Replace manual layer path construction with obilayeredmap::layer_dir

Standardizes layer directory path resolution across obikindex, obikpartitionner, and obikphylo by replacing inline string formatting and join calls with the centralized obilayeredmap::layer_dir utility. This refactoring removes redundant path construction logic while preserving existing iteration bounds, control flow, and public APIs.

src/obikindex/examples/compare_sparse.rs

@@ -5,6 +5,7 @@
 
 use obicompactvec::{PersistentBitMatrix, PersistentSparseBitMatrix};
 use obikindex::KmerIndex;
+use obilayeredmap::layer_dir;
 
 fn main() -> anyhow::Result<()> {
     let sparse_root = std::env::args().nth(1).expect("usage: compare_sparse <sparse_root> <dense_root>");
@@ -33,8 +34,10 @@ fn main() -> anyhow::Result<()> {
         }
 
         for layer in 0..n_layers {
-            let layer_dir_sparse = part_dir_sparse.join("index").join(format!("layer_{layer}"));
-            let layer_dir_dense = part_dir_dense.join("index").join(format!("layer_{layer}"));
+            let index_dir_sparse = part_dir_sparse.join("index");
+            let index_dir_dense = part_dir_dense.join("index");
+            let layer_dir_sparse = layer_dir(&index_dir_sparse, layer);
+            let layer_dir_dense = layer_dir(&index_dir_dense, layer);
 
             if !layer_dir_sparse.exists() || !layer_dir_dense.exists() {
                 continue;

src/obikindex/src/index.rs

@@ -264,10 +264,8 @@ impl KmerIndex {
 
     /// Path to the unitigs file for partition `part`, layer `layer`.
     pub fn layer_unitigs_path(&self, part: usize, layer: usize) -> PathBuf {
-        self.partition.part_dir(part)
-            .join("index")
-            .join(format!("layer_{layer}"))
-            .join("unitigs.bin")
+        let index_dir = self.partition.part_dir(part).join("index");
+        obilayeredmap::layer_dir(&index_dir, layer).join("unitigs.bin")
     }
 
     /// Pack all partition matrices into single-file format (presence → .pbmx, counts → .pcmx).
@@ -295,7 +293,7 @@ impl KmerIndex {
                 let meta = PartitionMeta::load(&index_dir)
                     .map_err(|e| OKIError::Io(std::io::Error::new(std::io::ErrorKind::Other, e.to_string())))?;
                 for l in 0..meta.n_layers {
-                    let layer_dir = index_dir.join(format!("layer_{l}"));
+                    let layer_dir = obilayeredmap::layer_dir(&index_dir, l);
                     let presence_dir = layer_dir.join("presence");
                     let counts_dir   = layer_dir.join("counts");
                     if presence_dir.exists() {
@@ -335,7 +333,7 @@ impl KmerIndex {
                     Err(e) => return Some(OKIError::Io(std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))),
                 };
                 for l in 0..meta.n_layers {
-                    let layer_dir = index_dir.join(format!("layer_{l}"));
+                    let layer_dir = obilayeredmap::layer_dir(&index_dir, l);
                     let meta_path = layer_dir.join(LayerMeta::FILENAME);
                     if meta_path.exists() { continue; }
                     let unitigs_path = layer_dir.join("unitigs.bin");

src/obikindex/src/reindex.rs

@@ -1,6 +1,6 @@
 use std::fs;
 use std::path::Path;
-use obilayeredmap::{IndexMode, layer::Layer};
+use obilayeredmap::{layer_dir, IndexMode, layer::Layer};
 use obilayeredmap::meta::PartitionMeta;
 use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
@@ -72,8 +72,7 @@ fn reindex_partition(index_dir: &Path, target: &IndexMode, block_bits: u8) -> OK
     }
     let pm = PartitionMeta::load(index_dir).map_err(olm_to_oki)?;
     for layer_idx in 0..pm.n_layers {
-        let layer_dir = index_dir.join(format!("layer_{layer_idx}"));
-        reindex_layer(&layer_dir, target, block_bits)?;
+        reindex_layer(&layer_dir(index_dir, layer_idx), target, block_bits)?;
     }
     Ok(())
 }

src/obikindex/src/stats.rs

@@ -3,6 +3,7 @@ use std::path::Path;
 
 use obicompactvec::{LayerMeta, PersistentBitMatrix, PersistentCompactIntMatrix};
 use obicompactvec::traits::ColumnWeights;
+use obilayeredmap::layer_dir;
 use obilayeredmap::meta::PartitionMeta;
 use rayon::prelude::*;
 
@@ -98,7 +99,7 @@ impl KmerIndex {
                     .unwrap_or(0);
 
                 (0..n_layers).fold((0usize, 0u64, 0u64, 0u64), |acc, l| {
-                    let lb = layer_bytes(&index_dir.join(format!("layer_{l}")));
+                    let lb = layer_bytes(&layer_dir(&index_dir, l));
                     (acc.0 + lb.n_kmers, acc.1 + lb.mphf, acc.2 + lb.evidence, acc.3 + lb.matrix)
                 })
             })