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ci: Small cleanup of the Github Actions in the PR workflow (#465)
* Update GHA actions to their latest versions Keep only the release related actions as is. The action is deprecated and should be replaces by a new one. Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Test on Linux ARM64 too Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Fix clippy errors for Rust 1.84.1 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Use dependabot to send PRs for new versions of the used Github Actions Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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‎.github/dependabot.yml‎

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@@ -4,3 +4,9 @@ updates:
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directory: "/"
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schedule:
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interval: "weekly"
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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‎.github/workflows/release-please.yml‎

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if: github.repository_owner == 'rust-bio'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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bump-minor-pre-major: true
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- name: Install stable toolchain
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uses: actions-rs/toolchain@v1
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uses: dtolnay/rust-toolchain@stable
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if: ${{ steps.release_main.outputs.release_created }}
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with:
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toolchain: stable
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override: true
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- name: Install system dependencies
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if: ${{ steps.release_main.outputs.release_created }}
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run: |
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sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
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- uses: Swatinem/rust-cache@v1.3.0
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- uses: Swatinem/rust-cache@v2
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if: ${{ steps.release_main.outputs.release_created }}
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- name: Publish rust-htslib
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if: ${{ steps.release_main.outputs.release_created }}
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uses: actions-rs/cargo@v1
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with:
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command: publish
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args: --token ${{ secrets.CRATES_IO_TOKEN }}
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run: cargo publish --token ${{ secrets.CRATES_IO_TOKEN }}
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# - uses: katyo/publish-crates@v1
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# if: ${{ steps.release_main.outputs.release_created || steps.release_sys.outputs.release_created }}

‎.github/workflows/rust.yml‎

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jobs:
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Formatting:
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runs-on: ubuntu-latest
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runs-on: ubuntu-22.04
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Install stable toolchain
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uses: actions-rs/toolchain@v1.0.6
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uses: dtolnay/rust-toolchain@stable
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with:
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toolchain: stable
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override: true
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components: rustfmt
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- name: Check format
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run: cargo fmt -- --check
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Linting:
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runs-on: ubuntu-latest
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runs-on: ubuntu-22.04
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Install stable toolchain
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uses: actions-rs/toolchain@v1.0.6
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uses: dtolnay/rust-toolchain@stable
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with:
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toolchain: stable
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override: true
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components: clippy
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- name: Lint with clippy
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uses: actions-rs/clippy-check@v1
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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run: RUSTFLAGS="-Dwarnings" cargo clippy --all-features --all-targets -- -Dclippy::all -Dunused_imports
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Testing:
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needs: Formatting
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runs-on: ubuntu-latest
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strategy:
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matrix:
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os: [ubuntu-22.04, ubuntu-22.04-arm]
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Install nightly toolchain
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uses: actions-rs/toolchain@v1.0.6
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uses: dtolnay/rust-toolchain@stable
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with:
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toolchain: nightly
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override: true
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- name: Install system dependencies
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run: |
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sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
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- uses: Swatinem/rust-cache@v1.3.0
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- uses: Swatinem/rust-cache@v2
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- name: Run cargo-tarpaulin
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uses: actions-rs/[email protected]
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with:
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# TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
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version: "0.22.0"
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args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
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run: |
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set -x
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cargo install cargo-tarpaulin
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cargo tarpaulin --all-features --tests --doc --out Lcov -- --test-threads 1
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- name: Upload coverage
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uses: coverallsapp/github-action@v1
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uses: coverallsapp/github-action@v2
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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path-to-lcov: ./lcov.info
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Testing-Features:
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needs: Formatting
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runs-on: ubuntu-latest
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strategy:
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matrix:
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os: [ubuntu-22.04, ubuntu-22.04-arm]
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target:
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- no-default-features
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- all-features
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include:
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- target: no-default-features
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args: --no-default-features
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use_cross: false
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- target: all-features
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os: ubuntu-22.04
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args: --all-features
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toolchain_target: x86_64-unknown-linux-musl
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use_cross: false
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- target: all-features
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os: ubuntu-22.04-arm
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args: --all-features
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toolchain_target: aarch64-unknown-linux-musl
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Install stable toolchain
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uses: actions-rs/toolchain@v1.0.6
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uses: dtolnay/rust-toolchain@stable
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with:
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toolchain: stable
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override: true
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- name: Install system dependencies
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run: |
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sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
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- uses: Swatinem/rust-cache@v1.3.0
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- uses: Swatinem/rust-cache@v2
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- name: Test
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uses: actions-rs/cargo@v1
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with:
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command: test
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args: ${{ matrix.args }}
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use-cross: ${{ matrix.use_cross }}
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run: |
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cargo test ${{ matrix.args }}
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Testing-MacOS:
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needs: Formatting
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Install stable toolchain
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uses: actions-rs/toolchain@v1.0.6
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uses: dtolnay/rust-toolchain@stable
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with:
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toolchain: ${{ matrix.toolchain }}
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target: ${{ matrix.toolchain_target }}
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targets: ${{ matrix.toolchain_target }}
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override: true
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default: ${{ matrix.default }}
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- name: Install htslib dependencies
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run: brew install bzip2 zlib xz curl-openssl
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- name: Test
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uses: actions-rs/[email protected]
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with:
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use-cross: false # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
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command: test
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args: --release --all-features --verbose ${{ matrix.aux_args }}
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run: |
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cargo test --release --all-features --verbose ${{ matrix.aux_args }}
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# Testing-OSX-MUSL-BigSur:
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# needs: Formatting
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# runs-on: macOS-11.0

‎src/bam/buffer.rs‎

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#[test]
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fn test_buffer() {
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let reader = bam::IndexedReader::from_path(&"test/test.bam").unwrap();
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let reader = bam::IndexedReader::from_path("test/test.bam").unwrap();
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let mut buffer = RecordBuffer::new(reader, false);
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buffer.fetch(b"CHROMOSOME_I", 1, 5).unwrap();

‎src/bam/ext.rs‎

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//// Copyright 2019 Johannes Köster and Florian Finkernagel.
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// Copyright 2019 Johannes Köster and Florian Finkernagel.
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// Licensed under the MIT license (http://opensource.org/licenses/MIT)
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// This file may not be copied, modified, or distributed
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// except according to those terms.

‎src/bam/header.rs‎

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fn test_push_tag() {
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let mut record = HeaderRecord::new(b"HD");
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record.push_tag(b"X1", 0);
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record.push_tag(b"X2", &0);
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record.push_tag(b"X2", 0);
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let x = "x".to_string();
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record.push_tag(b"X3", x.as_str());

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