feat: Add progress tracking and timing instrumentation to index

Introduces comprehensive progress tracking and timing instrumentation using indicatif and obisys::Reporter/Stage. Adds an EMA-based throughput calculator for the scatter phase and wraps parallel progress bars in Arc<Mutex> for thread-safe concurrent updates across all pipeline stages.

src/obikmer/src/cmd/index.rs

@@ -1,10 +1,13 @@
 use std::fs;
 use std::path::PathBuf;
 use std::sync::atomic::{AtomicUsize, Ordering};
+use std::sync::{Arc, Mutex};
+use std::time::{Duration, Instant};
 
 use cacheline_ef::{CachelineEf, CachelineEfVec};
 use clap::Args;
 use epserde::prelude::*;
+use indicatif::{ProgressBar, ProgressStyle};
 use obicompactvec::PersistentCompactIntMatrix;
 use obicompactvec::PersistentCompactIntVec;
 use obidebruinj::GraphDeBruijn;
@@ -12,6 +15,7 @@ use obikpartitionner::KmerPartition;
 use obikseq::{RoutableSuperKmer, set_k, set_m};
 use obiskio::SKFileReader;
 use obilayeredmap::layer::Layer;
+use obisys::{Reporter, Stage};
 use ptr_hash::{PtrHash, bucket_fn::CubicEps, hash::Xx64};
 use rayon::prelude::*;
 use tracing::info;
@@ -49,6 +53,8 @@ pub fn run(args: IndexArgs) {
 
     // ── Stage 1: scatter (skipped if partition already exists) ───────────────
     let partition_meta = output.join("partition.meta");
+    let mut rep = Reporter::new();
+
     let kp = if partition_meta.exists() {
         info!("resuming from existing partition at {}", output.display());
         let kp = KmerPartition::open(&output).unwrap_or_else(|e| {
@@ -76,7 +82,7 @@ pub fn run(args: IndexArgs) {
 
         let path_source = args.common.seqfile_paths();
 
-        info!("scattering...");
+        let t = Stage::start("scatter");
         let pipe = obipipeline::make_pipe! {
             PipelineData : PathBuf => Vec<RoutableSuperKmer>,
             ||? { |path| open_chunks(path) }                                               : Path     => RawChunk,
@@ -84,35 +90,78 @@ pub fn run(args: IndexArgs) {
             |   { move |rope| obiskbuilder::build_superkmers(rope, k, level_max, theta) }: NormChunk => Batch,
         };
 
+        let pb = ProgressBar::new_spinner();
+        pb.set_style(
+            ProgressStyle::with_template("{spinner} scatter — {msg}  {elapsed}")
+                .unwrap()
+                .tick_strings(&["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"]),
+        );
+        pb.enable_steady_tick(Duration::from_millis(100));
+
+        let mut total_bases: u64 = 0;
+        let mut ema_rate: f64 = 0.0;
+        let mut last_t = Instant::now();
+        let mut last_bases: u64 = 0;
+        const ALPHA: f64 = 0.15;
+
         for batch in pipe.apply(path_source, n_workers, 1) {
+            total_bases += batch.iter().map(|sk| sk.seql() as u64).sum::<u64>();
+            let now = Instant::now();
+            let dt = now.duration_since(last_t).as_secs_f64();
+            if dt > 0.1 {
+                let instant = (total_bases - last_bases) as f64 / dt;
+                ema_rate = ALPHA * instant + (1.0 - ALPHA) * ema_rate;
+                last_t = now;
+                last_bases = total_bases;
+                let bp = total_bases as f64;
+                let (count_str, rate_str) = if bp >= 1e9 {
+                    (format!("{:.2} Gbp", bp / 1e9), format!("{:.0} Mbp/s", ema_rate / 1e6))
+                } else {
+                    (format!("{:.0} Mbp", bp / 1e6), format!("{:.0} Mbp/s", ema_rate / 1e6))
+                };
+                pb.set_message(format!("{count_str}  {rate_str}"));
+            }
             kp.write_batch(batch).unwrap_or_else(|e| {
                 eprintln!("error: {e}");
                 std::process::exit(1);
             });
         }
+        pb.finish_and_clear();
         kp.close().expect("close error");
+        rep.push(t.stop());
         kp
     };
 
-    let k = kp.kmer_size();
     let n = kp.n_partitions();
 
     // ── Stage 2: dereplicate + count (skipped if already done) ───────────────
     let counting_done = output.join("kmer_spectrum_raw.json").exists();
     if !counting_done {
         info!("dereplicating...");
+        let t = Stage::start("dereplicate");
         kp.dereplicate().expect("dereplicate error");
+        rep.push(t.stop());
+
+        let t = Stage::start("count_kmer");
         info!("counting kmers...");
         kp.count_kmer().expect("count kmer error");
+        rep.push(t.stop());
     } else {
         info!("kmer counts already present, skipping dereplicate + count");
     }
 
     // ── Stage 3: build layered index per partition ────────────────────────────
-    info!("building index ({n} partitions, k={k})...");
+    let t = Stage::start("index");
     let total_kmers = AtomicUsize::new(0);
     let filter_active = min_ab > 1 || max_ab.is_some();
 
+    let pb = ProgressBar::new(n as u64);
+    pb.set_style(ProgressStyle::with_template(
+        "index — [{bar:20}] {pos}/{len} | {msg}",
+    ).unwrap());
+
+    let pb = Arc::new(Mutex::new(pb));
+
     (0..n).into_par_iter().for_each(|i| {
         let part_dir = output.join(format!("part_{i:05}"));
         let dedup_path = part_dir.join("dereplicated.skmer.zst");
@@ -206,11 +255,12 @@ pub fn run(args: IndexArgs) {
             std::process::exit(1);
         });
 
-        info!("partition {i}: {n_kmers} kmers indexed");
+        let pb = pb.lock().unwrap();
+        pb.inc(1);
+        pb.set_message(format!("{i}: {n_kmers} kmers"));
     });
 
-    info!(
+    pb.lock().unwrap().finish_and_clear();
-        "done — {} total kmers indexed across all partitions",
+    rep.push(t.stop());
-        total_kmers.load(Ordering::Relaxed)
+    rep.print();
-    );
 }