anndataR/.github/workflows/bench-pr-run.yaml at 7198d6d4fd45a527b876722dc223c32eb54ea74b · scverse/anndataR · GitHub

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# Run benchmarks on pull requests (fork-safe: no secrets needed)
# Results are uploaded as artifacts and tracked by bench-pr-track.yaml
name: Benchmarks (PR run)

on:
  pull_request:
    types: [opened, reopened, synchronize]

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

jobs:
  benchmark:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Install Linux dependencies
        run: |
          sudo apt-get update
          sudo apt-get -y install hdf5-tools libsz2 libaec-dev

      - name: Setup R and Bioconductor
        uses: grimbough/bioc-actions/setup-bioc@v1
        with:
          bioc-version: devel

      - name: Install R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: |
            any::bench
            any::devtools
            any::jsonlite
            any::reticulate

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version: '3.x'

      - name: Install Python dependencies
        run: pip install anndata dummy-anndata

      - name: Configure reticulate
        run: echo "RETICULATE_PYTHON=$(which python)" >> $GITHUB_ENV

      - name: Run benchmarks
        run: Rscript benchmarks/run_benchmarks.R --output benchmark_results.json

      - name: Upload benchmark results
        uses: actions/upload-artifact@v7
        with:
          name: benchmark_results.json
          path: ./benchmark_results.json

      - name: Upload PR event
        uses: actions/upload-artifact@v7
        with:
          name: event.json
          path: ${{ github.event_path }}