Release v1.04

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 "1.03.0")
+project(BioDynaMo LANGUAGES VERSION "1.04.0")
 
 #---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_v1.04.md

@@ -0,0 +1,16 @@
+---
+title: "BioDynaMo Version 1.04 Released"
+date: "2022-10-05"
+path: "/blog/release_v1.04/"
+meta_description: ""
+---
+
+</br>
+
+I am pleased to announce the release of BioDynaMo 1.04. 
+
+Please have a look at the [release notes](/docs/userguide/release_notes_v1.04/), [installation instructions](/docs/userguide/installation/) and [examples](/examples/demos/) for further information.
+
+Thanks and enjoy! </br>
+Lukas Breitwieser for the BioDynaMo team
+

doc/sidebars/userguide.yaml

@@ -55,6 +55,8 @@
         link: /docs/userguide/release_notes_v1.0/
       - title: BioDynaMo v1.02
         link: /docs/userguide/release_notes_v1.02/
+      - title: BioDynaMo v1.04
+        link: /docs/userguide/release_notes_v1.04/
   - group: Changelog
     items:
       - title: Log

doc/user_guide/release_notes_v1.04.md

@@ -0,0 +1,110 @@
+---
+title: "BioDynaMo Version 1.04 Release Notes"
+date: "2022-10-05"
+path: "/docs/userguide/release_notes_v1.04/"
+toc: true
+image: ""
+sidebar: "userguide"
+keywords:
+  -release
+  -v1.04
+  -1.04
+---
+
+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](https://github.com/BioDynaMo/biodynamo/pull/280)
+ * Generalize continuum integration [#260](https://github.com/BioDynaMo/biodynamo/pull/260)
+ * Improve scheduler information [#277](https://github.com/BioDynaMo/biodynamo/pull/277)
+ * Update flocking demo with local fluctuations [#256](https://github.com/BioDynaMo/biodynamo/pull/256)
+ * Added check for decay rate in diffusion grid [#271](https://github.com/BioDynaMo/biodynamo/pull/271)
+ * Make floating-point precision adjustable [#253](https://github.com/BioDynaMo/biodynamo/pull/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](https://github.com/BioDynaMo/biodynamo/pull/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](https://github.com/BioDynaMo/biodynamo/pull/264)
+ * Improve mechanism to reuse the index part of AgentUids [#263](https://github.com/BioDynaMo/biodynamo/pull/263)
+ * Update paraview build on macOS i386 [#261](https://github.com/BioDynaMo/biodynamo/pull/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](https://github.com/BioDynaMo/biodynamo/pull/257)
+ * Link Singularity in User Guide
+ * Add left-multiplication to MathArray [#255](https://github.com/BioDynaMo/biodynamo/pull/255)
+ * Minor code quality improvements [#252](https://github.com/BioDynaMo/biodynamo/pull/252)
+ * Create BioDynaMo singularity image [#244](https://github.com/BioDynaMo/biodynamo/pull/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](https://github.com/BioDynaMo/biodynamo/pull/247)
+ * Upgrade to ParaView 5.10 on macOS [#235](https://github.com/BioDynaMo/biodynamo/pull/235)
+ * Update continuum models [#241](https://github.com/BioDynaMo/biodynamo/pull/241)
+ * Add improvements suggested by Sonar Cloud [#246](https://github.com/BioDynaMo/biodynamo/pull/246)
+ * Add quality checks with `Sonar Cloud` [#245](https://github.com/BioDynaMo/biodynamo/pull/245)
+ * Add SWC export for neurons [#243](https://github.com/BioDynaMo/biodynamo/pull/243)
+ * Update link to endpoint package (CentOS CI)
+ * Add CLI wrapper for `bdm-config` [#238](https://github.com/BioDynaMo/biodynamo/pull/238)
+ * Add ProgressBar to visualise progress in `Simulate()` [#237](https://github.com/BioDynaMo/biodynamo/pull/237)
+ * Remove `benchmark` from default build target [#236](https://github.com/BioDynaMo/biodynamo/pull/236)
+ * Add SHA's for macOS 12.1 and Ubuntu 22.04.
+ * Extend functionality of `show_simulation_step` parameter [#234](https://github.com/BioDynaMo/biodynamo/pull/234)
+
+## Bug Fixes
+
+ * Fix issue with markupsafe which breaks nbconvert and thus the website  [#281](https://github.com/BioDynaMo/biodynamo/pull/281)
+ * Fix Python libraries on macOS [#279](https://github.com/BioDynaMo/biodynamo/pull/279)
+ * Fix warning in multi-simulation mode [#272](https://github.com/BioDynaMo/biodynamo/pull/272)
+ * Update GHA for macOS and fix notebooks on Ubuntu [#274](https://github.com/BioDynaMo/biodynamo/pull/274)
+ * Fix notebook related packages on CentOS [#275](https://github.com/BioDynaMo/biodynamo/pull/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](https://github.com/BioDynaMo/biodynamo/pull/248)
+ * Add fixes for code-smells [#249](https://github.com/BioDynaMo/biodynamo/pull/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](https://github.com/BioDynaMo/biodynamo/pull/262)
+ * Fix normalization of the diffusion gradient [#259](https://github.com/BioDynaMo/biodynamo/pull/259)
+ * Fix static agents bug in mechanical_forces_op
+ * Fix compiler warnings [#254](https://github.com/BioDynaMo/biodynamo/pull/254)
+ * Fix date-format in userguide/Singularity.md
+
+## Examples
+
+### New Demos
+
+ * Cell monolayer growth [#278](https://github.com/BioDynaMo/biodynamo/pull/278)
+ * Flocking Demo [#240](https://github.com/BioDynaMo/biodynamo/pull/240)
+
+## Supported Platforms
+
+ * Ubuntu 18.04, 20.04
+ * CentOS 7
+ * MacOS 11.7 and 12.6 (Intel and ARM) 
+