Exclude coverage testing of abstract properties, methods (#128)

* Exclude coverage testing of abstract properties, methods

* Replace calls to deprecated abc.abstractmethod

* Improve tests

.coveragerc

@@ -2,3 +2,8 @@
 branch = True
 source = src/
 omit = src/hdmf/_version.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    @abstract

src/hdmf/container.py

@@ -1,4 +1,4 @@
-import abc
+from abc import abstractmethod
 from uuid import uuid4
 from six import with_metaclass
 from .utils import docval, getargs, ExtenderMeta
@@ -131,27 +131,32 @@ def parent(self, parent_container):
 
 class Data(Container):
 
-    @abc.abstractproperty
+    @property
+    @abstractmethod
     def data(self):
         '''
         The data that is held by this Container
         '''
         pass
 
-    def __nonzero__(self):
+    def __bool__(self):
+        if not hasattr(self.data, '__len__'):
+            raise NotImplementedError('__bool__ must be implemented when data has no __len__')
         return len(self.data) != 0
 
 
 class DataRegion(Data):
 
-    @abc.abstractproperty
+    @property
+    @abstractmethod
     def data(self):
         '''
         The target data that this region applies to
         '''
         pass
 
-    @abc.abstractproperty
+    @property
+    @abstractmethod
     def region(self):
         '''
         The region that indexes into data e.g. slice or list of indices

src/hdmf/data_utils.py

@@ -1,4 +1,4 @@
-from abc import ABCMeta, abstractmethod, abstractproperty
+from abc import ABCMeta, abstractmethod
 try:
     from collections.abc import Iterable  # Python 3
 except ImportError:
@@ -83,7 +83,8 @@ def recommended_data_shape(self):
         """
         raise NotImplementedError("recommended_data_shape not implemented for derived class")
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def dtype(self):
         """
         Define the data type of the array
@@ -92,7 +93,8 @@ def dtype(self):
         """
         raise NotImplementedError("dtype not implemented for derived class")
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def maxshape(self):
         """
         Property describing the maximum shape of the data array that is being iterated over
@@ -556,11 +558,13 @@ def target(self):
     def slice(self):
         return self.__slice
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def __getitem__(self, idx):
         pass
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def __len__(self):
         pass
 

tests/unit/test_container.py

@@ -1,6 +1,6 @@
 import unittest2 as unittest
 
-from hdmf.container import Container
+from hdmf.container import Container, Data
 
 
 class Subcontainer(Container):
@@ -119,5 +119,42 @@ def test_type_hierarchy(self):
         self.assertEqual(Subcontainer.type_hierarchy(), (Subcontainer, Container, object))
 
 
+class SubData(Data):
+
+    def __init__(self, name, data):
+        super(SubData, self).__init__(name=name)
+        self.__data = data
+
+    @property
+    def data(self):
+        return self.__data
+
+
+class TestData(unittest.TestCase):
+
+    def test_bool_true(self):
+        """Test that __bool__ method works correctly on data with len
+        """
+        data_obj = SubData('my_data', [1, 2, 3, 4, 5])
+        self.assertTrue(data_obj)
+
+    def test_bool_false(self):
+        """Test that __bool__ method works correctly on empty data
+        """
+        data_obj = SubData('my_data', '')
+        self.assertFalse(data_obj)
+
+        data_obj = SubData('my_data', [])
+        self.assertFalse(data_obj)
+
+    def test_bool_no_len(self):
+        """Test that__bool__ method works correctly on data with no len
+        """
+        data_obj = SubData('my_data', Container(''))
+        err_msg = '__bool__ must be implemented when data has no __len__'
+        with self.assertRaisesRegex(NotImplementedError, err_msg):
+            bool(data_obj)
+
+
 if __name__ == '__main__':
     unittest.main()

tests/unit/test_io_hdf5_h5tools.py

@@ -523,6 +523,41 @@ def test_roundtrip_empty_group(self):
             self.assertListEqual([], read_foofile.buckets[0].foos)
 
 
+class TestHDF5IO(unittest.TestCase):
+
+    def setUp(self):
+        self.manager = _get_manager()
+        self.path = get_temp_filepath()
+
+        foo1 = Foo('foo1', [1, 2, 3, 4, 5], "I am foo1", 17, 3.14)
+        foobucket = FooBucket('test_bucket', [foo1])
+        self.foofile = FooFile([foobucket])
+
+        self.file_obj = None
+
+    def tearDown(self):
+        if os.path.exists(self.path):
+            os.remove(self.path)
+
+        if self.file_obj is not None:
+            fn = self.file_obj.filename
+            self.file_obj.close()
+            if os.path.exists(fn):
+                os.remove(fn)
+
+    def test_constructor(self):
+        with HDF5IO(self.path, manager=self.manager, mode='w') as io:
+            self.assertEquals(io.manager, self.manager)
+            self.assertEquals(io.source, self.path)
+
+    def test_set_file_mismatch(self):
+        self.file_obj = File(get_temp_filepath())
+        err_msg = re.escape("You argued %s as this object's path, but supplied a file with filename: %s"
+                            % (self.path, self.file_obj.filename))
+        with self.assertRaisesRegex(ValueError, err_msg):
+            HDF5IO(self.path, manager=self.manager, mode='w', file=self.file_obj)
+
+
 class TestCacheSpec(unittest.TestCase):
 
     def setUp(self):