Initial commit #1
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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: | |
| workflow_call: | |
| jobs: | |
| pylint: | |
| name: PyLint | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| - name: Install Infrastructure | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e . | |
| pip install toml | |
| pip install pylint | |
| - name: Analysing the code with pylint | |
| run: | | |
| pylint $(git ls-files '*.py') | |
| black_lint: | |
| name: Black Code Formatter Check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| - name: Install Black | |
| run: pip install black[jupyter] | |
| - name: Check code formatting with Black | |
| run: black . --exclude '\.ipynb$' | |
| unit_tests: | |
| name: Unit Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| - name: Install Infrastructure | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -e . | |
| - name: Run Unit Tests | |
| run: pytest tests/*.py --cov=. --cov-report=xml -vv | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| slug: StanfordSpezi/SpeziDataPipelineTemplate | |
| build_and_test_notebook: | |
| 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: Update apt-get | |
| run: sudo apt-get update | |
| - name: Setup LaTex | |
| run: | | |
| sudo apt-get install -y --fix-missing 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 and Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -e . | |
| - 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 |