fgumi 0.2.0

High-performance tools for UMI-tagged sequencing data: extraction, grouping, and consensus calling
Documentation 
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name: Check and Test

on:
  push:
    branches:
      - main
  pull_request:

env:
  CARGO_TERM_COLOR: always
  CARGO_INCREMENTAL: 0
  SCCACHE_GHA_ENABLED: "true"
  RUSTC_WRAPPER: "sccache"

jobs:
  test:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@7d986dd989559c6ecdb630a3fd2557667be217ad # v0.0.9
      - name: Install nextest
        uses: taiki-e/install-action@6ef672efc2b5aabc787a9e94baf4989aa02a97df # v2.70.3
        with:
          tool: nextest
      - name: Unit tests
        run: cargo ci-test
  
  lint:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
        with:
          components: clippy
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@7d986dd989559c6ecdb630a3fd2557667be217ad # v0.0.9
      - name: Clippy check
        run: cargo ci-lint

  coverage:
    runs-on: ubuntu-latest
    if: github.actor != 'dependabot[bot]'
    environment: github-actions
    steps:
      - name: Checkout code
        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@7d986dd989559c6ecdb630a3fd2557667be217ad # v0.0.9
      - name: Install cargo-llvm-cov
        uses: taiki-e/install-action@6ef672efc2b5aabc787a9e94baf4989aa02a97df # v2.70.3
        with:
          tool: cargo-llvm-cov
      - name: Install nextest
        uses: taiki-e/install-action@6ef672efc2b5aabc787a9e94baf4989aa02a97df # v2.70.3
        with:
          tool: nextest
      - name: Generate coverage
        run: cargo llvm-cov nextest --features compare,simulate,profile-adjacency --no-tests=pass --lcov --output-path lcov.info
      - name: Upload to Codecov
        uses: codecov/codecov-action@75cd11691c0faa626561e295848008c8a7dddffe # v5.5.4
        with:
          files: lcov.info
          fail_ci_if_error: true
          token: ${{ secrets.CODECOV_TOKEN }}

  format:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
        with:
          components: rustfmt
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@7d986dd989559c6ecdb630a3fd2557667be217ad # v0.0.9
      - name: Rustfmt check
        run: cargo ci-fmt

  security:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
      - name: Install cargo-audit
        uses: taiki-e/install-action@6ef672efc2b5aabc787a9e94baf4989aa02a97df # v2.70.3
        with:
          tool: cargo-audit
      - name: Audit dependencies for known vulnerabilities
        run: cargo audit