From c1d6f277ced705b30b8d624325ef86ff8ca9a5d3 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 21 Jun 2026 19:07:15 +0200
Subject: [PATCH] feat(select): add metrics reporting to selection methods

Integrates an obisys::Reporter across indexing and command modules to capture execution metrics. Replaces discarded timer stops with explicit rep.push() calls, adds timing instrumentation for the pack stage, and prints collected reports after each selection branch.
---
 src/obikindex/src/select.rs   | 16 +++++++++-------
 src/obikmer/src/cmd/select.rs |  9 +++++++--
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/src/obikindex/src/select.rs b/src/obikindex/src/select.rs
index 1db57bd..a27125b 100644
--- a/src/obikindex/src/select.rs
+++ b/src/obikindex/src/select.rs
@@ -3,7 +3,7 @@ use std::io;
 use std::path::Path;
 
 use obikpartitionner::{KmerPartition, OutputCol, PARTITIONS_SUBDIR};
-use obisys::{Stage, progress_bar};
+use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
 
 use crate::error::{OKIError, OKIResult};
@@ -25,6 +25,7 @@ impl KmerIndex {
         threshold: u32,
         output_presence: bool,
         force: bool,
+        rep: &mut Reporter,
     ) -> OKIResult<Self> {
         let output = output.as_ref();
 
@@ -80,13 +81,14 @@ impl KmerIndex {
         ).map_err(OKIError::Partition)?;
 
         pb.finish_and_clear();
-
-        let _ = t.stop();
+        rep.push(t.stop());
 
         fs::File::create(output.join(SENTINEL_INDEXED))?;
 
         let idx = KmerIndex::open(output)?;
+        let t_pack = Stage::start("pack");
         idx.pack_matrices()?;
+        rep.push(t_pack.stop());
         Ok(idx)
     }
 
@@ -98,6 +100,7 @@ impl KmerIndex {
         specs: &[OutputCol],
         threshold: u32,
         output_presence: bool,
+        rep: &mut Reporter,
     ) -> OKIResult<()> {
         if self.state() != IndexState::Indexed {
             return Err(OKIError::NotIndexed(self.root_path.clone()));
@@ -106,7 +109,6 @@ impl KmerIndex {
         let n_src_genomes = self.meta.genomes.len();
         let n_partitions  = self.partition.n_partitions();
 
-        // Open a second handle to the same path so we can borrow src and dst simultaneously.
         let src_partition = KmerPartition::open_with_config(
             &self.root_path,
             self.meta.config.kmer_size,
@@ -132,17 +134,17 @@ impl KmerIndex {
         ).map_err(OKIError::Partition)?;
 
         pb.finish_and_clear();
+        rep.push(t.stop());
 
-        let _ = t.stop();
-
-        // Update index.meta with new genome list and with_counts flag.
         self.meta.config.with_counts = !output_presence;
         self.meta.genomes = specs.iter()
             .map(|s| GenomeInfo::new(s.label.clone()))
             .collect();
         self.meta.write(&self.root_path)?;
 
+        let t_pack = Stage::start("pack");
         self.pack_matrices()?;
+        rep.push(t_pack.stop());
         Ok(())
     }
 }
diff --git a/src/obikmer/src/cmd/select.rs b/src/obikmer/src/cmd/select.rs
index e021b36..35719e8 100644
--- a/src/obikmer/src/cmd/select.rs
+++ b/src/obikmer/src/cmd/select.rs
@@ -4,6 +4,7 @@ use std::path::PathBuf;
 use clap::{Args, ValueEnum};
 use obikindex::{GenomeInfo, KmerIndex};
 use obikpartitionner::{AggOp, OutputCol};
+use obisys::Reporter;
 use tracing::info;
 
 use super::predicate::matching_genome_indices;
@@ -229,20 +230,24 @@ pub fn run(args: SelectArgs) {
         if output_presence { "presence" } else { "count" },
     );
 
+    let mut rep = Reporter::new();
+
     if args.in_place {
-        src.select_in_place(&specs, args.presence_threshold, output_presence)
+        src.select_in_place(&specs, args.presence_threshold, output_presence, &mut rep)
             .unwrap_or_else(|e| {
                 eprintln!("select error: {e}");
                 std::process::exit(1);
             });
+        rep.print();
         info!("selected in-place → {}", args.source.display());
     } else {
         let output = args.output.unwrap();
-        KmerIndex::select(&output, &src, &specs, args.presence_threshold, output_presence, args.force)
+        KmerIndex::select(&output, &src, &specs, args.presence_threshold, output_presence, args.force, &mut rep)
             .unwrap_or_else(|e| {
                 eprintln!("select error: {e}");
                 std::process::exit(1);
             });
+        rep.print();
         info!("selected index → {}", output.display());
     }
 }