Add ECG Data Pipeline Tool

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

@@ -49,3 +49,48 @@ 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 install 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 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=spezidatapipelinetemplate" >> $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
+

.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