Notebook setup documentation & minor notebook fixes

[jasonheld-msft]

Purpose

This pull request introduces improvements to notebook setup and logging configuration, simplifies notebook code, and updates dependencies for compatibility and reliability. The main changes include adding a dedicated Jupyter notebook setup guide, refactoring logging initialization to be more consistent and flexible, and updating requirements to ensure proper package versions. Additionally, some minor bug fixes and code cleanups have been made across notebooks and source files.

Notebook setup and documentation:

• Added a new notebooks/README.md guide for setting up and running Jupyter notebooks, including troubleshooting steps and kernel setup instructions.
• Updated docs/evaluation.md to reference the new notebook setup guide for additional instructions.

Logging and initialization improvements:

• Refactored logging setup in src/app.py and src/config.py to ensure logging is initialized with the correct log level and handlers, and moved Application Insights setup into the application context. [1] [2] [3] [4]
• Updated notebook scripts to consistently use the new logging setup via create_app_context(log_level) and removed redundant setup_logging calls. [1] [2] [3] [4]

Dependency and compatibility updates:

• Added jupyter and ipykernel to src/requirements-notebooks.txt to ensure notebooks run reliably.
• Updated minimum versions for several Azure-related packages in src/requirements.txt for compatibility, and fixed a version regression for azure-keyvault-secrets. [1] [2]
• Changed import statements to use asynchronous Azure credentials for improved reliability.

Code and path corrections:

• Fixed the path calculation for loading agent configuration in src/evaluation/metrics/base.py to prevent file-not-found errors.
• Corrected a typo in the reference data directory path in notebooks/evaluations/evaluation.ipynb.

Notebook code cleanup:

• Removed unnecessary code cells and outputs from test and evaluation notebooks, and improved formatting for data structures. [1] [2] [3] [4] [5] [6]

Does this introduce a breaking change?

[ ] Yes
[x] No

Pull Request Type

What kind of change does this Pull Request introduce?

[ ] Bugfix
[x] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Documentation content changes
[ ] Other... Please describe:

How to Test

• Get the code

git clone https://github.com/jasonheld-msft/healthcare-agent-orchestrator.git
cd healthcare-agent-orchestrator
git checkout jasonheld-msft/notebook-setup

• Test the code

Set up infra and run notebooks

What to Check

Verify that the following are valid

• No unexpected errors during notebook execution
• No unexpected errors outside of notebooks

Other Information