Release v1.02

Author: LukasBreitwieser

CMakeLists.txt

@@ -24,7 +24,7 @@ endforeach()
 # Project name and current version. We do not specify any language for
 # this project. Therefore, we will be able to check manually which compiler
 # is detected on the system.
-project(BioDynaMo LANGUAGES VERSION "1.01.0")
+project(BioDynaMo LANGUAGES VERSION "1.02.0")
 
 #---Set the locale to default C to prevent issued due to localization of commands---------------
 # This is necessary as we for example call `clang -v` and parse its output. But on a localized

doc/blog/release_v1.02.md

@@ -0,0 +1,22 @@
+---
+title: "BioDynaMo Version 1.02 Released"
+date: "2021-11-29"
+path: "/blog/release_v1.02/"
+meta_description: ""
+---
+
+</br>
+
+I am pleased to announce the release of BioDynaMo 1.02. 
+
+Please have a look at the [release notes](/docs/userguide/release_notes_v1.02/), [installation instructions](/docs/userguide/installation/) and [examples](/examples/demos/) for further information.
+
+The following publication gives a good overview about BioDynaMo's features and capabilities.
+
+**BioDynaMo: a modular platform for high-performance agent-based simulation** </br>
+*Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer* </br>
+Bioinformatics, 2021, doi: (https://doi.org/10.1093/bioinformatics/btab649)[https://doi.org/10.1093/bioinformatics/btab649]
+
+Thanks and enjoy! </br>
+Lukas Breitwieser for the BioDynaMo team
+

doc/sidebars/userguide.yaml

@@ -49,6 +49,8 @@
     items:
       - title: BioDynaMo v1.0
         link: /docs/userguide/release_notes_v1.0/
+      - title: BioDynaMo v1.02
+        link: /docs/userguide/release_notes_v1.02/
   - group: Changelog
     items:
       - title: Log

doc/user_guide/release_notes_v1.02.md

@@ -0,0 +1,87 @@
+---
+title: "BioDynaMo Version 1.02 Release Notes"
+date: "2021-11-29"
+path: "/docs/userguide/release_notes_v1.02/"
+toc: true
+image: ""
+sidebar: "userguide"
+keywords:
+  -release
+  -v1.02
+  -1.02
+---
+
+BioDynaMo version 1.02 was released on November 29, 2021.
+
+The following people have contributed to this version
+(ordered by the number of contributions):
+
+* Lukas Breitwieser
+* Tobias Duswald
+* Fons Rademakers
+* Ahmad Hesam
+* Will Hemsley
+
+## New Features
+
+* Enabled one-line install script to install arbitrary BioDynaMo versions [#231](https://github.com/BioDynaMo/biodynamo/pull/231)
+* Add Scheduler function to print operation information
+* Added parallelized optimization manager [#205](https://github.com/BioDynaMo/biodynamo/pull/205)
+* Added googletest support for simulations [#187](https://github.com/BioDynaMo/biodynamo/pull/187)
+* Improved biodynamo cli [#215](https://github.com/BioDynaMo/biodynamo/pull/215)
+* Added experimental version of the automated benchmarking suite [#202](https://github.com/BioDynaMo/biodynamo/pull/202)
+* Added CopyExecutionContext
+* Added support for different execution orders
+* Introduced execution context interface [#189](https://github.com/BioDynaMo/biodynamo/pull/189)
+* Reduced memory consumption of the BDM memory manager [#186](https://github.com/BioDynaMo/biodynamo/pull/186)
+* Added SphericalAgent
+* Added toroidal space boundary condition
+* Added RandomizedRm to randomize the iteration over all agents
+* Added support for hierarchical agent-based models
+* Added analysis classes to simplify data collection and plotting [#177](https://github.com/BioDynaMo/biodynamo/pull/177)
+* Improved random number generation
+* Added `Scheduler::SimulateUntil(exit_condition)`
+* Added class LambdaFunctor and function L2F to simplify functor creation [#175](https://github.com/BioDynaMo/biodynamo/pull/175)
+* Added octree and kd-tree as alternative environments [#169](https://github.com/BioDynaMo/biodynamo/pull/169)
+
+## Bug Fixes
+
+* Fixed environment inconsistencies [#226](https://github.com/BioDynaMo/biodynamo/pull/226)
+* Added simulation dependent diffusion time step [#198](https://github.com/BioDynaMo/biodynamo/pull/198)
+* Fixed bug in diffusion grid initialization [#199](https://github.com/BioDynaMo/biodynamo/pull/199)
+* Fixed MathArray::Norm and Normalize for zero vector [#194](https://github.com/BioDynaMo/biodynamo/pull/194)
+* Do not call `Rm::EndOfIteration` in `ExecCtxt::SetupIterationAll`
+* Fixed errors in the static agent detection mechanism [#191](https://github.com/BioDynaMo/biodynamo/pull/191)
+* Fixed race condition in `DiffusionGrid::ChangeConcentrationBy`
+* Changed BioDynaMo version from `vXX.YY-ZZ-gSHA` to `vXX.YY.ZZ-SHA` [#216](https://github.com/BioDynaMo/biodynamo/pull/216)
+
+## Examples
+
+### New Demos
+
+* Binding cells
+* Pyramidal cell growth
+
+### New Notebooks
+
+* ST01-model-initializer.ipynb
+* ST02-user-defined-random-number-distribution.ipynb
+* ST03-agent-reproduction-mortality.ipynb
+* ST04-agent-reproduction-with-behaviors.ipynb
+* ST05-agent-reproduction-advanced.ipynb
+* ST06-environment-search.ipynb
+* ST07-multi-scale-simulation.ipynb
+* ST08-histograms.ipynb
+* ST09-timeseries-plotting-basic.ipynb
+* ST10-timeseries-plotting-and-analysis.ipynb
+* ST11-multiple-experiments-statistical-analysis.ipynb
+* ST12-hierarchical-model.ipynb
+* ST13-dynamic-scheduling.ipynb
+* ST14-randomize-iteration-order.ipynb
+* ST15-replace-interaction-force.ipynb
+
+## Supported Platforms
+
+*  Ubuntu 18.04, 20.04
+*  CentOS 7
+*  macOS 10.15, >=11.6 and >=12.0