minimappers2-update

.github/workflows/build-test-rust-minimappers2.yaml

@@ -4,41 +4,71 @@ on:
   pull_request:
     branches: [ "main" ]
     paths: 
-      - 'minimappers2/src/'
-      - 'minimappers2/Cargo.toml'
+      - minimappers2/src/
+      - minimappers2/Cargo.toml
+      - minimappers2/**
+      - .github/workflows/build-test-rust-minimappers2.yaml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 env:
+  RUSTFLAGS: -C debuginfo=0  # Do not produce debug symbols to keep memory usage down
+  RUST_BACKTRACE: 1
+  PYTHONUTF8: 1
   CARGO_TERM_COLOR: always
 
+defaults:
+  run:
+    working-directory: minimappers2
+    shell: bash
+
 jobs:
-  test:
-    runs-on: ubuntu-latest
+  test-python:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.9', '3.12', '3.13']
+
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: 'recursive'
-    - run: cd minimappers2
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Create virtual environment
+      env:
+        BIN: ${{ matrix.os == 'windows-latest' && 'Scripts' || 'bin' }}
+      run: |
+        python -m venv .venv
+        echo "$GITHUB_WORKSPACE/minimappers2/.venv/$BIN" >> $GITHUB_PATH
+        echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/minimappers2/.venv" >> $GITHUB_ENV
+
+    - name: Set up Rust
+      run: rustup show
+
+    - name: Cache Rust
+      uses: Swatinem/rust-cache@v2
+      with:
+        workspaces: minimappers2
+        save-if: ${{ github.ref_name == 'main' }}
+
+    - name: Install Python dependencies
+      run: |
+        pip install uv
+        uv pip install maturin
+
+    - name: Install minimappers2
+      run: maturin develop
+
     - name: Build
       run: cargo build --verbose
+
     - name: Run tests
-      run: cargo test --verbose
-
-  build-manylinux-x64_64:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
-
-      - name: Test build
-        uses: messense/maturin-action@v1
-        env:
-          RUSTFLAGS: -C target-feature=+fxsr,+sse,+sse2,+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt,+avx,+fma
-        with:
-          rust-toolchain: nightly-2025-01-08
-          maturin-version: '1.8.0'
-          command: build
-          args: -m minimappers2/Cargo.toml
+      run: cargo test --verbose

.github/workflows/create-python-release.yaml

@@ -1,86 +1,185 @@
-# Taken from Polar-rs github action
-
-name: Create Python release
+# This file is autogenerated by maturin v1.8.1
+# To update, run
+#
+#    maturin generate-ci github
+#
+name: CI
 
 on:
   push:
+    branches:
+      - main
+      - master
     tags:
-      - py-*
+      - '*'
+  pull_request:
+  workflow_dispatch:
 
 defaults:
   run:
     shell: bash
 
+permissions:
+  contents: read
+
 jobs:
-  manylinux-x64_64:
-    runs-on: ubuntu-latest
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        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
-        with:
-          submodules: 'recursive'
+      - run: cd minimappers2
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.7'
-
-      - name: Publish wheel
+          python-version: 3.x
+      - name: Build wheels
         uses: PyO3/maturin-action@v1
-        env:
-          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
-          RUSTFLAGS: -C target-feature=+fxsr,+sse,+sse2,+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt,+avx,+fma
         with:
-          rust-toolchain: nightly-2024-02-04
-          maturin-version: '1.6.0'
-          command: publish
-          args: -m minimappers2/Cargo.toml --skip-existing -o wheels -u jguhlin
-
-  # Needed for Docker on Apple M1
-#  manylinux-aarch64:
-#    runs-on: ubuntu-latest
-#    steps:
-#      - uses: actions/checkout@v3
-#      - uses: actions/setup-python@v4
-#        with:
-#          python-version: '3.7'
-#
-#      - name: Publish wheel
-#        uses: messense/maturin-action@v1
-#        env:
-#          MATURIN_PASSWORD: ${{ secrets.PYPI_PASS }}
-#        with:
-#          rust-toolchain: nightly-2023-01-19
-#          target: aarch64-unknown-linux-gnu
-#          maturin-version: '0.14.10'
-#          command: publish
-#          args: -m minimappers2/Cargo.toml --skip-existing -o wheels -u jguhlin
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: 'true'
+          manylinux: auto
+      - name: Build free-threaded wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist -i python3.13t
+          sccache: 'true'
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
 
-  # uncomment to build a universal2 wheel
-  # we don't run it because it is twice as big and not needed because we build for both architectures separately
-  # macos-aarch64-universal:
-  #   runs-on: macos-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-  #     - uses: actions/setup-python@v4
-  #       with:
-  #         python-version: '3.7'
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        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
+    steps:
+      - uses: actions/checkout@v4
+      - run: cd minimappers2
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: 'true'
+          manylinux: musllinux_1_2
+      - name: Build free-threaded wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist -i python3.13t
+          sccache: 'true'
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
 
-  #     - name: Fix README symlink
-  #       run: |
-  #         rm py-polars/README.md
-  #         cp README.md py-polars/README.md
+  # No support for minimap2 for windows 
 
-  #     - name: Set up Rust
-  #       uses: dtolnay/rust-toolchain@master
-  #       with:
-  #         toolchain: nightly-2023-01-19
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-13
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - run: cd minimappers2
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist
+          sccache: 'true'
+      - name: Build free-threaded wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist -i python3.13t
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
 
-  #     - name: Set up Rust targets
-  #       run: rustup target add aarch64-apple-darwin
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: cd minimappers2
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
 
-  #     - name: Publish wheel
-  #       uses: messense/maturin-action@v1
-  #       env:
-  #         MATURIN_PASSWORD: ${{ secrets.PYPI_PASS }}
-  #       with:
-  #         maturin-version: '0.14.10'
-  #         command: publish
-  #         args: -m py-polars/Cargo.toml --no-sdist --universal2 -o wheels -i python -u ritchie46
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: ${{ startsWith(github.ref, 'refs/tags/py-') || github.event_name == 'workflow_dispatch' }}
+    needs: [linux, musllinux, macos, sdist]
+    permissions:
+      # Use to sign the release artifacts
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v4
+      - run: cd minimappers2
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-path: 'wheels-*/*'
+      - name: Publish to PyPI
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*

minimappers2/.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

minimappers2/.gitignore

@@ -0,0 +1,3 @@
+# pixi environments
+.pixi
+*.egg-info

minimappers2/Cargo.toml

@@ -1,21 +1,20 @@
 [package]
 name = "minimappers2"
-version = "0.1.6"
+version = "0.1.7"
 edition = "2021"
 
 [lib]
 name = "minimappers2"
 crate-type = ["cdylib", "rlib"]
 
 [dependencies]
-minimap2 = { version = "0.1.18", features = ["simde"] }
-minimap2-sys = { version = "0.1.19", features = ["simde"] }
+minimap2 = { version = "0.1.23", features = ["simde"], path = ".." }
 crossbeam = "0.8.4"
 mimalloc = {version = "0.1", default-features = false }
 
-pyo3 = { version = "0.21" }
-polars = "0.40"
-pyo3-polars = "0.14"
+pyo3 = { version = "0.22" }
+polars = "0.45"
+pyo3-polars = "0.19"
 
 [profile.release]
 opt-level = 3

minimappers2/example/.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

minimappers2/example/.gitignore

@@ -0,0 +1,3 @@
+# pixi environments
+.pixi
+*.egg-info

minimappers2/example/pixi.toml

@@ -0,0 +1,20 @@
+[project]
+authors = ["Joseph Guhlin <joseph.guhlin@gmail.com>"]
+channels = ["conda-forge", "bioconda"]
+description = "Add a short description here"
+name = "example"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+maturin = ">=1.8.1,<2"
+uv = ">=0.5.14,<0.6"
+jupyter = ">=1.1.1,<2"
+jupyterlab = ">=4.3.4,<5"
+polars = ">=1.17.1,<2"
+pandas = ">=2.2.3,<3"
+pyarrow = ">=18.1.0,<19"
+plotly = ">=5.24.1,<6"
+needletail = ">=0.6.1,<0.7"

minimappers2/pixi.toml

@@ -0,0 +1,13 @@
+[project]
+authors = ["Joseph Guhlin <joseph.guhlin@gmail.com>"]
+channels = ["conda-forge", "bioconda"]
+description = "Add a short description here"
+name = "minimappers2"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+uv = ">=0.5.14,<0.6"
+maturin = ">=1.8.1,<2"

minimappers2/pyproject.toml

@@ -13,16 +13,17 @@ license = { file = "LICENSE" }
 description = "A Python wrapper for minimap2-rs"
 keywords = ["minimap2", "bioinformatics", "alignment", "mapping"]
 dependencies = [
-    "polars>=0.15.15",
-    "pyarrow>=10.0.1",
+    "polars>=1.19.0",
+    "pyarrow>=18.1.0",
 ]
+version = "0.1.7"
 
 [project.urls]
 homepage = "https://github.com/jguhlin/minimap2-rs"
 repository = "https://github.com/jguhlin/minimap2-rs"
 
 [build-system]
-requires = ["maturin>=0.14,<0.15"]
+requires = ["maturin>=1.8"]
 build-backend = "maturin"
 
 [tool.maturin]