Refactor: rewrite in rust

.github/workflows/release.yml

@@ -0,0 +1,310 @@
+# This file is autogenerated by maturin v1.13.3
+# To update, run
+#
+#    maturin generate-ci github --pytest -o .github/workflows/release.yml
+#
+# Builds + tests wheels on every push/PR; publishes to PyPI on tag push.
+name: Release
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+  # Publishing a GitHub Release is the single source of truth for a release:
+  # the version is taken from the release tag and the wheels go to PyPI.
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Mainstream glibc targets with working test emulation. Other arches
+        # (s390x/ppc64le/32-bit) install from the sdist.
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.8"
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+      - uses: astral-sh/setup-uv@v7
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        shell: bash
+        run: |
+          set -e
+          uv venv .venv
+          source .venv/bin/activate
+          uv pip install seqfold --no-index --no-deps --find-links dist --reinstall
+          uv pip install seqfold pytest
+          pytest
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'x86') && matrix.platform.target != 'ppc64' }}
+        uses: uraimo/run-on-arch-action@v2
+        with:
+          arch: ${{ matrix.platform.target }}
+          # run-on-arch-action@v2 ships no ubuntu24.04 image; ubuntu22.04 has
+          # the aarch64 image needed to run the emulated test step.
+          distro: ubuntu22.04
+          githubToken: ${{ github.token }}
+          install: |
+            apt-get update
+            apt-get install -y --no-install-recommends python3 python3-venv
+          run: |
+            set -e
+            python3 -m venv .venv
+            source .venv/bin/activate
+            pip install pytest
+            pip install seqfold --no-index --no-deps --find-links dist --force-reinstall
+            pip install seqfold
+            pytest
+
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.8"
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        run: |
+          set -e
+          docker run --rm -v ${{ github.workspace }}:/io -w /io alpine:latest sh -c '
+            apk add py3-pip py3-virtualenv
+            python3 -m virtualenv .venv
+            source .venv/bin/activate
+            pip install seqfold --no-index --no-deps --find-links dist --force-reinstall
+            pip install seqfold pytest
+            pytest
+          '
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'x86') }}
+        uses: uraimo/run-on-arch-action@v2
+        with:
+          arch: ${{ matrix.platform.target }}
+          distro: alpine_latest
+          githubToken: ${{ github.token }}
+          install: |
+            apk add py3-virtualenv
+          run: |
+            set -e
+            python3 -m virtualenv .venv
+            source .venv/bin/activate
+            pip install seqfold --no-index --no-deps --find-links dist --force-reinstall
+            pip install seqfold pytest
+            pytest
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # 32-bit Windows (x86) is dropped: setup-python can't reliably provide
+        # 32-bit CPython 3.13, and it's a legacy target with ~no users. Those
+        # install from the sdist.
+        platform:
+          - runner: windows-latest
+            target: x64
+            python_arch: x64
+          - runner: windows-11-arm
+            target: aarch64
+            python_arch: arm64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+          architecture: ${{ matrix.platform.python_arch }}
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+      - uses: astral-sh/setup-uv@v7
+      - name: pytest
+        shell: bash
+        run: |
+          set -e
+          uv venv .venv
+          source .venv/Scripts/activate
+          uv pip install seqfold --no-index --no-deps --find-links dist --reinstall
+          uv pip install seqfold pytest
+          pytest
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - runner: macos-15-intel
+            target: x86_64
+          - runner: macos-latest
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.8"
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+      - uses: astral-sh/setup-uv@v7
+      - name: pytest
+        run: |
+          set -e
+          uv venv .venv
+          source .venv/bin/activate
+          uv pip install seqfold --no-index --no-deps --find-links dist --reinstall
+          uv pip install seqfold pytest
+          pytest
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set version from release tag
+        if: github.event_name == 'release'
+        shell: bash
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          V="${TAG#v}"   # strip an optional leading "v"
+          sed -i.bak "s/^version = .*/version = \"$V\"/" Cargo.toml && rm -f Cargo.toml.bak
+          echo "building seqfold $V"
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'release' || github.event_name == 'workflow_dispatch' }}
+    needs: [linux, musllinux, windows, macos, sdist]
+    # Dedicated publishing environment. Configure it under repo Settings ->
+    # Environments (and name it as the PyPI trusted publisher's "Environment").
+    # Add required reviewers there to gate who can actually publish to PyPI.
+    environment: pypi
+    permissions:
+      # Mint the OIDC token PyPI trusted publishing exchanges (no API token).
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v7
+      - name: Generate artifact attestation
+        uses: actions/attest@v4
+        with:
+          subject-path: 'wheels-*/*'
+      - name: Install uv
+        if: ${{ github.event_name == 'release' }}
+        uses: astral-sh/setup-uv@v7
+      # No token: uv uses GitHub OIDC trusted publishing (id-token: write above).
+      - name: Publish to PyPI
+        if: ${{ github.event_name == 'release' }}
+        run: uv publish --trusted-publishing always 'wheels-*/*'

.gitignore

@@ -135,6 +135,10 @@ dmypy.json
 seqfold/*.c
 seqfold/*.html
 
+# Rust / maturin build artifacts
+/target
+.venv/
+
 # development/test files
 /data/dna
 *.stats