v1.0.3

1.0.3 (2020-08-22)

Added

• thinning parameter to control sampling in Simulation.plot

Fix setup.py and add antimony keyword warning

Added

• Warnings about antimony keyword usage in tutorial, ModelIO class

Fixed

• setup.py setup requirements are automatically installed
• antimony version incompatibility issue

Fix interpolation bug in Results.get_state

0.9.1 (2020-05-23)

Fixed

• Results.get_state function now adds an epsilon to time to avoid integer time points.

Replace numba with Cython

0.9.0 (2020-01-05)

Replace numba implementation with Cython implementation

Fixed

• Propensity calculation in all algorithms
• Considerable speed-up in algorithm runtimes
• Remove volume from Simulation.simulate parameters

Added

• direct algorithm in Cython
• tau_leaping algorithm in Cython
• tau_adaptive algorithm in Cython (experimental)
• Cython to Azure pipeline
• Accuracy tests from sbml-test-suite
• HOR property and tests for it
• Code coverage for Cython
• Algorithms page to the documentation
• Examples page to the documentation

Changed

• Remove numba algorithms
• Remove interpolation for direct algorithm
• sim.plot now plots post step curve
• Updated tutorial page of the documentation

Tau adaptive and multiprocessing

Added

• Support for the tau_adaptive algorithm
• Support for multiprocessing

Fixed

• Transpose stoichiometric matrix
• Update references in doc strings

Changed

• Use TINY and HIGH for status estimation
• Use np.int64 and np.float64 explicitly

Chore

• Update dependencies
• Add azure pipelines for testing on Windows

Tau leaping

Added

• Updated direct_naive docstring
• Support for the tau_leaping algorithm
• Species name support for plotting

Fixed

• Check for sum propensities uses threshold instead of equality
• Add check for type of max_iter

Updates to documentation and readme

Added

plot to pypi

Changed

fix bumpversion/black issue
remove history from package long_description

First public release!!

Added

• pypi deployment
• pyup security checking
• readthedocs deployment
• Tutorials and documentation
• Plotting functionality through Simulation.plot

Changed

• Simulation.results is now a property
• Updated tests to support the new api changes

Chore

• Updated the README

Refactor everything into classes

Added

• Simulation class - main class for running simulations
• Results class - for storing and accessing simulation results
• Simulation.simulate a function that returns an instance of the Results class

Changed

• Refactor get_kstoc and roulette_selection into utils.py
• Refactor direct_naive into direct_naive.py
• Delete pyssa.py and replace with Simulation class

Chore

• Add license and code-style badges
• Use black for code-formatting

Numba implementation of the naive Gillespie algorithm

Added

• Naive implementation of the Gillepsie algorithm in numba
• Tests - sanity checks, bifurcation and long-running simulation
• CI on travis