Version updates

kno10 · Sep 10, 2024 · ccb60aa · ccb60aa
1 parent 67e48ac
commit ccb60aa
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diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -12,15 +12,16 @@ jobs:
     strategy:
       matrix:
         container:
+          - "quay.io/pypa/musllinux_1_2_x86_64"
           - "quay.io/pypa/manylinux2014_x86_64"
           - "quay.io/pypa/manylinux_2_28_x86_64"
     container: ${{ matrix.container }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build wheels
         run: |
           bash .github/workflows/build-wheels.sh
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: wheels
           path: wheelhouse
@@ -31,17 +32,18 @@ jobs:
     strategy:
       matrix:
         container:
+          - "quay.io/pypa/musllinux_1_2_aarch64"
           - "quay.io/pypa/manylinux2014_aarch64"
           - "quay.io/pypa/manylinux_2_28_aarch64"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install QEMU
         run: |
           docker run --privileged --rm tonistiigi/binfmt --install arm64
       - name: Build wheels
         run: |
           docker run --platform linux/arm64 --workdir /src -v ${PWD}:/src ${{ matrix.container }} /bin/bash .github/workflows/build-wheels.sh
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: wheels
           path: wheelhouse
@@ -51,9 +53,9 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions-rs/toolchain@v1
         with:
           toolchain: stable
@@ -68,7 +70,7 @@ jobs:
           maturin build --release --strip --target universal2-apple-darwin
           python3 -m pip install kmedoids --no-index --find-links target/wheels
           cd tests && python3 -m unittest discover && cd ..
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: wheels
           path: target/wheels
@@ -78,9 +80,9 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions-rs/toolchain@v1
         with:
           toolchain: stable
@@ -94,7 +96,7 @@ jobs:
           maturin build --release --strip
           python -m pip install kmedoids --no-index --find-links target/wheels
           cd tests && python -m unittest discover && cd ..
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: wheels
           path: target/wheels
@@ -106,7 +108,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Collect artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: wheels
           path: wheels/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,12 @@
 
 For changes to the main Rust package, please see <https://github.com/kno10/rust-kmedoids/blob/main/CHANGELOG.md>
 
+## kmedoids 0.5.2 (2024-09-10)
+
+- fix clippy warnings
+- update to pyo3 0.21, numpy 0.21
+- update github action for python 3.13 and musllinux
+
 ## kmedoids 0.5.1 (2024-03-14)
 
 - DynMSC: best loss reported incorrectly if best k=2

diff --git a/CITATION.cff b/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: 0.5.1
-date-released: 2024-03-14
+version: 0.5.2
+date-released: 2024-09-10
 license: GPL-3.0
 preferred-citation:
   title: "Fast k-medoids Clustering in Rust and Python"

diff --git a/Cargo.toml b/Cargo.toml
@@ -1,7 +1,7 @@
 [package]
 edition = "2021"
 name = "kmedoids"
-version = "0.5.1"
+version = "0.5.2"
 authors = ["Erich Schubert <[email protected]>", "Lars Lenssen <[email protected]>"]
 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 = "0.5.1", package = "kmedoids", git = "https://github.com/kno10/rust-kmedoids" }
-numpy = "0.20"
+rustkmedoids = { version = "0.5.2", package = "kmedoids", git = "https://github.com/kno10/rust-kmedoids" }
+numpy = "0.21"
 ndarray = "0.15"
 rand = "0.8"
-rayon = "1.9"
+rayon = "1.10"
 
 [dependencies.pyo3]
-version = "0.20"
+version = "^0.21"
 features = ["extension-module"]
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "kmedoids"
-version = "0.5.1"
+version = "0.5.2"
 description = "k-Medoids Clustering in Python with FasterPAM"
 requires-dist = ["numpy"]
 classifier = [

diff --git a/src/lib.rs b/src/lib.rs
@@ -1,9 +1,7 @@
 use pyo3::prelude::*;
 use pyo3::wrap_pyfunction;
-use numpy::{PyArray1, PyReadonlyArray1, PyReadonlyArray2};
+use numpy::{PyArray1, PyReadonlyArray1, PyReadonlyArray2, PyArrayMethods, PyUntypedArrayMethods};
 use rand::{rngs::StdRng, SeedableRng};
-use rayon;
-use rustkmedoids;
 
 macro_rules! variant_call {
 ($name:ident, $variant:ident, $type: ty, $ltype: ty) => {
@@ -24,7 +22,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
     let mut meds = meds.to_vec()?;
     let (loss, assi, n_iter, n_swap): ($ltype, _, _, _) = rustkmedoids::$variant(&dist.as_array(), &mut meds, max_iter);
     Python::with_gil(|py| -> PyResult<Py<PyAny>> {
-      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+      Ok((loss, PyArray1::from_vec_bound(py, assi), PyArray1::from_vec_bound(py, meds), n_iter, n_swap).to_object(py))
     })
 }
 }}
@@ -71,7 +69,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
     let mut rnd = StdRng::seed_from_u64(seed);
     let (loss, assi, n_iter, n_swap): ($ltype, _, _, _) = rustkmedoids::$variant(&dist.as_array(), &mut meds, max_iter, &mut rnd);
     Python::with_gil(|py| -> PyResult<Py<PyAny>> {
-      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter, n_swap).to_object(py))
+      Ok((loss, PyArray1::from_vec_bound(py, assi), PyArray1::from_vec_bound(py, meds), n_iter, n_swap).to_object(py))
     })
 }
 }}
@@ -108,7 +106,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
         rustkmedoids::$variant(&dist, &mut meds, max_iter, &mut rnd)
     });
     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))
+      Ok((loss, PyArray1::from_vec_bound(py, assi), PyArray1::from_vec_bound(py, meds), n_iter, n_swap).to_object(py))
     })
 }
 }}
@@ -133,7 +131,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, k: usize) -> PyResult<Py<PyAny>> {
     assert_eq!(dist.shape()[0], dist.shape()[1]);
     let (loss, assi, meds): ($ltype, _, _) = rustkmedoids::pam_build(&dist.as_array(), k);
     Python::with_gil(|py| -> PyResult<Py<PyAny>> {
-      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), 1).to_object(py))
+      Ok((loss, PyArray1::from_vec_bound(py, assi), PyArray1::from_vec_bound(py, meds), 1).to_object(py))
     })
 }
 }}
@@ -161,7 +159,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
     let mut meds = meds.to_vec()?;
     let (loss, assi, n_iter): ($ltype, _, _) = rustkmedoids::alternating(&dist.as_array(), &mut meds, max_iter);
     Python::with_gil(|py| -> PyResult<Py<PyAny>> {
-      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, meds), n_iter).to_object(py))
+      Ok((loss, PyArray1::from_vec_bound(py, assi), PyArray1::from_vec_bound(py, meds), n_iter).to_object(py))
     })
 }
 }}
@@ -191,7 +189,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, m
     let (loss, assi, n_iter, n_swap, best_meds, losses): ($ltype, _, _, _, _, _) = rustkmedoids::dynmsc(&dist.as_array(), &mut meds, minimum_k, max_iter);
     let bestk = best_meds.len();
     Python::with_gil(|py| -> PyResult<Py<PyAny>> {
-      Ok((loss, PyArray1::from_vec(py, assi), PyArray1::from_vec(py, best_meds), bestk, PyArray1::from_vec(py, losses), (minimum_k..maxk).collect::<Vec<usize>>(), n_iter, n_swap).to_object(py))
+      Ok((loss, PyArray1::from_vec_bound(py, assi), PyArray1::from_vec_bound(py, best_meds), bestk, PyArray1::from_vec_bound(py, losses), (minimum_k..maxk).collect::<Vec<usize>>(), n_iter, n_swap).to_object(py))
     })
 }
 }}
@@ -216,7 +214,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, assi: PyReadonlyArray1<'_, usize>, s
     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| -> PyResult<Py<PyAny>> {
-      Ok((sil, PyArray1::from_vec(py, sils)).to_object(py))
+      Ok((sil, PyArray1::from_vec_bound(py, sils)).to_object(py))
     })
 }
 }}
@@ -271,7 +269,7 @@ fn $name(dist: PyReadonlyArray2<'_, $type>, meds: PyReadonlyArray1<'_, usize>, s
     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| -> PyResult<Py<PyAny>> {
-      Ok((sil, PyArray1::from_vec(py, sils)).to_object(py))
+      Ok((sil, PyArray1::from_vec_bound(py, sils)).to_object(py))
     })
 }
 }}
@@ -282,7 +280,7 @@ medoid_silhouette_call!(medoid_silhouette_i32, i32);
 
 #[pymodule]
 #[allow(unused_variables)]
-fn kmedoids(py: Python, m: &PyModule) -> PyResult<()> {
+fn kmedoids(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add("_fasterpam_f32", wrap_pyfunction!(fasterpam_f32, m)?)?;
     m.add("_fasterpam_f64", wrap_pyfunction!(fasterpam_f64, m)?)?;
     m.add("_fasterpam_i32", wrap_pyfunction!(fasterpam_i32, m)?)?;
@@ -335,4 +333,3 @@ fn kmedoids(py: Python, m: &PyModule) -> PyResult<()> {
     // not supported: m.add("_medoid_silhouette_i64", wrap_pyfunction!(medoid_silhouette_i64, m)?)?;
     Ok(())
 }
-