dirty scan speed testing

.gitignore

@@ -38,6 +38,10 @@ test.db
 .env.*
 
 
-# === Other ===
+# === Other Files ===
 repo-context.txt
-saved_config.yaml
+saved_config.yaml
+
+# === Other Dirs ===
+/bench/corpus
+/bench/backups

bench/dirty-vs-full.md

@@ -0,0 +1,4 @@
+| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
+|:---|---:|---:|---:|---:|
+| `full-scan` | 427.0 ± 30.5 | 402.2 | 467.4 | 6.36 ± 0.49 |
+| `dirty-scan` | 67.2 ± 2.1 | 64.7 | 71.6 | 1.00 |

bench/dirty-vs-full.sh

@@ -0,0 +1,91 @@
+#!/usr/bin/env bash
+#
+# bench/dirty-vs-full.sh
+#
+# Compare full-scan vs dirty-scan performance on a large corpus,
+# simulating a random set of file modifications before each dirty scan,
+# and reporting corpus size, number of dirty files, and speedup.
+#
+
+set -euo pipefail
+IFS=$'\n\t'
+
+# Path to the marlin binary (adjust if you build elsewhere)
+MARLIN_BIN=${MARLIN_BIN:-target/release/marlin}
+
+# Directory containing your test corpus (100k+ files)
+CORPUS_DIR=${CORPUS_DIR:-bench/corpus}
+
+# Where to put the ephemeral DB
+DB_PATH=${DB_PATH:-bench/index.db}
+
+# How many files to mark dirty before each dirty‐scan run
+DIRTY_COUNT=${DIRTY_COUNT:-100}
+
+# Number of warm‐up runs
+WARMUPS=${WARMUPS:-3}
+
+# Tell Marlin where to write its DB
+export MARLIN_DB_PATH="$DB_PATH"
+
+# Ensure hyperfine is installed
+if ! command -v hyperfine &>/dev/null; then
+  echo "Error: hyperfine not found. Please install it and try again." >&2
+  exit 1
+fi
+
+# Ensure our corpus exists
+if [ ! -d "$CORPUS_DIR" ]; then
+  echo "Error: corpus directory '$CORPUS_DIR' not found." >&2
+  exit 1
+fi
+
+# Count corpus size
+CORPUS_SIZE=$(find "$CORPUS_DIR" -type f | wc -l | tr -d ' ')
+echo "→ Corpus size: $CORPUS_SIZE files"
+echo "→ Will mark $DIRTY_COUNT files dirty per dirty‐scan run"
+echo
+
+# Clean up any old database
+rm -f "$DB_PATH"
+
+# First, populate the DB once so that dirty-scan has something to do
+echo "→ Initial full scan to populate DB"
+"$MARLIN_BIN" scan "$CORPUS_DIR" >/dev/null 2>&1
+
+echo
+echo "→ Benchmarking full vs dirty scan with hyperfine"
+hyperfine \
+  --warmup "$WARMUPS" \
+  --prepare "
+    # wipe and re-populate
+    rm -f '$DB_PATH'
+    mkdir -p bench
+    export MARLIN_DB_PATH='$DB_PATH'
+    $MARLIN_BIN scan '$CORPUS_DIR' >/dev/null 2>&1
+
+    # seed $DIRTY_COUNT random files as 'dirty' in the DB
+    sqlite3 '$DB_PATH' \"INSERT OR IGNORE INTO file_changes(file_id, marked_at)
+      SELECT id, strftime('%s','now') FROM files
+      ORDER BY RANDOM()
+      LIMIT $DIRTY_COUNT;\"
+  " \
+  --command-name "full-scan"  "MARLIN_DB_PATH='$DB_PATH' $MARLIN_BIN scan       '$CORPUS_DIR' >/dev/null 2>&1" \
+  --command-name "dirty-scan" "MARLIN_DB_PATH='$DB_PATH' $MARLIN_BIN scan --dirty '$CORPUS_DIR' >/dev/null 2>&1" \
+  --export-markdown bench/dirty-vs-full.md
+
+echo
+echo "Results written to bench/dirty-vs-full.md"
+
+# Extract the speedup factor from the markdown table:
+#   the "Relative" column on the full-scan row tells us how many times
+#   slower full-scan is relative to dirty-scan (baseline = 1.00).
+SPEEDUP=$(grep '\`full-scan\`' bench/dirty-vs-full.md \
+         | awk -F'|' '{print $5}' \
+         | xargs)
+
+echo
+echo "→ Summary:"
+echo "   Corpus size:        $CORPUS_SIZE files"
+echo "   Dirty files seeded: $DIRTY_COUNT"
+echo "   Dirty‐scan speedup: dirty-scan ran $SPEEDUP times faster than full-scan"

bench/gen-corpus.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+#
+# bench/gen-corpus.sh
+#
+# Generate a synthetic corpus of N files in nested directories.
+# Defaults to 1 000 files so it stays laptop-friendly.
+#
+
+set -euo pipefail
+IFS=$'\n\t'
+
+# How many files? (default: 1 000)
+COUNT=${COUNT:-100000}
+# Where to put them
+TARGET=${TARGET:-bench/corpus}
+
+# Wipe any old corpus
+rm -rf "$TARGET"
+mkdir -p "$TARGET"
+
+echo "🚀 Generating $COUNT files under $TARGET…"
+for i in $(seq 1 "$COUNT"); do
+  # bucket into 100 sub-dirs so walkdir has some structure
+  dir_index=$(( (i - 1) / (COUNT / 100 + 1) ))
+  subdir="$TARGET/dir$(printf "%03d" "$dir_index")"
+  mkdir -p "$subdir"
+  echo "This is file #$i" > "$subdir/file_$i.txt"
+done
+
+echo "✅ Done: $(find "$TARGET" -type f | wc -l) files created."

cli-bin/src/cli.rs

@@ -1,4 +1,5 @@
 // src/cli.rs
+
 pub mod link;
 pub mod coll;
 pub mod view;
@@ -42,6 +43,10 @@ pub enum Commands {
 
     /// Scan one or more directories and populate the file index
     Scan {
+        /// Only re-index files marked dirty by `marlin watch`
+        #[arg(long)]
+        dirty: bool,
+
         /// Directories to scan (defaults to cwd)
         paths: Vec<std::path::PathBuf>,
     },

cli-bin/src/main.rs

@@ -16,6 +16,7 @@ use libmarlin::{
     scan,
     utils::determine_scan_root,
 };
+use libmarlin::db::take_dirty;
 
 use anyhow::{Context, Result};
 use clap::{CommandFactory, Parser};
@@ -83,13 +84,31 @@ fn main() -> Result<()> {
         }
 
         /* ---- scan ------------------------------------------------ */
-        Commands::Scan { paths } => {
-            let scan_paths = if paths.is_empty() {
+        Commands::Scan { dirty, paths } => {
+            // Determine full-scan roots
+            let scan_paths: Vec<std::path::PathBuf> = if paths.is_empty() {
                 vec![env::current_dir()?]
-            } else { paths };
+            } else {
+                paths.into_iter().collect()
+            };
 
-            for p in scan_paths {
-                scan::scan_directory(&mut conn, &p)?;
+            if dirty {
+                // Incremental: only re-index the files marked dirty
+                let dirty_ids = take_dirty(&conn)?;
+                for id in dirty_ids {
+                    // look up each path by its file_id
+                    let path: String = conn.query_row(
+                        "SELECT path FROM files WHERE id = ?1",
+                        [id],
+                        |r| r.get(0),
+                    )?;
+                    scan::scan_directory(&mut conn, Path::new(&path))?;
+                }
+            } else {
+                // Full rescan of the given directories
+                for p in scan_paths {
+                    scan::scan_directory(&mut conn, &p)?;
+                }
             }
         }
 

libmarlin/src/db/migrations/0005_add_dirty_table.sql

@@ -0,0 +1,8 @@
+PRAGMA foreign_keys = ON;
+PRAGMA journal_mode = WAL;
+
+-- Track which files need re-indexing
+CREATE TABLE IF NOT EXISTS file_changes (
+  file_id   INTEGER PRIMARY KEY REFERENCES files(id) ON DELETE CASCADE,
+  marked_at INTEGER NOT NULL             -- UNIX timestamp
+);

libmarlin/src/db/mod.rs

@@ -15,7 +15,7 @@ use rusqlite::{
     Connection,
     OpenFlags,
     OptionalExtension,
-    TransactionBehavior,  
+    TransactionBehavior,
 };
 use tracing::{debug, info, warn};
 
@@ -26,6 +26,7 @@ const MIGRATIONS: &[(&str, &str)] = &[
     ("0002_update_fts_and_triggers.sql", include_str!("migrations/0002_update_fts_and_triggers.sql")),
     ("0003_create_links_collections_views.sql", include_str!("migrations/0003_create_links_collections_views.sql")),
     ("0004_fix_hierarchical_tags_fts.sql", include_str!("migrations/0004_fix_hierarchical_tags_fts.sql")),
+    ("0005_add_dirty_table.sql", include_str!("migrations/0005_add_dirty_table.sql")),
 ];
 
 /* ─── connection bootstrap ────────────────────────────────────────── */
@@ -39,13 +40,12 @@ pub fn open<P: AsRef<Path>>(db_path: P) -> Result<Connection> {
     conn.pragma_update(None, "foreign_keys", "ON")?;
 
     // Wait up to 30 s for a competing writer before giving up
-    conn.busy_timeout(std::time::Duration::from_secs(30))?;   // ← tweaked
+    conn.busy_timeout(std::time::Duration::from_secs(30))?;
 
     apply_migrations(&mut conn)?;
     Ok(conn)
 }
 
-
 /* ─── migration runner ────────────────────────────────────────────── */
 
 pub(crate) fn apply_migrations(conn: &mut Connection) -> Result<()> {
@@ -85,7 +85,7 @@ pub(crate) fn apply_migrations(conn: &mut Connection) -> Result<()> {
 
         info!("applying migration {}", fname);
         tx.execute_batch(sql)
-            .with_context(|| format!("could not apply migration {fname}"))?;
+            .with_context(|| format!("could not apply migration {}", fname))?;
 
         tx.execute(
             "INSERT INTO schema_version (version, applied_on) VALUES (?1, ?2)",
@@ -158,7 +158,12 @@ pub fn upsert_attr(conn: &Connection, file_id: i64, key: &str, value: &str) -> R
 
 /* ─── links ───────────────────────────────────────────────────────── */
 
-pub fn add_link(conn: &Connection, src_file_id: i64, dst_file_id: i64, link_type: Option<&str>) -> Result<()> {
+pub fn add_link(
+    conn: &Connection,
+    src_file_id: i64,
+    dst_file_id: i64,
+    link_type: Option<&str>,
+) -> Result<()> {
     conn.execute(
         "INSERT INTO links(src_file_id, dst_file_id, type)
          VALUES (?1, ?2, ?3)
@@ -168,7 +173,12 @@ pub fn add_link(conn: &Connection, src_file_id: i64, dst_file_id: i64, link_type
     Ok(())
 }
 
-pub fn remove_link(conn: &Connection, src_file_id: i64, dst_file_id: i64, link_type: Option<&str>) -> Result<()> {
+pub fn remove_link(
+    conn: &Connection,
+    src_file_id: i64,
+    dst_file_id: i64,
+    link_type: Option<&str>,
+) -> Result<()> {
     conn.execute(
         "DELETE FROM links
          WHERE src_file_id = ?1
@@ -190,8 +200,10 @@ pub fn list_links(
     // Files matching pattern
     let mut stmt = conn.prepare("SELECT id, path FROM files WHERE path LIKE ?1")?;
     let rows = stmt
-        .query_map(params![like_pattern], |r| Ok((r.get::<_, i64>(0)?, r.get::<_, String>(1)?)))?
-        .collect::<Result<Vec<_>, _>>()?;
+        .query_map(params![like_pattern], |r| {
+            Ok((r.get::<_, i64>(0)?, r.get::<_, String>(1)?))
+        })?
+        .collect::<StdResult<Vec<_>, _>>()?;
 
     let mut out = Vec::new();
     for (fid, fpath) in rows {
@@ -210,8 +222,10 @@ pub fn list_links(
 
         let mut stmt2 = conn.prepare(&sql)?;
         let links = stmt2
-            .query_map(params![fid, link_type], |r| Ok((r.get::<_, String>(0)?, r.get::<_, Option<String>>(1)?)))?
-            .collect::<Result<Vec<_>, _>>()?;
+            .query_map(params![fid, link_type], |r| {
+                Ok((r.get::<_, String>(0)?, r.get::<_, Option<String>>(1)?))
+            })?
+            .collect::<StdResult<Vec<_>, _>>()?;
 
         for (other, typ) in links {
             out.push((fpath.clone(), other, typ));
@@ -238,11 +252,11 @@ pub fn find_backlinks(
         Ok((r.get::<_, String>(0)?, r.get::<_, Option<String>>(1)?))
     })?;
 
-    let out = rows.collect::<StdResult<Vec<_>, _>>()?;   // rusqlite → anyhow via `?`
+    let out = rows.collect::<StdResult<Vec<_>, _>>()?;
     Ok(out)
 }
 
-/* ─── NEW: collections helpers ────────────────────────────────────── */
+/* ─── collections helpers ────────────────────────────────────────── */
 
 pub fn ensure_collection(conn: &Connection, name: &str) -> Result<i64> {
     conn.execute(
@@ -281,7 +295,7 @@ pub fn list_collection(conn: &Connection, name: &str) -> Result<Vec<String>> {
     Ok(list)
 }
 
-/* ─── NEW: saved views (smart folders) ────────────────────────────── */
+/* ─── saved views (smart folders) ───────────────────────────────── */
 
 pub fn save_view(conn: &Connection, name: &str, query: &str) -> Result<()> {
     conn.execute(
@@ -295,7 +309,6 @@ pub fn save_view(conn: &Connection, name: &str, query: &str) -> Result<()> {
 
 pub fn list_views(conn: &Connection) -> Result<Vec<(String, String)>> {
     let mut stmt = conn.prepare("SELECT name, query FROM views ORDER BY name")?;
-
     let rows = stmt.query_map([], |r| Ok((r.get::<_, String>(0)?, r.get::<_, String>(1)?)))?;
     let list = rows.collect::<StdResult<Vec<_>, _>>()?;
     Ok(list)
@@ -307,7 +320,32 @@ pub fn view_query(conn: &Connection, name: &str) -> Result<String> {
         [name],
         |r| r.get::<_, String>(0),
     )
-    .context(format!("no view called '{name}'"))
+    .context(format!("no view called '{}'", name))
+}
+
+/* ─── dirty‐scan helpers ─────────────────────────────────────────── */
+
+/// Mark a file as “dirty” so it’ll be picked up by `scan_dirty`.
+pub fn mark_dirty(conn: &Connection, file_id: i64) -> Result<()> {
+    conn.execute(
+        "INSERT OR IGNORE INTO file_changes(file_id, marked_at)
+         VALUES (?1, strftime('%s','now'))",
+        params![file_id],
+    )?;
+    Ok(())
+}
+
+/// Take and clear all dirty file IDs for incremental re-scan.
+pub fn take_dirty(conn: &Connection) -> Result<Vec<i64>> {
+    let mut ids = Vec::new();
+    {
+        let mut stmt = conn.prepare("SELECT file_id FROM file_changes")?;
+        for row in stmt.query_map([], |r| r.get(0))? {
+            ids.push(row?);
+        }
+    }
+    conn.execute("DELETE FROM file_changes", [])?;
+    Ok(ids)
 }
 
 /* ─── backup / restore helpers ────────────────────────────────────── */

libmarlin/src/scan.rs

@@ -11,7 +11,10 @@ use walkdir::WalkDir;
 /// Recursively walk `root` and upsert file metadata.
 /// Triggers keep the FTS table in sync.
 pub fn scan_directory(conn: &mut Connection, root: &Path) -> Result<usize> {
+    // Begin a transaction so we batch many inserts/updates together
     let tx = conn.transaction()?;
+
+    // Prepare the upsert statement once
     let mut stmt = tx.prepare(
         r#"
         INSERT INTO files(path, size, mtime)
@@ -23,12 +26,15 @@ pub fn scan_directory(conn: &mut Connection, root: &Path) -> Result<usize> {
     )?;
 
     let mut count = 0usize;
+
+    // Walk the directory recursively
     for entry in WalkDir::new(root)
         .into_iter()
         .filter_map(Result::ok)
         .filter(|e| e.file_type().is_file())
     {
         let path = entry.path();
+
         // Skip the database file and its WAL/SHM siblings
         if let Some(name) = path.file_name().and_then(|n| n.to_str()) {
             if name.ends_with(".db") || name.ends_with("-wal") || name.ends_with("-shm") {
@@ -36,6 +42,7 @@ pub fn scan_directory(conn: &mut Connection, root: &Path) -> Result<usize> {
             }
         }
 
+        // Gather file metadata
         let meta = fs::metadata(path)?;
         let size = meta.len() as i64;
         let mtime = meta
@@ -43,14 +50,18 @@ pub fn scan_directory(conn: &mut Connection, root: &Path) -> Result<usize> {
             .duration_since(std::time::UNIX_EPOCH)?
             .as_secs() as i64;
 
+        // Execute the upsert
         let path_str = path.to_string_lossy();
         stmt.execute(params![path_str, size, mtime])?;
         count += 1;
+
         debug!(file = %path_str, "indexed");
     }
 
+    // Finalize and commit
     drop(stmt);
     tx.commit()?;
+
     info!(indexed = count, "scan complete");
     Ok(count)
 }

target/.rustc_info.json

@@ -1 +1 @@
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target/release/marlin.d

@@ -1 +1 @@
-/home/user/Documents/GitHub/Marlin/target/release/marlin: /home/user/Documents/GitHub/Marlin/cli-bin/build.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/annotate.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/coll.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/event.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/link.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/remind.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/state.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/task.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/version.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/view.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/main.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/config.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0001_initial_schema.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0002_update_fts_and_triggers.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0003_create_links_collections_views.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0004_fix_hierarchical_tags_fts.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/mod.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/lib.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/logging.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/scan.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/utils.rs
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