clean up

src/hdmf/build/manager.py

@@ -421,10 +421,6 @@ def __init__(self, **kwargs):
     def namespace_catalog(self):
         return self.__ns_catalog
 
-    @property
-    def data_types(self):
-        return self.__data_types
-
     @property
     def container_types(self):
         return self.__container_types

tests/unit/common/test_table.py

@@ -37,36 +37,6 @@
 except ImportError:
     LINKML_INSTALLED = False
 
-class TestVDConfig(TestCase):
-    def test_init_config(self):
-        load_termset_config(config_path='/Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/test_config2.yaml')
-        vd = VectorData(name='data', description='',data=['Homo sapiens'])
-        # tb = DynamicTable(name="with_table_columns", description='a test table', columns=[vd])
-        # from hdmf.common import get_type_map
-        # htm = get_type_map()
-        # om = htm.get_map(tb)
-        # from datetime import datetime
-        # from uuid import uuid4
-
-        # import numpy as np
-        # from dateutil.tz import tzlocal
-        #
-        # from pynwb import NWBHDF5IO, NWBFile
-        # from pynwb.behavior import SpatialSeries
-        # from pynwb import get_type_map
-        # tm = get_type_map()
-        # timestamps = np.linspace(0, 50) / 200
-        # position_data = np.array([np.linspace(0, 10, 50), np.linspace(0, 8, 50)]).T
-        #
-        # position_spatial_series = SpatialSeries(
-        #     name="SpatialSeries",
-        #     description="Position (x, y) in an open field.",
-        #     data=position_data,
-        #     timestamps=timestamps,
-        #     reference_frame="(0,0) is bottom left corner",
-        # )
-        breakpoint()
-
 
 class TestDynamicTable(TestCase):
 

tests/unit/test_config.yaml

@@ -1,12 +1,11 @@
-VectorData:
-    namespace:
-    namespace_version:
-    fields:
-      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
-      field2: ...
-DynamicTable:
-    namespace:
-    namespace_version:
-    fields:
-      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
-      field2: ...
+namespaces:
+  hdmf-common:
+    version: TBD
+    data_types:
+      VectorData:
+        data: '/Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml'
+        field2: '...'
+      type2:
+        field1: '...'
+  hdmf-experimental:
+    version: TBD

tests/unit/test_container.py

@@ -32,10 +32,6 @@ def test_link_and_get_resources(self):
         er_get = em.get_linked_resources()
         self.assertEqual(er, er_get)
 
-class TestContainerConfig(TestCase):
-    def test_init_config(self):
-        obj = Container('obj1')
-
 
 class TestContainer(TestCase):
 
@@ -190,21 +186,15 @@ def test_set_modified_parent(self):
         child_obj.set_modified()
         self.assertTrue(child_obj.parent.modified)
 
-    def test_vd(self):
-        col1 = VectorData(
-            name='Species_1',
-            description='...',
-            data=['Homo sapiens'],
-        )
     def test_all_children(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
             data=['Homo sapiens'],
         )
-        # species = DynamicTable(name='species', description='My species', columns=[col1])
-        # obj = species.all_objects
-        # self.assertEqual(sorted(list(obj.keys())), sorted([species.object_id, species.id.object_id, col1.object_id]))
+        species = DynamicTable(name='species', description='My species', columns=[col1])
+        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

tests/unit/test_extension_config.yaml

@@ -1,12 +1,11 @@
-VectorData:
-    namespace:
-    namespace_version:
-    fields:
-      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
-      field2: ...
-DataType2:
-    namespace:
-    namespace_version:
-    fields:
-      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
-      field2: ...
+namespaces:
+  hdmf-common:
+    version: TBD
+    data_types:
+      VectorData:
+        data: '/Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml'
+        field2: '...'
+      type2:
+        field1: '...'
+  hdmf-experimental:
+    version: TBD