Partition and layer caching (discussion)

Superseded (2026-08-21): obikpartition and obilayeredmap are no longer separate workspace crates — both were folded back into obikindex as submodules (obikindex::partition, obikindex::layer), alongside the crate's original content as obikindex::index, purely to reduce the crate count (no behavior change). Every mention of obikpartition/ obilayeredmap as a crate below, and every dependency-direction argument phrased in terms of "which crate depends on which" (e.g. "this crate depends only on obilayeredmap and below, never on obikindex"), describes that now-superseded split-crate architecture and is kept as-is for historical context — read obikpartition::X as obikindex:: partition::X and obilayeredmap::X as obikindex::layer::X throughout. The underlying module boundary and its rationale (Layer tier / Partition tier / Index tier, each depending only downward) are unchanged; only the crate-vs-module packaging changed. See obikindex::layer for the current module doc.

Status (2026-08-20, latest pass): (1) done — obilayeredmap::Layer exists, Mat is gone. (1b) done — Layer::Empty, the first non-ready state, added (panics on every read method). (2a) done — the obikpartition crate and KmerPartition itself exist (open/n_layers/ layer/layers/find). (2b) — migrating PartitionCache/QueryLayer onto it — not started, deliberately deferred. (3) done — the obikindex ↔ obikpartitionner dependency inverted: PartitionRouter now takes &mut KmerIndex and produces Layer::Empty shells directly, closing the gap Layer::Empty was built for in (1b) — see "(3) done" below. (4) done — dereplication split out into its own crate, obikderep, first step of an incremental "one algorithm at a time" split of obikpartitionner's remaining bundle (count_kmer/build_layers not yet moved) — see "(4) done" below. (5) — full design agreed, not yet implemented — KmerPartition was found to be wired into nothing (KmerIndex never calls it; every path is still computed via free functions), and the fix turned out to be bigger than KmerPartition alone: Layer's own constructors don't self-name either. Full redesign of both, agreed in detail, session ended (budget) before implementation — see "(5) design agreed" below; read it before touching KmerPartition/Layer signatures, the shape is fully specified. 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 merged into KmerIndex — see "Major restructuring" below), and never retracted that usage before this section was rewritten. An agent working from that stale wording built the wrong thing. If you are about to implement (2), read "Definitions: obikpartition and KmerPartition" below — it is the current, authoritative naming — before touching any other section of this file, some of which still describe superseded states of the code and are kept only as dated history.

Definitions: `obikpartition` and `KmerPartition` (not yet created)

obikpartition — a new workspace crate, not created yet. Holds the Partition tier of the Index { Partition { Layer } } model, the same way obilayeredmap already holds the Layer tier as its own crate rather than living inside obikindex. Depends only on obilayeredmap (for Layer) and lower (obikseq, obiskio). Does not depend on obikindex, obikpartitionner, or obikphylo. Dependency direction: obikindex → obikpartition → obilayeredmap; obikphylo → obikindex (and/or obikpartition directly if it ends up needing it without going through KmerIndex).

KmerPartition (singular) — the one type this crate exists for. Represents one partition's already-open layers — a read cache, built once per partition and held for the run, not rebuilt per lookup. Shape:

pub struct KmerPartition {
    layers: Vec<obilayeredmap::Layer>,
}

Nothing else. In particular: - No path computation. KmerPartition::open takes an already-resolved index_dir: &Path (plus mode: &IndexMode, n_layers: usize, with_counts: bool — whatever it needs, as plain arguments), the same discipline obikpartitionner::PartitionRouter::open already follows. Computing index_dir/layer_dir from a partition number is KmerIndex's job (obikindex, which owns that already — see "Major restructuring" below); KmerPartition never reaches back into KmerIndex to get it (would require obikpartition → obikindex, the wrong direction). - No routing/write state. Writing raw superkmers, dereplicate, count_kmer stay in obikpartitionner::PartitionRouter — a completely different crate, a completely different phase (pre-layer, whereas KmerPartition only makes sense once layers exist). - No multi-partition collection baked in. KmerPartition is one partition. Whatever ends up caching several of them (replacing obikphylo::siblings::cache::PartitionCache's Vec<Vec<Layer>> and obikindex::query_layer's per-call reopen) holds Vec<KmerPartition> — that collection can live in obikpartition too, or in obikindex alongside KmerIndex; not yet decided, secondary to getting KmerPartition itself right first.

Do not confuse with KmerPartitions (plural — note the s): that type is gone. It used to be obikpartitionner's (nee obikpartition, briefly — see the crate-rename history below, itself a separate rename from this one) do-everything struct — routing, dereplication, and path lookups all in one. It was deleted on 2026-08-20; its read-side (paths, n_layers, partition_meta) was absorbed into KmerIndex, its write-side became PartitionRouter. KmerPartition (this section, singular, no final s) is a brand-new type with a different job, in a crate that doesn't exist yet — not a revival, not a renaming, of KmerPartitions.

Type-to-concept mapping: Index / Partition / Layer

The conceptual nesting Index { Partition { Layer { MPHF, Evidence, Matrix } } } }, current state:

Index = obikindex::KmerIndex — { root_path, meta: IndexMeta }. Also directly exposes the partition-path/metadata accessors (partition_dir(i), index_dir(i), layer_dir(i, l), partition_meta(i), n_layers(i), partition_mode(i), n_partitions()) since KmerPartitions merged into it (see "Major restructuring" below) — KmerIndex today is "index + collection of partitions' paths & metadata," just without a Vec of open layers.
Partition, the collection = no dedicated type today; the closest thing is KmerIndex itself (previous bullet). Once KmerPartition (singular, see Definitions above) exists, a Vec<KmerPartition> somewhere would be this — still open, see "Direction agreed" below.
Partition, one of them = obikpartition::KmerPartition — to be built, see Definitions above. Nothing plays this role today; obikphylo::siblings::cache::PartitionCache and obikindex::query_layer::QueryLayer each independently reinvent a fragment of it.
Layer = obilayeredmap::Layer (format-erased: Count/Presence, each wrapping a TypedLayer<D>) — see "(1) done" below for how this came to be; TypedLayer<D> ({ mphf: MphfLayer, data: D }, monomorphic) is the lower-level, D-fixed building block Layer is built on, not what other crates should reach for directly.
MPHF = MphfLayer.mphf: MemCase<MphfEps> — kmer → slot.
Evidence = MphfLayer.ev: LayerEvidence (Exact/Approx/ Hybrid — evidence.bin/fingerprint.bin; see EvidenceKind).
Matrix = TypedLayer<D>.data: D — PersistentBitMatrix / PersistentCompactIntMatrix.

Target nesting once KmerPartition exists:

KmerIndex                                    (obikindex)
 └─ (opened on demand, per i)  KmerPartition  (obikpartition — not yet built)
     └─ layers: Vec<Layer>                    (obilayeredmap)
         └─ Layer::Count/Presence(TypedLayer<D>)
             └─ TypedLayer<D> { mphf: MphfLayer, data: D }
                 ├─ mphf.mphf   → MPHF
                 ├─ mphf.ev     → Evidence
                 └─ data        → Matrix

Major restructuring (2026-08-20): `KmerPartitions` merged into `KmerIndex`

Prompted by a direct question: why keep KmerIndex/KmerPartitions split when, one level down, KmerPartitions is going to directly hold Vec<KmerPartition> rather than being split again into "collection-holder" + "collection"? Investigating the actual justification ("KmerPartitions has an independent lifecycle, used before an index exists") turned out to be false — KmerPartitions::create was called in exactly one place, inside KmerIndex::create, and every open_with_config reopen outside KmerIndex's own constructors was a redundant re-derivation of a KmerPartitions already reachable via index.partition() (the exact kind of duplication this whole doc has been tracking). Once that was gone, so was the reason to keep them separate.

Second correction, from the same conversation: obikpartitionner had accumulated query/merge/select/rebuild/dump/distance logic that has nothing to do with partitioning super-kmers — it operates on layers, which don't exist yet at the phase obikpartitionner is actually responsible for (scatter → dereplicate → count, all pre-layer). That logic moved to obikindex, which already depends on obilayeredmap and never needed obikpartitionner for it. No crate-dependency inversion was needed — obikindex → obikpartitionner stays the same direction as before.

Result: - obikpartitionner (renamed back from obikpartition) now contains only PartitionRouter (superkmer routing: write/write_batch/flush/ close, dereplicate, count_kmer, KmerSpectrum) and the partition_dir(root, i) naming primitive both PartitionRouter and KmerIndex build on. KmerPartitions no longer exists as a type. - KmerIndex (obikindex) absorbed KmerPartitions's read-side entirely: partition_dir/index_dir/layer_dir/partition_meta/n_layers/ partition_mode/n_partitions (the last now derived from 2^config.n_bits, no longer a stored, independently-set duplicate field — kmer_size/minimizer_size used to be double-stored, in both KmerPartitions and IndexMeta.config, a latent-drift risk flagged earlier in this doc; now single-sourced from IndexMeta.config). Seven whole files moved from obikpartitionner into obikindex verbatim as impl KmerIndex blocks, kept as separate files (not merged into existing same-topic files): index_layer.rs, query_layer.rs, merge_layer/, select_layer.rs, rebuild_layer.rs, dump_layer.rs, plus distance.rs's count_store/presence_store (renamed matrix_store.rs to avoid colliding with obikindex's own pre-existing distance.rs), and their shared support (common.rs's load_meta/ olm_to_sk, filter.rs, graph_pipeline.rs). - obikphylo::siblings::cache::PartitionCache::build now takes &KmerIndex directly instead of a separately-opened &KmerPartitions — this deleted the redundant-reopen pattern at all 8 call sites (alignment/build/cardinality/distance/entropy×2/ sankoff_bundle/stats), the same bug flagged earlier in this conversation as a side effect of investigating the false "independent lifecycle" claim. - KmerIndex::partition()/partition_mut() are gone; scatter() (obikmer) and any write-side code get a transient PartitionRouter via KmerIndex::partition_router(). - A real bug caught by the test suite during this move: PartitionRouter::open initially defaulted to closed: true (inherited from KmerPartitions::open_with_config's old read-only-reopen semantics), which broke every write through a router obtained via partition_router(). Fixed — PartitionRouter is exclusively a write/processing tool now, so open always starts open.

Full workspace test suite green (0 failed) after, including all 27 obikphylo::siblings tests.

(1) done (2026-08-20): `Layer` is now the heterogeneous handle, `Mat` is gone

Resolved the naming question left open above. Layer<D> (the old generic/monomorphic type) renamed to TypedLayer<D> throughout (obilayeredmap, obikindex, obikphylo — 12 files, mechanical) to free Layer for the type that's actually meant to be everyone's default handle. obilayeredmap::content_layer::Layer (re-exported at the crate root) is that type — Count(TypedLayer<PersistentCompactIntMatrix>)/ Presence(TypedLayer<PersistentBitMatrix>), Layer::open doing the same disk probe Mat::open used to, find_slot/index_batch/n_cols/ fill_sub_matrix_carries dispatching per variant exactly as Mat did.

obikphylo::siblings::cache::Mat deleted outright — PartitionCache now holds Vec<Vec<obilayeredmap::Layer>> directly. The one sibling-specific method Mat carried (iter_minorants_batch) is not on obilayeredmap:: Layer (phylo concepts don't belong in obilayeredmap) — it's an impl SiblingLayerExt for obilayeredmap::Layer in iter.rs, dispatching to each variant's existing impl<D: LayerData> SiblingLayerExt for TypedLayer<D>.

Full workspace suite green (0 failed) after, including all 27 obikphylo::siblings tests.

Still not built: (2) — KmerPartition (singular, one partition's open Vec<Layer>) and a multi-partition cache in obikpartitionner to replace obikphylo::siblings::cache::PartitionCache and obikindex::query_layer's still-separate QueryLayer (which still independently bundles MPHF+matrix, 2-way not using Layer at all). Both remaining consumers now sit one Layer::open call away from unifying onto (2) once it exists.

(1b) done (2026-08-20): `Layer::Empty` — the first non-ready-to-read state

First step toward Layer representing a layer's whole life, not just the open-for-reading end of it (see "Definitions" above: KmerPartition will hold Vec<Layer> regardless of each layer's state, states in between included). Added one variant:

pub enum Layer {
    Empty { dir: PathBuf },
    Count(TypedLayer<PersistentCompactIntMatrix>),
    Presence(TypedLayer<PersistentBitMatrix>),
}

Layer::create(dir) makes the directory and returns Empty { dir } — nothing else; no MPHF/unitigs/evidence construction yet (that's the deferred next step: build_mphf()/build_unitigs()/build_evidence() methods to progress Empty → eventually Count/Presence). Empty carries path accessors so builder code has one place to get mphf_path()/unitigs_path()/evidence_path()/fingerprint_path()/ counts_dir()/presence_dir() from, instead of redeclaring the mphf.bin/unitigs.bin/… filenames at each write site — reusing the constants layer.rs/mphf_layer.rs already own (COUNTS_DIR/ PRESENCE_DIR widened from private to pub(crate), file-name constants already were).

Every read method (content/evidence_kind/n/find_slot/ index_batch/n_cols/fill_sub_matrix_carries) panics on Empty with a one-line message naming the method — confirmed as the right behaviour: calling any of them on an Empty layer means the caller assumed a layer was ready when it wasn't, an implementation error to surface loudly, not a case to design around (Option/Result would let it silently propagate instead of failing at the actual mistake). Same panic added to obikphylo::siblings::iter.rs's impl SiblingLayerExt for obilayeredmap::Layer (4 methods), the one other place that exhaustively matched Layer's variants.

Full workspace suite green (cargo check --workspace --all-targets then cargo test --workspace, exit code 0) after.

Still deferred, per explicit instruction: build_mphf()/ build_unitigs()/build_evidence() to progress Empty further, and (2) — KmerPartition itself — unchanged from above (see "(2a) done" below, added next).

(2a) done (2026-08-20): `obikpartition` crate + `KmerPartition`

Built exactly the shape "Definitions" (top of file) specifies, nothing more — deliberately scoped down from the full "Direction agreed" plan below: only steps 1–2 (open/n_layers/layer/layers/find), not 3–4 (migrating PartitionCache/QueryLayer onto it), per explicit instruction to implement KmerPartition first and decide the wiring ("comment on branche tout ça dans la construction") separately, later.

pub struct KmerPartition {
    layers: Vec<obilayeredmap::Layer>,
}

impl KmerPartition {
    pub fn open(index_dir: &Path, mode: &IndexMode, n_layers: usize, with_counts: bool) -> OLMResult<Self>;
    pub fn n_layers(&self) -> usize;
    pub fn layer(&self, i: usize) -> &Layer;
    pub fn layers(&self) -> &[Layer];
    pub fn find(&self, kmer: CanonicalKmer) -> Option<usize>;
}

open takes index_dir/mode/n_layers/with_counts as plain arguments — no reach-back into KmerIndex (would need obikpartition → obikindex, the wrong direction) — and builds each layer's path via obilayeredmap::layer_dir(index_dir, l), the same shared naming primitive KmerIndex::layer_dir itself delegates to, not a second copy of the layer_N convention. find mirrors PartitionCache::find's semantics (first layer that carries the kmer wins) but doesn't yet cover find_presence_batch/find_presence_batch_fast — those exist only to serve PartitionCache, so they're part of the (2b) migration, not this step; building them now against the current sibling-specific tuple shape (CanonicalKmer, usize, u8, u8) would either bake phylo vocabulary (family_idx, base) into obikpartition or require deciding a generic payload shape — a real design fork, deferred to when (2b) is actually tackled rather than guessed at here.

Crate deps: obikseq, obilayeredmap only (dev-deps add obiskio, obicompactvec, tempfile for tests) — matches the "Definitions" constraint (obikpartition depends on obilayeredmap and below, never obikindex/obikpartitionner/obikphylo). Registered as a new workspace member (src/Cargo.toml). 3 new tests (open_reads_every_layer_in_order, find_reports_the_first_layer_that_carries_the_kmer, find_returns_none_for_an_absent_kmer). Full workspace suite green (cargo check --workspace --all-targets then cargo test --workspace) after.

Still not done: (2b) — migrating obikphylo::siblings::cache:: PartitionCache (currently Vec<Vec<Layer>>) and obikindex::query_layer::QueryLayer (currently uncached, bypasses Layer entirely) onto KmerPartition/Vec<KmerPartition>; deciding whether that collection lives in obikpartition or obikindex; deciding the batch-lookup surface's exact shape (generic payload vs. as-is sibling tuple moved in wholesale); scan_layer_families's still-independent PartitionMeta::load (see "Remaining instance…" below) — all explicitly deferred to whenever wiring is tackled next.

(3) done (2026-08-20): `obikindex ↔ obikpartitionner` dependency inverted, `PartitionRouter` now fills `Layer::Empty` shells

Resolved a question left implicit since "Major restructuring": that pass set the direction obikindex → obikpartitionner (so KmerIndex could delegate partition_dir to it) without questioning whether that was the right direction at all. Challenged directly: obikpartitionner is an algorithm (superkmer routing/dereplication/counting) operating on an index (KmerIndex, the data structure) — algorithms depend on the data types they need, not the other way around. [[feedback_no_precedent_defense]] applied here: "that's the direction we already picked" was not treated as a justification for keeping it.

New direction: obikpartitionner → obikindex (+ obilayeredmap, obipipeline, obiread directly, for what run's pipeline itself needs). obikindex → obikpartitionner is gone entirely — KmerIndex no longer imports PartitionRouter/KmerSpectrum in any form. Two path-naming primitives that used to make this edge necessary moved down a tier instead of staying put: - partition_dir/PARTITIONS_SUBDIR moved from obikpartitionner into obikpartition (the Partition-tier crate KmerPartition already lives in), alongside a new index_dir(root, i) — both free functions, mirroring obilayeredmap::layer_dir one tier down. KmerIndex:: partition_dir/index_dir now delegate here instead of to obikpartitionner/an inline .join("index"). - KmerIndex::create/create_skeleton no longer call PartitionRouter::create to lay out an empty partitions/ skeleton upfront — turned out to be dead weight once traced: select_layer.rs/ rebuild_layer.rs already create_dir_all their own partition/layer directories on demand, and Layer::create's directory-creation covers the scatter path the same way. Partitions and their layer-0 shells now come into existence lazily, on first write, with nothing to pre-create. KmerIndex::create's now-unused force: bool parameter was dropped (4 call sites updated) rather than left as a dead parameter.

PartitionRouter reshaped (obikpartitionner/src/partition/router.rs) around the "création, paramétrage, run()" shape agreed on: new(index: &mut KmerIndex) -> Self (no disk access), chainable setters (level_max/theta/workers/max_open, defaults matching the CLI's old hardcoded values), then run(path_source, on_progress). write/ write_batch/flush/close/dereplicate/count_kmer stay public, unconsumed (&self/&mut self, not self) — callers needing fine-grained control (tests, obikphylo's test harness) still get it, run is a convenience layered on top, not the only way in.

run absorbs the entire body of what used to be the free function obikmer::steps::scatter (now deleted, along with the steps module entirely) — the obipipeline::make_pipe! two-stage pipeline (file→pages→superkmers), throttling, per-file logging. What changed: - Every ensure_writer(partition) call now does Layer::create(&layer0_dir) (layer0_dir = obilayeredmap::layer_dir(&index.index_dir(i), 0)) before opening raw.{ext} inside it — raw/dereplicated superkmer files and the provisional mphf1.bin/counts1.bin/kmer_spectrum_raw.json now live under <partition>/index/layer_0/, not flat under <partition>/ as before. This is Layer::Empty actually being used as the "builder code holding an Empty layer" its own (1b) docs anticipated, not just a shell with no consumer. - Caught by an end-to-end smoke test, not by cargo test: this path move broke obikindex::index_layer::build_index_layer and remove_build_artifacts, both of which still read/deleted dereplicated.skmer.zst/mphf1.bin/counts1.bin from self.partition_dir(i) (the old flat location) — no test in the workspace suite exercises the real CLI's file-reading scatter path end-to-end (obikphylo's test harness and obikpartitionner's own tests both call write_batch directly, bypassing run/file discovery entirely), so the whole suite stayed green while obikmer index on real FASTA silently indexed 0 kmers. Found by running the actual CLI against a small FASTA and noticing count.json's f0 (870, correct) didn't match "0 total kmers indexed" at the final stage. Fixed by retargeting both functions to self.layer_dir(i, 0). Lesson, consistent with the retracted-claim lesson above: a green test suite is not proof a refactor is correct when no test in it exercises the specific path that changed — for anything touching the CLI's own file-driven entry point, running the CLI for real is not optional verification. - The internal obisys::spinner("scatter") + hand-rolled EMA-rate display is gone from the library entirely, replaced by an Option<impl FnMut(obisys::Progress)> parameter — a new, deliberately generic progress-reporting type (obisys::Progress { position: u64, total: Option<u64> }, alongside the existing TracedBar/spinner/ progress_bar) added specifically so every future algo crate's run() reports progress the same shape, once, rather than each inventing its own. total: None here (bases processed isn't knowable without pre-scanning every input file) — deliberately simpler than the old in-library rate/file-count/thread-count message; the caller can recompute a Mbp/s rate from consecutive position values + wall-clock time itself, which is exactly what cmd/index/mod.rs now does to reproduce the old spinner message. This is a real, intentional restriction of the library's job: it reports raw ticks, the CLI decides what a human sees — same "generic vs. domain-specific" split applied again, this time to progress reporting rather than to Layer content. Explicitly not the same mechanism as Stage/Reporter (per [[feedback_stage_reporter_in_cmd_layer]]): Stage/Reporter measures a whole call's wall time from outside it; a progress callback has to fire from inside a loop mid-call, which wrapping from outside cannot express — two different needs, not the same rule reapplied under a new name. Stage::start("scatter")/rep.push(...) stayed in cmd/index/mod.rs, wrapping the whole run() call, unchanged in kind. - dereplicate/count_kmer keep their existing internal obisys::progress_bar(...) calls as-is (unconverted to the callback) — explicitly out of scope for this pass, by agreement.

Forced, not optional, consequence of the dependency inversion: KmerIndex::dereplicate_and_count/partition_router/write_spectrum(& KmerSpectrum) could not stay on KmerIndex at all once obikindex can no longer name obikpartitionner::{PartitionRouter, KmerSpectrum} in any position — not a design choice, a mechanical requirement of severing the edge. Replaced by: KmerIndex::write_spectrum(f0: u64, f1: u64, counts: &BTreeMap<u32, u64>) (plain values, no KmerSpectrum dependency) and a new KmerIndex::mark_counted() (symmetric to the already-existing mark_scattered), with the orchestration itself (router.dereplicate() → router.count_kmer() → write_spectrum → mark_counted()) now living in cmd/index/mod.rs, not obikindex.

Every PartitionRouter::new(&mut index) call in this codebase runs into the same NLL trap once: PartitionRouter has a Drop impl (auto-close on scope exit), which extends its &mut KmerIndex borrow to the end of the enclosing scope even after its last real use — idx.mark_scattered() right after router.run(...) (or idx.write_spectrum(...) right after router.count_kmer(...)) fails to borrow-check unless the router is drop()-ed explicitly first. Hit and fixed identically at all three call sites that needed it (cmd/index/mod.rs ×2, obikphylo's test harness, obikpartitionner's own tests).

Full workspace suite green (cargo check --workspace --all-targets + cargo test --workspace, exit code 0) both before and after the index_layer.rs fix above — the smoke test is what actually caught the regression the suite missed.

(4) done (2026-08-20): `obikderep` — dereplication split out of `obikpartitionner`, one algorithm at a time

Follow-on question after (3): the indexing pipeline has 4 stages (scatter, dereplicate, count_kmer, index-build — see the CLI's own Reporter output, one line per stage), but obikpartitionner — a name that says partitioning — owned three of them (routing, dereplication, counting). Challenged directly, same as (3)'s dependency-direction question: a crate should hold what its name says, not accumulate unrelated stages just because they happened to land there first. Two ways to fix it — one crate renamed to hold all remaining stages, or one crate per stage — decided in favour of the latter, explicitly incremental: build the second algo crate first (obikderep, dereplication only), only then look at what it and PartitionRouter actually have in common, and factor a shared Algorithm trait (future obikalgorithm crate) from that real overlap — not guessed at from a single example. count_kmer and build_layers (currently KmerIndex inherent methods — itself flagged as inconsistent with "KmerIndex is a data structure, not a compute structure") are left alone this round, on purpose — one stage moves at a time.

obikderep (new crate): Dereplicator<'a> { index: &'a KmerIndex, n_partitions, level } — new(index: &KmerIndex) (shared borrow, not &mut: dereplication never writes index metadata), no setters yet (nothing to configure), run(on_progress) does the two-phase split+merge dereplication in parallel across partitions, ported unchanged from PartitionRouter::dereplicate (moved wholesale: optimal_buckets/dereplicate_partition/load_bucket/flush_map/ remove_skmer_file, now private to this crate in dereplicate.rs). obikpartitionner::PartitionRouter::dereplicate is gone; count_kmer stays.

A real signature difference from PartitionRouter::run, not an inconsistency: Dereplicator::run takes Option<impl Fn(Progress) + Sync>, not FnMut. PartitionRouter::run's callback is invoked from one sequential loop (FnMut is fine); Dereplicator::run's work is rayon::par_iter, so the callback can be invoked concurrently from multiple worker threads — same reason obisys::TracedBar's own methods take &self, not &mut self. Progress position is tracked with an AtomicU64, incremented from inside the parallel closure so each completed partition reports immediately — collecting all results first and reporting after (the first draft of this) would have delivered every tick in one burst at the very end, defeating the point of a live progress bar. total: Some(n_partitions) (known up front, unlike scatter's bases count) — cmd/index/mod.rs renders a real progress_bar, not a spinner, driven by the callback exactly like scatter's spinner is.

A second, pre-existing instance of the exact bug (3) fixed, caught before it shipped: dereplicated.skmer.zst was hand-built as a string literal independently in three places — obikpartitionner's dereplicate.rs/count.rs and obikindex's index_layer.rs (a literal that already predated this session, never caught until now). Splitting dereplication into its own crate turns this from "two places, still matching by luck" into "three independent crates that must agree on a filename with no shared dependency forcing them to" — no longer deferrable. Fixed by adding obilayeredmap::{raw_superkmers_path, dereplicated_superkmers_path} (free functions, layer_dir: &Path -> PathBuf, mirroring layer_dir itself) — the filename lives in one place, in the Layer-tier crate every consumer here already depends on (obikpartitionner, obikderep, obikindex all reach it without a new edge), and no external crate ever sees the literal "skmer.zst" again. This reverses (3)'s own earlier call to keep SK_EXT private to obikpartitionner — that call assumed a single owner; a second owner appearing (obikderep) removed the assumption it rested on, so the decision changed with it, not out of inconsistency.

Every count_kmer call site that used to run after router.dereplicate() on the same PartitionRouter now runs after a separate Dereplicator::new(&idx).run(...) call, on a freshly-constructed PartitionRouter — PartitionRouter no longer offers a combined "dereplicate then count" path. Updated at all three call sites that had one: cmd/index/mod.rs, obikphylo's test harness, obikpartitionner's own tests.

Full workspace suite green (cargo check --workspace --all-targets + cargo test --workspace, exit code 0), plus an end-to-end CLI smoke test against real FASTA data (scatter → dereplicate → count → index-build → query, same numbers as (3)'s smoke test: 870 kmers) — required this time too, per (3)'s own lesson: no test in the suite exercises obikmer index's real file-driven path.

Still not done: count_kmer/build_layers staying where they are, the obikalgorithm shared-trait extraction (deliberately deferred until a third data point exists), and everything already listed under (2b).

(5) design agreed, not yet implemented (2026-08-20): `KmerPartition` rewritten, `Layer` gains self-naming, a future cache crate over `KmerIndex`

Session ended (out of budget) before any of this was coded. Everything below is a fully specified plan, agreed sentence by sentence with the user — not a sketch to re-derive, not a proposal to re-litigate. Implement it as written; if something here turns out to be wrong once coded, fix it and update this section, don't restart the design conversation.

How this was found

Direct question from the user: "tu as bien créé une structure KmerPartition ?" — yes (2a), but investigating exposed that it is wired into nothing. KmerIndex has no partition(i) method at all; partition_dir/index_dir/layer_dir still call obikpartition:: partition_dir/index_dir and obilayeredmap::layer_dir as bare free functions directly, never touching a KmerPartition/Layer object to get there. The end result on disk is identical (same paths), which is exactly why no test caught it — but the responsibility is in the wrong place: one function (on KmerIndex) knows the whole three-tier naming convention, instead of each tier asking the one below it for its own path. User's framing, verbatim, now saved as [[feedback_no_spaghetti_petits_pois]]: "spaghetti" (logic untraceable, split across too many unrelated crates) and "petits pois" (small bits of naming logic dispersed with no owning object) are strictly forbidden — this was a live example of both.

Pushed further, twice: 1. First correction: Layer::create(&obilayeredmap::layer_dir(&dir, 0)) — still a free-function call from outside Layer to compute where it should live. "Le layer n'est pas con, c'est lui qui dit où est-ce qu'il doit être sauvé" (the layer isn't stupid, it says itself where it should be saved). 2. Second correction, the general principle: "une partition est juste identifiée par un numéro, tout se calcule à partir du numéro, et un layer est identifié à partir d'un numéro et tout se calcule à partir de ce numéro." Concretely: each object stores its own local identifying number plus its immediate parent's path (captured once, at construction) — never a path handed in again later by a caller, and never a free function outside the object that can compute that path independently. Explicitly rejected along the way: making users pass "the partition's path that contains the layer" to open a layer — the parent path is captured once, at the child's construction, not re-supplied at every call.

The agreed shape

Layer (obilayeredmap) — identified by l + its parent partition's directory, both captured at construction, never received again:

pub enum Layer {
    Empty { partition_dir: PathBuf, l: usize },   // pure identification, no disk I/O
    Count(TypedLayer<PersistentCompactIntMatrix>),
    Presence(TypedLayer<PersistentBitMatrix>),
}

impl Layer {
    pub fn at(partition_dir: &Path, l: usize) -> Self;                 // identify only
    fn dir(&self) -> PathBuf;                                          // private — layer_dir() no longer a public free function, folded in here
    pub fn create(self) -> io::Result<Self>;                           // creates the directory if needed; no path parameter anymore
    pub fn open(self, mode: &IndexMode, with_counts: bool) -> OLMResult<Self>;  // no path parameter anymore
    // mphf_path()/unitigs_path()/evidence_path()/fingerprint_path()/counts_dir()/presence_dir()
    // unchanged in spirit, implemented via self.dir() instead of a stored `dir` field read directly
}

Note this replaces Layer::Empty { dir: PathBuf } from (1b) — dir becomes a computed value (partition_dir.join(format!("layer_{l}"))), not a stored field. obilayeredmap::layer_dir/raw_superkmers_path/ dereplicated_superkmers_path (currently public free functions, introduced in (3)/(4)) stop being called from outside obilayeredmap entirely once this lands — they were the right fix for their moment (a second crate, obikderep, needed to agree on a filename with no owner), but the real fix, now visible with a third data point, is that Layer itself should be the only thing anyone asks.

KmerPartition (obikpartition) — same principle, one tier up:

pub struct KmerPartition {
    index_root: PathBuf,   // the parent KmerIndex's root, captured once
    i: usize,
}

impl KmerPartition {
    pub fn new(index_root: PathBuf, i: usize) -> Self;                 // identify only, no disk I/O
    pub fn create(index_root: PathBuf, i: usize) -> io::Result<Self>;  // creates this partition's directory + an empty layer 0 (a partition is never born without one — that knowledge lives here, not in whoever calls create)
    pub fn partition_dir(&self) -> PathBuf;                            // part_{i:05}
    pub fn index_dir(&self) -> PathBuf;                                // part_{i:05}/index
    pub fn layer(&self, l: usize) -> Layer;                            // Layer::at(&self.index_dir(), l) — caller never touches a path
    pub fn meta(&self) -> SKResult<PartitionMeta>;                     // n_layers + mode; must absorb the recovery-on-missing-file logic
                                                                         // currently private in obikindex::common::load_meta (obikpartition
                                                                         // can't depend on obikindex to reuse it — this logic moves down)
    pub fn n_layers(&self) -> SKResult<usize>;                         // meta()?.n_layers
    pub fn mode(&self) -> SKResult<IndexMode>;                         // meta()?.mode — "exact/approximatif"
    pub fn is_filled(&self) -> bool;                                   // does this partition's directory exist at all
    pub fn n_kmers(&self) -> io::Result<usize>;                        // LayerMeta::load(&self.layer(0).dir()).n — reads layer 0's count as
                                                                         // a representative figure, same "read the first one" trick
                                                                         // n_layers_per_partition() already uses at the KmerIndex level
}

This replaces (2a)'s KmerPartition { layers: Vec<Layer> } entirely — no eagerly-opened Vec<Layer>, no find() (both belong to the future cache, see below, which is the thing that actually holds opened layers alive across many lookups). (2a)'s version is safe to delete outright: it was never wired into anything (confirmed above), so nothing depends on its current shape. New dependencies needed: obikpartition gains obiskio (for SKResult) and obicompactvec (for LayerMeta).

Deliberately not built this round: cross-level consistency checks ("verify everything below me is in the same state") — a real idea, raised by the user, but nothing concrete needs it yet; building it speculatively would be exactly the premature-abstraction pattern this project avoids.

KmerIndex (obikindex) — becomes the sole entry point:

pub fn partition(&self, i: usize) -> KmerPartition;   // KmerPartition::new(self.root_path.clone(), i)

partition_dir(i)/index_dir(i)/layer_dir(i, l) stay as public methods (≈30 existing call sites across obikindex/obikphylo — see (3)'s option A, applied identically here) but become pure delegations: self.partition(i).partition_dir(), self.partition(i).index_dir(), self.partition(i).layer(l).dir() (needs Layer::dir() to be visible enough for this — likely pub(crate) in obilayeredmap plus a thin public wrapper, or a public accessor on Layer itself; not fully nailed down, decide while implementing). No caller outside obikindex changes.

Known blast radius (why this wasn't done in the same session)

14 files call Layer::open/Layer::create directly today (obikphylo/siblings/{cache,build,family_scan,tests}.rs, obikpartitionner/partition/router.rs, obikpartition/src/lib.rs, obikindex/{rebuild_layer,dump_layer,index,query_layer}.rs, obilayeredmap/{mphf_layer,layer,map,content_layer}.rs) — every one loses its path parameter and gains a (partition_dir, l) or an already-identified Layer to call .create()/.open() on instead.
≈30 files call KmerIndex::partition_dir/index_dir/layer_dir — unaffected in their own code (same public signatures), but worth re-checking once (5) lands that none of them were relying on the old free-function-based implementation in a way the new delegation breaks.
obikpartitionner::PartitionRouter::ensure_writer and obikderep's run both currently call obilayeredmap::{layer_dir, raw_superkmers_path, dereplicated_superkmers_path} directly (from (3)/(4)) — both need to switch to going through index.partition(i).layer(0) instead.

Also agreed, separately: `PartitionRouter::new` never needed `&mut KmerIndex`

Verified by reading the code: every call PartitionRouter makes on index is &self (index.kmer_size(), index.index_dir(i)). The &mut in its current signature (from (3)) was inherited from the original "the router writes to the partitions" reasoning, never actually required by any method call. This is exactly what caused every drop(router) workaround needed throughout (3)/(4) (cmd/index/mod.rs ×2, obikphylo's test harness, obikpartitionner's own tests) — PartitionRouter holds a Drop impl, which extends a &mut borrow to the end of its scope even past its last real use. Fix alongside (5): change PartitionRouter::new(index: &'a mut KmerIndex) to &'a KmerIndex, and remove the now-unnecessary drop(router) calls at all four sites.

Also discussed: a future cache crate, not part of (5), not `obikalgorithm` either

Separate idea, explicitly not part of this design and not started: a new crate whose only job is to cache open KmerPartitions (and their opened Layers) across one run — replacing both obikphylo::siblings:: cache::PartitionCache (today, sibling-specific, holds Vec<Vec<Layer>>) and obikindex::query_layer::QueryLayer (today, uncached, bypasses Layer entirely) — the two consumers (2b) already identified as each reinventing a fragment of the same thing.

User's framing: this is not a third obikalgorithm data point — an algorithm has a new → run → done shape; a cache has a fundamentally different one (open, stay alive for a whole run, serve lookups, maybe evict) — "on crée un cache sur un index, ça consomme un index." Two distinct crate roles in this ecosystem (data crates: obikpartition/ obilayeredmap; algorithm crates: obikpartitionner/obikderep/future obikalgorithm implementors; and now a cache/service crate), not one unified shape to force everything into.

Depends on (5) being done first: the cache crate's whole job is holding Vec<KmerPartition>/opened Layers alive, built via KmerIndex:: partition(i) as its factory — nothing to build it on top of until (5) lands. Still open once (5) is done: eviction policy vs. holding everything open for the process lifetime (the never-measured mmap/VM-mapping-count question from earlier in this doc), and whether it lives in obikpartition itself or a new crate.

Order of remaining work, as currently understood

(5) — Layer/KmerPartition/KmerIndex rewrite described above, plus the PartitionRouter &mut → & fix (same root cause, same session, do together).
The future cache crate (name not chosen), consuming KmerIndex:: partition(i) — unblocks migrating PartitionCache/QueryLayer (2b).
obikalgorithm — still deliberately waiting for a third run()-shaped data point (count_kmer or build_layers migrating out of KmerIndex/PartitionRouter) before extracting a shared trait; two examples were judged not enough to be sure of the shape (Fn+Sync vs FnMut callback bound already diverged between the two that exist).

The problem

Reading a layer's data (MPHF + matrix) is not free: MphfLayer::open mmaps mphf.bin plus (evidence.bin/fingerprint.bin + unitigs.bin), and the matrix side mmaps matrix.pbmx/matrix.pcmx (or one file per genome column if not yet packed). Any code path that reopens a layer per lookup instead of once per run pays this cost repeatedly.

obikphylo::siblings::cache::PartitionCache was built to avoid exactly this for build_sibling_annex/sibling_annex_stats: those commands probe many partitions, once per source layer, over the whole run. Profiling a real run showed wall-clock time dominated by repeated open()/mmap syscalls, not computation — parallelising the naive per-lookup opens spread the cost across cores without reducing it. PartitionCache::build opens every partition's every layer once, up front, in parallel, and keeps the handles alive for the run.

Three independent implementations of the same bundle (historical — (1) fixed this)

As of 2026-08-20 this table describes the pre-(1) state. Mat no longer exists (deleted when obilayeredmap::Layer replaced it — see "(1) done" above); Layer<D> in the table below is what's now called TypedLayer<D>. QueryLayer is unaffected and still stands as described — still uncached, still not using Layer at all — which is exactly what (2) needs to fix. Kept for the original motivation, not as current fact:

Searching the codebase for "who bundles MPHF + matrix, with per-layer format auto-detection" turned up three unrelated implementations:

	lives in	scope	cached?
`Layer<D>` (now `TypedLayer<D>`)	`obilayeredmap`	one layer, `D` fixed at compile time	held alive by whoever owns the `Layer`, no policy of its own
`Mat` (now deleted; superseded by `obilayeredmap::Layer`)	`obikphylo::siblings::cache`	one layer, format resolved per instance from an enum of 3 `Layer<D>` variants	yes, via `PartitionCache`
`QueryLayer` (unchanged, still current)	`obikindex::query_layer` (moved crates since this was written — see "Major restructuring")	one layer, `(MphfLayer, PersistentBitMatrix\\|PersistentCompactIntMatrix)` pair, bypasses `TypedLayer<D>`/`Layer` entirely	no — opened fresh inside `query_partition_with` on every call

query_partition_with is obikmer query's normal query path — the one most exposed to repeated cross-partition lookups — and it is still the one with no cache at all. obikphylo built a cache first only because sibling-annex construction hits the cost hardest, not because the need is sibling-specific.

The gap in `obilayeredmap`'s existing cache (historical — (1) fixed this)

obilayeredmap::LayeredMap<D> already caches correctly at the granularity of one partition: open(root) opens every layer once, keeps Vec<TypedLayer<D>> alive for the LayeredMap's lifetime. But it is monomorphic — every layer in the Vec must share the same concrete D. In practice this was false: layers in the same partition are packed independently over time (pack --sparse converts one layer's presence matrix at a time). This motivated (1) — obilayeredmap::Layer, done — but note the specific PersistentSparseBitMatrix-mixing scenario described here turned out to be moot: PersistentBitMatrix itself absorbed sparse storage as a 4th internal variant before (1) was built (see "One bug found … one earlier claim retracted" below), so the only heterogeneity Layer actually needs to represent is Count vs. Presence, not dense-vs-sparse presence. LayeredMap<D> itself is unaffected by any of this — it's still monomorphic, still not used by Layer/KmerPartition (which bypass it entirely, opening each TypedLayer<D> directly, the same way Mat did).

Resource cost: mmap does not hold a file descriptor

Before deciding how many layers/partitions a cache may hold open simultaneously, the binding constraint needs to be identified correctly.

Confirmed against upstream documentation, not inferred from behaviour:

"After the mmap() call has returned, the file descriptor, fd, can be closed immediately without invalidating the mapping." — mmap(2), man7.org

"The close(2) function does not unmap pages" — mmap(2), Apple Developer

"A file backed Mmap ... will remain valid even after the File is dropped. ... the Mmap handle is completely independent of the File used to create it." — memmap2::Mmap, docs.rs

Every read-only mmap in this codebase already follows this: Mmap::map(&File::open(path)?)? — the File is a temporary, dropped (fd closed) immediately after the mapping is established; every persistent struct (PersistentBitVec, PersistentCompactIntVec, PackedBitMatrix, Evidence, FingerprintVec, ...) stores only the Mmap, never the File. So a cache built on these types does not consume the process's open-file-descriptor budget (ulimit -n, notoriously low by default on macOS) proportionally to how many mmapped files it holds.

It does consume a different resource — the process's virtual-memory mapping table (one entry per active mmap() region). Linux exposes this as vm.max_map_count (default 65530). No documented macOS equivalent (fixed numeric ceiling) was found; the constraint there appears to be virtual address space rather than an explicit mapping counter, but this is not sourced and should not be assumed. This is the resource actually worth measuring before deciding on cache size, not fd count — and it is why packing (matrix.pbmx/matrix.pcmx, one mmap for all columns) matters independently of any caching decision: an unpacked Columnar matrix opens one mmap per genome column, multiplying the mapping count a cache would have to hold by n_genomes.

Layering: who owns what (superseded — see Definitions above)

This section used to argue nobody owned "the collection of partitions." That's resolved: KmerIndex (obikindex) owns it now, directly (see "Major restructuring" below). What's still genuinely unowned is one partition's open layers — KmerPartition, in the not-yet-created obikpartition — see "Definitions" at the top of this file for the current, authoritative answer. Left here only so old links/references to this heading don't 404; don't read this section for current facts.

Direction agreed, not yet implemented

Only (2) remains — (1) shipped as obilayeredmap::Layer (see "(1) done" above). Concretely, in order:

Create the obikpartition crate (obikindex → obikpartition → obilayeredmap, no other edges — see "Definitions" above for the exact constraint and why).
KmerPartition { layers: Vec<obilayeredmap::Layer> } — open, n_layers, layer(i), find, plus whatever batch-lookup surface obikphylo::siblings::cache::PartitionCache currently needs (find_presence_batch/find_presence_batch_fast; fast_mode is sibling-specific bookkeeping and should probably stay in obikphylo, wrapping a KmerPartition/Vec<KmerPartition> rather than living inside it — same "generic vs. domain-specific" split iter_minorants_batch already went through for Layer in (1)).
Migrate obikphylo::siblings::cache::PartitionCache to hold Vec<KmerPartition> instead of Vec<Vec<Layer>>.
Migrate obikindex::query_layer::QueryLayer/query_partition_with to use KmerPartition too, closing the "no cache at all" gap on obikmer's normal query path (see "Three independent implementations," historical, above).

Open before implementing: exact API shape of KmerPartition (propose, confirm before coding — non-trivial), and whether the multi-partition Vec<KmerPartition> needs an eviction policy or can simply hold every partition open for the process lifetime (revisit once the VM-mapping-count question above has a real number behind it for this codebase's scale — still not measured).

Preparatory work done (2026-08-20)

Groundwork for (1)/(2), landed ahead of the design itself. Note: at the time this was written, the collection type these bullets describe was named KmerPartition (singular) in this doc; it was renamed KmerPartitions (plural) shortly after, then deleted entirely and merged into KmerIndex (see "Major restructuring" above). The bullets below are edited to say KmerPartitions throughout, to not collide with the unrelated, brand-new singular KmerPartition defined at the top of this file — the accessors described here live on KmerIndex today, not on any type called KmerPartition.

KmerPartitions (obikpartitionner, at the time) gained partition_dir/index_dir/layer_dir as the single source of truth for a partition's on-disk layout, replacing per-module duplicated const INDEX_SUBDIR: &str = "index" (7 copies) and ad hoc path joins — including one found duplicated inside the struct itself (ensure_writer rebuilt part_dir's own logic by hand).
Same struct gained partition_meta/n_layers/index_mode, wrapping obilayeredmap::meta::PartitionMeta::load (via the existing common::load_meta, which also recovers indexes built before meta.json existed). Before this, obikphylo and obikindex imported obilayeredmap::meta::PartitionMeta directly and called ::load() themselves at 21 call sites, each redoing its own error-mapping — every one of those crates knew the on-disk metadata format instead of going through an interface. Fixed everywhere except one remaining spot (below). Caught as a side effect: dump_layer.rs/query_layer.rs had been calling PartitionMeta::load directly, bypassing load_meta entirely — they never got the missing-meta.json recovery the other callers did.
Layer introspection API discussed but not yet implemented — three axes, deliberately kept separate after an initial draft conflated them:
LayerContent { Count, Presence } — what the layer stores; a const on LayerData (compile-time, zero-cost), not a runtime field.
StorageKind { Implicit, Columnar, Packed, Sparse } — how it's stored; only meaningful for D that actually carry data (Layer<()> has neither this nor LayerContent — it's a write-time-only state, never a queryable content: once a layer is closed, "no matrix file" reads back as Presence/Implicit via PersistentBitMatrix::open's own fallback, not as some third "empty" content).
EvidenceKind { Exact, Approx, Hybrid } — from MphfLayer's own already-in-memory LayerEvidence discriminant.
Not all (LayerContent, StorageKind) pairs are legal: Count never has Implicit or Sparse.

Implemented (2026-08-20). LayerContent/StorageKind/EvidenceKind now exist, each with two forms: - A runtime accessor on an already-open value (Layer<D>::content()/ storage_kind()/evidence_kind(), PersistentBitMatrix::storage_kind(), PersistentCompactIntMatrix::storage_kind(), MphfLayer::evidence_kind()) — reads a discriminant already in memory, zero disk access. - A lightweight detect()/detect_storage() disk probe that mirrors the corresponding open()'s own priority order by hand (file-existence checks only, no mmap) — usable before committing to a D, unlike the runtime accessors. Exposed per-layer on LayeredMap<D> as detect_layer_content/detect_layer_storage/detect_layer_evidence (work regardless of D, since they only use self.root + the layer index).

StorageKind lives in obicompactvec (owner of PersistentBitMatrix/ PersistentCompactIntMatrix); LayerContent/EvidenceKind live in obilayeredmap. HasLayerContent/HasStorageKind gate Layer<()> out of content()/storage_kind() (no matrix, nothing to report), matching the "empty is transitional" conclusion above. 42 new tests across obilayeredmap's tests/layer.rs and tests/map.rs; full workspace suite green (0 failed) after.

Not done: these detect() probes don't yet replace Mat::open's or QueryLayer::open's own hand-rolled equivalents (still duplicated content/ storage decisions, now a third copy of the same logic to keep in sync) — that consolidation is (1)/(2)'s job, not this prep step's.

One bug found while reading around this (signalled, not fixed); one earlier claim retracted

obicompactvec::bitmatrix::sparse.rs's module doc says "Not used by any production code path yet" — false since obikmer pack --sparse (cmd/pack/mod.rs) is wired to pack_sparse_bit_matrix and Mat::open already reads the result back in the sibling-annex path. Stale comment, not corrected.
Retracted (2026-08-20): an earlier pass through this doc claimed obikpartition::query_layer::QueryLayer::open had no sparse-format detection and would silently corrupt reads on a pack --sparsed layer. False — PersistentBitMatrix (obicompactvec::bitmatrix::persistent) is a 4-way enum (Columnar/Packed/Sparse/Implicit), not 3-way as first read; its open() already detects Sparse via presence/sparse_meta.json, and every method on the type (row, fill_row, nonzero_iter, …) already dispatches all 4 arms. QueryLayer::open's PersistentBitMatrix::open(layer_dir) call was never the bug. Root cause of the false claim: a grep -n "Implicit\|Columnar\|Packed" used to read the enum definition silently skipped the Sparse(...) line because it matched none of those three words — a self-inflicted blind spot from a filtered read, not a fact about the code. Lesson: for a pub enum whose variant list matters, read the definition unfiltered, don't grep for the variant names you expect to find.
One real consequence of that same correction, fixed (2026-08-20): obikphylo::siblings::cache::Mat::SparsePresence(Layer< PersistentSparseBitMatrix>) was redundant — Mat::Presence(Layer< PersistentBitMatrix>) alone already handles sparse layers transparently, since PersistentBitMatrix absorbs Sparse internally. Removed the variant, the presence/is_multi.prsb probe in Mat::open (now just opens Layer::<PersistentBitMatrix> unconditionally for the non-count case — sparse-vs-dense is PersistentBitMatrix::open's own concern), and every now-single-armed match in find_slot/index_batch/ iter_minorants_batch/n_cols/fill_sub_matrix_carries. Full workspace test suite green after, including the 27 obikphylo::siblings tests that exercise pack_matrices(true)/sparse through Mat.

Remaining instance of the PartitionMeta-encapsulation problem

obikphylo::siblings::family_scan::scan_layer_families still re-derives index_dir from layer_dir.parent() and calls PartitionMeta::load itself, purely to get .mode for obilayeredmap::Layer::open (was Mat::open, same gap, survived the Mat → Layer swap in (1) unchanged). Fixing it the way the 21 other call sites were fixed needs more than a 1:1 swap: scan_layer_families only receives a bare layer_dir: &Path, not a (partition, part, layer) triple, and its single upstream source of layer paths, sibling_layer_dirs, returns a flat Vec<PathBuf> with the partition/layer indices already discarded. Fixing it properly means either having sibling_layer_dirs return (PathBuf, IndexMode) (or (part, layer)) pairs, or threading &KmerIndex + indices through instead of paths (not &KmerPartition — that type doesn't exist yet, and once it does it still won't know IndexMode, which lives on KmerIndex/ PartitionMeta) — and touching every one of scan_layer_families's 8 callers (distance.rs, alignment.rs, cardinality.rs, entropy.rs ×2, sankoff_bundle.rs ×2, stats.rs). Left alone this round; worth doing as part of the same pass that builds KmerPartition, since those callers are exactly the sibling-annex consumers it's meant to serve.

Partition and layer caching (discussion)

Definitions: obikpartition and KmerPartition (not yet created)