Merge branch 'main' into doc

Author: Remi-Gau

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -95,6 +95,10 @@ body:
          - `git rev-parse --abbrev-ref HEAD`
          - `git rev-parse --short HEAD`
 
+        In the MATLAB command line
+
+         - `[branch, commit] = getRepoInfo()`
+
       render: markdown
       value: |
         - main 29b689dd

src/infra/getEnvInfo.m

@@ -17,8 +17,12 @@
     opt.dryRun = false;
   end
 
+  [branch, commit] = getRepoInfo();
+
   generatedBy(1).name = 'CPP SPM';
   generatedBy(1).Version =  getVersion();
+  generatedBy(1).Branch = branch;
+  generatedBy(1).Commit = commit;
   generatedBy(1).Description = '';
   generatedBy(1).CodeURL = returnRepoURL();
   generatedBy(1).DOI = 'https://doi.org/10.5281/zenodo.3554331';

src/infra/getRepoInfo.m

@@ -0,0 +1,34 @@
+function [branch, commit] = getRepoInfo(rootDir)
+  %
+  % Return the branch and commit shasum
+  %
+  % USAGE::
+  %
+  %   [branch, commit] = getRepoInfo()
+  %
+  % (C) Copyright 2022 CPP_SPM developers
+
+  if nargin < 1
+    rootDir = returnRootDir;
+  end
+
+  WD = pwd;
+  cd(rootDir);
+
+  try
+    [~, branch] = system('git rev-parse --abbrev-ref HEAD');
+    branch = strrep(branch, newline, '');
+  catch
+    branch = 'unknown';
+  end
+
+  try
+    [~, commit] = system('git rev-parse --short HEAD');
+    commit = strrep(commit, newline, '');
+  catch
+    commit = 'unknown';
+  end
+
+  cd(WD);
+
+end

src/messages/errorHandling.m

@@ -5,13 +5,17 @@ function errorHandling(varargin)
   %  errorHandling(functionName, id, msg, tolerant, verbose)
   %
   % :param functionName:
-  % :type functionName: string
+  % :type functionName: char
+  %
   % :param id: Error or warning id
-  % :type id: string
+  % :type id: char
+  %
   % :param msg: Message to print
-  % :type msg: string
+  % :type msg: char
+  %
   % :param tolerant: If set to ``true`` errors are converted into warnings
   % :type tolerant: boolean
+  %
   % :param verbose: If set to ``0`` or ``false`` this will silence any warning
   % :type verbose: boolean
   %

src/utils/designMatrixFigureName.m

@@ -32,8 +32,7 @@
   nameStructure = struct( ...
                          'suffix', 'designmatrix', ...
                          'ext', '.png', ...
-                         'entities', struct( ...
-                                            'sub', args.Results.subLabel, ...
+                         'entities', struct('sub', args.Results.subLabel, ...
                                             'task', strjoin(args.Results.opt.taskName, ''), ...
                                             'space', args.Results.opt.space));
   nameStructure.entities.desc = args.Results.desc;

src/utils/renamePng.m

@@ -1,7 +1,9 @@
-function renamePng(directory)
+function renamePng(directory, prefix)
   %
-  % removes the _XXX suffix before the PNG extension in files generated by SPM
-  % in a directory
+  % Removes the _XXX suffix before the PNG extension
+  % in files generated by SPM in a directory
+  %
+  % Wil overwrite any file that already exists
   %
   % USAGE::
   %
@@ -10,13 +12,37 @@ function renamePng(directory)
   %
   % (C) Copyright 2021 CPP_SPM developers
 
-  pngFiles = spm_select('FPList', directory, '^sub-.*[0-9].png$');
+  if nargin < 1
+    directory = pwd;
+  end
+  if nargin < 2
+    prefix = 'sub';
+  end
+
+  pngFiles = spm_select('FPList', directory, ['^' prefix '-.*[0-9].png$']);
 
   for iFile = 1:size(pngFiles, 1)
+
     source = deblank(pngFiles(iFile, :));
+
     basename = spm_file(source, 'basename');
     target = spm_file(source, 'basename', basename(1:end - 4));
-    movefile(source, target);
+
+    if exist(target, 'file')
+      delete(target);
+    end
+
+    try
+      movefile(source, target);
+
+    catch
+      tolerant = true;
+      verbosity = 2;
+      msg = sprintf('Could not move file %s to %s', source, target);
+      errorHandling(mfilename(), 'cannotMoveFile', msg, tolerant, verbosity);
+
+    end
+
   end
 
 end

src/workflows/stats/bidsRFX.m

@@ -127,25 +127,13 @@
                                             contrastsList, ...
                                             groups);
 
-        % make sure there is no SPM.mat in the target dir
-        %
-        % folders where the model is to be specified have already been emptied
-        % if at this stage they are not, something has gone horribly wrong.
-        %
-        % also if we continued SPM would ask us to manually confirm the over-write
-        % by clicking buttons and no one has got time this
-        for j = 1:numel(matlabbatch)
-
-          if isfield(matlabbatch{j}.spm, 'stats') && ...
-              isfield(matlabbatch{j}.spm.stats, 'fmri_est')
-            if exist(matlabbatch{j}.spm.stats.fmri_est.spmmat{1}, 'file')
-              error('PANIC! About to overwrite a model. That should not happen');
-            end
-          end
+        checkDirIsEmpty(matlabbatch);
 
-        end
+        status = saveAndRunWorkflow(matlabbatch, ...
+                                    'group_level_model_specification_estimation', ...
+                                    opt);
 
-        saveAndRunWorkflow(matlabbatch, 'group_level_model_specification_estimation', opt);
+        renameDesignMatrixFigure(status, matlabbatch);
 
       end
 
@@ -163,6 +151,7 @@
     opt.pipeline.type = 'groupStats';
     initBids(opt, 'description', description, 'force', false);
   end
+
 end
 
 function checks(opt)
@@ -172,3 +161,41 @@ function checks(opt)
     errorHandling(mfilename(), 'tooManySpaces', msg, false, opt.verbosity);
   end
 end
+
+function checkDirIsEmpty(matlabbatch)
+
+  % make sure there is no SPM.mat in the target dir
+  %
+  % folders where the model is to be specified have already been emptied
+  % if at this stage they are not, something has gone horribly wrong.
+  %
+  % also if we continued SPM would ask us to manually confirm the over-write
+  % by clicking buttons and no one has got time this
+  for i = 1:numel(matlabbatch)
+
+    if isfield(matlabbatch{i}.spm, 'stats') && ...
+        isfield(matlabbatch{i}.spm.stats, 'fmri_est')
+      if exist(matlabbatch{i}.spm.stats.fmri_est.spmmat{1}, 'file')
+        error('PANIC! About to overwrite a model. That should not happen');
+      end
+    end
+
+  end
+
+end
+
+function renameDesignMatrixFigure(status, matlabbatch)
+
+  if ~status
+    return
+  end
+
+  for j = 1:numel(matlabbatch)
+    if isfield(matlabbatch{j}.spm, 'stats') && ...
+        isfield(matlabbatch{j}.spm.stats, 'fmri_est')
+      directory = fileparts(matlabbatch{j}.spm.stats.fmri_est.spmmat{1});
+      renamePng(directory, 'task');
+    end
+  end
+
+end

src/workflows/stats/bidsResults.m

@@ -440,7 +440,7 @@
 
   matlabbatch = setBatchGroupLevelResults(matlabbatch, opt, result);
 
-  matlabbatch = setBatchPrintFigure(matlabbatch, opt, fullfile(result.dir, figureName(opt)));
+  %   matlabbatch = setBatchPrintFigure(matlabbatch, opt, fullfile(result.dir, figureName(opt)));
 
   results{end + 1} = result;