activate mtpy test env before jupyter install #437
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| name: TestingInConda | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - '*' | |
| jobs: | |
| setup-build: | |
| name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Conda | |
| uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: false | |
| conda-channels: conda-forge | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Env | |
| shell: bash | |
| run: | | |
| python --version | |
| conda env create -f environment.yml | |
| source activate mtpy-v2-test | |
| pip install git+https://github.com/simpeg/pydiso.git | |
| conda install pytest | |
| conda install pytest-subtests | |
| conda install pytest-cov | |
| pip install git+https://github.com/kujaku11/mt_metadata.git@main | |
| pip install git+https://github.com/kujaku11/mth5.git@master | |
| pip install git+https://github.com/simpeg/aurora@main | |
| git clone https://github.com/MTgeophysics/mtpy_data.git | |
| git clone --single-branch --branch mtpy_tests https://github.com/simpeg/aurora | |
| cd mtpy_data | |
| pip install -e . | |
| cd .. | |
| - name: Install Our Package | |
| shell: bash | |
| run: | | |
| source activate mtpy-v2-test | |
| pip install -e . | |
| conda list | |
| - name: Install Jupyter and dependencies | |
| run: | | |
| source activate mtpy-v2-test | |
| pip install jupyter | |
| pip install ipykernel | |
| python -m ipykernel install --user --name mtpy-v2-test | |
| # Install any other dependencies you need | |
| - name: Execute Jupyter Notebooks | |
| run: | | |
| source activate mtpy-v2-test | |
| cd aurora | |
| jupyter nbconvert --to notebook --execute docs/examples/dataset_definition.ipynb | |
| # jupyter nbconvert --to notebook --execute docs/examples/operate_aurora.ipynb | |
| #jupyter nbconvert --to notebook --execute docs/tutorials/pole_zero_fitting/lemi_pole_zero_fitting_example.ipynb | |
| #jupyter nbconvert --to notebook --execute docs/tutorials/processing_configuration.ipynb | |
| #jupyter nbconvert --to notebook --execute docs/tutorials/process_cas04_single_station.ipynb | |
| #jupyter nbconvert --to notebook --execute docs/tutorials/synthetic_data_processing.ipynb | |
| #jupyter nbconvert --to notebook --execute tests/test_run_on_commit.ipynb | |
| cd ../ | |
| # Replace "notebook.ipynb" with your notebook's filename | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| source activate mtpy-v2-test | |
| pytest -rA --cov=./ --cov-report=xml --cov=mtpy | |
| - name: "Upload coverage to Codecov" | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| with: | |
| fail_ci_if_error: false | |
| verbose: true | |
| flags: tests | |