From 5c8fec5d404ad0c093adf08008b8fbd440c6acba Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 4 Apr 2024 12:00:34 +0200
Subject: [PATCH] [FIX] install MACS toobox during initialisation (#1203)

* copy macs tooolbox during init

* update changelog

* fix and refactor
---
 .github/workflows/run_tests_notebooks.yml |  3 ---
 .github/workflows/tests.yml               |  3 ---
 .github/workflows/tests_octave.yml        |  3 ---
 .github/workflows/tests_windows.yml       |  3 ---
 CHANGELOG.md                              |  1 +
 bidspm.m                                  | 19 +++++++++++++++++
 src/infra/checkToolbox.m                  | 25 ++++++++++++++++-------
 7 files changed, 38 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/run_tests_notebooks.yml b/.github/workflows/run_tests_notebooks.yml
index e1295b19c..8219d8c3a 100644
--- a/.github/workflows/run_tests_notebooks.yml
+++ b/.github/workflows/run_tests_notebooks.yml
@@ -45,9 +45,6 @@ jobs:
       run: |
         git clone https://github.com/spm/spm12.git --depth 1
 
-    - name: Copy Macs toolbox to SPM inputs_folder
-      run: cp -rv lib/MACS spm12/toolbox/MACS
-
     - name: Test notebooks
       uses: matlab-actions/run-command@v2.1.0
       with:
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 7349a3e40..43bc98f97 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -105,9 +105,6 @@ jobs:
       run: |
         git clone https://github.com/spm/spm12.git --depth 1
 
-    - name: Copy Macs toolbox to SPM inputs_folder
-      run: cp -rv lib/MACS spm12/toolbox/MACS
-
     - name: Get moae fmriprep data from OSF
       run: |
         mkdir -p demos/MoAE/inputs/
diff --git a/.github/workflows/tests_octave.yml b/.github/workflows/tests_octave.yml
index 26f029d2d..d918e3169 100644
--- a/.github/workflows/tests_octave.yml
+++ b/.github/workflows/tests_octave.yml
@@ -86,9 +86,6 @@ jobs:
       run: |
         git clone https://github.com/spm/spm12.git --depth 1
 
-    - name: Copy Macs toolbox to SPM inputs_folder
-      run: cp -rv lib/MACS spm12/toolbox/MACS
-
     - name: Get moae fmriprep data from OSF
       run: |
         mkdir -p demos/MoAE/inputs/
diff --git a/.github/workflows/tests_windows.yml b/.github/workflows/tests_windows.yml
index ba731d0c7..1d6affe54 100644
--- a/.github/workflows/tests_windows.yml
+++ b/.github/workflows/tests_windows.yml
@@ -84,9 +84,6 @@ jobs:
       run: |
         git clone https://github.com/spm/spm12.git --depth 1
 
-    - name: Copy Macs toolbox to SPM inputs_folder
-      run: Copy-Item -Recurse -Verbose -Path ".\lib\MACS" -Destination ".\spm12\toolbox\MACS"
-
     - name: Get moae fmriprep data from OSF
       run: |
         New-Item -ItemType Directory -Path ".\demos\MoAE\inputs\" -Force
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 697489ffb..5067496c7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -50,6 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation #1203 by @Remi-Gau
 * [FIX] save onsets.mat directly in subject stats folder #1187 by @Remi-Gau
 * [FIX] do not compute subject level contrast when running dataset level #1102 by @Remi-Gau
 * [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in #1099 by @Remi-Gau
diff --git a/bidspm.m b/bidspm.m
index 35c108f51..578dd5363 100644
--- a/bidspm.m
+++ b/bidspm.m
@@ -171,6 +171,9 @@ function initBidspm(dev)
                          fullfile(rootDir(), 'tests', 'utils'));
     end
 
+    % Make sure MACS toolbox used by SPM is the one from bidspm
+    installMacstoolbox();
+
     % for some reasons this folder was otherwise not added to the path in Octave
     BIDSPM_PATHS = cat(2, BIDSPM_PATHS, ...
                        pathSep, ...
@@ -256,6 +259,22 @@ function initBidspm(dev)
 
 end
 
+function installMacstoolbox()
+
+  SPM_DIR = spm('dir');
+  target_dir = fullfile(SPM_DIR, 'toolbox', 'MACS');
+  MACS_TOOLBOX_DIR = fullfile(rootDir(), 'lib', 'MACS');
+
+  msg = sprintf('installing MACS toolbox in:\n%s.\n\n', target_dir);
+  fprintf(1, msg);
+
+  if exist(target_dir, 'dir') == 7
+    rmdir(target_dir, 's');
+  end
+  mkdir(target_dir);
+  copyfile(MACS_TOOLBOX_DIR, target_dir);
+end
+
 function uninitBidspm()
   %
   % Removes the added folders from the path for a given session.
diff --git a/src/infra/checkToolbox.m b/src/infra/checkToolbox.m
index f54771c72..f513c265a 100644
--- a/src/infra/checkToolbox.m
+++ b/src/infra/checkToolbox.m
@@ -65,13 +65,7 @@
 
       if ~status && install
 
-        msg = sprintf('installing MACS toolbox in:\n%s.\n\n', ...
-                      fullfile(spm('dir'), 'toolbox', 'MACS'));
-        id = 'installingMacsToolbox';
-        logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
-
-        copyfile(fullfile(returnRootDir(), 'lib', 'MACS'), ...
-                 fullfile(spm('dir'), 'toolbox', 'MACS'));
+        installMacstoolbox(opt);
 
         status = checkToolbox(toolboxName);
 
@@ -94,3 +88,20 @@
   end
 
 end
+
+function installMacstoolbox(opt)
+  SPM_DIR = spm('dir');
+  MACS_TOOLBOX_DIR = fullfile(returnRootDir(), 'lib', 'MACS');
+
+  target_dir = fullfile(SPM_DIR, 'toolbox', 'MACS');
+
+  msg = sprintf('installing MACS toolbox in:\n%s.\n\n', target_dir);
+  id = 'installingMacsToolbox';
+  logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
+
+  if exist(target_dir, 'dir') == 7
+    rmdir(target_dir, 's');
+  end
+  mkdir(target_dir);
+  copyfile(MACS_TOOLBOX_DIR, target_dir);
+end