try to fix failing tests #893
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| on: [push] | |
| name: "Tests and validation" | |
| jobs: | |
| python-tests: | |
| name: Python unit and integration tests | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # This is necessary for the conda action. It replaces `conda init` as | |
| # the shell does not load ,profile or .bashrc. | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-version: latest | |
| - name: Install nanover dependancies | |
| run: conda install -y mpi4py openmm | |
| - name: Install tests dependancies | |
| run: python -m pip install -r python-libraries/requirements.test | |
| - name: Compile | |
| run: ./compile.sh --no-dotnet | |
| - name: Parallel tests | |
| run: python -m pytest --cov nanover python-libraries -n auto -m 'not serial' | |
| - name: Serial tests | |
| run: python -m pytest --cov nanover python-libraries -n 1 -m 'serial' | |
| mypy: | |
| name: Type analysis for python | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # This is necessary for the conda action. It replaces `conda init` as | |
| # the shell does not load ,profile or .bashrc. | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-version: latest | |
| - name: Install nanover dependancies | |
| run: conda install -y mpi4py openmm | |
| - name: Install tests dependancies | |
| run: python -m pip install -r python-libraries/requirements.test | |
| - name: Compile (mypy requires --no-edit) | |
| run: ./compile.sh --no-dotnet --no-edit | |
| - name: mypy | |
| run: | | |
| # Mypy accepts paths, modules or packages as inputs. However, only | |
| # packages work reasonably well with packages. So we need to generate | |
| # a list of the packages we want to test. | |
| packages=$(find python-libraries -name __init__.py \ | |
| | sed 's/__init__.py//g' \ | |
| | awk '{split($0, a, /src/); print(a[2])}' \ | |
| | sed 's#/#.#g' \ | |
| | cut -c 2- \ | |
| | sed 's/\.$//g' \ | |
| | grep -v '^$' \ | |
| | grep -v protocol \ | |
| | sed 's/^/-p /g' \ | |
| | grep -v '\..*\.' \ | |
| | tr '\n' ' ') | |
| mypy --ignore-missing-imports --namespace-packages --check-untyped-defs --allow-redefinition $packages | |
| ruff: | |
| name: Ruff to lint python code | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # This is necessary for the conda action. It replaces `conda init` as | |
| # the shell does not load ,profile or .bashrc. | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniforge-version: latest | |
| - name: Install nanover dependancies | |
| run: conda install -y mpi4py openmm | |
| - name: Install ruff | |
| run: python -m pip install ruff black | |
| - name: Compile | |
| run: ./compile.sh --no-dotnet | |
| - name: Ruff | |
| run: ruff check ./python-libraries | |
| - name: Black | |
| run: black --diff --check ./python-libraries | |
| csharp-tests: | |
| name: C# unit and integration tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-dotnet@v3 | |
| with: | |
| dotnet-version: '2.1.x' | |
| - name: Compile | |
| run: ./compile.sh --no-python | |
| - name: Tests | |
| run: cd ./csharp-libraries && dotnet test |