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Release 0.21.2
Merge pull request #2287 from dweindl/release_0.21.2
2 parents ec4ee25 + 5e64ed4 commit fa7c0bd

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‎.github/actions/setup-swig/action.yml‎

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swig_version:
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description: 'Swig version to build'
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required: false
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default: '4.1.1'
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default: '4.2.0'
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runs:
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using: "composite"

‎.github/workflows/deploy_branch.yml‎

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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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fetch-depth: 20
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scripts/buildSdist.sh
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- name: "Upload artifact: sdist"
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: sdist
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path: python/sdist/dist/amici-*.gz

‎.github/workflows/deploy_protected.yml‎

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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2

‎.github/workflows/deploy_release.yml‎

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matrix:
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python-version: [3.9]
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environment:
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name: pypi
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url: https://pypi.org/p/amici
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permissions:
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id-token: write
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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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fetch-depth: 20
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- name: Publish a Python distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.pypi_password }}
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packages-dir: python/sdist/dist
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bioSimulatorsUpdateCliAndDockerImage:

‎.github/workflows/test_benchmark_collection_models.yml‎

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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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fetch-depth: 20
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- name: Install AMICI sdist
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run: |
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pip3 install --user petab[vis] && \
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AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
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AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
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$(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
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# retrieve test models
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- name: Download and test benchmark collection
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run: |
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git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
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&& export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
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&& AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh
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&& AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
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# run gradient checks
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- name: Run Gradient Checks
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&& cd tests/benchmark-models && pytest ./test_petab_benchmark.py
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# upload results
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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with:
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name: computation times
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name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}
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path: |
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tests/benchmark-models/computation_times.csv
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tests/benchmark-models/computation_times.png

‎.github/workflows/test_doc.yml‎

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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- run: git fetch --prune --unshallow
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- name: Set up doxygen
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- run: git fetch --prune --unshallow
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

‎.github/workflows/test_install.yml‎

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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- run: git fetch --prune --unshallow
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- run: git fetch --prune --unshallow
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- run: git fetch --prune --unshallow
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

‎.github/workflows/test_matlab.yml‎

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runs-on: ubuntu-20.04
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- run: git fetch --prune --unshallow
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- run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

‎.github/workflows/test_performance.yml‎

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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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fetch-depth: 20
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- name: Install AMICI sdist
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run: |
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AMICI_PARALLEL_COMPILE=2 check_time.sh \
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AMICI_PARALLEL_COMPILE="" check_time.sh \
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install_sdist pip3 install -v --user \
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$(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
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AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import
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- name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: model_performance_test
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path: model_performance_test

‎.github/workflows/test_petab_test_suite.yml‎

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steps:
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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fetch-depth: 20
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- name: Run PEtab test suite
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source ./build/venv/bin/activate \
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&& AMICI_PARALLEL_COMPILE=2 pytest -v \
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&& AMICI_PARALLEL_COMPILE="" pytest -v \
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--cov-report=xml:coverage.xml \
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--cov-append \
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--cov=amici \
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tests/petab_test_suite/
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- name: Codecov
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if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
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uses: codecov/[email protected]
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: coverage.xml

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