MRG: improve downsampling behavior on KmerMinHash; fix RevIndex::gather bug around scaled.
#5810
Workflow file for this run
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| 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 | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| profile: minimal | |
| toolchain: stable | |
| override: true | |
| - name: Run cargo check | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: 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: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: ${{ matrix.rust }} | |
| override: true | |
| - name: Run tests | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: test | |
| args: --no-fail-fast | |
| test_all_features: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - uses: actions-rs/[email protected] | |
| with: | |
| crate: cargo-all-features | |
| version: latest | |
| use-tool-cache: true | |
| - name: Run tests for all feature combinations | |
| run: cargo test-all-features --no-fail-fast --all | |
| coverage: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - name: Install cargo-binstall | |
| run: | | |
| wget https://github.com/ryankurte/cargo-binstall/releases/latest/download/cargo-binstall-x86_64-unknown-linux-gnu.tgz | |
| tar xf cargo-binstall-x86_64-unknown-linux-gnu.tgz | |
| chmod +x cargo-binstall | |
| mv cargo-binstall "$HOME/.cargo/bin" | |
| - name: Install cargo-tarpaulin | |
| run: cargo binstall --no-confirm cargo-tarpaulin | |
| - name: Coverage with tarpaulin | |
| run: cargo tarpaulin --all --all-features --timeout 600 --out xml -- --test-threads 1 | |
| - name: Upload Rust coverage to codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| flags: rust | |
| fail_ci_if_error: true | |
| 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: actions-rs/toolchain@v1 | |
| with: | |
| profile: minimal | |
| toolchain: ${{ matrix.rust }} | |
| override: true | |
| components: rustfmt, clippy | |
| - name: Run cargo fmt | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: fmt | |
| args: --all -- --check | |
| - name: Run cargo clippy | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: clippy | |
| args: --all -- -D warnings | |
| wasm-pack: | |
| name: Check if wasm-pack builds a valid package for the sourmash crate | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| target: wasm32-unknown-unknown | |
| - name: Install wasm-pack | |
| run: "curl https://rustwasm.github.io/wasm-pack/installer/init.sh -sSf | sh" | |
| - name: Prepare node for running tests | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: 16 | |
| registry-url: https://registry.npmjs.org/ | |
| - name: run wasm tests | |
| continue-on-error: true ## TODO: remove this when tests works again... | |
| run: wasm-pack test --node src/core | |
| - name: run wasm-pack build | |
| run: wasm-pack build src/core -d ../../pkg | |
| - name: Prepare package for NPM publishing | |
| working-directory: pkg | |
| run: npm pack | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| path: 'pkg/sourmash*.tgz' | |
| wasm32-wasi: | |
| name: Run tests under wasm32-wasi | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install wasm32-wasi target | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| target: wasm32-wasi | |
| - name: Install wasmtime | |
| run: "curl https://wasmtime.dev/install.sh -sSf | bash" | |
| - name: Add wasmtime to PATH | |
| run: echo "$HOME/.wasmtime/bin" >> $GITHUB_PATH | |
| - name: Install cargo-wasi command | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: install | |
| args: --force cargo-wasi | |
| - name: Build code with cargo-wasi | |
| uses: actions-rs/cargo@v1 | |
| continue-on-error: true ## TODO: remove this when build works... | |
| with: | |
| command: wasi | |
| args: build | |
| - name: Run tests under wasm32-wasi | |
| uses: actions-rs/cargo@v1 | |
| continue-on-error: true ## TODO: remove this when tests work... | |
| with: | |
| command: wasi | |
| args: test | |
| publish: | |
| name: Publish (dry-run) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout sources | |
| uses: actions/checkout@v4 | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| profile: minimal | |
| toolchain: stable | |
| override: true | |
| - 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 | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: publish | |
| args: --dry-run --manifest-path src/core/Cargo.toml | |
| minimum_rust_version: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: "1.65.0" | |
| override: true | |
| - name: check if README matches MSRV defined here | |
| run: grep '1.65.0' src/core/README.md | |
| - name: Check if it builds properly | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: build | |
| args: --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: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - uses: actions-rs/[email protected] | |
| with: | |
| crate: cbindgen | |
| version: 0.20.0 | |
| use-tool-cache: true | |
| - 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?" |