Sherlock optimizations #105
Workflow file for this run
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| # Modified from GitHub Actions template | |
| name: Workflow | |
| # Improves reproducibility and speed | |
| env: | |
| OPENBLAS_NUM_THREADS: 1 | |
| OMP_NUM_THREADS: 1 | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| jobs: | |
| Reproducibility: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip wheel | |
| pip install numpy==1.26.4 | |
| pip install -r requirements.txt | |
| - name: Compile Cython components | |
| run: | | |
| make clean compile | |
| - name: Set PYTHONPATH | |
| run: | | |
| echo "PYTHONPATH=." >> $GITHUB_ENV | |
| - name: Test ParCa reproducibility | |
| run: | | |
| python runscripts/parca.py --config ecoli/composites/ecoli_configs/run_parca.json \ | |
| -c 3 -o out/parca_1 | |
| python runscripts/parca.py --config ecoli/composites/ecoli_configs/run_parca.json \ | |
| -c 3 -o out/parca_2 | |
| python runscripts/debug/compare_pickles.py out/parca_1/kb out/parca_2/kb | |
| - name: Test simulation reproducibility | |
| run: | | |
| python ecoli/experiments/ecoli_master_sim.py \ | |
| --generations 1 --emitter parquet --emitter_arg out_dir='out' \ | |
| --experiment_id "parca_1" --daughter_outdir "out/parca_1" \ | |
| --sim_data_path "out/parca_1/kb/simData.cPickle" --fail_at_total_time & | |
| python ecoli/experiments/ecoli_master_sim.py \ | |
| --generations 1 --emitter parquet --emitter_arg out_dir='out' \ | |
| --experiment_id "parca_2" --daughter_outdir "out/parca_2" \ | |
| --sim_data_path "out/parca_2/kb/simData.cPickle" --fail_at_total_time | |
| python runscripts/debug/diff_simouts.py -o "out" "parca_1*" "parca_2*" | |
| Two-gens: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip wheel | |
| pip install numpy==1.26.4 mypy | |
| pip install -r requirements.txt | |
| - name: Install nextflow edge | |
| run: | | |
| curl -s https://get.nextflow.io | bash | |
| chmod +x nextflow | |
| echo "PATH=.:$PATH" >> $GITHUB_ENV | |
| NXF_EDGE=1 ./nextflow self-update | |
| - name: Compile Cython components | |
| run: | | |
| make clean compile | |
| - name: Set PYTHONPATH | |
| run: | | |
| echo "PYTHONPATH=." >> $GITHUB_ENV | |
| - name: Two generations | |
| run: | | |
| python runscripts/workflow.py --config ecoli/composites/ecoli_configs/two_generations.json |