feat!: bam header to_hashmap method now returns a result in order to deal with header parsing issues #875
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1.0.6 | |
| with: | |
| toolchain: stable | |
| override: true | |
| components: rustfmt | |
| - name: Check format | |
| run: cargo fmt -- --check | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1.0.6 | |
| with: | |
| toolchain: stable | |
| override: true | |
| components: clippy | |
| - name: Lint with clippy | |
| uses: actions-rs/clippy-check@v1 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| Testing: | |
| needs: Formatting | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: Install nightly toolchain | |
| uses: actions-rs/toolchain@v1.0.6 | |
| with: | |
| toolchain: nightly | |
| override: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev | |
| - uses: Swatinem/rust-cache@v1.3.0 | |
| - name: Run cargo-tarpaulin | |
| uses: actions-rs/tarpaulin@v0.1 | |
| with: | |
| # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23 | |
| version: "0.22.0" | |
| args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1" | |
| - name: Upload coverage | |
| uses: coverallsapp/github-action@v1 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| path-to-lcov: ./lcov.info | |
| Testing-Features: | |
| needs: Formatting | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| target: | |
| - no-default-features | |
| - all-features | |
| include: | |
| - target: no-default-features | |
| args: --no-default-features | |
| use_cross: false | |
| - target: all-features | |
| args: --all-features | |
| toolchain_target: x86_64-unknown-linux-musl | |
| use_cross: false | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1.0.6 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev | |
| - uses: Swatinem/rust-cache@v1.3.0 | |
| - name: Test | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: test | |
| args: ${{ matrix.args }} | |
| use-cross: ${{ matrix.use_cross }} | |
| Testing-MacOS: | |
| needs: Formatting | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| target: | |
| - intel-monterey | |
| - intel-ventura | |
| - silicon-sonoma | |
| include: | |
| - target: intel-monterey | |
| os: macOS-12.0 | |
| toolchain_target: x86_64-apple-darwin | |
| toolchain: stable | |
| aux_args: --target x86_64-apple-darwin | |
| default: true | |
| - target: intel-ventura | |
| os: macOS-13.0 | |
| toolchain_target: x86_64-apple-darwin | |
| toolchain: stable | |
| aux_args: --target x86_64-apple-darwin | |
| default: true | |
| - target: silicon-sonoma | |
| os: macOS-14.0 | |
| toolchain_target: aarch64-apple-darwin | |
| toolchain: stable | |
| aux_args: "" | |
| default: false | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1.0.6 | |
| with: | |
| toolchain: ${{ matrix.toolchain }} | |
| target: ${{ matrix.toolchain_target }} | |
| override: true | |
| default: ${{ matrix.default }} | |
| - name: Install htslib dependencies | |
| run: brew install bzip2 zlib xz curl-openssl | |
| - name: Test | |
| uses: actions-rs/cargo@v1.0.1 | |
| with: | |
| use-cross: false # cross is not supported on GHA OSX runner, see: https://github.saobby.my.eu.orgmunity/t/why-is-docker-not-installed-on-macos/17017 | |
| command: test | |
| args: --release --all-features --verbose ${{ matrix.aux_args }} | |
| # Testing-OSX-MUSL-BigSur: | |
| # needs: Formatting | |
| # runs-on: macOS-11.0 | |
| # steps: | |
| # Test MUSL builds on OSX | |
| # | |
| # - uses: actions-rs/toolchain@v1.0.6 | |
| # with: | |
| # toolchain: stable | |
| # target: x86_64-unknown-linux-musl | |
| # override: true | |
| # - name: Install OSX musl-cross | |
| # run: brew install FiloSottile/musl-cross/musl-cross | |
| # # https://github.com/FiloSottile/homebrew-musl-cross/issues/16 | |
| # - name: Provide musl-gcc symlink for the right musl arch | |
| # run: ln -sf /usr/local/opt/musl-cross/libexec/bin/x86_64-linux-musl-gcc /usr/local/bin/musl-gcc | |
| # - name: Test musl build without default features | |
| # uses: actions-rs/cargo@v1 | |
| # with: | |
| # use-cross: false # cross is not supported on GHA OSX runner, see: https://github.saobby.my.eu.orgmunity/t/why-is-docker-not-installed-on-macos/17017 | |
| # command: test | |
| # args: --release --target x86_64-unknown-linux-musl --no-default-features | |
| # - name: Test musl build with all features and debug symbols (non --release) on OSX | |
| # uses: actions-rs/cargo@v1.0.1 | |
| # with: | |
| # use-cross: false | |
| # command: test | |
| # args: --target x86_64-unknown-linux-musl --all-features --verbose |