pr_tests.yml

# 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: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        pip install --upgrade pip wheel
        pip install numpy==1.26.4 mypy
        pip install -r requirements.txt
    - name: Install nextflow
      run: |
        curl -s https://get.nextflow.io | bash
        chmod +x nextflow
        echo "PATH=.:$PATH" >> $GITHUB_ENV
    - 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