update pyo3/polars

Author: niklasmueboe

Cargo.toml

@@ -2,7 +2,7 @@
 name         = "_utils_rust"
 version      = "0.1.0"
 edition      = "2021"
-rust-version = "1.76.0"
+rust-version = "1.85.0"
 
 [lib]
 name       = "_utils_rust"
@@ -15,10 +15,10 @@ itertools     = { version = "0.12.1" }
 ndarray       = { version = "0.15.6", features = ["rayon"] }
 ndarray-stats = { version = "0.5.1" }
 num           = { version = "0.4.1" }
-numpy         = { version = "0.21" }
-polars        = { version = "0.44", features = ["partition_by", "dtype-categorical"] }
-polars-arrow  = { version = "0.44" }
-pyo3          = { version = "0.21", features = ["extension-module"] }
-pyo3-polars   = { version = "0.18", features = ["dtype-categorical"] }
+numpy         = { version = "0.24" }
+polars        = { version = "0.48", features = ["partition_by", "dtype-categorical"] }
+polars-arrow  = { version = "0.48" }
+pyo3          = { version = "0.24.2", features = ["extension-module"] }
+pyo3-polars   = { version = "0.21", features = ["dtype-categorical"] }
 rayon         = { version = "1.8" }
 sprs          = { version = "= 0.11.1", features = ["serde"] }

src/coordinates.rs

@@ -20,9 +20,7 @@ pub fn coordinate_as_string<'py>(
     n_threads: Option<usize>,
 ) -> PyResult<Bound<'py, PyArray1<PyFixedString<12>>>> {
     match string_coordinate_index_(x.as_array(), y.as_array(), n_threads) {
-        Ok(string_coordinates) => Ok(string_coordinates
-            .map(|s| (*s).into())
-            .into_pyarray_bound(py)),
+        Ok(string_coordinates) => Ok(string_coordinates.map(|s| (*s).into()).into_pyarray(py)),
         Err(e) => Err(PyRuntimeError::new_err(e.to_string())),
     }
 }
@@ -40,10 +38,7 @@ pub fn categorical_coordinate<'py>(
     Bound<'py, PyArray2<CoordInt>>,
 )> {
     match categorical_coordinate_(x.as_array(), y.as_array(), n_threads) {
-        Ok((codes, coordinates)) => Ok((
-            codes.into_pyarray_bound(py),
-            coordinates.into_pyarray_bound(py),
-        )),
+        Ok((codes, coordinates)) => Ok((codes.into_pyarray(py), coordinates.into_pyarray(py))),
         Err(e) => Err(PyRuntimeError::new_err(e.to_string())),
     }
 }

src/cosine.rs

@@ -56,9 +56,9 @@ macro_rules! build_cos_ct_fn {
 
             match cos_ct {
                 Ok((cosine, score, celltype_map)) => Ok((
-                    cosine.into_pyarray_bound(py),
-                    score.into_pyarray_bound(py),
-                    celltype_map.into_pyarray_bound(py),
+                    cosine.into_pyarray(py),
+                    score.into_pyarray(py),
+                    celltype_map.into_pyarray(py),
                 )),
                 Err(e) => Err(PyValueError::new_err(e.to_string())),
             }

src/gridcounts.rs

@@ -281,7 +281,7 @@ impl GridCounts {
 
     fn __getstate__<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyBytes>> {
         match serialize(&(&self.counts, self.shape, self.resolution, self.n_threads)) {
-            Ok(bytes) => Ok(PyBytes::new_bound(py, &bytes)),
+            Ok(bytes) => Ok(PyBytes::new(py, &bytes)),
             Err(e) => Err(PyRuntimeError::new_err(e.to_string())),
         }
     }
@@ -379,7 +379,7 @@ impl GridCounts {
         });
 
         let gridcounts = triplet_to_dense(TriMatI::from_triplets(self.shape, i, j, v));
-        Python::with_gil(|py| gridcounts.into_pyarray_bound(py).unbind())
+        Python::with_gil(|py| gridcounts.into_pyarray(py).unbind())
     }
 
     fn select_genes(&mut self, genes: HashSet<String>) {

src/sparsearray_conversion.rs

@@ -22,7 +22,7 @@ static SPMATRIX: GILOnceCell<Py<PyAny>> = GILOnceCell::new();
 pub struct WrappedCsx<N, I: SpIndex, Iptr: SpIndex>(pub CsMatI<N, I, Iptr>);
 
 fn get_scipy_sparse(py: Python) -> PyResult<&Py<PyModule>> {
-    SP_SPARSE.get_or_try_init(py, || Ok(py.import_bound("scipy.sparse")?.unbind()))
+    SP_SPARSE.get_or_try_init(py, || Ok(py.import("scipy.sparse")?.unbind()))
 }
 
 fn get_scipy_sparse_attr(py: Python, attr: &str) -> PyResult<PyObject> {
@@ -46,16 +46,20 @@ where
     let (indptr, indices, data) = cs.into_raw_storage();
 
     return (
-        data.into_pyarray_bound(py),
-        indices.into_pyarray_bound(py),
-        indptr.into_pyarray_bound(py),
+        data.into_pyarray(py),
+        indices.into_pyarray(py),
+        indptr.into_pyarray(py),
     );
 }
 
-impl<N: Element, I: SpIndex + Element, Iptr: SpIndex + Element> IntoPy<PyObject>
+impl<'py, N: Element, I: SpIndex + Element, Iptr: SpIndex + Element> IntoPyObject<'py>
     for WrappedCsx<N, I, Iptr>
 {
-    fn into_py(self, py: Python<'_>) -> PyObject {
+    type Target = PyAny;
+    type Output = Bound<'py, Self::Target>;
+    type Error = PyErr; // TODO: propagate better errors?
+
+    fn into_pyobject(self, py: Python<'py>) -> Result<Self::Output, Self::Error> {
         let csx = self.0;
         let shape = csx.shape();
 
@@ -67,16 +71,14 @@ impl<N: Element, I: SpIndex + Element, Iptr: SpIndex + Element> IntoPy<PyObject>
         sparray
             .unwrap()
             .call1(py, (make_csx_tuple(py, csx), shape))
-            .unwrap()
-            .extract(py)
-            .unwrap()
+            .map(move |x| x.into_bound(py))
     }
 }
-impl<'py, N: Element, I: SpIndex + Element, Iptr: SpIndex + Element> FromPyObject<'py>
+impl<'py, N: Element + Clone, I: SpIndex + Element, Iptr: SpIndex + Element> FromPyObject<'py>
     for WrappedCsx<N, I, Iptr>
 {
     fn extract_bound(obj: &Bound<'py, PyAny>) -> PyResult<Self> {
-        fn boundpyarray_to_vec<T: Element>(obj: Bound<'_, PyAny>) -> PyResult<Vec<T>> {
+        fn boundpyarray_to_vec<T: Element + Clone>(obj: Bound<'_, PyAny>) -> PyResult<Vec<T>> {
             Ok(obj.extract::<PyReadonlyArray1<T>>()?.as_array().to_vec())
         }