mcell/CHANGELOG.txt

CHANGELOG
===============================================================================

Changes in MCell 4.0.5
-------------------------------------------------------------------------------
* API changes:
  * All usages of Vec3 and Vec2 were replaced in API with List[double] 
  * Numpy float and int arrays are accepted as arguments 
  
* Reaction callback now allows to cancel the current reaction 
  
Changes in MCell 4.0.4
-------------------------------------------------------------------------------  
* New features:
  * Added support for paired molecules, paired molecules represent two 
    membrane-bound proteins bound togehert and when one membrane (wall)
    is moved through dynamic geometry, the second membrane is moved as well 

Changes in MCell 4.0.3
-------------------------------------------------------------------------------  
* New features:
  * Handling of overlapped walls (overlapped walls must use vertices with identical coordinates)

* Minor changes:
  * Support for default VizOutput and Count output directories/files
  
* Bug Fixes:
  * Fixed timed count buffer flush  

Changes in MCell 4.0.2
-------------------------------------------------------------------------------
* Bug Fixes:
  * Fixed case when having a transparent surface did not correctly adjust 
    volume reaction rate
  * Partial fix for geometry import using SBML in CellBlender
  * Check for scheduling events such as Counts too far into the future
  
* Minor changes:
  * Project base name 'Scene' is not used when exporting MCell4 Python files

Changes in MCell 4.0.1
-------------------------------------------------------------------------------
* Bug Fixes:
  * Fixed dependency on system Python3.9.so

* Minor changes:
  * Exporting counts information in export_viz_data_model
  * Support for region expressions for counts in exported data model

Changes in MCell 4.0.0
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* Completely new MCell implementation


Changes in MCell 3.5.1
-------------------------------------------------------------------------------

* Major changes:
  * Integration of mesh processing tool GAMer 2
  * Integration of mesh import tool Neuropil Tools
  * Using BNGSim library for compartmental BNGL import

* Bug Fixes:
  * Fixed multiple surface-surface reaction handling when the reactions had the same reactants
  * Fixed MCell-R conversion step when the number of molecules to release was 0

* Minor changes:
  * MCell-R/NFsim now prints out less messages
  * Integrated tck-tk for Linux and MacOS builds so the base operating system does not need to provide them 

* Known limitations:
  * MacOS version must be extracted into the /Applications/ directory manually and should be run from 
    terminal with the current directory being the root directory '/'
  * Part of Neuropil Tools volFixAll might not work out of the box on all MacOS instalation and tweaking 
    to install Qt4 correctly is needed, however, this tool is not needed for all the use cases for Neuropil Tools
  * Windows version does not contain the Neuropil Tools plugin 
  
* Known issues:
  * Some models stored a a .blend file from 3.5.0 and older releases might fail to import, 
    it is possible to export them as data model and import data model
  * Adding surface regions before creating an object might cause an error, it is possible 
    to create an object first 
  
Changes in MCell 3.5.0
-------------------------------------------------------------------------------

* Requirements:
  * BNGL style reactions (MCell-R) require Perl to be installed, Windows variant is known to work with Perl from strawberryper.com and must be as the first perl.exe in PATH 
  * To use Matplotlib, Debian 9 and 10 require package 'tk' to be installed; instead of installing it, it is possible to run export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/2.79/python/lib/ in Blender-2.79-CellBlender before running the ./blender executable     

* Known limitations:
  * Windows build does not contain GAMER plugin for mesh refinement
  * Older settings might interfere on Windows, to fix this, please erase C:\Users\USER_NAME\AppData\Roaming\Blender Foundation
  * MacOS version must be extracted into the /Applications/ directory manually and must be run from terminal with working directory being the root directory '/' 
  
* Major changes:
  * NFSim reaction engine gets the same seed as mcell, no longer it generates its seed from current time 
  * Several improvements in CellBlender plugin with regards to BNGL type reactions
  * Automated build and test system

* Bug Fixes:
  * Fixed several issues for BNGL type reactions in compartments support 
  * Fixed case when memory usage grew indefinitely when logging BNGL type reactions
  * Fixed variable release scheduling rate when checkpoint with different timestep is loaded
  
* Optimizations:
  * Optimized search in nfSim reaction cache (up to 2x speedup for some MCellR models)