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Update Dependencies & Fix Build Errors #432

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Update Dependencies & Fix Build Errors

Update Dependencies & Fix Build Errors #432

Workflow file for this run

.github/workflows/build-and-test.yml at a19f9d0
#
# 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: build
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
with:
node-version: '22'
- 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: Install Cloud Functions Dependencies
run: |
npm install --prefix functions
- 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/ECG Reviewer.ipynb'"
env:
CI: true
- uses: actions/upload-artifact@v4
with:
name: ECGReviewer_ColabBasic.pdf
path: ECGReviewer_ColabBasic.pdf