3.5.0 Release (#19)

Changes
==========================

Python API
----------
1. values for unknown tetrahedron and triangle identifiers changed from
   -1 to `steps.geom.UNKNOWN_TET` and `steps.geom.UNKNOWN_TRI`
   respectively.
   You may use these 2 constants instead of -1.

    A Python 3 Flake8 extension is available to help you migrate your code.

    ```
    $ pip3 install flake8 flake8-oist-steps
    $ cat test.py
    import steps.utilities.meshio as meshio

    mesh = meshio.loadMesh('axon_cube_L1000um_D866m_1135tets')[0]
    idx = mesh.findTetByPoint([0, 0, 0])
    if idx == -1:
        print('boundary')
    $ flake8 test.py
    ./test.py:5:4: E421 consider using steps.geom.UNKNOWN_TET constant instead of -1.
    ```

    You may use the following snippet in your scripts header to have backward
    compatible code:

   ```python
   try:
       from steps.geom import UNKNOWN_TET, UNKNOWN_TRI
   except ImportError:
       UNKNOWN_TET = -1
       UNKNOWN_TRI = -1
   ```

2. A new constant `steps.geom.INDEX_DTYPE` provides the proper NumPy datatype according
to whether STEPS has been built with 32 bits or 64 bits identifiers.

Build and Packaging
-------------------
1. New `USE_64_BITS_INDICES` CMake option to use 64bits unsigned integers
   for identifiers instead of 32bits.
2. New CMake variables to use either system libraries or bundle code.
    * `USE_BUNDLE_EASYLOGGINGP`
    * `USE_BUNDLE_RANDOM123`
    * `USE_BUNDLE_SUNDIALS`
3. Improve spack support
4. Improve support of GCC 7 and higher
5. Improve support of AppleClang compiler

Internal code base
------------------
1. Disable OpenMP instructions in TetOpSplit solver
2. Modernize code base by using most of C++11
3. Increase code safety by using strong types to distinguish
   identifiers from tetrahedrons, triangles, and vertices

fix critical bug where reac rate is computed incorrectly in tetopsplit (

#14)

3.4.0 Release

3.3.0 release (#12)

Version 3.3.0 (2018-04)

1. Implemented Rejection-based SSA (Thanh V, Zunino R, Priami C (n.d.) On the rejection-based algorithm for simulation and analysis of large-scale reaction networks. The Journal of Chemical Physics 142:244106) as a faster alternative to Wmdirect
2. Assertion and Exception logging overhaul
3. Remove SWIG interface
4. Matlab Simbiology support utility

3.2 Release (#11)

Version 3.2.0 (2017-10)
==========================
1. Extensive rework on Cython binding and documentation with Jupyter notebook.
2. Extend support for Python 3.4~.
3. several bug fixs.
Note: SWIG Binding will be removed in 3.3 release.

3.1.0 release (#9)

This is the release of STEPS 3.1.0

Bug fix: abort CMake if SWIG is REQUIRED but not found (#4)

3.0.1 bug fix patch (#1)

Bug fix for crash problem when providing fractional value to
setCompCount() and setPatchCount() in tetexact

STEPS 3.0.0

STEPS 3.0.0 Release.

tag 1.2.1