update deps #472
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| name: Rust | |
| on: | |
| push: | |
| branches: [ master, develop ] | |
| pull_request: | |
| branches: [ master, develop ] | |
| env: | |
| CARGO_TERM_COLOR: always | |
| jobs: | |
| Formatting: | |
| if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Install stable toolchain | |
| uses: dtolnay/rust-toolchain@stable | |
| with: | |
| toolchain: stable | |
| components: rustfmt | |
| - name: Check format | |
| run: cargo fmt -- --check | |
| build: | |
| if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build | |
| run: cargo build --verbose | |
| - name: Run tests | |
| run: cargo test --verbose | |
| Linting: | |
| if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Install stable toolchain | |
| uses: dtolnay/rust-toolchain@stable | |
| with: | |
| toolchain: stable | |
| components: clippy | |
| - name: Lint with clippy | |
| uses: actions-rs-plus/clippy-check@cbcfbff5103c40b26d7077f164f0ec6052036081 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| sample_run: | |
| if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install | |
| run: cargo build --release | |
| - name: sample run | |
| run: | | |
| wget https://umd.box.com/shared/static/75a80udhx51fjndbgnm6dmm25qsia5ks.gz -O toy_set.tar.gz | |
| tar xzf toy_set.tar.gz | |
| fry="target/release/alevin-fry" | |
| threads=2 | |
| map_dir="toy_set/alevin_map" | |
| gpl_dir="gpl" | |
| quant_dir="quant" | |
| permitmode="-u toy_set/10x_v3_permit.txt" | |
| t2g="toy_set/t2g_3col.tsv" | |
| res="cr-like" | |
| ### generate permit list | |
| cmd="$fry generate-permit-list $permitmode -d fw -i $map_dir -o $gpl_dir" | |
| eval $cmd | |
| ### collate | |
| cmd="$fry collate -i $gpl_dir -r $map_dir -t $threads" | |
| eval $cmd | |
| ### quant | |
| cmd="$fry quant -r $res --use-mtx -m $t2g -i $gpl_dir -o $quant_dir -t $threads" | |
| eval $cmd | |
| # Coverage: | |
| # if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| # needs: Formatting | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Checkout repository | |
| # uses: actions/checkout@v2 | |
| # - name: Install nightly toolchain | |
| # uses: actions-rs/toolchain@v1 | |
| # with: | |
| # toolchain: nightly | |
| # override: true | |
| # - name: Install cargo-tarpaulin | |
| # uses: actions-rs/install@v0.1 | |
| # with: | |
| # crate: cargo-tarpaulin | |
| # version: latest | |
| # use-tool-cache: true | |
| # - name: Coverage with tarpaulin | |
| # run: cargo tarpaulin --all --all-features --timeout 600 --out Lcov -- --test-threads 1 | |
| # - name: Upload coverage | |
| # uses: coverallsapp/github-action@master | |
| # with: | |
| # github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # path-to-lcov: ./lcov.info |