Merge branch 'fix_extra_column' of https://github.com/Remi-Gau/CPP_BIDS into fix_extra_column

Remi-Gau · Remi-Gau · commit 83ba9161b706 · 2021-10-28T20:47:03.000+02:00
diff --git a/.github/workflows/bids_validator.yml b/.github/workflows/bids_validator.yml
@@ -23,7 +23,7 @@ jobs:
     - name: Make jsonread for octave
       run: |
         sudo apt-get -y -qq update
-        sudo apt-get -y install octave 
+        sudo apt-get -y install octave
         sudo apt-get -y install liboctave-dev
         cd lib/JSONio
         mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
@@ -32,18 +32,13 @@ jobs:
     - name: Update octave path
       run: |
         octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
-        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();" 
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
 
     - name: Install BIDS validator
       run: |
         sudo npm install -g bids-validator@1.6.2
 
-    - name: Create dummy dataset and validate it 
+    - name: Create dummy dataset and validate it
       run: |
         cd tests/manualTests
         octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
-
-  
-
-
-
diff --git a/.github/workflows/check_markdown.yml b/.github/workflows/check_markdown.yml
@@ -26,9 +26,7 @@ jobs:
     - name: Install dependencies and check markdown
       run: |
         npm install `cat npm-requirements.txt`
-        npx remark README.md --frail  
+        npx remark README.md --frail
         npx remark ./notebooks/ --frail
         npx remark ./tests/ --frail
         npx remark ./docs/ --frail
-
-
diff --git a/.github/workflows/check_md_links.yml b/.github/workflows/check_md_links.yml
@@ -14,4 +14,4 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -21,7 +21,7 @@ jobs:
     - name: Make jsonread for octave
       run: |
         sudo apt-get -y -qq update
-        sudo apt-get -y install octave 
+        sudo apt-get -y install octave
         sudo apt-get -y install liboctave-dev
         cd lib/JSONio
         mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
@@ -30,7 +30,7 @@ jobs:
       uses: joergbrech/moxunit-action@master
       with:
         tests: tests # files or directories containing the MOxUnit test cases
-        src: src # directories to be added to the Octave search path before running the tests. 
+        src: src # directories to be added to the Octave search path before running the tests.
         ext: tests/utils # External resources to add to the search put (excluded from coverage)
         # data: # Directory for test data
         with_coverage: true
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -23,4 +23,4 @@ formats:
 python:
   version: 3.7
   install:
-    - requirements: requirements.txt
+    - requirements: requirements.txt
diff --git a/.travis.yml b/.travis.yml
@@ -11,7 +11,7 @@ node_js:
   - "11"
 
 branches:
-  only:  # only run the CI for those branches 
+  only:  # only run the CI for those branches
   - master
   - dev
 
diff --git a/.zenodo.json b/.zenodo.json
@@ -32,4 +32,4 @@
   ],
   "license": "MIT license",
   "upload_type": "software"
-}
+}
diff --git a/binder/postBuild b/binder/postBuild
@@ -1,3 +1,2 @@
 cd ${HOME}
 cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..
-
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -31,7 +31,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinxcontrib.matlab', 
+    'sphinxcontrib.matlab',
     'sphinx.ext.autodoc']
 matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
 primary_domain = 'mat'
@@ -88,4 +88,4 @@
         'searchbox.html',
         'donate.html',
     ]
-}
+}
diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -48,7 +48,7 @@ Template proposal
 
    end
 
-.. autofunction:: templateFunction  
+.. autofunction:: templateFunction
 
 
 Example code in the help section
@@ -100,6 +100,3 @@ Example code in the help section
    end
 
 .. autofunction:: templateFunctionExample
-
-
-
diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst
@@ -1,11 +1,11 @@
 Function description
 ********************
-  
-List of functions in the ``src`` folder.  
+
+List of functions in the ``src`` folder.
 
 ----
 
-.. automodule:: src 
+.. automodule:: src
 
 .. autofunction:: convertSourceToRaw
 .. autofunction:: createDataDictionary
@@ -14,13 +14,13 @@ List of functions in the ``src`` folder.
 .. autofunction:: createJson
 
 ``createJson`` can be used to save in a
-human readable format the extra parameters that you used to run your experiment. 
+human readable format the extra parameters that you used to run your experiment.
 This will most likely make the json file non-bids compliant but it can prove useful,
 to keep this information in your source dataset
 for when you write your methods sections 2 years later after running the experiment.
-This ensures that those are the exact parameters you used and you won't have 
-to read them from the ``setParameters.m`` file and wonder 
-if those might have been modified when running the experiment 
+This ensures that those are the exact parameters you used and you won't have
+to read them from the ``setParameters.m`` file and wonder
+if those might have been modified when running the experiment
 and you did not commit and tagged that change with git.
 
 And for the love of the flying spaghetti monster do not save all your
@@ -30,5 +30,3 @@ Octave installed on a computer (plus not everyone uses those).
 .. autofunction:: readAndFilterLogfile
 .. autofunction:: saveEventsFile
 .. autofunction:: userInputs
-
-
diff --git a/docs/source/gui.rst b/docs/source/gui.rst
@@ -1,17 +1,15 @@
 Graphic interface
 *****************
-  
+
 List of functions in the ``gui`` folder: those are mostly to handle the "graphic interface"
 that can be used to deal with ``userInputs()``.
 
 ----
 
-.. automodule:: src.gui 
+.. automodule:: src.gui
 
 .. autofunction:: askForGroupAndOrSession
 .. autofunction:: askUserGui
 .. autofunction:: createQuestionList
 .. autofunction:: getIsQuestionToAsk
 .. autofunction:: setDefaultResponses
-
-
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -38,11 +38,11 @@ A session folder will ALWAYS be created even if not requested (default will be `
 Task labels will be printed in ``camelCase`` in the filenames.
 
 Time stamps are added directly in the filename by adding a suffix
-``_date-*`` (default format is ``YYYYMMDDHHMM``) which makes the file name non-BIDS compliant. 
-This was added to prevent overwriting files in case a certain run needs to be done 
-a second time because of a crash. 
-Some of us are paranoid about keeping even cancelled runs during my experiments. 
-This suffix should be removed to make the data set BIDS compliant. 
+``_date-*`` (default format is ``YYYYMMDDHHMM``) which makes the file name non-BIDS compliant.
+This was added to prevent overwriting files in case a certain run needs to be done
+a second time because of a crash.
+Some of us are paranoid about keeping even cancelled runs during my experiments.
+This suffix should be removed to make the data set BIDS compliant.
 See ``convertSourceToRaw()`` for more details.
 
 For example::
diff --git a/docs/source/set_up.rst b/docs/source/set_up.rst
@@ -23,8 +23,8 @@ Group, subject, session and run
 ===============================
 
 You can use the ``userInputs()`` function to easily set the group name as well as
-the subject, session and run number. You can ask the function to not bother you with 
-group and session 
+the subject, session and run number. You can ask the function to not bother you with
+group and session
 
 
 .. todo:
@@ -50,4 +50,4 @@ group and session
     session
 
     If you use it with `cfg.subject.askGrpSess = [1 1]`, it will ask you about both.
-    This is the default behavior.
+    This is the default behavior.
diff --git a/lib/utils/abspath.m b/lib/utils/abspath.m
@@ -18,14 +18,14 @@
 %   Example
 %   fpath = abspath(fpath)
 %
-%   See also 
+%   See also
 
 %% Copyright notice
 %   --------------------------------------------------------------------
 %   Copyright (C) 2010 Deltares
 %       Bas Hoonhout
 %
-%       bas.hoonhout@deltares.nl	
+%       bas.hoonhout@deltares.nl
 %
 %       Rotterdamseweg 185
 %       2629HD Delft
@@ -45,9 +45,9 @@
 %   --------------------------------------------------------------------
 
 % This tool is part of <a href="http://OpenEarth.nl">OpenEarthTools</a>.
-% OpenEarthTools is an online collaboration to share and manage data and 
+% OpenEarthTools is an online collaboration to share and manage data and
 % programming tools in an open source, version controlled environment.
-% Sign up to recieve regular updates of this function, and to contribute 
+% Sign up to recieve regular updates of this function, and to contribute
 % your own tools.
 
 %% Version <http://svnbook.red-bean.com/en/1.5/svn.advanced.props.special.keywords.html>
@@ -114,4 +114,4 @@
 if isunix && ...
         (isempty(fpath) || ~strcmp(fpath(1), '~'))
     fpath = [filesep fpath];
-end
+end
diff --git a/lib/utils/file_utils.m b/lib/utils/file_utils.m
@@ -96,7 +96,7 @@
     % constructs
     % t must be a cell array of (relative or absolute) paths, d must be a
     % single cell containing the base path of relative paths in t
-    
+
     if ispc % valid absolute paths
         % Allow drive letter or UNC path
         mch = '^([a-zA-Z]:)|(\\\\[^\\]*)';
@@ -106,20 +106,20 @@
     if (nargin < 2) || isempty(basepath)
         basepath = {pwd};
     end
-    
+
     % Find partial paths, prepend them with d
     ppsel    = cellfun(@isempty, regexp(t, mch, 'once'));
     t(ppsel) = cellfun(@(t1)fullfile(basepath{1}, t1), t(ppsel), 'UniformOutput', false);
-    
+
     % Break paths into cell lists of folder names
     pt = pathparts(t);
-    
+
     % Remove single '.' folder names
     sd = cellfun(@(pt1)strcmp(pt1, '.'), pt, 'UniformOutput', false);
     for cp = 1:numel(pt)
         pt{cp} = pt{cp}(~sd{cp});
     end
-    
+
     % Go up one level for '..' folders, don't remove drive letter/server name
     % from PC path
     if ispc
@@ -142,14 +142,14 @@
             pt{cp} = tmppt;
         end
     end
-    
+
     % Assemble paths
     if ispc
         t = cellfun(@(pt1)fullfile(pt1{:}), pt, 'UniformOutput', false);
     else
         t = cellfun(@(pt1)fullfile(filesep, pt1{:}), pt, 'UniformOutput', false);
     end
-    
+
 end
 
     % ==========================================================================
@@ -160,14 +160,14 @@
     % returns cell array of path component cellstr arrays
     % For PC (WIN) targets, both '\' and '/' are accepted as filesep, similar
     % to MATLAB fileparts
-    
+
     if ispc
         fs = '\\/';
     else
         fs = filesep;
     end
     pp = cellfun(@(p1)textscan(p1, '%s', 'delimiter', fs, 'MultipleDelimsAsOne', 1), p);
-    
+
     if ispc
         for k = 1:numel(pp)
             if ~isempty(regexp(pp{k}{1}, '^[a-zA-Z]:$', 'once'))
@@ -198,14 +198,14 @@
         otherwise
             error('Invalid action: ''%s''.', action);
     end
-    
+
     if nargin < 2
         d = pwd;
     else
         d = file_utils(d, 'cpath');
     end
     dirMode = false;
-    
+
     if nargin < 3
         expr = '.*';
     else
@@ -220,16 +220,16 @@
             expr = varargin{1};
         end
     end
-    
+
     dd = dir(d);
-    
+
     if isempty(dd)
         return
     end
     files = sort({dd(~[dd.isdir]).name})';
     dirs = sort({dd([dd.isdir]).name})';
     dirs = setdiff(dirs, {'.', '..'});
-    
+
     if dirMode
         t = regexp(dirs, expr);
         if numel(dirs) == 1 && ~iscell(t)
@@ -244,12 +244,12 @@
         end
         files = files(~cellfun(@isempty, t));
     end
-    
+
     if fullpath
         files = cellfun(@(x) fullfile(d, x), files, 'UniformOutput', false);
         dirs = cellfun(@(x) fullfile(d, x), dirs, 'UniformOutput', false);
     end
     files = char(files);
     dirs = char(dirs);
-    
+
 end
diff --git a/notebooks/README.md b/notebooks/README.md
@@ -10,7 +10,7 @@
     install it. If using miniconda, run `conda install jupyter` to download and
     install the Jupyter Notebook package.
 
-1.  Install [Octave kernel](https://pypi.org/project/octave-kernel/): 
+1.  Install [Octave kernel](https://pypi.org/project/octave-kernel/):
     `pip install octave_kernel`
 
 1.  Run `jupyter notebook` in your terminal. `Octave` should appear on the list
diff --git a/npm-requirements.txt b/npm-requirements.txt
@@ -3,4 +3,3 @@ remark-lint@6.0.2
 remark-preset-lint-recommended@3.0.2
 remark-preset-lint-markdown-style-guide@2.1.2
 remark-preset-lint-consistent
-
diff --git a/templates/CHANGES b/templates/CHANGES
@@ -1,3 +1,3 @@
 1.0.0 YYYY-MM-DD
 
-  -  initial release
+  -  initial release
diff --git a/templates/README b/templates/README
diff --git a/tests/testData/eventsDataDictionary.json b/tests/testData/eventsDataDictionary.json
diff --git a/tests/testData/extra_bold.json b/tests/testData/extra_bold.json
diff --git a/tests/testData/stimDataDictionary.json b/tests/testData/stimDataDictionary.json
diff --git a/version.txt b/version.txt

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,2 @@`
`1`	`1`	`cd ${HOME}`
`2`	`2`	`cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..`
`3`		`-`