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1.0.3 (2020-08-22)

Added

  • thinning parameter to control sampling in Simulation.plot

1.0.2 (2020-08-08)

Added

  • Warnings about antimony keyword usage in tutorial, ModelIO class

Fixed

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

1.0.0 (2020-07-18)

Added

  • Antimony support and ModelIO class, giving easier entry point to load models
  • Support for custom species names in plotting and Results
  • Support for automatic cpu core detection
  • New logo for cayenne

Changed

  • Package name changed from pyssa to cayenne
  • Update docs for new API

0.9.1 (2020-05-23)

Fix interpolation bug in Results.get_state

Fixed

  • Results.get_state function now adds an epsilon to time

0.9.0 (2019-12-14)

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

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