From b5ec0122d0a4d167c96a41593c26fe084ce28111 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 20 Aug 2026 13:33:56 +0200 Subject: [PATCH] Rename obikpartition crate to obikpartitionner Update all dependent crates and internal imports to reference the renamed module. Expose configuration parameters and genome metadata through new public accessor methods in the index API, and update documentation comments to align with the new package name. --- src/Cargo.lock | 8 ++--- src/Cargo.toml | 2 +- src/obicompactvec/src/bitmatrix/packed.rs | 2 +- src/obicompactvec/src/intmatrix.rs | 2 +- src/obikindex/Cargo.toml | 2 +- src/obikindex/src/dump.rs | 2 +- src/obikindex/src/index.rs | 29 ++++++++++++++++++- src/obikindex/src/merge.rs | 4 +-- src/obikindex/src/predicate.rs | 2 +- src/obikindex/src/rebuild.rs | 2 +- src/obikindex/src/reindex.rs | 2 +- src/obikindex/src/select.rs | 2 +- src/obikmer/Cargo.toml | 2 +- src/obikmer/src/cmd/filter/mod.rs | 2 +- src/obikmer/src/cmd/predicate.rs | 2 +- src/obikmer/src/cmd/query/batch.rs | 2 +- src/obikmer/src/cmd/query/chunk.rs | 2 +- src/obikmer/src/cmd/select/mod.rs | 2 +- src/obikmer/src/steps/scatter.rs | 2 +- .../Cargo.toml | 2 +- .../src/common.rs | 0 .../src/distance.rs | 0 .../src/dump_layer.rs | 0 .../src/filter.rs | 0 .../src/graph_pipeline.rs | 0 .../src/index_layer.rs | 0 .../src/kmer_sort.rs | 0 .../src/lib.rs | 0 .../src/merge_layer/mod.rs | 0 .../src/merge_layer/src_layer.rs | 0 .../src/partition/count.rs | 0 .../src/partition/dereplicate.rs | 0 .../src/partition/kmer_partition.rs | 2 +- .../src/partition/mod.rs | 0 .../src/partition/tests.rs | 0 .../src/query_layer.rs | 0 .../src/rebuild_layer.rs | 0 .../src/select_layer.rs | 0 .../src/tests/query_layer.rs | 0 src/obikphylo/Cargo.toml | 2 +- src/obikphylo/src/siblings/alignment.rs | 2 +- src/obikphylo/src/siblings/build.rs | 2 +- src/obikphylo/src/siblings/cache.rs | 2 +- src/obikphylo/src/siblings/cardinality.rs | 2 +- src/obikphylo/src/siblings/distance.rs | 2 +- src/obikphylo/src/siblings/entropy.rs | 2 +- src/obikphylo/src/siblings/sankoff_bundle.rs | 2 +- src/obikphylo/src/siblings/stats.rs | 2 +- src/obilayeredmap/src/layer.rs | 2 +- 49 files changed, 62 insertions(+), 35 deletions(-) rename src/{obikpartition => obikpartitionner}/Cargo.toml (97%) rename src/{obikpartition => obikpartitionner}/src/common.rs (100%) rename src/{obikpartition => obikpartitionner}/src/distance.rs (100%) rename src/{obikpartition => obikpartitionner}/src/dump_layer.rs (100%) rename src/{obikpartition => obikpartitionner}/src/filter.rs (100%) rename src/{obikpartition => obikpartitionner}/src/graph_pipeline.rs (100%) rename src/{obikpartition => obikpartitionner}/src/index_layer.rs (100%) rename src/{obikpartition => obikpartitionner}/src/kmer_sort.rs (100%) rename src/{obikpartition => obikpartitionner}/src/lib.rs (100%) rename src/{obikpartition => obikpartitionner}/src/merge_layer/mod.rs (100%) rename src/{obikpartition => obikpartitionner}/src/merge_layer/src_layer.rs (100%) rename src/{obikpartition => obikpartitionner}/src/partition/count.rs (100%) rename src/{obikpartition => obikpartitionner}/src/partition/dereplicate.rs (100%) rename src/{obikpartition => obikpartitionner}/src/partition/kmer_partition.rs (99%) rename src/{obikpartition => obikpartitionner}/src/partition/mod.rs (100%) rename src/{obikpartition => obikpartitionner}/src/partition/tests.rs (100%) rename src/{obikpartition => obikpartitionner}/src/query_layer.rs (100%) rename src/{obikpartition => obikpartitionner}/src/rebuild_layer.rs (100%) rename src/{obikpartition => obikpartitionner}/src/select_layer.rs (100%) rename src/{obikpartition => obikpartitionner}/src/tests/query_layer.rs (100%) diff --git a/src/Cargo.lock b/src/Cargo.lock index e77fa39b..b90d56a3 100644 --- a/src/Cargo.lock +++ b/src/Cargo.lock @@ -1600,7 +1600,7 @@ dependencies = [ "indicatif", "ndarray", "obicompactvec", - "obikpartition", + "obikpartitionner", "obikseq", "obilayeredmap", "obiread", @@ -1626,7 +1626,7 @@ dependencies = [ "obidebruinj", "obifastwrite", "obikindex", - "obikpartition", + "obikpartitionner", "obikphylo", "obikrope", "obikseq", @@ -1648,7 +1648,7 @@ dependencies = [ ] [[package]] -name = "obikpartition" +name = "obikpartitionner" version = "0.1.0" dependencies = [ "cacheline-ef", @@ -1685,7 +1685,7 @@ dependencies = [ "ndarray", "obicompactvec", "obikindex", - "obikpartition", + "obikpartitionner", "obikseq", "obilayeredmap", "obipipeline", diff --git a/src/Cargo.toml b/src/Cargo.toml index 54b49f0e..f34f6918 100644 --- a/src/Cargo.toml +++ b/src/Cargo.toml @@ -1,5 +1,5 @@ [workspace] resolver = "3" -members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartition","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo"] +members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap", "obicompactvec", "obisys", "obikindex", "obitaxonomy", "obikentropy", "obikphylo"] [profile.release] debug = 1 diff --git a/src/obicompactvec/src/bitmatrix/packed.rs b/src/obicompactvec/src/bitmatrix/packed.rs index bc1d3b9b..fcae6466 100644 --- a/src/obicompactvec/src/bitmatrix/packed.rs +++ b/src/obicompactvec/src/bitmatrix/packed.rs @@ -129,7 +129,7 @@ pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> { // A `matrix.pbmx` can already exist here even though columnar data is // still pending — e.g. copied verbatim from a merge's base source // before this layer was widened with more genome columns (see - // `obikpartition::merge_partition`). Only skip (re-)packing if the + // `obikpartitionner::merge_partition`). Only skip (re-)packing if the // existing file already reflects the current column count; otherwise // the columnar files are newer and must be (re-)packed, overwriting the // stale one — never silently discarded as "leftover cleanup". diff --git a/src/obicompactvec/src/intmatrix.rs b/src/obicompactvec/src/intmatrix.rs index 96072be0..2131e461 100644 --- a/src/obicompactvec/src/intmatrix.rs +++ b/src/obicompactvec/src/intmatrix.rs @@ -232,7 +232,7 @@ pub fn pack_compact_int_matrix(dir: &Path) -> io::Result<()> { // A `matrix.pcmx` can already exist here even though columnar data is // still pending — e.g. copied verbatim from a merge's base source // before this layer was widened with more genome columns (see - // `obikpartition::merge_partition`). Only skip (re-)packing if the + // `obikpartitionner::merge_partition`). Only skip (re-)packing if the // existing file already reflects the current column count; otherwise // the columnar files are newer and must be (re-)packed, overwriting the // stale one — never silently discarded as "leftover cleanup". diff --git a/src/obikindex/Cargo.toml b/src/obikindex/Cargo.toml index ae8bda1f..e0707278 100644 --- a/src/obikindex/Cargo.toml +++ b/src/obikindex/Cargo.toml @@ -5,7 +5,7 @@ edition = "2024" [dependencies] obikseq = { path = "../obikseq" } -obikpartition = { path = "../obikpartition" } +obikpartitionner = { path = "../obikpartitionner" } obitaxonomy = { path = "../obitaxonomy" } obiskio = { path = "../obiskio" } obisys = { path = "../obisys" } diff --git a/src/obikindex/src/dump.rs b/src/obikindex/src/dump.rs index f5310ff8..756243fb 100644 --- a/src/obikindex/src/dump.rs +++ b/src/obikindex/src/dump.rs @@ -5,7 +5,7 @@ use rayon::prelude::*; use crate::error::{OKIError, OKIResult}; use crate::index::KmerIndex; -use obikpartition::KmerFilter; +use obikpartitionner::KmerFilter; impl KmerIndex { /// Write a CSV table of all indexed kmers to `out`. diff --git a/src/obikindex/src/index.rs b/src/obikindex/src/index.rs index 47e3ee16..b8e973ad 100644 --- a/src/obikindex/src/index.rs +++ b/src/obikindex/src/index.rs @@ -2,7 +2,7 @@ use std::collections::BTreeMap; use std::fs; use std::path::{Path, PathBuf}; -use obikpartition::{KmerPartitions, KmerSpectrum, PARTITIONS_SUBDIR}; +use obikpartitionner::{KmerPartitions, KmerSpectrum, PARTITIONS_SUBDIR}; use obisys::{Reporter, Stage, progress_bar}; use rayon::prelude::*; use tracing::info; @@ -157,6 +157,33 @@ impl KmerIndex { pub fn minimizer_size(&self) -> usize { self.meta.config.minimizer_size } + pub fn n_bits(&self) -> usize { + self.meta.config.n_bits + } + pub fn with_counts(&self) -> bool { + self.meta.config.with_counts + } + pub fn evidence_mode(&self) -> &obilayeredmap::IndexMode { + &self.meta.config.evidence + } + /// Coarse evidence mode (`Exact`/`Approx`/`Hybrid`, no `b`/`z` + /// parameters) — see [`evidence_mode`](Self::evidence_mode) for the + /// full `IndexMode`. Same discriminant as `Layer::evidence_kind`, so a + /// layer's own evidence kind can be compared directly against the + /// index's. + pub fn evidence_kind(&self) -> obilayeredmap::EvidenceKind { + match self.meta.config.evidence { + obilayeredmap::IndexMode::Exact => obilayeredmap::EvidenceKind::Exact, + obilayeredmap::IndexMode::Approx { .. } => obilayeredmap::EvidenceKind::Approx, + obilayeredmap::IndexMode::Hybrid { .. } => obilayeredmap::EvidenceKind::Hybrid, + } + } + pub fn block_bits(&self) -> u8 { + self.meta.config.block_bits + } + pub fn genomes(&self) -> &[GenomeInfo] { + &self.meta.genomes + } pub fn n_partitions(&self) -> usize { self.partition.n_partitions() } diff --git a/src/obikindex/src/merge.rs b/src/obikindex/src/merge.rs index 8943d9fe..444dc487 100644 --- a/src/obikindex/src/merge.rs +++ b/src/obikindex/src/merge.rs @@ -13,7 +13,7 @@ use crate::index::KmerIndex; use crate::meta::{GenomeInfo, IndexMeta}; use crate::state::{IndexState, SENTINEL_INDEXED}; -pub use obikpartition::MergeMode; +pub use obikpartitionner::MergeMode; // ── per-partition diagnostic record ────────────────────────────────────────── @@ -193,7 +193,7 @@ impl KmerIndex { let block_bits = dst.meta.config.block_bits; // Pre-build source list once (avoid rebuilding per partition) - let srcs: Vec<(&obikpartition::KmerPartitions, usize)> = remaining_sources + let srcs: Vec<(&obikpartitionner::KmerPartitions, usize)> = remaining_sources .iter() .map(|s| (&s.partition, s.meta.genomes.len())) .collect(); diff --git a/src/obikindex/src/predicate.rs b/src/obikindex/src/predicate.rs index 842f4534..b98286ef 100644 --- a/src/obikindex/src/predicate.rs +++ b/src/obikindex/src/predicate.rs @@ -1,6 +1,6 @@ use std::collections::HashMap; -use obikpartition::GroupQuorumFilter; +use obikpartitionner::GroupQuorumFilter; use obitaxonomy::{TaxPath, TaxPattern}; use crate::meta::{GenomeInfo, IndexMeta}; diff --git a/src/obikindex/src/rebuild.rs b/src/obikindex/src/rebuild.rs index 06d4e052..3db37f2f 100644 --- a/src/obikindex/src/rebuild.rs +++ b/src/obikindex/src/rebuild.rs @@ -1,6 +1,6 @@ use std::path::Path; -use obikpartition::{KmerFilter, MergeMode}; +use obikpartitionner::{KmerFilter, MergeMode}; use obisys::{Reporter, Stage, progress_bar}; use tracing::info; diff --git a/src/obikindex/src/reindex.rs b/src/obikindex/src/reindex.rs index b8d9ab56..a58f6dee 100644 --- a/src/obikindex/src/reindex.rs +++ b/src/obikindex/src/reindex.rs @@ -1,4 +1,4 @@ -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obilayeredmap::{IndexMode, layer::Layer}; use obisys::{Reporter, Stage, progress_bar}; use std::fs; diff --git a/src/obikindex/src/select.rs b/src/obikindex/src/select.rs index 350e4f85..1f6591f5 100644 --- a/src/obikindex/src/select.rs +++ b/src/obikindex/src/select.rs @@ -1,6 +1,6 @@ use std::path::Path; -use obikpartition::{KmerPartitions, OutputCol}; +use obikpartitionner::{KmerPartitions, OutputCol}; use obisys::{Reporter, Stage, progress_bar}; use tracing::info; diff --git a/src/obikmer/Cargo.toml b/src/obikmer/Cargo.toml index 3a5434b1..bec904c2 100644 --- a/src/obikmer/Cargo.toml +++ b/src/obikmer/Cargo.toml @@ -15,7 +15,7 @@ obifastwrite = { path = "../obifastwrite" } obidebruinj = { path = "../obidebruinj" } obipipeline = { path = "../obipipeline" } obikrope = { path = "../obikrope" } -obikpartition = { path = "../obikpartition" } +obikpartitionner = { path = "../obikpartitionner" } obisys = { path = "../obisys" } obiskio = { path = "../obiskio" } obikindex = { path = "../obikindex", default-features = false } diff --git a/src/obikmer/src/cmd/filter/mod.rs b/src/obikmer/src/cmd/filter/mod.rs index 0edce233..b2ca626a 100644 --- a/src/obikmer/src/cmd/filter/mod.rs +++ b/src/obikmer/src/cmd/filter/mod.rs @@ -2,7 +2,7 @@ use std::path::PathBuf; use clap::Args; use obikindex::{KmerIndex, MergeMode}; -use obikpartition::filter::{MaxTotalCount, MinComplexity, MinTotalCount}; +use obikpartitionner::filter::{MaxTotalCount, MinComplexity, MinTotalCount}; use obisys::Reporter; use tracing::info; diff --git a/src/obikmer/src/cmd/predicate.rs b/src/obikmer/src/cmd/predicate.rs index 5cb786c2..6d0f953e 100644 --- a/src/obikmer/src/cmd/predicate.rs +++ b/src/obikmer/src/cmd/predicate.rs @@ -1,6 +1,6 @@ use clap::Args; use obikindex::{GroupFilterParams, IndexMeta, MetaPred}; -use obikpartition::KmerFilter; +use obikpartitionner::KmerFilter; /// CLI args for ingroup/outgroup filtering — embeddable in any command via `#[command(flatten)]`. #[derive(Args)] diff --git a/src/obikmer/src/cmd/query/batch.rs b/src/obikmer/src/cmd/query/batch.rs index 09b48fbb..55cd9452 100644 --- a/src/obikmer/src/cmd/query/batch.rs +++ b/src/obikmer/src/cmd/query/batch.rs @@ -1,6 +1,6 @@ use std::collections::HashMap; -use obikpartition::KmerDesc; +use obikpartitionner::KmerDesc; use obikseq::CanonicalKmer; use obiread::record::SeqRecord; use obiskbuilder::SuperKmerIter; diff --git a/src/obikmer/src/cmd/query/chunk.rs b/src/obikmer/src/cmd/query/chunk.rs index f2e56fdb..509d84b1 100644 --- a/src/obikmer/src/cmd/query/chunk.rs +++ b/src/obikmer/src/cmd/query/chunk.rs @@ -1,7 +1,7 @@ use std::time::Instant; use obikindex::KmerIndex; -use obikpartition::{KmerDesc, QueryHit, QueryStats}; +use obikpartitionner::{KmerDesc, QueryHit, QueryStats}; use obikrope::Rope; use obikseq::CanonicalKmer; use obiread::record::parse_chunk; diff --git a/src/obikmer/src/cmd/select/mod.rs b/src/obikmer/src/cmd/select/mod.rs index 4f61960f..5f4180ad 100644 --- a/src/obikmer/src/cmd/select/mod.rs +++ b/src/obikmer/src/cmd/select/mod.rs @@ -3,7 +3,7 @@ use std::path::PathBuf; use clap::{Args, ValueEnum}; use obikindex::{IndexMeta, KmerIndex}; -use obikpartition::{AggOp, OutputCol}; +use obikpartitionner::{AggOp, OutputCol}; use obisys::Reporter; use tracing::info; diff --git a/src/obikmer/src/steps/scatter.rs b/src/obikmer/src/steps/scatter.rs index c8359260..a6b3b2f2 100644 --- a/src/obikmer/src/steps/scatter.rs +++ b/src/obikmer/src/steps/scatter.rs @@ -3,7 +3,7 @@ use std::sync::Arc; use std::sync::atomic::{AtomicU32, AtomicU64, Ordering}; use std::time::Instant; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obipipeline::{ThrottleGuard, Throttled, throttle}; use obiread::NucPage; use obisys::spinner; diff --git a/src/obikpartition/Cargo.toml b/src/obikpartitionner/Cargo.toml similarity index 97% rename from src/obikpartition/Cargo.toml rename to src/obikpartitionner/Cargo.toml index b762afbe..310b746d 100644 --- a/src/obikpartition/Cargo.toml +++ b/src/obikpartitionner/Cargo.toml @@ -1,5 +1,5 @@ [package] -name = "obikpartition" +name = "obikpartitionner" version = "0.1.0" edition = "2024" diff --git a/src/obikpartition/src/common.rs b/src/obikpartitionner/src/common.rs similarity index 100% rename from src/obikpartition/src/common.rs rename to src/obikpartitionner/src/common.rs diff --git a/src/obikpartition/src/distance.rs b/src/obikpartitionner/src/distance.rs similarity index 100% rename from src/obikpartition/src/distance.rs rename to src/obikpartitionner/src/distance.rs diff --git a/src/obikpartition/src/dump_layer.rs b/src/obikpartitionner/src/dump_layer.rs similarity index 100% rename from src/obikpartition/src/dump_layer.rs rename to src/obikpartitionner/src/dump_layer.rs diff --git a/src/obikpartition/src/filter.rs b/src/obikpartitionner/src/filter.rs similarity index 100% rename from src/obikpartition/src/filter.rs rename to src/obikpartitionner/src/filter.rs diff --git a/src/obikpartition/src/graph_pipeline.rs b/src/obikpartitionner/src/graph_pipeline.rs similarity index 100% rename from src/obikpartition/src/graph_pipeline.rs rename to src/obikpartitionner/src/graph_pipeline.rs diff --git a/src/obikpartition/src/index_layer.rs b/src/obikpartitionner/src/index_layer.rs similarity index 100% rename from src/obikpartition/src/index_layer.rs rename to src/obikpartitionner/src/index_layer.rs diff --git a/src/obikpartition/src/kmer_sort.rs b/src/obikpartitionner/src/kmer_sort.rs similarity index 100% rename from src/obikpartition/src/kmer_sort.rs rename to src/obikpartitionner/src/kmer_sort.rs diff --git a/src/obikpartition/src/lib.rs b/src/obikpartitionner/src/lib.rs similarity index 100% rename from src/obikpartition/src/lib.rs rename to src/obikpartitionner/src/lib.rs diff --git a/src/obikpartition/src/merge_layer/mod.rs b/src/obikpartitionner/src/merge_layer/mod.rs similarity index 100% rename from src/obikpartition/src/merge_layer/mod.rs rename to src/obikpartitionner/src/merge_layer/mod.rs diff --git a/src/obikpartition/src/merge_layer/src_layer.rs b/src/obikpartitionner/src/merge_layer/src_layer.rs similarity index 100% rename from src/obikpartition/src/merge_layer/src_layer.rs rename to src/obikpartitionner/src/merge_layer/src_layer.rs diff --git a/src/obikpartition/src/partition/count.rs b/src/obikpartitionner/src/partition/count.rs similarity index 100% rename from src/obikpartition/src/partition/count.rs rename to src/obikpartitionner/src/partition/count.rs diff --git a/src/obikpartition/src/partition/dereplicate.rs b/src/obikpartitionner/src/partition/dereplicate.rs similarity index 100% rename from src/obikpartition/src/partition/dereplicate.rs rename to src/obikpartitionner/src/partition/dereplicate.rs diff --git a/src/obikpartition/src/partition/kmer_partition.rs b/src/obikpartitionner/src/partition/kmer_partition.rs similarity index 99% rename from src/obikpartition/src/partition/kmer_partition.rs rename to src/obikpartitionner/src/partition/kmer_partition.rs index e8ba9037..aad39b4f 100644 --- a/src/obikpartition/src/partition/kmer_partition.rs +++ b/src/obikpartitionner/src/partition/kmer_partition.rs @@ -197,7 +197,7 @@ impl KmerPartitions { } /// Partition `i`'s metadata (layer count, evidence mode) — the single - /// entry point for this, so that callers outside `obikpartition` + /// entry point for this, so that callers outside `obikpartitionner` /// never need to know it's a `meta.json` loaded via /// `obilayeredmap::meta::PartitionMeta`, nor handle its own recovery /// path for indexes built before that file existed (see diff --git a/src/obikpartition/src/partition/mod.rs b/src/obikpartitionner/src/partition/mod.rs similarity index 100% rename from src/obikpartition/src/partition/mod.rs rename to src/obikpartitionner/src/partition/mod.rs diff --git a/src/obikpartition/src/partition/tests.rs b/src/obikpartitionner/src/partition/tests.rs similarity index 100% rename from src/obikpartition/src/partition/tests.rs rename to src/obikpartitionner/src/partition/tests.rs diff --git a/src/obikpartition/src/query_layer.rs b/src/obikpartitionner/src/query_layer.rs similarity index 100% rename from src/obikpartition/src/query_layer.rs rename to src/obikpartitionner/src/query_layer.rs diff --git a/src/obikpartition/src/rebuild_layer.rs b/src/obikpartitionner/src/rebuild_layer.rs similarity index 100% rename from src/obikpartition/src/rebuild_layer.rs rename to src/obikpartitionner/src/rebuild_layer.rs diff --git a/src/obikpartition/src/select_layer.rs b/src/obikpartitionner/src/select_layer.rs similarity index 100% rename from src/obikpartition/src/select_layer.rs rename to src/obikpartitionner/src/select_layer.rs diff --git a/src/obikpartition/src/tests/query_layer.rs b/src/obikpartitionner/src/tests/query_layer.rs similarity index 100% rename from src/obikpartition/src/tests/query_layer.rs rename to src/obikpartitionner/src/tests/query_layer.rs diff --git a/src/obikphylo/Cargo.toml b/src/obikphylo/Cargo.toml index 38d52483..35b1f7f0 100644 --- a/src/obikphylo/Cargo.toml +++ b/src/obikphylo/Cargo.toml @@ -6,7 +6,7 @@ edition = "2024" [dependencies] obikindex = { path = "../obikindex", default-features = false } obikseq = { path = "../obikseq" } -obikpartition = { path = "../obikpartition" } +obikpartitionner = { path = "../obikpartitionner" } obiskio = { path = "../obiskio" } obisys = { path = "../obisys" } obicompactvec = { path = "../obicompactvec" } diff --git a/src/obikphylo/src/siblings/alignment.rs b/src/obikphylo/src/siblings/alignment.rs index 5f5f6ab6..754fd577 100644 --- a/src/obikphylo/src/siblings/alignment.rs +++ b/src/obikphylo/src/siblings/alignment.rs @@ -1,6 +1,6 @@ use std::sync::Arc; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obisys::progress_bar; use obikindex::KmerIndex; diff --git a/src/obikphylo/src/siblings/build.rs b/src/obikphylo/src/siblings/build.rs index ee8d09c4..6d125e19 100644 --- a/src/obikphylo/src/siblings/build.rs +++ b/src/obikphylo/src/siblings/build.rs @@ -4,7 +4,7 @@ use std::sync::atomic::Ordering; use rayon::prelude::*; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obikseq::CanonicalKmer; use obilayeredmap::MphfLayer; use obilayeredmap::meta::IndexMode; diff --git a/src/obikphylo/src/siblings/cache.rs b/src/obikphylo/src/siblings/cache.rs index d00bdd12..8bc8f4f2 100644 --- a/src/obikphylo/src/siblings/cache.rs +++ b/src/obikphylo/src/siblings/cache.rs @@ -3,7 +3,7 @@ use rayon::prelude::*; use std::path::Path; use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix}; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obikseq::CanonicalKmer; use obilayeredmap::meta::IndexMode; use obilayeredmap::{Layer, OLMResult}; diff --git a/src/obikphylo/src/siblings/cardinality.rs b/src/obikphylo/src/siblings/cardinality.rs index 6f296d24..211a1f63 100644 --- a/src/obikphylo/src/siblings/cardinality.rs +++ b/src/obikphylo/src/siblings/cardinality.rs @@ -2,7 +2,7 @@ use std::sync::Arc; use ndarray::Array2; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obisys::progress_bar; use obikindex::KmerIndex; diff --git a/src/obikphylo/src/siblings/distance.rs b/src/obikphylo/src/siblings/distance.rs index 9426bd2c..8b8b15e6 100644 --- a/src/obikphylo/src/siblings/distance.rs +++ b/src/obikphylo/src/siblings/distance.rs @@ -2,7 +2,7 @@ use std::sync::Arc; use ndarray::Array2; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obisys::progress_bar; use obikindex::KmerIndex; diff --git a/src/obikphylo/src/siblings/entropy.rs b/src/obikphylo/src/siblings/entropy.rs index 1d1140b0..16aef5e3 100644 --- a/src/obikphylo/src/siblings/entropy.rs +++ b/src/obikphylo/src/siblings/entropy.rs @@ -13,7 +13,7 @@ use std::io::{BufWriter, Write}; use std::path::{Path, PathBuf}; use std::sync::Arc; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obisys::progress_bar; use obikindex::KmerIndex; diff --git a/src/obikphylo/src/siblings/sankoff_bundle.rs b/src/obikphylo/src/siblings/sankoff_bundle.rs index 36c3dfc8..b360721b 100644 --- a/src/obikphylo/src/siblings/sankoff_bundle.rs +++ b/src/obikphylo/src/siblings/sankoff_bundle.rs @@ -29,7 +29,7 @@ use std::sync::Arc; use ndarray::Array2; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obisys::progress_bar; use obikindex::KmerIndex; diff --git a/src/obikphylo/src/siblings/stats.rs b/src/obikphylo/src/siblings/stats.rs index dd71ccf6..2a636187 100644 --- a/src/obikphylo/src/siblings/stats.rs +++ b/src/obikphylo/src/siblings/stats.rs @@ -2,7 +2,7 @@ use std::sync::Arc; use rayon::prelude::*; -use obikpartition::KmerPartitions; +use obikpartitionner::KmerPartitions; use obisys::progress_bar; use obikindex::KmerIndex; diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs index f056375a..eea8ed81 100644 --- a/src/obilayeredmap/src/layer.rs +++ b/src/obilayeredmap/src/layer.rs @@ -33,7 +33,7 @@ pub trait LayerData: Sized { /// /// `obilayeredmap` operates within a single partition's index root; it has /// no notion of "partition" at all. Turning a partition number into that -/// root is `obikpartition::KmerPartition::part_dir`'s job, one layer up +/// root is `obikpartitionner::KmerPartition::part_dir`'s job, one layer up /// — callers here only ever name a layer *number*, never build the path /// themselves. pub fn layer_dir(root: &Path, i: usize) -> PathBuf {