Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.1.0] - 2025-04-19

Added

  • Initial release of PhosKinTime, a Python toolkit for ODE-based modeling of phosphorylation kinetics and transcriptional time-series.
  • Features include:
    • Parameter estimation.
    • Sensitivity analysis.
    • Steady-state computation.
    • Interactive visualization.
  • Support for Python 3.10, 3.11, and 3.12.
  • Dependencies include numpy, pandas, seaborn, matplotlib, scipy, and more.
  • CLI entry point phoskintime via bin.main:main in root.
  • Packaged directories: bin, config, kinopt, models, paramest, plotting, sensitivity, steady, tfopt, and utils.
  • Documentation and homepage available at https://bibymaths.github.io/phoskintime/.

[0.2.0] - 2025-04-24

Added

  • Added light grid in plotting of model.
  • Added CHANGELOG.md.
  • Added direct link to open file from CLI.
  • Added CLI wrappers for entry point.
  • Added deployment configuration file.
  • Added support for network via Cytoscape.
  • Added configuration file for PhosKinTime settings.
  • Enhanced analysis and plotting functions: added upper bound parameter, updated loss type defaults, and improved legend formatting.

Changed

  • Updated parameter bounds and model settings in configuration files.
  • Refactored logging statements and improved data filtering in main processing files.

Fixed

  • Fixed display of missing kinases in output before optimization in kinopt.

Removed

  • Removed clipping of predicted expression.
  • Deleted abopt directory.

[0.3.0] - 2025-04-24

Added

  • Support for non-psite time series in kinase data.
  • New results directory for structured output saving.
  • Detailed docstrings and inline documentation for key functions.

Changed

  • Refactored powell.jl: cleaner function names, improved parameter handling, and threading support.
  • Updated threading configuration and residuals calculation.
  • Replaced print statements with logger output in Python modules.
  • Adjusted beta bounds and default loss function settings.
  • Improved ODE system equations, plotting aesthetics, and documentation structure.

Fixed

  • LaTeX formatting in README.md.
  • Sheet name for estimated values in Excel export.

Removed

  • Obsolete abopt directory.
  • Outdated module references and unused code.
  • Removed julia implementation of kinopt
  • Removed Project.toml for Julia dependency management.

[0.4.0] - alpha

Added
- Phase space plots and strip plots for state distributions in sensitivity analysis.
- Time-state grid visualization replacing old time-wise plots.
- Enhanced logging format for parameter bounds and model configuration.
- Increased number of trajectories to 10,000 for improved sensitivity resolution.
- Support for parameter relationship plots and top parameter pair visualizations.

Changed
- Refactored sensitivity analysis functions and configuration parameters.
- Updated site parameter labels and adjusted development mode flags.
- Improved aesthetics of phase space and strip plots.
- Adjusted ODE model references (ODE_MODEL) and refined output normalization logic.
- Replaced hardcoded values with computed perturbations for sensitivity analysis.

Fixed
- Markdown formatting in README and PYPI_README.
- Sheet name bug in Excel export for estimated values.

Removed
- Deprecated analysis modes and unused constants.
- Combined time-weight calculation from data preprocessing.

[0.4.0] – Unreleased

Added

  • Model error plotting in the visualization pipeline.
  • Detailed descriptions for new Y_METRIC options in metric reports.

Changed

  • Streamlined argument parsing and enhanced logging details (now logs additional configuration parameters).
  • Updated default ODE model constant from randmod to succmod for improved simulation accuracy.
  • Disabled development mode by default; enhanced HTML‐report structure and log‐file handling.
  • Refactored output‐directory parameter to a list format and reorganized output files with improved naming conventions across display and plotting modules.
  • Updated upper bound ranges and default values for key parameters in config files.
  • Adjusted figure sizing and label management in plotting functions; updated regex for parameter‐label matching to support multi‐digit labels.
  • Improved plotting file naming and handling of perturbation values.
  • Enhanced Excel sheet processing for parameter imports and added regularization checks during data import.
  • Improved confidence‐interval logging format and enhanced regularization‐term computation in normest.py.
  • Updated lambda‐range handling in normest.py.

Fixed

None yet.

Removed

None.