[WIP] Replace Spec classes with Pydantic models

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.2
     hooks:
-    -   id: ruff
+    -   id: ruff-check
 # -   repo: https://github.com/econchick/interrogate
 #     rev: 1.5.0
 #     hooks:

pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
     'numpy>=1.19.3',
     "pandas>=1.2.0",
     "ruamel.yaml>=0.16",
+    "pydantic>=2.0.0",
 ]
 dynamic = ["version"]
 
@@ -84,6 +85,7 @@ min-reqs = [
     "numpy==1.19.3",
     "pandas==1.2.0",
     "ruamel.yaml==0.16.0",
+    "pydantic==2.0.0",
     "scipy==1.7.0",
     "tqdm==4.41.0",
     "zarr==2.12.0",
@@ -151,11 +153,11 @@ omit = [
     "*/hdmf/testing/*",
 ]
 
-# [tool.black]
-# line-length = 120
-# preview = true
-# exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb"
-# force-exclude = "src/hdmf/common/hdmf-common-schema|docs/gallery"
+[tool.black]
+line-length = 120
+preview = true
+exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb"
+force-exclude = "src/hdmf/common/hdmf-common-schema|docs/gallery"
 
 [tool.ruff]
 lint.select = ["E", "F", "T100", "T201", "T203", "C901"]

src/hdmf/build/classgenerator.py

@@ -5,8 +5,7 @@
 import numpy as np
 
 from ..container import Container, Data, MultiContainerInterface
-from ..spec import AttributeSpec, LinkSpec, RefSpec, GroupSpec
-from ..spec.spec import BaseStorageSpec, ZERO_OR_MANY, ONE_OR_MANY
+from ..spec import AttributeSpec, LinkSpec, RefSpec, GroupSpec, BaseStorageSpec
 from ..utils import docval, getargs, ExtenderMeta, get_docval, popargs, AllowPositional
 
 
@@ -379,7 +378,7 @@ class MCIClassGenerator(CustomClassGenerator):
     @classmethod
     def apply_generator_to_field(cls, field_spec, bases, type_map):
         """Return True if the field spec has quantity * or +, False otherwise."""
-        return getattr(field_spec, 'quantity', None) in (ZERO_OR_MANY, ONE_OR_MANY)
+        return isinstance(field_spec, (BaseStorageSpec, LinkSpec)) and field_spec.is_many()
 
     @classmethod
     def process_field_spec(cls, classdict, docval_args, parent_cls, attr_name, not_inherited_fields, type_map, spec):

src/hdmf/build/manager.py

@@ -7,8 +7,7 @@
 from .classgenerator import ClassGeneratorManager, CustomClassGenerator, MCIClassGenerator
 from ..container import AbstractContainer, Container, Data
 from ..term_set import TypeConfigurator
-from ..spec import DatasetSpec, GroupSpec, NamespaceCatalog, RefSpec
-from ..spec.spec import BaseStorageSpec
+from ..spec import BaseStorageSpec, DatasetSpec, GroupSpec, NamespaceCatalog, RefSpec
 from ..utils import docval, getargs, ExtenderMeta, get_docval
 
 

src/hdmf/build/objectmapper.py

@@ -19,8 +19,7 @@
 from ..term_set import TermSetWrapper
 from ..data_utils import DataIO, AbstractDataChunkIterator
 from ..query import ReferenceResolver
-from ..spec import Spec, AttributeSpec, DatasetSpec, GroupSpec, LinkSpec, RefSpec
-from ..spec.spec import BaseStorageSpec
+from ..spec import BaseStorageSpec, Spec, AttributeSpec, DatasetSpec, GroupSpec, LinkSpec, RefSpec
 from ..utils import docval, getargs, ExtenderMeta, get_docval, get_data_shape, StrDataset
 
 _const_arg = '__constructor_arg'

src/hdmf/spec/__init__.py

@@ -1,5 +1,9 @@
 from .catalog import SpecCatalog
 from .namespace import NamespaceCatalog, SpecNamespace, SpecReader
-from .spec import (AttributeSpec, DatasetSpec, DtypeHelper, DtypeSpec, GroupSpec, LinkSpec,
-                   NAME_WILDCARD, RefSpec, Spec)
+# from .spec import (AttributeSpec, DatasetSpec, DtypeHelper, DtypeSpec, GroupSpec, LinkSpec,
+#                    NAME_WILDCARD, RefSpec, Spec)
+from .spec2 import (
+    AttributeSpec, DatasetSpec, DtypeHelper, DtypeSpec, GroupSpec, LinkSpec, RefSpec, Spec, BaseStorageSpec,
+    QuantityEnum
+)
 from .write import NamespaceBuilder, SpecWriter, export_spec

src/hdmf/spec/catalog.py

@@ -2,7 +2,7 @@
 import warnings
 from collections import OrderedDict
 
-from .spec import BaseStorageSpec, GroupSpec
+from .spec2 import BaseStorageSpec, GroupSpec
 from ..utils import docval, getargs
 
 

src/hdmf/spec/namespace.py

@@ -9,7 +9,7 @@
 import graphlib
 
 from .catalog import SpecCatalog
-from .spec import DatasetSpec, GroupSpec, BaseStorageSpec
+from .spec2 import DatasetSpec, GroupSpec, BaseStorageSpec
 from ..utils import docval, getargs, popargs, get_docval, is_newer_version
 
 _namespace_args = [
@@ -567,9 +567,9 @@ def __register_type(self, ndt, inc_ns, catalog, registered_types):
             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)
+                built_spec = spec  # TODO self.dataset_spec_cls.build_spec(spec)
             else:
-                built_spec = self.group_spec_cls.build_spec(spec)
+                built_spec = spec  # TODO self.group_spec_cls.build_spec(spec)
             registered_types.add(ndt)
             catalog.register_spec(built_spec, spec_file)