chore: v2.1.0 version upgrade and code cleanup

CHANGELOG.md

@@ -5,7 +5,25 @@ All notable changes to SeqMatcher will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [2.0.0] - Unreleased
+## [2.1.0] - 2026-07-14
+
+### Added
+- `build-release.sh` cross-platform release builder (macOS/Linux/Windows targets)
+- `--no-report` flag to suppress run summary report generation
+- Pre-built release binaries for macOS (arm64/x86_64) and Linux (amd64/arm64 musl)
+
+### Changed
+- Simplified `progress` module: removed unused `count_lines` public API in favor of `estimate_total_lines`
+- Renamed internal `count_lines_in_buf` to `count_lines_exact` for clarity
+- Updated `rustfmt.toml` to use only stable-channel formatting options
+- `ThreadResult` now derives `Default` instead of manual implementation
+
+### Fixed
+- Clippy `too_many_arguments` warning on `process_sequences` (annotated allowed)
+- Clippy `derivable_impls` warning on `ThreadResult::Default`
+- Unused `create_temp_seq` helper in integration tests (annotated reserved)
+
+## [2.0.0] - 2026-07-14
 
 ### Added
 - Comprehensive IUPAC degenerate base support (S, W, B, D, H, V) in reverse complement table
@@ -17,42 +35,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `--timestamp-output` flag for time-stamped output filenames
 - Input data validation with health checks
 - Run summary report (`run_summary.json` and `run_summary.txt`)
-- Statistical summary with primer hit ranking and coverage metrics
-- Reproducibility features: SHA256 hashing of inputs, full CLI arg recording
-- ASCII bar chart visualization for top primer hits
+- Reproducibility features: full CLI arg recording in summary reports
 - `CITATION.cff` for academic citation
-- Benchmark suite using Criterion (AC matching, primer matching, reverse complement)
+- Benchmark suite using Criterion (AC matching, reverse complement)
 - Integration tests with end-to-end pipeline coverage
 - Public library API via `src/lib.rs` for downstream crate consumption
 - Comprehensive rustdoc documentation for all public APIs
 
 ### Changed
-- Refactored `main.rs` (436 lines) into 5 focused modules: `cli`, `progress`, `matcher`, `pipeline`, `main`
+- Refactored `main.rs` (436 lines) into focused modules: `cli`, `progress`, `matcher`, `pipeline`
 - Replaced manual `csv_to_line` serialization with `csv::Writer` for correctness
 - Optimized `write_variant_counts` O(P*V) HashMap lookups to O(1) array indexing
 - Replaced `eprintln!` diagnostics with `tracing` structured logging
 - Unified error messages to English (CLI help text remains bilingual)
 - Eliminated double I/O from `count_lines` pre-scan; uses file-size estimation
 
 ### Fixed
-- IUPAC degenerate bases S, W, B, D, H, V now correctly reverse-complemented
+- **Critical**: IUPAC degenerate bases S, W, B, D, H, V now correctly reverse-complemented
   (previously mapped to themselves, producing incorrect results for degenerate sequences)
 - Version inconsistency between `Cargo.toml` (1.4.0) and `Cargo.lock` (1.3.0)
 
 ### Removed
 - Unused `serde` dependency from `Cargo.toml`
 - Manual `csv_to_line` function in favor of `csv::Writer`
-- Redundant `num_primers` parameter from `process_sequences` and `process_chunk`
 
 ## [1.4.0] - 2025-06-25
 
 ### Added
 - Streaming I/O with reusable hit buffer for reduced allocations
 - In-place ASCII uppercase conversion
 
-### Changed
-- Performance optimization: streaming chunk processing replaces full-file buffering
-
 ## [1.3.0] - 2025-06-25
 
 ### Added

CITATION.cff

@@ -7,8 +7,8 @@ authors:
     given-names: Jiwen
     orcid: "https://orcid.org/0000-0000-0000-0000"
     url: "https://github.com/CropCoder"
-version: 2.0.0
-date-released: 2026-07-13
+version: 2.1.0
+date-released: 2026-07-14
 repository-code: "https://github.com/CropCoder/SeqMatcher"
 url: "https://github.com/CropCoder/SeqMatcher"
 abstract: >

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "seq_matcher"
-version = "2.0.0"
+version = "2.1.0"
 edition = "2021"
 
 [dependencies]

src/progress.rs

@@ -1,7 +1,7 @@
 //! Progress bar and line counting utilities.
 //!
 //! Provides real-time progress display with throughput and ETA estimation,
-//! plus efficient file line counting for progress tracking.
+//! plus efficient file line estimation for progress tracking.
 
 use std::fs::File;
 use std::io::{Read, Seek, SeekFrom, Write};
@@ -51,31 +51,17 @@ pub fn estimate_total_lines(path: &str, sample_lines: usize) -> Result<(u64, u64
         Ok((estimated.max(1), file_size))
     } else {
         // File is too short to sample — count exactly
-        file.seek(SeekFrom::Start(0))?;
-        let exact = count_lines_in_buf(&mut file)?;
+        let exact = count_lines_exact(&mut file)?;
         file.seek(SeekFrom::Start(0))?;
         Ok((exact, file_size))
     }
 }
 
-/// Count newlines in a file by scanning raw bytes (256KB buffer).
-///
-/// Fast line counting that avoids UTF-8 validation overhead of
-/// line-by-line reading. Handles files with or without trailing newline.
-/// Seeks back to the beginning of the file after counting.
-///
-/// Note: for pipeline progress estimation, [`estimate_total_lines`] is
-/// preferred as it avoids a full file scan.
-#[allow(dead_code)]
-pub fn count_lines(path: &str) -> Result<u64> {
-    let mut file = File::open(path)?;
-    let count = count_lines_in_buf(&mut file)?;
-    file.seek(SeekFrom::Start(0))?;
-    Ok(count)
-}
-
 /// Count newlines in an already-open file using a 256KB read buffer.
-fn count_lines_in_buf(file: &mut File) -> Result<u64> {
+///
+/// Accurate but requires a full scan. Prefer [`estimate_total_lines`] for
+/// progress-bar use; use this only when an exact count is required.
+fn count_lines_exact(file: &mut File) -> Result<u64> {
     let mut buf = [0u8; 256 * 1024];
     let mut count = 0u64;
     let mut non_empty = false;
@@ -104,12 +90,24 @@ fn count_lines_in_buf(file: &mut File) -> Result<u64> {
 /// Uses `\r` to overwrite the same line. The bar width is configurable.
 /// Callers should flush stderr after this to ensure immediate display.
 pub fn print_progress(processed: u64, total: u64, start: &std::time::Instant, bar_width: usize) {
-    let pct = if total > 0 { processed as f64 / total as f64 } else { 0.0 };
+    let pct = if total > 0 {
+        processed as f64 / total as f64
+    } else {
+        0.0
+    };
     let filled = (bar_width as f64 * pct) as usize;
     let bar = "\u{2588}".repeat(filled) + &"\u{2591}".repeat(bar_width.saturating_sub(filled));
     let elapsed = start.elapsed().as_secs_f64();
-    let rate = if elapsed > 0.0 { processed as f64 / elapsed } else { 0.0 };
-    let eta = if rate > 0.0 { (total.saturating_sub(processed)) as f64 / rate } else { 0.0 };
+    let rate = if elapsed > 0.0 {
+        processed as f64 / elapsed
+    } else {
+        0.0
+    };
+    let eta = if rate > 0.0 {
+        (total.saturating_sub(processed)) as f64 / rate
+    } else {
+        0.0
+    };
 
     eprint!(
         "\r    [{bar}] {pct:5.1}%  {processed}/{total}  {rate:.0} seq/s  ETA: {eta:.0}s",