Update GHA for macOS and fix notebooks on Ubuntu

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

@@ -126,22 +126,22 @@ jobs:
           -B build
         cmake --build build --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
-    - name: Run notebooks
-      shell: bash
-      run: |
-        export PATH="$HOME/.pyenv/bin:$PATH"
-        eval "$(pyenv init --path)"
-        eval "$(pyenv init -)"
-        pyenv shell 3.9.1
-        . scl_source enable devtoolset-8 || true
-        . /etc/profile.d/modules.sh || true
-        module load mpi
-        cmake \
-          -Dnotebooks=ON \
-          -B build
-        cmake --build build --config Release --target notebooks -- -j1
+    # # 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
+    # - name: Run notebooks
+    #   shell: bash
+    #   run: |
+    #     export PATH="$HOME/.pyenv/bin:$PATH"
+    #     eval "$(pyenv init --path)"
+    #     eval "$(pyenv init -)"
+    #     pyenv shell 3.9.1
+    #     . scl_source enable devtoolset-8 || true
+    #     . /etc/profile.d/modules.sh || true
+    #     module load mpi
+    #     cmake \
+    #       -Dnotebooks=ON \
+    #       -B build
+    #     cmake --build build --config Release --target notebooks -- -j1
 
     - name: Run system tests
       shell: bash

.github/workflows/macos-ci.yml

@@ -10,21 +10,20 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-10.15, macos-11]
+        os: [macos-11, macos-12]
 
     runs-on: ${{ matrix.os }}
 
     steps:
-    - name: Make sure Xcode 12.4 is used on macOS 10.15 as the default /Application/Xcode.app
+    - name: Make sure Xcode 13.1 is used on macOS 12 as the default /Application/Xcode.app
       shell: bash
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-
-        sudo ln -s /Applications/Xcode_12.4.app /Applications/Xcode.app
+        sudo ln -s /Applications/Xcode_13.1.app /Applications/Xcode.app
         sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
-      if: matrix.os == 'macos-10.15'
+      if: matrix.os == 'macos-12'
 
-    # It's not possible to specify 11.6 but we hope that this remains the latest.
-    - name: Make sure Xcode 13.1 is used on macOS 11.6 as the default /Application/Xcode.app
+    - name: Make sure Xcode 13.1 is used on macOS 11 as the default /Application/Xcode.app
       shell: bash
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-

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

@@ -17,21 +17,20 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-10.15, macos-11]
+        os: [macos-11, macos-12]
 
     runs-on: ${{ matrix.os }}
 
     steps:
-    - name: Make sure Xcode 12.4 is used on macOS 10.15 as the default /Application/Xcode.app
+    - name: Make sure Xcode 13.1 is used on macOS 12 as the default /Application/Xcode.app
       shell: zsh {0}
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-
-        sudo ln -s /Applications/Xcode_12.4.app /Applications/Xcode.app
+        sudo ln -s /Applications/Xcode_13.1.app /Applications/Xcode.app
         sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
-      if: matrix.os == 'macos-10.15'
+      if: matrix.os == 'macos-12'
 
-    # It's not possible to specify 11.6 but we hope that this remains the latest.
-    - name: Make sure Xcode 13.1 is used on macOS 11.6 as the default /Application/Xcode.app
+    - name: Make sure Xcode 13.1 is used on macOS 11 as the default /Application/Xcode.app
       shell: bash
       run: |
         sudo mv /Applications/Xcode.app /Applications/Xcode.app-

CMakeLists.txt

@@ -58,6 +58,7 @@ else()
     SET(DETECTED_OS_VERS ${OS})
     check_detected_os(${DETECTED_OS})
 endif()
+message(STATUS "Detected OS: ${DETECTED_OS_VERS}")
 
 
 # Find a suitable compiler

cmake/external/ROOT.cmake

@@ -6,13 +6,18 @@ SET(ROOT_SOURCE_DIR "${CMAKE_THIRD_PARTY_DIR}/root")
 set(ROOT_TAR_FILE root_v6.22.06_python3.9_${DETECTED_OS_VERS}.tar.gz)
 if(APPLE)
   if("${DETECTED_OS_VERS}" MATCHES "^osx-12" OR
-     "${DETECTED_OS_VERS}" MATCHES "^osx-11.6")
+     "${DETECTED_OS_VERS}" MATCHES "^osx-11.6" OR
+     "${DETECTED_OS_VERS}" MATCHES "^osx-11.7")
     set(ROOT_TAR_FILE root_v6.25.01_cxx14_python3.9_${DETECTED_OS_VERS}.tar.gz)
   elseif("${DETECTED_OS_VERS}" MATCHES "^osx-11")
-    message(FATAL_ERROR "We officialy only support the latest macOS 11 version: 11.6.")
+    message(FATAL_ERROR "We officialy only support the latest macOS 11 versions 11.6, 11.7.")
   endif()
 endif()
 
+message(STATUS "Using ROOT tarball: ${ROOT_TAR_FILE}")
+message(STATUS "Using ROOT source dir: ${ROOT_SOURCE_DIR}")
+message(STATUS "Using ROOT version: ${${DETECTED_OS_VERS}-ROOT}")
+
 download_verify_extract(
   http://cern.ch/biodynamo-lfs/third-party/${ROOT_TAR_FILE}
   ${ROOT_SOURCE_DIR}

cmake/external/SHA256Digests.cmake

@@ -24,10 +24,15 @@ SET(osx-11.5-i386-Qt 7af9eed30be9f25bbdcf7e5747ab53eaaf077c6b2a974c2e520ac678f5a
 SET(osx-11.5-i386-ROOT 92c2fd4f6af11a64f9b0c9a7a5b19d92b65653b1b4e7a0f84afac7fa3abaffc2)
 SET(osx-11.5-arm64-ROOT 70a2ef099275e4720c1a5fc46c1fa8ad9dfd407049fcb2b1b91b39bd07a1575a)
 SET(osx-11.6-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
+SET(osx-11.6-arm64-ROOT 62bd493f45b13baa15a29713c4fd989eca235a77545f56c9a9ecd6667bafaf85)
 SET(osx-11.6-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e80554f7fa617ccb)
 SET(osx-11.6-i386-Qt 7af9eed30be9f25bbdcf7e5747ab53eaaf077c6b2a974c2e520ac678f5a147a7)
 SET(osx-11.6-i386-ROOT 90060674515211b98b4b5349fdb0de96f73b7d12768331217e8c833acb7ed307)
-SET(osx-11.6-arm64-ROOT 62bd493f45b13baa15a29713c4fd989eca235a77545f56c9a9ecd6667bafaf85)
+SET(osx-11.7-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
+SET(osx-11.7-arm64-ROOT 62bd493f45b13baa15a29713c4fd989eca235a77545f56c9a9ecd6667bafaf85)
+SET(osx-11.7-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e80554f7fa617ccb)
+SET(osx-11.7-i386-Qt 7af9eed30be9f25bbdcf7e5747ab53eaaf077c6b2a974c2e520ac678f5a147a7)
+SET(osx-11.7-i386-ROOT 90060674515211b98b4b5349fdb0de96f73b7d12768331217e8c833acb7ed307)
 SET(osx-12.0-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e80554f7fa617ccb)
 SET(osx-12.0-i386-Qt 7af9eed30be9f25bbdcf7e5747ab53eaaf077c6b2a974c2e520ac678f5a147a7)
 SET(osx-12.0-i386-ROOT be97dd72022c8d082fbe4394f18b55c4920f20b138cfff1b5fc2b41d397ac203)

util/installation/ubuntu-18.04/prerequisites.sh

@@ -72,7 +72,7 @@ pyenv shell $PYVERS
 # Install optional packages
 if [ $1 == "all" ]; then
   # this updates pip, but installs the updated version in $HOME/.local/bin
-  PIP_PACKAGES="nbformat jupyter metakernel jupyterlab"
+  PIP_PACKAGES="jupyter metakernel jupyterlab nbformat==5.4.0 nbconvert==6.5.3 nbclient==0.6.6"
   # Don't install --user: the packages should end up in the PYENV_ROOT directory
   python -m pip install $PIP_PACKAGES