Merge branch 'master' into umar_neurite_test

.github/workflows/macos-ci.yml

@@ -14,7 +14,7 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-11, macos-12, macos-13]
+        os: [macos-12, macos-13]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/macos-system-ci.yml

@@ -21,7 +21,7 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-11, macos-12, macos-13]
+        os: [macos-12, macos-13]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/sonar-source.yml

@@ -15,21 +15,15 @@ jobs:
     name: Sonar Source Analysis
     runs-on: ubuntu-20.04
     env:
-      SONAR_SCANNER_VERSION: 4.6.1.2450 # Find the latest version in the "Linux" link on this page:
-                                        # https://sonarcloud.io/documentation/analysis/scan/sonarscanner/
       SONAR_SERVER_URL: "https://sonarcloud.io"
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
     steps:
       - name: Download BioDynaMo
         uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
-      - name: Set up JDK 11
-        uses: actions/setup-java@v1
-        with:
-          java-version: 11
       - name: Install sonar-scanner and build-wrapper
-        uses: SonarSource/sonarcloud-github-c-cpp@v1
+        uses: SonarSource/sonarcloud-github-c-cpp@v2
       - name: Install dependencies
         run: |
           sudo apt-get update

cmake/external/ROOT.cmake

@@ -13,7 +13,11 @@ if(APPLE)
      "${DETECTED_OS_VERS}" MATCHES "^osx-11.7")
     execute_process(COMMAND bash "-c" "xcodebuild -version | sed -En 's/Xcode[[:space:]]+([0-9\.]*)/\\1/p'" OUTPUT_VARIABLE XCODE_VERS)
     message(STATUS "##### XCODE version: ${XCODE_VERS}")
-    if("${XCODE_VERS}" GREATER_EQUAL "14.3")
+    if("${XCODE_VERS}" GREATER_EQUAL "15.0")
+      message(STATUS "##### Using ROOT builds for XCODE 15.0.1")
+      set(ROOT_TAR_FILE root_v6.28.10_cxx14_python3.9_osx-xcode-15.0.1-${DETECTED_ARCH}.tar.gz)
+      set(ROOT_SHA_KEY osx-xcode-15.0.1-${DETECTED_ARCH}-ROOT)
+    elseif("${XCODE_VERS}" GREATER_EQUAL "14.3")
       message(STATUS "##### Using ROOT builds for XCODE 14.3")
       set(ROOT_TAR_FILE root_v6.29.01_cxx14_python3.9_osx-xcode-14.3-${DETECTED_ARCH}.tar.gz)
       set(ROOT_SHA_KEY osx-xcode-14.3-${DETECTED_ARCH}-ROOT)

cmake/external/SHA256Digests.cmake

@@ -60,6 +60,8 @@ SET(osx-xcode-14.1-i386-ROOT 001311608512b24535bb9710b8baf006bd00e9b0595fd6bdf90
 SET(osx-xcode-14.1-arm64-ROOT 12ad32f7d49e2c5dfd4124923bd87f49a31a670d99e390b0a9b71a8ff2f2f035)
 SET(osx-xcode-14.3-i386-ROOT c4f4c7a9848121ae19f3fe3c40c5812813ed42d9dfa7f1948f67907ed47fa083)
 SET(osx-xcode-14.3-arm64-ROOT 6ffcfaadd4de627cffde2e42fded9175b730769071396d7abdabeefc2714839a)
+SET(osx-xcode-15.0.1-i386-ROOT a88b770a1848f41be23a6cfe166d9e4da6c73f985865fb96d473dba966fee3b4)
+SET(osx-xcode-15.0.1-arm64-ROOT de60b679f09e7ccde3f5d117e728ffb28d705196935ada5b29f5cc27f2c03091)
 
 SET(ubuntu-18.04-Libroadrunner bf9293c1c95d0b65227bd7e08c0048116ba851bcec5028ef72ea13762ef79276)
 SET(ubuntu-18.04-ParaView e3fd74b13e9a4086988c5104c6b8d95c56365d25b491706a8e72018d0e5c76f1)

doc/user_guide/Singularity.md

@@ -90,3 +90,22 @@ If you wish to read further about Singularity, you can find a substantial amount
 singularity home website: https://sylabs.io/guides/3.5/user-guide/introduction.html. Including many tutorials and more 
 complex use cases.
 
+
+## Exporting visualisations on HPC's
+By default, BioDynaMo uses ParaView for visualization, which needs an X-display server to function. Since the Singularity image does not provide a graphical desktop environment and hence no X-server, there are two workarounds.
+
+### Option 1: Using xvfb
+```xvfb``` stands for X virtual frame buffer and emulates the required display server. Start a virtual frame buffer with: 
+```
+/biodynamo/util/xvfb-initd.sh start
+```
+The buffer can be managed with the arguments ```start```|```stop```|```restart```
+
+Note: Some systems may require display forwarding **before** starting the frame buffer. This can be achived through ```export DISPLAY=0```.
+
+### Option 2: Setting Paraview to work in a headless mode using the CMAKE flag
+Paraview with the osmesa or EGL backend does not require an X-server. To change the backend, you have to edit the cmake options in [1], build paraview, and replace the ParaView version that BioDynaMo installs. See also [2].
+
+[1] https://github.com/BioDynaMo/biodynamo/blob/HPC-documentation/util/build-third-party/paraview/build.sh
+
+[2] https://discourse.paraview.org/t/pvpython-offscreen-rendering-segfault/246/3

doc/user_guide/installation.md

@@ -61,7 +61,7 @@ curl https://biodynamo.github.io/install | bash
 
 *  Ubuntu 20.04, 22.04
 *  CentOS 7
-*  MacOS 11.7 and 12.6 (Intel and ARM)
+*  MacOS > 12.0 (Intel and ARM)
 
 Currently, we do **not** support Windows or Windows subsystem for Linux.
 

doc/user_guide/prerequisites.md

@@ -219,7 +219,7 @@ sudo yum install -y llvm-toolset-7 llvm-toolset-7-clang-tools-extra \
 Requirements to build on macOS are:
 
  * A 64-bit Intel CPU or Apple Silicon CPU
- * macOS Catalina (10.15) or higher
+ * macOS 12.0 or higher
  * [Xcode](https://itunes.apple.com/us/app/xcode/id497799835) and the Command Line Tools (CLT) for Xcode: `xcode-select --install`  
     (or from [developer.apple.com/downloads](https://developer.apple.com/downloads))
  * An up to date [Homebrew](https://brew.sh) installation (MacPorts and Fink are not supported)