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

Author: rly

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:
@@ -113,6 +113,7 @@ def get_type_map(**kwargs):
     if extensions is None:
         type_map = deepcopy(__TYPE_MAP)
     else:
+        warnings.warn("The 'extensions' argument is deprecated and will be removed in HDMF 5.0", DeprecationWarning)
         if isinstance(extensions, TypeMap):
             type_map = extensions
         else:
@@ -538,7 +539,7 @@ 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 +557,18 @@ 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 +586,17 @@ 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 +608,18 @@ 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 +643,7 @@ def read_nwb(**kwargs):
     # Functions
     'get_type_map',
     'get_manager',
-    'load_namespaces', 
+    'load_namespaces',
     'available_namespaces',
     'clear_cache_dir',
     'register_class',
@@ -653,11 +654,11 @@ def read_nwb(**kwargs):
     'unload_type_config',
     'read_nwb',
     'get_nwbfile_version',
-    
+
     # Classes
     'NWBHDF5IO',
     'NWBContainer',
-    'NWBData', 
+    'NWBData',
     'TimeSeries',
     'ProcessingModule',
     'NWBFile',

src/pynwb/core.py

@@ -32,7 +32,7 @@ class NWBMixin(AbstractContainer):
 
     __nwbfields__ = tuple()
 
-    __type_map = get_type_map()  # static type map created at module import
+    __type_map = None
 
     @docval({'name': 'neurodata_type', 'type': str, 'doc': 'the data_type to search for', 'default': None})
     def get_ancestor(self, **kwargs):
@@ -63,6 +63,10 @@ def _error_on_new_pass_on_construct(self, error_msg: str):
             raise ValueError(error_msg)
 
     def _get_type_map(self):
+        # Cache the type map to avoid repeated calls to get_type_map()
+        if self.__type_map is None:
+            self.__type_map = get_type_map()
+
         return self.__type_map
 
     @property

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):