remove random print statements #101
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| # Workflow for running Pytest against g3t | |
| # Optionally debug via SSH | |
| # Ref: https://fleetdm.com/engineering/tips-for-github-actions-usability | |
| # | |
| # To use this step uncomment and place anywhere in the build steps. The build will pause on this step and | |
| # output a ssh address associated with the Github action worker. Helpful for debugging build steps and | |
| # and intermediary files/artifacts. | |
| # | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| name: Pytest | |
| on: | |
| push: | |
| jobs: | |
| pytest: | |
| # We're testing 'cbds' by default so we can use the self-hosted runner to access htps://idp.cbds.ohsu.edu | |
| # https://github.com/ACED-IDP/gen3_util/settings/actions/runners/21 | |
| # https://docs.github.com/en/actions/hosting-your-own-runners/managing-self-hosted-runners/adding-self-hosted-runners#adding-a-self-hosted-runner-to-a-repository | |
| environment: cbds | |
| runs-on: self-hosted | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.12" | |
| - name: Install gen3-client | |
| id: install-gen3-client | |
| run: | | |
| wget https://github.com/ACED-IDP/cdis-data-client/releases/latest/download/gen3-client-linux-amd64.zip | |
| unzip gen3-client-linux-amd64.zip | |
| mkdir -p ~/.gen3 | |
| mv gen3-client ~/.gen3/gen3-client | |
| echo 'export PATH=$PATH:~/.gen3' >> ~/.bash_profile | |
| source ~/.bash_profile | |
| gen3-client | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| pip install -e . | |
| - name: Configure gen3-client | |
| id: configure-gen3-client | |
| env: | |
| CREDENTIALS: ${{ secrets.CREDENTIALS }} | |
| run: | | |
| source ~/.bash_profile | |
| echo $CREDENTIALS > ~/.gen3/credentials.json | |
| # Hardcoding the endpoint for now | |
| # TODO: Should we make this configurable to run `pytest` against all Gen3 instances? | |
| export ENDPOINT="https://idp.cbds.ohsu.edu" | |
| gen3-client configure --profile=CALIPER --cred=~/.gen3/credentials.json --apiendpoint="$ENDPOINT" | |
| export G3T_PROFILE=CALIPER | |
| echo "G3T_PROFILE=CALIPER" >> $GITHUB_ENV | |
| g3t ping | |
| # A 'local' profile appears to be required for the `pytest` tests | |
| # So we just "duplicate" the existing 'CALIPER' profile | |
| gen3-client configure --profile=local --cred=~/.gen3/credentials.json --apiendpoint="$ENDPOINT" | |
| - name: Pytest | |
| run: | | |
| pytest tests/ --cov=gen3_util |