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BioDynaMo 1.04

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@LukasBreitwieser LukasBreitwieser released this 05 Oct 16:16
· 122 commits to master since this release
v1.04
1101305

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 with bdm 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
  • Reenable 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 mechanical_forces_op
  • Fix compiler warnings #254
  • Fix date-format in userguide/Singularity.md

Examples

New Demos

  • Cell monolayer growth #278
  • Flocking Demo #240

Supported Platforms

  • Ubuntu 18.04, 20.04
  • CentOS 7
  • MacOS 11.7 and 12.6 (Intel and ARM)
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