add logging. less janky adapter instantiation using model validators. correctly propagate properties from ancestor classes when building

nwb_linkml/pyproject.toml

@@ -74,7 +74,9 @@ addopts = [
 ]
 markers = [
     "dev: tests that are just for development rather than testing correctness",
-    "provider: tests for providers!"
+    "provider: tests for providers!",
+    "linkml: tests related to linkml generation",
+    "pydantic: tests related to pydantic generation"
 ]
 testpaths = [
     "src/nwb_linkml",

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -5,16 +5,8 @@ Base class for adapters
 import sys
 from abc import abstractmethod
 from dataclasses import dataclass, field
-from typing import (
+from typing import Any, Generator, List, Literal, Optional, Tuple, Type, TypeVar, Union, overload
-    Any,
+from logging import Logger
-    Generator,
-    List,
-    Optional,
-    Tuple,
-    Type,
-    TypeVar,
-    Union,
-)
 
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import (
@@ -26,6 +18,7 @@ from linkml_runtime.linkml_model import (
 )
 from pydantic import BaseModel
 
+from nwb_linkml.logging import init_logger
 from nwb_schema_language import Attribute, CompoundDtype, Dataset, Group, Schema
 
 if sys.version_info.minor >= 11:
@@ -107,6 +100,14 @@ class BuildResult:
 class Adapter(BaseModel):
     """Abstract base class for adapters"""
 
+    _logger: Optional[Logger] = None
+
+    @property
+    def logger(self) -> Logger:
+        if self._logger is None:
+            self._logger = init_logger(self.__class__.__name__)
+        return self._logger
+
     @abstractmethod
     def build(self) -> "BuildResult":
         """
@@ -152,8 +153,8 @@ class Adapter(BaseModel):
                 # SchemaAdapters that should be located under the same
                 # NamespacesAdapter when it's important to query across SchemaAdapters,
                 # so skip to avoid combinatoric walking
-                if key == "imports" and type(input).__name__ == "SchemaAdapter":
+                # if key == "imports" and type(input).__name__ == "SchemaAdapter":
-                    continue
+                #     continue
                 val = getattr(input, key)
                 yield (key, val)
                 if isinstance(val, (BaseModel, dict, list)):
@@ -196,6 +197,14 @@ class Adapter(BaseModel):
             if isinstance(item, tuple) and item[0] in field and item[1] is not None:
                 yield item[1]
 
+    @overload
+    def walk_field_values(
+        self,
+        input: Union[BaseModel, dict, list],
+        field: Literal["neurodata_type_def"],
+        value: Optional[Any] = None,
+    ) -> Generator[Group | Dataset, None, None]: ...
+
     def walk_field_values(
         self, input: Union[BaseModel, dict, list], field: str, value: Optional[Any] = None
     ) -> Generator[BaseModel, None, None]:
@@ -248,6 +257,9 @@ def is_1d(cls: Dataset | Attribute) -> bool:
     * a single-layer dim/shape list of length 1, or
     * a nested dim/shape list where every nested spec is of length 1
     """
+    if cls.dims is None:
+        return False
+
     return (
         not any([isinstance(dim, list) for dim in cls.dims]) and len(cls.dims) == 1
     ) or (  # nested list
@@ -270,4 +282,8 @@ def has_attrs(cls: Dataset) -> bool:
     """
     Check if a dataset has any attributes at all without defaults
     """
-    return len(cls.attributes) > 0 and all([not a.value for a in cls.attributes])
+    return (
+        cls.attributes is not None
+        and len(cls.attributes) > 0
+        and all([not a.value for a in cls.attributes])
+    )

nwb_linkml/src/nwb_linkml/adapters/classes.py

@@ -119,9 +119,12 @@ class ClassAdapter(Adapter):
         Returns:
             list[:class:`.SlotDefinition`]
         """
+        if cls.attributes is not None:
             results = [AttributeAdapter(cls=attr).build() for attr in cls.attributes]
             slots = [r.slots[0] for r in results]
             return slots
+        else:
+            return []
 
     def _get_full_name(self) -> str:
         """The full name of the object in the generated linkml

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -784,6 +784,12 @@ class MapCompoundDtype(DatasetMap):
         Make a new class for this dtype, using its sub-dtypes as fields,
         and use it as the range for the parent class
         """
+        # all the slots share the same ndarray spec if there is one
+        array = {}
+        if cls.dims or cls.shape:
+            array_adapter = ArrayAdapter(cls.dims, cls.shape)
+            array = array_adapter.make_slot()
+
         slots = {}
         for a_dtype in cls.dtype:
             slots[a_dtype.name] = SlotDefinition(
@@ -791,8 +797,13 @@ class MapCompoundDtype(DatasetMap):
                 description=a_dtype.doc,
                 range=handle_dtype(a_dtype.dtype),
                 **QUANTITY_MAP[cls.quantity],
+                **array,
             )
         res.classes[0].attributes.update(slots)
+
+        # the compound dtype replaces the ``value`` slot, if present
+        if "value" in res.classes[0].attributes:
+            del res.classes[0].attributes["value"]
         return res
 
 

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -13,13 +13,13 @@ from typing import Dict, List, Optional
 
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import Annotation, SchemaDefinition
-from pydantic import Field, PrivateAttr
+from pydantic import Field, model_validator
 
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.schema import SchemaAdapter
 from nwb_linkml.lang_elements import NwbLangSchema
 from nwb_linkml.ui import AdapterProgress
-from nwb_schema_language import Namespaces
+from nwb_schema_language import Namespaces, Group, Dataset
 
 
 class NamespacesAdapter(Adapter):
@@ -31,12 +31,6 @@ class NamespacesAdapter(Adapter):
     schemas: List[SchemaAdapter]
     imported: List["NamespacesAdapter"] = Field(default_factory=list)
 
-    _imports_populated: bool = PrivateAttr(False)
-
-    def __init__(self, **kwargs: dict):
-        super().__init__(**kwargs)
-        self._populate_schema_namespaces()
-
     @classmethod
     def from_yaml(cls, path: Path) -> "NamespacesAdapter":
         """
@@ -70,8 +64,6 @@ class NamespacesAdapter(Adapter):
         """
         Build the NWB namespace to the LinkML Schema
         """
-        if not self._imports_populated and not skip_imports:
-            self.populate_imports()
 
         sch_result = BuildResult()
         for sch in self.schemas:
@@ -129,6 +121,7 @@ class NamespacesAdapter(Adapter):
 
         return sch_result
 
+    @model_validator(mode="after")
     def _populate_schema_namespaces(self) -> None:
         """
         annotate for each schema which namespace imports it
@@ -143,6 +136,7 @@ class NamespacesAdapter(Adapter):
                     sch.namespace = ns.name
                     sch.version = ns.version
                     break
+        return self
 
     def find_type_source(self, name: str) -> SchemaAdapter:
         """
@@ -182,7 +176,8 @@ class NamespacesAdapter(Adapter):
         else:
             raise KeyError(f"No schema found that define {name}")
 
-    def populate_imports(self) -> None:
+    @model_validator(mode="after")
+    def populate_imports(self) -> "NamespacesAdapter":
         """
         Populate the imports that are needed for each schema file
 
@@ -199,11 +194,46 @@ class NamespacesAdapter(Adapter):
                 if depends_on not in sch.imports:
                     sch.imports.append(depends_on)
 
-        # do so recursively
+        return self
-        for imported in self.imported:
-            imported.populate_imports()
 
-        self._imports_populated = True
+    @model_validator(mode="after")
+    def _populate_inheritance(self):
+        """
+        ensure properties from `neurodata_type_inc` are propaged through to inheriting classes.
+
+        This seems super expensive but we'll optimize for perf later if that proves to be the case
+        """
+        # don't use walk_types here so we can replace the objects as we mutate them
+        for sch in self.schemas:
+            for i, group in enumerate(sch.groups):
+                if getattr(group, "neurodata_type_inc", None) is not None:
+                    merged_attrs = self._merge_inheritance(group)
+                    sch.groups[i] = Group(**merged_attrs)
+            for i, dataset in enumerate(sch.datasets):
+                if getattr(dataset, "neurodata_type_inc", None) is not None:
+                    merged_attrs = self._merge_inheritance(dataset)
+                    sch.datasets[i] = Dataset(**merged_attrs)
+        return self
+
+    def _merge_inheritance(self, obj: Group | Dataset) -> dict:
+        obj_dict = obj.model_dump(exclude_none=True)
+        if obj.neurodata_type_inc:
+            name = obj.neurodata_type_def if obj.neurodata_type_def else obj.name
+            self.logger.debug(f"Merging {name} with {obj.neurodata_type_inc}")
+            # there must be only one type with this name
+            parent: Group | Dataset = next(
+                self.walk_field_values(self, "neurodata_type_def", obj.neurodata_type_inc)
+            )
+            if obj.neurodata_type_def == "TimeSeriesReferenceVectorData":
+                pdb.set_trace()
+            parent_dict = copy(self._merge_inheritance(parent))
+            # children don't inherit the type_def
+            del parent_dict["neurodata_type_def"]
+            # overwrite with child values
+            parent_dict.update(obj_dict)
+            return parent_dict
+
+        return obj_dict
 
     def to_yaml(self, base_dir: Path) -> None:
         """

nwb_linkml/src/nwb_linkml/adapters/schema.py

@@ -42,7 +42,8 @@ class SchemaAdapter(Adapter):
         """
         The namespace.schema name for a single schema
         """
-        return ".".join([self.namespace, self.path.with_suffix("").name])
+        namespace = self.namespace if self.namespace is not None else ""
+        return ".".join([namespace, self.path.with_suffix("").name])
 
     def __repr__(self):
         out_str = "\n" + self.name + "\n"

nwb_linkml/src/nwb_linkml/config.py

@@ -2,10 +2,12 @@
 Manage the operation of nwb_linkml from environmental variables
 """
 
+from typing import Optional, Literal
 import tempfile
 from pathlib import Path
 
 from pydantic import (
+    BaseModel,
     DirectoryPath,
     Field,
     FieldValidationInfo,
@@ -15,15 +17,68 @@ from pydantic import (
 )
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
+LOG_LEVELS = Literal["DEBUG", "INFO", "WARNING", "ERROR"]
+
+
+class LogConfig(BaseModel):
+    """
+    Configuration for logging
+    """
+
+    level: LOG_LEVELS = "INFO"
+    """
+    Severity of log messages to process.
+    """
+    level_file: Optional[LOG_LEVELS] = None
+    """
+    Severity for file-based logging. If unset, use ``level``
+    """
+    level_stdout: Optional[LOG_LEVELS] = "WARNING"
+    """
+    Severity for stream-based logging. If unset, use ``level``
+    """
+    file_n: int = 5
+    """
+    Number of log files to rotate through
+    """
+    file_size: int = 2**22  # roughly 4MB
+    """
+    Maximum size of log files (bytes)
+    """
+
+    @field_validator("level", "level_file", "level_stdout", mode="before")
+    @classmethod
+    def uppercase_levels(cls, value: Optional[str] = None) -> Optional[str]:
+        """
+        Ensure log level strings are uppercased
+        """
+        if value is not None:
+            value = value.upper()
+        return value
+
+    @model_validator(mode="after")
+    def inherit_base_level(self) -> "LogConfig":
+        """
+        If loglevels for specific output streams are unset, set from base :attr:`.level`
+        """
+        levels = ("level_file", "level_stdout")
+        for level_name in levels:
+            if getattr(self, level_name) is None:
+                setattr(self, level_name, self.level)
+        return self
+
 
 class Config(BaseSettings):
     """
     Configuration for nwb_linkml, populated by default but can be overridden
     by environment variables.
 
+    Nested models can be assigned from .env files with a __ (see examples)
+
     Examples:
 
         export NWB_LINKML_CACHE_DIR="/home/mycache/dir"
+        export NWB_LINKML_LOGS__LEVEL="debug"
 
     """
 
@@ -32,6 +87,11 @@ class Config(BaseSettings):
         default_factory=lambda: Path(tempfile.gettempdir()) / "nwb_linkml__cache",
         description="Location to cache generated schema and models",
     )
+    log_dir: Path = Field(
+        Path("logs"),
+        description="Location to store logs. If a relative directory, relative to ``cache_dir``",
+    )
+    logs: LogConfig = Field(LogConfig(), description="Log configuration")
 
     @computed_field
     @property
@@ -62,6 +122,15 @@ class Config(BaseSettings):
         assert v.exists()
         return v
 
+    @model_validator(mode="after")
+    def log_dir_relative_to_cache_dir(self) -> "Config":
+        """
+        If log dir is relative, put it beneath the cache_dir
+        """
+        if not self.log_dir.is_absolute():
+            self.log_dir = self.cache_dir / self.log_dir
+        return self
+
     @model_validator(mode="after")
     def folders_exist(self) -> "Config":
         """

nwb_linkml/src/nwb_linkml/io/schema.py

@@ -70,6 +70,7 @@ def load_namespace_adapter(
     namespace: Path | NamespaceRepo | Namespaces,
     path: Optional[Path] = None,
     version: Optional[str] = None,
+    imported: Optional[list[NamespacesAdapter]] = None,
 ) -> NamespacesAdapter:
     """
     Load all schema referenced by a namespace file
@@ -115,6 +116,9 @@ def load_namespace_adapter(
             yml_file = (path / schema.source).resolve()
             sch.append(load_schema_file(yml_file))
 
+    if imported is not None:
+        adapter = NamespacesAdapter(namespaces=namespaces, schemas=sch, imported=imported)
+    else:
         adapter = NamespacesAdapter(namespaces=namespaces, schemas=sch)
 
     return adapter
@@ -148,8 +152,6 @@ def load_nwb_core(
     if hdmf_only:
         schema = hdmf_schema
     else:
-        schema = load_namespace_adapter(NWB_CORE_REPO, version=core_version)
+        schema = load_namespace_adapter(NWB_CORE_REPO, version=core_version, imported=[hdmf_schema])
-
-        schema.imported.append(hdmf_schema)
 
     return schema

nwb_linkml/src/nwb_linkml/logging.py

@@ -0,0 +1,100 @@
+"""
+Logging factory and handlers
+"""
+
+import logging
+from logging.handlers import RotatingFileHandler
+from pathlib import Path
+from typing import Optional, Union
+
+from rich.logging import RichHandler
+
+from nwb_linkml.config import LOG_LEVELS, Config
+
+
+def init_logger(
+    name: str,
+    log_dir: Union[Optional[Path], bool] = None,
+    level: Optional[LOG_LEVELS] = None,
+    file_level: Optional[LOG_LEVELS] = None,
+    log_file_n: Optional[int] = None,
+    log_file_size: Optional[int] = None,
+) -> logging.Logger:
+    """
+    Make a logger.
+
+    Log to a set of rotating files in the ``log_dir`` according to ``name`` ,
+    as well as using the :class:`~rich.RichHandler` for pretty-formatted stdout logs.
+
+    Args:
+        name (str): Name of this logger. Ideally names are hierarchical
+            and indicate what they are logging for, eg. ``miniscope_io.sdcard``
+            and don't contain metadata like timestamps, etc. (which are in the logs)
+        log_dir (:class:`pathlib.Path`): Directory to store file-based logs in. If ``None``,
+            get from :class:`.Config`. If ``False`` , disable file logging.
+        level (:class:`.LOG_LEVELS`): Level to use for stdout logging. If ``None`` ,
+            get from :class:`.Config`
+        file_level (:class:`.LOG_LEVELS`): Level to use for file-based logging.
+             If ``None`` , get from :class:`.Config`
+        log_file_n (int): Number of rotating file logs to use.
+            If ``None`` , get from :class:`.Config`
+        log_file_size (int): Maximum size of logfiles before rotation.
+            If ``None`` , get from :class:`.Config`
+
+    Returns:
+        :class:`logging.Logger`
+    """
+    config = Config()
+    if log_dir is None:
+        log_dir = config.log_dir
+    if level is None:
+        level = config.logs.level_stdout
+    if file_level is None:
+        file_level = config.logs.level_file
+    if log_file_n is None:
+        log_file_n = config.logs.file_n
+    if log_file_size is None:
+        log_file_size = config.logs.file_size
+
+    if not name.startswith("nwb_linkml"):
+        name = "nwb_linkml." + name
+
+    logger = logging.getLogger(name)
+    logger.setLevel(level)
+
+    # Add handlers for stdout and file
+    if log_dir is not False:
+        logger.addHandler(_file_handler(name, file_level, log_dir, log_file_n, log_file_size))
+
+    logger.addHandler(_rich_handler())
+
+    return logger
+
+
+def _file_handler(
+    name: str,
+    file_level: LOG_LEVELS,
+    log_dir: Path,
+    log_file_n: int = 5,
+    log_file_size: int = 2**22,
+) -> RotatingFileHandler:
+    # See init_logger for arg docs
+
+    filename = Path(log_dir) / ".".join([name, "log"])
+    file_handler = RotatingFileHandler(
+        str(filename), mode="a", maxBytes=log_file_size, backupCount=log_file_n
+    )
+    file_formatter = logging.Formatter("[%(asctime)s] %(levelname)s [%(name)s]: %(message)s")
+    file_handler.setLevel(file_level)
+    file_handler.setFormatter(file_formatter)
+    return file_handler
+
+
+def _rich_handler() -> RichHandler:
+    rich_handler = RichHandler(rich_tracebacks=True, markup=True)
+    rich_formatter = logging.Formatter(
+        "[bold green]\[%(name)s][/bold green] %(message)s",
+        datefmt="[%y-%m-%dT%H:%M:%S]",
+    )
+    rich_handler.setFormatter(rich_formatter)
+    return rich_handler

nwb_linkml/tests/fixtures.py

@@ -82,7 +82,6 @@ def tmp_output_dir_mod(tmp_output_dir) -> Path:
 @pytest.fixture(scope="session", params=[{"core_version": "2.7.0", "hdmf_version": "1.8.0"}])
 def nwb_core_fixture(request) -> NamespacesAdapter:
     nwb_core = io.load_nwb_core(**request.param)
-    nwb_core.populate_imports()
     assert (
         request.param["core_version"] in nwb_core.versions["core"]
     )  # 2.6.0 is actually 2.6.0-alpha

nwb_linkml/tests/test_adapters/test_adapter_namespaces.py

@@ -46,3 +46,17 @@ def test_skip_imports(nwb_core_fixture):
     # we shouldn't have any of the hdmf-common schema in with us
     namespaces = [sch.annotations["namespace"].value for sch in res.schemas]
     assert all([ns == "core" for ns in namespaces])
+
+
+@pytest.mark.skip()
+def test_populate_inheritance(nwb_core_fixture):
+    """
+    Classes should receive and override the properties of their parents
+    when they have neurodata_type_inc
+    Args:
+        nwb_core_fixture:
+
+    Returns:
+
+    """
+    pass

nwb_linkml/tests/test_generate.py

@@ -76,6 +76,7 @@ def test_generate_pydantic(tmp_output_dir):
         initfile.write("# Autogenerated module indicator")
 
 
+@pytest.mark.linkml
 @pytest.mark.provider
 @pytest.mark.dev
 def test_generate_linkml_provider(tmp_output_dir, nwb_core_fixture):
@@ -84,6 +85,7 @@ def test_generate_linkml_provider(tmp_output_dir, nwb_core_fixture):
     result = provider.build(nwb_core_fixture)
 
 
+@pytest.mark.pydantic
 @pytest.mark.provider
 @pytest.mark.dev
 def test_generate_pydantic_provider(tmp_output_dir):

nwb_linkml/tests/test_includes/conftest.py

@@ -0,0 +1,120 @@
+from typing import Tuple
+
+import numpy as np
+import pytest
+
+from nwb_linkml.models import (
+    ElectricalSeries,
+    ExtracellularEphysElectrodes,
+    Device,
+    ElectrodeGroup,
+    DynamicTableRegion,
+    Units,
+    IntracellularElectrode,
+    IntracellularElectrodesTable,
+    IntracellularResponsesTable,
+    IntracellularStimuliTable,
+    IntracellularRecordingsTable,
+)
+
+
+@pytest.fixture()
+def electrical_series() -> Tuple["ElectricalSeries", "ExtracellularEphysElectrodes"]:
+    """
+    Demo electrical series with adjoining electrodes
+    """
+    n_electrodes = 5
+    n_times = 100
+    data = np.arange(0, n_electrodes * n_times).reshape(n_times, n_electrodes).astype(float)
+    timestamps = np.linspace(0, 1, n_times)
+
+    device = Device(name="my electrode")
+
+    # electrode group is the physical description of the electrodes
+    electrode_group = ElectrodeGroup(
+        name="GroupA",
+        device=device,
+        description="an electrode group",
+        location="you know where it is",
+    )
+
+    # make electrodes tables
+    electrodes = ExtracellularEphysElectrodes(
+        description="idk these are also electrodes",
+        id=np.arange(0, n_electrodes),
+        x=np.arange(0, n_electrodes).astype(float),
+        y=np.arange(n_electrodes, n_electrodes * 2).astype(float),
+        group=[electrode_group] * n_electrodes,
+        group_name=[electrode_group.name] * n_electrodes,
+        location=[str(i) for i in range(n_electrodes)],
+        extra_column=["sup"] * n_electrodes,
+    )
+
+    electrical_series = ElectricalSeries(
+        name="my recording!",
+        electrodes=DynamicTableRegion(
+            table=electrodes,
+            value=np.arange(n_electrodes - 1, -1, step=-1),
+            name="electrodes",
+            description="hey",
+        ),
+        timestamps=timestamps,
+        data=data,
+    )
+    return electrical_series, electrodes
+
+
+def _ragged_array(n_units: int) -> tuple[list[np.ndarray], np.ndarray]:
+    generator = np.random.default_rng()
+    spike_times = [
+        np.full(shape=generator.integers(10, 50), fill_value=i, dtype=float) for i in range(n_units)
+    ]
+    spike_idx = []
+    for i in range(n_units):
+        if i == 0:
+            spike_idx.append(len(spike_times[0]))
+        else:
+            spike_idx.append(len(spike_times[i]) + spike_idx[i - 1])
+    spike_idx = np.array(spike_idx)
+    return spike_times, spike_idx
+
+
+@pytest.fixture(params=[True, False])
+def units(request) -> Tuple[Units, list[np.ndarray], np.ndarray]:
+    """
+    Test case for units
+
+    Parameterized by extra_column because pandas likes to pivot dataframes
+    to long when there is only one column and it's not len() == 1
+    """
+    spike_times, spike_idx = _ragged_array(24)
+
+    spike_times_flat = np.concatenate(spike_times)
+
+    kwargs = {
+        "description": "units!!!!",
+        "spike_times": spike_times_flat,
+        "spike_times_index": spike_idx,
+    }
+    if request.param:
+        kwargs["extra_column"] = ["hey!"] * 24
+    units = Units(**kwargs)
+    return units, spike_times, spike_idx
+
+
+@pytest.fixture()
+def intracellular_recordings_table() -> IntracellularRecordingsTable:
+    n_recordings = 10
+    device = Device(name="my device")
+    electrode = IntracellularElectrode(
+        name="my_electrode", description="an electrode", device=device
+    )
+    electrodes = IntracellularElectrodesTable(
+        name="intracellular_electrodes", electrode=[electrode] * n_recordings
+    )
+    stimuli = IntracellularStimuliTable(
+        name="intracellular_stimuli",
+    )
+    responses = IntracellularResponsesTable()
+
+    recordings_table = IntracellularRecordingsTable()

nwb_linkml/tests/test_includes/test_hdmf.py

@@ -1,103 +1,13 @@
-from typing import Tuple
-
 import numpy as np
-import pytest
 
 # FIXME: Make this just be the output of the provider by patching into import machinery
 from nwb_linkml.models.pydantic.core.v2_7_0.namespace import (
-    Device,
     DynamicTable,
     DynamicTableRegion,
-    ElectricalSeries,
     ElectrodeGroup,
-    ExtracellularEphysElectrodes,
-    Units,
     VectorIndex,
 )
-
+from .conftest import _ragged_array
-
-@pytest.fixture()
-def electrical_series() -> Tuple["ElectricalSeries", "ExtracellularEphysElectrodes"]:
-    """
-    Demo electrical series with adjoining electrodes
-    """
-    n_electrodes = 5
-    n_times = 100
-    data = np.arange(0, n_electrodes * n_times).reshape(n_times, n_electrodes).astype(float)
-    timestamps = np.linspace(0, 1, n_times)
-
-    device = Device(name="my electrode")
-
-    # electrode group is the physical description of the electrodes
-    electrode_group = ElectrodeGroup(
-        name="GroupA",
-        device=device,
-        description="an electrode group",
-        location="you know where it is",
-    )
-
-    # make electrodes tables
-    electrodes = ExtracellularEphysElectrodes(
-        description="idk these are also electrodes",
-        id=np.arange(0, n_electrodes),
-        x=np.arange(0, n_electrodes).astype(float),
-        y=np.arange(n_electrodes, n_electrodes * 2).astype(float),
-        group=[electrode_group] * n_electrodes,
-        group_name=[electrode_group.name] * n_electrodes,
-        location=[str(i) for i in range(n_electrodes)],
-        extra_column=["sup"] * n_electrodes,
-    )
-
-    electrical_series = ElectricalSeries(
-        name="my recording!",
-        electrodes=DynamicTableRegion(
-            table=electrodes,
-            value=np.arange(n_electrodes - 1, -1, step=-1),
-            name="electrodes",
-            description="hey",
-        ),
-        timestamps=timestamps,
-        data=data,
-    )
-    return electrical_series, electrodes
-
-
-def _ragged_array(n_units: int) -> tuple[list[np.ndarray], np.ndarray]:
-    generator = np.random.default_rng()
-    spike_times = [
-        np.full(shape=generator.integers(10, 50), fill_value=i, dtype=float) for i in range(n_units)
-    ]
-    spike_idx = []
-    for i in range(n_units):
-        if i == 0:
-            spike_idx.append(len(spike_times[0]))
-        else:
-            spike_idx.append(len(spike_times[i]) + spike_idx[i - 1])
-    spike_idx = np.array(spike_idx)
-    return spike_times, spike_idx
-
-
-@pytest.fixture(params=[True, False])
-def units(request) -> Tuple[Units, list[np.ndarray], np.ndarray]:
-    """
-    Test case for units
-
-    Parameterized by extra_column because pandas likes to pivot dataframes
-    to long when there is only one column and it's not len() == 1
-    """
-    spike_times, spike_idx = _ragged_array(24)
-
-    spike_times_flat = np.concatenate(spike_times)
-
-    kwargs = {
-        "description": "units!!!!",
-        "spike_times": spike_times_flat,
-        "spike_times_index": spike_idx,
-    }
-    if request.param:
-        kwargs["extra_column"] = ["hey!"] * 24
-    units = Units(**kwargs)
-    return units, spike_times, spike_idx
 
 
 def test_dynamictable_indexing(electrical_series):

nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py

@@ -220,8 +220,8 @@ class DtypeMixin(ConfiguredBaseModel):
 class Attribute(DtypeMixin):
 
     name: str = Field(...)
-    dims: Optional[List[Union[Any, str]]] = Field(default_factory=list)
+    dims: Optional[List[Union[Any, str]]] = Field(None)
-    shape: Optional[List[Union[Any, int, str]]] = Field(default_factory=list)
+    shape: Optional[List[Union[Any, int, str]]] = Field(None)
     value: Optional[Any] = Field(
         None, description="""Optional constant, fixed value for the attribute."""
     )
@@ -233,9 +233,7 @@ class Attribute(DtypeMixin):
         True,
         description="""Optional boolean key describing whether the attribute is required. Default value is True.""",
     )
-    dtype: Optional[Union[List[CompoundDtype], FlatDtype, ReferenceDtype]] = Field(
+    dtype: Optional[Union[List[CompoundDtype], FlatDtype, ReferenceDtype]] = Field(None)
-        default_factory=list
-    )
 
 
 class Dataset(DtypeMixin):
@@ -250,8 +248,8 @@ class Dataset(DtypeMixin):
     )
     name: Optional[str] = Field(None)
     default_name: Optional[str] = Field(None)
-    dims: Optional[List[Union[Any, str]]] = Field(default_factory=list)
+    dims: Optional[List[Union[Any, str]]] = Field(None)
-    shape: Optional[List[Union[Any, int, str]]] = Field(default_factory=list)
+    shape: Optional[List[Union[Any, int, str]]] = Field(None)
     value: Optional[Any] = Field(
         None, description="""Optional constant, fixed value for the attribute."""
     )
@@ -261,7 +259,5 @@ class Dataset(DtypeMixin):
     doc: str = Field(..., description="""Description of corresponding object.""")
     quantity: Optional[Union[QuantityEnum, int]] = Field(1)
     linkable: Optional[bool] = Field(None)
-    attributes: Optional[List[Attribute]] = Field(default_factory=list)
+    attributes: Optional[List[Attribute]] = Field(None)
-    dtype: Optional[Union[List[CompoundDtype], FlatDtype, ReferenceDtype]] = Field(
+    dtype: Optional[Union[List[CompoundDtype], FlatDtype, ReferenceDtype]] = Field(None)
-        default_factory=list
-    )