build: support 3.13 python version (#190)

* build: support python version
* build: update exon version
* build: update signatures for pyclass

.github/workflows/test.yml

@@ -20,7 +20,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.13'
 
       - name: Run clippy
         run: cargo clippy --all-targets --all-features -- -D warnings

Cargo.toml

@@ -8,10 +8,10 @@ crate-type = ["cdylib"]
 name = "biobear"
 
 [dependencies]
-arrow = { version = "52.1.0", features = ["pyarrow"] }
-datafusion = "41"
-exon = { version = "0.32.3", features = ["default"] }
-pyo3 = "0.21.2"
+arrow = { version = "53.3.0", features = ["pyarrow"] }
+datafusion = "43"
+exon = { version = "0.32.4", features = ["default"] }
+pyo3 = "0.22.2"
 tokio = { version = "1", features = ["rt"] }
 noodles = { version = "0.86", features = ["core"] }
 

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 build-backend = "maturin"
-requires = ["maturin==1.5.1"]
+requires = ["maturin==1.7.8"]
 
 [project]
 authors = [{ name = "WHERE TRUE devs", email = "[email protected]" }]
@@ -13,7 +13,7 @@ dependencies = ["pyarrow>=15"]
 license = { file = "LICENSE" }
 name = "biobear"
 readme = "README.md"
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.9"
 description = "A package for working with Bioinformatics data with SQL and Arrow"
 version = "0.23.2"
 

src/bam_reader.rs

@@ -57,6 +57,7 @@ impl BamIndexedReader {
 #[pymethods]
 impl BamIndexedReader {
     #[new]
+    #[pyo3(signature = (path, batch_size=None))]
     fn new(path: &str, batch_size: Option<usize>) -> PyResult<Self> {
         Self::open(path, batch_size).map_err(|e| {
             PyErr::new::<pyo3::exceptions::PyIOError, _>(format!(

src/bcf_reader.rs

@@ -58,6 +58,7 @@ impl BCFIndexedReader {
 #[pymethods]
 impl BCFIndexedReader {
     #[new]
+    #[pyo3(signature = (path, batch_size=None))]
     fn new(path: &str, batch_size: Option<usize>) -> PyResult<Self> {
         Self::open(path, batch_size).map_err(PyErr::new::<pyo3::exceptions::PyValueError, _>)
     }

src/datasources/bam.rs

@@ -27,6 +27,7 @@ pub struct BAMReadOptions {
 #[pymethods]
 impl BAMReadOptions {
     #[new]
+    #[pyo3(signature = (region=None))]
     pub fn try_new(region: Option<String>) -> PyResult<Self> {
         let region = parse_region(region)?;
 

src/datasources/cram.rs

@@ -28,6 +28,7 @@ pub struct CRAMReadOptions {
 #[pymethods]
 impl CRAMReadOptions {
     #[new]
+    #[pyo3(signature = (region=None, fasta_reference=None))]
     pub fn try_new(region: Option<String>, fasta_reference: Option<String>) -> PyResult<Self> {
         let region = parse_region(region)?;
 

src/datasources/fasta.rs

@@ -20,8 +20,8 @@ use pyo3::{pyclass, pymethods};
 
 const DEFAULT_FASTA_FILE_EXTENSION: &str = "fasta";
 
-#[derive(Debug, Clone)]
-#[pyclass]
+#[derive(Debug, Clone, PartialEq, Eq)]
+#[pyclass(eq, eq_int)]
 pub enum FastaSequenceDataType {
     UTF8,
     #[allow(non_camel_case_types)]

src/datasources/fcs.rs

@@ -27,6 +27,7 @@ pub struct FCSReadOptions {
 #[pymethods]
 impl FCSReadOptions {
     #[new]
+    #[pyo3(signature = (file_compression_type=None))]
     pub fn new(file_compression_type: Option<FileCompressionType>) -> Self {
         Self {
             file_compression_type: file_compression_type.unwrap_or_default(),

src/datasources/genbank.rs

@@ -32,6 +32,7 @@ impl_settable_from_file_options!(GenBankReadOptions);
 #[pymethods]
 impl GenBankReadOptions {
     #[new]
+    #[pyo3(signature = (file_compression_type=None))]
     fn new(file_compression_type: Option<FileCompressionType>) -> Self {
         Self {
             file_compression_type,

src/datasources/gtf.rs

@@ -38,6 +38,7 @@ impl_settable_from_file_options!(GTFReadOptions);
 #[pymethods]
 impl GTFReadOptions {
     #[new]
+    #[pyo3(signature = (file_compression_type=None))]
     pub fn new(file_compression_type: Option<FileCompressionType>) -> Self {
         Self {
             file_compression_type,

src/datasources/hmm_dom_tab.rs

@@ -39,6 +39,7 @@ impl SettableFromFileOptions for HMMDomTabReadOptions {
 #[pymethods]
 impl HMMDomTabReadOptions {
     #[new]
+    #[pyo3(signature = (file_extension=None, file_compression_type=None))]
     fn new(
         file_extension: Option<String>,
         file_compression_type: Option<FileCompressionType>,

src/datasources/mzml.rs

@@ -39,6 +39,7 @@ impl Default for MzMLReadOptions {
 #[pymethods]
 impl MzMLReadOptions {
     #[new]
+    #[pyo3(signature = (file_compression_type=None))]
     fn new(file_compression_type: Option<FileCompressionType>) -> Self {
         Self {
             file_compression_type: Some(

src/exon_reader.rs

@@ -76,6 +76,7 @@ impl ExonReader {
 #[pymethods]
 impl ExonReader {
     #[new]
+    #[pyo3(signature = (path, file_type, compression=None, batch_size=None))]
     fn new(
         path: &str,
         file_type: &str,

src/file_compression_type.rs

@@ -22,8 +22,8 @@ use pyo3::prelude::*;
 
 use crate::error::BioBearError;
 
-#[pyclass]
 #[derive(Debug, Clone, PartialEq)]
+#[pyclass(eq, eq_int)]
 pub enum FileCompressionType {
     GZIP,
     ZSTD,

src/session_context.rs

@@ -44,6 +44,7 @@ impl BioBearSessionContext {
     }
 
     /// Read one or more VCF files from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_vcf_file(
         &mut self,
         file_path: &str,
@@ -62,6 +63,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a HMM Dom Tab file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_hmm_dom_tab_file(
         &mut self,
         file_path: &str,
@@ -80,6 +82,7 @@ impl BioBearSessionContext {
     }
 
     /// Read an SDF file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_sdf_file(
         &mut self,
         file_path: &str,
@@ -98,6 +101,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a bigwig file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_bigwig_file(
         &mut self,
         file_path: &str,
@@ -126,6 +130,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a gff file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_gff_file(
         &mut self,
         file_path: &str,
@@ -143,6 +148,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a fastq file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_fastq_file(
         &mut self,
         file_path: &str,
@@ -161,6 +167,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a genbank file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_genbank_file(
         &mut self,
         file_path: &str,
@@ -179,6 +186,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a CRAM file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_cram_file(
         &mut self,
         file_path: &str,
@@ -194,6 +202,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a mzml file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_mzml_file(
         &mut self,
         file_path: &str,
@@ -212,6 +221,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a GTF file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_gtf_file(
         &mut self,
         file_path: &str,
@@ -230,6 +240,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a BCF file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_bcf_file(
         &mut self,
         file_path: &str,
@@ -245,6 +256,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a fasta file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_fasta_file(
         &mut self,
         file_path: &str,
@@ -263,6 +275,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a BED file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_bed_file(
         &mut self,
         file_path: &str,
@@ -281,6 +294,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a BAM file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_bam_file(
         &mut self,
         file_path: &str,
@@ -296,6 +310,7 @@ impl BioBearSessionContext {
     }
 
     /// Read a SAM file from the given path.
+    #[pyo3(signature = (file_path, options=None))]
     fn read_sam_file(
         &mut self,
         file_path: &str,

src/vcf_reader.rs

@@ -59,6 +59,7 @@ impl VCFIndexedReader {
 #[pymethods]
 impl VCFIndexedReader {
     #[new]
+    #[pyo3(signature = (path, batch_size=None))]
     fn new(path: &str, batch_size: Option<usize>) -> PyResult<Self> {
         Self::open(path, batch_size).map_err(PyErr::new::<pyo3::exceptions::PyValueError, _>)
     }