Define an API surface between Spezi Data Pipeline and Python notebook #54
Workflow file for this run
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| # | |
| # This source file is part of the Stanford Spezi open-source project | |
| # | |
| # SPDX-FileCopyrightText: 2024 Stanford University and the project authors (see CONTRIBUTORS.md) | |
| # | |
| # SPDX-License-Identifier: MIT | |
| # | |
| name: Build and Test | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| pylint: | |
| name: Pylint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| - name: Install Infrastructure | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pylint | |
| - name: Install SpeziDataPipelineTemplate Dependencies | |
| run: | | |
| pip install pandas numpy matplotlib firebase-admin fhir.resources | |
| - name: Analysing the code with pylint | |
| run: | | |
| pylint $(git ls-files '*.py') | |
| build_and_test: | |
| name: Build and Test Notebook | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| - name: Setup NodeJS | |
| uses: actions/setup-node@v3 | |
| - name: Setup Java | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'microsoft' | |
| java-version: '17' | |
| - name: Setup LaTex | |
| run: | | |
| sudo apt-get install pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic | |
| - name: Cache Firebase Emulators | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/firebase/emulators | |
| key: ${{ runner.os }}-${{ runner.arch }}-firebase-emulators-${{ hashFiles('~/.cache/firebase/emulators/**') }} | |
| - name: Install Firebase CLI Tools | |
| run: npm install -g firebase-tools | |
| - name: Install Infrastructure | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install jupyterlab | |
| - name: Install SpeziDataPipelineTemplate Dependencies | |
| run: | | |
| pip install pandas numpy matplotlib firebase-admin fhir.resources | |
| - name: Set Firestore Emulator Environment Variable | |
| run: | | |
| echo "FIRESTORE_EMULATOR_HOST=localhost:8080" >> $GITHUB_ENV | |
| echo "GCLOUD_PROJECT=spezidatapipelinetemplate" >> $GITHUB_ENV | |
| - name: Run Firebase Emulator & Execute Notebook | |
| run: | | |
| firebase emulators:exec --import=./sample_data "jupyter nbconvert --to pdf --execute SpeziDataPipelineTemplate.ipynb" | |
| env: | |
| CI: true | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: SpeziDataPipelineTemplate.pdf | |
| path: SpeziDataPipelineTemplate.pdf |