fix extra tab added at the end of tsv lines

Author: Remi-Gau

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+repos:
+
+-   repo: local
+
+    hooks:
+
+    - id: mh_version
+      name: mh_version
+      entry: mh_style
+      args: [-v]
+      verbose: true
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    # - id: mh_style
+    #   name: mh_style
+    #   entry: mh_style
+    #   args: [--process-slx, --fix]
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit_core]
+
+    # - id: mh_metric
+    #   name: mh_metric
+    #   entry: mh_metric
+    #   args: [--ci]
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit_core]
+
+    # - id: mh_lint
+    #   name: mh_lint
+    #   entry: mh_lint
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.0.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files

checkCppBidsDependencies.m

@@ -0,0 +1,65 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function checkCppBidsDependencies(cfg)
+    %
+    % Adds dependencies to the Matlab / Octave path and make sure we got all of them.
+    %
+    % USAGE::
+    %
+    %   checkCppBidsDependencies(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+
+    if nargin < 1
+        cfg.verbose = 2;
+    end
+
+    global CPP_BIDS_INITIALIZED
+
+    if isempty(CPP_BIDS_INITIALIZED)
+
+        GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE');
+
+        if strcmp(GITHUB_WORKSPACE, '/github/workspace')
+
+            pth = GITHUB_WORKSPACE;
+            addpath(genpath(fullfile(pth, 'lib')));
+
+        elseif isempty(GITHUB_WORKSPACE)  % local
+
+            pth = fullfile(fileparts(mfilename('fullpath')));
+
+            addpath(pth);
+
+            addpath(fullfile(pth, 'lib', 'utils'));
+
+            checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
+            checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
+
+            addpath(genpath(fullfile(pth, 'src')));
+
+        end
+
+        printCreditsCppBids(cfg);
+
+        CPP_BIDS_INITIALIZED = true();
+
+    else
+        fprintf(1, '\n\nCPP_BIDS already initialized\n\n');
+
+    end
+
+end
+
+function checkSubmodule(pth)
+    % If external dir is empty throw an exception
+    % and ask user to update submodules.
+    if numel(dir(pth)) <= 2 % Means that the external is empty
+        error(['Git submodules are not cloned!', ...
+               'Try this in your terminal:', ...
+               ' git submodule update --recursive ']);
+    else
+        addpath(pth);
+    end
+end

miss_hit.cfg

@@ -1,11 +1,13 @@
 # style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
+regex_parameter_name: "[a-z0-9]+(([A-Z]){1}[A-Za-z]+)*"
+
 exclude_dir: "lib"
 copyright_entity: "CPP_BIDS developers"
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
 metric "file_length": limit 500
 metric "cyc": limit 15
-metric "parameters": limit 6
+metric "parameters": limit 6

requirements.txt

@@ -2,6 +2,6 @@ Sphinx
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
 sphinx_rtd_theme
-miss_hit==0.9.15
+miss_hit==0.9.29
 notebook
-octave_kernel
+octave_kernel

src/saveEventsFile.m

@@ -378,9 +378,9 @@ function printToFile(cfg, logFile, skipEvent, iEvent)
     if ~skipEvent
 
         if ~logFile(1).isStim
-            printData(logFile(1).fileID, logFile(iEvent).onset, cfg);
-            printData(logFile(1).fileID, logFile(iEvent).duration, cfg);
-            printData(logFile(1).fileID, logFile(iEvent).trial_type, cfg);
+            printData(logFile(1).fileID, logFile(iEvent).onset, cfg, true);
+            printData(logFile(1).fileID, logFile(iEvent).duration, cfg, true);
+            printData(logFile(1).fileID, logFile(iEvent).trial_type, cfg, false);
         end
 
         printExtraColumns(logFile, iEvent, cfg);
@@ -394,26 +394,41 @@ function printToFile(cfg, logFile, skipEvent, iEvent)
 function printExtraColumns(logFile, iEvent, cfg)
     % loops through the extra columns and print them
     namesExtraColumns = returnNamesExtraColumns(logFile);
+    if ~logFile(1).isStim && numel(namesExtraColumns) > 0
+        fprintf(logFile(1).fileID, '\t');
+        talkToMe(cfg, '\t');
+    end
+    addTab = true;
     for iExtraColumn = 1:numel(namesExtraColumns)
         data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
-        printData(logFile(1).fileID, data, cfg);
+        if iExtraColumn == numel(namesExtraColumns)
+            addTab = false;
+        end
+        printData(logFile(1).fileID, data, cfg, addTab);
     end
 end
 
-function printData(output, data, cfg)
+function printData(output, data, cfg, addTab)
     % write char
     % for numeric data we replace any nan by n/a
+
+    if addTab
+        separator = '\t';
+    else
+        separator = '';
+    end
+
     if ischar(data)
-        content = sprintf('%s\t', data);
+        content = sprintf('%s%s', data, separator);
         fprintf(output, content);
         talkToMe(cfg, content);
 
     else
         for i = 1:numel(data)
             if isnan(data(i))
-                content = sprintf('%s\t', 'n/a');
+                content = sprintf('%s%s', 'n/a', separator);
             else
-                content = sprintf('%f\t', data(i));
+                content = sprintf('%f%s', data(i), separator);
             end
             fprintf(output, content);
             talkToMe(cfg, content);

src/templates/miss_hit.cfg

@@ -1,9 +1,10 @@
 # style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
+regex_parameter_name: "test_suite|[a-z0-9]+(([A-Z]){1}[A-Za-z]+)*"
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
 metric "file_length": limit 500
 metric "cyc": limit 15
-metric "parameters": limit 5
+metric "parameters": limit 5

src/utils/checkCppBidsDependencies.m

@@ -1,9 +1,10 @@
 # style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
+regex_parameter_name: "test_suite|[a-z0-9]+(([A-Z]){1}[A-Za-z]+)*"
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
 metric "file_length": limit 500
 metric "cyc": limit 15
-metric "parameters": limit 5
+metric "parameters": limit 5

tests/miss_hit.cfg

@@ -46,6 +46,54 @@ function test_saveEventsFileSaveBasic()
 
 end
 
+function test_saveEventsFileSaveNoExtraTab()
+
+    cfg.verbose = 2;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
+    cfg = createFilename(cfg);
+
+    logFile.extraColumns.Speed.length = 1;
+    logFile.extraColumns.LHL24.length = 3;
+    logFile.extraColumns.is_Fixation.length = 1;
+
+    logFile = saveEventsFile('init', cfg, logFile);
+    logFile = saveEventsFile('open', cfg, logFile);
+
+    %     logFile.onset = 2;
+    %     logFile.duration = 3;
+
+    % ROW 2: normal events : all info is there
+    logFile(1, 1).onset = 2;
+    logFile(end, 1).trial_type = 'MotionUp';
+    logFile(end, 1).duration = 3;
+    logFile(end, 1).Speed = 2;
+    logFile(end, 1).is_Fixation = true;
+    logFile(end, 1).LHL24 = 1:3;
+
+    logFile = saveEventsFile('save', cfg, logFile);
+
+    saveEventsFile('close', cfg, logFile);
+
+    funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
+    eventFilename = cfg.fileName.events;
+
+    %         FID = fopen(fullfile(funcDir, eventFilename), 'r');
+    %         content = fread(FID, 900, 'uint8=>char')
+
+    FID = fopen(fullfile(funcDir, eventFilename), 'r');
+    content = fread(FID, 900);
+    tab = 9;
+    eol = 10;
+    assert(content(end) == 10);
+    assert(content(end - 1) ~= 9);
+
+end
+
 function test_saveEventsFileSaveStim()
 
     %% set up

tests/test_saveEventsFileSave.m

@@ -2,7 +2,7 @@
 
 function [cfg, logFile] = setUp()
 
-    cfg.verbose = 2;
+    cfg.verbose = 0;
 
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;