fqgrep 1.1.2

Search a pair of fastq files for reads that match a given ref or alt sequence
Documentation 
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name: Manage Release PRs and Publish Crate

permissions:
  pull-requests: write
  contents: write

on:
  push:
    branches:
      - main

concurrency:
  group: release-plz-${{ github.ref }}
  cancel-in-progress: false

jobs:
  release-pr:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
        with:
          fetch-depth: 0
          token: ${{ secrets.RELEASE_PLZ_TOKEN }}
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Create or update release PR
        uses: release-plz/action@1528104d2ca23787631a1c1f022abb64b34c1e11 # v0.5
        with:
          command: release-pr
        env:
          GITHUB_TOKEN: ${{ secrets.RELEASE_PLZ_TOKEN }}

  publish:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
        with:
          fetch-depth: 0
          token: ${{ secrets.RELEASE_PLZ_TOKEN }}
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Publish crate
        id: publish
        env:
          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
        run: |
          set -euo pipefail

          VERSION=$(cargo metadata --no-deps --format-version 1 | jq -r \
            '.packages[] | select(.name == "fqgrep") | .version')
          echo "version=$VERSION" >> "$GITHUB_OUTPUT"

          PUBLISHED_VERSION=$(curl -sS \
            -H "User-Agent: fqgrep-ci (https://github.com/fulcrumgenomics/fqgrep)" \
            "https://crates.io/api/v1/crates/fqgrep" | jq -r \
            '.crate.max_version // "0.0.0"')

          if [ "$VERSION" = "$PUBLISHED_VERSION" ]; then
            echo "fqgrep v$VERSION already on crates.io -- nothing to publish"
            echo "published=false" >> "$GITHUB_OUTPUT"
            exit 0
          fi

          echo "Publishing fqgrep v$VERSION..."
          cargo publish
          echo "published=true" >> "$GITHUB_OUTPUT"

      - name: Create GitHub release
        if: steps.publish.outputs.published == 'true'
        env:
          GITHUB_TOKEN: ${{ secrets.RELEASE_PLZ_TOKEN }}
        run: |
          set -euo pipefail
          VERSION="${{ steps.publish.outputs.version }}"
          TAG="v${VERSION}"

          # Idempotent: skip if tag/release already exist (e.g. from a
          # previous partial run that published crates but failed here).
          if ! git rev-parse "$TAG" >/dev/null 2>&1; then
            git tag "$TAG"
          fi
          if ! git ls-remote --tags origin "$TAG" | grep -q "$TAG"; then
            git push origin "$TAG"
          fi
          if ! gh release view "$TAG" >/dev/null 2>&1; then
            gh release create "$TAG" \
              --title "v${VERSION}" \
              --generate-notes \
              --latest
          else
            echo "Release $TAG already exists -- skipping"
          fi