From b204b101ea612391c148eab80c7060fadb9d08b5 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 19 Jul 2020 23:39:32 +0200
Subject: [PATCH 1/3] apply mh_linter autofix

---
 checkCFG.m                  |  91 +++++-----
 createFilename.m            | 280 +++++++++++++++----------------
 miss_hit.cfg                |   3 +
 saveEventsFile.m            | 323 ++++++++++++++++++------------------
 tests/runtests.m            |  92 +++++-----
 tests/test_createFilename.m | 122 +++++++-------
 tests/test_saveEventsFile.m | 113 +++++++------
 userInputs.m                | 111 ++++++-------
 8 files changed, 565 insertions(+), 570 deletions(-)
 create mode 100644 miss_hit.cfg

diff --git a/checkCFG.m b/checkCFG.m
index c97834ce..59ea4d15 100644
--- a/checkCFG.m
+++ b/checkCFG.m
@@ -1,57 +1,56 @@
 function [expParameters, cfg] = checkCFG(cfg, expParameters)
-% check that we have all the fields that we need in the experiment
-% parameters
+    % check that we have all the fields that we need in the experiment
+    % parameters
 
-if ~isfield(expParameters, 'verbose') || isempty(expParameters.verbose)
-    expParameters.verbose = 0;
-end
+    if ~isfield(expParameters, 'verbose') || isempty(expParameters.verbose)
+        expParameters.verbose = 0;
+    end
 
-if ~isfield(expParameters, 'outputDir')
-    expParameters.outputDir = fullfile(...
-        fileparts(mfilename('fullpath')), ...
-        '..', ...
-        'output');
-end
+    if ~isfield(expParameters, 'outputDir')
+        expParameters.outputDir = fullfile( ...
+            fileparts(mfilename('fullpath')), ...
+            '..', ...
+            'output');
+    end
 
-% set empty values for a series of field if they have not been specified
-% 'ce'
-% 'dir'        For BIDS file naming: phase encoding direction of acquisition for fMRI
-% 'rec'        For BIDS file naming: reconstruction of fMRI images
-% 'echo'       For BIDS file naming: echo fMRI images
-% 'acq'        For BIDS file naming: acquisition of fMRI images
-% 'subjectGrp' in case no group was provided
-% 'sessionNb'  in case no session was provided
-
-fields2Check = { ...
-    'ce', ...
-    'dir', ...  
-    'rec', ...  
-    'echo', ... 
-    'acq', ...  
-    'subjectGrp', ... 
-    'sessionNb'};
-
-for iField = 1:numel(fields2Check)
-    if ~isfield(expParameters, fields2Check{iField})
-        expParameters = setfield(expParameters, fields2Check{iField}, []); %#ok<SFLD>
+    % set empty values for a series of field if they have not been specified
+    % 'ce'
+    % 'dir'        For BIDS file naming: phase encoding direction of acquisition for fMRI
+    % 'rec'        For BIDS file naming: reconstruction of fMRI images
+    % 'echo'       For BIDS file naming: echo fMRI images
+    % 'acq'        For BIDS file naming: acquisition of fMRI images
+    % 'subjectGrp' in case no group was provided
+    % 'sessionNb'  in case no session was provided
+
+    fields2Check = { ...
+        'ce', ...
+        'dir', ...
+        'rec', ...
+        'echo', ...
+        'acq', ...
+        'subjectGrp', ...
+        'sessionNb'};
+
+    for iField = 1:numel(fields2Check)
+        if ~isfield(expParameters, fields2Check{iField})
+            expParameters = setfield(expParameters, fields2Check{iField}, []); %#ok<SFLD>
+        end
     end
-end
 
-% set false value for a series of field if they have not been specified
-fields2CheckFalse = { ...
-    'eyeTracker'
-    };
+    % set false value for a series of field if they have not been specified
+    fields2CheckFalse = { ...
+        'eyeTracker'
+        };
 
-for iField = 1:numel(fields2CheckFalse)
-    if ~isfield(cfg, fields2CheckFalse{iField})
-        cfg = setfield(cfg, fields2CheckFalse{iField}, false); %#ok<SFLD>
+    for iField = 1:numel(fields2CheckFalse)
+        if ~isfield(cfg, fields2CheckFalse{iField})
+            cfg = setfield(cfg, fields2CheckFalse{iField}, false); %#ok<SFLD>
+        end
     end
-end
-
-% other defaults
-if ~isfield(expParameters, 'askGrpSess')
-    expParameters.askGrpSess = [true true];
-end
 
+    % other defaults
+    if ~isfield(expParameters, 'askGrpSess')
+        expParameters.askGrpSess = [true true];
+    end
 
 end
diff --git a/createFilename.m b/createFilename.m
index 0ef65a67..ab9f4eda 100644
--- a/createFilename.m
+++ b/createFilename.m
@@ -1,159 +1,153 @@
 function expParameters = createFilename(cfg, expParameters)
-% create the BIDS compliant directories and filenames for the behavioral output for this subject /
-% session / run using the information from cfg and expParameters.
-% Will also create the right filename for the eyetracking data file.
-%
-% For the moment the date of acquisition is appended to the filename
-%
-% can work for behavioral experiment if cfg.device is set to 'PC'
-% can work for fMRI experiment if cfg.device is set to 'scanner'
-% can work for simple eyetracking data if cfg.eyeTracker is set to 1
-%
-% BOLD
-% sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
-%
-% iEEG
-% sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
-%
-% EEG
-% sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
-%
-% EYETRACKER
-% sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>
-%
-%
-% See test_createFilename in the test folder for more details on how to use it.
-
-zeroPadding = 3;
-pattern = ['%0' num2str(zeroPadding) '.0f'];
-
-dateFormat = 'yyyymmdd_HHMM';
-
-% Setting some defaults: no need to change things here
-[expParameters, cfg] = checkCFG(cfg,expParameters);
-
-% extract input
-subjectGrp = expParameters.subjectGrp;
-subjectNb = expParameters.subjectNb;
-sessionNb = expParameters.sessionNb;
-runNb = expParameters.runNb;
-
-expParameters.date = datestr(now, dateFormat);
-
-% output dir
-expParameters.outputDir = fullfile (...
-    expParameters.outputDir, ...
-    'source', ...
-    ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
-    ['ses-', sprintf(pattern, sessionNb)]);
-
-% create base filename
-expParameters.fileName.base = ...
-    ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
-    '_ses-', sprintf(pattern, sessionNb) , ...
-    '_task-', expParameters.task];
-
-runSuffix = ['_run-' sprintf(pattern, runNb)];
-
-
-switch lower(cfg.device)
-    case 'pc'
-        modality = 'beh';
-    case 'scanner'
-        modality = 'func';
-    otherwise
-        modality = 'beh';
-end
+    % create the BIDS compliant directories and filenames for the behavioral output for this subject /
+    % session / run using the information from cfg and expParameters.
+    % Will also create the right filename for the eyetracking data file.
+    %
+    % For the moment the date of acquisition is appended to the filename
+    %
+    % can work for behavioral experiment if cfg.device is set to 'PC'
+    % can work for fMRI experiment if cfg.device is set to 'scanner'
+    % can work for simple eyetracking data if cfg.eyeTracker is set to 1
+    %
+    % BOLD
+    % sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
+    %
+    % iEEG
+    % sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
+    %
+    % EEG
+    % sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
+    %
+    % EYETRACKER
+    % sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>
+    %
+    %
+    % See test_createFilename in the test folder for more details on how to use it.
+
+    zeroPadding = 3;
+    pattern = ['%0' num2str(zeroPadding) '.0f'];
+
+    dateFormat = 'yyyymmdd_HHMM';
+
+    % Setting some defaults: no need to change things here
+    [expParameters, cfg] = checkCFG(cfg, expParameters);
+
+    % extract input
+    subjectGrp = expParameters.subjectGrp;
+    subjectNb = expParameters.subjectNb;
+    sessionNb = expParameters.sessionNb;
+    runNb = expParameters.runNb;
+
+    expParameters.date = datestr(now, dateFormat);
+
+    % output dir
+    expParameters.outputDir = fullfile ( ...
+        expParameters.outputDir, ...
+        'source', ...
+        ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
+        ['ses-', sprintf(pattern, sessionNb)]);
+
+    % create base filename
+    expParameters.fileName.base = ...
+        ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
+        '_ses-', sprintf(pattern, sessionNb), ...
+        '_task-', expParameters.task];
+
+    runSuffix = ['_run-' sprintf(pattern, runNb)];
+
+    switch lower(cfg.device)
+        case 'pc'
+            modality = 'beh';
+        case 'scanner'
+            modality = 'func';
+        otherwise
+            modality = 'beh';
+    end
 
-expParameters.modality = modality;
-
-
-% set values for the suffixes for the different fields in the BIDS name
-fields2Check = { ...
-    'ce', ...
-    'dir', ...  % For BIDS file naming: phase encoding direction of acquisition for fMRI
-    'rec', ...  % For BIDS file naming: reconstruction of fMRI images
-    'echo', ... % For BIDS file naming: echo fMRI images
-    'acq'       % For BIDS file naming: acquisition of fMRI images
-    };
-
-for iField = 1:numel(fields2Check)
-    if isempty (getfield(expParameters, fields2Check{iField}) ) %#ok<*GFLD>
-        expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
-            ''); %#ok<*SFLD>
-    else
-        expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
-            ['_' fields2Check{iField} '-' getfield(expParameters, fields2Check{iField})]);
+    expParameters.modality = modality;
+
+    % set values for the suffixes for the different fields in the BIDS name
+    fields2Check = { ...
+        'ce', ...
+        'dir', ...  % For BIDS file naming: phase encoding direction of acquisition for fMRI
+        'rec', ...  % For BIDS file naming: reconstruction of fMRI images
+        'echo', ... % For BIDS file naming: echo fMRI images
+        'acq'       % For BIDS file naming: acquisition of fMRI images
+        };
+
+    for iField = 1:numel(fields2Check)
+        if isempty (getfield(expParameters, fields2Check{iField})) %#ok<*GFLD>
+            expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
+                ''); %#ok<*SFLD>
+        else
+            expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
+                ['_' fields2Check{iField} '-' getfield(expParameters, fields2Check{iField})]);
+        end
     end
-end
 
+    %% create directories
+    [~, ~, ~] = mkdir(expParameters.outputDir);
+    [~, ~, ~] = mkdir(fullfile(expParameters.outputDir, modality));
 
-%% create directories
-[~, ~, ~] = mkdir(expParameters.outputDir);
-[~, ~, ~] = mkdir(fullfile(expParameters.outputDir, modality));
+    if cfg.eyeTracker
+        [~, ~, ~] = mkdir(fullfile(expParameters.outputDir, 'eyetracker'));
+    end
 
-if cfg.eyeTracker
-    [~, ~, ~] = mkdir(fullfile(expParameters.outputDir, 'eyetracker'));
-end
+    %% create filenames
 
+    switch modality
 
-%% create filenames
-
-switch modality
-    
-    case 'beh'
-        
-        expParameters.fileName.events = ...
-            [expParameters.fileName.base, runSuffix, '_events_date-' expParameters.date '.tsv'];
-        
-        expParameters.fileName.stim = ...
-            [expParameters.fileName.base, runSuffix, '_stim_date-' expParameters.date '.tsv'];
-        
-    case 'func'
-        
-        expParameters.fileName.events = ...
-            [expParameters.fileName.base, ...
-            expParameters.acqSuffix, expParameters.ceSuffix, ...
-            expParameters.dirSuffix, expParameters.recSuffix, ...
-            runSuffix, expParameters.echoSuffix, ...
-            '_events_date-' expParameters.date '.tsv'];
-        
-        expParameters.fileName.stim = ...
-            [expParameters.fileName.base, ...
-            expParameters.acqSuffix, expParameters.ceSuffix, ...
-            expParameters.dirSuffix, expParameters.recSuffix, ...
-            runSuffix, expParameters.echoSuffix, ...
-            '_stim_date-' expParameters.date '.tsv'];
-        
-end
+        case 'beh'
 
+            expParameters.fileName.events = ...
+                [expParameters.fileName.base, runSuffix, '_events_date-' expParameters.date '.tsv'];
 
-if cfg.eyeTracker
-    expParameters.fileName.eyetracker = ...
-        [expParameters.fileName.base, expParameters.acqSuffix, ...
-        runSuffix, '_eyetrack_date-' expParameters.date '.edf'];
-    
-end
+            expParameters.fileName.stim = ...
+                [expParameters.fileName.base, runSuffix, '_stim_date-' expParameters.date '.tsv'];
+
+        case 'func'
+
+            expParameters.fileName.events = ...
+                [expParameters.fileName.base, ...
+                expParameters.acqSuffix, expParameters.ceSuffix, ...
+                expParameters.dirSuffix, expParameters.recSuffix, ...
+                runSuffix, expParameters.echoSuffix, ...
+                '_events_date-' expParameters.date '.tsv'];
+
+            expParameters.fileName.stim = ...
+                [expParameters.fileName.base, ...
+                expParameters.acqSuffix, expParameters.ceSuffix, ...
+                expParameters.dirSuffix, expParameters.recSuffix, ...
+                runSuffix, expParameters.echoSuffix, ...
+                '_stim_date-' expParameters.date '.tsv'];
+
+    end
 
-if expParameters.verbose
-    
-    fprintf(1,'\nData will be saved in this directory:\n\t%s\n', ...
-        fullfile(expParameters.outputDir, modality));
-    
-    fprintf(1,'\nData will be saved in this file:\n\t%s\n', ...
-        expParameters.fileName.events);
-    
     if cfg.eyeTracker
-        
-        fprintf(1,'\nEyetracking data will be saved in this directory:\n\t%s\n', ...
-            fullfile(expParameters.outputDir, 'eyetracker'));
-        
-        fprintf(1,'\nEyetracking data will be saved in this file:\n\t%s\n', ...
-            expParameters.fileName.eyetracker);
-        
+        expParameters.fileName.eyetracker = ...
+            [expParameters.fileName.base, expParameters.acqSuffix, ...
+            runSuffix, '_eyetrack_date-' expParameters.date '.edf'];
+
     end
-    
-end
 
+    if expParameters.verbose
+
+        fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
+            fullfile(expParameters.outputDir, modality));
+
+        fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
+            expParameters.fileName.events);
+
+        if cfg.eyeTracker
+
+            fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
+                fullfile(expParameters.outputDir, 'eyetracker'));
+
+            fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
+                expParameters.fileName.eyetracker);
+
+        end
+
+    end
 
 end
diff --git a/miss_hit.cfg b/miss_hit.cfg
new file mode 100644
index 00000000..bf034a66
--- /dev/null
+++ b/miss_hit.cfg
@@ -0,0 +1,3 @@
+line_length: 100
+regex_function_name: "[a-z]+(([A-Z]|[0-9]){1}[a-z]+)*"
+suppress_rule: "copyright_notice"
\ No newline at end of file
diff --git a/saveEventsFile.m b/saveEventsFile.m
index cf438b2a..2e39a46e 100644
--- a/saveEventsFile.m
+++ b/saveEventsFile.m
@@ -1,174 +1,173 @@
-function [ logFile ] = saveEventsFile(action, expParameters, logFile, varargin)
-% Function to save output files for events that will be BIDS compliant.
-%
-% INPUTS
-%
-% logFile:
-%   When you want to save your data logFile contains the data you want to save. 
-% The logFile variable that contains the n events you want to % save must be a nx1 structure. 
-% Each field will be saved in a separate column.
-%
-% example:
-% logFile(1,1).onset = 2;
-% logFile(1,1).trial_type = 'motion_up';
-% logFile(1,1).duration = 1;
-% logFile(1,1).speed = 2;
-% logFile(1,1).is_fixation = true;
-% 
-% logFile(2,1).onset = 3;
-% logFile(2,1).trial_type = 'static';
-% logFile(2,1).duration = 4;
-% logFile(2,1).is_fixation = 3;
-%
-%
-% logFile:
-%   When you want to save your data logFile contains the data you want to save.
-% The logFile variable that contains the n events you want to % save must be a nx1 structure.
-% Each field will be saved in a separate column.
-%
-% example:
-% logFile(1,1).onset = 2;
-% logFile(1,1).trial_type = 'motion_up';
-% logFile(1,1).duration = 1;
-% logFile(1,1).speed = 2;
-% logFile(1,1).is_fixation = true;
-%
-% logFile(2,1).onset = 3;
-% logFile(2,1).trial_type = 'static';
-% logFile(2,1).duration = 4;
-% logFile(2,1).is_fixation = 3;
-%
-%
-% action:
-%  - 'open': will create the file ID and return it in logFile.fileID using the information in
-% the expParameters structure. This file ID is then reused when calling that function to save data
-% into this file.
-% This creates the header with the obligatory 'onset', 'trial_type', 'duration' required bt BIDS and other
-% coluns can be specified in varargin.
-%
-% example : logFile = saveEventsFile('open', expParameters, [], 'direction', 'speed', 'target');
-%
-%  - 'save': will save the data contained in logfile by using the file ID logFile.fileID;
-% logfile must then contain:
-%     - logFile.onset
-%     - logFile.trial_type
-%     - logFile.duration
-% The name of any extra column whose content must be saved should be listed in varargin.
-%
-%  - 'close': closes the file with file ID logFile.fileID. If expParameters.verbose is set to true
-% then this will tell you where the file is located.
-%
-% See test_saveEventsFile in the test folder for more details on how to use it.
-
-if nargin<3 || isempty(logFile)
-    logFile = struct();
-end
+function [logFile] = saveEventsFile(action, expParameters, logFile, varargin)
+    % Function to save output files for events that will be BIDS compliant.
+    %
+    % INPUTS
+    %
+    % logFile:
+    %   When you want to save your data logFile contains the data you want to save.
+    % The logFile variable that contains the n events you want to % save must be a nx1 structure.
+    % Each field will be saved in a separate column.
+    %
+    % example:
+    % logFile(1,1).onset = 2;
+    % logFile(1,1).trial_type = 'motion_up';
+    % logFile(1,1).duration = 1;
+    % logFile(1,1).speed = 2;
+    % logFile(1,1).is_fixation = true;
+    %
+    % logFile(2,1).onset = 3;
+    % logFile(2,1).trial_type = 'static';
+    % logFile(2,1).duration = 4;
+    % logFile(2,1).is_fixation = 3;
+    %
+    %
+    % logFile:
+    %   When you want to save your data logFile contains the data you want to save.
+    % The logFile variable that contains the n events you want to % save must be a nx1 structure.
+    % Each field will be saved in a separate column.
+    %
+    % example:
+    % logFile(1,1).onset = 2;
+    % logFile(1,1).trial_type = 'motion_up';
+    % logFile(1,1).duration = 1;
+    % logFile(1,1).speed = 2;
+    % logFile(1,1).is_fixation = true;
+    %
+    % logFile(2,1).onset = 3;
+    % logFile(2,1).trial_type = 'static';
+    % logFile(2,1).duration = 4;
+    % logFile(2,1).is_fixation = 3;
+    %
+    %
+    % action:
+    %  - 'open': will create the file ID and return it in logFile.fileID using the information in
+    % the expParameters structure. This file ID is then reused when calling that function to save data
+    % into this file.
+    % This creates the header with the obligatory 'onset', 'trial_type', 'duration' required bt BIDS and other
+    % coluns can be specified in varargin.
+    %
+    % example : logFile = saveEventsFile('open', expParameters, [], 'direction', 'speed', 'target');
+    %
+    %  - 'save': will save the data contained in logfile by using the file ID logFile.fileID;
+    % logfile must then contain:
+    %     - logFile.onset
+    %     - logFile.trial_type
+    %     - logFile.duration
+    % The name of any extra column whose content must be saved should be listed in varargin.
+    %
+    %  - 'close': closes the file with file ID logFile.fileID. If expParameters.verbose is set to true
+    % then this will tell you where the file is located.
+    %
+    % See test_saveEventsFile in the test folder for more details on how to use it.
 
-switch action
-    
-    case 'open'
-        
-        logFile = struct();
-        
-        % Initialize txt logfiles and empty fields for the standard BIDS
-        %  event file
-        logFile.fileID = fopen(...
-            fullfile(...
-            expParameters.outputDir, ...
-            expParameters.modality, ...
-            expParameters.fileName.events), ...
-            'w');
-        
-        initializeHeader(logFile, varargin);
-        
-        
-    case 'open_stim'
+    if nargin < 3 || isempty(logFile)
         logFile = struct();
-        
-        % Initialize txt logfiles and empty fields for the standard BIDS
-        %  event file
-        logFile.fileID = fopen(...
-            fullfile(...
-            expParameters.outputDir, ...
-            expParameters.modality, ...
-            expParameters.fileName.stim), ...
-            'w');
-        
-        initializeHeader(logFile, varargin);
-        
-    case 'save'
-        
-        if ~isstruct(logFile) || size(logFile, 2)>1
-            error('The logFile variable that contains the n events you want to save must be a nx1 structure.')
-        end
-        
-        % appends to the logfile all the data stored in the structure
-        % first with the standard BIDS data and then any extra things
-        for iEvent = 1:size(logFile,1)
-            
-            fprintf(logFile(1).fileID,'%f\t%s\t%f\t',...
-                logFile(iEvent).onset, ...
-                logFile(iEvent).trial_type, ...
-                logFile(iEvent).duration);
-            
-            for iExtraColumn = 1:numel(varargin)
-                
-                % if the field we are looking for does not exist or is empty in the
-                % action logFile structure we will write a NaN otherwise we
-                % write its content
-                
-                if ~isfield(logFile, varargin{iExtraColumn})
-                    data = [];
-                else
-                    data = getfield(logFile(iEvent), varargin{iExtraColumn});
-                end
-                
-                if isempty(data)
-                    data = NaN;
-                end
-                
-                if ischar(data)
-                    fprintf(logFile(1).fileID, '%s\t', data);
-                else
-                    fprintf(logFile(1).fileID, '%f\t', data);
-                end
-                
-            end
-            
-            fprintf(logFile(1).fileID, '\n');
-        end
-        
-    case 'close'
-        
-        % close txt log file
-        fclose(logFile(1).fileID);
-        
-        if expParameters.verbose
-            fprintf(1,'\nData were saved in this file:\n\n%s\n\n', ...
-                fullfile(...
+    end
+
+    switch action
+
+        case 'open'
+
+            logFile = struct();
+
+            % Initialize txt logfiles and empty fields for the standard BIDS
+            %  event file
+            logFile.fileID = fopen( ...
+                fullfile( ...
                 expParameters.outputDir, ...
                 expParameters.modality, ...
-                expParameters.fileName.events));
-            
-        end
-        
-end
+                expParameters.fileName.events), ...
+                'w');
+
+            initializeHeader(logFile, varargin);
+
+        case 'open_stim'
+            logFile = struct();
+
+            % Initialize txt logfiles and empty fields for the standard BIDS
+            %  event file
+            logFile.fileID = fopen( ...
+                fullfile( ...
+                expParameters.outputDir, ...
+                expParameters.modality, ...
+                expParameters.fileName.stim), ...
+                'w');
+
+            initializeHeader(logFile, varargin);
+
+        case 'save'
+
+            if ~isstruct(logFile) || size(logFile, 2) > 1
+                error('The logFile variable that contains the n events you want to save must be a nx1 structure.');
+            end
+
+            % appends to the logfile all the data stored in the structure
+            % first with the standard BIDS data and then any extra things
+            for iEvent = 1:size(logFile, 1)
+
+                fprintf(logFile(1).fileID, '%f\t%s\t%f\t', ...
+                    logFile(iEvent).onset, ...
+                    logFile(iEvent).trial_type, ...
+                    logFile(iEvent).duration);
+
+                for iExtraColumn = 1:numel(varargin)
+
+                    % if the field we are looking for does not exist or is empty in the
+                    % action logFile structure we will write a NaN otherwise we
+                    % write its content
+
+                    if ~isfield(logFile, varargin{iExtraColumn})
+                        data = [];
+                    else
+                        data = getfield(logFile(iEvent), varargin{iExtraColumn});
+                    end
+
+                    if isempty(data)
+                        data = NaN;
+                    end
+
+                    if ischar(data)
+                        fprintf(logFile(1).fileID, '%s\t', data);
+                    else
+                        fprintf(logFile(1).fileID, '%f\t', data);
+                    end
+
+                end
+
+                fprintf(logFile(1).fileID, '\n');
+            end
+
+        case 'close'
+
+            % close txt log file
+            fclose(logFile(1).fileID);
+
+            if expParameters.verbose
+                fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
+                    fullfile( ...
+                    expParameters.outputDir, ...
+                    expParameters.modality, ...
+                    expParameters.fileName.events));
+
+            end
+
+    end
 
 end
 
 function initializeHeader(logFile, varargin)
 
-% print the basic BIDS columns
-fprintf(logFile.fileID, '%s\t%s\t%s\t', 'onset', 'trial_type', 'duration');
+    % print the basic BIDS columns
+    fprintf(logFile.fileID, '%s\t%s\t%s\t', 'onset', 'trial_type', 'duration');
 
-% print any extra column specified by the user
-%  also prepare an empty field in the structure to collect data
-%  for those
-for iExtraColumn = 1:numel(varargin{1})
-    fprintf(logFile.fileID,'%s\t', lower(varargin{1}{iExtraColumn}));
-end
+    % print any extra column specified by the user
+    %  also prepare an empty field in the structure to collect data
+    %  for those
+    for iExtraColumn = 1:numel(varargin{1})
+        fprintf(logFile.fileID, '%s\t', lower(varargin{1}{iExtraColumn}));
+    end
 
-% next line so we start printing at the right place
-fprintf(logFile.fileID, '\n');
+    % next line so we start printing at the right place
+    fprintf(logFile.fileID, '\n');
 
-end
\ No newline at end of file
+end
diff --git a/tests/runtests.m b/tests/runtests.m
index a1b006fd..6facd137 100644
--- a/tests/runtests.m
+++ b/tests/runtests.m
@@ -1,51 +1,53 @@
 function results = runtests(pth)
-% Run tests
-% List all the 'test_*.m' files located in the same directory as this
-% function, run them and keep track of how many passed, failed or are
-% incomplete.
-%__________________________________________________________________________
-
-% Copyright (C) 2019, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
-% Copyright (C) 2020--, CPP_BIDS developers
-
-%-Get the path of where this file is located
-if ~nargin, pth = fileparts(mfilename('fullpath')); end
-
-%-List all the 'test_*.m' files located in the same directory as this
-% function
-d = dir(pth);
-d([d.isdir]) = [];
-d(arrayfun(@(x) isempty(regexp(x.name,'^test_.*\.m$','once')),d)) = [];
-
-results = struct('Passed',{},'Failed',{},'Incomplete',{},'Duration',{});
-for i=1:numel(d)
-
-    results(i).Failed = false;
-    results(i).Passed = false;
-    results(i).Incomplete = false;
-
-    tstart = tic;
-
-    %-Run each test file and catch error message in case of failure
-    try
-
-        fprintf('%s',d(i).name(1:end-2));
-        feval(d(i).name(1:end-2));
-        results(i).Passed = true;
-        
-    catch err
-        results(i).Failed = true;
-        fprintf('\n%s',err.message);
+    % Run tests
+    % List all the 'test_*.m' files located in the same directory as this
+    % function, run them and keep track of how many passed, failed or are
+    % incomplete.
+    % __________________________________________________________________________
+
+    % Copyright (C) 2019, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
+    % Copyright (C) 2020--, CPP_BIDS developers
+
+    % -Get the path of where this file is located
+    if ~nargin
+        pth = fileparts(mfilename('fullpath'));
     end
 
-    results(i).Duration = toc(tstart);
+    % -List all the 'test_*.m' files located in the same directory as this
+    % function
+    d = dir(pth);
+    d([d.isdir]) = [];
+    d(arrayfun(@(x) isempty(regexp(x.name, '^test_.*\.m$', 'once')), d)) = [];
 
-    fprintf('\n');
+    results = struct('Passed', {}, 'Failed', {}, 'Incomplete', {}, 'Duration', {});
+    for i = 1:numel(d)
 
-end
+        results(i).Failed = false;
+        results(i).Passed = false;
+        results(i).Incomplete = false;
 
-if ~nargout
-    fprintf(['Totals (%d tests):\n\t%d Passed, %d Failed, %d Incomplete.\n' ...
-        '\t%f seconds testing time.\n\n'],numel(results),nnz([results.Passed]),...
-        nnz([results.Failed]),nnz([results.Incomplete]),sum([results.Duration]));
-end
+        tstart = tic;
+
+        % -Run each test file and catch error message in case of failure
+        try
+
+            fprintf('%s', d(i).name(1:end - 2));
+            feval(d(i).name(1:end - 2));
+            results(i).Passed = true;
+
+        catch err
+            results(i).Failed = true;
+            fprintf('\n%s', err.message);
+        end
+
+        results(i).Duration = toc(tstart);
+
+        fprintf('\n');
+
+    end
+
+    if ~nargout
+        fprintf(['Totals (%d tests):\n\t%d Passed, %d Failed, %d Incomplete.\n' ...
+            '\t%f seconds testing time.\n\n'], numel(results), nnz([results.Passed]), ...
+            nnz([results.Failed]), nnz([results.Incomplete]), sum([results.Duration]));
+    end
diff --git a/tests/test_createFilename.m b/tests/test_createFilename.m
index 6c964e01..a3e34544 100644
--- a/tests/test_createFilename.m
+++ b/tests/test_createFilename.m
@@ -1,87 +1,87 @@
 function test_createFilename()
-% test for filename creation and their directories
+    % test for filename creation and their directories
 
-%% check directory and filename creation (PC)
+    %% check directory and filename creation (PC)
 
-%%% set up part
+    %%% set up part
 
-expParameters.subjectGrp = '';
-expParameters.subjectNb = 1;
-expParameters.sessionNb = 1;
-expParameters.runNb = 1;
-expParameters.task = 'testtask';
-expParameters.verbose = 1;
+    expParameters.subjectGrp = '';
+    expParameters.subjectNb = 1;
+    expParameters.sessionNb = 1;
+    expParameters.runNb = 1;
+    expParameters.task = 'testtask';
+    expParameters.verbose = 1;
 
-cfg.eyeTracker = false;
-cfg.device = 'PC';
+    cfg.eyeTracker = false;
+    cfg.device = 'PC';
 
-% set up the output directories
-outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-expParameters.outputDir = outputDir;
+    % set up the output directories
+    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+    expParameters.outputDir = outputDir;
 
-behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
-eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
+    behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
+    eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
 
-expParameters = checkCFG(cfg,expParameters);
-expParameters = createFilename(cfg,expParameters);
+    expParameters = checkCFG(cfg, expParameters);
+    expParameters = createFilename(cfg, expParameters);
 
-%%% test part
+    %%% test part
 
-% make sure the beh dir is created
-assert(exist(behDir, 'dir')==7)
+    % make sure the beh dir is created
+    assert(exist(behDir, 'dir') == 7);
 
-% make sure the eyetracker dir is not created
-assert(exist(eyetrackerDir, 'dir')==0)
+    % make sure the eyetracker dir is not created
+    assert(exist(eyetrackerDir, 'dir') == 0);
 
-% make sure the events filename is created
-assert(strcmp(...
-    expParameters.fileName.events, ...
-    ['sub-001_ses-001_task-testtask_run-001_events_date-' expParameters.date '.tsv']));
+    % make sure the events filename is created
+    assert(strcmp( ...
+        expParameters.fileName.events, ...
+        ['sub-001_ses-001_task-testtask_run-001_events_date-' expParameters.date '.tsv']));
 
-% make sure the stim filename is created
-assert(strcmp(...
-    expParameters.fileName.stim, ...
-    ['sub-001_ses-001_task-testtask_run-001_stim_date-' expParameters.date '.tsv']));
+    % make sure the stim filename is created
+    assert(strcmp( ...
+        expParameters.fileName.stim, ...
+        ['sub-001_ses-001_task-testtask_run-001_stim_date-' expParameters.date '.tsv']));
 
-%% check directory and filename creation (fMRI and eye tracker)
+    %% check directory and filename creation (fMRI and eye tracker)
 
-clear
+    clear;
 
-%%% set up part
+    %%% set up part
 
-expParameters.subjectGrp = 'ctrl';
-expParameters.subjectNb = 2;
-expParameters.sessionNb = 2;
-expParameters.runNb = 2;
-expParameters.task = 'testtask';
+    expParameters.subjectGrp = 'ctrl';
+    expParameters.subjectNb = 2;
+    expParameters.sessionNb = 2;
+    expParameters.runNb = 2;
+    expParameters.task = 'testtask';
 
-cfg.eyeTracker = true;
-cfg.device = 'scanner';
+    cfg.eyeTracker = true;
+    cfg.device = 'scanner';
 
-outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-funcDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
-eyetrackerDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'eyetracker');
+    funcDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
+    eyetrackerDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'eyetracker');
 
-expParameters.outputDir = outputDir;
-expParameters = checkCFG(cfg,expParameters);
-expParameters = createFilename(cfg,expParameters);
+    expParameters.outputDir = outputDir;
+    expParameters = checkCFG(cfg, expParameters);
+    expParameters = createFilename(cfg, expParameters);
 
-%%% test part
+    %%% test part
 
-% make sure the func dir is created
-assert(exist(funcDir, 'dir')==7)
+    % make sure the func dir is created
+    assert(exist(funcDir, 'dir') == 7);
 
-% make sure the eyetracker dir is created
-assert(exist(eyetrackerDir, 'dir')==7)
+    % make sure the eyetracker dir is created
+    assert(exist(eyetrackerDir, 'dir') == 7);
 
-% make sure the events filename is created
-assert(strcmp(expParameters.fileName.base, 'sub-ctrl002_ses-002_task-testtask'))
-assert(strcmp(...
-    expParameters.fileName.events, ...
-    ['sub-ctrl002_ses-002_task-testtask_run-002_events_date-' expParameters.date '.tsv']));
+    % make sure the events filename is created
+    assert(strcmp(expParameters.fileName.base, 'sub-ctrl002_ses-002_task-testtask'));
+    assert(strcmp( ...
+        expParameters.fileName.events, ...
+        ['sub-ctrl002_ses-002_task-testtask_run-002_events_date-' expParameters.date '.tsv']));
 
-% make sure the eyetracker filename is created
-assert(strcmp(...
-    expParameters.fileName.eyetracker, ...
-    ['sub-ctrl002_ses-002_task-testtask_run-002_eyetrack_date-' expParameters.date '.edf']));
+    % make sure the eyetracker filename is created
+    assert(strcmp( ...
+        expParameters.fileName.eyetracker, ...
+        ['sub-ctrl002_ses-002_task-testtask_run-002_eyetrack_date-' expParameters.date '.edf']));
diff --git a/tests/test_saveEventsFile.m b/tests/test_saveEventsFile.m
index b5091227..475154f2 100644
--- a/tests/test_saveEventsFile.m
+++ b/tests/test_saveEventsFile.m
@@ -1,84 +1,83 @@
 function test_saveEventsFile()
-% test for events.tsv file creation
+    % test for events.tsv file creation
 
-%% set up
+    %% set up
 
-expParameters.subjectGrp = '';
-expParameters.subjectNb = 1;
-expParameters.sessionNb = 1;
-expParameters.runNb = 1;
-expParameters.task = 'testtask';
-expParameters.verbose = 1;
+    expParameters.subjectGrp = '';
+    expParameters.subjectNb = 1;
+    expParameters.sessionNb = 1;
+    expParameters.runNb = 1;
+    expParameters.task = 'testtask';
+    expParameters.verbose = 1;
 
-cfg.eyeTracker = false;
-cfg.device = 'scanner';
+    cfg.eyeTracker = false;
+    cfg.device = 'scanner';
 
-outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-expParameters.outputDir = outputDir;
-expParameters = checkCFG(cfg,expParameters);
-expParameters = createFilename(cfg,expParameters);
+    expParameters.outputDir = outputDir;
+    expParameters = checkCFG(cfg, expParameters);
+    expParameters = createFilename(cfg, expParameters);
 
-%% create the events and stim files
+    %% create the events and stim files
 
-logFile = saveEventsFile('open', expParameters, [], 'Speed', 'is_Fixation');
+    logFile = saveEventsFile('open', expParameters, [], 'Speed', 'is_Fixation');
 
-stimFile = saveEventsFile('open_stim', expParameters, []);
+    stimFile = saveEventsFile('open_stim', expParameters, []);
 
-%%% test section
+    %%% test section
 
-fileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events);
-stimFileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.stim);
+    fileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events);
+    stimFileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.stim);
 
-% check that the file has the right path and name
-assert(exist(fileName, 'file')==2)
-assert(exist(stimFileName, 'file')==2)
+    % check that the file has the right path and name
+    assert(exist(fileName, 'file') == 2);
+    assert(exist(stimFileName, 'file') == 2);
 
+    %%  write things in it
 
-%%  write things in it
+    logFile(1).onset = 1;
+    logFile(1).trial_type = 'motion_up';
+    logFile(1).duration = 1;
+    logFile(1).speed = [];
+    logFile(1).is_fixation = 'true';
 
-logFile(1).onset = 1;
-logFile(1).trial_type = 'motion_up';
-logFile(1).duration = 1;
-logFile(1).speed = [];
-logFile(1).is_fixation = 'true';
+    saveEventsFile('save', expParameters, logFile, 'speed', 'is_fixation');
 
-saveEventsFile('save', expParameters, logFile, 'speed', 'is_fixation');
+    logFile(1, 1).onset = 2;
+    logFile(1, 1).trial_type = 'motion_up';
+    logFile(1, 1).duration = 1;
+    logFile(1, 1).speed = 2;
+    logFile(1, 1).is_fixation = true;
 
-logFile(1,1).onset = 2;
-logFile(1,1).trial_type = 'motion_up';
-logFile(1,1).duration = 1;
-logFile(1,1).speed = 2;
-logFile(1,1).is_fixation = true;
+    logFile(2, 1).onset = 3;
+    logFile(2, 1).trial_type = 'static';
+    logFile(2, 1).duration = 4;
+    logFile(2, 1).is_fixation = 3;
 
-logFile(2,1).onset = 3;
-logFile(2,1).trial_type = 'static';
-logFile(2,1).duration = 4;
-logFile(2,1).is_fixation = 3;
+    saveEventsFile('save', expParameters, logFile, 'speed', 'is_fixation');
 
-saveEventsFile('save', expParameters, logFile, 'speed', 'is_fixation');
+    % close the file
+    saveEventsFile('close', expParameters, logFile);
 
-% close the file
-saveEventsFile('close', expParameters, logFile);
+    %%% test section
 
-%%% test section
+    % check the extra columns of the header and some of the content
 
-% check the extra columns of the header and some of the content
+    FID = fopen(fileName, 'r');
+    C = textscan(FID, '%s%s%s%s%s', 'Delimiter', '\t', 'EndOfLine', '\n');
 
-FID = fopen(fileName, 'r');
-C = textscan(FID,'%s%s%s%s%s','Delimiter', '\t', 'EndOfLine', '\n');
+    % check header
+    assert(isequal(C{4}{1}, 'speed'));
 
-% check header
-assert(isequal(C{4}{1}, 'speed')); 
+    % check that empty values are entered as NaN
+    assert(isequal(C{4}{2}, 'NaN'));
 
-% check that empty values are entered as NaN
-assert(isequal(C{4}{2}, 'NaN')); 
+    % check that missing fields are entered as NaN
+    assert(isequal(C{4}{4}, 'NaN'));
 
-% check that missing fields are entered as NaN
-assert(isequal(C{4}{4}, 'NaN')); 
+    % check values entered properly
+    assert(isequal(str2double(C{4}{3}), 2));
 
-% check values entered properly
-assert(isequal(str2double(C{4}{3}), 2)); 
-
-% check values entered properly
-assert(isequal(str2double(C{5}{4}), 3)); 
+    % check values entered properly
+    assert(isequal(str2double(C{5}{4}), 3));
diff --git a/userInputs.m b/userInputs.m
index f1863148..6561f2a2 100644
--- a/userInputs.m
+++ b/userInputs.m
@@ -1,67 +1,66 @@
 function [expParameters] = userInputs(cfg, expParameters)
-% Get subject, run and session number and make sure they are
-% positive integer values
-%
-% expParameters.askGrpSess
-% a 1 X 2 array of booleans (default is [true true] ):
-%    - the first value set to false will skip asking for the participants
-%    group
-%    - the second value set to false will skip asking for the session
+    % Get subject, run and session number and make sure they are
+    % positive integer values
+    %
+    % expParameters.askGrpSess
+    % a 1 X 2 array of booleans (default is [true true] ):
+    %    - the first value set to false will skip asking for the participants
+    %    group
+    %    - the second value set to false will skip asking for the session
 
-if nargin<1 || isempty(cfg.debug)
-    cfg.debug = false;
-end
-if nargin<2
-    expParameters = [];
-end
-if ~isfield(expParameters, 'askGrpSess') || isempty(expParameters.askGrpSess)
-    askGrpSess = [true true];
-else
-    askGrpSess = expParameters.askGrpSess;
-end
+    if nargin < 1 || isempty(cfg.debug)
+        cfg.debug = false;
+    end
+    if nargin < 2
+        expParameters = [];
+    end
+    if ~isfield(expParameters, 'askGrpSess') || isempty(expParameters.askGrpSess)
+        askGrpSess = [true true];
+    else
+        askGrpSess = expParameters.askGrpSess;
+    end
 
+    % When in debug more this function returns some dummy values
+    if cfg.debug
+        subjectGrp = 'ctrl';
+        subjectNb = 666;
+        runNb = 666;
+        sessionNb = 666;
+
+        % Otherwise it prompts the user for some information
+    else
+
+        % subject group
+        if askGrpSess(1)
+            subjectGrp = lower(input('Enter subject group (leave empty if none): ', 's'));
+        end
+
+        % the subject number
+        subjectNb = str2double(input('Enter subject number (1-999): ', 's'));
+        subjectNb = checkInput(subjectNb);
+
+        % the session number
+        if  numel(askGrpSess) > 1 && askGrpSess(2)
+            sessionNb = str2double(input('Enter the session (i.e day - 1-999)) number: ', 's'));
+            sessionNb = checkInput(sessionNb);
+        end
+
+        % the run number
+        runNb = str2double(input('Enter the run number (1-999): ', 's'));
+        runNb = checkInput(runNb);
 
-% When in debug more this function returns some dummy values
-if cfg.debug
-    subjectGrp = 'ctrl';
-    subjectNb = 666;
-    runNb = 666;
-    sessionNb = 666;
-    
-    % Otherwise it prompts the user for some information
-else
-    
-    % subject group
-    if askGrpSess(1)
-        subjectGrp = lower(input('Enter subject group (leave empty if none): ', 's'));
-    end
-    
-    % the subject number
-    subjectNb = str2double(input('Enter subject number (1-999): ', 's') );
-    subjectNb = checkInput(subjectNb);
-    
-    % the session number
-    if  numel(askGrpSess)>1 && askGrpSess(2)
-        sessionNb = str2double(input('Enter the session (i.e day - 1-999)) number: ', 's'));
-        sessionNb = checkInput(sessionNb);
     end
-    
-    % the run number
-    runNb = str2double(input('Enter the run number (1-999): ', 's'));
-    runNb = checkInput(runNb);
-    
-end
 
-expParameters.subjectGrp = subjectGrp;
-expParameters.subjectNb = subjectNb;
-expParameters.sessionNb = sessionNb;
-expParameters.runNb = runNb;
+    expParameters.subjectGrp = subjectGrp;
+    expParameters.subjectNb = subjectNb;
+    expParameters.sessionNb = sessionNb;
+    expParameters.runNb = runNb;
 
 end
 
 function input2check = checkInput(input2check)
-% this function checks the input to makes sure the user enters a positive integer
-while isnan(input2check) || fix(input2check) ~= input2check || input2check<0
-    input2check = str2double(input('Please enter a positive integer: ', 's'));
-end
+    % this function checks the input to makes sure the user enters a positive integer
+    while isnan(input2check) || fix(input2check) ~= input2check || input2check < 0
+        input2check = str2double(input('Please enter a positive integer: ', 's'));
+    end
 end

From 416f3c6be9d5e3ddb04bd5dffc8472bc5ff61679 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 19 Jul 2020 23:52:13 +0200
Subject: [PATCH 2/3] additional linting fix

---
 .travis.yml                      |  2 +-
 createFilename.m                 |  4 ++--
 saveEventsFile.m                 | 14 +++++++-------
 tests/miss_hit.cfg               |  3 +++
 tests/{runtests.m => runTests.m} |  0
 tests/test_saveEventsFile.m      | 10 ++++++++--
 6 files changed, 21 insertions(+), 12 deletions(-)
 create mode 100644 tests/miss_hit.cfg
 rename tests/{runtests.m => runTests.m} (100%)

diff --git a/.travis.yml b/.travis.yml
index 235ce2a1..ca362514 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -31,4 +31,4 @@ before_script:
   - cd tests
 
 script:
-  - octave $OCTFLAGS --eval "results = runtests; assert(all(~[results.Failed]))"
+  - octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
diff --git a/createFilename.m b/createFilename.m
index ab9f4eda..ba46389d 100644
--- a/createFilename.m
+++ b/createFilename.m
@@ -1,6 +1,6 @@
 function expParameters = createFilename(cfg, expParameters)
-    % create the BIDS compliant directories and filenames for the behavioral output for this subject /
-    % session / run using the information from cfg and expParameters.
+    % create the BIDS compliant directories and filenames for the behavioral output
+    % for this subject / session / run using the information from cfg and expParameters.
     % Will also create the right filename for the eyetracking data file.
     %
     % For the moment the date of acquisition is appended to the filename
diff --git a/saveEventsFile.m b/saveEventsFile.m
index 2e39a46e..3a09d6a6 100644
--- a/saveEventsFile.m
+++ b/saveEventsFile.m
@@ -41,10 +41,10 @@
     %
     % action:
     %  - 'open': will create the file ID and return it in logFile.fileID using the information in
-    % the expParameters structure. This file ID is then reused when calling that function to save data
-    % into this file.
-    % This creates the header with the obligatory 'onset', 'trial_type', 'duration' required bt BIDS and other
-    % coluns can be specified in varargin.
+    % the expParameters structure. This file ID is then reused when calling that function
+    % to save data into this file.
+    % This creates the header with the obligatory 'onset', 'trial_type', 'duration' required
+    % by BIDS and other columns can be specified in varargin.
     %
     % example : logFile = saveEventsFile('open', expParameters, [], 'direction', 'speed', 'target');
     %
@@ -55,8 +55,8 @@
     %     - logFile.duration
     % The name of any extra column whose content must be saved should be listed in varargin.
     %
-    %  - 'close': closes the file with file ID logFile.fileID. If expParameters.verbose is set to true
-    % then this will tell you where the file is located.
+    %  - 'close': closes the file with file ID logFile.fileID. If expParameters.verbose is set
+    % to true then this will tell you where the file is located.
     %
     % See test_saveEventsFile in the test folder for more details on how to use it.
 
@@ -98,7 +98,7 @@
         case 'save'
 
             if ~isstruct(logFile) || size(logFile, 2) > 1
-                error('The logFile variable that contains the n events you want to save must be a nx1 structure.');
+                error('The variable containing the n events to save must be a nx1 structure.');
             end
 
             % appends to the logfile all the data stored in the structure
diff --git a/tests/miss_hit.cfg b/tests/miss_hit.cfg
new file mode 100644
index 00000000..bbb08b15
--- /dev/null
+++ b/tests/miss_hit.cfg
@@ -0,0 +1,3 @@
+line_length: 100
+regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]|[0-9]){1}[a-z]+)*"
+suppress_rule: "copyright_notice"
\ No newline at end of file
diff --git a/tests/runtests.m b/tests/runTests.m
similarity index 100%
rename from tests/runtests.m
rename to tests/runTests.m
diff --git a/tests/test_saveEventsFile.m b/tests/test_saveEventsFile.m
index 475154f2..f2a8019c 100644
--- a/tests/test_saveEventsFile.m
+++ b/tests/test_saveEventsFile.m
@@ -27,8 +27,14 @@ function test_saveEventsFile()
 
     %%% test section
 
-    fileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events);
-    stimFileName = fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.stim);
+    fileName = fullfile( ...
+        expParameters.outputDir, ...
+        expParameters.modality, ...
+        expParameters.fileName.events);
+    stimFileName = fullfile( ...
+        expParameters.outputDir, ...
+        expParameters.modality, ...
+        expParameters.fileName.stim);
 
     % check that the file has the right path and name
     assert(exist(fileName, 'file') == 2);

From a7e22bff8d916ca9df64180ebafe101f7b222cc9 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 19 Jul 2020 23:55:25 +0200
Subject: [PATCH 3/3] update readme

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 99b6b4fe..5cf60913 100644
--- a/README.md
+++ b/README.md
@@ -16,6 +16,7 @@
   - [Contributing](#contributing)
     - [Guidestyle](#guidestyle)
     - [BIDS naming convention](#bids-naming-convention)
+    - [Contributors ✨](#contributors-)
 
 <!-- /TOC -->
 
@@ -184,7 +185,8 @@ Feel free to open issues to report a bug and ask for improvements.
 ### Guidestyle
 
 -   We use camelCase.
--   We keep the McCabe complexity as reported by the [check_my_code function](https://github.com/Remi-Gau/matlab_checkcode) below 15.
+-   We keep the McCabe complexity as reported by the [check_my_code function](https://github.com/Remi-Gau/check_my_code) below 15.
+-   We use the [MISS_HIT linter](https://florianschanda.github.io/miss_hit/style_checker.html) to automatically fix some linting issues.
 
 ### BIDS naming convention