test_benchmark_collection_models.yml

name: Benchmark Collection
on:
  push:
    branches:
      - develop
      - master
  pull_request:
    branches:
      - master
      - develop
  merge_group:
  workflow_dispatch:
  schedule:
    - cron:  '48 4 * * *'

jobs:
  build:
    name: Benchmark Collection

    runs-on: ubuntu-22.04

    strategy:
      fail-fast: false
      matrix:
        python-version: [ "3.9" ]
        extract_subexpressions: ["true", "false"]
    env:
      AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}

    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: echo "${HOME}/.local/bin/" >> $GITHUB_PATH

    # install AMICI
    - name: Create AMICI sdist
      run: |
        pip3 install build && cd python/sdist && python3 -m build --sdist
    - name: Install AMICI sdist
      run: |
        pip3 install --user petab[vis] && \
        AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]

    # retrieve test models
    - name: Download and test benchmark collection
      run: |
        git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
          && AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh

    # run gradient checks
    - name: Run Gradient Checks
      run: |
        pip install git+https://github.com/ICB-DCM/fiddy.git \
          && cd tests/benchmark-models && pytest ./test_petab_benchmark.py

    # upload results
    - uses: actions/upload-artifact@v3
      with:
        name: computation times
        path: |
          tests/benchmark-models/computation_times.csv
          tests/benchmark-models/computation_times.png