show options in debug mode

cpp-lln-lab · Jul 7, 2024 · 1e4f4c9 · 1e4f4c9
1 parent 1546e50
commit 1e4f4c9
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Showing 6 changed files with 23 additions and 10 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -101,7 +101,7 @@ jobs:
                           --action default_model \
                           --task balloonanalogrisktask \
                           --space MNI152NLin2009cAsym \
-                          --verbosity 2
+                          --verbosity 3
 
                     cat ${HOME}/outputs/ds000001/derivatives/models/*.json
 
@@ -120,7 +120,7 @@ jobs:
                           --action default_model \
                           --task balloonanalogrisktask \
                           --space MNI152NLin2009cAsym \
-                          --verbosity 2
+                          --verbosity 3
 
                     cat ${HOME}/outputs/ds000001/derivatives/models/*.json
 
@@ -152,7 +152,7 @@ jobs:
                           --participant_label 01 02 \
                           --space MNI152NLin2009cAsym \
                           --fwhm 8 \
-                          --verbosity 2
+                          --verbosity 3
 
         # needed to access the model
         -   checkout
@@ -179,7 +179,7 @@ jobs:
                           --skip_validation \
                           --fwhm 0 \
                           --participant_label 01 02 \
-                          --verbosity 2 \
+                          --verbosity 3 \
                           --options /options/ds000001.json
 
         -   run:
@@ -201,7 +201,7 @@ jobs:
                           --space MNI152NLin2009cAsym \
                           --skip_validation \
                           --fwhm 0 \
-                          --verbosity 2 \
+                          --verbosity 3 \
                           --options /options/ds000001.json
 
     deploy:

diff --git a/bidspm.m b/bidspm.m
@@ -261,7 +261,7 @@ function updateMacstoolbox()
   end
 
   if exist(target_dir, 'dir') == 7
-    msg = sprintf('updating MACS toolbox: ');
+    msg = sprintf('updating MACS toolbox\n');
     fprintf(1, msg);
     [status, cmdout] = system(sprintf('git -C %s pull', target_dir));
     if status ~= 0

diff --git a/src/bidspm/matlab.py b/src/bidspm/matlab.py
@@ -2,12 +2,16 @@
 
 
 def matlab() -> str:
-    """Return the path to the Matlab executable.
+    r"""Return the path to the Matlab executable.
 
     Modify this value to match your Matlab installation.
 
     The MATLAB 'matlabroot' should tell you where MATLAB is installed.
 
     The 'matlab' executable is usually in the 'bin' subdirectory.
+
+    -   Windows: ``'C:\\Program Files\\MATLAB\\R20XXx\bin\\matlab.exe'``
+    -   Mac: ``'/Applications/Matlab_R20XXx.app/bin/matlab'``
+    -   Linux: ``'/usr/local/MATLAB/R20XXx/bin/matlab'``
     """
-    return "/usr/local/MATLAB/R2018a/ bin/matlab"
+    return "/usr/local/MATLAB/R2018a/bin/matlab"
diff --git a/src/bidspm/parsers.py b/src/bidspm/parsers.py
@@ -94,7 +94,7 @@ def common_parser() -> argparse.ArgumentParser:
         help="""
         Verbosity level.
         """,
-        choices=[0, 1, 2],
+        choices=[0, 1, 2, 3],
         default=2,
         type=int,
         nargs=1,

diff --git a/src/cli/getOptionsFromCliArgument.m b/src/cli/getOptionsFromCliArgument.m
@@ -74,6 +74,11 @@
     opt.toolbox.MACS.model.dir = args.Results.models_dir;
   end
 
+  if opt.verbosity > 3
+    unfold(opt);
+  end
+  unfold(opt);
+
 end
 
 function opt = optionsPreprocessing(opt, args, action)
@@ -147,10 +152,14 @@
 end
 
 function opt = getOptions(args)
+
   if isstruct(args.Results.options)
     opt = args.Results.options;
   elseif exist(args.Results.options, 'file') == 2
     opt = bids.util.jsondecode(args.Results.options);
+    opt = checkOptions(opt);
+    logger('INFO', ['options loaded from file:\n', args.Results.options], ...
+           'options', opt);
   end
   if isempty(opt)
     % set defaults

diff --git a/src/infra/checkToolbox.m b/src/infra/checkToolbox.m
@@ -100,7 +100,7 @@ function updateMacstoolbox()
   end
 
   if exist(target_dir, 'dir') == 7
-    msg = sprintf('updating MACS toolbox: ');
+    msg = sprintf('updating MACS toolbox\n');
     fprintf(1, msg);
     system(sprintf('git -C %s pull', ...
                    target_dir));