v1.4.0

GillesPy2 v.1.4.0 CHANGELOG

FEATURES

• New Solver : VariableSSACSolver
  This solver works identically to SSACSolver, but is
  optimized for multiple trajectories using variable input values
  for species and Parameters.
• Results and ensembles of Results now share an object type.
• Ensembles can now be created from separate runs using the '+' operator
  In order to add Results to an Ensemble, they must share the same model/solver
• Model objects are now comparable
• Added advanced string parsing for user inputs
• Now uses AST parsing, interpretation should now be consistent across solvers
• Results can now be properly pickled and unpickled
• Added getters for all model objects
• Added delete methods for all model objects

FIXES

• BasicODESolver now correctly accepts integrator args.
• Resolved incorrect rounding in BasicTauHybridSolver switching
• All model objects are now checked for unique names when added to model

v1.3.4

• removed further uses of isinstance with module objects to avoid potential errors
• Fix for pickling Results objects
• Fixed error where math definitions could overlap with Parameter/Species names in hybrid solver. Parameter/Species names will now take priority in evaluation.
• Added error checking layer for threads
• Re-Ran notebooks and fixed paths for Michaelis Menten notebooks
• added License to Manifest for conda-forge

v1.3.3

-This version contains a hotfix for an issue where using module class objects were not passing comparison checks. This was an issue with Python's isinstance method.

v1.3.2

• Fix for multiple unnamed Reactions
• Timeouts now work with Windows! Refactored using python threading instead of signals.
• Updated hybrid solver value testing and error messages for float/int initial values

v1.3.1

Fix for conda-forge
Updated Authors

v1.3.0

Changes:

Timeouts via signal handling
Privatized methods
Test scripts load Cython conditionally
Order Propensity Formulas / Sortable Elements
Fix: timesteps calculated by round now, instead of floor
Fix: matplotlib plot() is now resizeable
Fix: test runner wrappers python versioning
Fix: plot colors loopable beyond 10 species
Fix: uniform colors between plotplotly and plot
Opioid example model added
Plotly figures can be returned without plotting
SBML features:
Events [and all subentities of Events]
Assignment Rules
Initial Assignments
Initial Value Reassignments
Function Definitions
Species: Constant
Species: Boundary Condition
Non Constant Parameters
Local Parameters
Increased MathML support
Fix: Rate Rules nomenclature matches assignment rules and sbml
Fix: numpy float casting (response to user issue)
Added Pylint badge
Removed mxml and python_libsbml from requirements.txt
Updated Installation instructions
Reorganized example directory
Added auto-deployment to PyPi
Fix: multiple error / warning changes to provide more helpful information
Fix: tau selection fixed in response to hybrid dynamic error
Export to csv
Example UML Model added

v1.2.3

-Updated requirements.txt to no longer require python_libsbml or lxml on installation

v1.2.2

This release contains minor hotfixes for issues in release 1.2.1.

Changelist:

• Minor updates to README
• Hotfix for cython/numpy solvers resolving issue where timespan was sometimes getting a type error

v1.2.1

1.2.1 Changelist:

• contains edits to README for PyPI displaying and compatibility

1.2 Changelist:

New Features:

• model.run now returns a Results object for single trajectories
• model.run now returns an Ensemble object for multiple trajectories
• Added built-in plotting (matplotlib and plotly) for Results and Ensemble Objects (use .plot, .plotplotly)
• Added statistical plotting for Ensemble objects (use .plot_std_dev_error_bars
• Overhauled Readme with better layout, logos, and examples
• Added Code of Conduct
• Added notebooks for the following models:
  • Vilar Oscillator
  • Brusselator
  • Oregonator

Fixes / Updates:

• Made corrections to ssa_c_solver dependency graph to be non-symmetric. now runs vilar oscillator model [c_base/model.cpp]
• Fixed error where Cython solver was incorrectly parsing species [cython_ssa_solver.pyx]
• Fixed issue where propensities were being calculated incorrectly for bimolecular reactions of type 2X -> Y [gillespy2.py]
• Included check for RateRules empty strings [gillespy2.py]
• Included a check for RateRules valid associated species [gillespy2.py]
• Modified RateRule instantiation to be positional or keyword [gillespy2.py]
• Modified Tau Hybrid Switching Condition tests [basic_tau_hybrid_solver.py]
• Cleaned/updated basic_tau_leaping comments [basic_tau_hybrid_solver.py]
• Added loop break point for faster pure ode detection [basic_tau_hybrid_solver.py]