diff --git a/CMakeLists.txt b/CMakeLists.txt index 9cf1f9ef2..8eff58c75 100755 --- a/CMakeLists.txt +++ b/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 diff --git a/doc/blog/release_v1.04.md b/doc/blog/release_v1.04.md new file mode 100644 index 000000000..61a93fc0d --- /dev/null +++ b/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: "" +--- + +
+ +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!
+Lukas Breitwieser for the BioDynaMo team + diff --git a/doc/sidebars/userguide.yaml b/doc/sidebars/userguide.yaml index 476de47d3..edadf7bc0 100644 --- a/doc/sidebars/userguide.yaml +++ b/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 diff --git a/doc/user_guide/release_notes_v1.04.md b/doc/user_guide/release_notes_v1.04.md new file mode 100644 index 000000000..3782a115d --- /dev/null +++ b/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) +