rasusa 5.0.0

Randomly subsample reads or alignments
Documentation 
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name: Benchmark

on:
  release:
    types: [published]
  workflow_dispatch: {}
  schedule:
    # First of the month, 03:00 UTC - keeps the published numbers from going stale
    # between releases.
    - cron: "0 3 1 * *"

concurrency:
  group: ${{ github.workflow }}
  cancel-in-progress: false

jobs:
  update-readme-benchmark:
    name: Regenerate README benchmark tables
    # Pinned (not `ubuntu-latest`) since the whole point of this job is producing
    # numbers on a stable, known runner - a silent image bump shouldn't move them.
    runs-on: ubuntu-24.04
    steps:
      - name: Checkout sources
        uses: actions/checkout@v6
        with:
          ref: main
          # Needed so the commit-back step has a real branch to push to.
          fetch-depth: 1

      # Loop-guard: this workflow commits back to `main` with a tagged message. It isn't
      # push-triggered, so it can't retrigger itself directly, but `workflow_dispatch`/
      # `schedule` firing right after such a commit would otherwise just redo the same
      # work - skip in that case.
      - name: Check loop-guard
        id: guard
        run: |
          if git log -1 --pretty=%B | grep -qF '[skip benchmark]'; then
            echo "HEAD is a bench-refresh commit, skipping this run." >&2
            echo "skip=true" >> "$GITHUB_OUTPUT"
          else
            echo "skip=false" >> "$GITHUB_OUTPUT"
          fi

      - name: Install toolchain
        if: steps.guard.outputs.skip != 'true'
        uses: dtolnay/rust-toolchain@stable

      - uses: actions/cache@v5
        if: steps.guard.outputs.skip != 'true'
        with:
          path: |
            ~/.cargo/registry/index/
            ~/.cargo/registry/cache/
            ~/.cargo/git/db/
            target/
          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
          restore-keys: |
            ${{ runner.os }}-cargo-

      - name: Cache downloaded benchmark datasets
        if: steps.guard.outputs.skip != 'true'
        uses: actions/cache@v5
        with:
          path: data/download-cache
          key: bench-datasets-v1

      - name: Install hyperfine
        if: steps.guard.outputs.skip != 'true'
        uses: taiki-e/install-action@v2
        with:
          tool: hyperfine

      - name: Install filtlong, seqtk, fastaq (bioconda)
        if: steps.guard.outputs.skip != 'true'
        uses: mamba-org/setup-micromamba@v3
        with:
          environment-name: bench-tools
          create-args: -c bioconda -c conda-forge filtlong seqtk fastaq
          init-shell: bash

      - name: Regenerate README benchmark tables
        if: steps.guard.outputs.skip != 'true'
        shell: bash -leo pipefail {0}
        run: benches/update_readme.sh

      - name: Commit refreshed README
        if: steps.guard.outputs.skip != 'true'
        run: |
          if git diff --quiet -- README.md; then
            echo "No benchmark changes to commit."
            exit 0
          fi
          git config user.name "github-actions[bot]"
          git config user.email "github-actions[bot]@users.noreply.github.com"
          git add README.md
          git commit -m "chore(bench): refresh README benchmark tables [skip benchmark]"
          git push "https://x-access-token:${GH_PAT}@github.com/${{ github.repository }}.git" HEAD:main
        env:
          GH_PAT: ${{ secrets.PAT }}