Cayenne

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Added
+++++
- ``thinning`` parameter to control sampling in ``Simulation.plot``

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Added
+++++
- Warnings about antimony keyword usage in tutorial, ``ModelIO`` class

Fixed
+++++
- ``setup.py`` setup requirements are automatically installed
- ``antimony`` version incompatibility issue

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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

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Fix interpolation bug in ``Results.get_state``

Fixed
+++++
- ``Results.get_state`` function now adds an epsilon to time

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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 <https://github.com/sbmlteam/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

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Fixed
+++++
- Initialize ``algorithms`` submodule with ``__init__.py``
- Update ``setup.py`` to allow submodule detection