Remove unnecessary calls to deepcopy(get_type_map) (#2121)

* Remove unnecessary calls to deepcopy(get_type_map)

* Cache type map in container cls, use global map for type configs

* Caching doesn't work that way. Refactor with copy arg in get_type_map

* Discard changes to src/pynwb/legacy/__init__.py

* Update changelog

* Update src/pynwb/__init__.py

Co-authored-by: Copilot <[email protected]>

* Fixed rtype value in get_type_map

---------

Co-authored-by: Copilot <[email protected]>

Author: rly

CHANGELOG.md

@@ -5,6 +5,17 @@
 ### Fixed
 - Fixed parsing of the nwb_version attribute which followed the previous suggestion to have a `NWB-` prefix.
   @t-b [#2118](https://github.com/NeurodataWithoutBorders/pynwb/pull/2118)
+- Fixed a performance regression introduced in pynwb 2.8.0 that affected reading NWB files with a large
+  number of objects or fields of objects. @rly [#2121](https://github.com/NeurodataWithoutBorders/pynwb/pull/2121)
+- Fixed `load_type_config`, `unload_type_config`, and `get_loaded_type_config` acting on a copy of the global type map
+  instead of the global type map itself. @rly [#2121](https://github.com/NeurodataWithoutBorders/pynwb/pull/2121)
+
+### Changed
+- Added an argument `copy` to `get_type_map` to control whether a copy of the type map is returned or not.
+  If `copy=False`, the returned type map will be a direct reference to the global type map. @rly
+  [#2121](https://github.com/NeurodataWithoutBorders/pynwb/pull/2121)
+- Deprecated calling `get_type_map` with the `extensions` argument. Call `load_namespaces` on the returned `TypeMap`
+  instead. @rly [#2121](https://github.com/NeurodataWithoutBorders/pynwb/pull/2121)
 
 ## PyNWB 3.1.1 (July 22, 2025)
 

src/pynwb/__init__.py

@@ -46,14 +46,14 @@ def load_type_config(**kwargs):
     This method will either load the default config or the config provided by the path.
     """
     config_path = kwargs['config_path']
-    type_map = kwargs['type_map'] or get_type_map()
+    type_map = kwargs['type_map'] or __TYPE_MAP
 
     hdmf_load_type_config(config_path=config_path, type_map=type_map)
 
 @docval({'name': 'type_map', 'type': TypeMap, 'doc': 'The TypeMap.', 'default': None},
         is_method=False)
 def get_loaded_type_config(**kwargs):
-    type_map = kwargs['type_map'] or get_type_map()
+    type_map = kwargs['type_map'] or __TYPE_MAP
     return hdmf_get_loaded_type_config(type_map=type_map)
 
 @docval({'name': 'type_map', 'type': TypeMap, 'doc': 'The TypeMap.', 'default': None},
@@ -62,7 +62,7 @@ def unload_type_config(**kwargs):
     """
     Remove validation.
     """
-    type_map = kwargs['type_map'] or get_type_map()
+    type_map = kwargs['type_map'] or __TYPE_MAP
     hdmf_unload_type_config(type_map=type_map)
 
 def __get_resources() -> dict:
@@ -101,18 +101,28 @@ def __get_resources() -> dict:
 @docval({'name': 'extensions', 'type': (str, TypeMap, list),
          'doc': 'a path to a namespace, a TypeMap, or a list consisting of paths to namespaces and TypeMaps',
          'default': None},
-        returns="TypeMap loaded for the given extension or NWB core namespace", rtype=tuple,
+        {
+            'name': 'copy', 'type': bool,
+            'doc': 'Whether to return a deepcopy of the TypeMap. '
+            'If False, a direct reference may be returned (use with caution).',
+            'default': True
+        },
+        returns="TypeMap loaded for the given extension or NWB core namespace", rtype=TypeMap,
         is_method=False)
 def get_type_map(**kwargs):
     '''
     Get the TypeMap for the given extensions. If no extensions are provided,
     return the TypeMap for the core namespace
     '''
-    extensions = getargs('extensions', kwargs)
+    extensions, copy_map = getargs('extensions', 'copy', kwargs)
     type_map = None
     if extensions is None:
-        type_map = deepcopy(__TYPE_MAP)
+        if copy_map:
+            type_map = deepcopy(__TYPE_MAP)
+        else:
+            type_map = __TYPE_MAP
     else:
+        warn("The 'extensions' argument is deprecated and will be removed in PyNWB 4.0", DeprecationWarning)
         if isinstance(extensions, TypeMap):
             type_map = extensions
         else:
@@ -538,7 +548,7 @@ def read_nwb(**kwargs):
         # Retrieve the filepath
         path = popargs('path', kwargs)
         file = popargs('file', kwargs)
-        
+
         path = str(path) if path is not None else None
 
         # Streaming case
@@ -556,18 +566,18 @@ def read_nwb(**kwargs):
 
         return nwbfile
 
-@docval({'name': 'path', 'type': (str, Path), 
+@docval({'name': 'path', 'type': (str, Path),
          'doc': 'Path to the NWB file. Can be either a local filesystem path to '
-                'an HDF5 (.nwb) or Zarr (.zarr) file.'}, 
+                'an HDF5 (.nwb) or Zarr (.zarr) file.'},
         is_method=False)
 def read_nwb(**kwargs):
     """Read an NWB file from a local path.
 
-    High-level interface for reading NWB files. Automatically handles both HDF5 
-    and Zarr formats. For advanced use cases (parallel I/O, custom namespaces), 
+    High-level interface for reading NWB files. Automatically handles both HDF5
+    and Zarr formats. For advanced use cases (parallel I/O, custom namespaces),
     use NWBHDF5IO or NWBZarrIO.
 
-    See also 
+    See also
         * :py:class:`~pynwb.NWBHDF5IO`: Core I/O class for HDF5 files with advanced options.
         * :py:class:`~hdmf_zarr.nwb.NWBZarrIO`: Core I/O class for Zarr files with advanced options.
 
@@ -585,17 +595,17 @@ def read_nwb(**kwargs):
             * Write or append modes
             * Pre-opened HDF5 file objects or Zarr stores
             * Remote file access configuration
- 
+
     Example usage reading a local NWB file:
 
     .. code-block:: python
 
         from pynwb import read_nwb
-        nwbfile = read_nwb("path/to/file.nwb")    
+        nwbfile = read_nwb("path/to/file.nwb")
 
     :Returns: pynwb.NWBFile The loaded NWB file object.
     """
-    
+
     path = popargs('path', kwargs)
     # HDF5 is always available so we try that first
     backend_is_hdf5 = NWBHDF5IO.can_read(path=path)
@@ -607,18 +617,18 @@ def read_nwb(**kwargs):
             from hdmf_zarr import NWBZarrIO
             backend_is_zarr = NWBZarrIO.can_read(path=path)
             if backend_is_zarr:
-                return NWBZarrIO.read_nwb(path=path) 
+                return NWBZarrIO.read_nwb(path=path)
             else:
                 raise ValueError(
                     f"Unable to read file: '{path}'. The file is not recognized as "
                     "either a valid HDF5 or Zarr NWB file. Please ensure the file exists and contains valid NWB data."
-                )     
+                )
         except ImportError:
             raise ValueError(
                 f"Unable to read file: '{path}'. The file is not recognized as an HDF5 NWB file. "
                 "If you are trying to read a Zarr file, please install hdmf-zarr using: pip install hdmf-zarr"
             )
-    
+
 
 
 from . import io as __io  # noqa: F401,E402
@@ -642,7 +652,7 @@ def read_nwb(**kwargs):
     # Functions
     'get_type_map',
     'get_manager',
-    'load_namespaces', 
+    'load_namespaces',
     'available_namespaces',
     'clear_cache_dir',
     'register_class',
@@ -653,11 +663,11 @@ def read_nwb(**kwargs):
     'unload_type_config',
     'read_nwb',
     'get_nwbfile_version',
-    
+
     # Classes
     'NWBHDF5IO',
     'NWBContainer',
-    'NWBData', 
+    'NWBData',
     'TimeSeries',
     'ProcessingModule',
     'NWBFile',

src/pynwb/core.py

@@ -61,7 +61,7 @@ def _error_on_new_pass_on_construct(self, error_msg: str):
             raise ValueError(error_msg)
 
     def _get_type_map(self):
-        return get_type_map()
+        return get_type_map(copy=False)
 
     @property
     def data_type(self):

tests/integration/helpers/utils.py

@@ -19,7 +19,8 @@ def create_test_extension(specs, container_classes, mappers=None):
     export_spec(ns_builder, specs, output_dir.name)
 
     # this will copy the global pynwb TypeMap and add the extension types to the copy
-    type_map = get_type_map(f"{output_dir.name}/{NAMESPACE_NAME}.namespace.yaml")
+    type_map = get_type_map()
+    type_map.load_namespaces(f"{output_dir.name}/{NAMESPACE_NAME}.namespace.yaml")
     for type_name, container_cls in container_classes.items():
         type_map.register_container_type(NAMESPACE_NAME, type_name, container_cls)
     if mappers:

tests/unit/test_config.py

@@ -20,7 +20,7 @@ class TestPyNWBTypeConfig(TestCase):
     def setUp(self):
         if not REQUIREMENTS_INSTALLED:
             self.skipTest("optional LinkML module is not installed")
-        CUR_DIR = os.path.dirname(os.path.realpath(__file__))    
+        CUR_DIR = os.path.dirname(os.path.realpath(__file__))
         path_to_config = os.path.join(CUR_DIR, 'test_config/test_nwb_config.yaml')
         load_type_config(config_path=path_to_config)
 

tests/unit/test_extension.py

@@ -45,11 +45,13 @@ def test_export(self):
 
     def test_load_namespace(self):
         self.test_export()
-        get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
+        type_map = get_type_map()
+        type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path))
 
     def test_get_class(self):
         self.test_export()
-        type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
+        type_map = get_type_map()
+        type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path))
         type_map.get_dt_container_cls('TetrodeSeries', self.prefix)
 
     def test_load_namespace_with_reftype_attribute(self):
@@ -62,7 +64,8 @@ def test_load_namespace_with_reftype_attribute(self):
                                      neurodata_type_def='my_new_type')
         ns_builder.add_spec(self.ext_source, test_ds_ext)
         ns_builder.export(self.ns_path, outdir=self.tempdir)
-        get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
+        type_map = get_type_map()
+        type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path))
 
     def test_load_namespace_with_reftype_attribute_check_autoclass_const(self):
         ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
@@ -74,7 +77,8 @@ def test_load_namespace_with_reftype_attribute_check_autoclass_const(self):
                                      neurodata_type_def='my_new_type')
         ns_builder.add_spec(self.ext_source, test_ds_ext)
         ns_builder.export(self.ns_path, outdir=self.tempdir)
-        type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
+        type_map = get_type_map()
+        type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path))
         my_new_type = type_map.get_dt_container_cls('my_new_type', self.prefix)
         docval = None
         for tmp in get_docval(my_new_type.__init__):
@@ -172,7 +176,8 @@ def test_catch_dup_name(self):
                             neurodata_type_def='TetrodeSeries')
         ns_builder2.add_spec(self.ext_source2, ext2)
         ns_builder2.export(self.ns_path2, outdir=self.tempdir)
-        type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path1))
+        type_map = get_type_map()
+        type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path1))
         type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path2))
 
     def test_catch_dup_name_core_newer(self):