chore: Clippy and fmt fixes

Author: St4NNi

src/bias.rs

@@ -2514,11 +2514,11 @@ mod tests {
         let pos_counts = [100u64; 255];
         let neg_counts = [100u64; 255];
 
-        for i in 200..255 {
-            p_pos[i] = 1.0 / 55.0;
+        for value in p_pos.iter_mut().skip(200) {
+            *value = 1.0 / 55.0;
         }
-        for i in 0..55 {
-            p_neg[i] = 1.0 / 55.0;
+        for value in p_neg.iter_mut().take(55) {
+            *value = 1.0 / 55.0;
         }
 
         let pos_sum: f64 = p_pos.iter().sum();
@@ -2640,11 +2640,11 @@ mod tests {
         let pos_counts = [100u64; 255];
         let neg_counts = [100u64; 255];
 
-        for i in 180..255 {
-            p_pos[i] = 1.0 / 75.0;
+        for value in p_pos.iter_mut().skip(180) {
+            *value = 1.0 / 75.0;
         }
-        for i in 0..75 {
-            p_neg[i] = 1.0 / 75.0;
+        for value in p_neg.iter_mut().take(75) {
+            *value = 1.0 / 75.0;
         }
 
         let pos_sum: f64 = p_pos.iter().sum();

src/cli/handlers.rs

@@ -440,7 +440,7 @@ fn compute_distance_chunk_size(
 ) -> usize {
     debug_assert!(total_samples > 0);
 
-    let min_chunk_size = total_samples.min(100).max(1);
+    let min_chunk_size = total_samples.clamp(1, 100);
     let raw_chunk_size = budget_bytes / per_sample_bytes.max(1);
 
     raw_chunk_size.clamp(min_chunk_size, total_samples)

src/io.rs

@@ -65,7 +65,7 @@ pub fn is_sequence_file(path: &Path) -> bool {
 pub fn read_entries<P: AsRef<Path>>(path: P) -> io::Result<Vec<Entry>> {
     let file = File::open(path)?;
     let file_size = file.metadata()?.len() as usize;
-    if file_size % ENTRY_SIZE != 0 {
+    if !file_size.is_multiple_of(ENTRY_SIZE) {
         return Err(io::Error::new(
             io::ErrorKind::InvalidData,
             format!("entry file size {file_size} is not a multiple of {ENTRY_SIZE}"),

src/query.rs

@@ -318,6 +318,9 @@ pub struct QueryResult {
     pub total_query_weight: f64,
 }
 
+type SampleHitMap = HashMap<u32, (u32, f64)>;
+type QueryBucketHitMap = HashMap<usize, SampleHitMap>;
+
 impl QueryResult {
     pub fn top(&self, n: usize) -> Vec<&SampleMatch> {
         let mut sorted: Vec<_> = self.matches.iter().collect();
@@ -528,10 +531,10 @@ impl QueryEngine {
 
         let bias_table = &self.bias_table;
 
-        let bucket_maps: Vec<HashMap<usize, HashMap<u32, (u32, f64)>>> = (0..BUCKET_COUNT)
+        let bucket_maps: Vec<QueryBucketHitMap> = (0..BUCKET_COUNT)
             .into_par_iter()
             .map(|bucket_idx| {
-                let mut local_maps: HashMap<usize, HashMap<u32, (u32, f64)>> = HashMap::new();
+                let mut local_maps: QueryBucketHitMap = HashMap::new();
 
                 let query_bucket = sketch.bucket(bucket_idx);
                 if query_bucket.is_empty() {
@@ -627,10 +630,10 @@ impl QueryEngine {
             })
             .collect();
 
-        let merged: Vec<HashMap<u32, (u32, f64)>> = (0..chunk_len)
+        let merged: Vec<SampleHitMap> = (0..chunk_len)
             .into_par_iter()
             .map(|local_idx| {
-                let mut combined: HashMap<u32, (u32, f64)> = HashMap::new();
+                let mut combined: SampleHitMap = HashMap::new();
                 for per_bucket in &bucket_maps {
                     if let Some(local_map) = per_bucket.get(&local_idx) {
                         for (&db_id, &(count, weight)) in local_map {

tests/coverage_tests.rs

@@ -230,14 +230,21 @@ fn test_expand_input_paths_relative_paths() -> Result<()> {
 fn test_expand_input_paths_compressed_files() -> Result<()> {
     let env = CoverageTestEnvironment::new()?;
 
-    let gz_file = env.create_test_fasta("test.fa.gz", ">seq\nACGT\n")?;
-    let fq_gz_file = env.create_test_fasta("test.fq.gz", "@seq\nACGT\n+\nIIII\n")?;
+    let compressed_files = [
+        env.create_test_fasta("test.fa.gz", ">seq\nACGT\n")?,
+        env.create_test_fasta("test.fq.gz", "@seq\nACGT\n+\nIIII\n")?,
+        env.create_test_fasta("test.fa.bz2", ">seq\nACGT\n")?,
+        env.create_test_fasta("test.fasta.xz", ">seq\nACGT\n")?,
+        env.create_test_fasta("test.fastq.zst", "@seq\nACGT\n+\nIIII\n")?,
+        env.create_test_fasta("test.fq.zstd", "@seq\nACGT\n+\nIIII\n")?,
+    ];
 
-    let result = expand_input_paths(&[gz_file.clone(), fq_gz_file.clone()])?;
+    let result = expand_input_paths(&compressed_files)?;
 
-    assert_eq!(result.len(), 2);
-    assert!(result.contains(&gz_file));
-    assert!(result.contains(&fq_gz_file));
+    assert_eq!(result.len(), compressed_files.len());
+    for file in compressed_files {
+        assert!(result.contains(&file));
+    }
 
     Ok(())
 }
@@ -328,9 +335,19 @@ fn test_is_sequence_file_edge_cases() {
     assert!(is_sequence_file(Path::new("file.name.with.dots.fa")));
     assert!(is_sequence_file(Path::new("version.1.0.fasta")));
 
-    assert!(is_sequence_file(Path::new("file.fastq.gz")));
-    assert!(is_sequence_file(Path::new("file.fq.gz")));
-    assert!(!is_sequence_file(Path::new("file.fa.bz2")));
+    for filename in [
+        "file.fastq.gz",
+        "file.fq.gz",
+        "file.fa.bz2",
+        "file.fasta.xz",
+        "file.fastq.zst",
+        "file.fq.zstd",
+    ] {
+        assert!(
+            is_sequence_file(Path::new(filename)),
+            "Failed for {filename}"
+        );
+    }
 
     let mixed_case = vec![
         "File.Fa",