Build for Python 3.14 (#109)

Author: apcamargo

.github/workflows/release.yml

@@ -1,8 +1,3 @@
-# This file is autogenerated by maturin v1.8.2
-# To update, run
-#
-#    maturin generate-ci github
-#
 name: build wheels
 
 on:
@@ -33,6 +28,7 @@ jobs:
           - "3.11"
           - "3.12"
           - "3.13"
+          - "3.14"
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels
@@ -53,16 +49,17 @@ jobs:
     strategy:
       matrix:
         platform:
-          - runner: macos-13
+          - runner: macos-15
             target: x86_64
-          - runner: macos-14
+          - runner: macos-15
             target: aarch64
         python-version:
           - "3.9"
           - "3.10"
           - "3.11"
           - "3.12"
           - "3.13"
+          - "3.14"
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels

Cargo.toml

@@ -31,7 +31,7 @@ bytecount = { version = "0.6", features = ["runtime-dispatch-simd"] }
 bzip2 = { version = "0.4", optional = true }
 flate2 = { version = "1.0.30", optional = true }
 memchr = "2.7.2"
-pyo3 = { version = "0.24.1", optional = true }
+pyo3 = { version = "0.27.2", optional = true }
 liblzma = { version = "0.3.1", optional = true }
 zstd = { version = "0.13.2", optional = true }
 

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["maturin>=1.8,<2.0"]
+requires = ["maturin>=1.10,<2.0"]
 build-backend = "maturin"
 
 [project]

src/parser/fasta.rs

@@ -288,7 +288,7 @@ where
 }
 
 impl<R: io::Read + Send> FastxReader for Reader<R> {
-    fn next(&mut self) -> Option<Result<SequenceRecord, ParseError>> {
+    fn next(&mut self) -> Option<Result<SequenceRecord<'_>, ParseError>> {
         if self.finished {
             return None;
         }

src/parser/fastq.rs

@@ -385,7 +385,7 @@ where
 }
 
 impl<R: io::Read + Send> FastxReader for Reader<R> {
-    fn next(&mut self) -> Option<Result<SequenceRecord, ParseError>> {
+    fn next(&mut self) -> Option<Result<SequenceRecord<'_>, ParseError>> {
         // No more records to read
         if self.finished {
             return None;

src/parser/record.rs

@@ -84,7 +84,7 @@ impl<'a> SequenceRecord<'a> {
 
     /// Returns the cleaned up sequence of the record. For FASTQ it is the same as `raw_seq` but
     /// for FASTA it is `raw_seq` minus all the `\r\n`
-    pub fn seq(&self) -> Cow<[u8]> {
+    pub fn seq(&self) -> Cow<'_, [u8]> {
         match self.buf_pos {
             BufferPositionKind::Fasta(bp) => bp.seq(self.buffer),
             BufferPositionKind::Fastq(bp) => bp.seq(self.buffer).into(),

src/parser/utils.rs

@@ -120,7 +120,7 @@ pub trait FastxReader: Send {
     /// Gets the next record in the stream.
     /// This imitates the Iterator API but does not support any iterator functions.
     /// This returns None once we reached the EOF.
-    fn next(&mut self) -> Option<Result<SequenceRecord, ParseError>>;
+    fn next(&mut self) -> Option<Result<SequenceRecord<'_>, ParseError>>;
     /// Returns the current line/byte in the stream we are reading from
     fn position(&self) -> &Position;
     /// Returns whether the current stream uses Windows or Unix style line endings

src/python.rs

@@ -38,7 +38,7 @@ fn get_seq_snippet(seq: &str, max_len: usize) -> String {
     if seq.len() > max_len {
         let start = &seq[..max_len - 4];
         let end = &seq[seq.len() - 3..];
-        format!("{}…{}", start, end)
+        format!("{start}…{end}")
     } else {
         seq.to_string()
     }
@@ -156,7 +156,7 @@ impl Record {
     #[getter]
     pub fn description(&self) -> PyResult<Option<&str>> {
         if let Some(pos) = self.id.find(char::is_whitespace) {
-            Ok(Some(&self.id[pos..].trim_start()))
+            Ok(Some(self.id[pos..].trim_start()))
         } else {
             Ok(None)
         }
@@ -219,9 +219,8 @@ impl Record {
         let mut hasher = DefaultHasher::new();
         self.id.hash(&mut hasher);
         self.seq.hash(&mut hasher);
-        match &self.qual {
-            Some(qual) => qual.hash(&mut hasher),
-            None => {}
+        if let Some(qual) = &self.qual {
+            qual.hash(&mut hasher);
         }
         Ok(hasher.finish())
     }
@@ -249,7 +248,7 @@ impl Record {
 
     fn __repr__(&self) -> PyResult<String> {
         let id_snippet = match self.name() {
-            Ok(name) if name != self.id => format!("{}…", name),
+            Ok(name) if name != self.id => format!("{name}…"),
             Ok(name) => name.to_string(),
             Err(_) => self.id.clone(),
         };
@@ -259,8 +258,7 @@ impl Record {
             None => "None".to_string(),
         };
         Ok(format!(
-            "Record(id={}, seq={}, qual={})",
-            id_snippet, seq_snippet, quality_snippet
+            "Record(id={id_snippet}, seq={seq_snippet}, qual={quality_snippet})"
         ))
     }
 }
@@ -424,7 +422,7 @@ pub fn py_decode_phred(qual: &str, base_64: bool, py: Python<'_>) -> PyResult<Py
         PhredEncoding::Phred33
     };
     let scores = decode_phred(qual.as_bytes(), encoding)
-        .map_err(|e| PyValueError::new_err(format!("Invalid Phred quality: {}", e)))?;
+        .map_err(|e| PyValueError::new_err(format!("Invalid Phred quality: {e}")))?;
     Ok(PyTuple::new(py, &scores)?.into())
 }
 

src/sequence.rs

@@ -107,7 +107,7 @@ pub fn complement(n: u8) -> u8 {
 /// Taking in a sequence string, return the canonical form of the sequence
 /// (e.g. the lexigraphically lowest of either the original sequence or its
 /// reverse complement)
-pub fn canonical(seq: &[u8]) -> Cow<[u8]> {
+pub fn canonical(seq: &[u8]) -> Cow<'_, [u8]> {
     let mut buf: Vec<u8> = Vec::with_capacity(seq.len());
     // enough just keeps our comparisons from happening after they need to
     let mut enough = false;
@@ -136,7 +136,7 @@ pub fn canonical(seq: &[u8]) -> Cow<[u8]> {
 /// Find the lexigraphically smallest substring of `seq` of length `length`
 ///
 /// There's probably a faster algorithm for this somewhere...
-pub fn minimizer(seq: &[u8], length: usize) -> Cow<[u8]> {
+pub fn minimizer(seq: &[u8], length: usize) -> Cow<'_, [u8]> {
     let reverse_complement: Vec<u8> = seq.iter().rev().map(|n| complement(*n)).collect();
     let mut minmer = Cow::Borrowed(&seq[..length]);