on the "order of
+was in (4). (7) done — `LayerBuilder`, the fourth and last pipeline
-remaining work" list — see "(6) done" below. Earlier mix-up, for
+algorithm; the indexing pipeline is now fully decomposed into
+`obikindexer::algorithms::{partitionner, dereplicator, counter,
+layer_builder}`. (5) itself still not implemented, still first on the
+"order of remaining work" list — see "(7) done" below. Earlier mix-up, for
 context: an earlier
 version of this doc used the name `KmerPartition` (singular) for what was
 actually the *collection* type (later renamed `KmerPartitions`, later
@@ -851,6 +854,104 @@ Still not done: (5) (`Layer`/`KmerPartition` redesign, `PartitionRouter`'s
 `&mut`→`&`), the future cache crate, `build_layers` (still a `KmerIndex`
 inherent method, not an algorithm), and `obikalgorithm` itself.
 
+## (7) done (2026-08-21): `LayerBuilder` — fourth and last pipeline algorithm
+
+Closes out the indexing pipeline: `build_layers`/`build_index_layer`
+(the last stage still living as `KmerIndex` inherent methods, flagged as
+inconsistent since (6)) extracted into `obikindexer::algorithms::
+layer_builder::LayerBuilder`, same two-phase shape as the other three.
+
+```rust
+pub struct LayerBuilder<'a> {
+    index: &'a KmerIndex,
+    n_partitions: usize,
+    min_abundance: u32,
+    max_abundance: Option<u32>,
+    keep_intermediate: bool,
+}
+
+impl<'a> LayerBuilder<'a> {
+    pub fn new(index: &'a KmerIndex) -> Self;
+    pub fn min_abundance(mut self, v: u32) -> Self;
+    pub fn max_abundance(mut self, v: Option<u32>) -> Self;
+    pub fn keep_intermediate(mut self, v: bool) -> Self;
+    pub fn run(&self, on_progress: Option<impl FnMut(Progress) + Send>) -> SKResult<usize>;  // returns total kmers built
+}
+```
+
+**Different from all three prior extractions in one respect, deliberately
+not "fixed" to match them**: the actual per-partition construction logic
+(De Bruijn graph from dereplicated superkmers + provisional counts →
+unitigs → MPHF → matrix) stayed put as `KmerIndex::build_index_layer`/
+`remove_build_artifacts` (both already `pub`) — not moved into
+`obikindexer`. Checked first: unlike `dereplicate_partition`/
+`count_partition` (which only ever had one caller), `build_index_layer`
+depends on several `obikindex`-internal helpers (`graph_pipeline::
+{write_graph_as_unitigs, materialize_layer}`, `common::olm_to_sk`) that
+are `pub(crate)` and shared with `merge`/`select`/`rebuild`'s own
+layer-construction paths — moving `build_index_layer` out would have
+meant either exporting that internal surface just for this one algorithm
+or duplicating it. Neither was needed: `build_index_layer`/
+`remove_build_artifacts` were *already* public `KmerIndex` methods, so
+`LayerBuilder`'s job is purely the orchestration around them (scheduling,
+config, progress) — the exact same "algorithm calls already-public
+`KmerIndex` primitives" shape `PartitionRouter`/`Dereplicator`/`Counter`
+already have, just at a coarser grain for this one stage. This is the
+"is the producer's API actually deficient?" check from
+[[feedback_no_spaghetti_petits_pois]] applied and answered "no" — not
+skipped.
+
+**Two more real divergences, both forced by `PartitionRunner`, not
+arbitrary:**
+- Uses `obikindex::PartitionRunner` (NUMA-aware scheduler, already
+  `pub use`d from `obikindex`) instead of plain `rayon::into_par_iter`
+  like `Dereplicator`/`Counter` — matches what `build_layers` already used
+  before extraction; this stage is more CPU/memory-intensive per partition
+  (graph construction) than scatter/dereplicate/count.
+- Callback bound is `FnMut(Progress) + Send` — a third variant, not
+  matching either prior shape. `PartitionRunner::run`'s `on_done` is
+  invoked from its own single controller thread (never concurrently, so
+  no `Sync` needed, unlike `Dereplicator`/`Counter`'s `Fn + Sync`), but
+  that controller thread is itself `std::thread::scope`-spawned, so the
+  closure still has to be `Send` to cross into it — caught immediately by
+  the compiler (`cannot be sent between threads safely`) when `Send` was
+  first omitted, not a design guess. `obikalgorithm`'s eventual shared
+  trait now has three real callback-bound data points to reconcile
+  (`FnMut` alone for `PartitionRouter::run`'s sequential loop, `FnMut +
+  Send` here, `Fn + Sync` for `Dereplicator`/`Counter`'s `rayon`
+  `par_iter`), not two.
+
+`KmerIndex::build_layers` deleted outright (`KmerIndex` stays a pure data
+structure — no compute orchestration methods, consistent with `dereplicate`/
+`count_kmer`'s removal in (4)/(6)). New `KmerIndex::mark_indexed()` added,
+symmetric to `mark_scattered`/`mark_counted`, replacing the inline
+`touch(SENTINEL_INDEXED)` that used to live inside `build_layers`.
+`Stage::start("index")`/`rep.push(...)` and the `progress_bar`/
+`"{n} total kmers indexed"` log line both moved to `cmd/index/mod.rs`,
+same pattern as (3)/(4)/(6) — `LayerBuilder` renders nothing itself, just
+reports `Progress`.
+
+All callers updated: `cmd/index/mod.rs` (Stage 3), `obikphylo`'s test
+harness (also gained a `mark_indexed()` call it was missing — harmless
+before since nothing checked `IndexState::Indexed` in that test, but now
+correct).
+
+Full workspace suite green (`cargo check --workspace --all-targets` +
+`cargo test --workspace`, exit code 0), plus the end-to-end CLI smoke test
+(`scripts/smoke_test_index.sh`, built earlier specifically so this
+verification step is a one-liner from now on) — 870 kmers indexed, query
+round-trip confirmed, same numbers as (6).
+
+**The indexing pipeline is now fully decomposed**: `obikindexer::
+algorithms::{partitionner, dereplicator, counter, layer_builder}`, each a
+`new`/(setters)/`run` algorithm operating on a `&KmerIndex` (or `&mut` for
+`PartitionRouter`, not yet fixed — see (5)), `KmerIndex` itself holding no
+pipeline-orchestration logic anymore. Still not done: (5), the future
+cache crate, `obikalgorithm` (now unblocked — three real callback-bound
+variants observed, worth revisiting whether a single trait can express
+all three or whether that's itself the answer: it can't, and the trait
+should not force it).
+
 ## The problem
 
 Reading a layer's data (MPHF + matrix) is not free: `MphfLayer::open` mmaps

src/obikindex/src/index/kmer_index.rs

@@ -5,7 +5,6 @@ use std::path::{Path, PathBuf};
 use crate::layer::meta::PartitionMeta;
 use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
-use tracing::info;
 
 use obikseq::{set_k, set_m};
 
@@ -230,6 +229,12 @@ impl KmerIndex {
         Ok(())
     }
 
+    /// Mark layer construction as complete and write `index.done`.
+    pub fn mark_indexed(&self) -> OKIResult<()> {
+        touch(&self.root_path.join(SENTINEL_INDEXED))?;
+        Ok(())
+    }
+
     /// Write `spectrums/{label}.json` from an already-computed kmer
     /// spectrum (`f0`/`f1`/abundance histogram). Takes plain values rather
     /// than `obikindexer::algorithms::partitionner::KmerSpectrum` — `KmerIndex`
@@ -260,63 +265,6 @@ impl KmerIndex {
         Ok(())
     }
 
-    /// Build the layered MPHF index for all partitions in parallel.
-    ///
-    /// Writes `index.done` upon completion.
-    pub fn build_layers(
-        &self,
-        min_ab: u32,
-        max_ab: Option<u32>,
-        keep_intermediate: bool,
-        rep: &mut Reporter,
-    ) -> OKIResult<()> {
-        let n = self.n_partitions();
-        let t = Stage::start("index");
-        let with_counts = self.meta.config.with_counts;
-        let evidence = self.meta.config.evidence.clone();
-        let block_bits = self.meta.config.block_bits;
-        let mut total_kmers: usize = 0;
-        let pb = progress_bar("index", n as u64, "partitions");
-
-        let order: Vec<usize> = (0..n).collect();
-        let runner = crate::index::numa::PartitionRunner::new();
-        runner
-            .run(
-                &order,
-                |i| {
-                    self.build_index_layer(
-                        i,
-                        min_ab,
-                        max_ab,
-                        with_counts,
-                        &evidence,
-                        block_bits,
-                    )
-                },
-                |i, n_kmers, _| {
-                    if n_kmers > 0 {
-                        total_kmers += n_kmers;
-                        pb.inc(1);
-                        pb.set_message(format!("{i}: {n_kmers} kmers"));
-                    }
-                },
-            )
-            .map_err(OKIError::Partition)?;
-
-        pb.finish_and_clear();
-        info!("done — {} total kmers indexed", total_kmers);
-
-        if !keep_intermediate {
-            for i in 0..n {
-                self.remove_build_artifacts(i);
-            }
-        }
-
-        touch(&self.root_path.join(SENTINEL_INDEXED))?;
-        rep.push(t.stop());
-        Ok(())
-    }
-
     /// Path to the unitigs file for partition `part`, layer `layer`.
     pub fn layer_unitigs_path(&self, part: usize, layer: usize) -> PathBuf {
         self.layer_dir(part, layer).join("unitigs.bin")

src/obikindexer/src/algorithms/layer_builder/mod.rs

@@ -0,0 +1,109 @@
+//! Layer construction — the last stage of the indexing pipeline: turns
+//! each partition's dereplicated superkmers + provisional counts (from
+//! [`crate::algorithms::counter`]) into the real layer 0 (`mphf.bin` +
+//! `unitigs.bin` + matrix). See
+//! `DevDocMD/implementation/partition_layer_cache.md`.
+
+use obikindex::{KmerIndex, PartitionRunner};
+use obiskio::SKResult;
+use obisys::Progress;
+
+/// Builds every partition's real layer 0 in parallel.
+///
+/// Two-phase construction, same shape as the other pipeline algorithms:
+/// `new` (no disk access), optional setters (`min_abundance`/
+/// `max_abundance`/`keep_intermediate`), then `run`. The actual
+/// per-partition construction (De Bruijn graph, unitigs, MPHF, matrix)
+/// stays a `KmerIndex` method (`build_index_layer`) — unlike
+/// `Dereplicator`/`Counter`, it depends on several `obikindex`-internal
+/// helpers (`graph_pipeline`, `common::olm_to_sk`) already shared with
+/// `merge`/`select`/`rebuild`'s own layer-construction paths, so it
+/// belongs there, not duplicated or newly exported just for this
+/// algorithm. `LayerBuilder`'s own job is the orchestration around it:
+/// scheduling, configuration, and progress reporting.
+pub struct LayerBuilder<'a> {
+    index: &'a KmerIndex,
+    n_partitions: usize,
+    min_abundance: u32,
+    max_abundance: Option<u32>,
+    keep_intermediate: bool,
+}
+
+impl<'a> LayerBuilder<'a> {
+    pub fn new(index: &'a KmerIndex) -> Self {
+        Self {
+            index,
+            n_partitions: index.n_partitions(),
+            min_abundance: 1,
+            max_abundance: None,
+            keep_intermediate: false,
+        }
+    }
+
+    /// Minimum kmer abundance (inclusive) — kmers below this are filtered
+    /// out. Default 1 (no filtering).
+    pub fn min_abundance(mut self, v: u32) -> Self {
+        self.min_abundance = v;
+        self
+    }
+
+    /// Maximum kmer abundance (inclusive) — kmers above this are filtered
+    /// out. Default `None` (no ceiling).
+    pub fn max_abundance(mut self, v: Option<u32>) -> Self {
+        self.max_abundance = v;
+        self
+    }
+
+    /// Keep each partition's build artifacts (dereplicated superkmers,
+    /// `mphf1.bin`, `counts1.bin`) after their layer is built, instead of
+    /// deleting them (default: `false`).
+    pub fn keep_intermediate(mut self, v: bool) -> Self {
+        self.keep_intermediate = v;
+        self
+    }
+
+    /// Build every partition's layer 0 in parallel via `PartitionRunner`
+    /// (NUMA-aware scheduling — this stage is more CPU/memory-intensive
+    /// per partition than scatter/dereplicate/count, unlike those it
+    /// doesn't use plain rayon). Returns the total number of kmers built
+    /// across all partitions.
+    ///
+    /// `on_progress`, when set, is called once per completed partition —
+    /// `FnMut + Send`, not `Fn + Sync`: `PartitionRunner::run` calls
+    /// `on_done` from its own single controller thread, not concurrently
+    /// from workers, so (unlike `Dereplicator`/`Counter`) there's no need
+    /// for a `Sync` bound — but that controller runs in a spawned scoped
+    /// thread, so the closure itself still has to cross a thread boundary
+    /// once, hence `Send`. `total: Some(n_partitions)` — known up front.
+    pub fn run(&self, mut on_progress: Option<impl FnMut(Progress) + Send>) -> SKResult<usize> {
+        let with_counts = self.index.with_counts();
+        let evidence = self.index.evidence_mode().clone();
+        let block_bits = self.index.block_bits();
+        let min_ab = self.min_abundance;
+        let max_ab = self.max_abundance;
+        let mut total_kmers: usize = 0;
+        let mut done: u64 = 0;
+
+        let order: Vec<usize> = (0..self.n_partitions).collect();
+        let runner = PartitionRunner::new();
+        runner.run(
+            &order,
+            |i| self.index.build_index_layer(i, min_ab, max_ab, with_counts, &evidence, block_bits),
+            |_i, n_kmers, _elapsed| {
+                total_kmers += n_kmers;
+                done += 1;
+                if let Some(cb) = on_progress.as_mut() {
+                    cb(Progress { position: done, total: Some(self.n_partitions as u64) });
+                }
+            },
+        )?;
+
+        if !self.keep_intermediate {
+            for i in 0..self.n_partitions {
+                self.index.remove_build_artifacts(i);
+            }
+        }
+
+        Ok(total_kmers)
+    }
+}

src/obikindexer/src/algorithms/mod.rs

@@ -4,8 +4,11 @@
 //! algorithm is its own submodule: [`partitionner`] (routing raw super-kmers
 //! into partitions), [`dereplicator`] (deduplicating a partition's raw
 //! super-kmers), [`counter`] (counting unique canonical kmers from a
-//! partition's dereplicated super-kmers) — the three run in that order.
+//! partition's dereplicated super-kmers), [`layer_builder`] (turning
+//! dereplicated super-kmers + counts into the real layer 0) — the four run
+//! in that order.
 
 pub mod counter;
 pub mod dereplicator;
+pub mod layer_builder;
 pub mod partitionner;

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

@@ -4,6 +4,7 @@ use std::time::Instant;
 use clap::Args;
 use obikindexer::algorithms::counter::Counter;
 use obikindexer::algorithms::dereplicator::Dereplicator;
+use obikindexer::algorithms::layer_builder::LayerBuilder;
 use obikindexer::algorithms::partitionner::PartitionRouter;
 use obikindex::{validate_label, GenomeInfo, IndexConfig, IndexState, KmerIndex};
 use obikindex::layer::IndexMode;
@@ -328,15 +329,25 @@ pub fn run(args: IndexArgs) {
 
     // ── Stage 3: build layered index ─────────────────────────────────────────
     if idx.state() < IndexState::Indexed {
-        idx.build_layers(
+        let t = Stage::start("index");
-            args.min_abundance,
+        let pb = progress_bar("index", idx.n_partitions() as u64, "partitions");
-            args.max_abundance,
+        let total_kmers = LayerBuilder::new(&idx)
-            args.keep_intermediate,
+            .min_abundance(args.min_abundance)
-            &mut rep,
+            .max_abundance(args.max_abundance)
-        ).unwrap_or_else(|e| {
+            .keep_intermediate(args.keep_intermediate)
+            .run(Some(|_: Progress| pb.inc(1)))
+            .unwrap_or_else(|e| {
                 eprintln!("error: {e}");
                 std::process::exit(1);
             });
+        pb.finish_and_clear();
+        info!("done — {total_kmers} total kmers indexed");
+        rep.push(t.stop());
+
+        idx.mark_indexed().unwrap_or_else(|e| {
+            eprintln!("error marking index done: {e}");
+            std::process::exit(1);
+        });
     } else {
         info!("index already built, skipping");
     }

src/obikphylo/src/siblings/tests.rs

@@ -8,6 +8,7 @@ use tempfile::tempdir;
 
 use obikindexer::algorithms::counter::Counter;
 use obikindexer::algorithms::dereplicator::Dereplicator;
+use obikindexer::algorithms::layer_builder::LayerBuilder;
 use obikindexer::algorithms::partitionner::PartitionRouter;
 use obikindex::{GenomeInfo, IndexConfig, KmerIndex, MergeMode};
 
@@ -70,7 +71,6 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
     let mut idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)))
         .expect("create");
 
-    let mut rep = Reporter::new();
     let stream = obiread::open_nuc_stream(fasta_path.to_str().unwrap(), K).expect("open fasta");
     let mut router = PartitionRouter::new(&mut idx);
     for page in stream {
@@ -86,7 +86,10 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
     idx.mark_scattered().expect("mark_scattered");
     idx.write_spectrum(spectrum.f0, spectrum.f1, &spectrum.counts).expect("write_spectrum");
     idx.mark_counted().expect("mark_counted");
-    idx.build_layers(1, None, false, &mut rep).expect("build_layers");
+    LayerBuilder::new(&idx)
+        .run(None::<fn(obisys::Progress)>)
+        .expect("build_layers");
+    idx.mark_indexed().expect("mark_indexed");
     idx
 }