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Extend tests to other branches (#24)
Add a daily cronjob to try `main` and `dev` (and a shortlived hotfix branch) to install ob using miniforge and micromamba on a matrix of pythons/deps and run a small version of clustbench.
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‎.github/workflows/benchmark.yml‎

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cancel-in-progress: true
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- 'main'
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workflow_dispatch:
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permissions:

‎.github/workflows/micromamba.yml‎

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name: micromamba
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# concurrency:
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# group: ${{ github.head_ref || github.run_id }}
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# cancel-in-progress: true
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on:
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pull_request:
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workflow_dispatch:
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schedule:
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# - cron: "*/30 * * * *" # Runs every 30 minutes for testing
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- cron: "30 1 * * *" # at 1.30am
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## these permissions are only for deployment to gh pages
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# permissions:
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# id-token: write
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# pages: write
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jobs:
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run-benchmark-micromamba:
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name: run_clustbench_micromamba
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## runs-on: ubuntu-latest
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runs-on: self-hosted
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strategy:
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matrix:
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ob_branch: [dev, reduce_install_scope, main]
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micromamba-version: ['2.1.1-0', '2.0.5-0', '1.5.12-0', '1.5.8-0']
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fail-fast: false
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concurrency:
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group: micromamba-${{ matrix.micromamba-version }}-${{ matrix.ob_branch }}
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cancel-in-progress: false # true
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Install (with) micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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cache-environment: false # true
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micromamba-version: ${{ matrix.micromamba-version }}
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download-micromamba: true
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micromamba-binary-path: ${{ runner.temp }}/bin/micromamba-${{ matrix.micromamba-version }}/micromamba
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environment-name: test-env-${{matrix.ob_branch }}-${{ matrix.micromamba-version }}
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create-args: >-
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python=3.12
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pip
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conda
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post-cleanup: environment # all
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- name: Overwrite omnibenchmark CLI to branch
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shell: bash -l {0}
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run: |
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micromamba --version
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pip install git+https://github.com/omnibenchmark/omnibenchmark.git@${{ matrix.ob_branch }}
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# - name: Enable a benchmarking `out` cache
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# id: cache-benchmark
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# uses: actions/cache@v3
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# with:
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# path: out/
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# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}
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- name: Run benchmark
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shell: bash -l {0}
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run: |
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env
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output=$( echo "y" | ob run benchmark -b Clustering.yaml --local --cores 10 2>&1 )
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status=$?
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if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
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status=0
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fi
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echo -e $output
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sh -c "exit $status"
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if: matrix.ob_branch == 'dev' || matrix.ob_branch == 'reduce_install_scope'
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- name: Run benchmark
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shell: bash -l {0}
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run: |
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env
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output=$( ob run benchmark -b Clustering.yaml --local --threads 10 2>&1 )
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status=$?
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if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
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status=0
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fi
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echo -e $output
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sh -c "exit $status"
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if: matrix.ob_branch == 'main'
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# upload-artifact:
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# name: Benchmark Artifact
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# runs-on: ubuntu-latest
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# ## runs-on: self-hosted
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# needs: run-benchmark
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# if: always()
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# steps:
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# - name: Check out repository
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# uses: actions/checkout@v4
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# - name: Load cached output
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# uses: actions/cache@v3
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# with:
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# path: out/
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# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}
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# - name: Prepare output
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# run: |
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# zip -r benchmark_output.zip out/
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# mkdir -p gh-pages
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# cp out/plotting/plotting_report.html gh-pages/index.html
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# - name: Upload zipped output
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# uses: actions/upload-artifact@v4
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# with:
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# name: benchmark-output
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# path: benchmark_output.zip
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# retention-days: 7
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# - name: Upload Pages Artifact
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# uses: actions/upload-pages-artifact@v3
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# with:
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# path: gh-pages
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# - name: Deploy to GitHub Pages
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# uses: actions/deploy-pages@v4
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# - name: Create Job Summary
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# if: always()
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# run: |
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# echo "### Reports" >> $GITHUB_STEP_SUMMARY
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# echo "- [Plotting Report](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }})" >> $GITHUB_STEP_SUMMARY
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# echo "### All Outputs" >> $GITHUB_STEP_SUMMARY
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# echo "- [Complete Benchmark Output](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}#artifacts)" >> $GITHUB_STEP_SUMMARY
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‎.github/workflows/miniconda_miniforge.yml‎

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name: clustbench_miniforge
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# concurrency:
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# group: ${{ github.head_ref || github.run_id }}
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# cancel-in-progress: true
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on:
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pull_request:
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workflow_dispatch:
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schedule:
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# - cron: "*/30 * * * *" # Runs every 30 minutes for testing
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- cron: "30 1 * * *" # at 1.30am
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## these permissions are only for deployment to gh pages
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# permissions:
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# id-token: write
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# pages: write
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jobs:
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run-benchmark-miniforge:
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name: run_clustbench_miniforge
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## runs-on: ubuntu-latest
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runs-on: self-hosted
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strategy:
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matrix:
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ob_branch: [dev, reduce_install_scope, main]
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fail-fast: false
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concurrency:
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group: mambaforge-${{ matrix.ob_branch }}
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cancel-in-progress: false # true
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Install Mambaforge
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-variant: Miniforge3
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use-mamba: true
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activate-environment: test-env-${{matrix.ob_branch }}
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python-version: "3.12"
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auto-update-conda: true
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channels: conda-forge
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- name: Cache environment
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id: cache-env
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uses: actions/cache@v3
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with:
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path: |
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~/.conda/pkgs
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~/.conda/envs/omnibenchmark-env
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~/.cache/pip
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key: ${{ runner.os }}-conda-pip-${{ hashFiles('requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-conda-pip-
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- name: Install omnibenchmark CLI
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shell: bash -l {0}
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run: |
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mamba install -y pip
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pip install git+https://github.com/omnibenchmark/omnibenchmark.git@${{ matrix.ob_branch }}
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# - name: Enable a benchmarking `out` cache
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# id: cache-benchmark
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# uses: actions/cache@v3
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# with:
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# path: out/
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# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}
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- name: Run benchmark
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shell: bash -l {0}
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run: |
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env
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output=$( echo "y" | ob run benchmark -b Clustering.yaml --local --cores 10 2>&1 )
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status=$?
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if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
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status=0
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fi
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echo -e $output
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sh -c "exit $status"
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if: matrix.ob_branch == 'dev' || matrix.ob_branch == 'reduce_install_scope'
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- name: Run benchmark
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shell: bash -l {0}
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run: |
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env
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output=$( ob run benchmark -b Clustering.yaml --local --threads 10 2>&1 )
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status=$?
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if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
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status=0
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fi
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echo -e $output
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sh -c "exit $status"
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if: matrix.ob_branch == 'main'
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# upload-artifact:
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# name: Benchmark Artifact
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# runs-on: ubuntu-latest
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# ## runs-on: self-hosted
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# needs: run-benchmark
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# if: always()
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# steps:
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# - name: Check out repository
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# uses: actions/checkout@v4
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# - name: Load cached output
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# uses: actions/cache@v3
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# with:
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# path: out/
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# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}
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# - name: Prepare output
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# run: |
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# zip -r benchmark_output.zip out/
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# mkdir -p gh-pages
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# cp out/plotting/plotting_report.html gh-pages/index.html
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# - name: Upload zipped output
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# uses: actions/upload-artifact@v4
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# with:
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# name: benchmark-output
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# path: benchmark_output.zip
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# retention-days: 7
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# - name: Upload Pages Artifact
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# uses: actions/upload-pages-artifact@v3
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# with:
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# path: gh-pages
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# - name: Deploy to GitHub Pages
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# uses: actions/deploy-pages@v4
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# - name: Create Job Summary
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# if: always()
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# run: |
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# echo "### Reports" >> $GITHUB_STEP_SUMMARY
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# echo "- [Plotting Report](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }})" >> $GITHUB_STEP_SUMMARY
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# echo "### All Outputs" >> $GITHUB_STEP_SUMMARY
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# echo "- [Complete Benchmark Output](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}#artifacts)" >> $GITHUB_STEP_SUMMARY
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