BioDynaMo version 1.04 was released on October 5, 2022.
The following people have contributed to this version (ordered by the number of contributions):
- Lukas Breitwieser
- Tobias Duswald
- Nicolò Cogno
- Fons Rademakers
- Ahmad Hesam
- Jack Jennings
- Moritz Grabmann
New Features and Improvements
- Add check for PVSM output files to system tests #280
- Generalize continuum integration #260
- Improve scheduler information #277
- Update flocking demo with local fluctuations #256
- Added check for decay rate in diffusion grid #271
- Make floating-point precision adjustable #253
- Improve UniformGridEnvironment::Box::Iterator interface
- Add switch to turn off automatic sim size detection in UniformGridEnvironment
- Add missing ForEachNeighbor implementation for UniformGridEnvironment
- Add BinarySearch.DuplicatesLarge test
- Remove const specifier from Agent::RemoveFromSimulation
- Improve the time series collection API #266
- AgentPointer return nullptr directly for corresponding AgentUid
- Make InPlaceExecutionContext::remove_ protected
- Make Agent::RemoveFromSimulation virtual
- Remove all virtual functions from InlineVector
- Introduce different AgentPointer modes #264
- Improve mechanism to reuse the index part of AgentUids #263
- Update paraview build on macOS i386 #261
- Don't run Singularity GHA on all branches
- Avoid parsing of
bdm.json
withbdm test
- Add macOS packages to user guide
- Extend DiffusionGrid interface for full gradient information #257
- Link Singularity in User Guide
- Add left-multiplication to MathArray #255
- Minor code quality improvements #252
- Create BioDynaMo singularity image #244
- Re-enable gitpod image workflow but only for manual triggering
- Add additional LamdaFunctor tests
- Add safety check in function PlotNeighborMemoryHistogram
- Improve documentation of Agent::RemoveBehavior
- Add coverage reporting with SonarCloud #247
- Upgrade to ParaView 5.10 on macOS #235
- Update continuum models #241
- Add improvements suggested by Sonar Cloud #246
- Add quality checks with
Sonar Cloud
#245 - Add SWC export for neurons #243
- Update link to endpoint package (CentOS CI)
- Add CLI wrapper for
bdm-config
#238 - Add ProgressBar to visualise progress in
Simulate()
#237 - Remove
benchmark
from default build target #236 - Add SHA's for macOS 12.1 and Ubuntu 22.04.
- Extend functionality of
show_simulation_step
parameter #234
Bug Fixes
- Fix issue with markupsafe which breaks nbconvert and thus the website #281
- Fix Python libraries on macOS #279
- Fix warning in multi-simulation mode #272
- Update GHA for macOS and fix notebooks on Ubuntu #274
- Fix notebook related packages on CentOS #275
- Fix issues introduced due to the global edit from double to
real_t
in OpenCL code. - Fix to find python3.9 on macOS.
- Added version check and threshold fix for ParaView in epidemiology demo
- Attribute environment update time to the correct operation
- Reduce size of UniformGridEnvironment::Box
- Remove obsolete parameter from toml file
- Fix NUMA bug in ResourceManager::RemoveAgents
- Fix GHA copyright script for linux
- Fix DiffuseWithOpenEdge #248
- Add fixes for code-smells #249
- Fix bug in function GenerateSimulationInfoJson
- Add additional AgentPointer tests; fix bug in AgentPointer
- Fix possible race condition in user-defined thread-safety mechanism #262
- Fix normalization of the diffusion gradient #259
- Fix static agents bug in mechanicalforcesop
- Fix compiler warnings #254
- Fix date-format in userguide/Singularity.md
Examples
New Demos
Supported Platforms
- Ubuntu 18.04, 20.04
- CentOS 7
- MacOS 11.7 and 12.6 (Intel and ARM)