centralize layer path construction and data loading

Replace manual directory formatting and inline matrix opening with the newly introduced `layer_dir` and `open_data` helpers from the `obilayeredmap` crate. This standardizes filesystem access, encapsulates layer naming conventions, and simplifies error handling without altering computational behavior or test suites.

src/obikindex/src/stats.rs

@@ -149,21 +149,21 @@ impl KmerIndex {
                     .unwrap_or(0);
 
                 for l in 0..n_layers {
-                    let layer_dir = index_dir.join(format!("layer_{l}"));
+                    let this_layer_dir = obilayeredmap::layer_dir(&index_dir, l);
-                    if !layer_dir.exists() { continue; }
+                    if !this_layer_dir.exists() { continue; }
 
-                    n_kmers += LayerMeta::load(&layer_dir).map(|m| m.n).unwrap_or(0);
+                    n_kmers += LayerMeta::load(&this_layer_dir).map(|m| m.n).unwrap_or(0);
 
                     let mat: Box<dyn ColumnWeights> =
-                        if layer_dir.join("counts").exists()
+                        if this_layer_dir.join("counts").exists()
-                            && !layer_dir.join("presence").exists()
+                            && !this_layer_dir.join("presence").exists()
                         {
-                            match PersistentCompactIntMatrix::open(&layer_dir) {
+                            match obilayeredmap::open_data::<PersistentCompactIntMatrix>(&index_dir, l) {
                                 Ok(m)  => Box::new(m),
                                 Err(_) => continue,
                             }
                         } else {
-                            match PersistentBitMatrix::open(&layer_dir) {
+                            match obilayeredmap::open_data::<PersistentBitMatrix>(&index_dir, l) {
                                 Ok(m)  => Box::new(m),
                                 Err(_) => continue,
                             }

src/obikpartitionner/src/distance.rs

@@ -1,17 +1,12 @@
 use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
-use obilayeredmap::LayeredStore;
+use obilayeredmap::{layer_dir, open_data, LayeredStore};
-use obiskio::{SKError, SKResult};
+use obiskio::SKResult;
 
+use crate::common::{load_meta, olm_to_sk};
 use crate::partition::KmerPartition;
 
 const INDEX_SUBDIR: &str = "index";
 
-fn probe_n_layers(index_dir: &std::path::Path) -> usize {
-    let mut n = 0;
-    while index_dir.join(format!("layer_{n}")).exists() { n += 1; }
-    n
-}
-
 impl KmerPartition {
     /// Open all count matrices for partition `part`, one per layer.
     /// Layers without a `counts/` directory are skipped.
@@ -20,11 +15,11 @@ impl KmerPartition {
         if !index_dir.exists() {
             return Ok(LayeredStore::new(vec![]));
         }
-        let matrices = (0..probe_n_layers(&index_dir))
+        let n_layers = load_meta(&index_dir, "distance")?.n_layers;
+        let matrices = (0..n_layers)
             .filter_map(|l| {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
+                layer_dir(&index_dir, l).join("counts").exists()
-                layer_dir.join("counts").exists()
+                    .then(|| open_data(&index_dir, l).map_err(|e| olm_to_sk(e, "distance")))
-                    .then(|| PersistentCompactIntMatrix::open(&layer_dir).map_err(SKError::Io))
             })
             .collect::<SKResult<Vec<_>>>()?;
         Ok(LayeredStore::new(matrices))
@@ -37,11 +32,11 @@ impl KmerPartition {
         if !index_dir.exists() {
             return Ok(LayeredStore::new(vec![]));
         }
-        let matrices = (0..probe_n_layers(&index_dir))
+        let n_layers = load_meta(&index_dir, "distance")?.n_layers;
+        let matrices = (0..n_layers)
             .filter_map(|l| {
-                let layer_dir = index_dir.join(format!("layer_{l}"));
+                layer_dir(&index_dir, l).join("presence").exists()
-                layer_dir.join("presence").exists()
+                    .then(|| open_data(&index_dir, l).map_err(|e| olm_to_sk(e, "distance")))
-                    .then(|| PersistentBitMatrix::open(&layer_dir).map_err(SKError::Io))
             })
             .collect::<SKResult<Vec<_>>>()?;
         Ok(LayeredStore::new(matrices))

src/obilayeredmap/src/layer.rs

@@ -1,6 +1,6 @@
 use std::collections::HashMap;
 use std::fs;
-use std::path::Path;
+use std::path::{Path, PathBuf};
 
 use obicompactvec::{
     BinaryMatrix,
@@ -27,6 +27,34 @@ pub trait LayerData: Sized {
     fn read(&self, slot: usize) -> Self::Item;
 }
 
+/// Layer directory path for layer `i` within a partition's index root — the
+/// single source of truth for the on-disk `layer_N` naming convention
+/// (mirrors what `LayeredMap::open`/`push_layer` already use internally).
+///
+/// `obilayeredmap` operates within a single partition's index root; it has
+/// no notion of "partition" at all. Turning a partition number into that
+/// root is `obikpartitionner::KmerPartition::part_dir`'s job, one layer up
+/// — callers here only ever name a layer *number*, never build the path
+/// themselves.
+pub fn layer_dir(root: &Path, i: usize) -> PathBuf {
+    root.join(format!("layer_{i}"))
+}
+
+/// Opens layer `i`'s data only, skipping the MPHF — for callers that only
+/// need matrix-level operations (distance traits, column weights, group
+/// filters, sub-matrix extraction) and never look up a kmer for this layer.
+/// `Layer<D>::open` always pays for the MPHF too (and doesn't expose `data`
+/// once open), so it's the wrong tool for these; this is the other half of
+/// the same `D::open(layer_dir)` call, without the MPHF alongside it.
+///
+/// Takes `(root, i)`, not a pre-built path: the caller names a layer
+/// *number* within a partition it already knows the root of, the same
+/// vocabulary as [`layer_dir`] and `LayeredMap` — never the `layer_N`
+/// naming convention itself, which stays private to this crate.
+pub fn open_data<D: LayerData>(root: &Path, i: usize) -> OLMResult<D> {
+    D::open(&layer_dir(root, i))
+}
+
 impl LayerData for () {
     type Item = ();
     fn open(_layer_dir: &Path) -> OLMResult<Self> { Ok(()) }

src/obilayeredmap/src/lib.rs

@@ -8,7 +8,7 @@ pub mod meta;
 pub(crate) mod mphf_layer;
 
 pub use error::{OLMError, OLMResult};
-pub use layer::{Hit, Layer, LayerData};
+pub use layer::{layer_dir, open_data, Hit, Layer, LayerData};
 pub use layered_store::LayeredStore;
 pub use map::LayeredMap;
 pub use meta::{IndexMode, PartitionMeta};

src/obilayeredmap/src/map.rs

@@ -7,7 +7,7 @@ use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileWriter, DEFAULT_BLOCK_BITS};
 
 use crate::error::OLMResult;
-use crate::layer::{Hit, Layer, LayerData};
+use crate::layer::{layer_dir, Hit, Layer, LayerData};
 use crate::meta::{IndexMode, PartitionMeta};
 
 /// Layered kmer index for a single partition.
@@ -97,10 +97,6 @@ impl LayeredMap<PersistentCompactIntMatrix> {
     }
 }
 
-fn layer_dir(root: &Path, i: usize) -> PathBuf {
-    root.join(format!("layer_{i}"))
-}
-
 #[cfg(test)]
 #[path = "tests/map.rs"]
 mod tests;