Introduce obikalgorithm crate to unify pipeline algorithms

Define a shared Algorithm trait with an associated Output type and a parameterless run(&mut self) method. Refactor PartitionRouter, Dereplicator, Counter, and LayerBuilder to implement the trait, standardizing receivers to &mut self and moving configuration and progress callbacks to dedicated builder setters. Decouple error handling using a generic boxed error type and update workspace dependencies accordingly.

src/obikphylo/Cargo.toml

@@ -18,7 +18,8 @@ rayon            = "1"
 tracing          = "0.1.44"
 
 [dev-dependencies]
-obiread     = { path = "../obiread" }
-obikindexer = { path = "../obikindexer" }
+obiread       = { path = "../obiread" }
+obikindexer   = { path = "../obikindexer" }
+obikalgorithm = { path = "../obikalgorithm" }
 tempfile = "3"
 tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }

src/obikphylo/src/siblings/tests.rs

@@ -6,6 +6,7 @@ use obikindex::layer::MphfLayer;
 use obisys::Reporter;
 use tempfile::tempdir;
 
+use obikalgorithm::Algorithm;
 use obikindexer::algorithms::counter::Counter;
 use obikindexer::algorithms::dereplicator::Dereplicator;
 use obikindexer::algorithms::layer_builder::LayerBuilder;
@@ -68,11 +69,11 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
         evidence: obikindex::layer::IndexMode::Exact,
         block_bits: 0,
     };
-    let mut idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)))
+    let idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)))
         .expect("create");
 
     let stream = obiread::open_nuc_stream(fasta_path.to_str().unwrap(), K).expect("open fasta");
-    let mut router = PartitionRouter::new(&mut idx);
+    let mut router = PartitionRouter::new(&idx);
     for page in stream {
         let batch = obiskbuilder::build_superkmers_page(page, K, /* level_max */ 1, /* theta */ 0.0);
         router.write_batch(batch).expect("write_batch");
@@ -80,10 +81,10 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
     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");
-    Counter::new(&idx).run(None::<fn(obisys::Progress)>).expect("count_kmer"); // also writes the spectrum + marks counted
+    Dereplicator::new(&idx).run().expect("dereplicate");
+    Counter::new(&idx).run().expect("count_kmer"); // also writes the spectrum + marks counted
     LayerBuilder::new(&idx)
-        .run(None::<fn(obisys::Progress)>)
+        .run()
         .expect("build_layers"); // also marks indexed
     idx
 }