ruff

src/hdmf/container.py

@@ -143,7 +143,6 @@ def _field_config(self, arg_name, val):
                         return val
                     # From the spec, get the corresponding constructor name
                     else:
-                        constr_name = obj_mapper.get_const_arg(spec)
                         termset_path = os.path.join(CUR_DIR, config_namespace['data_types'][object_name][attr])
                         termset = TermSet(term_schema_path=termset_path)
                         # If the val has been manually wrapped then skip checking the config for the attr

src/hdmf/term_set.py

@@ -332,6 +332,12 @@ def load_termset_config(self,config_path):
         """
         Load the configuration file for validation on the fields defined for the objects within the file.
         """
+        try:
+            import yaml
+        except ImportError:
+            msg = "Install yaml."
+            raise ValueError(msg)
+
         with open(config_path, 'r') as config:
             termset_config = yaml.load(config, Loader=yaml.FullLoader)
             if self.config is None: # set the initial config/load after config has been unloaded
@@ -347,14 +353,13 @@ def load_termset_config(self,config_path):
                         if namespace not in self.config: # append namespace config if not present within self.config
                             self.config['namespaces'][namespace] = termset_config['namespaces'][namespace]
                         else: # check for any needed overrides within existing namespace configs
-                            breakpoint()
                             for data_type in termset_config['namespaces'][namespace]['data_types']:
                                 if data_type in self.config['namespaces'][namespace]['data_types']:
                                     replace_config = termset_config['namespaces'][namespace]['data_types'][data_type]
                                     self.config['namespaces'][namespace]['data_types'][data_type] = replace_config
                                 else: # append to config
-                                    new_data_type_config = termset_config['namespaces'][namespace]['data_types'][data_type]
-                                    self.config['namespaces'][namespace]['data_types'] = new_data_type_config
+                                    new_config = termset_config['namespaces'][namespace]['data_types'][data_type]
+                                    self.config['namespaces'][namespace]['data_types'] = new_config
 
                     # append path to self.path
                     self.path.append(config_path)

tests/unit/common/test_table.py

@@ -5,7 +5,7 @@
 import pandas as pd
 import unittest
 
-from hdmf import Container, Data
+from hdmf import Container
 from hdmf import TermSet, TermSetWrapper
 from hdmf.backends.hdf5 import H5DataIO, HDF5IO
 from hdmf.backends.hdf5.h5tools import H5_TEXT, H5PY_3
@@ -20,11 +20,9 @@
     SimpleMultiContainer,
     load_termset_config,
     unload_termset_config,
-    get_loaded_config,
-    get_type_map
-)
+    get_loaded_config)
 from hdmf.testing import TestCase, H5RoundTripMixin, remove_test_file
-from hdmf.utils import StrDataset, popargs, docval
+from hdmf.utils import StrDataset, popargs
 from hdmf.data_utils import DataChunkIterator
 
 from tests.unit.helpers.utils import (
@@ -36,7 +34,6 @@
 
 try:
     import linkml_runtime  # noqa: F401
-    import yaml
     REQUIREMENTS_INSTALLED = True
 except ImportError:
     REQUIREMENTS_INSTALLED = False
@@ -2804,18 +2801,27 @@ def test_load_config(self):
 
     def test_validate_with_config(self):
         data = VectorData(name='foo', data=[0], description='Homo sapiens')
+        self.assertEqual(data.description.value, 'Homo sapiens')
 
     def test_namespace_warn(self):
         with self.assertWarns(Warning):
-            container = ExtensionContainer(name='foo', namespace='foo', type_map=self.tm, description='Homo sapiens')
+            ExtensionContainer(name='foo',
+                               namespace='foo',
+                               type_map=self.tm,
+                               description='Homo sapiens')
 
     def test_container_type_warn(self):
         with self.assertWarns(Warning):
-            container = ExtensionContainer(name='foo', namespace='hdmf-common', type_map=self.tm, description='Homo sapiens')
+            ExtensionContainer(name='foo',
+                               namespace='hdmf-common',
+                               type_map=self.tm,
+                               description='Homo sapiens')
 
     def test_already_wrapped_warn(self):
         with self.assertWarns(Warning):
             terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
-            data = VectorData(name='foo', data=[0], description=TermSetWrapper(value='Homo sapiens', termset=terms))
+            VectorData(name='foo',
+                       data=[0],
+                       description=TermSetWrapper(value='Homo sapiens', termset=terms))
 
         unload_termset_config()