[INFRA] update miss hit config

.github/workflows/miss_hit.yml

@@ -28,12 +28,16 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install miss_hit
+        pip3 install -r requirements.txt
 
-    - name: Miss_hit code quality
+    - name: MISS_HIT Code style
       run: |
-        mh_metric . --ci
+        mh_style --process-slx
 
-    - name: Miss_hit code style
+    - name: MISS_HIT Metrics
       run: |
-        mh_style .
+        mh_metric --ci
+
+    - name: MISS_HIT Bug finder
+      run: |
+        mh_lint

demos/sourceDataProcessing/batchSource.m

@@ -21,4 +21,4 @@
 % defaceAnat(optSource); COMING SOON
 
 % GZip the volumes in a raw folder
-bidsGZipRawFolder(optSource, 0)
+bidsGZipRawFolder(optSource, 0);

demos/sourceDataProcessing/getOptionSource.m

@@ -17,7 +17,7 @@
 
   % Set the folder where sequences folders exist
   optSource.sourceDir = '/Users/barilari/Desktop/DICOM_UCL_leuven/renamed/sub-pilot001/ses-002/MRI';
-  
+
   optSource.dataDir = '/Users/barilari/Desktop/DICOM_UCL_leuven/raw';
 
   % List of the sequences that you want to skip (folder name pattern)

demos/spm_face_rep/face_rep_convert2BIDS.m

@@ -53,7 +53,7 @@ function face_rep_convert2BIDS()
                   ['sub-01_task-' strrep(task_name, ' ', '') '_bold.mat']));
 
   %% And everything else
-  create_events_tsv_file(WD, task_name, repetition_time)
+  create_events_tsv_file(WD, task_name, repetition_time);
   create_readme(WD);
   create_changelog(WD);
   create_datasetdescription(WD, opt);
@@ -62,7 +62,7 @@ function face_rep_convert2BIDS()
 end
 
 function create_events_tsv_file(WD, task_name, repetition_time)
-    
+
   % TODO
   % add the lag between presentations of each item necessary for the parametric
   % analysis.
@@ -86,7 +86,7 @@ function create_events_tsv_file(WD, task_name, repetition_time)
   [onset_column, idx] = sort(onset_column);
   duration_column = duration_column(idx);
   trial_type_column = trial_type_column(idx, :);
-  
+
   onset_column = repetition_time * onset_column;
 
   tsv_content = struct( ...

demos/spm_face_rep/face_rep_run.m

@@ -69,5 +69,5 @@
 bidsFFX('specifyAndEstimate', opt, FWHM);
 bidsFFX('contrasts', opt, FWHM);
 
-%TODO
+% TODO
 bidsResults(opt, FWHM);

requirements.txt

@@ -2,4 +2,4 @@ Sphinx
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
 sphinx_rtd_theme
-miss_hit
+miss_hit==0.9.15

src/QA/anatomicalQA.m

@@ -11,9 +11,9 @@ function anatomicalQA(opt)
   % :param opt: Options chosen for the analysis. See ``checkOptions()``.
   % :type opt: structure
   %
-  
+
   if isOctave()
-    warning('\nanatomicalQA is not yet supported on Octave. This step will be skipped.')
+    warning('\nanatomicalQA is not yet supported on Octave. This step will be skipped.');
   end
 
   % if input has no opt, load the opt.mat file

src/QA/functionalQA.m

@@ -25,9 +25,9 @@ function functionalQA(opt)
   %     resliced to the dimension of the functional with ``bidsResliceTpmToFunc()``
 
   if isOctave()
-    warning('\nfunctionalQA is not yet supported on Octave. This step will be skipped.')
+    warning('\nfunctionalQA is not yet supported on Octave. This step will be skipped.');
   end
-  
+
   % if input has no opt, load the opt.mat file
   if nargin < 1
     opt = [];
@@ -123,10 +123,10 @@ function functionalQA(opt)
           createDataDictionary(subFuncDataDir, fileName, size(confounds, 2));
 
           % create carpet plot
-          
-          % horrible hack to prevent the "abrupt" way spmup_volumecorr crashes 
+
+          % horrible hack to prevent the "abrupt" way spmup_volumecorr crashes
           % if nansum is not there
-          if exist('nansum','file') == 2 
+          if exist('nansum', 'file') == 2
             spmup_timeseriesplot(funcImage, TPMs(1, :), TPMs(2, :), TPMs(3, :), ...
                                  'motion', 'on', ...
                                  'nuisances', 'on', ...

src/batches/setBatchComputeVDM.m

@@ -10,10 +10,10 @@
   %
   % :param matlabbatch: list of SPM batches
   % :type matlabbatch: structure
-  % :param fmapType: 
-  % :type fmapType: 
+  % :param fmapType:
+  % :type fmapType:
   % :param refImage: Reference image
-  % :type refImage: 
+  % :type refImage:
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
   %

src/batches/setBatchReslice.m

@@ -19,7 +19,6 @@
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
   %
 
-
   printBatchName('reslicing');
 
   if ischar(referenceImg)

src/batches/setBatchSaveCoregistrationMatrix.m

@@ -8,16 +8,16 @@
   %
   %   matlabbatch = setBatchSaveCoregistrationMatrix(matlabbatch, BIDS, subID, opt)
   %
-  % :param matlabbatch: 
+  % :param matlabbatch:
   % :type matlabbatch: structure
   % :param BIDS: BIDS layout returned by ``getData``.
   % :type BIDS: structure
-  % :param subID: 
+  % :param subID:
   % :type subID:
-  % :param opt: 
+  % :param opt:
   % :type opt: Options chosen for the analysis. See ``checkOptions()``.
-  % 
-  % :returns: - :matlabbatch: 
+  %
+  % :returns: - :matlabbatch:
   %
 
   printBatchName('saving coregistration matrix');

src/batches/setBatchSmoothConImages.m

@@ -8,15 +8,15 @@
   %
   %   matlabbatch = setBatchSmoothConImages(group, funcFWHM, conFWHM, opt)
   %
-  % :param group: 
-  % :type group: 
-  % :param funcFWHM: 
+  % :param group:
+  % :type group:
+  % :param funcFWHM:
   % :type funcFWHM:
-  % :param conFWHM: 
+  % :param conFWHM:
   % :type conFWHM:
   % :param opt: Options chosen for the analysis. See ``checkOptions()``.
-  % :type opt:  
-  % 
+  % :type opt:
+  %
   % :returns: - :matlabbatch:
   %
 

src/defaults/createDefaultModel.m

@@ -46,7 +46,7 @@
   %   opt = checkOptions(opt);
   %
   %   [~, opt, BIDS] = getData(opt);
-  % 
+  %
   %   createDefaultModel(BIDS, opt);
   %
 

src/defaults/createEmptyModel.m

@@ -2,8 +2,8 @@
 
 function content = createEmptyModel()
   %
-  % Creates the content of a basic model.json file for GLM analysis with 
-  % some default options like high pass filter cut-off 
+  % Creates the content of a basic model.json file for GLM analysis with
+  % some default options like high pass filter cut-off
   % and the type of autocorrelation correction.
   %
   % USAGE::

src/fieldmaps/getMetadataFromIntendedForFunc.m

@@ -39,12 +39,12 @@
     fragments = bids.internal.parse_filename(filename);
 
     funcMetadata = bids.query(BIDS, 'metadata', ...
-                            'modality', 'func', ...
-                            'type', fragments.type, ...
-                            'sub', fragments.sub, ...
-                            'ses', fragments.ses, ...
-                            'run', fragments.run, ...
-                            'acq', fragments.acq);
+                              'modality', 'func', ...
+                              'type', fragments.type, ...
+                              'sub', fragments.sub, ...
+                              'ses', fragments.ses, ...
+                              'run', fragments.run, ...
+                              'acq', fragments.acq);
 
   end
 

src/fieldmaps/getVdmFile.m

@@ -27,8 +27,8 @@
   end
 
   modalities = bids.query(BIDS, 'modalities', ...
-                        'sub', fragments.sub, ...
-                        'ses', fragments.ses);
+                          'sub', fragments.sub, ...
+                          'ses', fragments.ses);
 
   if opt.useFieldmaps && any(ismember('fmap', modalities))
     % We loop through the field maps and find the one that is intended for this
@@ -37,14 +37,14 @@
     % We break the loop when the file has been found
 
     fmapFiles = bids.query(BIDS, 'data', ...
-                         'modality', 'fmap', ...
-                         'sub', fragments.sub, ...
-                         'ses', fragments.ses);
+                           'modality', 'fmap', ...
+                           'sub', fragments.sub, ...
+                           'ses', fragments.ses);
 
     fmapMetadata = bids.query(BIDS, 'metadata', ...
-                            'modality', 'fmap', ...
-                            'sub', fragments.sub, ...
-                            'ses', fragments.ses);
+                              'modality', 'fmap', ...
+                              'sub', fragments.sub, ...
+                              'ses', fragments.ses);
 
     for  iFile = 1:size(fmapFiles, 1)
 

src/getData.m

@@ -135,13 +135,13 @@
   switch type
     case 'bold'
       metadata = bids.query(BIDS, 'metadata', ...
-                          'task', opt.taskName, ...
-                          'sub', subjects{1}, ...
-                          'type', type);
+                            'task', opt.taskName, ...
+                            'sub', subjects{1}, ...
+                            'type', type);
     case 'T1w'
       metadata = bids.query(BIDS, 'metadata', ...
-                          'sub', subjects{1}, ...
-                          'type', type);
+                            'sub', subjects{1}, ...
+                            'type', type);
   end
 
   if iscell(metadata)

src/getInfo.m

@@ -41,8 +41,8 @@
     case 'sessions'
 
       sessions = bids.query(BIDS, 'sessions', ...
-                          'sub', subID, ...
-                          'task', opt.taskName);
+                            'sub', subID, ...
+                            'task', opt.taskName);
       nbSessions = size(sessions, 2);
       if nbSessions == 0
         nbSessions = 1;
@@ -56,10 +56,10 @@
       session = varargin{1};
 
       runs = bids.query(BIDS, 'runs', ...
-                      'sub', subID, ...
-                      'task', opt.taskName, ...
-                      'ses', session, ...
-                      'type', 'bold');
+                        'sub', subID, ...
+                        'task', opt.taskName, ...
+                        'ses', session, ...
+                        'type', 'bold');
       nbRuns = size(runs, 2);     % Get the number of runs
 
       if nbRuns == 0
@@ -74,11 +74,11 @@
       [session, run, type] = deal(varargin{:});
 
       varargout = bids.query(BIDS, 'data', ...
-                           'sub', subID, ...
-                           'run', run, ...
-                           'ses', session, ...
-                           'task', opt.taskName, ...
-                           'type', type);
+                             'sub', subID, ...
+                             'run', run, ...
+                             'ses', session, ...
+                             'task', opt.taskName, ...
+                             'type', type);
 
     otherwise
       error('Not sure what info you want me to get.');

src/setDerivativesDir.m

@@ -13,7 +13,7 @@
   % :param opt: Options chosen for the analysis. See ``checkOptions()``.
   % :type opt: structure
   %
-  % :returns: 
+  % :returns:
   %   - :opt: structure or json filename containing the options. See
   %           ``checkOptions()`` and ``loadAndCheckOptions()``.
   %

src/subject_level/convertOnsetTsvToMat.m

@@ -38,10 +38,10 @@
   end
 
   % assign all the tsv information to a variable called conds.
-  conds = t.trial_type; 
+  conds = t.trial_type;
 
-  % identify where the conditions to include that are specificed 
-  % in the run step of the model file  
+  % identify where the conditions to include that are specificed
+  % in the run step of the model file
   model = spm_jsonread(opt.model.file);
 
   for runIdx = 1:numel(model.Steps)

src/utils/validationInputFile.m

@@ -18,29 +18,29 @@
   % :param dir: Directory where the search will be conducted.
   % :type dir: string
   % :param fileName: file name pattern. Can be a regular expression except for
-  %                  the starting ``^`` and ending ``$``. For example: 
-  %                  ``'sub-.*_ses-.*_task-.*_bold.nii'``. 
+  %                  the starting ``^`` and ending ``$``. For example:
+  %                  ``'sub-.*_ses-.*_task-.*_bold.nii'``.
   % :type fileName: string
   % :param prefix: prefix to be added to the filename pattern. This can also be
   %                a regular expression (ish). For example ,f looking for the files that
   %                start with ``c1`` or ``c2`` or ``c3``, the prefix can be
   %                ``c[123]``.
   % :type prefix: string
   %
-  % :returns: 
+  % :returns:
   %
   %           :files: (string array) returns the fullpath file list of all the
   %                   files matching the required pattern.
-  %           
-  % 
+  %
+  %
   % See also: ``spm_select``.
   %
   %
   % Example:
-  % % 
+  % %
   % % tissueProbaMaps = validationInputFile(anatDataDir, anatImage, 'c[12]');
   %
-  % 
+  %
 
   if nargin < 3
     prefix = '';

src/workflows/bidsFFX.m

@@ -33,7 +33,7 @@ function bidsFFX(action, opt, funcFWHM)
   end
 
   [BIDS, opt, group] = setUpWorkflow(opt, 'subject level GLM');
-  
+
   if isempty(opt.model.file)
     opt = createDefaultModel(BIDS, opt);
   end