Merge pull request #515 from Remi-Gau/misc-bug-squashing

[FIX] Misc bug squashing 🐛 💀

.github/workflows/tests_matlab.m

@@ -11,6 +11,6 @@
 
 cd(fullfile(root_dir));
 
-initCppSpm(true);
+cpp_spm('dev');
 
 run run_tests();

.gitignore

@@ -1,4 +1,5 @@
 *_report.md
+
 # General
 .DS_Store
 
@@ -17,9 +18,9 @@ options_task-*date*.json
 onsets*_events.mat
 
 ## virtual env
-cpp_spm/*
-env/*
-venv/*
+cpp_spm
+env
+venv
 
 ## visual studio code
 .vscode

manualTests/test_ds114.m

@@ -18,7 +18,8 @@
 WD = fullfile(fileparts(mfilename('fullpath')), '..', 'demos', 'openneuro');
 cd(WD);
 
-run ../../initCppSpm.m;
+addpath(fullfile(pwd, '..', '..'));
+cpp_spm('init');
 
 optionsFilesList = { ...
                     'options_task-linebisection.json'; ...

manualTests/test_moae.m

@@ -18,7 +18,8 @@
 WD = fullfile(fileparts(mfilename('fullpath')), '..', 'demos', 'MoAE');
 cd(WD);
 
-run ../../initCppSpm.m;
+addpath(fullfile(pwd, '..', '..'));
+cpp_spm('init');
 
 %% Set up
 optionsFilesList = {'options_task-auditory.json'; ...

miss_hit.cfg

@@ -14,7 +14,7 @@ regex_method_name: "[a-z]+([A-Z0-9]+[a-z]*)*"
 # all uppercase or camelCase
 regex_parameter_name: "[A-Z]+(_[A-Z]+)*|[a-z]+([A-Z]+[a-z]*)*"
 
-suppress_rule: "naming_parameters"
+# suppress_rule: "naming_parameters"
 
 exclude_dir: "lib"
 

src/IO/saveSpmScript.m

@@ -49,6 +49,10 @@
     outputFilename = returnBatchFileName('', '.m');
   end
 
+  % matlab scripts cannot have hyphens
+  filename = spm_file(outputFilename, 'filename');
+  outputFilename = spm_file(outputFilename, 'filename', strrep(filename, '-', '_'));
+
   try
     str = gencode(matlabbatch);
   catch

src/infra/getEnvInfo.m

@@ -49,11 +49,12 @@
         if bids.internal.starts_with(keyname, 'LS_COLORS')
           % to prevent annoying warnign when field names are too long.
           OS.environmentVariables.LS_COLORS = vals{i};
+        else
+          OS.environmentVariables.(keyname) = vals{i};
         end
       end
     end
   catch
-    errorHandling;
     errorHandling(mfilename(), 'envUnknown', 'Could not get env info.', true, opt.verbosity);
   end
 

tests/tests_batches/test_saveMatlabBatch.m

@@ -16,16 +16,19 @@ function test_saveMatlabBatch_basic()
   opt.dir.jobs = pwd;
 
   matlabbatch = struct('test', 1);
+  saveMatlabBatch(matlabbatch, 'test', opt, subLabel);
 
   expectedOutput = fullfile(pwd, ['sub-' subLabel], ...
                             ['batch_test_' datestr(now, 'yyyy-mm-ddTHH-MM') '.mat']);
 
-  saveMatlabBatch(matlabbatch, 'test', opt, subLabel);
-
   assertEqual(exist(expectedOutput, 'file'), 2);
-  assertEqual(exist(spm_file(expectedOutput, 'ext', '.m'), 'file'), 2);
   assertEqual(exist(spm_file(expectedOutput, 'ext', '.json'), 'file'), 2);
 
+  expectedOutput = fullfile(pwd, ['sub-' subLabel], ...
+                            ['batch_test_' datestr(now, 'yyyy_mm_ddTHH_MM') '.m']);
+
+  assertEqual(exist(expectedOutput, 'file'), 2);
+
   cleanUp(fullfile(pwd, ['sub-' subLabel]));
 
 end
@@ -45,7 +48,7 @@ function test_saveMatlabBatch_group()
   saveMatlabBatch(matlabbatch, 'groupTest', opt);
 
   assertEqual(exist(expectedOutput, 'file'), 2);
-  assertEqual(exist(spm_file(expectedOutput, 'ext', '.m'), 'file'), 2);
+  assertEqual(exist(spm_file(strrep(expectedOutput, '-', '_'), 'ext', '.m'), 'file'), 2);
 
   cleanUp(fullfile(pwd, 'group'));
 

tests/tests_infra/test_getEnvInfo.m

@@ -0,0 +1,22 @@
+% (C) Copyright 2022 CPP_SPM developers
+
+function test_suite = test_getEnvInfo %#ok<*STOUT>
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+  initTestSuite;
+end
+
+function test_getEnvInfo_basic()
+
+  opt.dryRun = false;
+  opt.versbosity = false;
+
+  [OS, generatedBy] = getEnvInfo(opt);
+
+  %   OS.platform
+  %   OS.environmentVariables
+  %   generatedBy
+
+end