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Safer method of specifying None as default #499

Safer method of specifying None as default

Safer method of specifying None as default #499

name: create_test_conda_env
on: [push]
jobs:
build-linux:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- 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