make create_test_conda_env.yml run on pull_request #514
Workflow file for this run
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| name: create_test_conda_env | |
| on: [push, pull_request] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/noaa-gfdl/fre-cli:miniconda24.7.1_gcc14.2.0 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| - 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 | |
| # sets CONDA to wherever it may be on the image | |
| source /root/.bashrc | |
| # add conda env's executables and mkmf to github's PATH equiv. | |
| echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH | |
| echo $PWD/mkmf/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 $CONDA/envs/fre-cli . | |
| - name: Run pytest in fre-cli environment | |
| run: | | |
| # add spack installed binaries to front of path so that | |
| # conda's netcdf/hdf5 installs don't break compilation tests | |
| export path_save=$PATH | |
| export PATH="/opt/views/view/bin:$PATH" | |
| # run pytest | |
| pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/ | |
| # restore original path and install genbadge to generate coverage badge based on xml | |
| export PATH="$path_save" | |
| 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: | | |
| # 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 |