Merge pull request #2295 from yarikoptic/enh-codespell

codespell: config, workflow (fail if typos introduced) and some typos fixed

.codespellrc

@@ -0,0 +1,10 @@
+[codespell]
+skip = .git,*.pdf,*.svg,external,src
+ignore-words-list = ans,cfg,siz,pnt,pos,ori,ext,dum,siz,toi,homogenous,whos,nas,ini,lpa,rpa,als,ali,ars,ari,pls,pli,prs,pri,las,lai,ras,rai,lps,lpi,rps,rpi,asl,ail,asr,air,psl,pil,psr,pir,sal,ial,sar,iar,spl,ipl,spr,ipr,sla,ila,sra,ira,slp,ilp,srp,irp,lsa,lia,rsa,ria,lsp,lip,rsp,rip
+
+# case sensitive etc as regex
+# ignore-regex = \b(ALS|correctT)\b|n\(ot a
+
+# there is no files option yet: https://github.com/codespell-project/codespell/issues/2758
+# but for now - running codespell only for utilities
+# files = utilites

.github/workflows/codespell.yml

@@ -0,0 +1,24 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
+        with:
+          path: utilities

utilities/dccnpath.m

@@ -49,7 +49,7 @@
   filename = strrep(filename,'\','/');
 end
 
-% alternative1 alllows to test with local files in the present working directory
+% alternative1 allows to test with local files in the present working directory
 % this is often convenient when initially setting up a new test script while the data is not yet uploaded
 [p, f, x] = fileparts(filename);
 alternative1 = [f x];

utilities/ft_average_sens.m

@@ -81,7 +81,7 @@
 x1 = pos*u(:, 2);
 x2 = pos*u(:, 1);
 
-% detemine the indices of three reference sensors that are close to the three principal axes
+% determine the indices of three reference sensors that are close to the three principal axes
 [dum, ind1] = min(x1);
 [dum, ind2] = max(x1);
 [dum, ind3] = max(abs(x2 - mean(x2([ind1 ind2]))));

utilities/ft_channelcombination.m

@@ -100,7 +100,7 @@
 else
   % a combination is made for each row of the input selection after
   % translating the channel group (such as 'all') to the proper channel names
-  % and within each set, double occurences and autocombinations are removed
+  % and within each set, double occurrences and autocombinations are removed
 
   selmat = false(numel(datachannel));
   for sel=1:size(channelcmb,1)

utilities/ft_channelselection.m

@@ -244,7 +244,7 @@
 end
 
 if ~isempty(findreg)
-  findreg  = unique(findreg); % remove multiple occurances due to multiple wildcards
+  findreg  = unique(findreg); % remove multiple occurrences due to multiple wildcards
   labelreg = datachannel(labelreg);
 end
 
@@ -448,7 +448,7 @@
 findspike      = find(strcmpi(channel, 'spike'));
 findgui        = find(strcmpi(channel, 'gui'));
 
-% remove any occurences of groups in the channel list
+% remove any occurrences of groups in the channel list
 channel([
   findall
   findreg

utilities/ft_checkconfig.m

@@ -308,7 +308,7 @@
         if silent
           % don't mention it
         elseif loose
-          ft_warning('The field cfg.%s.%s is deprecated, pleae use cfg.%s\n', subname, fieldname{i}, fieldname{i});
+          ft_warning('The field cfg.%s.%s is deprecated, please use cfg.%s\n', subname, fieldname{i}, fieldname{i});
         elseif pedantic
           ft_error('The field cfg.%s.%s is not longer supported, please use cfg.%s\n', subname, fieldname{i}, fieldname{i});
         end
@@ -321,7 +321,7 @@
         if silent
           % don't mention it
         elseif loose
-          ft_warning('The field cfg.%s.%s is deprecated, pleae use cfg.%s\n', subname, fieldname{i}, fieldname{i});
+          ft_warning('The field cfg.%s.%s is deprecated, please use cfg.%s\n', subname, fieldname{i}, fieldname{i});
         elseif pedantic
           ft_error('The field cfg.%s.%s is not longer supported, please use cfg.%s\n', subname, fieldname{i}, fieldname{i});
         end
@@ -347,7 +347,7 @@
 % them in a separate substructure.
 %
 % This is to ensure backward compatibility of end-user scripts, FieldTrip functions
-% and documentation that do not use the nested detailled configuration but that use a
+% and documentation that do not use the nested detailed configuration but that use a
 % flat configuration.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 if ~isempty(createsubcfg)
@@ -574,7 +574,7 @@
         if silent
           % don't mention it
         elseif loose
-          ft_warning('The field cfg.%s is deprecated, pleae use cfg.%s.%s\n', fieldname{i}, subname, fieldname{i});
+          ft_warning('The field cfg.%s is deprecated, please use cfg.%s.%s\n', fieldname{i}, subname, fieldname{i});
         elseif pedantic
           ft_error('The field cfg.%s is not longer supported, please use cfg.%s.%s\n', fieldname{i}, subname, fieldname{i});
         end
@@ -587,7 +587,7 @@
         if silent
           % don't mention it
         elseif loose
-          ft_warning('The field cfg.%s is deprecated, pleae use cfg.%s.%s\n', fieldname{i}, subname, fieldname{i});
+          ft_warning('The field cfg.%s is deprecated, please use cfg.%s.%s\n', fieldname{i}, subname, fieldname{i});
         elseif pedantic
           ft_error('The field cfg.%s is not longer supported, please use cfg.%s.%s\n', fieldname{i}, subname, fieldname{i});
         end

utilities/ft_checkdata.m

@@ -1,7 +1,7 @@
 function [data] = ft_checkdata(data, varargin)
 
 % FT_CHECKDATA checks the input data of the main FieldTrip functions, e.g. whether the
-% type of data strucure corresponds with the required data. If necessary and possible,
+% type of data structure corresponds with the required data. If necessary and possible,
 % this function will adjust the data structure to the input requirements (e.g. change
 % dimord, average over trials, convert inside from index into logical).
 %
@@ -63,7 +63,7 @@
 %
 % $Id$
 
-% in case of an error this function could use dbstack for more detailled
+% in case of an error this function could use dbstack for more detailed
 % user feedback
 %
 % this function should replace/encapsulate

utilities/ft_compile_mex.m

@@ -8,7 +8,7 @@ function ft_compile_mex(force)
 % path. Subsequently you can rtun this function to recompile it on your platform with
 % your compiler settings
 %
-% The standards procedure for compiling mex files is detailled on
+% The standards procedure for compiling mex files is detailed on
 % http://www.fieldtriptoolbox.org/development/guidelines/code#compiling_mex_files
 %
 % Please note that this script does NOT set up your MEX environment for you, so in

utilities/ft_datatype_comp.m

@@ -11,8 +11,8 @@
 % An example of a decomposed raw data structure with 100 components that resulted from
 % a 151-channel MEG recording is shown here:
 %
-%           topo: [151x100 double]  the compoment topographies
-%       unmixing: [100x151 double]  the compoment unmixing matrix
+%           topo: [151x100 double]  the component topographies
+%       unmixing: [100x151 double]  the component unmixing matrix
 %      topolabel: {151x1 cell}      the channel labels (e.g. 'MRC13')
 %          label: {100x1 cell}      the component labels (e.g. 'runica001')
 %           time: {1x10 cell}       the time axis [1*Ntime double] per trial

utilities/ft_datatype_dip.m

@@ -2,7 +2,7 @@
 
 % FT_DATATYPE_DIP descripts the FieldTrip MATLAB structure for dip data
 %
-% The dip structure reprents a dipole model that has been fitted to
+% The dip structure represents a dipole model that has been fitted to
 % ERP or ERF data using a non-linear optimization approach. It is
 % usually generated by the FT_DIPOLEFITTING function.
 %

utilities/ft_datatype_freq.m

@@ -10,7 +10,7 @@
 % and 120 frequencies is
 %
 %       dimord: 'chan_freq'          defines how the numeric data should be interpreted
-%    powspctrm: [306x120 double]     the power spectum
+%    powspctrm: [306x120 double]     the power spectrum
 %        label: {306x1 cell}         the channel labels
 %         freq: [1x120 double]       the frequencies expressed in Hz
 %          cfg: [1x1 struct]         the configuration used by the function that generated this data structure
@@ -20,7 +20,7 @@
 % and 60 timepoints is
 %
 %       dimord: 'chan_freq_time'     defines how the numeric data should be interpreted
-%    powspctrm: [306x120x60 double]  the power spectum
+%    powspctrm: [306x120x60 double]  the power spectrum
 %        label: {306x1 cell}         the channel labels
 %         freq: [1x120 double]       the frequencies, expressed in Hz
 %         time: [1x60 double]        the time, expressed in seconds

utilities/ft_datatype_parcellation.m

@@ -7,7 +7,7 @@
 % A parcellation describes the tissue types for each of the surface elements.
 % Parcellations are often, but not always labeled. A parcellatoin can be used to
 % estimate the activity from MEG data in a known region of interest. A surface-based
-% atlas is basically a very detailled parcellation with an anatomical label for each
+% atlas is basically a very detailed parcellation with an anatomical label for each
 % vertex.
 %
 % An example of a surface based Brodmann parcellation looks like this

utilities/ft_datatype_raw.m

@@ -42,7 +42,7 @@
 % (2010v1) In 2010/Q3 it shortly contained the trialdef field which was a copy
 % of the trial definition (trl) is generated by FT_DEFINETRIAL.
 %
-% (2007) It used to contain the offset field, which correcponds to trl(:,3).
+% (2007) It used to contain the offset field, which corresponds to trl(:,3).
 % Since the offset field is redundant with the time axis, the offset field is
 % from now on not present any more. It can be recreated if needed.
 %

utilities/ft_datatype_spike.m

@@ -38,7 +38,7 @@
 % FT_SPIKE_MAKETRIALS function can be used to reorganise the SPIKE
 % structure such that the spike times are expressed relative to a trigger
 % instead of relative to the acquisition devices internal timestamp clock.
-% The time field then contains only those spikes that ocurred within one of
+% The time field then contains only those spikes that occurred within one of
 % the trials . The spike times are now expressed on seconds relative to the
 % trigger.
 %

utilities/ft_datatype_volume.m

@@ -45,7 +45,7 @@
 % with it here. However, keep this snippet of code for reference.
 %
 % (2011) The dimord field was deprecated and we agreed that volume
-% data should be 3-dimensional and not N-dimensional with arbitary
+% data should be 3-dimensional and not N-dimensional with arbitrary
 % dimensions. In case time-frequency recolved data has to be represented
 % on a 3-d grid, the source representation should be used.
 %

utilities/ft_determine_coordsys.m

@@ -19,7 +19,7 @@
 %   axisscale    = scaling factor for the reference axes and sphere (default = 1)
 %   clim         = lower and upper anatomical MRI limits (default = [0 1])
 %
-% This function wil pop up a figure that allows you to check whether the
+% This function will pop up a figure that allows you to check whether the
 % alignment of the object relative to the coordinate system axes is correct
 % and what the anatomical labels of the coordinate system axes are. You
 % should switch on the 3D rotation option in the figure panel to rotate and
@@ -65,7 +65,7 @@
 dtype = ft_datatype(data);
 
 % the high-level data structures are detected with ft_datatype, but there are
-% also some low-level data structures that need to be supproted here
+% also some low-level data structures that need to be supported here
 if strcmp(dtype, 'unknown')
   if isfield(data, 'fid') || (isfield(data, 'tri') && isfield(data, 'pos'))
     dtype = 'headshape';

utilities/ft_fetch_data.m

@@ -168,7 +168,7 @@
             ft_error('some of the requested samples occur twice in the data and have conflicting values');
           end
           % Otherwise rises a warning and exits the loop.
-          ft_warning('some of the requested samples occur twice in the data and have conflicting values, using only the last occurence of each sample');
+          ft_warning('some of the requested samples occur twice in the data and have conflicting values, using only the last occurrence of each sample');
           break
         end
       end

utilities/ft_hastoolbox.m

@@ -652,7 +652,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 function status = hasfunction(funname, toolbox)
 try
-  % call the function without any input arguments, which probably is inapropriate
+  % call the function without any input arguments, which probably is inappropriate
   feval(funname);
   % it might be that the function without any input already works fine
   status = true;

utilities/ft_headcoordinates.m

@@ -75,7 +75,7 @@
 %   the origin is the intersection of the line through LPA and RPA and a line orthogonal to L passing through the nasion
 %
 % The ASA coordinate system is defined as follows:
-%   the origin is at the orthogonal intersection of the line from rpa-lpa and the line trough nas
+%   the origin is at the orthogonal intersection of the line from rpa-lpa and the line through nas
 %   the X-axis goes towards nas
 %   the Y-axis goes through rpa and lpa
 %   the Z-axis goes approximately towards the vertex, orthogonal to X and Y

utilities/ft_platform_supports.m

@@ -16,7 +16,7 @@
 %   'onCleanup'                     onCleanup(...)
 %   'alim'                          alim(...)
 %   'int32_logical_operations'      bitand(a,b) with a, b of type int32
-%   'graphics_objects'              graphics sysem is object-oriented
+%   'graphics_objects'              graphics system is object-oriented
 %   'libmx_c_interface'             libmx is supported through mex in the C-language (recent MATLAB versions only support C++)
 %   'images'                        all image processing functions in FieldTrip's external/images directory
 %   'signal'                        all signal processing functions in FieldTrip's external/signal directory

utilities/ft_postamble.m

@@ -33,7 +33,7 @@ function ft_postamble(cmd, varargin)
 
 % ideally this would be a script, because the local variables would then be
 % shared with the calling function. Instead, this is a function which then
-% passes the variables explicitely to another script which is eval'ed.
+% passes the variables explicitly to another script which is eval'ed.
 
 % the following section ensures that these scripts are included as
 % dependencies when using the MATLAB compiler

utilities/ft_preamble.m

@@ -33,7 +33,7 @@ function ft_preamble(cmd, varargin)
 
 % ideally this would be a script, because the local variables would then be
 % shared with the calling function. Instead, this is a function which then
-% passes the variables explicitely to another script which is eval'ed.
+% passes the variables explicitly to another script which is eval'ed.
 
 % the following section ensures that these scripts are included as
 % dependencies when using the MATLAB compiler

utilities/ft_selectdata.m

@@ -34,7 +34,7 @@
 %   cfg.nanmean     = string, can be 'yes' or 'no' (default = 'no')
 %
 % When you average over a dimension, you can choose whether to keep that dimension in
-% the data representation or remove it alltogether.
+% the data representation or remove it altogether.
 %   cfg.keeprptdim     = 'yes' or 'no' (default is automatic)
 %   cfg.keepchandim    = 'yes' or 'no' (default = 'yes')
 %   cfg.keepchancmbdim = 'yes' or 'no' (default = 'yes')
@@ -509,7 +509,7 @@
 switch selmode
   case 'intersect'
     if iscell(selindx)
-      % there are multiple selections in multipe vectors, the selection is in the matrices contained within the cell-array
+      % there are multiple selections in multiple vectors, the selection is in the matrices contained within the cell-array
       for j=1:numel(selindx)
         if ~isempty(selindx{j}) && all(isnan(selindx{j}))
           % no selection needs to be made
@@ -999,7 +999,7 @@
   end
 
 elseif numel(cfg.latency)==2
-  % the [min max] range can be specifed with +inf or -inf, but should
+  % the [min max] range can be specified with +inf or -inf, but should
   % at least partially overlap with the time axis of the input data
   mintime = min(alltimevec);
   maxtime = max(alltimevec);
@@ -1137,7 +1137,7 @@
     end
 
   elseif numel(cfg.frequency)==2
-    % the [min max] range can be specifed with +inf or -inf, but should
+    % the [min max] range can be specified with +inf or -inf, but should
     % at least partially overlap with the freq axis of the input data
     minfreq = min(freqaxis);
     maxfreq = max(freqaxis);

utilities/ft_setopt.m

@@ -49,7 +49,7 @@
     valindex = keyindex+1;
     opt{valindex} = val;
   elseif length(sel)>1
-    % first remove all occurences
+    % first remove all occurrences
     keyindex = 2*sel-1;
     valindex = keyindex+1;
     opt([keyindex valindex]) = [];

utilities/ft_standalone.m

@@ -18,7 +18,7 @@ function ft_standalone(varargin)
 %   ft_standalone --option value scriptname.m
 % or on the Linux/macOS command line
 %   fieldtrip.sh <MATLABROOT> --option value scriptname.m
-% The options and their values are automaticallly made available as local
+% The options and their values are automatically made available as local
 % variables in the script execution environment.
 %
 % See also FT_COMPILE_STANDALONE

utilities/ft_transform_geometry.m

@@ -129,7 +129,7 @@
 
 % tfields must be rotated, translated and scaled
 % rfields must only be rotated
-% mfields must be simply multipied
+% mfields must be simply multiplied
 % recfields must be recursed into
 tfields   = {'pos' 'pnt' 'o' 'coilpos' 'elecpos' 'optopos' 'chanpos' 'chanposold' 'nas' 'lpa' 'rpa' 'zpoint'}; % apply rotation plus translation
 rfields   = {'ori' 'nrm'     'coilori' 'elecori' 'optoori' 'chanori' 'chanoriold' 'mom'                     }; % only apply rotation

utilities/ft_warp_error.m

@@ -6,7 +6,7 @@
 % Use as
 %   dist = ft_warp_error(M, input, target, 'method')
 %
-% It returns the mean Euclidian distance (i.e. the residual) for an interative
+% It returns the mean Euclidean distance (i.e. the residual) for an interactive
 % optimalization to transform the input towards the target using the
 % transformation M with the specified warping method.
 %
@@ -56,7 +56,7 @@
   % this is done here in one step, but can also be done in separate steps (see example code below)
   el = project_elec(input, target.pos, target.tri);
   dist = mean(el(:,4));
-  % the following example code is more elaborate, and can be used for detailled testing
+  % the following example code is more elaborate, and can be used for detailed testing
   if 0
     Npos = size(input,1);
     prj = zeros(Npos, 3);

utilities/ft_warp_optim.m

@@ -61,7 +61,7 @@
 %
 % $Id$
 
-% this can be used for printing detailled user feedback
+% this can be used for printing detailed user feedback
 fb = false;
 
 if nargin<3