Update dependencies, for Python 3.14 compatibility

Author: kno10

.gitignore

@@ -1 +1,6 @@
 /target
+/build
+/tests/__pycache__
+/kmedoids/__pycache__
+/kmedoids/*.so
+/Cargo.lock

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 For changes to the main Rust package, please see <https://github.com/kno10/rust-kmedoids/blob/main/CHANGELOG.md>
 
+## kmedoids 0.5.4 (2025-09-17)
+
+- no functionality changes
+- update Rust edition, rand, rayon
+- Python 3.14 compatibility
+- update to pyo3 0.26, numpy 0.26
+
 ## kmedoids 0.5.3.1 (2024-12-09)
 
 - no changes, but rebuild binary packages because of compile issue

CITATION.cff

@@ -10,8 +10,8 @@ authors:
 title: "Fast k-medoids Clustering in Rust and Python"
 journal: "J. Open Source Softw."
 doi: 10.21105/joss.04183
-version: 0.5.3
-date-released: 2024-12-02
+version: 0.5.4
+date-released: 2025-09-17
 license: GPL-3.0
 preferred-citation:
   title: "Fast k-medoids Clustering in Rust and Python"

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
-edition = "2021"
+edition = "2024"
 name = "kmedoids"
-version = "0.5.3"
+version = "0.5.4"
 authors = ["Erich Schubert <erich.schubert@tu-dortmund.de>", "Lars Lenssen <lars.lenssen@tu-dortmund.de>"]
 description = "k-Medoids clustering with the FasterPAM algorithm"
 homepage = "https://github.com/kno10/python-kmedoids"
@@ -14,13 +14,13 @@ name = "kmedoids"
 crate-type = ["cdylib"]
 
 [dependencies]
-rustkmedoids = { version = "0.5.3", package = "kmedoids", git = "https://github.com/kno10/rust-kmedoids" }
-numpy = "0.23"
+rustkmedoids = { version = "0.5.4", package = "kmedoids", git = "https://github.com/kno10/rust-kmedoids" }
+numpy = "0.26"
 ndarray = "0.16"
-rand = "0.8"
-rayon = "1.10"
+rand = "0.9"
+rayon = "1.11"
 
 [dependencies.pyo3]
-version = "^0.23"
+version = "^0.26"
 features = ["extension-module"]
 

src/lib.rs

@@ -22,7 +22,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, meds: PyReadonlyArray1<'py, us
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let mut meds = meds.to_vec()?;
     let (loss, assi, n_iter, n_swap): ($ltype, _, _, _) = rustkmedoids::$variant(&dist.as_array(), &mut meds, max_iter);
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).into_pyobject(py)?.unbind())
     })
 }
@@ -69,7 +69,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, meds: PyReadonlyArray1<'py, us
     let mut meds = meds.to_vec()?;
     let mut rnd = StdRng::seed_from_u64(seed);
     let (loss, assi, n_iter, n_swap): ($ltype, _, _, _) = rustkmedoids::$variant(&dist.as_array(), &mut meds, max_iter, &mut rnd);
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).into_pyobject(py)?.unbind())
     })
 }
@@ -106,7 +106,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, meds: PyReadonlyArray1<'py, us
         let mut rnd = StdRng::seed_from_u64(seed);
         rustkmedoids::$variant(&dist, &mut meds, max_iter, &mut rnd)
     });
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).into_pyobject(py)?.unbind())
     })
 }
@@ -131,7 +131,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, k: usize) -> PyResult<Py<PyTup
     assert_eq!(dist.ndim(), 2);
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let (loss, assi, meds): ($ltype, _, _) = rustkmedoids::pam_build(&dist.as_array(), k);
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), 1).into_pyobject(py)?.unbind())
     })
 }
@@ -159,7 +159,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, meds: PyReadonlyArray1<'py, us
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let mut meds = meds.to_vec()?;
     let (loss, assi, n_iter): ($ltype, _, _) = rustkmedoids::alternating(&dist.as_array(), &mut meds, max_iter);
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter).into_pyobject(py)?.unbind())
     })
 }
@@ -189,7 +189,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, meds: PyReadonlyArray1<'py, us
     let maxk = meds.len() + 1;
     let (loss, assi, n_iter, n_swap, best_meds, losses): ($ltype, _, _, _, _, _) = rustkmedoids::dynmsc(&dist.as_array(), &mut meds, minimum_k, max_iter);
     let bestk = best_meds.len();
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, best_meds), bestk, PyArray1::from_vec(py, losses), PyArray1::from_vec(py, (minimum_k..maxk).collect::<Vec<usize>>()), n_iter, n_swap).into_pyobject(py)?.unbind())
     })
 }
@@ -214,7 +214,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, assi: PyReadonlyArray1<'py, us
     assert_eq!(dist.ndim(), 2);
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let (sil, sils): (f64, _) = rustkmedoids::silhouette(&dist.as_array(), &assi.to_vec()?, samples);
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((sil, PyArray1::from_vec(py, sils)).into_pyobject(py)?.unbind())
     })
 }
@@ -269,7 +269,7 @@ fn $name<'py>(dist: PyReadonlyArray2<'py, $type>, meds: PyReadonlyArray1<'py, us
     assert_eq!(dist.ndim(), 2);
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let (sil, sils): (f64, _) = rustkmedoids::medoid_silhouette(&dist.as_array(), &meds.to_vec()?, samples);
-    Python::with_gil(|py| {
+    Python::attach(|py| {
         Ok((sil, PyArray1::from_vec(py, sils)).into_pyobject(py)?.unbind())
     })
 }
@@ -332,5 +332,6 @@ fn kmedoids(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add("_medoid_silhouette_f64", wrap_pyfunction!(medoid_silhouette_f64, m)?)?;
     m.add("_medoid_silhouette_i32", wrap_pyfunction!(medoid_silhouette_i32, m)?)?;
     // not supported: m.add("_medoid_silhouette_i64", wrap_pyfunction!(medoid_silhouette_i64, m)?)?;
+    // use m.sum(axis=1).argmin() instead of choose_medoid_within_partition
     Ok(())
 }