Separate testing notebooks from source code (#20)

# *Separate testing notebooks from source code*

## ♻️ Current situation & Problem
This pull request refactors the current project structure by separating
the testing notebooks from the source code. This refactoring aims to
streamline the repository by isolating the source code, enhancing
maintainability, and improving focus within the repository.


## ⚙️ Release Notes 
- Refactored project by moving notebooks out of the source code
repository to maintain a clean separation of concerns.
- Improved maintainability.


## 📝 Code of Conduct & Contributing Guidelines 

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

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

@@ -66,52 +66,4 @@ jobs:
           files: ./coverage.xml
           flags: unittests
           name: codecov-umbrella
-          slug: StanfordSpezi/SpeziDataPipelineTemplate
-  build_and_test_notebook:
-    name: Build and Test 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: Update apt-get
-        run: sudo apt-get update
-      - name: Setup LaTex
-        run: |
-            sudo apt-get install -y --fix-missing 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 SpeziDataPipelineTemplate and Dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -e .
-      - 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 SpeziDataPipelineTemplate.ipynb"
-        env:
-          CI: true
-      - uses: actions/upload-artifact@v4
-        with:
-          name: SpeziDataPipelineTemplate.pdf
-          path: SpeziDataPipelineTemplate.pdf
+          slug: StanfordSpezi/SpeziDataPipeline

README.md

@@ -8,13 +8,10 @@ SPDX-License-Identifier: MIT
 
 -->
 
-# Spezi Data Pipeline Template
+# Spezi Data Pipeline
 
-[![Build and Test](https://github.com/StanfordSpezi/SpeziDataPipelineTemplate/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/StanfordSpezi/SpeziDataPipelineTemplate/actions/workflows/build-and-test.yml)
-[![codecov](https://codecov.io/gh/StanfordSpezi/SpeziDataPipelineTemplate/branch/main/graph/badge.svg)](https://codecov.io/gh/StanfordSpezi/SpeziDataPipelineTemplate)
-<a target="_blank" href="https://colab.research.google.com/github/StanfordSpezi/SpeziDataPipelineTemplate/blob/main/SpeziDataPipelineTemplate.ipynb">
-<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
-</a>
+[![Build and Test](https://github.com/StanfordSpezi/SpeziDataPipeline/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/StanfordSpezi/SpeziDataPipeline/actions/workflows/build-and-test.yml)
+[![codecov](https://codecov.io/gh/StanfordSpezi/SpeziDataPipeline/branch/main/graph/badge.svg)](https://codecov.io/gh/StanfordSpezi/SpeziDataPipeline)
 
 The Spezi Data Pipeline offers a comprehensive suite of tools designed to facilitate the management, analysis, and visualization of healthcare data from Firebase Firestore. By adhering to the Fast Healthcare Interoperability Resources (FHIR) standards, this platform ensures that data handling remains robust, standardized, and interoperable across different systems and software.
 
@@ -24,7 +21,7 @@ The Spezi Data Pipeline is engineered to improve workflows associated with data
 
 ## Package Structure
 
-The SpeziDataPipelineTemplate is organized into several directories, each serving a specific function as part of the overall application. This guide will walk you through the package structure, highlighting the key components and their usage based on your needs and challenges.
+The Spezi Data Pipeline is organized into several directories, each serving a specific function as part of the overall application. This guide will walk you through the package structure, highlighting the key components and their usage based on your needs and challenges.
 
 1. `data_access/`
 
@@ -70,12 +67,12 @@ _DataExporter_
 
 
 ### How to Use Based on Your Needs
-- **Downloading Data from Firestore**: Start with FirebaseFHIRAccess to connect and fetch data.
-- **Converting and Structuring FHIR Data**: Use ResourceCreator and its subclasses to convert Firestore documents to FHIR resources.
-- **Flattening Nested FHIR Data**: Utilize ResourceFlattener and its specific implementations to transform data into flat DataFrames.
+- **Downloading Data from Firestore**: Start with `FirebaseFHIRAccess` to connect and fetch data.
+- **Converting and Structuring FHIR Data**: Use `ResourceCreator` and its subclasses to convert Firestore documents to FHIR resources.
+- **Flattening Nested FHIR Data**: Utilize `ResourceFlattener` and its specific implementations to transform data into flat `DataFrames`.
 - **Processing Data**: Apply FHIRDataProcessor for filtering, selecting, and general data processing tasks.
-- **Exploring and Visualizing Data**: Leverage DataExplorer and ECGExplorer to create visualizations and explore your data.
-- **Exporting Data**: Use DataExporter to save processed data and plots.
+- **Exploring and Visualizing Data**: Leverage `DataExplorer` and `ECGExplorer`, and `QuestionnaireResponseExplorer` to create visualizations and explore your data.
+- **Exporting Data**: Use `DataExporter` to save processed data and plots.
 
 
 ## Dependencies
@@ -185,8 +182,8 @@ visualizer.set_date_range(selected_start_date, selected_end_date)
 figs = visualizer.create_static_plot(processed_fhir_dataframe)
 ```
 
-![daily_steps_data_plot.png](https://github.com/StanfordSpezi/SpeziDataPipelineTemplate/blob/main/Figures/daily_steps_data_plot.png)
-![heart_rate_data_plot.png](https://github.com/StanfordSpezi/SpeziDataPipelineTemplate/blob/main/Figures/heart_rate_data_plot.png)
+![daily_steps_data_plot.png](https://github.com/StanfordSpezi/SpeziDataPipeline/blob/main/Figures/daily_steps_data_plot.png)
+![heart_rate_data_plot.png](https://github.com/StanfordSpezi/SpeziDataPipeline/blob/main/Figures/heart_rate_data_plot.png)
 
 ## ECG Observations
 
@@ -212,7 +209,7 @@ visualizer.set_date_range(selected_start_date, selected_end_date)
 figs = visualizer.plot_ecg_subplots(processed_fhir_dataframe)
 ```
 
-![ecg_data_plot.png](https://github.com/StanfordSpezi/SpeziDataPipelineTemplate/blob/main/Figures/ecg_data_plot.png)
+![ecg_data_plot.png](https://github.com/StanfordSpezi/SpeziDataPipeline/blob/main/Figures/ecg_data_plot.png)
 
 
 ### Questionnaire Responses