🐛 fix installation issue of pimms on PR using colab image #49
Workflow file for this run
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| name: Test that tutorial runs on latest colab image | |
| on: | |
| # push: | |
| # branches: [main] | |
| pull_request: | |
| branches: [main] | |
| schedule: | |
| - cron: '0 2 3 * *' | |
| jobs: | |
| test-tutorial-on-colab: | |
| name: Test tutorial on latest colab image | |
| runs-on: ubuntu-latest-4core # increase disk space | |
| # https://console.cloud.google.com/artifacts/docker/colab-images/europe/public/runtime | |
| container: | |
| image: europe-docker.pkg.dev/colab-images/public/runtime:latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-tags: true | |
| # fetch-depth: 0 | |
| # path: /pimms | |
| - name: Check out the repository | |
| run: | | |
| git clone https://github.com/RasmussenLab/pimms.git | |
| cd pimms | |
| echo $GITHUB_REF | |
| git checkout $GITHUB_REF | |
| git merge main | |
| - name: Install pimms-learn (from branch) and papermill | |
| if: github.event_name == 'pull_request' | |
| run: | | |
| cd pimms | |
| echo PWD: $(pwd) | |
| python -m build . | |
| pip install dist/pimms_learn-*.whl | |
| pip install papermill | |
| which papermill | |
| which python | |
| which pip | |
| cd project | |
| echo python3 -c "import pimmslearn; print(pimmslearn.__version__)" | |
| python3 -c "import pimmslearn; print(pimmslearn.__version__)" | |
| echo python3 -c "import pimmslearn; pimmslearn.io | |
| python3 -c "import pimmslearn; pimmslearn.io" | |
| echo python3 -c "import pimmslearn.io" | |
| python3 -c "import pimmslearn.io" | |
| python -m papermill 04_1_train_pimms_models.ipynb 04_1_train_pimms_models_output.ipynb | |
| papermill 04_1_train_pimms_models.ipynb 04_1_train_pimms_models_output.ipynb | |
| - name: Install pimms-learn (from PyPI) and papermill | |
| if: github.event_name == 'schedule' | |
| run: | | |
| pip install pimms-learn papermill | |
| - name: Run tutorial | |
| run: | | |
| cd project | |
| which papermill | |
| papermill 04_1_train_pimms_models.ipynb 04_1_train_pimms_models_output.ipynb | |
| papermill 04_1_train_pimms_models.ipynb 04_1_train_pimms_models_no_val.ipynb -p sample_splits False | |