diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0f486273b..0ad399734 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,7 +18,7 @@ repos: # hooks: # - id: black - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.9 + rev: v0.5.7 hooks: - id: ruff # - repo: https://github.com/econchick/interrogate diff --git a/CHANGELOG.md b/CHANGELOG.md index 38f3923fe..0d7489419 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ - Added new attribute "dimension_labels" on `DatasetBuilder` which specifies the names of the dimensions used in the dataset based on the shape of the dataset data and the dimension names in the spec for the data type. This attribute is available on build (during the write process), but not on read of a dataset from a file. @rly [#1081](https://github.com/hdmf-dev/hdmf/pull/1081) +- Speed up loading namespaces by skipping register_type when already registered. @magland [#1102](https://github.com/hdmf-dev/hdmf/pull/1102) +- Speed up namespace loading: return a shallow copy rather than a deep copy in build_const_args. @magland [#1103](https://github.com/hdmf-dev/hdmf/pull/1103) ## HDMF 3.14.2 (July 7, 2024) diff --git a/src/hdmf/spec/namespace.py b/src/hdmf/spec/namespace.py index 5f322e911..57232bd25 100644 --- a/src/hdmf/spec/namespace.py +++ b/src/hdmf/spec/namespace.py @@ -466,15 +466,19 @@ def __load_namespace(self, namespace, reader, resolve=True): return included_types def __register_type(self, ndt, inc_ns, catalog, registered_types): - spec = inc_ns.get_spec(ndt) - spec_file = inc_ns.catalog.get_spec_source_file(ndt) - self.__register_dependent_types(spec, inc_ns, catalog, registered_types) - if isinstance(spec, DatasetSpec): - built_spec = self.dataset_spec_cls.build_spec(spec) + if ndt in registered_types: + # already registered + pass else: - built_spec = self.group_spec_cls.build_spec(spec) - registered_types.add(ndt) - catalog.register_spec(built_spec, spec_file) + spec = inc_ns.get_spec(ndt) + spec_file = inc_ns.catalog.get_spec_source_file(ndt) + self.__register_dependent_types(spec, inc_ns, catalog, registered_types) + if isinstance(spec, DatasetSpec): + built_spec = self.dataset_spec_cls.build_spec(spec) + else: + built_spec = self.group_spec_cls.build_spec(spec) + registered_types.add(ndt) + catalog.register_spec(built_spec, spec_file) def __register_dependent_types(self, spec, inc_ns, catalog, registered_types): """Ensure that classes for all types used by this type are registered diff --git a/src/hdmf/spec/spec.py b/src/hdmf/spec/spec.py index 222e3ec5e..e10d5e43e 100644 --- a/src/hdmf/spec/spec.py +++ b/src/hdmf/spec/spec.py @@ -1,7 +1,6 @@ import re from abc import ABCMeta from collections import OrderedDict -from copy import deepcopy from warnings import warn from ..utils import docval, getargs, popargs, get_docval @@ -84,7 +83,7 @@ class ConstructableDict(dict, metaclass=ABCMeta): def build_const_args(cls, spec_dict): ''' Build constructor arguments for this ConstructableDict class from a dictionary ''' # main use cases are when spec_dict is a ConstructableDict or a spec dict read from a file - return deepcopy(spec_dict) + return spec_dict.copy() @classmethod def build_spec(cls, spec_dict):