[ENH] options are saved in a cfg folder in the working directory

.gitignore

@@ -20,6 +20,7 @@ demos/spm*/raw
 demos/spm*/source
 
 # test folder and dummy data
+tests/cfg/*.json
 tests/sub-01/*
 tests/group/*
 tests/models/*.json

src/utils/loadAndCheckOptions.m

@@ -25,7 +25,9 @@
   %    - add test for when the input is a structure.
 
   if nargin < 1 || isempty(optionJsonFile)
-    optionJsonFile = spm_select('FPList', pwd, '^options_task-.*.json$');
+    optionJsonFile = spm_select('FPList', ...
+                                fullfile(pwd, 'cfg'), ...
+                                '^options_task-.*.json$');
   end
 
   if isstruct(optionJsonFile)

src/utils/saveOptions.m

@@ -12,7 +12,9 @@ function saveOptions(opt)
   % :type opt: structure
   %
 
-  filename = fullfile(pwd, ['options', ...
+  optionDir = fullfile(pwd, 'cfg');
+  [~,~,~] = mkdir(optionDir);
+  filename = fullfile(optionDir, ['options', ...
                             '_task-', opt.taskName, ...
                             '_date-' datestr(now, 'yyyymmddHHMM'), ...
                             '.json']);

tests/test_loadAndCheckOptions.m

@@ -8,11 +8,12 @@
 
 function test_loadAndCheckOptionsBasic()
 
-  delete('*.json');
+  mkdir cfg;
+  delete(fullfile(pwd, 'cfg', '*.json'));
 
   % create dummy json file
   jsonContent.taskName = 'vismotion';
-  filename = 'options_task-vismotion.json';
+  filename = fullfile(pwd, 'cfg', 'options_task-vismotion.json');
   spm_jsonwrite(filename, jsonContent);
 
   % makes sure that it is picked up by default
@@ -27,6 +28,9 @@ function test_loadAndCheckOptionsBasic()
 
 function test_loadAndCheckOptionsStructure()
 
+  mkdir cfg;
+  delete(fullfile(pwd, 'cfg', '*.json'));
+
   % create dummy json file
   opt.taskName = 'vismotion';
 
@@ -42,19 +46,20 @@ function test_loadAndCheckOptionsStructure()
 
 function test_loadAndCheckOptionsFromFile()
 
-  delete('*.json');
+  mkdir cfg;
+  delete(fullfile(pwd, 'cfg', '*.json'));
 
   % create dummy json file
   jsonContent.taskName = 'vismotion';
   jsonContent.space = 'individual';
   jsonContent.groups = {''};
   jsonContent.subjects = {[]};
 
-  filename = 'options_task-vismotion_space-T1w.json';
+  filename = fullfile(pwd, 'cfg', 'options_task-vismotion_space-T1w.json');
   spm_jsonwrite(filename, jsonContent);
 
   % makes sure that it is read correctly from
-  opt = loadAndCheckOptions('options_task-vismotion_space-T1w.json');
+  opt = loadAndCheckOptions(filename);
 
   expectedOptions = defaultOptions();
   expectedOptions.taskName = 'vismotion';
@@ -68,30 +73,31 @@ function test_loadAndCheckOptionsFromFile()
 
 function test_loadAndCheckOptionsFromSeveralFiles()
 
-  delete('*.json');
+  mkdir cfg;
+  delete(fullfile(pwd, 'cfg', '*.json'));
 
   % create old dummy json file
   jsonContent.taskName = 'vismotion';
-  filename = fullfile(pwd, ['options', ...
-                            '_task-', jsonContent.taskName, ...
-                            '_date-151501011111', ...
-                            '.json']);
+  filename = fullfile(pwd, 'cfg', ['options', ...
+                                   '_task-', jsonContent.taskName, ...
+                                   '_date-151501011111', ...
+                                   '.json']);
   spm_jsonwrite(filename, jsonContent);
 
   % create dummy json file with no date
   jsonContent.taskName = 'vismotion';
   jsonContent.space = 'individual';
-  filename = 'options_task-vismotion_space-T1w.json';
+  filename = fullfile(pwd, 'cfg', 'options_task-vismotion_space-T1w.json');
   spm_jsonwrite(filename, jsonContent);
 
   % most recent option file that should be read from
   jsonContent.taskName = 'vismotion';
   jsonContent.space = 'individual';
   jsonContent.funcVoxelDims = [1 1 1];
-  filename = fullfile(pwd, ['options', ...
-                            '_task-', jsonContent.taskName, ...
-                            '_date-' datestr(now, 'yyyymmddHHMM'), ...
-                            '.json']);
+  filename = fullfile(pwd, 'cfg', ['options', ...
+                                   '_task-', jsonContent.taskName, ...
+                                   '_date-' datestr(now, 'yyyymmddHHMM'), ...
+                                   '.json']);
   spm_jsonwrite(filename, jsonContent);
 
   % makes sure that the right json is read