Pyssa

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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

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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

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Changed
+++++++
- Refactor ``tau_adaptive``
- Rename ``direct_naive`` to ``direct``

Fixed
+++++
- SSA part of ``tau_adaptive``
- Bug in linux compatibility of ``tau_adaptive``

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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