MRG: additional moltype specification needed for sig downsample with skipmers
#6238
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Rust checks | |
| on: | |
| push: | |
| branches: [latest] | |
| pull_request: | |
| schedule: | |
| - cron: "0 0 * * *" # daily | |
| jobs: | |
| check: | |
| name: Check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout sources | |
| uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| - uses: Swatinem/rust-cache@v2 | |
| - name: Run cargo check | |
| run: | | |
| cargo check | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| build: [beta, stable, windows, macos] | |
| include: | |
| - build: macos | |
| os: macos-latest | |
| rust: stable | |
| continue: false | |
| - build: windows | |
| os: windows-latest | |
| rust: stable | |
| continue: true | |
| - build: beta | |
| os: ubuntu-latest | |
| rust: beta | |
| continue: false | |
| - build: stable | |
| os: ubuntu-latest | |
| rust: stable | |
| continue: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@master | |
| with: | |
| toolchain: ${{ matrix.rust }} | |
| - uses: Swatinem/rust-cache@v2 | |
| - uses: taiki-e/install-action@nextest | |
| - name: Run tests | |
| run: | | |
| cargo nextest run | |
| test_all_features: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| - uses: Swatinem/rust-cache@v2 | |
| - uses: taiki-e/install-action@v2 | |
| with: | |
| tool: cargo-all-features | |
| - name: Run tests for all feature combinations | |
| run: cargo test-all-features --no-fail-fast --all | |
| coverage: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| with: | |
| components: llvm-tools-preview | |
| - uses: Swatinem/rust-cache@v2 | |
| - uses: taiki-e/install-action@cargo-llvm-cov | |
| - uses: taiki-e/install-action@nextest | |
| - name: Collect coverage data | |
| run: cargo llvm-cov nextest --all-features --lcov --output-path lcov.info | |
| - name: Upload Rust coverage to codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| flags: rust | |
| fail_ci_if_error: true | |
| files: lcov.info | |
| lints: | |
| name: Lints | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| build: [beta, stable] | |
| include: | |
| - build: beta | |
| rust: beta | |
| - build: stable | |
| rust: stable | |
| steps: | |
| - name: Checkout sources | |
| uses: actions/checkout@v4 | |
| - name: Install Rust toolchain | |
| uses: dtolnay/rust-toolchain@master | |
| with: | |
| toolchain: ${{ matrix.rust }} | |
| components: "clippy, rustfmt" | |
| - uses: Swatinem/rust-cache@v2 | |
| - name: Run cargo fmt | |
| run: | | |
| cargo fmt --all -- --check | |
| - name: Run cargo clippy | |
| run: | | |
| cargo clippy --all -- -D warnings | |
| wasm-pack: | |
| name: Check if wasm-pack builds a valid package for the sourmash crate | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| with: | |
| target: wasm32-unknown-unknown | |
| - uses: Swatinem/rust-cache@v2 | |
| - name: Install wasm-pack | |
| run: "curl https://rustwasm.github.io/wasm-pack/installer/init.sh -sSf | sh" | |
| - name: Prepare node for running tests | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: 16 | |
| registry-url: https://registry.npmjs.org/ | |
| - name: run wasm tests | |
| continue-on-error: true ## TODO: remove this when tests works again... | |
| run: wasm-pack test --node src/core | |
| - name: run wasm-pack build | |
| run: wasm-pack build src/core -d ../../pkg | |
| - name: Prepare package for NPM publishing | |
| working-directory: pkg | |
| run: npm pack | |
| - name: Publish to NPM | |
| if: startsWith(github.ref, 'refs/tags/r') | |
| working-directory: pkg | |
| run: npm publish | |
| env: | |
| NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }} | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| path: 'pkg/sourmash*.tgz' | |
| publish: | |
| name: Publish (on tags, dry-run otherwise) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout sources | |
| uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| - uses: Swatinem/rust-cache@v2 | |
| - name: Check semver | |
| uses: obi1kenobi/cargo-semver-checks-action@v2 | |
| with: | |
| crate-name: sourmash | |
| version-tag-prefix: r | |
| feature-group: default-features | |
| features: branchwater | |
| - name: Make sure we can publish the sourmash crate | |
| run: | | |
| cargo publish --dry-run --manifest-path src/core/Cargo.toml | |
| # Login to crates.io on tags | |
| - name: login to crates.io | |
| if: startsWith(github.ref, 'refs/tags/r') | |
| run: | | |
| cargo login ${{ secrets.CRATES_IO_TOKEN }} | |
| # Publish to crates.io on tags | |
| - name: Publish to crates.io | |
| if: startsWith(github.ref, 'refs/tags/r') | |
| run: | | |
| cargo publish --manifest-path src/core/Cargo.toml | |
| minimum_rust_version: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@master | |
| with: | |
| toolchain: "1.66.0" | |
| - uses: Swatinem/rust-cache@v2 | |
| - name: check if README matches MSRV defined here | |
| run: grep '1.66.0' src/core/README.md | |
| - name: Check if it builds properly | |
| run: | | |
| cargo build --all-features | |
| check_cbindgen: | |
| name: "Check if cbindgen runs cleanly for generating the C headers" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| - uses: Swatinem/rust-cache@v2 | |
| - uses: taiki-e/install-action@v2 | |
| with: | |
| tool: [email protected] | |
| - run: make include/sourmash.h | |
| - name: check if headers have the same content | |
| run: | | |
| git update-index --refresh | |
| git diff | |
| git diff-index --quiet HEAD -- include/sourmash.h || echo "::error file=include/sourmash.h::Header doesn't match committed file, did you forget to rerun cbindgen?" |