refactor: extract index construction state tracking into extension trait

Moves pipeline state bookkeeping, including sentinel file marking and spectrum persistence, into the algorithms' run and close methods. Introduces a crate-private extension trait to satisfy Rust's orphan rule while implementing construction-only operations on KmerIndex. Updates helper function visibility for cross-crate access and removes the now-empty index_layer module.

DevDocMD/implementation/partition_layer_cache.md

@@ -56,8 +56,12 @@ algorithm, extracted from `PartitionRouter` the same way `Dereplicator`
 was in (4). (7) done — `LayerBuilder`, the fourth and last pipeline
 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
+layer_builder}`. (8) design agreed, item 1 (`obikindexer::extensions::
-"order of remaining work" list — see "(7) done" below. Earlier mix-up, for
+IndexBuilder`) done in (9) — private extension trait, six construction-only
+`KmerIndex` methods moved out; item 2 (`obikalgorithm::Algorithm`) still
+not started. Note: `Layer` renamed `KmerLayer` (2026-08-21, outside this
+conversation). (5) itself still not implemented, still first on the
+"order of remaining work" list. 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
@@ -952,6 +956,198 @@ 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).
 
+## (8) design agreed, not yet implemented (2026-08-21): `obikalgorithm::Algorithm` trait + `obikindexer::extensions` — private/public extension-trait split, `KmerLayer` rename
+
+Session note: `Layer` was renamed `KmerLayer` (user, outside this
+conversation, alongside other naming homogenisation with `KmerIndex`/
+`KmerPartition`) — every reference to `Layer` in this doc from before
+2026-08-21 means today's `obikindex::layer::KmerLayer`.
+
+### Why this came up
+
+Verifying "does `cmd/index` now rest entirely on the algorithm structs"
+(it doesn't quite — see below) led to sorting `KmerIndex`'s own methods by
+a criterion the user was explicit is **semantic, not mechanical**: "les
+méthodes qui, sémantiquement, n'ont pas d'intérêt hors de la construction
+de l'index" (methods that have no semantic interest outside index
+construction) — not "methods only called from `cmd/index` today," which
+a grep could answer but would miss methods construction-adjacent code
+elsewhere (`merge`/`select`/`rebuild`/`reindex`) also depends on for the
+same reason.
+
+**Checked, not assumed** (grepped every call site before classifying):
+
+- **Construction-only, real candidates for a private extension trait**:
+  `KmerIndex::{mark_scattered, mark_counted, mark_indexed, write_spectrum,
+  build_index_layer, remove_build_artifacts, clear_output_for_create,
+  create_skeleton, finalize_indexed, state}`. The last four are called
+  from `merge.rs`/`select.rs`/`rebuild.rs`/`reindex.rs` too (as
+  precondition checks — "is my source `Indexed`?" — or shared
+  skeleton/finalize machinery), not just from the 4-stage pipeline — so
+  this extension trait's scope is "construction of any kind," not
+  narrowly "the initial build pipeline."
+- **Looked construction-only by name, checked, and kept on `KmerIndex`**:
+  `layer_unitigs_path` (unitigs are the only way to recover a built
+  index's kmer sequences — read by `rebuild_layer.rs` and others, well
+  beyond construction — see [[project_unitigs_always_kept]]),
+  `pack_matrices` (re-runnable maintenance on an already-finished index
+  via `obikmer pack`, not just a pipeline step), `upgrade_layer_meta`
+  (migration, runnable on any existing index at any time).
+
+### The general pattern (not obikindexer-specific)
+
+`KmerIndex`/`KmerPartition`/`KmerLayer` stay generic, in `obikindex` —
+every domain-specific consumer crate gets to attach its own extension
+trait(s), of two kinds:
+
+- **Private** (`pub(crate)`, invisible outside the defining crate) — for
+  plumbing only that crate's own algorithms need. `obikindexer` gets
+  exactly one of these (see below); no public counterpart makes sense for
+  it — "l'index est tellement central que le second trait n'a pas
+  vraiment d'intérêt" for construction specifically: nothing external
+  should ever want to call `mark_scattered` or `build_index_layer`.
+- **Public** — for a genuinely reusable domain extension. The user's own
+  example, found while discussing this, not hypothetical: `obikindex/src/
+  index/distance.rs` (phylogenetic distance metrics) is currently an
+  `impl KmerIndex` block **inside `obikindex` itself** — under this
+  principle it should be a public extension trait owned by `obikphylo`
+  instead (distance metrics are a phylo concept, `obikindex` has no more
+  business defining them than `obikindex::layer` has defining
+  "family"/"minorant", the reasoning `SiblingLayerExt` already followed
+  for `KmerLayer` — see `obikphylo/src/siblings/iter.rs`). **Explicitly
+  deferred** — noted here so it isn't lost, not part of this round.
+- The future cache-manager crate (still blocked on (5), see above) will
+  add its own **public** extension trait mirroring part of `KmerIndex`'s/
+  `KmerPartition`'s own read API in cached form (e.g. a cached
+  `.partition(i)` that doesn't re-touch disk) — same pattern, third data
+  point once built.
+
+### Concretely, next to implement (two items, in order)
+
+1. **`obikindexer::extensions`** — a private (`pub(crate)`) extension
+   trait, most likely named something like `IndexBuildExt` (final name
+   not yet chosen), implemented for `KmerIndex`, carrying the ten methods
+   listed above, moved out of `obikindex::index::{kmer_index,
+   index_layer}`. Every algorithm in `obikindexer::algorithms::*` that
+   currently calls `idx.mark_scattered()`/etc. keeps the same call syntax
+   (extension trait methods are called the same way as inherent ones,
+   just need the trait in scope) — `cmd/index/mod.rs` itself would need
+   `use obikindexer::extensions::IndexBuildExt;` (or the module re-exports
+   it) to keep compiling, since it's the one place outside `obikindexer`'s
+   own algorithms that currently calls `mark_scattered`/`write_spectrum`/
+   `mark_counted`/`mark_indexed` directly. **Not yet decided**: exact
+   trait name, whether it's one trait or split further (e.g. sentinel
+   marking vs. skeleton/finalize machinery), and whether `merge`/`select`/
+   `rebuild`/`reindex` (not yet extracted into algorithms themselves) move
+   onto it now too or keep calling the soon-to-be-inherent-no-longer
+   methods some other way in the meantime — **ask before implementing**,
+   this changes the blast radius significantly (4 more `obikindex`
+   internal files depend on `clear_output_for_create`/`create_skeleton`/
+   `finalize_indexed`/`state`).
+2. **`obikalgorithm::Algorithm` trait** — new crate, the shared trait
+   `obikpartitionner`→`obikindexer` merge (session start of 2026-08-21)
+   and (6)/(7) were deliberately building toward, now with four real
+   `new`/(setters)/`run` examples and three distinct callback-bound
+   shapes to reconcile (plain `FnMut` for `PartitionRouter`, `FnMut +
+   Send` for `LayerBuilder`, `Fn + Sync` for `Dereplicator`/`Counter` —
+   see (7)). Exact shape not yet drafted in this doc — do that as its own
+   design pass before coding, same discipline as everything above.
+
+Both items: **design only, nothing implemented yet** — this section is
+the record to resume from, not a plan already executed.
+
+## (9) done (2026-08-21): `obikindexer::extensions::IndexBuilder` — item 1 above, implemented
+
+Scoped down from (8)'s six-method list to the concrete set that's
+genuinely movable without further ripple — checked, not assumed, before
+writing anything:
+
+```rust
+pub(crate) trait IndexBuilder {
+    fn mark_scattered(&mut self) -> OKIResult<()>;
+    fn mark_counted(&self) -> OKIResult<()>;
+    fn mark_indexed(&self) -> OKIResult<()>;
+    fn write_spectrum(&self, f0: u64, f1: u64, counts: &BTreeMap<u32, u64>) -> OKIResult<()>;
+    fn build_index_layer(&self, i: usize, min_ab: u32, max_ab: Option<u32>, with_counts: bool, mode: &IndexMode, block_bits: u8) -> Result<usize, SKError>;
+    fn remove_build_artifacts(&self, i: usize);
+}
+impl IndexBuilder for KmerIndex { ... }
+```
+
+All six moved bodily out of `obikindex::index::{kmer_index, index_layer}`
+into `obikindexer::extensions` (new module, `pub(crate)`) — `index_layer.rs`
+is now empty and deleted outright.
+`clear_output_for_create`/`create_skeleton`/`finalize_indexed`/`state`
+stayed inherent on `KmerIndex`, per (8)'s reasoning: `merge`/`select`/
+`rebuild`/`reindex` — living *inside* `obikindex` itself — call them too,
+and `obikindex` can never depend on `obikindexer` to reach a trait defined
+there. Moving those four is real future work (extract
+merge/select/rebuild/reindex into algorithms first), not part of this
+step.
+
+**One new, small, deliberate API widening in `obikindex`**: `build_index_layer`
+depends on three helpers that were `pub(crate)` to `obikindex`
+(`graph_pipeline::{write_graph_as_unitigs, materialize_layer}`,
+`common::olm_to_sk`) — widened to `pub` (re-exported from `obikindex`'s
+crate root) so `obikindexer` could reach them. This is exactly the
+"enrich shared/lower-level APIs instead of ad hoc local code" call the
+project's own rules ask for, made explicitly rather than routed around:
+three functions, already generically written (no rewrite needed), now
+serve a second caller instead of being duplicated.
+
+**Why the trait had to be defined in `obikindexer`, not `obikindex`**:
+Rust's orphan rule — implementing a trait for a foreign type requires
+either the trait or the type to be local to the current crate. `KmerIndex`
+is foreign to `obikindexer`, so the trait must be the local half; if it
+were defined in `obikindex` instead, `pub(crate)` there would make it
+invisible to `obikindexer` too (crate-private means private to *that*
+crate, not "private except to one named dependent") — the opposite of
+what was wanted.
+
+**A real design decision made while wiring callers up, not a mechanical
+rename**: `IndexBuilder` being genuinely `pub(crate)` to `obikindexer`
+means `obikmer::cmd::index` (a different crate) can no longer call
+`mark_scattered`/`mark_counted`/`mark_indexed`/`write_spectrum` directly —
+it never could have, once privacy was real rather than aspirational. Each
+algorithm now marks its own completion as part of `run()`/`close()`
+instead of leaving it to the caller:
+- `PartitionRouter::close()` (not `run()`) calls `mark_scattered()` —
+  `close()`, not `run()`, is the actual shared completion point between
+  the file-driven `run()` path and the manual `write`/`write_batch`+
+  `close()` path low-level callers (tests) use; putting it in `run()`
+  alone would have silently skipped marking for every caller that never
+  calls `run()`. `run()` already calls `self.close()` at its own end, so
+  this covers both paths through one line, not two.
+- `Counter::run` calls `write_spectrum` then `mark_counted` before
+  returning.
+- `LayerBuilder::run` calls `mark_indexed` before returning.
+
+`cmd/index/mod.rs` lost all four direct calls (`mark_scattered`/
+`write_spectrum`/`mark_counted`/`mark_indexed`) — each stage's `if
+idx.state() < IndexState::X { ... }` block is now purely "run the
+algorithm," no separate bookkeeping call after it. Confirms, precisely
+this time (checked by re-reading the whole file, not assumed): `cmd/index`
+now rests on the four algorithms for every read/write of pipeline state
+except `KmerIndex::{exists, create, state, n_partitions}`, which are
+genuinely index-identity concerns, not construction bookkeeping — the
+original question this whole design pass started from.
+
+Same fix applied to `obikphylo`'s test harness (its four explicit
+`mark_*`/`write_spectrum` calls removed, relying on the algorithms now
+doing it themselves) — `obikindexer::algorithms::partitionner`'s own
+`pipeline_counts` test needed no change (never called `mark_*` directly).
+
+Full workspace suite green (`cargo check --workspace --all-targets` +
+`cargo test --workspace`, exit code 0), plus the CLI smoke test — 870
+kmers, same as (6)/(7).
+
+Still not done: item 2 from (8) (`obikalgorithm::Algorithm`), (5), the
+future cache crate, the `distance.rs` → `obikphylo` relocation (noted in
+(8), explicitly deferred), and extracting
+`merge`/`select`/`rebuild`/`reindex` into algorithms (which would unblock
+moving `clear_output_for_create`/`create_skeleton`/`finalize_indexed`/
+`state` the same way).
+
 ## The problem
 
 Reading a layer's data (MPHF + matrix) is not free: `MphfLayer::open` mmaps

src/Cargo.lock

@@ -1563,6 +1563,7 @@ dependencies = [
  "memmap2",
  "niffler",
  "obicompactvec",
+ "obidebruinj",
  "obikindex",
  "obikrope",
  "obikseq",

src/obikindex/src/index/common.rs

@@ -7,7 +7,7 @@ use obiskio::{SKError, SKResult};
 
 // ── olm_to_sk ────────────────────────────────────────────────────────────────
 
-pub(crate) fn olm_to_sk(e: OLMError, context: &'static str) -> SKError {
+pub fn olm_to_sk(e: OLMError, context: &'static str) -> SKError {
     match e {
         OLMError::Io(e) => SKError::Io(e),
         other => SKError::InvalidData {

src/obikindex/src/index/graph_pipeline.rs

@@ -121,7 +121,7 @@ where
 /// Phase 2 (write unitigs only): compute degrees, write unitigs to `layer_dir`, drop graph.
 ///
 /// Returns n_kmers. Does NOT build the MPHF — caller does it.
-pub(crate) fn write_graph_as_unitigs(g: GraphDeBruijn, layer_dir: &Path) -> SKResult<usize> {
+pub fn write_graph_as_unitigs(g: GraphDeBruijn, layer_dir: &Path) -> SKResult<usize> {
     let n_kmers = g.len();
     g.compute_degrees_and_mark_starts();
     std::fs::create_dir_all(layer_dir)?;
@@ -137,7 +137,7 @@ pub(crate) fn write_graph_as_unitigs(g: GraphDeBruijn, layer_dir: &Path) -> SKRe
 /// Phase 2 (full): write_graph_as_unitigs + `TypedLayer::<()>::build`.
 ///
 /// Returns n_kmers.
-pub(crate) fn materialize_layer(
+pub fn materialize_layer(
     g: GraphDeBruijn,
     layer_dir: &Path,
     block_bits: u8,

src/obikindex/src/index/index_layer.rs

@@ -1,132 +0,0 @@
-use std::fs;
-use std::io;
-
-use cacheline_ef::{CachelineEf, CachelineEfVec};
-use epserde::prelude::*;
-use obicompactvec::{PersistentCompactIntMatrix, PersistentCompactIntVec};
-use obidebruinj::GraphDeBruijn;
-use crate::layer::meta::PartitionMeta;
-use crate::layer::{IndexMode, TypedLayer};
-use obiskio::{SKError, SKFileMeta, SKFileReader};
-use ptr_hash::{PtrHash, bucket_fn::CubicEps, hash::Xx64};
-
-use crate::index::common::olm_to_sk;
-use crate::index::graph_pipeline::{materialize_layer, write_graph_as_unitigs};
-use crate::index::kmer_index::KmerIndex;
-
-type Mphf = PtrHash<u64, CubicEps, CachelineEfVec<Vec<CachelineEf>>, Xx64, Vec<u8>>;
-
-fn remove_if_exists(path: &std::path::Path) {
-    if let Err(e) = fs::remove_file(path) {
-        if e.kind() != io::ErrorKind::NotFound {
-            eprintln!("warning: could not remove {}: {e}", path.display());
-        }
-    }
-}
-
-impl KmerIndex {
-    /// Build the layered MPHF index for partition `i`.
-    ///
-    /// Returns the number of canonical k-mers indexed, or 0 if the partition
-    /// has no data or its layer was already built (resume-safe).
-    ///
-    /// Abundance filtering is applied when `min_ab > 1` or `max_ab.is_some()`,
-    /// using `mphf1.bin` + `counts1.bin` if they exist.
-    /// Count payload is stored iff `with_counts` is true.
-    pub fn build_index_layer(
-        &self,
-        i: usize,
-        min_ab: u32,
-        max_ab: Option<u32>,
-        with_counts: bool,
-        mode: &IndexMode,
-        block_bits: u8,
-    ) -> Result<usize, SKError> {
-        let layer0_dir = self.layer_dir(i, 0);
-        let dedup_path = crate::layer::dereplicated_superkmers_path(&layer0_dir);
-        if !dedup_path.exists() {
-            return Ok(0);
-        }
-
-        if layer0_dir.join("mphf.bin").exists() {
-            return Ok(0);
-        }
-
-        let filter_active = min_ab > 1 || max_ab.is_some();
-        let need_counts = filter_active || with_counts;
-
-        let mphf1_opt: Option<Mphf> = if need_counts {
-            let p = layer0_dir.join("mphf1.bin");
-            p.exists().then(|| Mphf::load_full(&p).ok()).flatten()
-        } else {
-            None
-        };
-
-        let counts1_opt: Option<PersistentCompactIntVec> = if need_counts {
-            let p = layer0_dir.join("counts1.bin");
-            p.exists()
-                .then(|| PersistentCompactIntVec::open(&p).ok())
-                .flatten()
-        } else {
-            None
-        };
-
-        let mut g = GraphDeBruijn::new();
-        let mut reader = SKFileReader::open(&dedup_path)?;
-        for sk in reader.iter() {
-            for kmer in sk.iter_canonical_kmers() {
-                let accept = if filter_active {
-                    match (&mphf1_opt, &counts1_opt) {
-                        (Some(mphf), Some(counts)) => {
-                            let ab = counts.get(mphf.index(&kmer.raw()));
-                            ab >= min_ab && max_ab.map_or(true, |max| ab <= max)
-                        }
-                        _ => true,
-                    }
-                } else {
-                    true
-                };
-                if accept {
-                    g.push(kmer);
-                }
-            }
-        }
-
-        let n_kmers =
-            if with_counts {
-                let n = write_graph_as_unitigs(g, &layer0_dir)?;
-                TypedLayer::<PersistentCompactIntMatrix>::build(&layer0_dir, block_bits, mode, |kmer| {
-                    match (&mphf1_opt, &counts1_opt) {
-                        (Some(mphf), Some(counts)) => counts.get(mphf.index(&kmer.raw())),
-                        _ => 1,
-                    }
-                })
-                .map_err(|e| olm_to_sk(e, "layer build"))?;
-                n
-            } else {
-                materialize_layer(g, &layer0_dir, block_bits, mode)?
-            };
-
-        let index_dir = layer0_dir.parent().expect("layer_dir has a parent");
-        PartitionMeta {
-            n_layers: 1,
-            mode: mode.clone(),
-        }
-        .save(index_dir)
-        .map_err(|e| olm_to_sk(e, "layer build"))?;
-
-        Ok(n_kmers)
-    }
-
-    /// Remove intermediate build artifacts for partition `i`.
-    ///
-    /// Deletes `dereplicated.skmer.zst` (+ sidecar), `mphf1.bin`, `counts1.bin`.
-    pub fn remove_build_artifacts(&self, i: usize) {
-        let layer0_dir = self.layer_dir(i, 0);
-        let dedup = crate::layer::dereplicated_superkmers_path(&layer0_dir);
-        remove_if_exists(&SKFileMeta::sidecar_path(&dedup));
-        remove_if_exists(&dedup);
-        remove_if_exists(&layer0_dir.join("mphf1.bin"));
-        remove_if_exists(&layer0_dir.join("counts1.bin"));
-    }
-}

src/obikindex/src/index/kmer_index.rs

@@ -1,4 +1,3 @@
-use std::collections::BTreeMap;
 use std::fs;
 use std::path::{Path, PathBuf};
 
@@ -11,7 +10,7 @@ use obikseq::{set_k, set_m};
 use crate::index::common::load_meta;
 use crate::index::error::{OKIError, OKIResult};
 use crate::index::meta::{GenomeInfo, IndexConfig, IndexMeta};
-use crate::index::state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
+use crate::index::state::{IndexState, SENTINEL_INDEXED};
 
 pub struct KmerIndex {
     pub(crate) root_path: PathBuf,
@@ -209,62 +208,6 @@ impl KmerIndex {
         Ok(self.n_layers(0)?)
     }
 
-    /// Mark scatter as complete and write `scatter.done`.
-    ///
-    /// If no genome label was set at creation time, one is derived from
-    /// the index root directory name (stripped of all extensions).
-    pub fn mark_scattered(&mut self) -> OKIResult<()> {
-        if self.meta.genomes.is_empty() {
-            let label = label_from_path(&self.root_path);
-            self.meta.genomes.push(GenomeInfo::new(label));
-            self.meta.write(&self.root_path)?;
-        }
-        touch(&self.root_path.join(SENTINEL_SCATTERED))?;
-        Ok(())
-    }
-
-    /// Mark dereplicate+count as complete and write `count.done`.
-    pub fn mark_counted(&self) -> OKIResult<()> {
-        touch(&self.root_path.join(SENTINEL_COUNTED))?;
-        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`
-    /// is the data model, `PartitionRouter` the algorithm that depends on
-    /// it (see `DevDocMD/implementation/partition_layer_cache.md`), not
-    /// the other way around, and this is the only field of that type it
-    /// actually uses.
-    pub fn write_spectrum(&self, f0: u64, f1: u64, counts: &BTreeMap<u32, u64>) -> OKIResult<()> {
-        let label = self
-            .meta
-            .genomes
-            .first()
-            .map(|g| g.label.as_str())
-            .unwrap_or("unknown");
-        let spectrums_dir = self.root_path.join("spectrums");
-        fs::create_dir_all(&spectrums_dir)?;
-        let path = spectrums_dir.join(format!("{label}.json"));
-        let spectrum_map: BTreeMap<String, u64> = counts
-            .iter()
-            .map(|(&c, &f)| (format!("{c:010}"), f))
-            .collect();
-        let f = fs::File::create(&path)?;
-        serde_json::to_writer_pretty(
-            f,
-            &serde_json::json!({ "f0": f0, "f1": f1, "spectrum": spectrum_map }),
-        )
-        .map_err(OKIError::Json)?;
-        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")
@@ -370,23 +313,4 @@ impl KmerIndex {
     }
 }
 
-fn label_from_path(path: &Path) -> String {
-    let name = path
-        .file_name()
-        .unwrap_or(path.as_os_str())
-        .to_string_lossy()
-        .into_owned();
-    let mut s = name;
-    while let Some(pos) = s.rfind('.') {
-        s.truncate(pos);
-    }
-    if s.is_empty() {
-        "unknown".to_string()
-    } else {
-        s
-    }
-}
 
-fn touch(path: &Path) -> Result<(), std::io::Error> {
-    fs::File::create(path).map(|_| ())
-}

src/obikindex/src/index/mod.rs

@@ -9,7 +9,6 @@ mod dump_layer;
 pub mod filter;
 mod graph_pipeline;
 mod kmer_index;
-mod index_layer;
 mod matrix_store;
 mod merge;
 mod merge_layer;
@@ -23,6 +22,8 @@ mod select_layer;
 mod stats;
 
 pub use error::{OKIError, OKIResult};
+pub use common::olm_to_sk;
+pub use graph_pipeline::{materialize_layer, write_graph_as_unitigs};
 pub use distance::{DistanceMetric, DistanceOutput};
 pub use filter::{GroupQuorumFilter, KmerFilter, passes_all};
 pub use kmer_index::KmerIndex;

src/obikindex/src/lib.rs

@@ -17,6 +17,6 @@ pub use index::{
     GroupQuorumFilter, IndexBitsPerKmer, IndexConfig, IndexMeta, IndexState, KmerDesc, KmerFilter,
     KmerIndex, MergeMode, MetaPred, OKIError, OKIResult, OutputCol, PartitionRunner, QueryHit,
     QueryStats, META_FILENAME, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED,
-    passes_all,
+    materialize_layer, olm_to_sk, write_graph_as_unitigs, passes_all,
 };
 pub use index::{filter, meta};

src/obikindexer/Cargo.toml

@@ -6,6 +6,7 @@ edition = "2024"
 [dependencies]
 obikindex        = { path = "../obikindex" }
 obikseq          = { path = "../obikseq" }
+obidebruinj      = { path = "../obidebruinj" }
 obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }

src/obikindexer/src/algorithms/counter/mod.rs

@@ -22,6 +22,8 @@ use sysinfo::System;
 use count::count_partition;
 use kmer_sort::chunk_size_from_ram;
 
+use crate::extensions::PrivateBuilder;
+
 pub struct KmerSpectrum {
     pub f0: u64,
     pub f1: u64,
@@ -67,7 +69,9 @@ impl<'a> Counter<'a> {
     /// `FnMut`, same reason as `Dereplicator::run`: the counting pass itself
     /// is a parallel `par_iter`, so the callback must tolerate concurrent
     /// calls. `total: Some(n_partitions)` — known up front. This algorithm
-    /// never renders anything itself.
+    /// never renders anything itself. Writes `spectrums/{label}.json` and
+    /// marks the index as counted (`count.done`) once every partition
+    /// succeeds.
     pub fn run(&self, on_progress: Option<impl Fn(Progress) + Sync>) -> SKResult<KmerSpectrum> {
         let sys = System::new_all();
         // available_memory() can return 0 on macOS when the compressor page count exceeds
@@ -92,7 +96,10 @@ impl<'a> Counter<'a> {
                 };
                 if let Some(cb) = &on_progress {
                     let pos = done.fetch_add(1, Ordering::Relaxed) + 1;
-                    cb(Progress { position: pos, total: Some(self.n_partitions as u64) });
+                    cb(Progress {
+                        position: pos,
+                        total: Some(self.n_partitions as u64),
+                    });
                 }
                 result
             })
@@ -128,6 +135,13 @@ impl<'a> Counter<'a> {
             }
         }
 
+        self.index
+            .write_spectrum(f0, f1, &counts)
+            .map_err(|e| io::Error::other(e.to_string()))?;
+        self.index
+            .mark_counted()
+            .map_err(|e| io::Error::other(e.to_string()))?;
+
         Ok(KmerSpectrum { f0, f1, counts })
     }
 }

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

@@ -8,6 +8,8 @@ use obikindex::{KmerIndex, PartitionRunner};
 use obiskio::SKResult;
 use obisys::Progress;
 
+use crate::extensions::PrivateBuilder;
+
 /// Builds every partition's real layer 0 in parallel.
 ///
 /// Two-phase construction, same shape as the other pipeline algorithms:
@@ -65,8 +67,9 @@ impl<'a> LayerBuilder<'a> {
     /// 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
+    /// doesn't use plain rayon). Marks the index as fully built
-    /// across all partitions.
+    /// (`index.done`) once every partition succeeds. 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
@@ -88,12 +91,18 @@ impl<'a> LayerBuilder<'a> {
         let runner = PartitionRunner::new();
         runner.run(
             &order,
-            |i| self.index.build_index_layer(i, min_ab, max_ab, with_counts, &evidence, block_bits),
+            |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) });
+                    cb(Progress {
+                        position: done,
+                        total: Some(self.n_partitions as u64),
+                    });
                 }
             },
         )?;
@@ -104,6 +113,10 @@ impl<'a> LayerBuilder<'a> {
             }
         }
 
+        self.index
+            .mark_indexed()
+            .map_err(|e| std::io::Error::other(e.to_string()))?;
+
         Ok(total_kmers)
     }
 }

src/obikindexer/src/algorithms/partitionner/router.rs

@@ -18,6 +18,8 @@ use obiskio::SKFileWriter;
 use obipipeline::{ThrottleGuard, Throttled, throttle};
 use obiread::NucPage;
 
+use crate::extensions::PrivateBuilder;
+
 // ── Pipeline plumbing, private to `run` ─────────────────────────────────────
 
 /// Carrier enum for `obipipeline::make_pipe!`'s two-stage transform — local
@@ -160,6 +162,12 @@ impl<'a> PartitionRouter<'a> {
         Ok(())
     }
 
+    /// Closes every open writer and marks scatter as complete
+    /// (`scatter.done`) — the single completion point shared by `run`
+    /// (the file-driven pipeline) and manual `write`/`write_batch` callers
+    /// (e.g. tests feeding in-memory superkmers directly): whichever path
+    /// was used, `close` is what both agree means "scatter is done".
+    /// Idempotent — a second call is a no-op, sentinel included.
     pub fn close(&mut self) -> SKResult<()> {
         if self.closed {
             return Ok(());
@@ -168,6 +176,9 @@ impl<'a> PartitionRouter<'a> {
         for writer in self.writers.iter_mut().flatten() {
             writer.close()?;
         }
+        self.index
+            .mark_scattered()
+            .map_err(|e| std::io::Error::other(e.to_string()))?;
         Ok(())
     }
 

src/obikindexer/src/extensions/mod.rs

@@ -0,0 +1,261 @@
+//! Construction-only `KmerIndex` operations — semantically meaningless
+//! once an index is built and being used for reading (query, dump, phylo,
+//! or as a `merge`/`select`/`rebuild` *source*): sentinel marking, the
+//! per-partition layer-build primitive, and cleanup of build-time scratch
+//! files. Private to this crate — no consumer outside the
+//! indexing-pipeline algorithms in `obikindexer::algorithms` should ever
+//! need them. See `DevDocMD/implementation/partition_layer_cache.md`,
+//! "(8)".
+//!
+//! Defined here, not in `obikindex`, so it can be genuinely `pub(crate)`
+//! while extending a foreign type (`KmerIndex`) — Rust's orphan rule
+//! requires the trait itself to be local to the crate that implements it
+//! for a foreign type; `obikindex` has no way to make a trait "private
+//! except to `obikindexer`" from its own side.
+//!
+//! Scoped to the six methods exclusive to this crate's own pipeline
+//! (`partitionner`/`dereplicator`/`counter`/`layer_builder`).
+//! `clear_output_for_create`/`create_skeleton`/`finalize_indexed`/`state`
+//! stay inherent on `KmerIndex`, deliberately not moved here: they're also
+//! called from `obikindex`'s own `merge`/`select`/`rebuild`/`reindex`
+//! modules, which — living inside `obikindex` itself — could never reach a
+//! trait defined in `obikindexer` (the dependency only runs
+//! `obikindexer → obikindex`, never the other way). Moving those four
+//! would require extracting `merge`/`select`/`rebuild`/`reindex` into
+//! algorithms first — separate, larger future work, not this one.
+
+use std::collections::BTreeMap;
+use std::fs;
+use std::io;
+use std::path::Path;
+
+use cacheline_ef::{CachelineEf, CachelineEfVec};
+use epserde::prelude::*;
+use obicompactvec::{PersistentCompactIntMatrix, PersistentCompactIntVec};
+use obidebruinj::GraphDeBruijn;
+use obikindex::layer::IndexMode;
+use obikindex::layer::{TypedLayer, meta::PartitionMeta};
+use obikindex::{GenomeInfo, KmerIndex, OKIError, OKIResult};
+use obikindex::{SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
+use obikindex::{materialize_layer, olm_to_sk, write_graph_as_unitigs};
+use obiskio::{SKError, SKFileMeta, SKFileReader};
+use ptr_hash::{PtrHash, bucket_fn::CubicEps, hash::Xx64};
+
+type Mphf = PtrHash<u64, CubicEps, CachelineEfVec<Vec<CachelineEf>>, Xx64, Vec<u8>>;
+
+pub(crate) trait PrivateBuilder {
+    /// Mark scatter as complete and write `scatter.done`.
+    ///
+    /// If no genome label was set at creation time, one is derived from
+    /// the index root directory name (stripped of all extensions).
+    fn mark_scattered(&mut self) -> OKIResult<()>;
+
+    /// Mark dereplicate+count as complete and write `count.done`.
+    fn mark_counted(&self) -> OKIResult<()>;
+
+    /// Mark layer construction as complete and write `index.done`.
+    fn mark_indexed(&self) -> OKIResult<()>;
+
+    /// Write `spectrums/{label}.json` from an already-computed kmer
+    /// spectrum (`f0`/`f1`/abundance histogram). Takes plain values rather
+    /// than `algorithms::counter::KmerSpectrum` — `KmerIndex` is the data
+    /// model, `Counter` the algorithm that depends on it, not the other
+    /// way around, and this is the only field of that type it actually
+    /// uses.
+    fn write_spectrum(&self, f0: u64, f1: u64, counts: &BTreeMap<u32, u64>) -> OKIResult<()>;
+
+    /// Build the layered MPHF index for partition `i`.
+    ///
+    /// Returns the number of canonical k-mers indexed, or 0 if the
+    /// partition has no data or its layer was already built
+    /// (resume-safe).
+    ///
+    /// Abundance filtering is applied when `min_ab > 1` or
+    /// `max_ab.is_some()`, using `mphf1.bin` + `counts1.bin` if they
+    /// exist. Count payload is stored iff `with_counts` is true.
+    fn build_index_layer(
+        &self,
+        i: usize,
+        min_ab: u32,
+        max_ab: Option<u32>,
+        with_counts: bool,
+        mode: &IndexMode,
+        block_bits: u8,
+    ) -> Result<usize, SKError>;
+
+    /// Remove intermediate build artifacts for partition `i`: dereplicated
+    /// superkmers (+ sidecar), `mphf1.bin`, `counts1.bin`.
+    fn remove_build_artifacts(&self, i: usize);
+}
+
+impl PrivateBuilder for KmerIndex {
+    fn mark_scattered(&mut self) -> OKIResult<()> {
+        if self.meta().genomes.is_empty() {
+            let label = label_from_path(self.root_path());
+            self.meta_mut().genomes.push(GenomeInfo::new(label));
+            self.meta().write(self.root_path())?;
+        }
+        touch(&self.root_path().join(SENTINEL_SCATTERED))?;
+        Ok(())
+    }
+
+    fn mark_counted(&self) -> OKIResult<()> {
+        touch(&self.root_path().join(SENTINEL_COUNTED))?;
+        Ok(())
+    }
+
+    fn mark_indexed(&self) -> OKIResult<()> {
+        touch(&self.root_path().join(SENTINEL_INDEXED))?;
+        Ok(())
+    }
+
+    fn write_spectrum(&self, f0: u64, f1: u64, counts: &BTreeMap<u32, u64>) -> OKIResult<()> {
+        let label = self
+            .meta()
+            .genomes
+            .first()
+            .map(|g| g.label.as_str())
+            .unwrap_or("unknown");
+        let spectrums_dir = self.root_path().join("spectrums");
+        fs::create_dir_all(&spectrums_dir)?;
+        let path = spectrums_dir.join(format!("{label}.json"));
+        let spectrum_map: BTreeMap<String, u64> = counts
+            .iter()
+            .map(|(&c, &f)| (format!("{c:010}"), f))
+            .collect();
+        let f = fs::File::create(&path)?;
+        serde_json::to_writer_pretty(
+            f,
+            &serde_json::json!({ "f0": f0, "f1": f1, "spectrum": spectrum_map }),
+        )
+        .map_err(OKIError::Json)?;
+        Ok(())
+    }
+
+    fn build_index_layer(
+        &self,
+        i: usize,
+        min_ab: u32,
+        max_ab: Option<u32>,
+        with_counts: bool,
+        mode: &IndexMode,
+        block_bits: u8,
+    ) -> Result<usize, SKError> {
+        let layer0_dir = self.layer_dir(i, 0);
+        let dedup_path = obikindex::layer::dereplicated_superkmers_path(&layer0_dir);
+        if !dedup_path.exists() {
+            return Ok(0);
+        }
+
+        if layer0_dir.join("mphf.bin").exists() {
+            return Ok(0);
+        }
+
+        let filter_active = min_ab > 1 || max_ab.is_some();
+        let need_counts = filter_active || with_counts;
+
+        let mphf1_opt: Option<Mphf> = if need_counts {
+            let p = layer0_dir.join("mphf1.bin");
+            p.exists().then(|| Mphf::load_full(&p).ok()).flatten()
+        } else {
+            None
+        };
+
+        let counts1_opt: Option<PersistentCompactIntVec> = if need_counts {
+            let p = layer0_dir.join("counts1.bin");
+            p.exists()
+                .then(|| PersistentCompactIntVec::open(&p).ok())
+                .flatten()
+        } else {
+            None
+        };
+
+        let mut g = GraphDeBruijn::new();
+        let mut reader = SKFileReader::open(&dedup_path)?;
+        for sk in reader.iter() {
+            for kmer in sk.iter_canonical_kmers() {
+                let accept = if filter_active {
+                    match (&mphf1_opt, &counts1_opt) {
+                        (Some(mphf), Some(counts)) => {
+                            let ab = counts.get(mphf.index(&kmer.raw()));
+                            ab >= min_ab && max_ab.map_or(true, |max| ab <= max)
+                        }
+                        _ => true,
+                    }
+                } else {
+                    true
+                };
+                if accept {
+                    g.push(kmer);
+                }
+            }
+        }
+
+        let n_kmers = if with_counts {
+            let n = write_graph_as_unitigs(g, &layer0_dir)?;
+            TypedLayer::<PersistentCompactIntMatrix>::build(
+                &layer0_dir,
+                block_bits,
+                mode,
+                |kmer| match (&mphf1_opt, &counts1_opt) {
+                    (Some(mphf), Some(counts)) => counts.get(mphf.index(&kmer.raw())),
+                    _ => 1,
+                },
+            )
+            .map_err(|e| olm_to_sk(e, "layer build"))?;
+            n
+        } else {
+            materialize_layer(g, &layer0_dir, block_bits, mode)?
+        };
+
+        let index_dir = layer0_dir.parent().expect("layer_dir has a parent");
+        PartitionMeta {
+            n_layers: 1,
+            mode: mode.clone(),
+        }
+        .save(index_dir)
+        .map_err(|e| olm_to_sk(e, "layer build"))?;
+
+        Ok(n_kmers)
+    }
+
+    fn remove_build_artifacts(&self, i: usize) {
+        let layer0_dir = self.layer_dir(i, 0);
+        let dedup = obikindex::layer::dereplicated_superkmers_path(&layer0_dir);
+        remove_if_exists(&SKFileMeta::sidecar_path(&dedup));
+        remove_if_exists(&dedup);
+        remove_if_exists(&layer0_dir.join("mphf1.bin"));
+        remove_if_exists(&layer0_dir.join("counts1.bin"));
+    }
+}
+
+// ── private helpers ──────────────────────────────────────────────────────
+
+fn label_from_path(path: &Path) -> String {
+    let name = path
+        .file_name()
+        .unwrap_or(path.as_os_str())
+        .to_string_lossy()
+        .into_owned();
+    let mut s = name;
+    while let Some(pos) = s.rfind('.') {
+        s.truncate(pos);
+    }
+    if s.is_empty() {
+        "unknown".to_string()
+    } else {
+        s
+    }
+}
+
+fn touch(path: &Path) -> Result<(), io::Error> {
+    fs::File::create(path).map(|_| ())
+}
+
+fn remove_if_exists(path: &Path) {
+    if let Err(e) = fs::remove_file(path) {
+        if e.kind() != io::ErrorKind::NotFound {
+            eprintln!("warning: could not remove {}: {e}", path.display());
+        }
+    }
+}

src/obikindexer/src/lib.rs

@@ -6,8 +6,11 @@
 //! and `obikindex` doesn't grow every algorithm's own dependencies.
 //!
 //! [`algorithms`] holds each algorithm as its own submodule: `partitionner`
-//! (routing raw super-kmers into partitions, then counting), `dereplicator`
+//! (routing raw super-kmers into partitions), `dereplicator` (deduplicating
-//! (deduplicating a partition's raw super-kmers before counting). A future
+//! a partition's raw super-kmers), `counter` (counting unique canonical
-//! `extensions` module will sit alongside it.
+//! kmers), `layer_builder` (turning dereplicated super-kmers + counts into
+//! the real layer 0). [`extensions`] (private — see its own module docs)
+//! holds construction-only `KmerIndex` operations these algorithms share.
 
 pub mod algorithms;
+pub(crate) mod extensions;

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

@@ -280,12 +280,7 @@ pub fn run(args: IndexArgs) {
             });
         pb.finish_and_clear();
         rep.push(t.stop());
-        drop(router); // ends the borrow of `idx` early — `PartitionRouter`'s `Drop` impl would otherwise extend it to the end of scope
+        drop(router); // ends the borrow of `idx` early — `PartitionRouter`'s `Drop` impl would otherwise extend it to the end of scope (`run()` already called `close()`, which marks scatter done, internally)
-
-        idx.mark_scattered().unwrap_or_else(|e| {
-            eprintln!("error marking scatter done: {e}");
-            std::process::exit(1);
-        });
     } else {
         info!("scatter already done, skipping");
     }
@@ -305,7 +300,9 @@ pub fn run(args: IndexArgs) {
 
         let t = Stage::start("count_kmer");
         let pb = progress_bar("counting", idx.n_partitions() as u64, "partitions");
-        let spectrum = Counter::new(&idx)
+        // `Counter::run` writes `spectrums/{label}.json` and marks count
+        // done (`count.done`) internally once every partition succeeds.
+        Counter::new(&idx)
             .keep_partial(args.keep_intermediate)
             .run(Some(|_: Progress| pb.inc(1)))
             .unwrap_or_else(|e| {
@@ -314,15 +311,6 @@ pub fn run(args: IndexArgs) {
             });
         pb.finish_and_clear();
         rep.push(t.stop());
-
-        idx.write_spectrum(spectrum.f0, spectrum.f1, &spectrum.counts).unwrap_or_else(|e| {
-            eprintln!("error: {e}");
-            std::process::exit(1);
-        });
-        idx.mark_counted().unwrap_or_else(|e| {
-            eprintln!("error marking count done: {e}");
-            std::process::exit(1);
-        });
     } else {
         info!("dereplicate+count already done, skipping");
     }
@@ -343,11 +331,8 @@ pub fn run(args: IndexArgs) {
         pb.finish_and_clear();
         info!("done — {total_kmers} total kmers indexed");
         rep.push(t.stop());
-
+        // `LayerBuilder::run` marks the index done (`index.done`) internally
-        idx.mark_indexed().unwrap_or_else(|e| {
+        // once every partition succeeds.
-            eprintln!("error marking index done: {e}");
-            std::process::exit(1);
-        });
     } else {
         info!("index already built, skipping");
     }

src/obikphylo/src/siblings/tests.rs

@@ -77,19 +77,14 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
         let batch = obiskbuilder::build_superkmers_page(page, K, /* level_max */ 1, /* theta */ 0.0);
         router.write_batch(batch).expect("write_batch");
     }
-    router.close().expect("close partition writers");
+    router.close().expect("close partition writers"); // also marks scatter done
     drop(router); // ends the borrow of `idx` early — `PartitionRouter`'s `Drop` impl would otherwise extend it to the end of scope
 
     Dereplicator::new(&idx).run(None::<fn(obisys::Progress)>).expect("dereplicate");
-    let spectrum = Counter::new(&idx).run(None::<fn(obisys::Progress)>).expect("count_kmer");
+    Counter::new(&idx).run(None::<fn(obisys::Progress)>).expect("count_kmer"); // also writes the spectrum + marks counted
-
-    idx.mark_scattered().expect("mark_scattered");
-    idx.write_spectrum(spectrum.f0, spectrum.f1, &spectrum.counts).expect("write_spectrum");
-    idx.mark_counted().expect("mark_counted");
     LayerBuilder::new(&idx)
         .run(None::<fn(obisys::Progress)>)
-        .expect("build_layers");
+        .expect("build_layers"); // also marks indexed
-    idx.mark_indexed().expect("mark_indexed");
     idx
 }