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brainstorm-tools · Aug 21, 2024 · 764b8a0 · 764b8a0
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diff --git a/.github/workflows/startup_test.yml b/.github/workflows/startup_test.yml
@@ -0,0 +1,65 @@
+# Workflow to perform a minimal startup test of Brainstorm source
+
+# Workflow name
+name: Startup test
+
+# Environment variables
+env:
+  MATLAB_VER: R2021b             # Oldest "b" available (Feb2024)
+  TMP_ERROR_FILE: tmp_error.txt  # Flag file to indicate error
+  MATLAB_SCRIPT_FILE: scripto.m  # Matlab script to handle errors
+
+# Run manually from GitHub Actions tab, it must be in the default branch
+on:
+  workflow_dispatch:
+
+# Name for each run
+run-name: "Startup test: ${{ github.ref_name }}"
+jobs:
+  Run-Ubuntu:
+    name: Run on Linux (Ubuntu 20.04)
+    runs-on: ubuntu-20.04
+    steps:
+      # Get the Brainstorm code to test
+      - name: Checkout 'brainstorm3'
+        uses: actions/checkout@v3
+      # Setting Matlab
+      - name: Set up Matlab
+        uses: matlab-actions/setup-matlab@v1
+        with:
+          release: ${{ env.MATLAB_VER }}
+      # Create error file and Matlab test script
+      - name: Create required files
+        run: |
+             touch $TMP_ERROR_FILE
+             echo "function scripto()" > $MATLAB_SCRIPT_FILE
+             MATLAB_SCRIPT_TEXT="try brainstorm server local; catch ME; disp(getReport(ME)); exit; end; delete('$TMP_ERROR_FILE'); brainstorm stop; exit;"
+             echo $MATLAB_SCRIPT_TEXT >> $MATLAB_SCRIPT_FILE
+             cat $MATLAB_SCRIPT_FILE
+             ls -al
+             pwd
+      # Run test script
+      - name: Run test script
+        uses: matlab-actions/run-command@v1
+        with:
+          command: scripto()
+          startup-options: -nodisplay
+      # Check error file was deleted
+      - id: startuptest
+        name: Check error file
+        continue-on-error: true
+        run: |
+             if [ -f "$TMP_ERROR_FILE" ]; then
+               echo "ERROR: Brainstorm could not start on GitHub runner"
+               exit 1
+             fi
+      # Actions depending of outcome
+      - id: succeeded
+        if: steps.startuptest.outcome == 'success'
+        run: |
+             echo "Success action"
+      - id: failed
+        if: steps.startuptest.outcome == 'failure'
+        run: |
+             echo "Failure action"
+             exit 1
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -24,6 +24,8 @@ This is a brief list of resources to get started with MATLAB if you are new or c
 - [Introduction to MATLAB for Python Users](https://blogs.mathworks.com/student-lounge/2021/02/19/introduction-to-matlab-for-python-users/)
 - [MATLAB for Brain and Cognitive Scientists](https://mitpress.mit.edu/9780262035828/)
 - [Brainstorm scripting](https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting)
+- [Debug MATLAB Code Files](https://www.mathworks.com/help/matlab/matlab_prog/debugging-process-and-features.html)
+- [MATLAB Debugging Tutorial (video)](https://www.youtube.com/watch?v=PdNY9n8lV1Y)
 
 ## Git and GitHub resources
 Before starting a new contribution, you need to be familiar with [Git](https://git-scm.com/) and [GitHub](https://github.com/) concepts like: ***commit, branch, push, pull, remote, fork, repository***, etc. There are plenty resources online to learn Git and GitHub, for example:
@@ -101,7 +103,7 @@ See: [Git tools rewriting history](https://git-scm.com/book/en/v2/Git-Tools-Rewr
 6. ### **Create a new Pull Request**
 
     Once you're **happy** with all the changes that you have done, and you have pushed them to your remote repo, using the GitHub website, create a [Pull Request (PR)](https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) from your **remote branch** to the **master** branch in the official Brainstorm repo.
-    
+
     > :warning: For greater collaboration, select the option [Allow edits by maintainers](https://docs.github.com/en/github/collaborating-with-pull-requests/working-with-forks/allowing-changes-to-a-pull-request-branch-created-from-a-fork) before creating your PR. This will allow Brainstorm maintainers to add commits to your PR branch before merging it. You can always change this setting later.
 
  ![image](https://user-images.githubusercontent.com/8238803/135626746-aaaac892-8c44-494e-a79d-b7195e3b2b5e.png)

diff --git a/bin/R2022b/brainstorm3.bat → bin/R2023a/brainstorm3.bat b/bin/R2022b/brainstorm3.bat → bin/R2023a/brainstorm3.bat
@@ -1,8 +1,8 @@
 @ECHO.
 @SET MATLABROOT=
-@SET VER_NAME=R2022b
-@SET VER_NUMBER=9.13
-@SET MCR_FOLDER=v913
+@SET VER_NAME=R2023a
+@SET VER_NUMBER=9.14
+@SET MCR_FOLDER=R2023a
 
 
 @REM ===== SKIP DETECTION =====

diff --git a/bin/R2022b/brainstorm3.command → bin/R2023a/brainstorm3.command b/bin/R2022b/brainstorm3.command → bin/R2023a/brainstorm3.command
@@ -4,17 +4,17 @@
 #         brainstorm3.command <MATLABROOT> <script.m> <arguments>
 #
 # If MATLABROOT argument is specified, the Matlab root path is saved
-# in the file ~/.brainstorm/MATLABROOTXX.txt.
+# in the file ~/.brainstorm/MATLABROOT_R20YYx.txt
 # Else, MATLABROOT is read from this file
 #
 # AUTHOR: Francois Tadel, 2011-2022
+#         Raymundo Cassani, 2024
 
 # Configuration
-VER_NAME="2022b"
-VER_NUMBER="9.13"
-VER_DIR="913"
+VER_YEAR_VERSION="2023a"
+VER_NAME="R$VER_YEAR_VERSION"
 MDIR="$HOME/.brainstorm"
-MFILE="$MDIR/MATLABROOT$VER_DIR.txt"
+MFILE="$MDIR/MATLABROOT_$VER_NAME.txt"
 
 #########################################################################
 # Detect system type
@@ -38,7 +38,7 @@ SH_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 # JAR is in the same folder (Linux)
 if [ -f "$SH_DIR/brainstorm3.jar" ]; then
     JAR_FILE=$SH_DIR/brainstorm3.jar
-# JAR is 3 levels up (on MacOSX: brainstorm3.app/Contents/MacOS/brainstorm3.command)
+# JAR is 3 levels up (on macOS: brainstorm3.app/Contents/MacOS/brainstorm3.command)
 elif [ -f "$SH_DIR/../../../brainstorm3.jar" ]; then
     JAR_FILE=$SH_DIR/../../../brainstorm3.jar
 else
@@ -52,14 +52,21 @@ if [ "$1" ]; then
 # Read the folder from the file
 elif [ -f $MFILE ]; then
     MATLABROOT=$(<$MFILE)
-# MacOS: Try the default installation folders for Matlab or the MCR
-elif [ $SYST == "maci64" ] && [ -d "/Applications/MATLAB/MATLAB_Runtime/v$VER_DIR" ]; then
-    MATLABROOT="/Applications/MATLAB/MATLAB_Runtime/v$VER_DIR"
-    echo "MATLAB Runtime library was found in folder:"
-    echo "$MATLABROOT"
+# macOS: Try the default installation folder for Matlab
+elif [ $SYST == "maci64" ] && [ -d "/Applications/MATLAB_$VER_NAME.app" ]; then
+    MATLABROOT="/Applications/MATLAB_$VER_NAME.app"
+# macOS: Try the default installation folder for Matlab Runtime
+elif [ $SYST == "maci64" ] && [ -d "/Applications/MATLAB/MATLAB_Runtime/$VER_NAME" ]; then
+    MATLABROOT="/Applications/MATLAB/MATLAB_Runtime/$VER_NAME"
+# Linux: Try the default installation folder for Matlab
+elif ([ $SYST == "glnx86" ] || [ $SYST == "glnxa64" ]) && [ -d "/usr/local/MATLAB/$VER_NAME" ]; then
+    MATLABROOT="/usr/local/MATLAB/$VER_NAME"
+# Linux: Try the default installation folder for Matlab Runtime
+elif ([ $SYST == "glnx86" ] || [ $SYST == "glnxa64" ]) && [ -d "/usr/local/MATLAB/MATLAB_Runtime/$VER_NAME" ]; then
+    MATLABROOT="/usr/local/MATLAB/MATLAB_Runtime/$VER_NAME"
 # Run the java file selector
 else
-    java -classpath "$JAR_FILE" org.brainstorm.file.SelectMcr$VER_NAME
+    java -classpath "$JAR_FILE" org.brainstorm.file.SelectMcr$VER_YEAR_VERSION
     # Read again the folder from the file
     if [ -f $MFILE ]; then
         MATLABROOT=$(<$MFILE)
@@ -73,17 +80,16 @@ if [ -z "$MATLABROOT" ]; then
     echo "USAGE: brainstorm3.command <MATLABROOT>"
 	echo "       brainstorm3.command <MATLABROOT> <script.m> <arguments>"
     echo " "
-    echo "MATLABROOT is the installation folder of the Runtime $VER_NUMBER (R$VER_NAME)"
-    echo "The Matlab Runtime $VER_NUMBER is the library needed to"
+    echo "MATLABROOT is the installation folder of the Runtime ($VER_NAME)"
+    echo "The Matlab Runtime $VER_NAME is the library needed to"
     echo "run executables compiled with Matlab $VER_NAME."
     echo " "
-    echo "Examples:"
-    echo "    Linux:  /usr/local/MATLAB_Runtime/v$VER_DIR"
-    echo "    Linux:  $HOME/MATLAB_Runtime_$VER_NAME"
-    echo "    MacOSX: /Applications/MATLAB/MATLAB_Runtime/v$VER_DIR"
+    echo "Default Matlab Runtime installation folders:"
+    echo "    Linux: /usr/local/MATLAB_Runtime/$VER_NAME"
+    echo "    macOS: /Applications/MATLAB/MATLAB_Runtime/v$VER_NAME"
     echo " "
     echo "MATLABROOT has to be specified only at the first call,"
-    echo "then it is saved in the file ~/.brainstorm/MATLABROOT$VER_DIR.txt"
+    echo "then it is saved in the file ~/.brainstorm/MATLABROOT_$VER_NAME.txt"
     echo " "
     exit 1
 # If folder not a valid Matlab root path
@@ -110,6 +116,9 @@ fi
 if [ ! -d "$MDIR" ]; then
     mkdir $MDIR
 fi
+# Matlab path found
+echo "Matlab $VER_NAME found:"
+echo "$MATLABROOT"
 # Save Matlab path in user folder
 echo "$MATLABROOT" > $MFILE
 
@@ -119,10 +128,10 @@ export JVM_DIR=$MATLABROOT/sys/java/jre/$SYST/jre
 export JAVA_EXE=$JVM_DIR/bin/java
 
 ##########################################################################
-# Setting library path for MACOSX
+# Setting library path for macOS
 if [ $SYST == "maci64" ]; then
     export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$MATLABROOT/runtime/maci64:$MATLABROOT/sys/os/maci64:$MATLABROOT/bin/maci64
-# Setting library path for LINUX
+# Setting library path for Linux
 else
     export PATH=$PATH:$MATLABROOT/runtime/$SYST
     JAVA_SUBDIR=$(find $MATLABROOT/sys/java/jre -type d | tr '\n' ':') 
@@ -144,7 +153,7 @@ echo " "
 # Run Brainstorm
 "$JAVA_EXE" -jar "$JAR_FILE" "${@:2}"
 
-# Force shell death on MacOSX
+# Force shell death on macOS
 if [ $SYST == "maci64" ]; then
     exit 0
 fi

diff --git a/brainstorm.m b/brainstorm.m
@@ -102,6 +102,9 @@
     javaaddpath(BstJar);
 end
 
+% Default anatomy template
+TemplateName = 'ICBM152_2023b';
+
 % Default action : start
 if (nargin == 0)
     action = 'start';
@@ -120,17 +123,17 @@
 switch action
     case 'start'
         bst_set_path(BrainstormHomeDir);
-        bst_startup(BrainstormHomeDir, 1, BrainstormDbDir);
+        bst_startup(BrainstormHomeDir, 1, BrainstormDbDir, TemplateName);
     case 'nogui'
         bst_set_path(BrainstormHomeDir);
-        bst_startup(BrainstormHomeDir, 0, BrainstormDbDir);
+        bst_startup(BrainstormHomeDir, 0, BrainstormDbDir, TemplateName);
     case 'server'
         bst_set_path(BrainstormHomeDir);
-        bst_startup(BrainstormHomeDir, -1, BrainstormDbDir);
+        bst_startup(BrainstormHomeDir, -1, BrainstormDbDir, TemplateName);
     case 'autopilot'
         if ~isappdata(0, 'BrainstormRunning')
             bst_set_path(BrainstormHomeDir);
-            bst_startup(BrainstormHomeDir, 2, BrainstormDbDir);
+            bst_startup(BrainstormHomeDir, 2, BrainstormDbDir, TemplateName);
         end
         res = bst_autopilot(varargin{2:end});
     case 'digitize'
@@ -211,7 +214,7 @@
         % Runs Brainstorm normally (asks for brainstorm_db)
         if ~isappdata(0, 'BrainstormRunning')
             bst_set_path(BrainstormHomeDir);
-            bst_startup(BrainstormHomeDir, 1, BrainstormDbDir);
+            bst_startup(BrainstormHomeDir, 1, BrainstormDbDir, TemplateName);
         end
         % Message
         java_dialog('msgbox', 'Brainstorm will now download additional files needed for the workshop.', 'Workshop');

diff --git a/deploy/bst_compile.m b/deploy/bst_compile.m
@@ -52,10 +52,26 @@ function bst_compile(isPlugs)
     error('You must install the toolboxes "Matlab Compiler" and "Matlab Compiler SDK" to run this function.');
 end
 % Start brainstorm without the GUI
-isNogui = ~brainstorm('status');
-if isNogui
+wasBstRunning = brainstorm('status');
+if ~wasBstRunning
     brainstorm nogui
 end
+isGUI = bst_get('isGUI');
+% Delete current default anatomy and download it
+templateDir = bst_fullfile(bst_get('BrainstormHomeDir'), 'defaults', 'anatomy');
+if exist(templateDir, 'dir')
+    brainstorm stop
+    try
+        rmdir(templateDir, 's');
+    catch
+        disp(['COMPILE> Error: Could not delete folder: ' templateDir]);
+    end
+    if isGUI
+        brainstorm start
+    else
+        brainstorm nogui
+    end
+end
 % Remove .brainstorm from the path
 rmpath(bst_get('UserMexDir'));
 rmpath(bst_get('UserProcessDir'));
@@ -258,13 +274,15 @@ function bst_compile(isPlugs)
     delete(bstJar);
 end
 if ispc
-    cmdSeparator = '&';
+    cdCall = 'cd /d';
+    cmdSeparator = '&&';
     jarExePath = '\bin\jar.exe'; 
-else   
+else
+    cdCall = 'cd';
     cmdSeparator = ';';
     jarExePath = '/bin/jar'; 
 end
-system(['cd "' jarDir '" ' cmdSeparator ' "' JdkDir, jarExePath '" cmf manifest.txt "' bstJar '" bst_javabuilder_' ReleaseName(2:end) ' org com']);
+system([cdCall ' "' jarDir '" ' cmdSeparator ' "' JdkDir, jarExePath '" cmf manifest.txt "' bstJar '" bst_javabuilder_' ReleaseName(2:end) ' org com']);