Add ECG Data Pipeline Tool (#53)

# *Add ECG Data Pipeline Tool*

## ♻️ Current situation & Problem
This PR adds the ECG Data Pipeline tool into a separate folder in the
root of the project repository. Currently, the project lacks a dedicated
pipeline for processing, analyzing and visualising the ECG data. This
addition aims to provide a streamlined way to handle ECG data with
enhanced analysis and visualisation capabilities.


## ⚙️ Release Notes 
- Added ECG Data Pipeline folder containing the pipeline tool for
processing, analyzing, and visualising ECG data.
- The pipeline includes modules for data preparation, access to
Firebase, utility functions, and data visualization, alongside an
interactive Python notebook (ECGDataPipelineTemplate.ipynb) for ECG data
review.
- Migration Guide: No breaking changes introduced. Users can integrate
the pipeline tool into their workflow by cloning the repository and
following the setup instructions in the README.

```python
!git clone https://github.com/StanfordBDHG/PediatricAppleWatchStudy.git
%cd PediatricAppleWatchStudy/ECGDataPipeline
```

## 📚 Documentation
The ECG Data Pipeline tool is fully documented. The README within the
ECG Data Pipeline folder provides an overview, setup instructions, and
usage examples for integration and utilization of the tool.

## ✅ Testing
A job to build and test the ECG Data Pipeline notebook was added into
the existing workflow build-and-test. This includes setting up Python,
NodeJS, Java, and LaTeX environments; installing necessary dependencies;
and executing the notebook with Firebase emulators to validate the data
pipeline's functionality. The notebook is then converted to a PDF
document, which is uploaded as an artifact for review.

### Code of Conduct & Contributing Guidelines 

By submitting creating this pull request, you agree to follow our [Code
of
Conduct](https://github.com/StanfordBDHG/.github/blob/main/CODE_OF_CONDUCT.md)
and [Contributing
Guidelines](https://github.com/StanfordBDHG/.github/blob/main/CONTRIBUTING.md):
- [x] I agree to follow the [Code of
Conduct](https://github.com/StanfordBDHG/.github/blob/main/CODE_OF_CONDUCT.md)
and [Contributing
Guidelines](https://github.com/StanfordBDHG/.github/blob/main/CONTRIBUTING.md).

---------

Co-authored-by: Paul Schmiedmayer <[email protected]>

.github/workflows/build-and-test.yml

@@ -49,3 +49,53 @@ jobs:
       coveragereports: PAWS.xcresult
     secrets:
       token: ${{ secrets.CODECOV_TOKEN }}
+  buildandtestdatapipelinenotebook:
+    name: Build and Test ECG Data pipeline 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 ECGDataPipelineTemplate Dependencies
+      run: |
+        pip install pandas numpy matplotlib firebase-admin requests ipywidgets pytz
+    - name: Set Firestore Emulator Environment Variable
+      run: |
+        echo "FIRESTORE_EMULATOR_HOST=localhost:8080" >> $GITHUB_ENV
+        echo "GCLOUD_PROJECT=ecgdatapipelinetemplate" >> $GITHUB_ENV
+    - name: Run Firebase Emulator & Execute Notebook
+      run: |
+        firebase emulators:exec --import=./ECGDataPipelineTemplate/sample_data "jupyter nbconvert --to pdf --execute ./ECGDataPipelineTemplate/ECGDataPipelineTemplate.ipynb"
+      env:
+        CI: true
+    - uses: actions/upload-artifact@v4
+      with:
+        name: ECGDataPipelineTemplate.pdf
+        path: ECGDataPipelineTemplate.pdf
+

.gitignore

@@ -46,3 +46,20 @@ firebase-debug.*.log*
 
 # Swift Package List
 PAWS/package-list.json
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+.virtual_documents
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class

.reuse/dep5

@@ -0,0 +1,13 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+
+Files: ECGDataPipelineTemplate/Figures/*
+Copyright: 2024 Stanford University and the project authors (see CONTRIBUTORS.md)
+License: MIT
+Comment: All figures are part of the Stanford Spezi Data Pipeline Template open source project.
+
+Files: ECGDataPipelineTemplate/sample_data/*
+Copyright: 2024 Stanford University and the project authors (see CONTRIBUTORS.md)
+License: MIT
+Comment: All files are part of the Stanford Spezi Data Pipeline Template open source project.
+
+

ECGDataPipelineTemplate/.gitignore

@@ -0,0 +1,171 @@
+#
+# 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
+#
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+.virtual_documents
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+.DS_Store