Update the build-and-test workflow to incorporate CI for ECGDataPipel…

…ineTemplate
StanfordBDHG · Mar 9, 2024 · 70f64d1 · 70f64d1
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diff --git a/.github/workflows/build-and-test.yml b/.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=./sample_data "jupyter nbconvert --to pdf --execute ECGDataPipelineTemplate.ipynb"
+      env:
+        CI: true
+    - uses: actions/upload-artifact@v4
+      with:
+        name: ECGDataPipelineTemplate.pdf
+        path: ECGDataPipelineTemplate.pdf
+
diff --git a/ECGDataPipeline/requirements.txt b/ECGDataPipeline/requirements.txt
diff --git a/ECGDataPipeline/.gitignore → ECGDataPipelineTemplate/.gitignore b/ECGDataPipeline/.gitignore → ECGDataPipelineTemplate/.gitignore
diff --git a/...Pipeline/SpeziECGDataIteractiveTool.ipynb → ...ineTemplate/ECGDataPipelineTemplate.ipynb b/...Pipeline/SpeziECGDataIteractiveTool.ipynb → ...ineTemplate/ECGDataPipelineTemplate.ipynb
diff --git a/...es/ecg_data_interactive_tool_snapshot.png → ...es/ecg_data_interactive_tool_snapshot.png b/...es/ecg_data_interactive_tool_snapshot.png → ...es/ecg_data_interactive_tool_snapshot.png
diff --git a/ECGDataPipeline/Modules/__init__.py → ECGDataPipelineTemplate/Modules/__init__.py b/ECGDataPipeline/Modules/__init__.py → ECGDataPipelineTemplate/Modules/__init__.py
diff --git a/ECGDataPipeline/Modules/data_preparation.py → ...elineTemplate/Modules/data_preparation.py b/ECGDataPipeline/Modules/data_preparation.py → ...elineTemplate/Modules/data_preparation.py
diff --git a/ECGDataPipeline/Modules/firebase_access.py → ...pelineTemplate/Modules/firebase_access.py b/ECGDataPipeline/Modules/firebase_access.py → ...pelineTemplate/Modules/firebase_access.py
diff --git a/ECGDataPipeline/Modules/utils.py → ECGDataPipelineTemplate/Modules/utils.py b/ECGDataPipeline/Modules/utils.py → ECGDataPipelineTemplate/Modules/utils.py
diff --git a/ECGDataPipeline/Modules/visualization.py → ...PipelineTemplate/Modules/visualization.py b/ECGDataPipeline/Modules/visualization.py → ...PipelineTemplate/Modules/visualization.py
diff --git a/ECGDataPipeline/README.md → ECGDataPipelineTemplate/README.md b/ECGDataPipeline/README.md → ECGDataPipelineTemplate/README.md
@@ -10,7 +10,7 @@ SPDX-License-Identifier: MIT
 
 # Spezi ECG Data Pipeline
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/[YourGitHub]/SpeziECGDataAnalysisPipeline/blob/main/SpeziECGDataInteractiveTool.ipynbhttps://colab.research.google.com/github/StanfordBDHG/PediatricAppleWatchStudy/blob/main/ECGDataPipeline/SpeziECGDataIteractiveTool.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/[YourGitHub]/SpeziECGDataAnalysisPipeline/blob/main/SpeziECGDataInteractiveTool.ipynbhttps://colab.research.google.com/github/StanfordBDHG/PediatricAppleWatchStudy/blob/main/ECGDataPipelineTemplate/ECGDataPipelineTemplate.ipynb)
 <!-- [![Build Status](https://github.com/[YourGitHub]/SpeziECGDataAnalysisPipeline/actions/workflows/main.yml/badge.svg)](https://github.com/[YourGitHub]/SpeziECGDataAnalysisPipeline/actions/workflows/main.yml)
 [![codecov](https://codecov.io/gh/[YourGitHub]/SpeziECGDataAnalysisPipeline/graph/badge.svg?token=[YourToken])](https://codecov.io/gh/[YourGitHub]/SpeziECGDataInteractiveTool.)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.0000000.svg)](https://doi.org/10.5281/zenodo.0000000) -->
@@ -26,11 +26,11 @@ The Spezi ECG Data Pipeline adopts a modular structure, comprising several Pytho
 - `data_preparation.py`: Prepares and processes raw ECG data.
 - `utils.py`: Provides utility functions for data processing.
 - `visualization.py`: Contains functions for data visualization.
-- `SpeziECGDataIteractiveTool.ipynb`: An interactive notebook for analyzing and reviewing ECG data.
+- `SpeziECGDataIteractECGDataPipelineTemplateiveTool.ipynb`: An interactive notebook for analyzing and reviewing ECG data.
 
 ## Running the Notebook in Google Colab
 
-You can open the `SpeziECGDataIteractiveTool.ipynb` notebook in Google Colab by clicking the "Open In Colab" badge above.
+You can open the `ECGDataPipelineTemplate.ipynb` notebook in Google Colab by clicking the "Open In Colab" badge above.
 
 ### Setup Instructions in Colab
 

diff --git a/ECGDataPipeline/__init__.py → ECGDataPipelineTemplate/__init__.py b/ECGDataPipeline/__init__.py → ECGDataPipelineTemplate/__init__.py
diff --git a/ECGDataPipelineTemplate/requirements.txt b/ECGDataPipelineTemplate/requirements.txt
@@ -0,0 +1,5 @@
+firebase_admin
+pandas
+numpy
+matplotlib
+ipywidgets
diff --git a/...ine/sample_data/auth_export/accounts.json → ...ate/sample_data/auth_export/accounts.json b/...ine/sample_data/auth_export/accounts.json → ...ate/sample_data/auth_export/accounts.json
diff --git a/...eline/sample_data/auth_export/config.json → ...plate/sample_data/auth_export/config.json b/...eline/sample_data/auth_export/config.json → ...plate/sample_data/auth_export/config.json
diff --git a/...sample_data/firebase-export-metadata.json → ...sample_data/firebase-export-metadata.json b/...sample_data/firebase-export-metadata.json → ...sample_data/firebase-export-metadata.json
diff --git a/.../all_namespaces_all_kinds.export_metadata → .../all_namespaces_all_kinds.export_metadata b/.../all_namespaces_all_kinds.export_metadata → .../all_namespaces_all_kinds.export_metadata
diff --git a/..._export/all_namespaces/all_kinds/output-0 → ..._export/all_namespaces/all_kinds/output-0 b/..._export/all_namespaces/all_kinds/output-0 → ..._export/all_namespaces/all_kinds/output-0
diff --git a/.../firestore_export.overall_export_metadata → .../firestore_export.overall_export_metadata b/.../firestore_export.overall_export_metadata → .../firestore_export.overall_export_metadata
diff --git a/...e/sample_data/storage_export/buckets.json → ...e/sample_data/storage_export/buckets.json b/...e/sample_data/storage_export/buckets.json → ...e/sample_data/storage_export/buckets.json