kractor 4.0.0

Extract reads from a FASTQ file based on taxonomic classification via Kraken2.
# adapted from https://github.com/jonhoo/rust-ci-conf/blob/fabb82abd53e0052c8b70ae197a80e6203ede26d/.github/workflows/test.yml
# This is the main CI workflow that runs the test suite on all pushes to main and all pull requests.
# It runs the following jobs:
# - required: runs the test suite on ubuntu with stable and beta rust toolchains
# - minimal: runs the test suite with the minimal versions of the dependencies that satisfy the
#   requirements of this crate, and its dependencies
# - os-check: runs the test suite on mac and windows
# See check.yml for information about how the concurrency cancellation and workflow triggering works
permissions:
  contents: read
on:
  push:
    branches: [ main ]
  pull_request:
concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
  cancel-in-progress: true
name: test
jobs:
  required:
    runs-on: ubuntu-latest
    name: ubuntu / ${{ matrix.toolchain }}
    strategy:
      matrix:
        # run on stable and beta to ensure that tests won't break on the next version of the rust
        # toolchain
        toolchain: [ stable, beta ]
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: true
      - name: Install ${{ matrix.toolchain }}
        uses: dtolnay/rust-toolchain@master
        with:
          toolchain: ${{ matrix.toolchain }}
      - name: cargo generate-lockfile
        # enable this ci template to run regardless of whether the lockfile is checked in or not
        if: hashFiles('Cargo.lock') == ''
        run: cargo generate-lockfile
      # https://twitter.com/jonhoo/status/1571290371124260865
      - name: cargo test --locked
        run: cargo test --locked --all-features --all-targets
  os-check:
    # run cargo test on mac and windows
    runs-on: ${{ matrix.os }}
    name: ${{ matrix.os }} / stable
    strategy:
      fail-fast: false
      matrix:
        os: [ macos-latest ]
    steps:
      # if your project needs OpenSSL, uncomment this to fix Windows builds.
      # it's commented out by default as the install command takes 5-10m.
      # - run: echo "VCPKG_ROOT=$env:VCPKG_INSTALLATION_ROOT" | Out-File -FilePath $env:GITHUB_ENV -Append
      #   if: runner.os == 'Windows'
      # - run: vcpkg install openssl:x64-windows-static-md
      #   if: runner.os == 'Windows'
      - uses: actions/checkout@v4
        with:
          submodules: true
      - name: Install stable
        uses: dtolnay/rust-toolchain@stable
      - name: cargo generate-lockfile
        if: hashFiles('Cargo.lock') == ''
        run: cargo generate-lockfile
      - name: cargo test
        run: cargo test --locked --all-features --all-targets