feat: add obisys crate for standardized CLI progress reporting

This commit introduces the `obisys` crate, which wraps `indicatif` to provide reusable `spinner` and `progress_bar` utilities with consistent styling and tick intervals. It refactors progress reporting across `obikindex`, `obikpartitionner`, and `obikmer` to use these shared functions, eliminating inline UI configuration and ensuring uniform terminal feedback.

src/obikindex/src/index.rs

@@ -4,10 +4,9 @@ use std::path::{Path, PathBuf};
 use std::sync::atomic::{AtomicUsize, Ordering};
 use std::sync::{Arc, Mutex};
 
-use indicatif::{ProgressBar, ProgressStyle};
 use obikpartitionner::{KmerPartition, KmerSpectrum};
 use obilayeredmap;
-use obisys::{Reporter, Stage};
+use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
 use tracing::info;
 
@@ -155,11 +154,7 @@ impl KmerIndex {
         let block_bits = self.meta.config.block_bits;
         let total_kmers = AtomicUsize::new(0);
 
-        let pb = Arc::new(Mutex::new(
-            ProgressBar::new(n as u64).with_style(
-                ProgressStyle::with_template("index — [{bar:20}] {pos}/{len} | {msg}").unwrap(),
-            ),
-        ));
+        let pb = Arc::new(Mutex::new(progress_bar("index", n as u64, "partitions")));
 
         (0..n).into_par_iter().for_each(|i| {
             match self.partition.build_index_layer(i, min_ab, max_ab, with_counts, &evidence, block_bits) {

src/obikindex/src/merge.rs

@@ -2,10 +2,7 @@ use std::collections::HashMap;
 use std::fs;
 use std::io;
 use std::path::Path;
-use std::time::Duration;
-
-use indicatif::{ProgressBar, ProgressStyle};
-use obisys::{Reporter, Stage};
+use obisys::{Reporter, Stage, progress_bar, spinner};
 use rayon::prelude::*;
 use tracing::info;
 
@@ -124,7 +121,8 @@ impl KmerIndex {
             sources[0].meta.genomes.len(),
         );
         let t = Stage::start("bootstrap");
-        let pb = spinner("bootstrap — copying index …");
+        let pb = spinner("bootstrap");
+        pb.set_message("copying index …");
         copy_dir_all(&sources[0].root_path, output)?;
 
         // Rewrite index.meta with final genome labels and the effective mode.
@@ -146,7 +144,8 @@ impl KmerIndex {
         // Drop the spectrums/ that were copied from source_0 and rebuild from scratch.
         info!("rebuilding spectrums for {} source(s)", sources.len());
         let t = Stage::start("spectrums");
-        let pb = spinner("spectrums — copying …");
+        let pb = spinner("spectrums");
+        pb.set_message("copying …");
         let spectrums_dir = output.join("spectrums");
         if spectrums_dir.exists() {
             fs::remove_dir_all(&spectrums_dir)?;
@@ -172,7 +171,7 @@ impl KmerIndex {
                 n_partitions, n_src_genomes, n_dst_genomes,
             );
             let t = Stage::start("merge_partitions");
-            let pb = partition_bar(n_partitions as u64);
+            let pb = progress_bar("merge", n_partitions as u64, "partitions");
 
             let dst_partition = &dst.partition;
             let block_bits = dst.meta.config.block_bits;
@@ -199,7 +198,8 @@ impl KmerIndex {
         // ── Pack matrices after merge ─────────────────────────────────────────
         {
             let t = Stage::start("pack");
-            let pb = spinner("pack — consolidating column files …");
+            let pb = spinner("pack");
+            pb.set_message("consolidating column files …");
             let dst2 = KmerIndex::open(output)?;
             dst2.pack_matrices()?;
             pb.finish_and_clear();
@@ -285,30 +285,6 @@ fn remove_dirs_named(root: &Path, name: &str) -> io::Result<()> {
     Ok(())
 }
 
-fn spinner(msg: &'static str) -> ProgressBar {
-    let pb = ProgressBar::new_spinner();
-    pb.set_style(
-        ProgressStyle::with_template("{spinner} {msg}  {elapsed}")
-            .unwrap()
-            .tick_strings(&["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"]),
-    );
-    pb.set_message(msg);
-    pb.enable_steady_tick(Duration::from_millis(100));
-    pb
-}
-
-fn partition_bar(n: u64) -> ProgressBar {
-    let pb = ProgressBar::new(n);
-    pb.set_style(
-        ProgressStyle::with_template(
-            "{spinner} merge — {bar:40.cyan/blue} {pos}/{len} partitions  {elapsed}",
-        )
-        .unwrap()
-        .tick_strings(&["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"]),
-    );
-    pb.enable_steady_tick(Duration::from_millis(100));
-    pb
-}
 
 fn format_evidence(ev: &IndexMode) -> String {
     match ev {

src/obikindex/src/rebuild.rs

@@ -1,11 +1,9 @@
 use std::fs;
 use std::io;
 use std::path::Path;
-use std::time::Duration;
 
-use indicatif::{ProgressBar, ProgressStyle};
 use obikpartitionner::{KmerFilter, KmerPartition, MergeMode};
-use obisys::{Reporter, Stage};
+use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
 use tracing::info;
 
@@ -80,12 +78,7 @@ impl KmerIndex {
         );
 
         let t = Stage::start("rebuild");
-        let pb = ProgressBar::new(n_partitions as u64).with_style(
-            ProgressStyle::with_template("rebuild — [{bar:20}] {pos}/{len} | {msg}")
-                .unwrap()
-                .progress_chars("=> "),
-        );
-        pb.enable_steady_tick(Duration::from_millis(100));
+        let pb = progress_bar("rebuild", n_partitions as u64, "partitions");
 
         let src_partition = &src.partition;
         let block_bits = meta.config.block_bits;

src/obikindex/src/reindex.rs

@@ -1,11 +1,8 @@
 use std::fs;
 use std::path::Path;
-use std::time::Duration;
-
-use indicatif::{ProgressBar, ProgressStyle};
 use obilayeredmap::{IndexMode, layer::Layer};
 use obilayeredmap::meta::PartitionMeta;
-use obisys::{Reporter, Stage};
+use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
 use tracing::info;
 
@@ -46,14 +43,7 @@ impl KmerIndex {
         );
 
         let t = Stage::start("reindex");
-        let pb = ProgressBar::new(n as u64).with_style(
-            ProgressStyle::with_template(
-                "reindex — [{bar:20}] {pos}/{len} | {msg}",
-            )
-            .unwrap()
-            .tick_strings(&["⠋","⠙","⠹","⠸","⠼","⠴","⠦","⠧","⠇","⠏"]),
-        );
-        pb.enable_steady_tick(Duration::from_millis(80));
+        let pb = progress_bar("reindex", n as u64, "partitions");
 
         let errors: Vec<String> = (0..n)
             .into_par_iter()