update pyo3 version

Author: kno10

Cargo.toml

@@ -15,7 +15,7 @@ crate-type = ["cdylib"]
 
 [dependencies]
 rustkmedoids = { version = "0.4.0", package = "kmedoids", git = "https://github.com/kno10/rust-kmedoids" }
-numpy = "0.16"
+numpy = "0.17"
 ndarray = "0.15"
 rand = "0.8"
 rayon = "1.5"
@@ -24,18 +24,3 @@ rayon = "1.5"
 version = "0.17.1"
 features = ["extension-module"]
 
-[package.metadata.maturin]
-classifier = [
-        "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "Programming Language :: Python",
-        "Programming Language :: Rust",
-        "Operating System :: POSIX",
-        "Operating System :: MacOS",
-        "Operating System :: Microsoft :: Windows",
-        "Topic :: Scientific/Engineering :: Artificial Intelligence",
-        "Topic :: Software Development :: Libraries"
-]
-requires-dist = ["numpy"]
-project-url = { "ReadTheDocs" = "https://python-kmedoids.readthedocs.io/", "Rust Source Code" = "https://github.com/kno10/rust-kmedoids" }

README.md

@@ -22,11 +22,12 @@ an earlier (slower, and now obsolete) version was published as:
 This is a port of the original Java code from [ELKI](https://elki-project.github.io/) to Rust.
 The [Rust version](https://github.com/kno10/rust-kmedoids) is then wrapped for use with Python.
 
-For further details on the implemented algorithm FasterMSC, see:
+For further details on medoid Silhouette clustering with FasterMSC, see:
 
-> Lars Lenssen, Erich Schubert  
+> Lars Lenssen, Erich Schubert:  
 > **Clustering by Direct Optimization of the Medoid Silhouette**  
-> In: 15th International Conference on Similarity Search and Applications (SISAP 2022)
+> In: 15th International Conference on Similarity Search and Applications (SISAP 2022)  
+> <https://doi.org/10.1007/978-3-031-17849-8_15>
 
 If you use this code in scientific work, please cite above papers. Thank you.
 
@@ -64,6 +65,7 @@ maturin develop --release
 ```
 Integration test to validate the installation.
 ```sh
+pip install numpy
 python -m unittest discover tests
 ```
 

pyproject.toml

@@ -1,3 +1,22 @@
 [build-system]
-requires = ["maturin>=0.11,<0.12"]
+requires = ["maturin>=0.13,<0.14"]
 build-backend = "maturin"
+
+[project]
+name = "kmedoids"
+version = "0.4.0"
+description = "k-Medoids Clustering in Python with FasterPAM"
+requires-dist = ["numpy"]
+classifier = [
+        "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "Programming Language :: Python",
+        "Programming Language :: Rust",
+        "Operating System :: POSIX",
+        "Operating System :: MacOS",
+        "Operating System :: Microsoft :: Windows",
+        "Topic :: Scientific/Engineering :: Artificial Intelligence",
+        "Topic :: Software Development :: Libraries"
+]
+project-url = { "ReadTheDocs" = "https://python-kmedoids.readthedocs.io/", "Rust Source Code" = "https://github.com/kno10/rust-kmedoids" }

src/lib.rs

@@ -23,9 +23,9 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let mut meds = meds.to_vec()?;
     let (loss, assi, n_iter, n_swap): ($ltype, _, _, _) = rustkmedoids::$variant(&dist.as_array(), &mut meds, max_iter);
-    let gil = Python::acquire_gil();
-    let py = gil.python();
-    Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+    Python::with_gil(|py| -> PyResult<Py<PyAny>> {
+      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+    })
 }
 }}
 variant_call!(fasterpam_f32, fasterpam, f32, f64);
@@ -70,9 +70,9 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
     let mut meds = meds.to_vec()?;
     let mut rnd = StdRng::seed_from_u64(seed);
     let (loss, assi, n_iter, n_swap): ($ltype, _, _, _) = rustkmedoids::$variant(&dist.as_array(), &mut meds, max_iter, &mut rnd);
-    let gil = Python::acquire_gil();
-    let py = gil.python();
-    Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+    Python::with_gil(|py| -> PyResult<Py<PyAny>> {
+      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+    })
 }
 }}
 rand_call!(rand_fasterpam_f32, rand_fasterpam, f32, f64);
@@ -107,9 +107,9 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
         let mut rnd = StdRng::seed_from_u64(seed);
         rustkmedoids::$variant(&dist, &mut meds, max_iter, &mut rnd)
     });
-    let gil = Python::acquire_gil();
-    let py = gil.python();
-    Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+    Python::with_gil(|py| -> PyResult<Py<PyAny>> {
+      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+    })
 }
 }}
 par_call!(par_fasterpam_f32, par_fasterpam, f32, f64);
@@ -132,9 +132,9 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, k: usize) -> PyResult<Py<PyAny>> {
     assert_eq!(dist.ndim(), 2);
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let (loss, assi, meds): ($ltype, _, _) = rustkmedoids::pam_build(&dist.as_array(), k);
-    let gil = Python::acquire_gil();
-    let py = gil.python();
-    Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), 1).to_object(py))
+    Python::with_gil(|py| -> PyResult<Py<PyAny>> {
+      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), 1).to_object(py))
+    })
 }
 }}
 pam_build_call!(pam_build_f32, f32, f64);
@@ -160,9 +160,9 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let mut meds = meds.to_vec()?;
     let (loss, assi, n_iter): ($ltype, _, _) = rustkmedoids::alternating(&dist.as_array(), &mut meds, max_iter);
-    let gil = Python::acquire_gil();
-    let py = gil.python();
-    Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter).to_object(py))
+    Python::with_gil(|py| -> PyResult<Py<PyAny>> {
+      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter).to_object(py))
+    })
 }
 }}
 alternating_call!(alternating_f32, f32, f64);
@@ -187,9 +187,9 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, assi: PyReadonlyArray1<'_, usize>, s
     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);
-    let gil = Python::acquire_gil();
-    let py = gil.python();
-    Ok((sil, PyArray1::from_vec(py, sils)).to_object(py))
+    Python::with_gil(|py| -> PyResult<Py<PyAny>> {
+      Ok((sil, PyArray1::from_vec(py, sils)).to_object(py))
+    })
 }
 }}
 silhouette_call!(silhouette_f32, f32);