v1.3.0

This release introduces updates focused on computational performance, an expanded sensitivity analysis, and improved dependency management.

Performance

• Parallel Execution: Multi-simulation analyses in the figures.ipynb and hypotheses.ipynb notebooks, including the parameter sweeps and pathological model comparisons, have been refactored to run in parallel using Joblib. This significantly reduces the total runtime on multi-core systems.

Expanded Sensitivity Analysis

• Wider Parameter Sweep: A more thorough sensitivity analysis has been performed, expanding the parameter sweep from the original ±5% to a more comprehensive ±25% range.
• New Supplementary Figure: The results of this new analysis are presented in a heatmap which has been added to the supplementary materials.

Dependency and Reproducibility Improvements

• Updated Requirements: The requirements.txt file has been updated to include new dependencies (seaborn, joblib).
• Removed Dependencies: The brian2 package is no longer a dependency, with its functionality replaced by standard NumPy functions.

v1.2.0

This release updates the repository to correspond with a revised version of the manuscript. The changes focus on updating the figure reproduction process and refactoring the model code for better usability.

Manuscript & Figure Updates

• New Figures: The figures.ipynb notebook now generates the updated figures included in the latest version of the manuscript.
• Simplified Setup: The requirement for a local LaTeX installation has been removed from the figure notebook. This makes the environment easier to configure and the results more reproducible.

Code Refinements

• Model Restructuring: The core model code, LUT_Model.py, has been refactored to make it easier to externally manipulate model parameters and generate the data for the sensitivity analysis figure.

v1.1.0

This release introduces significant updates to the repository, focusing on data validation, reproducibility, and model enhancements. Key changes include:

• Data Validation:
  • Added raw rat data files to support model validation.
• Paper Figure Reproduction:
  • Included a paper_figures folder with a Jupyter notebook to reproduce the figures from the associated paper.
  • Added copies of the generated figures for easy access.
• Pathological Model Variants:
  • Implemented example variants of the LUT model to simulate pathological trends.
  • Added a Jupyter notebook to reproduce associated hypotheses from the paper.
• Documentation Improvements:
  • Updated the README.md file with relevant information and usage instructions.
  • Updated the CITATION.cff file.
  • Updated the requirements.txt file to specify software dependencies.

This release aims to improve the reproducibility and extend the functionality of the LUT model.

v1.0.0

Public release of the lower urinary tract simulator.