deps

src/hdmf/build/manager.py

@@ -501,7 +501,7 @@ def get_dt_container_cls(self, **kwargs):
         If no class has been associated with the ``data_type`` from ``namespace``, a class will be dynamically
         created and returned.
 
-        Replaces get_container_cls but namespace is optional. If namespace is unknown, it will be looked up from
+        Namespace is optional. If namespace is unknown, it will be looked up from
         all namespaces.
         """
         namespace, data_type, post_init_method, autogen = getargs('namespace', 'data_type',

src/hdmf/common/table.py

@@ -775,8 +775,8 @@ def add_column(self, **kwargs):  # noqa: C901
         index, table, enum, col_cls, check_ragged = popargs('index', 'table', 'enum', 'col_cls', 'check_ragged', kwargs)
 
         if isinstance(index, VectorIndex):
-            warn("Passing a VectorIndex in for index may lead to unexpected behavior. This functionality will be "
-                 "deprecated in a future version of HDMF.", category=FutureWarning, stacklevel=3)
+            msg = "Passing a VectorIndex may lead to unexpected behavior. This functionality is not supported."
+            raise ValueError(msg)
 
         if name in self.__colids:  # column has already been added
             msg = "column '%s' already exists in %s '%s'" % (name, self.__class__.__name__, self.name)

src/hdmf/container.py

@@ -467,21 +467,6 @@ def set_modified(self, **kwargs):
     def children(self):
         return tuple(self.__children)
 
-    @docval({'name': 'child', 'type': 'Container',
-             'doc': 'the child Container for this Container', 'default': None})
-    def add_child(self, **kwargs):
-        warn(DeprecationWarning('add_child is deprecated. Set the parent attribute instead.'))
-        child = getargs('child', kwargs)
-        if child is not None:
-            # if child.parent is a Container, then the mismatch between child.parent and parent
-            # is used to make a soft/external link from the parent to a child elsewhere
-            # if child.parent is not a Container, it is either None or a Proxy and should be set to self
-            if not isinstance(child.parent, AbstractContainer):
-                # actually add the child to the parent in parent setter
-                child.parent = self
-        else:
-            warn('Cannot add None as child to a container %s' % self.name)
-
     @classmethod
     def type_hierarchy(cls):
         return cls.__mro__
@@ -913,20 +898,6 @@ def shape(self):
         """
         return get_data_shape(self.__data)
 
-    @docval({'name': 'dataio', 'type': DataIO, 'doc': 'the DataIO to apply to the data held by this Data'})
-    def set_dataio(self, **kwargs):
-        """
-        Apply DataIO object to the data held by this Data object
-        """
-        warn(
-            "Data.set_dataio() is deprecated. Please use Data.set_data_io() instead.",
-            DeprecationWarning,
-            stacklevel=3,
-        )
-        dataio = getargs('dataio', kwargs)
-        dataio.data = self.__data
-        self.__data = dataio
-
     def set_data_io(
         self,
         data_io_class: Type[DataIO],

tests/unit/common/test_table.py

@@ -429,9 +429,7 @@ def test_add_column_vectorindex(self):
         table.add_column(name='qux', description='qux column')
         ind = VectorIndex(name='quux', data=list(), target=table['qux'])
 
-        msg = ("Passing a VectorIndex in for index may lead to unexpected behavior. This functionality will be "
-               "deprecated in a future version of HDMF.")
-        with self.assertWarnsWith(FutureWarning, msg):
+        with self.assertRaises(ValueError):
             table.add_column(name='bad', description='bad column', index=ind)
 
     def test_add_column_multi_index(self):

tests/unit/test_container.py

@@ -213,18 +213,6 @@ def test_all_children(self):
         obj = species.all_objects
         self.assertEqual(sorted(list(obj.keys())), sorted([species.object_id, species.id.object_id, col1.object_id]))
 
-    def test_add_child(self):
-        """Test that add child creates deprecation warning and also properly sets child's parent and modified
-        """
-        parent_obj = Container('obj1')
-        child_obj = Container('obj2')
-        parent_obj.set_modified(False)
-        with self.assertWarnsWith(DeprecationWarning, 'add_child is deprecated. Set the parent attribute instead.'):
-            parent_obj.add_child(child_obj)
-        self.assertIs(child_obj.parent, parent_obj)
-        self.assertTrue(parent_obj.modified)
-        self.assertIs(parent_obj.children[0], child_obj)
-
     def test_parent_set_link_warning(self):
         col1 = VectorData(
             name='col1',

tests/unit/utils_test/test_core_DataIO.py

@@ -1,10 +1,8 @@
 from copy import copy, deepcopy
 
 import numpy as np
-from hdmf.container import Data
 from hdmf.data_utils import DataIO
 from hdmf.testing import TestCase
-import warnings
 
 
 class DataIOTests(TestCase):
@@ -30,34 +28,13 @@ def test_dataio_slice_delegation(self):
         dset = DataIO(indata)
         self.assertTrue(np.all(dset[1:3, 5:8] == indata[1:3, 5:8]))
 
-    def test_set_dataio(self):
-        """
-        Test that Data.set_dataio works as intended
-        """
-        dataio = DataIO()
-        data = np.arange(30).reshape(5, 2, 3)
-        container = Data('wrapped_data', data)
-        msg = "Data.set_dataio() is deprecated. Please use Data.set_data_io() instead."
-        with self.assertWarnsWith(DeprecationWarning, msg):
-            container.set_dataio(dataio)
-        self.assertIs(dataio.data, data)
-        self.assertIs(dataio, container.data)
-
-    def test_set_dataio_data_already_set(self):
+    def test_set_data_io_data_already_set(self):
         """
         Test that Data.set_dataio works as intended
         """
         dataio = DataIO(data=np.arange(30).reshape(5, 2, 3))
-        data = np.arange(30).reshape(5, 2, 3)
-        container = Data('wrapped_data', data)
         with self.assertRaisesWith(ValueError, "cannot overwrite 'data' on DataIO"):
-            with warnings.catch_warnings(record=True):
-                warnings.filterwarnings(
-                    action='ignore',
-                    category=DeprecationWarning,
-                    message="Data.set_dataio() is deprecated. Please use Data.set_data_io() instead.",
-                )
-                container.set_dataio(dataio)
+            dataio.data=[1,2,3,4]
 
     def test_dataio_options(self):
         """