Fix CI (#457) #28
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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)" >> $GITHUB_ENV | |
| - name: Install Bencher CLI | |
| uses: bencherdev/bencher@v0.6.4 | |
| - name: Run benchmarks | |
| run: Rscript benchmarks/run_benchmarks.R --output results.json | |
| - name: Track benchmarks with Bencher | |
| run: | | |
| bencher run \ | |
| --project anndatar \ | |
| --token '${{ 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 |