369.fre-cli mkmf dependency #1476
Workflow file for this run
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| name: create_test_conda_env | ||
| on: | ||
| pull_request: | ||
| branches: | ||
| - main | ||
| push: | ||
| branches: | ||
| - main | ||
| # cancel running jobs if theres a newer push | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.ref }} | ||
| cancel-in-progress: true | ||
| jobs: | ||
| build-linux: | ||
| runs-on: ubuntu-latest | ||
| container: | ||
| image: ghcr.io/noaa-gfdl/fre-cli:miniconda24_gcc14_v2 | ||
| options: "--privileged --cap-add=sys_admin --cap-add=mknod --device=/dev/fuse --security-opt seccomp=unconfined --security-opt label=disable --security-opt apparmor=unconfined" # needed for podman | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| submodules: 'recursive' | ||
| - name: Create fre-cli environment | ||
| run: | | ||
| # create env holding all deps, the env cant be explicitly activated in 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 as module 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:$PATH" | ||
| # run pytest | ||
| coverage run -m pytest --durations=20 --log-level INFO --junit-xml=pytest_results.xml --config-file=pytest.ini --cov-config=coveragerc --cov-report=xml --cov=fre fre/ | ||
| # restore original path and install genbadge to generate coverage badge based on xml | ||
| export PATH="$path_save" | ||
| # install genbadge to make badge from coverage/test stats | ||
| pip install defusedxml genbadge | ||
| # genbadge coverage | ||
| genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg | ||
| # genbadge tests | ||
| genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg | ||
| - name: Archive code coverage results | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: code-coverage-report | ||
| path: coverage.xml | ||
| - name: Run pylint in fre-cli environment | ||
| run: | | ||
| # run pylint, ignored modules avoid warnings arising from code internal to those modules | ||
| pylint --max-line-length 120 --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 and themes, upgrade theme | ||
| pip install sphinx renku-sphinx-theme sphinx-rtd-theme | ||
| pip install --upgrade sphinx-rtd-theme | ||
| # have sphinx build the docs | ||
| sphinx-apidoc --ext-autodoc --output-dir docs fre/ --separate | ||
| sphinx-build -E docs build | ||
| - name: Deploy to GitHub Pages | ||
| uses: peaceiris/actions-gh-pages@v4 | ||
| if: ${{ github.ref == 'refs/heads/main' }} | ||
| with: | ||
| publish_branch: gh-pages | ||
| github_token: ${{ secrets.GITHUB_TOKEN }} | ||
| publish_dir: build/ | ||
| force_orphan: true | ||
