History

0.8.2 (2019-04-20)

Fixed

  • Initialize algorithms submodule with __init__.py

  • Update setup.py to allow submodule detection

0.8.0 (2019-04-13)

Added

  • Results.get_states method - returns state at time t

  • Accuracy tests for all algorithms

  • Additional consistency checks for X0 and k_det

Changed

  • Refactor algorithms into sub module algorithms

  • Refactor algorithm independent tests

Fixed

  • Indexing issue in propensity calculation in direct algorithm

  • Indexing issue in propensity calculation in tau_leaping algorithm

  • Address edge case X->2X in tau_adaptive algorithm

0.7.1 (2019-03-23)

Changed

  • Refactor tau_adaptive

  • Rename direct_naive to direct

Fixed

  • SSA part of tau_adaptive

  • Bug in linux compatibility of tau_adaptive

0.7.0 (2019-02-02)

Added

  • Support for the tau_adaptive algorithm

  • Support for multiprocessing

Fixed

  • Transpose stoichiometric matrix

  • Update references in docstrings

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

0.6.0 (2018-12-16)

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

Changed

  • Update roulette_selection to use np.searchsorted

  • Minor changes to numpy style usage

Chore

  • Add codecov

  • Travis pypi autodepolyment

  • Parameterize tests with algorithm name

  • Add details about tau_leaping to docs and README

0.5.4 (2018-12-02)

Added

  • badge to readme

0.5.3 (2018-12-02)

Added

  • plot to pypi

Changed

  • fix bumpversion/black issue

  • remove history from package long_description

0.5.0 (2018-12-01)

First public release!!

Added

  • testpypi 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

0.4.0 (2018-11-23)

Added

  • Simulation class - main class for running simulations

  • Results class - for storing and acessing simulation results

  • Simulation.simulate 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

0.2.0 (2018-11-10)

Added

  • Naive implementation of the Gillepsie algorithm in numba

  • Tests - sanity checks, bifurcation and long running simulation

  • CI on travis

0.1.0 (2018-08-08)

  • First commit