Update freyamltools.py #431
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| name: create_test_conda_env | |
| on: [push] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '>=3.9' | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an env var pointing to root of miniconda dir | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Create fre-cli environment | |
| run: | | |
| # create environment containing all dependencies | |
| # the env cannot be explicitly activated in github CI/CD | |
| conda env create -f environment.yml --name fre-cli | |
| # add conda env's executables to github's PATH equiv. | |
| echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH | |
| # use *conda environment's pip* to install fre-cli | |
| # called w/ full path to conda's python for explicitness | |
| # called as a module (-m pip) for explicitness | |
| $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli . | |
| - name: Run pytest in fre-cli environment | |
| run: | | |
| # try to make sure the right things are in GITHUB_PATH | |
| echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH | |
| # are we talking to the right python? | |
| which python | |
| python --version | |
| $CONDA/envs/fre-cli/bin/python --version | |
| # run pytest | |
| pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/ | |
| # install genbadge to generate coverage badge based on xml | |
| pip install genbadge | |
| genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg | |
| genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg | |
| - name: Run pylint in fre-cli environment | |
| run: | | |
| # try to make sure the right things are in GITHUB_PATH | |
| echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH | |
| # are we talking to the right python? | |
| which python | |
| python --version | |
| $CONDA/envs/fre-cli/bin/python --version | |
| # run pylint, ignored modules avoid warnings arising from code internal to those modules | |
| pylint --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo." | |
| - name: Install Sphinx and Build Documentation | |
| run: | | |
| pip install sphinx renku-sphinx-theme sphinx-rtd-theme | |
| pip install --upgrade sphinx-rtd-theme | |
| sphinx-apidoc --output-dir docs fre/ --separate | |
| sphinx-build docs build | |
| - name: Deploy to GitHub Pages | |
| uses: peaceiris/actions-gh-pages@v3 | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| with: | |
| publish_branch: gh-pages | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: build/ | |
| force_orphan: true |