Merge branch 'master' into cppmodules

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

@@ -32,6 +32,7 @@ jobs:
         if [ "${{ github.event_name }}" = "schedule" ]; then
           echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
         fi
+        echo "GHA_REPOSITORY=${{ github.repository }}" >> $GITHUB_ENV
 
     - name: Set OSVERS
       run: |
@@ -62,7 +63,7 @@ jobs:
       run: |
         yum update -y
         yum install -y sudo curl
-        curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/${GHA_BRANCH_NAME}/util/install | bash
+        curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash
         # remove whole BioDynaMo repository to catch errors related to paths pointing into the build dir
         mktemp -d
         find /tmp -iname biodynamo -type d || true

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

@@ -33,7 +33,7 @@ jobs:
         sudo ln -s /Applications/Xcode_14.2.app /Applications/Xcode.app
         sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
       if: matrix.os == 'macos-12'
-    
+
     - name: Make sure Xcode 15.2 is used on macOS 13 as the default /Application/Xcode.app
       shell: bash
       run: |
@@ -53,12 +53,14 @@ jobs:
         if [ "${{ github.event_name }}" = "schedule" ]; then
           echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
         fi
-    
+
+        echo "GHA_REPOSITORY=${{ github.repository}}" >> $GITHUB_ENV
+
     - name: Install BioDynaMo
       shell: zsh {0}
       run: |
         brew install curl
-        curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/${GHA_BRANCH_NAME}/util/install | bash
+        curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash
         # remove whole bidynamo repository to catch errors related to paths pointing into the build dir
         mktemp -d
         find /tmp -iname biodynamo -type d || true
@@ -102,7 +104,7 @@ jobs:
         cmake --build build --parallel --config Release
 
     # Don't do this in the `Build BioDynaMo step`, because notebooks might time out in GHA
-    # runners, while waiting for other targets to be compiled. Run notebooks only on 
+    # runners, while waiting for other targets to be compiled. Run notebooks only on
     # macOS 10.15 until we managed to compile ROOT for 11.6 again.
     - name: Run notebooks
       shell: zsh {0}

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

@@ -34,6 +34,8 @@ jobs:
           echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
         fi
 
+        echo "GHA_REPOSITORY=${{ github.repository }}" >> $GITHUB_ENV
+
     - name: Set OSVERS
       run: |
         ID=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"')
@@ -55,7 +57,7 @@ jobs:
       run: |
         sudo apt update
         sudo apt install -y curl
-        curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/${GHA_BRANCH_NAME}/util/install | bash
+        curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash
         # remove whole bidynamo repository to catch errors related to paths pointing into the build dir
         mktemp -d
         find /tmp -iname biodynamo -type d || true
@@ -133,7 +135,7 @@ jobs:
           -B build
         cmake --build build --parallel --config Release --target notebooks  -- -j1
       if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-22.04'
-      
+
 
     - name: Build BioDynaMo
       shell: bash

README.md

@@ -24,7 +24,7 @@
   <a href="https://github.com/BioDynaMo/biodynamo/actions/workflows/centos-system-ci.yml"><img src="https://github.com/BioDynaMo/biodynamo/actions/workflows/centos-system-ci.yml/badge.svg"/></a>
   <a href="https://github.com/BioDynaMo/biodynamo/actions/workflows/macos-system-ci.yml"><img src="https://github.com/BioDynaMo/biodynamo/actions/workflows/macos-system-ci.yml/badge.svg"/></a>
   <a href="https://sonarcloud.io/project/overview?id=BioDynaMo_biodynamo"><img src="https://sonarcloud.io/api/project_badges/measure?project=BioDynaMo_biodynamo&metric=alert_status"/></a>
-  <a href="https://discord.gg/9hNCbNYwcT"><img src="https://img.shields.io/discord/1029690454574370816"/></a>
+  <a href="https://discord.com/invite/kTcTTNFy"><img src="https://img.shields.io/discord/1029690454574370816"/></a>
   <a href="https://opensource.org/licenses/Apache-2.0"><img src="https://img.shields.io/badge/License-Apache%202.0-blue.svg"/></a>
 </p>
 

cmake/FindROOT.cmake

@@ -104,4 +104,4 @@ if(NOT BDM_OUT_OF_SOURCE)
   set(LAUNCHER ${CMAKE_BINARY_DIR}/launcher.sh)
 endif()
 
-include(${CMAKE_SOURCE_DIR}/cmake/RootMacros.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake/RootMacros.cmake)

cmake/external/SHA256Digests.cmake

@@ -62,6 +62,8 @@ SET(osx-14.4-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e8055
 SET(osx-14.4-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
 SET(osx-14.5-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e80554f7fa617ccb)
 SET(osx-14.5-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
+SET(osx-14.6-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e80554f7fa617ccb)
+SET(osx-14.6-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
 SET(osx-xcode-13.1-i386-ROOT be97dd72022c8d082fbe4394f18b55c4920f20b138cfff1b5fc2b41d397ac203)
 SET(osx-xcode-13.1-arm64-ROOT 0a55b91c6df42d152b7943912e134f05c3872a73e73fcc129ee87fd847240ec8)
 SET(osx-xcode-14.1-i386-ROOT 001311608512b24535bb9710b8baf006bd00e9b0595fd6bdf900d28b1e22c395)

util/install

@@ -1,14 +1,14 @@
 #!/usr/bin/env bash
 # Adapted from https://github.com/pyenv/pyenv-installer/
-# Usage: curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/master/util/install | bash 
+# Usage: curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/master/util/install | bash
 
 set -e
 
 if [ -z ${BDM_INSTALL} ]; then
   export BDM_INSTALL=v1.04-patches
 fi
 echo "BDM_INSTALL is set to: $BDM_INSTALL"
-  
+
 temp_dir=$(mktemp -d)
 BDM_SRC="${temp_dir}/biodynamo"
 mkdir "$BDM_SRC"
@@ -34,8 +34,9 @@ FailedCheckout() {
 
 Checkout() {
   # In Github Actions we checkout the branch that is running the install script
+  REPO_URL="${GITHUB}/${GHA_REPOSITORY}.git"
   if [ ! -z ${GITHUB_ACTIONS+x} ]; then
-    git clone --branch ${GHA_BRANCH_NAME} "$1" . || FailedClone "$1"
+    git clone --branch ${GHA_BRANCH_NAME} "$REPO_URL" . || FailedClone "$REPO_URL"
   else
     git clone "$1" . || FailedClone "$1"
     git checkout "$BDM_INSTALL" || FailedCheckout "$BDM_INSTALL"