Update CI to build for Python 3.13 and linux-aarch64

.github/workflows/release.yml

@@ -25,9 +25,12 @@ jobs:
         platform:
           - runner: ubuntu-22.04
             target: x86_64
+          - runner: ubuntu-22.04
+            target: aarch64
         python-version:
           - "3.11"
           - "3.12"
+          - "3.13"
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels
@@ -55,6 +58,7 @@ jobs:
         python-version:
           - "3.11"
           - "3.12"
+          - "3.13"
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels

Cargo.toml

@@ -28,7 +28,7 @@ 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 = "0.21.2", optional = true }
+pyo3 = { version = "0.24.0", optional = true }
 liblzma = { version = "0.3.1", optional = true }
 zstd = { version = "0.13.2", optional = true }
 

pyproject.toml

@@ -1,13 +1,14 @@
 [build-system]
-requires = ["maturin>=1.7,<2.0"]
+requires = ["maturin>=1.8,<2.0"]
 build-backend = "maturin"
 
 [project]
 name = "needletail"
+requires-python = ">=3.8"
 dynamic = ["version"]
 classifier = [
     "Intended Audience :: Science/Research",
-    "Programming Language :: Python :: 3",
+    "Programming Language :: Rust",
     "License :: OSI Approved :: MIT License",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]

src/python.rs

@@ -19,6 +19,7 @@ use pyo3::{create_exception, wrap_pyfunction};
 use std::hash::{DefaultHasher, Hash, Hasher};
 use std::io::Cursor;
 use std::path::PathBuf;
+use std::sync::Mutex;
 
 create_exception!(needletail, NeedletailError, pyo3::exceptions::PyException);
 
@@ -56,7 +57,7 @@ fn get_seq_snippet(seq: &str, max_len: usize) -> String {
 ///     A class representing a FASTA/FASTQ sequence record.
 #[pyclass]
 pub struct PyFastxReader {
-    reader: Box<dyn FastxReader>,
+    reader: Mutex<Box<dyn FastxReader>>,
 }
 
 #[pymethods]
@@ -69,8 +70,8 @@ impl PyFastxReader {
         slf
     }
 
-    fn __next__(mut slf: PyRefMut<Self>) -> PyResult<Option<Record>> {
-        if let Some(rec) = slf.reader.next() {
+    fn __next__(slf: PyRefMut<Self>) -> PyResult<Option<Record>> {
+        if let Some(rec) = slf.reader.lock().unwrap().next() {
             let record = py_try!(rec);
             Ok(Some(Record::from_sequence_record(&record)))
         } else {
@@ -280,7 +281,9 @@ impl Record {
 #[pyfunction]
 fn parse_fastx_file(path: PathBuf) -> PyResult<PyFastxReader> {
     let reader = py_try!(rs_parse_fastx_file(path));
-    Ok(PyFastxReader { reader })
+    Ok(PyFastxReader {
+        reader: reader.into(),
+    })
 }
 
 /// Parse sequence records from a FASTA/FASTQ string.
@@ -310,7 +313,9 @@ fn parse_fastx_file(path: PathBuf) -> PyResult<PyFastxReader> {
 #[pyfunction]
 fn parse_fastx_string(content: &str) -> PyResult<PyFastxReader> {
     let reader = py_try!(parse_fastx_reader(Cursor::new(content.to_owned())));
-    Ok(PyFastxReader { reader })
+    Ok(PyFastxReader {
+        reader: reader.into(),
+    })
 }
 
 /// Normalize the sequence string of nucleotide records by:
@@ -383,6 +388,6 @@ fn needletail(py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_wrapped(wrap_pyfunction!(parse_fastx_string))?;
     m.add_wrapped(wrap_pyfunction!(normalize_seq))?;
     m.add_wrapped(wrap_pyfunction!(reverse_complement))?;
-    m.add("NeedletailError", py.get_type_bound::<NeedletailError>())?;
+    m.add("NeedletailError", py.get_type::<NeedletailError>())?;
     Ok(())
 }