🧪 Add unit test for simulate_cellular_relaxation

[Sir-Ripley]

🎯 What: The simulate_cellular_relaxation function in QAG_Truth.ipynb was previously untested. It only generated data and plotted it, without verifying the correctness of the generated arrays.

📊 Coverage: The function is now refactored to return its internal arrays (t and final_path) and accept a plot=False argument. A new unit test test_simulate_cellular_relaxation was added to verify:

• The shape of the generated arrays (1000 elements).
• The correct initial zeta condition (-15.0).
• The upper and lower bounds of the final path, ensuring it stays within expected bounds.

✨ Result: The simulate_cellular_relaxation function now has dedicated programmatic test coverage, improving the reliability of the cellular healing simulation code. Additionally, a syntax error (importimport numpy as np) at the top of the notebook was fixed.

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PR created automatically by Jules for task 9337776552491887765 started by @Sir-Ripley

Summary by Sourcery

Add test coverage and programmatic access for the cellular relaxation simulation in the QAG notebook.

New Features:

• Expose simulate_cellular_relaxation outputs and plotting toggle to enable programmatic use and testing.
• Introduce a unit test for simulate_cellular_relaxation that validates output length, initial conditions, and value bounds.

Bug Fixes:

• Fix a syntax error in the QAG notebook import statement to allow proper execution.

Enhancements:

• Update the main execution block to run unit tests before executing the full QAG simulation pipeline.

[google-labs-jules]

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[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly enhances the reliability of the cellular healing simulation by introducing dedicated unit testing for the simulate_cellular_relaxation function. The function itself was modified to facilitate testing by allowing plot suppression and returning its computed data. This ensures that the core simulation logic produces expected results, improving the overall robustness of the codebase.

Highlights

• Unit Test Added: A new unit test, test_simulate_cellular_relaxation, was added to verify the correctness of the simulate_cellular_relaxation function, checking array shapes, initial conditions, and bounds.
• Function Refactoring: The simulate_cellular_relaxation function was refactored to accept a plot argument (defaulting to True) and now returns the generated t (time) and final_path arrays, enabling programmatic testing.
• Syntax Fix: A minor syntax error, importimport numpy as np, was corrected to import numpy as np.

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Changelog

• QAG_Truth.ipynb
  • Fixed a duplicate 'import' keyword for the numpy library.
  • Modified the simulate_cellular_relaxation function to accept a plot boolean argument and return the t and final_path arrays.
  • Encapsulated the plotting logic within an if plot: block in simulate_cellular_relaxation.
  • Corrected a unicode character for 'µg' in a print statement within run_thrust_simulation.
  • Added a new test_simulate_cellular_relaxation function to verify the output of the simulation function.
  • Integrated the execution of the new unit test into the main execution block (if __name__ == "__main__":).

Activity

• PR created automatically by Jules for task 9337776552491887765, started by @Sir-Ripley.

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[sourcery-ai]

Reviewer's Guide

Refactors the simulate_cellular_relaxation routine to be testable by returning its computed arrays and gating plotting behind a flag, adds a lightweight unit test that validates array shape, initial conditions, and bounds, wires the test into the script’s main execution block, and fixes minor notebook issues including an import typo and a print formatting tweak.

Sequence diagram for running tests and simulation in main execution block

sequenceDiagram
    actor User
    participant QAG_Truth_main
    participant test_simulate_cellular_relaxation
    participant simulate_cellular_relaxation
    participant matplotlib_pyplot

    User->>QAG_Truth_main: run script
    QAG_Truth_main->>QAG_Truth_main: check __name__ == __main__
    QAG_Truth_main->>QAG_Truth_main: print initializing message

    QAG_Truth_main->>QAG_Truth_main: print running unit tests
    QAG_Truth_main->>test_simulate_cellular_relaxation: call

    test_simulate_cellular_relaxation->>simulate_cellular_relaxation: simulate_cellular_relaxation plot=False
    activate simulate_cellular_relaxation
    simulate_cellular_relaxation-->>test_simulate_cellular_relaxation: return t, final_path
    deactivate simulate_cellular_relaxation

    test_simulate_cellular_relaxation->>test_simulate_cellular_relaxation: assert lengths and values
    test_simulate_cellular_relaxation-->>QAG_Truth_main: print test passed

    QAG_Truth_main->>QAG_Truth_main: print tests passed

    QAG_Truth_main->>simulate_cellular_relaxation: simulate_cellular_relaxation plot=True
    activate simulate_cellular_relaxation
    simulate_cellular_relaxation->>matplotlib_pyplot: create figure and plot data
    matplotlib_pyplot-->>simulate_cellular_relaxation: render plot
    simulate_cellular_relaxation-->>QAG_Truth_main: return t, final_path
    deactivate simulate_cellular_relaxation

    QAG_Truth_main->>QAG_Truth_main: run other simulations

Loading

Flow diagram for simulate_cellular_relaxation refactor

flowchart TD
    A["Start simulate_cellular_relaxation"] --> B["Create time array t with 1000 points"]
    B --> C["Set initial_zeta = -15.0"]
    C --> D["Set zeta_target = -55.0"]
    D --> E["Compute zeta_curve using exponential decay"]
    E --> F["Compute vortex_hum as sinusoidal term"]
    F --> G["Compute final_path = zeta_curve + vortex_hum"]
    G --> H{Plot flag plot}
    H --> I["Create figure"]:::plotting
    I --> J["Plot final_path vs t"]:::plotting
    J --> K["Draw horizontal line at zeta_target"]:::plotting
    K --> L["Set title and labels"]:::plotting
    L --> M["Show plot"]:::plotting
    H --> N["Skip plotting"]
    M --> O["Return t, final_path"]
    N --> O["Return t, final_path"]

    classDef plotting fill:#e0f7ff,stroke:#0099cc,stroke-width:1.5;

Loading

File-Level Changes

Change	Details	Files
Make simulate_cellular_relaxation testable and non-plotting by default in tests.	Add a plot parameter (default True) to allow disabling plotting when running tests or in non-interactive contexts. Return the computed time array and final_path from the function so that callers and tests can assert on numeric outputs. Guard plotting code with an if plot condition so functional behavior is preserved while enabling headless use.	QAG_Truth.ipynb
Introduce an inline unit test for simulate_cellular_relaxation and hook it into the notebook’s main execution path.	Add test_simulate_cellular_relaxation that calls simulate_cellular_relaxation(plot=False) and asserts on array length, initial zeta value, and acceptable upper/lower bounds of the simulated path. Print a simple success message from the test to give immediate feedback when run as a script. Extend the main execution block to run the new unit test suite before running the main simulations, with surrounding log messages indicating test execution.	QAG_Truth.ipynb
Fix small correctness and formatting issues in the notebook.	Correct a syntax error in the NumPy import statement by changing a duplicated keyword to a valid import. Adjust a propulsion print statement to use a proper micro symbol in the formatted string for psychon_ug display.	QAG_Truth.ipynb

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[gemini-code-assist]

Code Review

This pull request effectively adds unit test coverage for the simulate_cellular_relaxation function, which is a great step towards improving the reliability of the simulation code. The refactoring to make the function testable by adding a plot parameter and returning the generated data is well-implemented. The fix for the import syntax error is also appreciated. I have one suggestion to improve the maintainability of the new test by making the assertion bounds more explicit.