Improve test coverage (#589)

* Improve coverage for nwbRead/nwbExport

* Remove tutorialTest (function-based)

* Create TutorialTest (class-based unit test)

* Add test classes (issue #583 )

* Update description for PynwbTutorialTest

* Add specific tests for io.timestamp2datetime

* Update unit tests

* Create getTutorialNwbFilePath.m

Add function to create a filepath for saving tutorial nwb files in a fixed folder

* Fix: Add starting_time when creating TimeSeries objects (#584)

Also, use misc.getTutorialNwbFilePath to create a filepath for saving tutorial nwb file

* Update several tutorials: Specify timezone or NWBFile's session_start_time property

* Fix bug in io.timestamp2datetime (Issue #585)

Some dates are assigned wrongly when Day, Month and Year are set individually, as the datetime object internally/silently adjusts month if day is not valid

* Update timestamp2datetime.m

Fix: Should not preallocate datetimeArray as it is not known beforehand whether the timestamp has a timezone or not (datetime.empty contrains to datetime w/o timezone)

* Update GenerationTest.m

Ensure test can be run from any current working directory, not just the matnwb repo folder

* Update getMatnwbDir.m

Simplyfy function by using mfilename instead of dbstack

* Delete file which was introduced with issue #585

* Change nwbtest: Add selector options as input; Add cleanup routine

* Add test for constructing Anon with name, value input

* Add specific testing of types.untyped.Set

When writing test, also discovered a but in types.untyped.Set which is fixed

* Remove function call used for debugging

---------

Co-authored-by: Ben Dichter <[email protected]>

+misc/getMatnwbDir.m

@@ -1,23 +1,7 @@
-function [matnwbDir] = getMatnwbDir(varargin)
-
-try
-    % Get the actual location of the matnwb directory. This assumes "getMatnwbDir" is
-    % within the +misc matnwb package folder.
-    fnLoc = dbstack('-completenames');
-    fnLoc = fnLoc(1).file;
-    [fnDir,~,~] = fileparts(fnLoc);
-    [matnwbDir,~,~] = fileparts(fnDir);
-
-    if 7 ~= exist(matnwbDir, 'dir')
-        warning('NWB:GetMatnwbDir:NotFound',...
-            'Did not find "matnwb" root directory at %s. Using defaults.',...
-            matnwbDir);
-    end
-catch err
-    atLine = repmat('@', 1, 7);
-    fprintf('%s\n%s\n%s\n',...
-        atLine,...
-        getReport(err, 'extended', 'hyperlinks', 'on'),...
-        atLine);
-end
+function matnwbDir = getMatnwbDir(varargin)
+% Get the absolute path for the matnwb directory.
+
+    % This assumes "getMatnwbDir" is within the +misc matnwb package folder.
+    miscFolder = fileparts(mfilename('fullpath'));
+    matnwbDir = fileparts(miscFolder);
 end

+tests/+sanity/GenerationTest.m

@@ -1,6 +1,6 @@
 classdef GenerationTest < matlab.unittest.TestCase
     properties (MethodSetupParameter)
-        schemaVersion = setdiff({dir('nwb-schema').name}, {'.', '..'});
+        schemaVersion = listSchemaVersions()
     end
 
     methods (TestClassSetup)
@@ -62,3 +62,7 @@ function dynamicTableMethodsTest(testCase)
     end
 end
 
+function schemaVersions = listSchemaVersions()
+    nwbSchemaDir = fullfile(misc.getMatnwbDir, 'nwb-schema');
+    schemaVersions = setdiff({dir(nwbSchemaDir).name}, {'.', '..'});
+end

+tests/+system/NWBFileIOTest.m

@@ -22,5 +22,94 @@ function addContainer(testCase, file) %#ok<INUSL>
             c = file;
         end
     end
+
+    methods (Test)
+        function writeMultipleFiles(testCase)
+
+            fileA = testCase.file;
+            fileB = NwbFile( ...
+                'session_description', 'a second test NWB File', ...
+                'identifier', 'TEST456', ...
+                'session_start_time', '2018-12-02T12:57:27.371444-08:00', ...
+                'file_create_date', '2017-04-15T12:00:00.000000-08:00',...
+                'timestamps_reference_time', '2018-12-02T12:57:27.371444-08:00');
+
+            fileNameA = ['MatNWB.' testCase.className() '.testWriteMultiA.nwb'];
+            fileNameB = ['MatNWB.' testCase.className() '.testWriteMultiB.nwb'];
+
+            nwbExport([fileA, fileB], {fileNameA, fileNameB});
+        end
+
+        function readWithStringArg(testCase)
+            fileName = ['MatNWB.' testCase.className() '.testReadWithStringArg.nwb'];
+            fileName = string(fileName);
+            nwbExport(testCase.file, fileName)
+            nwbRead(fileName, "ignorecache");
+        end
+
+        function readFileWithoutSpec(testCase)
+            fileName = ['MatNWB.' testCase.className() '.testReadFileWithoutSpec.nwb'];
+            nwbExport(testCase.file, fileName)
+
+            testCase.deleteGroupFromFile(fileName, 'specifications')
+            nwbRead(fileName);
+        end
+
+        function readFileWithoutSpecLoc(testCase)
+            fileName = ['MatNWB.' testCase.className() '.testReadFileWithoutSpecLoc.nwb'];
+            nwbExport(testCase.file, fileName)
+
+            testCase.deleteAttributeFromFile(fileName, '/', '.specloc')
+
+            nwbRead(fileName);
+        end
+
+        function readFileWithUnsupportedVersion(testCase)
+            fileName = ['MatNWB.' testCase.className() '.testReadFileWithUnsupportedVersion.nwb'];
+            nwbExport(testCase.file, fileName)
+
+            testCase.deleteAttributeFromFile(fileName, '/', 'nwb_version')
+
+            file_id = H5F.open(fileName, 'H5F_ACC_RDWR', 'H5P_DEFAULT');
+            io.writeAttribute(file_id, '/nwb_version', '1.0.0')
+            H5F.close(file_id);
+
+            nwbRead(fileName);
+        end
+    end
+
+    methods (Static, Access = private)
+        function deleteGroupFromFile(fileName, groupName)
+            if ~startsWith(groupName, '/')
+                groupName = ['/', groupName];
+            end
+
+            % Open the HDF5 file in read-write mode
+            file_id = H5F.open(fileName, 'H5F_ACC_RDWR', 'H5P_DEFAULT');
+
+            % Delete the group
+            H5L.delete(file_id, groupName, 'H5P_DEFAULT');
+
+            % Close the HDF5 file
+            H5F.close(file_id);
+        end
+
+        function deleteAttributeFromFile(fileName, objectName, attributeName)
+            % Open the HDF5 file in read-write mode
+            file_id = H5F.open(fileName, 'H5F_ACC_RDWR', 'H5P_DEFAULT');
+
+            % Open the object (dataset or group)
+            object_id = H5O.open(file_id, objectName, 'H5P_DEFAULT');
+
+            % Delete the attribute
+            H5A.delete(object_id, attributeName);
+
+            % Close the object
+            H5O.close(object_id);
+
+            % Close the HDF5 file
+            H5F.close(file_id);
+        end
+    end
 end
 

+tests/+unit/anonTest.m

@@ -27,3 +27,9 @@ function testAnonDataset(testCase)
 
 tests.util.verifyContainerEqual(testCase, nwbRead('testanon.nwb', 'ignorecache'), nwbExpected);
 end
+
+function testAnonTypeWithNameValueInput(testCase)
+    anon = types.untyped.Anon('a', 1);
+    testCase.verifyEqual(anon.name, 'a')
+    testCase.verifyEqual(anon.value, 1)
+end

+tests/+unit/dataPipeTest.m

@@ -255,6 +255,11 @@ function testBoundPipe(testCase)
     warning('on', debugId);
 end
 
+function testConfigurationFromData(testCase)
+    conf = types.untyped.datapipe.Configuration.fromData(zeros(10,10), 1);
+    testCase.verifyClass(conf, 'types.untyped.datapipe.Configuration')
+end
+
 function data = createData(dataType, size)
     data = randi(intmax(dataType), size, dataType);
 end

+tests/+unit/untypedSetTest.m

@@ -0,0 +1,68 @@
+function tests = untypedSetTest()
+    tests = functiontests(localfunctions);
+end
+
+function setupOnce(testCase)
+    rootPath = fullfile(fileparts(mfilename('fullpath')), '..', '..');
+    testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath));
+end
+
+function setup(testCase)
+    testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture);
+end
+
+function testCreateSetWithFunctionInput(testCase)
+    set = types.untyped.Set(@(key, value) true);
+    testCase.verifyNotEmpty(set.ValidationFcn)
+end
+
+function testCreateSetFromStruct(testCase)
+    untypedSet = types.untyped.Set( struct('a',1, 'b', 2) );
+    testCase.verifyEqual(untypedSet.get('a'), 1)
+end
+
+function testCreateSetFromNvPairs(testCase)
+    untypedSet = types.untyped.Set( 'a',1, 'b', 2 );
+    testCase.verifyEqual(untypedSet.get('a'), 1)
+end
+
+function testCreateSetFromNvPairsPlusFunctionHandle(testCase)
+    untypedSet = types.untyped.Set( 'a',1, 'b', 2, @(key, value) disp('Hello World'));
+    testCase.verifyEqual(untypedSet.get('a'), 1)
+end
+
+function testDisplayEmptyObject(testCase)
+    emptyUntypedSet = types.untyped.Set();
+    disp(emptyUntypedSet)
+end
+
+function testDisplayScalarObject(testCase)
+    scalarSet = types.untyped.Set('a',1)
+    disp(scalarSet)
+end
+
+function testGetSetSize(testCase)
+    untypedSet = types.untyped.Set( 'a',1, 'b', 2 );
+
+    [nRowsA, nColsA] = size(untypedSet);
+
+     nRowsB = size(untypedSet, 1);
+     nColsB = size(untypedSet, 2);
+
+     testCase.verifyEqual(nRowsA, nRowsB);
+     testCase.verifyEqual(nColsA, nColsB);
+end
+
+function testHorizontalConcatenation(testCase)
+    untypedSetA = types.untyped.Set( struct('a',1, 'b', 2) );
+    untypedSetB = types.untyped.Set( struct('c',3, 'd', 3) );
+
+    testCase.verifyError(@() [untypedSetA, untypedSetB], 'NWB:Set:Unsupported') 
+end
+
+function testVerticalConcatenation(testCase)
+    untypedSetA = types.untyped.Set( struct('a',1, 'b', 2) );
+    untypedSetB = types.untyped.Set( struct('c',3, 'd', 3) );
+
+    testCase.verifyError(@() [untypedSetA; untypedSetB], 'NWB:Set:Unsupported') 
+end

+types/+untyped/Set.m

@@ -83,7 +83,7 @@
                 if nargout == 1
                     varargout{1} = [obj.Count, 1];
                 else
-                    [varargout{:}] = ones(nargout,1);
+                    varargout = num2cell( ones(1, nargout) );
                     varargout{1} = obj.Count;
                 end
             end

nwbtest.m

@@ -40,13 +40,19 @@
         parser = inputParser;
         parser.KeepUnmatched = true;
         parser.addParameter('Verbosity', 1);
+        parser.addParameter('Selector', [])
         parser.parse(varargin{:});
 
         ws = pwd;
 
-        nwbClearGenerated(); % clear default files if any.
+        nwbClearGenerated(); % Clear default files if any.
+        cleaner = onCleanup(@generateCore); % Regenerate core when finished
+
         pvcell = struct2pvcell(parser.Unmatched);
         suite = TestSuite.fromPackage('tests', 'IncludingSubpackages', true, pvcell{:});
+        if ~isempty(parser.Results.Selector)
+            suite = suite.selectIf(parser.Results.Selector);
+        end
 
         runner = TestRunner.withTextOutput('Verbosity', parser.Results.Verbosity);