Release Notes

Version 1.0.0 (2010-01-05)
==========================
First release.

Version 1.0.1 (2010-01-28)
==========================
1. Bug fix of utilities.meshio.importTetgen() method crashing.
2. Changes to 'def' classes so that these classes no longer store
   a pointer to model level objects or access data from those objects, 
   instead coping all data during construction and setup. 
   Also modified rng.py to be directly created by swig for 
   compatability with python3.
   
Version 1.1.0 (2010-03-20)
==========================
1. Replace GNU distrubution system with Python Distutils.
2. Provide a visualization toolkit for mesh based simulation 
    (steps.utilitis.visual)
3. Provide checkpointing support for Wmdirect and Tetexact solvers.
    (Please check user manual for more details)
4. New user manual and API reference
    
Version 1.1.1 (2010-04-7)
==========================
1. New setup.py to fix undefined symbol error in Linux
2. function name fix in utilities/visual.py
    
Version 1.1.2 (2010-05-8)
==========================
1. Solve crash problem of Tetexact solver in some Linux system.
Binary packages of version 1.1.1 are not affected, 
so only source package is released.

Version 1.2.0 (2011-04-13)
==========================
1. SBML support in steps/utilities/sbml.py
2. Addition of Diffusion Boundary object, which allows for optional 
chemical diffusion between connected compartments.  
3. Initial conditions improvement for Tetexact solver, resulting
in a  uniform initial spatial concentration across the 
compartment (or patch) regardless of tetrahedron volumes (or triangle 
areas), important where tetrahedrons vary considerably in volume. 
Thanks to Haroon Anwar for bringing this issue to our attention.
4. Bugfix on Wmrk4 deterministic solver on the reset() function, 
which previously did not reset counts in Patches. 
5. Changed zero-order reaction constants to the conventional M/s. 
Previously was /s.
6. Bugfix on surface-reactions. Now reaction constants for reactions 
that involve reactants only on a patch (nothing in a volume) are 
correctly scaled in 2D, as opposed to previous 3D scaling. Thanks 
to Gabriela Antunes for pointing out this one. 
7. Additions to examples folder to include scripts that link to the 
user documentation, found in examples/tutorial.

Version 1.2.1 (2011-06-10)
==========================
1. Important bugfix in Tetexact to fix a problem that was causing 
crashes during construction.

Version 2.0.0 (2013-04-22)
==========================
1. First version to include E-Field and related objects. Allows 
simulation of the potential across a membrane specifed as a collection of 
triangles comprising a surface in the tetrahedral mesh. See documentation for
more information.
2. Addition of solver TetODE for spatial deterministic simulations. Uses the CVODE
library for solutions. 
3. Addition of surface diffusion in mesh-based solvers (Tetexct and TetODE), which models a 
diffusive flux between triangles that form part of a patch surface, analogous to 
volume diffusion between tetrahedral elements in a compartment.
4. Several other smaller additions and fixes. 

Version 2.1.0 (2013-09-05)
==========================
1. Add steps.geom.castToTmComp and steps.geom.castToTmPatch methods for casting Comp and Patch
objects to their TetMesh counterpart (if possible).
2. Added direct connection between TetODE and E-Field. Previously connection was possible
only through the python interface.
3. Other small additions such as optional percentage of starting nodes tested for mesh breadth
first search in E-Field setup.

Version 2.2.0 (2014-04-16)
==========================
1. Add CUBIT-STEPS geometry praparation toolkit and visualization toolkit.
2. Add "Region of Interest" dataset in Tetmesh Geometry and related functions in Tetexact solver
3. Add direct NumPy access functions in Tetmesh geometry and Tetexact solver


