feat(obikmer): add obisys profiling to partition pipeline

Added obisys as a local dependency and integrated its Reporter and Stage instrumentation into the partition command. Each major phase (scatter, dereplicate, and kmer-counting) is now wrapped in timing blocks, with aggregated execution times printed to stdout upon completion.

src/Cargo.lock

@@ -1734,6 +1734,7 @@ dependencies = [
  "obiread",
  "obiskbuilder",
  "obiskio",
+ "obisys",
  "ph",
  "pprof",
  "rayon",

src/obikmer/Cargo.toml

@@ -17,6 +17,7 @@ obidebruinj  = { path = "../obidebruinj" }
 clap         = { version = "4", features = ["derive"] }
 obikrope          = { path = "../obikrope" }
 obikpartitionner  = { path = "../obikpartitionner" }
+obisys            = { path = "../obisys" }
 obiskio           = { path = "../obiskio" }
 niffler      = "3"
 rayon        = "1"

src/obikmer/src/cmd/partition.rs

@@ -2,6 +2,7 @@ use std::path::PathBuf;
 
 use clap::Args;
 use obikpartitionner::KmerPartition;
+use obisys::{Reporter, Stage};
 use obikseq::{RoutableSuperKmer, set_k, set_m};
 use tracing::info;
 
@@ -39,14 +40,15 @@ pub fn run(args: PartitionArgs) {
         });
 
     let path_source = args.common.seqfile_paths();
+    let mut rep = Reporter::new();
 
+    let t = Stage::start("scatter");
     let pipe = obipipeline::make_pipe! {
         PipelineData : PathBuf => Vec<RoutableSuperKmer>,
         ||? { |path| open_chunks(path) }                                               : Path     => RawChunk,
         |?  { move |rope| obiread::normalize_sequence_chunk(rope, k) }                : RawChunk => NormChunk,
         |   { move |rope| obiskbuilder::build_superkmers(rope, k, level_max, theta) }: NormChunk => Batch,
     };
-
     for batch in pipe.apply(path_source, n_workers, 1) {
         kp.write_batch(batch).unwrap_or_else(|e| {
             eprintln!("error: {e}");
@@ -54,8 +56,16 @@ pub fn run(args: PartitionArgs) {
         });
     }
     kp.close().expect("close error");
+    rep.push(t.stop());
 
     info!("dereplicating...");
+    let t = Stage::start("dereplicate");
     kp.dereplicate().expect("dereplicate error");
+    rep.push(t.stop());
+
+    let t = Stage::start("count_kmer");
     kp.count_kmer().expect("count kmer error");
+    rep.push(t.stop());
+
+    rep.print();
 }