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CompuCell3D Changelog

What's new in CompuCell3D 4.4.1.0

Jul 9, 2023
  • Improvements and new features:
  • New features:
  • Added support for all Python versions >= 3.7
  • Updated muParser to the latest version
  • Changed the way updates are handled: we are now redirecting users to sourceforge to download the new package
  • Improved package resolution - results in much faster download and installation times
  • Bug fixes:
  • Fixed integration between Twedit and Player
  • Fixed cc3d.init to run with python versions > 3.7
  • Fixed Python bindings and Python scripts to behave properly when working with Python> 3.7 and newer versions of numpy
  • Minor fixes to C++ code to compile properly with the latest versions of C++ compilers and use a newer versions of OpenMP on linux/OSX

New in CompuCell3D 4.4.0.0 (Apr 6, 2023)

  • New features:
  • Added all-Python frontend
  • Implemented interactive execution and visualization in pure Python
  • Added support for Jupyter Notebook
  • Added select Jupyter Notebook widgets for interactive execution and visualization
  • Added finite volume reaction diffusion solver
  • Improved glyphs rendering
  • Added backend logging
  • Upgraded VTK to 9.x
  • Upgraded SWIG to 4.x
  • Improved conda builds
  • Bug fixes:
  • Fixed 3D concentration visualization
  • Fixed ordering of cell type ID generation
  • Fixed python-based rendering
  • Fixed random number generator
  • Fixed randomization of cleavage plane during random orientation mitosis
  • Known Issues:
  • GPU solvers on OSX 10.14 or higher may not work properly. Windows GPU solvers may not work on all machines

New in CompuCell3D 4.2.4 Revision 20210118 (Jan 19, 2021)

  • Improvements and new features:
  • Added regression test suite
  • Added Callable CC3D renderer
  • Added DerivedProperty for read-only attributes in python calculated on-demand in C++
  • Added derived properties for cells: pressure, surface tension,
  • Added derived properties to regular and internal links: length, tension, linked cells
  • Added derived properties to anchor links: length, tension, linked cell
  • Major overhaul of FocalPointPlasticity Plugin including:
  • Added regular, internal and anchor link objects
  • Revised plugin throughout on the basis of link objects
  • Added link attributes and methods for link-specific manipulations
  • Added link inventory management methods to SteppableBasePy
  • Multiple bug fixes including:
  • Minor bug fixes
  • Known Issues:
  • GPU solvers on OSX 10.14 or higher may not work properly
  • Binary distribution packages:
  • Windows - 32-bit and 64-bit:
  • CompuCell3D 4.2.4 - Windows (select one of the exe files) Download
  • Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D
  • IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

New in CompuCell3D 4.2.3 Revision 20200822 (Aug 29, 2020)

  • Improvements and new features:
  • Added on_stop function to steppable - called if user stops the simulation
  • Added ability to open zipped project from both Player and Twedit++
  • Improved commenting / uncommenting of XML scripts
  • Added more natural syntax to refer to cell types
  • eg, selfcell_typeCondensing
  • Added pre-check for cell types and fields
  • Added Add Steppable function to CC3D Python menu, making it easier to add steppables in Twedit
  • Multiple bug fixes including:
  • Fixed settings handling in Twedit++
  • Fixed display of line numbers in Twedit++
  • Fixed issues with 25D simulations where dim z=2
  • Fixed behavior of cell_list_by_cell type when using nested loops
  • Improved random seed generation (matters if two identical simulations are started within less than a second of each other)

New in CompuCell3D 4.2.2 Revision 20200725 (Jul 26, 2020)

  • Improvements and new features:
  • Added ability top open zipped .cc3d project directly from Twedit++ - no need to do unzipping using 3rd party tools
  • Added saving of simulation layout on simulation stop or simulation finish events
  • Added automatic zip file name fill-in in Twedit++ when zipping .cc3d project
  • Added Simulation menu action to reset global settings - as of now users can reset simulation-specific and global settings directly from Player menu
  • Added option to reset Twedit++ settings directly from Twedit++ GUI
  • Multiple bug fixes including:
  • Fixed saving of windows layout - including plots and steering panel
  • Fixed screenshot color issues - as of now coloring is based on specification inside screenshot description file, and not on current player settings
  • Fixed handling of secretion in ReactionDiffusionSolverFE
  • Fixed "Check for New Version" functionality in the player
  • Fixed behavior of simulations that use plots but are run in gui-less mode
  • Fixed Twedit++ zoom in / zoom out issues
  • Fixed CC3D version printout issues
  • Known Issues:
  • GPU solvers on OSX 10.14 or higher may not work properly

New in CompuCell3D 4.2.1 Revision 20200606 (Jun 9, 2020)

  • Improvements and new features:
  • Added new convenience function to FieldSecretor class to compute total concentration "seen" by a cell as well as total amount of field in the entire lattice
  • Multiple bug fixes including:
  • Fixed Replay of saved simulation snapshots - Fixed simulation shutdown function call sequence to avoid crashes after last MCS was not a multiple of screen update frequency
  • Known Issues:
  • GPU solvers on OSX 10.14 or higher may not work properly

New in CompuCell3D 4.1.0 Revision 20190921 (Sep 22, 2019)

  • New Features:
  • New , intuitive way to launch parameter scans
  • Added 3D vascularized tumor demo from Shirinifard PLoS One 2009
  • Added basic, in-player simulation stats output
  • Added "WeightEnergyByDistance" in all contact energy plugins
  • Expanded Developer's manual and added new , documented DeveloperZone steppables examples
  • Added convenience Michaelis-Menten and Hill functions to SteppableBasePy
  • Multiple bug fixes (including ability to resize screenshots)

New in CompuCell3D 3.7.9 Revision 20181205 (Dec 11, 2018)

  • New, intuitive handling of screenshots. Adjust graphical configuration in the Player, click "Camera" button and from now on every run of your simulation will have screenshots taken.
  • Support for screenshots on clusters, and in the non-GUI-based runs
  • Vastly improved Boundary Walker algorithm that provides major speedups for simulations with either very large cells or with very few cells on a large lattice
  • Refactored Player code
  • Multiple bug fixes

New in CompuCell3D 3.7.8 Revision 20180722 (Jul 23, 2018)

  • New Features:
  • Python parameter Steering via Interactive Slider
  • Multiple Bug Fixes

New in CompuCell3D 3.7.7 Revision 20171112 (Nov 13, 2017)

  • New Features:
  • Improved handling of Player settings - based on SQLite database
  • Significantly faster connectivity plugin that works in 2D , 3D and on any type of lattice
  • Multiple bug-fixes

New in CompuCell3D 3.7.6 Revision 20170723 (Jul 31, 2017)

  • New Features:
  • Windows, OSX, Linux versions ship with bundled Python distributions
  • Simplified Player menus
  • We added parameter optimization module based on user-defined cost function (we will develop tutorials soon)
  • One installer should work on all versions of OSX starting with 10.9 (Mavericks)
  • Starting from this version we will be only providing binaries for 64-bit Long Term Support Ubuntu releases (14.0 16.04 etc). Keep in mind that CC3D can be easily compiled on any linux distribution
  • Bug fixes in Twedit++
  • RoadRunner was upgraded to the latest version.
  • IMPORTANT: The RR upgrade eliminates the need to set steps options in in the Steppable file. If you have step options set remove it from your script

New in CompuCell3D 3.7.4 Revision 20150514 (May 20, 2015)

  • Player has been improved and has new layout with floating windows. This is the default and recommended setting for Mac users. Check here
  • Player settings are stored individually with each simulation. Thus several simulations running in parallel may have different set of settings. Previously there was one global setting file which made it inconvenient to run multiple simultaneous simulations with different settings
  • Window layout is saved in the settings each time user stops the simulation. This feature allows simulation to open in exactly the same state it was before user stopped simulation run.
  • Automatic cell labeling using scalar or vector cell attribute
  • Simplified access to cell python dictionary - not you type cell.dict
  • Simplified histograms and scientific plots setup
  • Added ability to subscribe/unsubscribe to CompuCell3D mailing list from the Player

New in CompuCell3D 3.7.3 Revision 20141125 (Nov 26, 2014)

  • New Features:
  • paramScan script that runs parameter scan in a fault-tolerant way.
  • New format to save plot data (csv)
  • Easier computations on he lattice with new hex2Cartesian and cartesin2Hex Py Steppable Base functions
  • Option to turn off comments in Python snippets inserted from CC3D Python menu
  • Support for VTK6
  • Stopped requiring PyQt/Qt for command line runs
  • Improved XML code checkers which do sanity checks for XML part of simulation description
  • Bug Fixes:
  • Fixed saving plots and plots data
  • Fixed saving .cc3d projects in the new directory aka Save Project As ...
  • Fixed visualization scaling for 2D projectsion on hex lattice
  • Fixed generation of higher neighbor orders on demand. Current implementation was good up to 8th nearest neighbor. Now we can use 20 or 30 or higher
  • Fixed how secretion plugin=- related bottleneck in openMP see manual for more details

New in CompuCell3D 3.7.2 Revision 20140307 (Apr 24, 2014)

  • Improved roadrunner SBML Solver - faster than before and with more user-configurable options
  • Improved GPU and CPU PDE Solvers - fixed small bugs on hex lattice with non-periodic boundary conditions
  • Updated Twedit helper menu
  • Fixed OSX player freeze when replaying VTK files
  • Added min/max functions to the chemical field for faster performance