Version 0.33.0

Minor features and bug fix release

• Improved performance of particle creation
• Upgrades to Python support for Windows
• Improved potential consistency, checks and performance
• Removed limitation on local populations in CUDA acceleration
• Added integration support in cmake projects
• Improved library interface
• Added C++ tests submodule
• Improved documentation
• Bug fixes
  • Disabled unreliable automated tests in pipelines conda build
  • Minor build fixes for gcc
  • Corrected pointers during fission
  • Fixed memory leak in I/O
  • Fixed incorrect install headers

Version 0.32.1

Patch release

• Added links to C API docs
• Reduced cost of docs build to support rendered notebooks online
• Mitigated bug related to pre-rendered notebooks with jpeg output
• Relaxed python library testing to mitigate random, erroneous errors on Azure for osx

Version 0.32.0

Minor features and bug fix release

• Adds C API
• Adds and integrates test suite
• Finishes all current features in lattice python module
• Updates Jupyter deployment and widgets
• Adds notebooks to distributed examples
• Adds rendered notebooks and gallery to docs examples
• Adds settable particle position, velocity and force
• Adds automatic destruction of angles and dihedrals connected to a destroyed particle
• Adds improved checks to particle handle and type
• Adds key modifiers to key events
• Adds support for multiple new screenshot file formats
• Splits language support and bindings into separate, self-contained modules
• Major cleanup of codebase
• Minor bug fixes
  • Fixes particle position details very close to boundaries
  • Removes redundant random force in Friction
  • Refactors Berendsen to correct typo
  • Fixes/improves argument handling in python particle construction
  • Fixes inventory tracking during particle destruction
  • Fixes cluster particle factory
  • Fixes visible types in particle become
  • Adds templates for universe grid

Version 0.31.0

Huge release, with completion of (hopefully) all features for Version 1.0.0

• Core features

  • Adds support for model specification in pure C++
  • Adds support for generating bindings in additional languages
  • Adds a formal event system, with callback capabilities in C++ and python
  • Implements universal naming of particle types: a registered type can now always be uniquely determined anywhere in a simulation
  • Adds "models" module for application-specific modeling features
  • Adds libSBML dependency
  • Removes carbon
  • Adds modular CUDA runtime support
  • Improves synchronization of SBML states and state vector dynamics
  • Adds simulation I/O based on JSON
  • Adds I/O support for 3D model format files

• Modeling features

  • Populates event system with events for

    • single events
    • time-dependent events
    • particle-dependent events
    • time- and particle-dependent events

  • Adds cell polarity model to models module

  • Adds "reset" boundary condition

  • Unifies bond interfaces

• Visualization / interactive features

  • Adds camera and basic visualization interfaces

  • Adds clip planes support for bonds rendering

  • Adds interactive interface for clip planes

  • Adds interface for random number generator

  • Adds interface to customize basic visualization (e.g., background color, scene decorations)

  • Adds screenshot interface

  • Adds rendering of space discretization

  • Adds visualization of view orientation

  • Adds keyboard commands for

    • pre-defined views
    • toggling scene decorations
    • toggling display of space discretization

• Documentation features

  • Adds documentation on (hopefully) all modeling and simulation features
  • Adds documentation on select back-end details
  • Adds automated C/C++ API documentation using Doxygen
  • Adds automated Python API documentation using Sphinx

• Build / distribution features

  • Adds automated local build using conda
  • Adds conda package recipe
  • Implements CI/CD using Azure