AMICI/.github/workflows/test_benchmark_collection_models.yml at ffb787d2ec2ac8bd2cc8af6c88d571b8a7cda3e6 · AMICI-dev/AMICI · GitHub

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

jobs:
  cpp:
    name: Benchmark Collection CPP

    runs-on: ubuntu-24.04

    strategy:
      fail-fast: false
      matrix:
        python-version: [ "3.14" ]
        extract_subexpressions: ["true", "false"]
    env:
      AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}
    steps:
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v6
      with:
        python-version: ${{ matrix.python-version }}

    - uses: actions/checkout@v5
      with:
        fetch-depth: 20

    - name: Install apt dependencies
      uses: ./.github/actions/install-apt-dependencies

    - 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="" pip3 install -v --user \
            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis,jax]

    - name: Install test dependencies
      run: |
        python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@main \
        &&  python3 -m pip install -U sympy \
        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@main

    - name: Download benchmark collection
      run: |
        pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python

    - name: Run tests
      env:
        AMICI_PARALLEL_COMPILE: ""
      run: |
        pytest tests/benchmark_models/test_petab_benchmark.py \
          --durations=10 \
          --cov=amici \
          --cov-report=xml:"coverage_py.xml" \
          --cov-append \

    - name: Codecov Python
      if: (github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev') && github.actor != 'dependabot[bot]'
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: coverage_py.xml
        flags: python
        fail_ci_if_error: true
        verbose: true

    # collect & upload results
    - name: Aggregate results
      run: |
          python3 tests/benchmark_models/evaluate_benchmark.py

    - uses: actions/upload-artifact@v5
      with:
        name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}
        path: |
          tests/benchmark_models/computation_times.csv
          tests/benchmark_models/computation_times.png

  jax:
    name: Benchmark Collection JAX
    runs-on: ubuntu-24.04
    strategy:
      fail-fast: false
      matrix:
        python-version: [ "3.14" ]
        extract_subexpressions: ["false"]
    env:
      AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}
    steps:
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v6
      with:
        python-version: ${{ matrix.python-version }}

    - uses: actions/checkout@v5
      with:
        fetch-depth: 20

    - name: Install apt dependencies
      uses: ./.github/actions/install-apt-dependencies

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

    - 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] && \
        pip3 install -v --user \
            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis,jax]

    - name: Install test dependencies
      run: |
        python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@main \
        &&  python3 -m pip install -U sympy \
        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@amici100

    - run: pip uninstall -y diffrax && pip install git+https://github.com/patrick-kidger/diffrax@dev # TODO FIXME https://github.com/patrick-kidger/diffrax/issues/654 + event dirs

    - name: Download benchmark collection
      run: |
        pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python

    - name: Run JAX tests
      env:
        AMICI_PARALLEL_COMPILE: ""
      run: |
        pytest tests/benchmark_models/test_petab_benchmark_jax.py \
          --durations=10 \
          --cov=amici \
          --cov-report=xml:"coverage_py.xml" \
          --cov-append

    - name: Codecov Python
      if: (github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev') && github.actor != 'dependabot[bot]'
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: coverage_py.xml
        flags: python
        fail_ci_if_error: true
        verbose: true