Merge pull request 'Push rrwpnquuzsvr' (#15) from push-rrwpnquuzsvr into main

Reviewed-on: #15

src/Cargo.lock

@@ -1561,6 +1561,7 @@ dependencies = [
  "obiread",
  "obiskbuilder",
  "obiskio",
+ "obisys",
  "ptr_hash",
  "rayon",
  "remove_dir_all",
@@ -1659,6 +1660,7 @@ dependencies = [
 name = "obisys"
 version = "0.1.0"
 dependencies = [
+ "indicatif",
  "libc",
  "sysinfo",
 ]

src/obicompactvec/src/bitmatrix.rs

@@ -190,6 +190,10 @@ pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
     file.write_all(&(n_cols as u64).to_le_bytes())?;
     for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
     for data in &col_files { file.write_all(data)?; }
+    drop(file);
+
+    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
+    fs::remove_file(dir.join("meta.json"))?;
     Ok(())
 }
 

src/obicompactvec/src/intmatrix.rs

@@ -293,6 +293,10 @@ pub fn pack_compact_int_matrix(dir: &Path) -> io::Result<()> {
     file.write_all(&(n_cols as u64).to_le_bytes())?;
     for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
     for data in &col_files { file.write_all(data)?; }
+    drop(file);
+
+    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
+    fs::remove_file(dir.join("meta.json"))?;
     Ok(())
 }
 

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(
+        let pb = Arc::new(Mutex::new(progress_bar("index", n as u64, "partitions")));
-            ProgressBar::new(n as u64).with_style(
-                ProgressStyle::with_template("index — [{bar:20}] {pos}/{len} | {msg}").unwrap(),
-            ),
-        ));
 
         (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 obisys::{Reporter, Stage, progress_bar, spinner};
-
-use indicatif::{ProgressBar, ProgressStyle};
-use obisys::{Reporter, Stage};
 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(
+        let pb = progress_bar("rebuild", n_partitions as u64, "partitions");
-            ProgressStyle::with_template("rebuild — [{bar:20}] {pos}/{len} | {msg}")
-                .unwrap()
-                .progress_chars("=> "),
-        );
-        pb.enable_steady_tick(Duration::from_millis(100));
 
         let src_partition = &src.partition;
         let block_bits = meta.config.block_bits;
@@ -112,6 +105,8 @@ impl KmerIndex {
         // Write SENTINEL_INDEXED — output is ready to use.
         fs::File::create(output.join(SENTINEL_INDEXED))?;
 
-        KmerIndex::open(output)
+        let idx = KmerIndex::open(output)?;
+        idx.pack_matrices()?;
+        Ok(idx)
     }
 }

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(
+        let pb = progress_bar("reindex", n as u64, "partitions");
-            ProgressStyle::with_template(
-                "reindex — [{bar:20}] {pos}/{len} | {msg}",
-            )
-            .unwrap()
-            .tick_strings(&["⠋","⠙","⠹","⠸","⠼","⠴","⠦","⠧","⠇","⠏"]),
-        );
-        pb.enable_steady_tick(Duration::from_millis(80));
 
         let errors: Vec<String> = (0..n)
             .into_par_iter()

src/obikmer/src/steps/scatter.rs

@@ -1,9 +1,9 @@
 use std::path::PathBuf;
 use std::sync::atomic::{AtomicU32, AtomicU64, Ordering};
 use std::sync::Arc;
-use std::time::{Duration, Instant};
+use std::time::Instant;
 
-use indicatif::{ProgressBar, ProgressStyle};
+use obisys::spinner;
 use obiread::NucPage;
 use obikpartitionner::KmerPartition;
 use obisys::{Reporter, Stage};
@@ -83,13 +83,7 @@ pub fn scatter(
         } : NucPage => Batch,
     };
 
-    let pb = ProgressBar::new_spinner();
+    let pb = spinner("scatter");
-    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;

src/obikpartitionner/Cargo.toml

@@ -28,3 +28,4 @@ memmap2 = "0.9.10"
 obicompactvec = { path = "../obicompactvec" }
 ptr_hash = "1.1"
 indicatif = "0.17"
+obisys    = { path = "../obisys" }

src/obikpartitionner/src/partition.rs

@@ -5,7 +5,7 @@ use std::path::{Path, PathBuf};
 use std::time::Instant;
 use tracing::debug;
 
-use indicatif::{ProgressBar, ProgressStyle};
+use obisys::progress_bar;
 
 use cacheline_ef::{CachelineEf, CachelineEfVec};
 use epserde::ser::Serialize as EpSerialize;
@@ -219,14 +219,7 @@ impl KmerPartition {
         let n_threads = rayon::current_num_threads().max(1) as u64;
         let available_per_thread = available / n_threads;
 
-        let pb = ProgressBar::new(self.n_partitions as u64);
+        let pb = progress_bar("dereplication", self.n_partitions as u64, "partitions");
-        pb.set_style(
-            ProgressStyle::with_template(
-                "dereplicating [{bar:40}] {pos}/{len} ({percent}%)  {per_sec}  eta {eta}  {msg}",
-            )
-            .unwrap()
-            .progress_chars("█▌░"),
-        );
 
         let results: Vec<SKResult<()>> = (0..self.n_partitions)
             .into_par_iter()
@@ -274,14 +267,7 @@ impl KmerPartition {
         let n_threads = rayon::current_num_threads().max(1) as u64;
         let chunk_kmers = chunk_size_from_ram(available / n_threads);
 
-        let pb = ProgressBar::new(self.n_partitions as u64);
+        let pb = progress_bar("counting", self.n_partitions as u64, "partitions");
-        pb.set_style(
-            ProgressStyle::with_template(
-                "counting [{bar:40}] {pos}/{len} ({percent}%)  {per_sec}  eta {eta}  {msg}",
-            )
-            .unwrap()
-            .progress_chars("█▌░"),
-        );
 
         let results: Vec<SKResult<()>> = (0..self.n_partitions)
             .into_par_iter()

src/obisys/Cargo.toml

@@ -6,3 +6,4 @@ edition = "2024"
 [dependencies]
 libc      = "0.2"
 sysinfo   = "0.33"
+indicatif = "0.17"

src/obisys/src/lib.rs

@@ -1,5 +1,37 @@
 use std::fmt;
-use std::time::Instant;
+use std::time::{Duration, Instant};
+
+use indicatif::{ProgressBar, ProgressStyle};
+
+const BRAILLE: &[&str] = &["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"];
+
+/// Spinner with the standard project look: `⠋ label — msg  0s`.
+/// Caller updates the message with `pb.set_message(...)`.
+pub fn spinner(label: &str) -> ProgressBar {
+    let pb = ProgressBar::new_spinner();
+    pb.set_style(
+        ProgressStyle::with_template(&format!("{{spinner}} {label} — {{msg}}  {{elapsed}}"))
+            .unwrap()
+            .tick_strings(BRAILLE),
+    );
+    pb.enable_steady_tick(Duration::from_millis(100));
+    pb
+}
+
+/// Progress bar with the standard project look:
+/// `⠋ label — [████░░░░] pos/len unit  elapsed`.
+pub fn progress_bar(label: &str, n: u64, unit: &str) -> ProgressBar {
+    let pb = ProgressBar::new(n);
+    pb.set_style(
+        ProgressStyle::with_template(&format!(
+            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}}"
+        ))
+        .unwrap()
+        .tick_strings(BRAILLE),
+    );
+    pb.enable_steady_tick(Duration::from_millis(100));
+    pb
+}
 
 use libc::{RUSAGE_SELF, getrusage, rusage, timeval};
 use sysinfo::System;