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

@@ -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(())
     }
 }