Add codespell support (config, workflow to detect/not fix) and make it fix few typos

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git*,.codespellrc,*.csv
+check-hidden = true
+# ignore-regex = 
+ignore-words-list = ans,nd,assignin,onl

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# Codespell configuration is within .codespellrc
+---
+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@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

Browsing Functions/allen_ccf_npx_4shank.m

@@ -540,7 +540,7 @@ function update_slice(probe_atlas_gui,varargin)
 
     end
 
-    % Get the coordiates on the plane
+    % Get the coordinates on the plane
     x_idx = round(plane_x);
     y_idx = round(plane_y);
     z_idx = round(plane_z);

Browsing Functions/allen_ccf_npx_4shank_spherical.m

@@ -529,7 +529,7 @@ function update_slice(probe_atlas_gui,varargin)
 
     end
 
-    % Get the coordiates on the plane
+    % Get the coordinates on the plane
     x_idx = round(plane_x);
     y_idx = round(plane_y);
     z_idx = round(plane_z);

Browsing Functions/distinguishable_colors.m

@@ -61,7 +61,7 @@
     bg = [1 1 1];  % default white background
   else
     if iscell(bg)
-      % User specified a list of colors as a cell aray
+      % User specified a list of colors as a cell array
       bgc = bg;
       for i = 1:length(bgc)
 	bgc{i} = parsecolor(bgc{i});

Browsing Functions/plotAsProbe.m

@@ -1,7 +1,7 @@
 
 
 function plotAsProbe(data, ann_percents, yc, cm, cm2, sqSizeY, active_site_start, rpl)
-% data is vector, same lenght as xc and yc
+% data is vector, same length as xc and yc
 % cm is colormap, size [n x 3]
 %
 % other usage: if data is empty and cm's first dimension is the same length

Browsing Functions/plotDistToNearestToTip.m

@@ -102,7 +102,7 @@
         cur_annotation_square = squeeze(annotation_square(ind,:,:));
         currSqVec = cur_annotation_square(:);
 
-        % find where the annotation isn't equal to that at the curent point
+        % find where the annotation isn't equal to that at the current point
         otherInd = find(currSqVec(distOrder)~=currSqVec(distOrder(1)),1); 
         if isempty(otherInd)
             otherDist(ind) = dists(end);

Browsing Functions/selectStructure.m

@@ -249,7 +249,7 @@ function doSelectAll(selectall_btn, evd, listbox) %#ok
 
 %% Listbox callback
 function doListboxClick(listbox, evd, selectall_btn) %#ok
-% if this is a doubleclick, doOK
+% if this is a double-click, doOK
 if strcmp(get(gcbf,'SelectionType'),'open')
     doOK([],[],listbox);
 elseif nargin == 3

SHARP-Track/Analyze_ROIs.m

@@ -94,7 +94,7 @@
 
 
 % initialize array of locations (AP, DV, ML relative to bregma) in reference space
-% and the correponding region annotations
+% and the corresponding region annotations
 roi_location = zeros(sum(rois(:)>0),3);
 roi_annotation = cell(sum(rois(:)>0),3);
 

SHARP-Track/Process_Histology.m

@@ -125,7 +125,7 @@
 % it also pads images smaller than the reference_size and requests that you
 % crop images larger than this size
 %
-% note -- presssing left or right arrow saves the modified image, so be
+% note -- pressing left or right arrow saves the modified image, so be
 % sure to do this even after modifying the last slice in the folder
 slice_figure = figure('Name','Slice Viewer');
 SliceFlipper(slice_figure, folder_processed_images, atlas_reference_size)