Run documentation generation on CI #368
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| - "!open-in-colab" | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: "0 0 * * THU" | |
| workflow_dispatch: | |
| jobs: | |
| test_library: | |
| runs-on: ubuntu-latest | |
| container: ubuntu:rolling | |
| steps: | |
| - name: Install git | |
| run: | | |
| apt update -y -q | |
| apt install -y -qq git | |
| - name: Mark workspace as safe | |
| run: | | |
| git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
| - uses: actions/checkout@v3 | |
| with: | |
| set-safe-directory: false | |
| - name: Install non-pip dependencies of the workflow call library | |
| run: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt install -y -qq imagemagick inkscape python3-pip wget | |
| wget https://github.com/rclone/rclone/releases/download/v1.59.1/rclone-v1.59.1-linux-amd64.deb -O /tmp/rclone-v1.59.1-linux-amd64.deb | |
| dpkg -i /tmp/rclone-v1.59.1-linux-amd64.deb | |
| rm /usr/lib/python3.*/EXTERNALLY-MANAGED | |
| - name: Install the workflow call library | |
| run: | | |
| python3 -m pip install .[docs,lint,tests] | |
| - name: Run flake8 and mypy checks | |
| run: | | |
| python3 -m flake8 . | |
| python3 -m mypy . | |
| python3 -m nbqa flake8 . | |
| python3 -m nbqa mypy . | |
| - name: Run documentation generation | |
| run: | | |
| cd docs && make html | |
| - name: Run tests | |
| run: | | |
| python3 -m coverage run --source=open_in_cloud_workflow -m pytest tests | |
| env: | |
| RCLONE_CONFIG_DRIVE_CLIENT_ID: "${{ secrets.RCLONE_CONFIG_DRIVE_CLIENT_ID }}" | |
| RCLONE_CONFIG_DRIVE_CLIENT_SECRET: "${{ secrets.RCLONE_CONFIG_DRIVE_CLIENT_SECRET }}" | |
| RCLONE_CONFIG_DRIVE_TOKEN: "${{ secrets.RCLONE_CONFIG_DRIVE_TOKEN }}" | |
| - name: Check test coverage | |
| run: | | |
| python3 -m coverage report --fail-under=100 --show-missing --skip-covered | |
| test_workflow_artifact: | |
| needs: [test_library] | |
| uses: fem-on-colab/open-in-colab-workflow/.github/workflows/workflow_call.yml@main | |
| with: | |
| work_directory: open_in_colab | |
| notebook_pattern: "**/*.ipynb" | |
| extra_files_pattern: "**/*.dat" | |
| notebook_preparation: | | |
| rsync -avz --include "*/" --include="*.ipynb" --exclude="*" tests open_in_colab/ | |
| extra_files_preparation: | | |
| rsync -avz --include "*/" --include="*.png" --include="*.jpg" --include="*.svg" --exclude="*" tests open_in_colab/ | |
| mkdir -p open_in_colab/tests/data/extras/ | |
| echo "This is an extra file" > open_in_colab/tests/data/extras/extra.dat | |
| fem_on_colab_packages: | | |
| mpi4py | |
| pip_packages: | | |
| python-dateutil$dateutil | |
| kaleido%plotly | |
| itkwidgets | |
| test_script: | | |
| python3 -m pip install plotly | |
| python3 -m pytest --nbval open_in_colab/tests | |
| publish_on: artifact@open-in-colab | |
| publish_if_repository: fem-on-colab/open-in-colab-workflow | |
| test_workflow_drive: | |
| needs: [test_library] | |
| uses: fem-on-colab/open-in-colab-workflow/.github/workflows/workflow_call.yml@main | |
| with: | |
| work_directory: open_in_colab | |
| notebook_pattern: "**/*.ipynb" | |
| extra_files_pattern: "**/*.dat" | |
| notebook_preparation: | | |
| rsync -avz --include "*/" --include="*.ipynb" --exclude="*" tests open_in_colab/ | |
| extra_files_preparation: | | |
| rsync -avz --include "*/" --include="*.png" --include="*.jpg" --include="*.svg" --exclude="*" tests open_in_colab/ | |
| mkdir -p open_in_colab/tests/data/extras/ | |
| echo "This is an extra file" > open_in_colab/tests/data/extras/extra.dat | |
| fem_on_colab_packages: | | |
| mpi4py | |
| pip_packages: | | |
| python-dateutil$dateutil | |
| kaleido%plotly | |
| itkwidgets | |
| test_script: | | |
| python3 -m pip install plotly | |
| python3 -m pytest --nbval open_in_colab/tests | |
| publish_on: drive@GitHub/open_in_colab_workflow | |
| publish_if_repository: fem-on-colab/open-in-colab-workflow | |
| secrets: | |
| RCLONE_CONFIG_DRIVE_CLIENT_ID: "${{ secrets.RCLONE_CONFIG_DRIVE_CLIENT_ID }}" | |
| RCLONE_CONFIG_DRIVE_CLIENT_SECRET: "${{ secrets.RCLONE_CONFIG_DRIVE_CLIENT_SECRET }}" | |
| RCLONE_CONFIG_DRIVE_TOKEN: "${{ secrets.RCLONE_CONFIG_DRIVE_TOKEN }}" | |
| test_workflow_github: | |
| needs: [test_library] | |
| uses: fem-on-colab/open-in-colab-workflow/.github/workflows/workflow_call.yml@main | |
| with: | |
| work_directory: open_in_colab | |
| notebook_pattern: "**/*.ipynb" | |
| extra_files_pattern: "**/*.dat" | |
| notebook_preparation: | | |
| rsync -avz --delete --include "*/" --include="*.ipynb" --exclude="*" tests open_in_colab/ | |
| extra_files_preparation: | | |
| rsync -avz --delete --include "*/" --include="*.png" --include="*.jpg" --include="*.svg" --exclude="*" tests open_in_colab/ | |
| mkdir -p open_in_colab/tests/data/extras/ | |
| echo "This is an extra file" > open_in_colab/tests/data/extras/extra.dat | |
| fem_on_colab_packages: | | |
| mpi4py | |
| pip_packages: | | |
| python-dateutil$dateutil | |
| kaleido%plotly | |
| itkwidgets | |
| test_script: | | |
| python3 -m pip install plotly | |
| python3 -m pytest --nbval open_in_colab/tests | |
| publish_on: github@fem-on-colab/open-in-colab-workflow@open-in-colab | |
| publish_if_repository: fem-on-colab/open-in-colab-workflow | |
| warn: | |
| runs-on: ubuntu-latest | |
| if: github.repository == 'fem-on-colab/open-in-colab-workflow' && github.ref == 'refs/heads/main' && github.event_name == 'schedule' | |
| steps: | |
| - name: Warn if scheduled workflow is about to be disabled | |
| uses: fem-on-colab/warn-workflow-about-to-be-disabled-action@main | |
| with: | |
| workflow-filename: ci.yml | |
| days-elapsed: 50 |