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/obikphylo/src/siblings/build.rs

@@ -7,7 +7,7 @@ use rayon::prelude::*;
 use obikpartitionner::KmerPartition;
 use obipipeline::ThrottleGuard;
 use obikseq::CanonicalKmer;
-use obilayeredmap::MphfLayer;
+use obilayeredmap::{layer_dir, MphfLayer};
 use obilayeredmap::meta::PartitionMeta;
 use obisys::progress_bar;
 
@@ -101,8 +101,7 @@ impl SiblingAnnexBuildExt for KmerIndex {
 
             let mut part_slots: u64 = 0;
             for l in 0..meta.n_layers {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
-                part_slots += build_layer_sibling_annex(self, &layer_dir, n_parts, l, &cache)?;
+                part_slots += build_layer_sibling_annex(self, &layer_dir(&index_dir, l), n_parts, l, &cache)?;
             }
             total_slots += part_slots;
             pb.inc(1);

src/obikphylo/src/siblings/cache.rs

@@ -5,7 +5,7 @@ use std::path::Path;
 use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix, PersistentSparseBitMatrix};
 use obikpartitionner::KmerPartition;
 use obikseq::CanonicalKmer;
-use obilayeredmap::{Layer, OLMResult};
+use obilayeredmap::{layer_dir, Layer, OLMResult};
 use obilayeredmap::meta::{IndexMode, PartitionMeta};
 use obisys::progress_bar;
 
@@ -182,8 +182,7 @@ impl PartitionCache {
                 let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
                 let mut mats = Vec::with_capacity(meta.n_layers);
                 for l in 0..meta.n_layers {
-                    let layer_dir = index_dir.join(format!("layer_{l}"));
-                    let Ok(mat) = Mat::open(&layer_dir, &meta.mode, with_counts) else { continue };
+                    let Ok(mat) = Mat::open(&layer_dir(&index_dir, l), &meta.mode, with_counts) else { continue };
                     mats.push(mat);
                 }
                 pb.inc(1);

src/obikphylo/src/siblings/family_scan.rs

@@ -54,6 +54,7 @@ use std::sync::atomic::{AtomicU8, Ordering};
 use rayon::prelude::*;
 
 use obikseq::CanonicalKmer;
+use obilayeredmap::layer_dir;
 use obilayeredmap::meta::PartitionMeta;
 use obipipeline::{ThrottleGuard, throttle};
 
@@ -111,15 +112,15 @@ pub(crate) fn sibling_layer_dirs(index: &KmerIndex) -> OKIResult<Vec<PathBuf>> {
         }
         let meta = PartitionMeta::load(&index_dir).map_err(olm_to_ok)?;
         for l in 0..meta.n_layers {
-            let layer_dir = index_dir.join(format!("layer_{l}"));
-            let annex_path = layer_dir.join(ANNEX_FILE_NAME);
+            let this_layer_dir = layer_dir(&index_dir, l);
+            let annex_path = this_layer_dir.join(ANNEX_FILE_NAME);
             if !annex_path.exists() {
                 return Err(OKIError::InvalidInput(format!(
                     "no sibling annex at {} — run build_sibling_annex first",
                     annex_path.display()
                 )));
             }
-            layer_dirs.push(layer_dir);
+            layer_dirs.push(this_layer_dir);
         }
     }
     Ok(layer_dirs)

src/obikphylo/src/siblings/tests.rs

@@ -3,6 +3,7 @@ use std::path::Path;
 
 use obikseq::{CanonicalKmer, Kmer, Sequence};
 use obilayeredmap::MphfLayer;
+use obilayeredmap::layer_dir;
 use obilayeredmap::meta::PartitionMeta;
 use obisys::Reporter;
 use tempfile::tempdir;
@@ -91,7 +92,7 @@ fn annex_info_for(idx: &KmerIndex, kmer: CanonicalKmer) -> FamilyMask {
     let index_dir = idx.partition().part_dir(0).join(INDEX_SUBDIR);
     let meta = PartitionMeta::load(&index_dir).unwrap();
     for l in 0..meta.n_layers {
-        let layer_dir = index_dir.join(format!("layer_{l}"));
+        let layer_dir = layer_dir(&index_dir, l);
         let mphf = MphfLayer::open(&layer_dir, &meta.mode).unwrap();
         if let Some(slot) = mphf.find(kmer) {
             let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME)).unwrap();
@@ -313,7 +314,7 @@ fn sibling_annex_no_empty_masks_after_build() {
     let index_dir = g1.partition().part_dir(0).join(INDEX_SUBDIR);
     let meta = PartitionMeta::load(&index_dir).expect("partition meta");
     for l in 0..meta.n_layers {
-        let layer_dir = index_dir.join(format!("layer_{l}"));
+        let layer_dir = layer_dir(&index_dir, l);
         let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME)).expect("annex open");
         for slot in 0..annex.len() {
             let mask = annex.get(slot).expect("slot must have an entry");