build-and-test.yml

#
# This source file is part of the PAWS application based on the Stanford Spezi Template Application project
#
# SPDX-FileCopyrightText: 2023 Stanford University
#
# SPDX-License-Identifier: MIT
#

name: Build and Test

on:
  pull_request:
  workflow_dispatch:
  workflow_call:

concurrency:
  group: build-${{ github.ref }}
  cancel-in-progress: true

jobs:
  reuse_action:
    name: REUSE Compliance Check
    uses: StanfordBDHG/.github/.github/workflows/reuse.yml@v2
    permissions:
      contents: read
  swiftlint:
    name: SwiftLint
    uses: StanfordBDHG/.github/.github/workflows/swiftlint.yml@v2
    permissions:
      contents: read
  markdownlinkcheck:
    name: Markdown Link Check
    uses: StanfordBDHG/.github/.github/workflows/markdown-link-check.yml@v2
    permissions:
      contents: read
  codeql:
    name: CodeQL
    uses: StanfordBDHG/.github/.github/workflows/xcodebuild-or-fastlane.yml@v2
    with:
      codeql: true
      fastlanelane: codeql
    permissions:
      security-events: write
      actions: read
  buildandtest:
    name: Build and Test
    uses: StanfordBDHG/.github/.github/workflows/xcodebuild-or-fastlane.yml@v2
    permissions:
      contents: read
    with:
      artifactname: PAWS.xcresult
      runsonlabels: '["macOS", "self-hosted"]'
      setupfirebaseemulator: true
      fastlanelane: test
      firebaseemulatorimport: ./firebase
    secrets:
      GOOGLE_APPLICATION_CREDENTIALS_BASE64: ${{ secrets.GOOGLE_APPLICATION_CREDENTIALS_BASE64 }}
  uploadcoveragereport:
    name: Upload Coverage Report
    needs: buildandtest
    uses: StanfordBDHG/.github/.github/workflows/create-and-upload-coverage-report.yml@v2
    permissions:
      contents: read
    with:
      coveragereports: PAWS.xcresult
    secrets:
      token: ${{ secrets.CODECOV_TOKEN }}
  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: |
          pip install pylint
      - name: Install ECGReviewer Dependencies
        run: |
          pip install -r ./ecg_data_manager/requirements.txt
      - name: Analysing the code with pylint
        run: |
          pylint $(git ls-files '*.py')
  black_lint:
    name: Black Code Formatter Check
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
      - name: Install Black
        run: pip install black[jupyter]
      - name: Check code formatting with Black
        run: black . --exclude '\.ipynb$'
  buildandtestdatapipelinenotebook:
    name: Build and Test ECG Reviewer 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 update -y
        sudo apt-get install -y --no-install-recommends pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic || true
        if ! dpkg -l pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic; then
          sudo apt-get update --fix-missing
          sudo apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic
        fi
    - 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 ECGReviewer Dependencies
      run: |
        pip install -r ./ecg_data_manager/requirements.txt
    - name: Set Firestore Emulator Environment Variable
      run: |
        echo "FIRESTORE_EMULATOR_HOST=localhost:8080" >> $GITHUB_ENV
        echo "GCLOUD_PROJECT=ecg_example_project" >> $GITHUB_ENV
    - name: Run Firebase Emulator & Execute Notebook
      run: |
        firebase emulators:exec --import=./ecg_data_manager/sample_data "jupyter nbconvert --to pdf --execute ./ecg_data_manager/ECGReviewer_ColabBasic.ipynb"
      env:
        CI: true
    - uses: actions/upload-artifact@v4
      with:
        name: ECGReviewer_ColabBasic.pdf
        path: ECGReviewer_ColabBasic.pdf