build: use updated maturin release workflow (#44)

Author: jsstevenson

.github/workflows/release.yaml

@@ -1,86 +1,103 @@
-# This file is autogenerated by maturin v1.2.3
-# To update, run
-#
-#    maturin generate-ci github
-#
-# Edited to incorporate genomicmedlab/software-templates Python template
-# See also https://www.maturin.rs/distribution#using-pypis-trusted-publishing
 name: Publish Python distribution to PyPI
 
 on:
-  release:
-    types: [created]
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  workflow_dispatch:
 
 permissions:
   contents: read
 
 jobs:
   linux:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x86_64, x86, aarch64, armv7, s390x, ppc64le]
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: x86
+          - runner: ubuntu-22.04
+            target: aarch64
+          - runner: ubuntu-22.04
+            target: armv7
+          - runner: ubuntu-22.04
+            target: s390x
+          - runner: ubuntu-22.04
+            target: ppc64le
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path rust/Cargo.toml
           sccache: 'true'
           manylinux: auto
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-linux-${{ matrix.platform.target }}
           path: dist
 
   windows:
-    runs-on: windows-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x64, x86]
+        platform:
+          - runner: windows-latest
+            target: x64
+          - runner: windows-latest
+            target: x86
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-          architecture: ${{ matrix.target }}
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path rust/Cargo.toml
           sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-windows-${{ matrix.platform.target }}
           path: dist
 
   macos:
-    runs-on: macos-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x86_64, aarch64]
+        platform:
+          - runner: macos-latest
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path rust/Cargo.toml
           sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-macos-${{ matrix.platform.target }}
           path: dist
 
   sdist:
@@ -95,25 +112,35 @@ jobs:
       - name: Upload sdist
         uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-sdist
           path: dist
 
   release:
     name: Release
     runs-on: ubuntu-latest
+    if: ${{ startsWith(github.ref, 'refs/tags/') }}
+    needs: [
+      linux,
+      windows,
+      macos,
+      sdist
+    ]
     environment:
       name: pypi
       url: https://pypi.org/p/agct
     permissions:
-      id-token: write # IMPORTANT: mandatory for trusted publishing
-    if: "startsWith(github.ref, 'refs/tags/')"
-    needs: [linux, windows, macos, sdist]
+      id-token: write
+      contents: write
+      attestations: write
     steps:
-      - uses: actions/download-artifact@v4
+      - name: Acquire build artifacts from parent jobs
+        uses: actions/download-artifact@v4
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
         with:
-          name: wheels
+          subject-path: 'wheels-*/*'
       - name: Publish to PyPI
         uses: PyO3/maturin-action@v1
         with:
           command: upload
-          args: --non-interactive --skip-existing *
+          args: --non-interactive --skip-existing wheels-*/*

rust/Cargo.toml

@@ -11,7 +11,4 @@ crate-type = ["cdylib"]
 chainfile = "0.3.0"
 directories = "5.0"
 omics = { version = "0.2.0", features = ["coordinate"] }
-
-[dependencies.pyo3]
-version = "0.20.2"
-features = ["abi3-py38"]
+pyo3 = { version = "0.23.3", features = ["abi3-py310"] }

rust/src/lib.rs

@@ -86,7 +86,7 @@ impl Converter {
 /// agct._core Python module. Collect Python-facing methods.
 #[pymodule]
 #[pyo3(name = "_core")]
-fn agct(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
+fn agct(_py: Python<'_>, m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<Converter>()?;
     m.add("NoLiftoverError", _py.get_type::<NoLiftoverError>())?;
     m.add("ChainfileError", _py.get_type::<ChainfileError>())?;