test_performance.yml

name: Performance Test
on:
  push:
    branches:
      - develop
      - master
      - fix_perftest

  pull_request:
    branches:
      - master

  workflow_dispatch:

  schedule:
    - cron:  '48 4 * * *'

jobs:
  build:
    name: Performance Test

    runs-on: ubuntu-22.04

    strategy:
      matrix:
        python-version: [3.9]

    steps:
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - uses: actions/checkout@v3
      with:
        fetch-depth: 20

    # install dependencies
    - name: apt
      run: |
        sudo apt-get update \
          && sudo apt-get install -y swig libatlas-base-dev
    - run: pip3 install petab shyaml build

    - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
    - run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH

    # install AMICI
    - name: Create AMICI sdist
      run: |
        cd python/sdist \
          && check_time.sh create_sdist python3 -m build --sdist

    - name: Install AMICI sdist
      run: |
        AMICI_PARALLEL_COMPILE=2 check_time.sh \
            install_sdist pip3 install -v --user \
            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)

    # retrieve test model
    - run: git clone --depth 1 https://github.com/ICB-DCM/CS_Signalling_ERBB_RAS_AKT

    # import test model
    - name: Import test model
      run: |
        AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import

    - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
      uses: actions/upload-artifact@v3
      with:
        name: model_performance_test
        path: model_performance_test

    # install model package
    - name: Install test model
      run: >
        check_time.sh install_model tests/performance/test.py compile;
        for opt in O0 O1 O2;
        do
          check_time.sh install_model_${opt} tests/performance/test.py compile_${opt};
        done

    # run simulations
    - name: forward_simulation
      run: >
        check_time.sh forward_simulation tests/performance/test.py  forward_simulation;
        for opt in O0 O1 O2;
        do
          check_time.sh forward_simulation tests/performance/test.py forward_simulation_${opt};
        done
    - name: forward_sensitivities
      run: >
        check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities;
        for opt in O0 O1 O2;
        do
          check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities_${opt};
        done
    - name: adjoint_sensitivities
      run: >
        check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities;
        for opt in O0 O1 O2;
        do
          check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities_${opt};
        done
    - name: forward_simulation_non_optimal_parameters
      run: |
        check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters;
        for opt in O0 O1 O2;
        do
          check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters_${opt};
        done
    - name: adjoint_sensitivities_non_optimal_parameters
      run: |
        check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters;
        for opt in O0 O1 O2;
        do
          check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters_${opt};
        done
    - name: forward_steadystate_sensitivities_non_optimal_parameters
      run: |
        check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters;
        for opt in O0 O1 O2;
        do
          check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters_${opt};
        done
    - name: adjoint_steadystate_sensitivities_non_optimal_parameters
      run: |
        check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters;
        for opt in O0 O1 O2;
        do
          check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters_${opt};
        done