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.

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")