Upgrade to Pydantic 2 (#767)

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Upcoming
 
+### Improvements
+
+* Upgraded Pydantic support to `>v2.0.0`. [PR #767](https://github.com/catalystneuro/neuroconv/pull/767)
+* Absorbed the `DatasetInfo` model into the `DatasetIOConfiguration` model. [PR #767](https://github.com/catalystneuro/neuroconv/pull/767)
+* Keyword argument `field_name` of the `DatasetIOConfiguration.from_neurodata_object` method has been renamed to `dataset_name` to be more consistent with its usage. This only affects direct initialization of the model; usage via the `BackendConfiguration` constructor and its associated helper functions in `neuroconv.tools.nwb_helpers` is unaffected. [PR #767](https://github.com/catalystneuro/neuroconv/pull/767)
+* Manual construction of a `DatasetIOConfiguration` now requires the field `dataset_name`, and will be validated to match the final path of `location_in_file`. Usage via the automated constructors is unchanged. [PR #767](https://github.com/catalystneuro/neuroconv/pull/767)
+
+
+
 # v0.4.7 (February 21, 2024)
 
 ### Deprecation

requirements-minimal.txt

@@ -4,10 +4,11 @@ jsonschema>=3.2.0
 PyYAML>=5.4
 scipy>=1.4.1
 h5py>=3.9.0
-hdmf>=3.12.1
+hdmf>=3.12.2
 hdmf_zarr>=0.4.0
 pynwb>=2.3.2;python_version>='3.8'
-pydantic>=1.10.13,<2.0.0
+pydantic>=2.0.0
+typing_extensions>=4.1.0
 psutil>=5.8.0
 tqdm>=4.60.0
 pandas

src/neuroconv/tools/nwb_helpers/__init__.py

@@ -6,7 +6,7 @@
 
 from ._backend_configuration import get_default_backend_configuration
 from ._configuration_models._base_backend import BackendConfiguration
-from ._configuration_models._base_dataset_io import DatasetInfo, DatasetIOConfiguration
+from ._configuration_models._base_dataset_io import DatasetIOConfiguration
 from ._configuration_models._hdf5_backend import HDF5BackendConfiguration
 from ._configuration_models._hdf5_dataset_io import (
     AVAILABLE_HDF5_COMPRESSION_METHODS,
@@ -37,21 +37,20 @@
     "BACKEND_CONFIGURATIONS",
     "DATASET_IO_CONFIGURATIONS",
     "BACKEND_NWB_IO",
+    "BackendConfiguration",
+    "HDF5BackendConfiguration",
+    "ZarrBackendConfiguration",
+    "DatasetIOConfiguration",
+    "HDF5DatasetIOConfiguration",
+    "ZarrDatasetIOConfiguration",
     "get_default_backend_configuration",
     "get_default_dataset_io_configurations",
     "configure_backend",
-    "BackendConfiguration",
-    "DatasetIOConfiguration",
     "get_default_dataset_io_configurations",
     "get_default_backend_configuration",
     "add_device_from_metadata",
     "get_default_nwbfile_metadata",
     "get_module",
     "make_nwbfile_from_metadata",
     "make_or_load_nwbfile",
-    "DatasetInfo",
-    "HDF5BackendConfiguration",
-    "HDF5DatasetIOConfiguration",
-    "ZarrBackendConfiguration",
-    "ZarrDatasetIOConfiguration",
 ]

src/neuroconv/tools/nwb_helpers/_configuration_models/_base_backend.py

@@ -3,8 +3,9 @@
 from typing import ClassVar, Dict, Literal, Type
 
 from hdmf.container import DataIO
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field
 from pynwb import NWBFile
+from typing_extensions import Self
 
 from ._base_dataset_io import DatasetIOConfiguration
 from .._dataset_configuration import get_default_dataset_io_configurations
@@ -13,10 +14,11 @@
 class BackendConfiguration(BaseModel):
     """A model for matching collections of DatasetConfigurations to a specific backend."""
 
-    backend: ClassVar[Literal["hdf5", "zarr"]] = Field(
-        description="The name of the backend used to configure the NWBFile."
-    )
-    data_io_class: Type[DataIO] = Field(description="The DataIO class that is specific to this backend.")
+    backend: ClassVar[Literal["hdf5", "zarr"]]
+    data_io_class: ClassVar[Type[DataIO]]
+
+    model_config = ConfigDict(validate_assignment=True)  # Re-validate model on mutation
+
     dataset_configurations: Dict[str, DatasetIOConfiguration] = Field(
         description=(
             "A mapping from object locations (e.g. `acquisition/TestElectricalSeriesAP/data`) "
@@ -38,10 +40,10 @@ def __str__(self) -> str:
         return string
 
     @classmethod
-    def from_nwbfile(cls, nwbfile: NWBFile) -> "BackendConfiguration":
+    def from_nwbfile(cls, nwbfile: NWBFile) -> Self:
         default_dataset_configurations = get_default_dataset_io_configurations(nwbfile=nwbfile, backend=cls.backend)
         dataset_configurations = {
-            default_dataset_configuration.dataset_info.location_in_file: default_dataset_configuration
+            default_dataset_configuration.location_in_file: default_dataset_configuration
             for default_dataset_configuration in default_dataset_configurations
         }