refactor: centralize index setup logic and add progress bar ETA

Extracts directory cleanup, partition initialization, and finalization into dedicated helper methods within KmerIndex. This centralizes force-flag handling and reduces boilerplate across merge, rebuild, and select workflows. Additionally updates the CLI progress bar template to display an ETA indicator following elapsed time.

src/obikindex/src/index.rs

@@ -2,7 +2,7 @@ use std::collections::BTreeMap;
 use std::fs;
 use std::path::{Path, PathBuf};
 
-use obikpartitionner::{KmerPartition, KmerSpectrum};
+use obikpartitionner::{KmerPartition, KmerSpectrum, PARTITIONS_SUBDIR};
 use obilayeredmap;
 use obisys::{Reporter, Stage, progress_bar};
 use rayon::prelude::*;
@@ -68,6 +68,65 @@ impl KmerIndex {
         IndexMeta::exists(path.as_ref())
     }
 
+    /// Make `output` ready to receive a newly created index.
+    ///
+    /// If an index already exists there, remove it when `force` is set,
+    /// otherwise fail. A bare directory with no `index.meta` (e.g. one left
+    /// behind by a `DirLock`) is not considered a pre-existing index.
+    pub fn clear_output_for_create<P: AsRef<Path>>(output: P, force: bool) -> OKIResult<()> {
+        let output = output.as_ref();
+        if Self::exists(output) {
+            if force {
+                fs::remove_dir_all(output).map_err(OKIError::Io)?;
+            } else {
+                return Err(OKIError::Io(std::io::Error::new(
+                    std::io::ErrorKind::AlreadyExists,
+                    format!("{}: output directory already exists", output.display()),
+                )));
+            }
+        }
+        Ok(())
+    }
+
+    /// Lay out a fresh index skeleton at `output`: the root directory,
+    /// `index.meta` (from `meta`), and an opened, empty partition set.
+    ///
+    /// For construction paths that build partitions from scratch (`select`,
+    /// `rebuild`). `merge` bootstraps by copying a source index instead, so
+    /// it does not use this.
+    pub(crate) fn create_skeleton<P: AsRef<Path>>(
+        output: P,
+        meta: &IndexMeta,
+    ) -> OKIResult<KmerPartition> {
+        let output = output.as_ref();
+        fs::create_dir_all(output).map_err(OKIError::Io)?;
+        meta.write(output).map_err(OKIError::Io)?;
+        fs::create_dir_all(output.join(PARTITIONS_SUBDIR)).map_err(OKIError::Io)?;
+        Ok(KmerPartition::open_with_config(
+            output,
+            meta.config.kmer_size,
+            meta.config.minimizer_size,
+            meta.config.n_bits,
+        )?)
+    }
+
+    /// Mark `output` as fully indexed, pack its column matrices, and reopen it.
+    ///
+    /// Shared tail of the `select`/`rebuild` construction paths, once their
+    /// partitions have been written.
+    pub(crate) fn finalize_indexed<P: AsRef<Path>>(
+        output: P,
+        rep: &mut Reporter,
+    ) -> OKIResult<Self> {
+        let output = output.as_ref();
+        fs::File::create(output.join(SENTINEL_INDEXED)).map_err(OKIError::Io)?;
+        let idx = KmerIndex::open(output)?;
+        let t_pack = Stage::start("pack");
+        idx.pack_matrices()?;
+        rep.push(t_pack.stop());
+        Ok(idx)
+    }
+
     /// Current construction state, as reported by sentinel files on disk.
     pub fn state(&self) -> IndexState {
         IndexState::detect(&self.root_path).unwrap_or(IndexState::Empty)

src/obikindex/src/merge.rs

@@ -130,16 +130,7 @@ impl KmerIndex {
         let (source_labels, all_genomes) = compute_labels(sources, rename_duplicates)?;
 
         // ── Prepare output directory ──────────────────────────────────────────
-        if output.exists() {
+        KmerIndex::clear_output_for_create(output, force)?;
-            if force {
-                fs::remove_dir_all(output)?;
-            } else {
-                return Err(OKIError::Io(io::Error::new(
-                    io::ErrorKind::AlreadyExists,
-                    format!("{}: output directory already exists", output.display()),
-                )));
-            }
-        }
 
         // ── Bootstrap: copy first source to output ────────────────────────────
         info!(

src/obikindex/src/rebuild.rs

@@ -1,15 +1,13 @@
-use std::fs;
-use std::io;
 use std::path::Path;
 
-use obikpartitionner::{KmerFilter, KmerPartition, MergeMode};
+use obikpartitionner::{KmerFilter, MergeMode};
 use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 use crate::meta::IndexMeta;
-use crate::state::{IndexState, SENTINEL_INDEXED};
+use crate::state::IndexState;
 
 impl KmerIndex {
     /// Rebuild `src` into a new compact single-layer index at `output`.
@@ -40,36 +38,18 @@ impl KmerIndex {
             ));
         }
 
-        if output.exists() {
+        KmerIndex::clear_output_for_create(output, force)?;
-            if force {
-                fs::remove_dir_all(output)?;
-            } else {
-                return Err(OKIError::Io(io::Error::new(
-                    io::ErrorKind::AlreadyExists,
-                    format!("{}: output directory already exists", output.display()),
-                )));
-            }
-        }
 
         // ── Create output directory + metadata ────────────────────────────────
-        fs::create_dir_all(output)?;
         let mut meta = IndexMeta::new(src.meta.config.clone());
         meta.config.with_counts = mode == MergeMode::Count;
         meta.genomes = src.meta.genomes.clone();
-        meta.write(output)?;
 
         let n_genomes = src.meta.genomes.len();
         let n_partitions = src.partition.n_partitions();
 
         // ── Create an empty destination KmerPartition ─────────────────────────
-        // Create the partitions/ subdirectory so KmerPartition::open_with_config works.
+        let dst_partition = KmerIndex::create_skeleton(output, &meta)?;
-        fs::create_dir_all(output.join(obikpartitionner::PARTITIONS_SUBDIR))?;
-        let dst_partition = KmerPartition::open_with_config(
-            output,
-            meta.config.kmer_size,
-            meta.config.minimizer_size,
-            meta.config.n_bits,
-        )?;
 
         info!(
             "rebuild: {} partition(s), {} genome(s), mode={:?}",
@@ -94,13 +74,6 @@ impl KmerIndex {
 
         rep.push(t.stop());
 
-        // Write SENTINEL_INDEXED — output is ready to use.
+        KmerIndex::finalize_indexed(output, rep)
-        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)
     }
 }

src/obikindex/src/select.rs

@@ -1,15 +1,13 @@
-use std::fs;
-use std::io;
 use std::path::Path;
 
-use obikpartitionner::{KmerPartition, OutputCol, PARTITIONS_SUBDIR};
+use obikpartitionner::{KmerPartition, OutputCol};
 use obisys::{Reporter, Stage, progress_bar};
 use tracing::info;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 use crate::meta::{GenomeInfo, IndexMeta};
-use crate::state::{IndexState, SENTINEL_INDEXED};
+use crate::state::IndexState;
 
 impl KmerIndex {
     /// Create a new index at `output` by projecting/aggregating the genome columns
@@ -33,35 +31,18 @@ impl KmerIndex {
             return Err(OKIError::NotIndexed(src.root_path.clone()));
         }
 
-        if output.exists() {
+        KmerIndex::clear_output_for_create(output, force)?;
-            if force {
-                fs::remove_dir_all(output)?;
-            } else {
-                return Err(OKIError::Io(io::Error::new(
-                    io::ErrorKind::AlreadyExists,
-                    format!("{}: output directory already exists", output.display()),
-                )));
-            }
-        }
 
-        fs::create_dir_all(output)?;
         let mut meta = IndexMeta::new(src.meta.config.clone());
         meta.config.with_counts = !output_presence;
         meta.genomes = specs.iter()
             .map(|s| GenomeInfo::new(s.label.clone()))
             .collect();
-        meta.write(output)?;
 
         let n_src_genomes  = src.meta.genomes.len();
         let n_partitions   = src.partition.n_partitions();
 
-        fs::create_dir_all(output.join(PARTITIONS_SUBDIR))?;
+        let dst_partition = KmerIndex::create_skeleton(output, &meta)?;
-        let dst_partition = KmerPartition::open_with_config(
-            output,
-            meta.config.kmer_size,
-            meta.config.minimizer_size,
-            meta.config.n_bits,
-        )?;
 
         info!(
             "select: {} partition(s), {} source genome(s) → {} output column(s)",
@@ -83,13 +64,7 @@ impl KmerIndex {
         pb.finish_and_clear();
         rep.push(t.stop());
 
-        fs::File::create(output.join(SENTINEL_INDEXED))?;
+        KmerIndex::finalize_indexed(output, rep)
-
-        let idx = KmerIndex::open(output)?;
-        let t_pack = Stage::start("pack");
-        idx.pack_matrices()?;
-        rep.push(t_pack.stop());
-        Ok(idx)
     }
 
     /// Rewrite the genome columns of this index in-place according to `specs`.

src/obisys/src/progress.rs

@@ -91,12 +91,12 @@ pub fn spinner(label: &str) -> TracedBar {
 }
 
 /// Progress bar with the standard project look:
-/// `⠋ label — [████░░░░] pos/len unit  elapsed`.
+/// `⠋ label — [████░░░░] pos/len unit  elapsed (eta: remaining)`.
 pub fn progress_bar(label: &str, n: u64, unit: &str) -> TracedBar {
     let pb = ProgressBar::new(n);
     pb.set_style(
         ProgressStyle::with_template(&format!(
-            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}}"
+            "{{spinner}} {label} — {{bar:40.cyan/blue}} {{pos}}/{{len}} {unit}  {{elapsed}} (eta: {{eta}})"
         ))
         .unwrap()
         .tick_strings(BRAILLE),