anndataR/.github/workflows/bench-base.yaml at 897914bb5abaed985c86664466b3cdd3c3f4a24e · scverse/anndataR · GitHub

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# Track benchmark results for the base (devel) branch on bencher.dev
on:
  push:
    branches:
      - devel

name: Benchmarks (base)

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

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

jobs:
  benchmark:
    runs-on: ubuntu-latest
    permissions:
      checks: write
    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: Install Bencher CLI
        uses: bencherdev/bencher@v0.6.5

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

      - name: Track benchmarks with Bencher
        run: |
          bencher run \
            --project anndatar \
            --token '${{ secrets.BENCHER_API_TOKEN }}' \
            --branch devel \
            --testbed ubuntu-latest \
            --threshold-measure latency \
            --threshold-test t_test \
            --threshold-max-sample-size 64 \
            --threshold-upper-boundary 0.99 \
            --threshold-measure memory \
            --threshold-test t_test \
            --threshold-max-sample-size 64 \
            --threshold-upper-boundary 0.99 \
            --thresholds-reset \
            --err \
            --adapter json \
            --github-actions '${{ secrets.GITHUB_TOKEN }}' \
            --file results.json