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workflows/pytest: disable full analysis tests
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‎.github/workflows/pytest.yaml

+91-91
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@@ -36,94 +36,94 @@ jobs:
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run: |
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pytest tests/test_coef.py tests/test_pytorch_core.py tests/test_scipy_stats.py tests/test_sklearn_metrics.py
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pytest:
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name: Python tests for analyses
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runs-on: ${{ matrix.os }}
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strategy:
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max-parallel: 4
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fail-fast: false
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matrix:
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python-version: ["3.9"]
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os: [ubuntu-latest, macOS-latest, windows-latest]
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steps:
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- name: Checkout git repo
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uses: actions/checkout@v3
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- name: Cache conda
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id: cache
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uses: actions/cache@v3
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with:
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path: "${{ env.PY_ENV }}.tar.gz"
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key: ${{ runner.os }}-${{ env.PY_CACHE_NUMBER }}-${{ hashFiles('environment/environment.yml', 'environment/scripts/install_r_packages.r', 'environment/scripts/install_other_packages.sh') }}
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- name: Setup Miniconda
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if: steps.cache.outputs.cache-hit != 'true'
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uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: ${{ env.PY_ENV }}
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environment-file: environment/environment.yml
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auto-activate-base: false
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miniforge-variant: Mambaforge
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miniforge-version: 'latest'
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use-mamba: true
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- name: Install other packages and Conda-Pack environment
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if: steps.cache.outputs.cache-hit != 'true'
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shell: bash -l {0}
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run: |
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# other packages (R packages mainly)
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bash environment/scripts/install_other_packages.sh
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# install conda-pack, and pack environment
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conda install --yes -c conda-forge conda-pack coverage
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conda pack -f -n ${{ env.PY_ENV }} -o "${{ env.PY_ENV }}.tar.gz"
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- name: Unpack environment
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shell: bash -l {0}
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run: |
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mkdir -p "${{ env.PY_ENV }}"
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tar -xzf "${{ env.PY_ENV }}.tar.gz" -C "${{ env.PY_ENV }}"
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- name: Setup data and run pytest (Windows systems)
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if: runner.os == 'Windows'
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env:
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PYTHONPATH: libs/
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shell: cmd
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run: |
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echo on
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cd ${{ env.PY_ENV }}
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call .\Scripts\activate.bat
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.\Scripts\conda-unpack.exe
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cd ..
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set R_HOME=%CONDA_PREFIX%\Lib\R
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python environment\scripts\setup_data.py --mode testing
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pytest -v -rs tests
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- name: Setup data and run pytest (non-Windows systems)
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if: runner.os != 'Windows'
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shell: bash
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env:
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PYTHONPATH: libs/
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run: |
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source ${{ env.PY_ENV }}/bin/activate
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conda-unpack
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python environment/scripts/setup_data.py --mode testing
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if [ "$RUNNER_OS" == "Linux" ]; then
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# for linux/ubuntu, run the tests once: with numba jit activated
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# (which is the expected implementation) and with the jit
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# deactivated (otherwise coverage does not work).
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# numba jit activated
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pytest -v -rs tests
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# numba jit deactivated + code coverage
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export NUMBA_DISABLE_JIT=1
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coverage run --source=libs/ -m pytest -v -rs tests
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coverage xml -o coverage.xml
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else
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pytest -v -rs tests
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fi
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- name: Codecov upload
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if: runner.os == 'Linux'
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uses: codecov/codecov-action@v2
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with:
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files: ./coverage.xml
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name: codecov-${{ matrix.os }}-python${{ matrix.python-version }}
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fail_ci_if_error: true
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verbose: true
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# pytest:
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# name: Python tests for analyses
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# runs-on: ${{ matrix.os }}
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# strategy:
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# max-parallel: 4
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# fail-fast: false
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# matrix:
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# python-version: ["3.9"]
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# os: [ubuntu-latest, macOS-latest, windows-latest]
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# steps:
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# - name: Checkout git repo
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# uses: actions/checkout@v3
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# - name: Cache conda
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# id: cache
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# uses: actions/cache@v3
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# with:
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# path: "${{ env.PY_ENV }}.tar.gz"
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# key: ${{ runner.os }}-${{ env.PY_CACHE_NUMBER }}-${{ hashFiles('environment/environment.yml', 'environment/scripts/install_r_packages.r', 'environment/scripts/install_other_packages.sh') }}
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# - name: Setup Miniconda
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# if: steps.cache.outputs.cache-hit != 'true'
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# uses: conda-incubator/setup-miniconda@v2
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# with:
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# activate-environment: ${{ env.PY_ENV }}
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# environment-file: environment/environment.yml
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# auto-activate-base: false
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# miniforge-variant: Mambaforge
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# miniforge-version: 'latest'
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# use-mamba: true
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# - name: Install other packages and Conda-Pack environment
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# if: steps.cache.outputs.cache-hit != 'true'
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# shell: bash -l {0}
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# run: |
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# # other packages (R packages mainly)
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# bash environment/scripts/install_other_packages.sh
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#
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# # install conda-pack, and pack environment
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# conda install --yes -c conda-forge conda-pack coverage
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# conda pack -f -n ${{ env.PY_ENV }} -o "${{ env.PY_ENV }}.tar.gz"
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# - name: Unpack environment
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# shell: bash -l {0}
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# run: |
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# mkdir -p "${{ env.PY_ENV }}"
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# tar -xzf "${{ env.PY_ENV }}.tar.gz" -C "${{ env.PY_ENV }}"
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# - name: Setup data and run pytest (Windows systems)
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# if: runner.os == 'Windows'
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# env:
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# PYTHONPATH: libs/
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# shell: cmd
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# run: |
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# echo on
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# cd ${{ env.PY_ENV }}
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# call .\Scripts\activate.bat
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# .\Scripts\conda-unpack.exe
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# cd ..
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# set R_HOME=%CONDA_PREFIX%\Lib\R
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# python environment\scripts\setup_data.py --mode testing
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# pytest -v -rs tests
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# - name: Setup data and run pytest (non-Windows systems)
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# if: runner.os != 'Windows'
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# shell: bash
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# env:
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# PYTHONPATH: libs/
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# run: |
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# source ${{ env.PY_ENV }}/bin/activate
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# conda-unpack
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#
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# python environment/scripts/setup_data.py --mode testing
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#
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# if [ "$RUNNER_OS" == "Linux" ]; then
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# # for linux/ubuntu, run the tests once: with numba jit activated
109+
# # (which is the expected implementation) and with the jit
110+
# # deactivated (otherwise coverage does not work).
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#
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# # numba jit activated
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# pytest -v -rs tests
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#
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# # numba jit deactivated + code coverage
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# export NUMBA_DISABLE_JIT=1
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# coverage run --source=libs/ -m pytest -v -rs tests
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# coverage xml -o coverage.xml
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# else
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# pytest -v -rs tests
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# fi
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# - name: Codecov upload
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# if: runner.os == 'Linux'
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# uses: codecov/codecov-action@v2
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# with:
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# files: ./coverage.xml
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# name: codecov-${{ matrix.os }}-python${{ matrix.python-version }}
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# fail_ci_if_error: true
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# verbose: true

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