update copyright format in help - closes #215

Remi-Gau · Remi-Gau · commit b18cb81e8dc6 · 2022-11-02T10:41:24.000+01:00
diff --git a/cpp_bids.m b/cpp_bids.m
@@ -16,6 +16,7 @@ function cpp_bids(varargin)
     %
     % Example::
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     p = inputParser;
@@ -35,7 +36,7 @@ function cpp_bids(varargin)
         case 'init'
 
             initCppBids(verbose);
-            
+
         case 'dev'
 
             initCppBids(verbose);
@@ -44,7 +45,6 @@ function cpp_bids(varargin)
             addpath(testFolder, '-begin');
             utilFolder = fullfile(thisDirectory, 'tests', 'utils');
             addpath(utilFolder, '-begin');
-            
 
         case 'uninit'
 
@@ -67,6 +67,7 @@ function initCppBids(verbose)
     %
     %   initCppPtb()
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     thisDirectory = fileparts(mfilename('fullpath'));
@@ -136,6 +137,7 @@ function uninitCppBids()
     %
     %   uninitCppPtb()
     %
+
     % (C) Copyright 2021 CPP_BIDS developers
 
     global CPP_BIDS_INITIALIZED
@@ -168,6 +170,7 @@ function uninitCppBids()
     %
     % :returns: :retval: (boolean)
     %
+
     % (C) Copyright 2020 Agah Karakuzu
     % (C) Copyright 2022 CPP_BIDS developers
 
diff --git a/requirements.txt b/requirements.txt
@@ -5,7 +5,7 @@ sphinx_rtd_theme
 myst-parser
 sphinx-copybutton
 
-miss_hit==0.9.29
+miss_hit==0.9.35
 pre-commit
 
 notebook
diff --git a/runTests.m b/runTests.m
@@ -1,5 +1,6 @@
 function runTests()
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     % Elapsed time is ??? seconds.
diff --git a/src/checkCFG.m b/src/checkCFG.m
@@ -180,6 +180,7 @@
     %    cfg.bids.meg.DigitizedLandmarks = [];
     %    cfg.bids.meg.DigitizedHeadPoints = [];
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if nargin < 1 || isempty(cfg)
diff --git a/src/convertSourceToRaw.m b/src/convertSourceToRaw.m
@@ -20,6 +20,7 @@ function convertSourceToRaw(varargin)
     %          - :removes: the date suffix ``_date-*`` from the files where it is present
     %          - :zips: the ``_stim.tsv`` files.
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     args = inputParser;
diff --git a/src/createDataDictionary.m b/src/createDataDictionary.m
@@ -12,6 +12,7 @@ function createDataDictionary(cfg, logFile)
     % :param logFile: Contains the data you want to save.
     % :type logFile: structure
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     fileName = strrep(logFile(1).filename, '.tsv', '.json');
diff --git a/src/createDatasetDescription.m b/src/createDatasetDescription.m
@@ -12,6 +12,7 @@ function createDatasetDescription(cfg)
     %
     % :output: - :``dataset_description.json``: (jsonfile)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     opts.Indent = '    ';
diff --git a/src/createFilename.m b/src/createFilename.m
@@ -33,6 +33,7 @@
     %
     % See ``test_createFilename`` in the ``tests`` folder for more details on how to use it.
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     cfg = checkCFG(cfg);
diff --git a/src/createJson.m b/src/createJson.m
@@ -31,6 +31,7 @@ function createJson(varargin)
     %                         on the arguments passed in.
     %
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     %% Parse inputs
diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
@@ -42,6 +42,7 @@
     % See also: bids.transformers.filter
     %
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     % Check if input is cfg or the file path and assign the output filename for later saving
diff --git a/src/saveCfg.m b/src/saveCfg.m
@@ -28,6 +28,7 @@
     % in the ``pwd`` under ``'date-yyyymmddHHMM_cfg.json'``.
     %
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     %% Parse inputs
diff --git a/src/saveEventsFile.m b/src/saveEventsFile.m
@@ -74,6 +74,7 @@
     %
     %       logFile = saveEventsFile('close', cfg, logFile)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if nargin < 2
diff --git a/src/ui/askForGroupAndOrSession.m b/src/ui/askForGroupAndOrSession.m
@@ -15,6 +15,7 @@
     %           :cfg: (structure) Configuration update with the instructions if to ask for ``group``
     %                 and ``session``.
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if isempty(cfg)
diff --git a/src/ui/askUserCli.m b/src/ui/askUserCli.m
@@ -20,6 +20,7 @@
     % See also: createQuestionnaire
     %
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     fields = fieldnames(items);
diff --git a/src/ui/askUserGui.m b/src/ui/askUserGui.m
@@ -16,6 +16,7 @@
     %
     % :returns: - :responses: (cell) Response updated with the user inputs.
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     fields = fieldnames(items);
diff --git a/src/ui/createQuestionnaire.m b/src/ui/createQuestionnaire.m
@@ -30,6 +30,7 @@
     %
     % See also: returnDefaultQuestionnaire
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if nargin < 1
diff --git a/src/ui/getIsQuestionToAsk.m b/src/ui/getIsQuestionToAsk.m
@@ -17,6 +17,7 @@
     % :returns: - :argout1: (type) (dimension)
     %           - :argout2: (type) (dimension)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     isQuestionToAsk = cell2mat(questions.questionsToAsk(:, 2));
diff --git a/src/ui/returnDefaultQuestionnaire.m b/src/ui/returnDefaultQuestionnaire.m
@@ -7,6 +7,7 @@
     %
     %     q = returnDefaultQuestionnaire()
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     if nargin < 1
diff --git a/src/userInputs.m b/src/userInputs.m
@@ -22,6 +22,7 @@
     % - 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
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if nargin < 1
diff --git a/src/utils/checkCppBidsDependencies.m b/src/utils/checkCppBidsDependencies.m
@@ -9,6 +9,7 @@ function checkCppBidsDependencies(cfg)
     % :param cfg: Configuration. See ``checkCFG()``.
     % :type cfg: structure
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     global CPP_BIDS_INITIALIZED
diff --git a/src/utils/checkInput.m b/src/utils/checkInput.m
@@ -8,6 +8,7 @@
     %
     %   data = checkInput(data)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if islogical(data) && data
diff --git a/src/utils/getFullFilename.m b/src/utils/getFullFilename.m
@@ -11,6 +11,7 @@
     % :param cfg: Configuration. See ``checkCFG()``.
     % :type cfg: structure
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if isfield(cfg, 'dir') && isfield(cfg.dir, 'outputSubject') && ...
diff --git a/src/utils/getVersion.m b/src/utils/getVersion.m
@@ -9,6 +9,7 @@
     %
     % :returns: :versionNumber: (string) Use semantic versioning format (like v0.1.0)
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     try
diff --git a/src/utils/initializeExtraColumns.m b/src/utils/initializeExtraColumns.m
@@ -17,6 +17,7 @@
     %   logFile = initializeExtraColumns(logFile)
     %
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     fieldsToSet.length = 1;
diff --git a/src/utils/isPositiveInteger.m b/src/utils/isPositiveInteger.m
@@ -11,6 +11,7 @@
     %
     % :returns: :trueOrFalse: (boolean)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if ~isnumeric(input2check)
diff --git a/src/utils/nanPadding.m b/src/utils/nanPadding.m
@@ -7,6 +7,7 @@
     %
     %  data = nanPadding(cfg, data, expectedLength)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if nargin < 2
diff --git a/src/utils/pathToPrint.m b/src/utils/pathToPrint.m
@@ -7,6 +7,7 @@
     %             recursively on it.
     % :type pth: char or cellstr
     %
+
     % (C) Copyright 2021 CPP_BIDS developers
 
     if isunix()
diff --git a/src/utils/printCreditsCppBids.m b/src/utils/printCreditsCppBids.m
@@ -10,6 +10,7 @@ function printCreditsCppBids(cfg)
     % :param cfg: Configuration. See ``checkCFG()``.
     % :type cfg: structure
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     version = getVersion();
diff --git a/src/utils/removeDateEntity.m b/src/utils/removeDateEntity.m
@@ -8,6 +8,7 @@ function removeDateEntity(varargin)
     %   removeDateEntity(pathToDataSet, 'filter', filter)
     %
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     args = inputParser;
diff --git a/src/utils/returnHeaderName.m b/src/utils/returnHeaderName.m
@@ -15,6 +15,7 @@
     %
     % :returns: - :headerName: (string) return the extra column name to be used as header
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if nbCol == 1
diff --git a/src/utils/returnNamesExtraColumns.m b/src/utils/returnNamesExtraColumns.m
@@ -12,6 +12,7 @@
     %
     % :returns: - :namesExtraColumns: (cell) (nx1)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     namesExtraColumns = [];
diff --git a/src/utils/returnNbColumns.m b/src/utils/returnNbColumns.m
@@ -15,6 +15,7 @@
     %           - :nbCol: (integer) The number of columns associated to one entry of the extra
     %                     column list.
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     thisExtraColumn = logFile(1).extraColumns.(nameExtraColumn);
diff --git a/src/utils/returnRootDir.m b/src/utils/returnRootDir.m
@@ -4,6 +4,7 @@
     %
     %   rootDir = returnRootDir()
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     Mfile = 'cpp_bids.m';
diff --git a/src/utils/setDefaultFields.m b/src/utils/setDefaultFields.m
@@ -14,6 +14,7 @@
     %
     % :returns: - :structure: (structure)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     fieldsToSet = orderfields(fieldsToSet);
diff --git a/src/utils/talkToMe.m b/src/utils/talkToMe.m
@@ -4,6 +4,7 @@ function talkToMe(cfg, message)
     %
     %   talkToMe(cfg, message)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if isfield(cfg, 'verbose') && cfg.verbose > 0
diff --git a/src/utils/throwWarning.m b/src/utils/throwWarning.m
@@ -4,6 +4,7 @@ function throwWarning(cfg, identifier, warningMessage)
     %
     %   throwWarning(cfg, identifier, warningMessage)
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     % TODO refactor with bids.internal.warning ?
diff --git a/src/utils/transferInfoToBids.m b/src/utils/transferInfoToBids.m
@@ -20,6 +20,7 @@
     % manually in ``cfg.mri.repetitionTime`` or in ``cfg.task.name``
     % will be passed to the correct field in right fields of ``cfg.bids``.
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     if isfield(cfg, 'task') && isfield(cfg.task, 'name')
diff --git a/templates_functions/templateFunction.m b/templates_functions/templateFunction.m
@@ -28,6 +28,7 @@
     %    - item 1
     %    - item 2
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     % The code goes below
diff --git a/templates_functions/templateFunctionExample.m b/templates_functions/templateFunctionExample.m
@@ -35,6 +35,7 @@ function templateFunctionExample()
     %
     % % tests end here because test indentation has ended
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     % The code goes below
diff --git a/tests/utils/globalTestSetUp.m b/tests/utils/globalTestSetUp.m
@@ -1,5 +1,6 @@
 function cfg = globalTestSetUp()
     %
+
     % (C) Copyright 2020 CPP_BIDS developers
 
     cfg.verbose = false;
diff --git a/tests/utils/isOctave.m b/tests/utils/isOctave.m
@@ -8,6 +8,7 @@
     %
     % :returns: :retval: (boolean)
     %
+
     % (C) Copyright 2022 CPP_BIDS developers
 
     persistent cacheval   % speeds up repeated calls

Original file line number	Diff line number	Diff line change
`@@ -16,6 +16,7 @@ function cpp_bids(varargin)`
`16`	`16`	`%`
`17`	`17`	`% Example::`
`18`	`18`	`%`
	`19`	`+`
`19`	`20`	`% (C) Copyright 2022 CPP_BIDS developers`
`20`	`21`
`21`	`22`	`p = inputParser;`
`@@ -35,7 +36,7 @@ function cpp_bids(varargin)`
`35`	`36`	`case 'init'`
`36`	`37`
`37`	`38`	`initCppBids(verbose);`
`38`		`-`
	`39`	`+`
`39`	`40`	`case 'dev'`
`40`	`41`
`41`	`42`	`initCppBids(verbose);`
`@@ -44,7 +45,6 @@ function cpp_bids(varargin)`
`44`	`45`	`addpath(testFolder, '-begin');`
`45`	`46`	`utilFolder = fullfile(thisDirectory, 'tests', 'utils');`
`46`	`47`	`addpath(utilFolder, '-begin');`
`47`		`-`
`48`	`48`
`49`	`49`	`case 'uninit'`
`50`	`50`
`@@ -67,6 +67,7 @@ function initCppBids(verbose)`
`67`	`67`	`%`
`68`	`68`	`% initCppPtb()`
`69`	`69`	`%`
	`70`	`+`
`70`	`71`	`% (C) Copyright 2022 CPP_BIDS developers`
`71`	`72`
`72`	`73`	`thisDirectory = fileparts(mfilename('fullpath'));`
`@@ -136,6 +137,7 @@ function uninitCppBids()`
`136`	`137`	`%`
`137`	`138`	`% uninitCppPtb()`
`138`	`139`	`%`
	`140`	`+`
`139`	`141`	`% (C) Copyright 2021 CPP_BIDS developers`
`140`	`142`
`141`	`143`	`global CPP_BIDS_INITIALIZED`
`@@ -168,6 +170,7 @@ function uninitCppBids()`
`168`	`170`	`%`
`169`	`171`	`% :returns: :retval: (boolean)`
`170`	`172`	`%`
	`173`	`+`
`171`	`174`	`% (C) Copyright 2020 Agah Karakuzu`
`172`	`175`	`% (C) Copyright 2022 CPP_BIDS developers`
`173`	`176`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,6 @@`
`1`	`1`	`function runTests()`
`2`	`2`	`%`
	`3`	`+`
`3`	`4`	`% (C) Copyright 2022 CPP_BIDS developers`
`4`	`5`
`5`	`6`	`% Elapsed time is ??? seconds.`
Original file line number	Diff line number	Diff line change
`@@ -180,6 +180,7 @@`
`180`	`180`	`% cfg.bids.meg.DigitizedLandmarks = [];`
`181`	`181`	`% cfg.bids.meg.DigitizedHeadPoints = [];`
`182`	`182`	`%`
	`183`	`+`
`183`	`184`	`% (C) Copyright 2020 CPP_BIDS developers`
`184`	`185`
`185`	`186`	`if nargin < 1 \|\| isempty(cfg)`
Original file line number	Diff line number	Diff line change
`@@ -20,6 +20,7 @@ function convertSourceToRaw(varargin)`
`20`	`20`	% - :removes: the date suffix ``_date-*`` from the files where it is present
`21`	`21`	% - :zips: the ``_stim.tsv`` files.
`22`	`22`	`%`
	`23`	`+`
`23`	`24`	`% (C) Copyright 2020 CPP_BIDS developers`
`24`	`25`
`25`	`26`	`args = inputParser;`
Original file line number	Diff line number	Diff line change
`@@ -12,6 +12,7 @@ function createDataDictionary(cfg, logFile)`
`12`	`12`	`% :param logFile: Contains the data you want to save.`
`13`	`13`	`% :type logFile: structure`
`14`	`14`	`%`
	`15`	`+`
`15`	`16`	`% (C) Copyright 2020 CPP_BIDS developers`
`16`	`17`
`17`	`18`	`fileName = strrep(logFile(1).filename, '.tsv', '.json');`
Original file line number	Diff line number	Diff line change
`@@ -12,6 +12,7 @@ function createDatasetDescription(cfg)`
`12`	`12`	`%`
`13`	`13`	% :output: - :``dataset_description.json``: (jsonfile)
`14`	`14`	`%`
	`15`	`+`
`15`	`16`	`% (C) Copyright 2020 CPP_BIDS developers`
`16`	`17`
`17`	`18`	`opts.Indent = ' ';`
Original file line number	Diff line number	Diff line change
`@@ -33,6 +33,7 @@`
`33`	`33`	`%`
`34`	`34`	% See ``test_createFilename`` in the ``tests`` folder for more details on how to use it.
`35`	`35`	`%`
	`36`	`+`
`36`	`37`	`% (C) Copyright 2020 CPP_BIDS developers`
`37`	`38`
`38`	`39`	`cfg = checkCFG(cfg);`
Original file line number	Diff line number	Diff line change
`@@ -31,6 +31,7 @@ function createJson(varargin)`
`31`	`31`	`% on the arguments passed in.`
`32`	`32`	`%`
`33`	`33`	`%`
	`34`	`+`
`34`	`35`	`% (C) Copyright 2020 CPP_BIDS developers`
`35`	`36`
`36`	`37`	`%% Parse inputs`
Original file line number	Diff line number	Diff line change
`@@ -42,6 +42,7 @@`
`42`	`42`	`% See also: bids.transformers.filter`
`43`	`43`	`%`
`44`	`44`	`%`
	`45`	`+`
`45`	`46`	`% (C) Copyright 2020 CPP_BIDS developers`
`46`	`47`
`47`	`48`	`% Check if input is cfg or the file path and assign the output filename for later saving`