build-and-test.yml

#
# 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/codecov-action@v4.0.1
        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