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Updated PyO3 from 0.17.3 to 0.24.2, specified minimum Python version as 3.9 #9

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Merged
tombch merged 1 commit into from
Apr 30, 2025
Merged

Updated PyO3 from 0.17.3 to 0.24.2, specified minimum Python version as 3.9 #9

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170 changes: 37 additions & 133 deletions Cargo.lock
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2 changes: 1 addition & 1 deletion Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,5 +9,5 @@ name = "maptide"
crate-type = ["cdylib"]

[dependencies]
pyo3 = { version = "0.17.3", features = ["extension-module", "abi3-py37"] }
pyo3 = { version = "0.24.2", features = ["extension-module", "abi3-py39"] }
noodles = { version = "0.31.1", features = ["core", "bam", "sam", "bgzf"] }
16 changes: 5 additions & 11 deletions src/lib.rs
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Expand Up @@ -13,15 +13,9 @@ use std::fs::File;
mod error;
use error::MapTideError;

#[derive(Debug, PartialEq, Eq, PartialOrd, Ord, Hash, Clone, Copy)]
#[derive(IntoPyObject, Debug, PartialEq, Eq, PartialOrd, Ord, Hash, Clone, Copy)]
struct Coordinate(usize, usize);

impl IntoPy<PyObject> for Coordinate {
fn into_py(self, py: Python<'_>) -> PyObject {
(self.0, self.1).into_py(py)
}
}

impl From<MapTideError> for PyErr {
fn from(e: MapTideError) -> Self {
match e {
Expand Down Expand Up @@ -379,7 +373,7 @@ fn merge_into_base_map(
Ok(ins_maps)
}

#[pyfunction]
#[pyfunction(signature = (bam_path, mapping_quality, base_quality))]
fn all(bam_path: String, mapping_quality: usize, base_quality: usize) -> PyResult<MapTide> {
// Create initial maps
let (mut ref_arrs, mut ins_maps, mut ref_lengths) = init_maps();
Expand Down Expand Up @@ -450,7 +444,7 @@ fn all(bam_path: String, mapping_quality: usize, base_quality: usize) -> PyResul
Ok(base_map)
}

#[pyfunction]
#[pyfunction(signature = (bam_path, bai_path, region, mapping_quality, base_quality))]
fn query(
bam_path: String,
bai_path: Option<String>,
Expand Down Expand Up @@ -571,7 +565,7 @@ fn query(
Ok(base_map)
}

#[pyfunction]
#[pyfunction(signature = (region))]
fn parse_region(region: String) -> PyResult<(String, Option<usize>, Option<usize>)> {
let region: Region = region
.parse()
Expand All @@ -591,7 +585,7 @@ fn parse_region(region: String) -> PyResult<(String, Option<usize>, Option<usize

/// A Python module implemented in Rust.
#[pymodule]
fn maptide(_py: Python, m: &PyModule) -> PyResult<()> {
fn maptide(m: &Bound<'_, PyModule>) -> PyResult<()> {
m.add_function(wrap_pyfunction!(all, m)?)?;
m.add_function(wrap_pyfunction!(query, m)?)?;
m.add_function(wrap_pyfunction!(parse_region, m)?)?;
Expand Down