barkit 0.1.1

BarKit — a cross-platform and ultrafast toolkit for barcodes manipulation in FASTQ files
Documentation 
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name: Continuous Integration

on:
  pull_request:
  push:
    branches:
      - main
  schedule:
    - cron: "0 0 * * 0"

permissions:
  pull-requests: write

jobs:
  check:
    name: Check
    runs-on: ubuntu-22.04
    steps:
      - name: Install toolchain
        uses: dtolnay/rust-toolchain@stable
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check
        uses: actions-rs/cargo@v1
        with:
          command: check
          args: --locked --verbose
      - name: Check without default features
        uses: actions-rs/cargo@v1
        with:
          command: check
          args: --locked --no-default-features --verbose

  typos:
    name: Typos
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check typos
        uses: crate-ci/typos@master

  test:
    name: Test suite
    runs-on: ubuntu-22.04
    steps:
      - name: Install toolchain
        uses: dtolnay/rust-toolchain@nightly
      - name: Checkout
        if: github.event_name != 'pull_request'
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Checkout
        if: github.event_name == 'pull_request'
        uses: actions/checkout@v4
        with:
          ref: ${{ github.event.pull_request.head.sha }}
          fetch-depth: 0
      - name: Setup cargo-tarpaulin
        uses: taiki-e/install-action@cargo-tarpaulin
      - name: Run tests
        run: |
          cargo test --all --no-default-features \
            -- --skip "repo::test::git_upstream_remote"
      - name: Run tests
        run: |
          cargo tarpaulin --out xml --verbose --all-features \
            -- --skip "repo::test::git_upstream_remote"
      - name: Upload reports to codecov
        uses: codecov/codecov-action@v4
        with:
          name: code-coverage-report
          file: cobertura.xml
          flags: unit-tests
          fail_ci_if_error: true
          verbose: true
          token: ${{ secrets.CODECOV_TOKEN }}

  clippy:
    name: Lints
    runs-on: ubuntu-22.04
    steps:
      - name: Install toolchain
        uses: dtolnay/rust-toolchain@nightly
        with:
          components: clippy
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check the lints
        uses: actions-rs/cargo@v1
        with:
          command: clippy
          args: --tests --verbose -- -D warnings

  rustfmt:
    name: Formatting
    runs-on: ubuntu-22.04
    steps:
      - name: Install toolchain
        uses: dtolnay/rust-toolchain@nightly
        with:
          components: rustfmt
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check the formatting
        uses: actions-rs/cargo@v1
        with:
          command: fmt
          args: --all -- --check --verbose

  msrv:
    name: Check Rust version
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Install cargo-binstall
        uses: taiki-e/install-action@cargo-binstall
      - name: Install cargo-msrv
        run: cargo binstall -y cargo-msrv
      - name: Run cargo-msrv
        shell: bash
        run: |
          for package in barkit-extract; do
            printf "Checking MSRV for %s..." "$package"
            cargo msrv --output-format json --path "$package" verify | tail -n 1 | jq --exit-status '.success'
          done