Merge pull request #1227 from AllenNeuralDynamics/1225-20-rename-aind…

…x-models

refactor: rename AindX classes to show their actual purposes

src/aind_data_schema/__init__.py

@@ -1,4 +1,4 @@
-""" imports for AindModel subclasses
+""" imports for DataModel subclasses
 """
 
 __version__ = "2.0.0"

src/aind_data_schema/base.py

@@ -75,7 +75,7 @@ def has_corrupt_keys(input) -> bool:
     return has_corrupt_keys(input_dict)
 
 
-class AindGeneric(BaseModel, extra="allow"):
+class GenericModel(BaseModel, extra="allow"):
     """Base class for generic types that can be used in AIND schema"""
 
     # extra="allow" is needed because BaseModel by default drops extra parameters.
@@ -91,10 +91,10 @@ def validate_fieldnames(self):
         return self
 
 
-AindGenericType = TypeVar("AindGenericType", bound=AindGeneric)
+GenericModelType = TypeVar("GenericModelType", bound=GenericModel)
 
 
-class AindModel(BaseModel, Generic[AindGenericType]):
+class DataModel(BaseModel, Generic[GenericModelType]):
     """BaseModel that disallows extra fields
 
     Also performs validation checks / coercion / upgrades where necessary
@@ -130,7 +130,7 @@ def unit_validator(cls, values):
         return values
 
 
-class AindCoreModel(AindModel):
+class DataCoreModel(DataModel):
     """Generic base class to hold common fields/validators/etc for all basic AIND schema"""
 
     _FILE_EXTENSION = PrivateAttr(default=".json")
@@ -154,7 +154,9 @@ def default_filename(cls):
         """
         Returns standard filename in snakecase
         """
-        parent_classes = [base_class for base_class in cls.__bases__ if base_class.__name__ != AindCoreModel.__name__]
+        parent_classes = [
+            base_class for base_class in cls.__bases__ if base_class.__name__ != DataCoreModel.__name__
+        ]
 
         name = cls.__name__
 

src/aind_data_schema/components/coordinates.py

@@ -8,7 +8,7 @@
 from pydantic import Field
 from typing_extensions import Annotated
 
-from aind_data_schema.base import AindModel
+from aind_data_schema.base import DataModel
 
 
 class CcfVersion(str, Enum):
@@ -45,7 +45,7 @@ class AnatomicalDirection(str, Enum):
     OTHER = "Other"
 
 
-class CoordinateTransform(AindModel):
+class CoordinateTransform(DataModel):
     """Generic base class for coordinate transform subtypes"""
 
     type: str = Field(..., title="transformation type")
@@ -83,15 +83,15 @@ class Affine3dTransform(CoordinateTransform):
     )
 
 
-class Size2d(AindModel):
+class Size2d(DataModel):
     """2D size of an object"""
 
     width: int = Field(..., title="Width")
     height: int = Field(..., title="Height")
     unit: SizeUnit = Field(SizeUnit.PX, title="Size unit")
 
 
-class Size3d(AindModel):
+class Size3d(DataModel):
     """3D size of an object"""
 
     width: int = Field(..., title="Width")
@@ -100,7 +100,7 @@ class Size3d(AindModel):
     unit: SizeUnit = Field(SizeUnit.M, title="Size unit")
 
 
-class Orientation3d(AindModel):
+class Orientation3d(DataModel):
     """3D orientation of an object"""
 
     pitch: Decimal = Field(..., title="Angle pitch", ge=0, le=360)
@@ -109,15 +109,15 @@ class Orientation3d(AindModel):
     unit: AngleUnit = Field(AngleUnit.DEG, title="Angle unit")
 
 
-class ModuleOrientation2d(AindModel):
+class ModuleOrientation2d(DataModel):
     """2D module orientation of an object"""
 
     arc_angle: Decimal = Field(..., title="Arc angle")
     module_angle: Decimal = Field(..., title="Module angle")
     unit: AngleUnit = Field(AngleUnit.DEG, title="Angle unit")
 
 
-class ModuleOrientation3d(AindModel):
+class ModuleOrientation3d(DataModel):
     """3D module orientation of an object"""
 
     arc_angle: Decimal = Field(..., title="Arc angle")
@@ -126,7 +126,7 @@ class ModuleOrientation3d(AindModel):
     unit: AngleUnit = Field(AngleUnit.DEG, title="Angle unit")
 
 
-class Coordinates3d(AindModel):
+class Coordinates3d(DataModel):
     """Coordinates in a 3D grid"""
 
     x: Decimal = Field(..., title="Position X")
@@ -135,7 +135,7 @@ class Coordinates3d(AindModel):
     unit: SizeUnit = Field(SizeUnit.UM, title="Position unit")
 
 
-class CcfCoords(AindModel):
+class CcfCoords(DataModel):
     """Coordinates in CCF template space"""
 
     ml: Decimal = Field(..., title="ML")
@@ -145,7 +145,7 @@ class CcfCoords(AindModel):
     ccf_version: CcfVersion = Field(CcfVersion.CCFv3, title="CCF version")
 
 
-class Axis(AindModel):
+class Axis(DataModel):
     """Description of an axis"""
 
     name: AxisName = Field(..., title="Axis")
@@ -168,7 +168,7 @@ class ImageAxis(Axis):
     unit: SizeUnit = Field(SizeUnit.UM, title="Axis physical units")
 
 
-class RelativePosition(AindModel):
+class RelativePosition(DataModel):
     """Position and rotation of a device in a rig or instrument"""
 
     device_position_transformations: List[

src/aind_data_schema/components/devices.py

@@ -19,7 +19,7 @@
 from pydantic import Field, ValidationInfo, field_validator, model_validator
 from typing_extensions import Annotated
 
-from aind_data_schema.base import AindGeneric, AindGenericType, AindModel, AwareDatetimeWithDefault
+from aind_data_schema.base import GenericModel, GenericModelType, DataModel, AwareDatetimeWithDefault
 from aind_data_schema.components.coordinates import RelativePosition, Size3d
 from aind_data_schema.components.reagent import Reagent
 
@@ -261,7 +261,7 @@ class MyomatrixArrayType(str, Enum):
     SUTURED = "Sutured"
 
 
-class Device(AindModel):
+class Device(DataModel):
     """Generic device"""
 
     device_type: str = Field(..., title="Device type")  # Needs to be set by child classes that inherits
@@ -273,31 +273,31 @@ class Device(AindModel):
         default=None, title="Path to CAD diagram", description="For CUSTOM manufactured devices"
     )
     port_index: Optional[str] = Field(default=None, title="Port index")
-    additional_settings: AindGenericType = Field(AindGeneric(), title="Additional parameters")
+    additional_settings: GenericModelType = Field(GenericModel(), title="Additional parameters")
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class Software(AindModel):
+class Software(DataModel):
     """Description of generic software"""
 
     name: str = Field(..., title="Software name")
     version: str = Field(..., title="Software version")
     url: Optional[str] = Field(default=None, title="URL to commit being used")
-    parameters: AindGenericType = Field(AindGeneric(), title="Software parameters")
+    parameters: GenericModelType = Field(GenericModel(), title="Software parameters")
 
 
-class Calibration(AindModel):
+class Calibration(DataModel):
     """Generic calibration class"""
 
     calibration_date: AwareDatetimeWithDefault = Field(..., title="Date and time of calibration")
     device_name: str = Field(..., title="Device name", description="Must match a device name in rig/instrument")
     description: str = Field(..., title="Description", description="Brief description of what is being calibrated")
-    input: AindGenericType = Field(AindGeneric(), description="Calibration input", title="inputs")
-    output: AindGenericType = Field(AindGeneric(), description="Calibration output", title="outputs")
+    input: GenericModelType = Field(GenericModel(), description="Calibration input", title="inputs")
+    output: GenericModelType = Field(GenericModel(), description="Calibration output", title="outputs")
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class Maintenance(AindModel):
+class Maintenance(DataModel):
     """Generic maintenance class"""
 
     maintenance_date: AwareDatetimeWithDefault = Field(..., title="Date and time of maintenance")
@@ -444,7 +444,7 @@ def validate_other(cls, value: Optional[str], info: ValidationInfo) -> Optional[
         return value
 
 
-class CameraAssembly(AindModel):
+class CameraAssembly(DataModel):
     """Named assembly of a camera and lens (and optionally a filter)"""
 
     # required fields
@@ -458,7 +458,7 @@ class CameraAssembly(AindModel):
     position: Optional[RelativePosition] = Field(default=None, title="Relative position of this assembly")
 
 
-class DAQChannel(AindModel):
+class DAQChannel(DataModel):
     """Named input or output channel on a DAQ device"""
 
     # required fields
@@ -560,7 +560,7 @@ class Lamp(Device):
     temperature_unit: Optional[TemperatureUnit] = Field(default=None, title="Temperature unit")
 
 
-class ProbePort(AindModel):
+class ProbePort(DataModel):
     """Port for a probe connection"""
 
     index: int = Field(..., title="One-based port index")
@@ -610,7 +610,7 @@ class Patch(Device):
     photobleaching_date: Optional[date] = Field(default=None, title="Photobleaching date")
 
 
-class LaserAssembly(AindModel):
+class LaserAssembly(DataModel):
     """Assembly for optogenetic stimulation"""
 
     name: str = Field(..., title="Laser assembly name")
@@ -638,7 +638,7 @@ class EphysProbe(Device):
     headstage: Optional[Headstage] = Field(default=None, title="Headstage for this probe")
 
 
-class EphysAssembly(AindModel):
+class EphysAssembly(DataModel):
     """Module for electrophysiological recording"""
 
     name: str = Field(..., title="Ephys assembly name")
@@ -659,7 +659,7 @@ class FiberProbe(Device):
     length_unit: SizeUnit = Field(default=SizeUnit.MM, title="Length unit")
 
 
-class FiberAssembly(AindModel):
+class FiberAssembly(DataModel):
     """Module for inserted fiber photometry recording"""
 
     name: str = Field(..., title="Fiber assembly name")
@@ -839,7 +839,7 @@ def validate_other(self):
         return self
 
 
-class RewardDelivery(AindModel):
+class RewardDelivery(DataModel):
     """Description of reward delivery system"""
 
     device_type: Literal["Reward delivery"] = "Reward delivery"
@@ -862,7 +862,7 @@ class ChannelType(Enum):
     CARRIER = "Carrier"
 
 
-class OlfactometerChannel(AindModel):
+class OlfactometerChannel(DataModel):
     """description of a Olfactometer channel"""
 
     channel_index: int = Field(..., title="Channel index")

src/aind_data_schema/components/reagent.py

@@ -7,10 +7,10 @@
 from aind_data_schema_models.pid_names import PIDName
 from pydantic import Field
 
-from aind_data_schema.base import AindModel
+from aind_data_schema.base import DataModel
 
 
-class Reagent(AindModel):
+class Reagent(DataModel):
     """Description of reagent used in procedure"""
 
     name: str = Field(..., title="Name")

src/aind_data_schema/components/stimulus.py

@@ -7,7 +7,7 @@
 from aind_data_schema_models.units import ConcentrationUnit, FrequencyUnit, PowerUnit, TimeUnit
 from pydantic import Field, model_validator
 
-from aind_data_schema.base import AindGeneric, AindGenericType, AindModel
+from aind_data_schema.base import GenericModel, GenericModelType, DataModel
 
 
 class PulseShape(str, Enum):
@@ -25,7 +25,7 @@ class FilterType(str, Enum):
     OTHER = "Other"
 
 
-class OptoStimulation(AindModel):
+class OptoStimulation(DataModel):
     """Description of opto stimulation parameters"""
 
     stimulus_type: Literal["Opto Stimulation"] = "Opto Stimulation"
@@ -49,17 +49,17 @@ class OptoStimulation(AindModel):
         description="Duration of baseline recording prior to first pulse train",
     )
     baseline_duration_unit: TimeUnit = Field(default=TimeUnit.S, title="Baseline duration unit")
-    other_parameters: AindGenericType = Field(AindGeneric(), title="Other parameters")
+    other_parameters: GenericModelType = Field(GenericModel(), title="Other parameters")
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class VisualStimulation(AindModel):
+class VisualStimulation(DataModel):
     """Description of visual stimulus parameters. Provides a high level description of stimulus."""
 
     stimulus_type: Literal["Visual Stimulation"] = "Visual Stimulation"
     stimulus_name: str = Field(..., title="Stimulus name")
-    stimulus_parameters: AindGenericType = Field(
-        AindGeneric(),
+    stimulus_parameters: GenericModelType = Field(
+        GenericModel(),
         title="Stimulus parameters",
         description="Define and list the parameter values used (e.g. all TF or orientation values)",
     )
@@ -71,7 +71,7 @@ class VisualStimulation(AindModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class PhotoStimulationGroup(AindModel):
+class PhotoStimulationGroup(DataModel):
     """Description of a photostimulation group"""
 
     group_index: int = Field(..., title="Group index")
@@ -84,11 +84,11 @@ class PhotoStimulationGroup(AindModel):
     spiral_duration_unit: TimeUnit = Field(default=TimeUnit.S, title="Spiral duration unit")
     inter_spiral_interval: Decimal = Field(..., title="Inter trial interval (s)")
     inter_spiral_interval_unit: TimeUnit = Field(default=TimeUnit.S, title="Inter trial interval unit")
-    other_parameters: AindGenericType = Field(AindGeneric(), title="Other parameters")
+    other_parameters: GenericModelType = Field(GenericModel(), title="Other parameters")
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class PhotoStimulation(AindModel):
+class PhotoStimulation(DataModel):
     """Description of a photostimulation session"""
 
     stimulus_type: Literal["Photo Stimulation"] = "Photo Stimulation"
@@ -97,11 +97,11 @@ class PhotoStimulation(AindModel):
     groups: List[PhotoStimulationGroup] = Field(..., title="Groups")
     inter_trial_interval: Decimal = Field(..., title="Inter trial interval (s)")
     inter_trial_interval_unit: TimeUnit = Field(default=TimeUnit.S, title="Inter trial interval unit")
-    other_parameters: AindGenericType = Field(AindGeneric(), title="Other parameters")
+    other_parameters: GenericModelType = Field(GenericModel(), title="Other parameters")
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class OlfactometerChannelConfig(AindModel):
+class OlfactometerChannelConfig(DataModel):
     """Description of olfactometer channel configurations"""
 
     channel_index: int = Field(..., title="Channel index")
@@ -111,7 +111,7 @@ class OlfactometerChannelConfig(AindModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class OlfactoryStimulation(AindModel):
+class OlfactoryStimulation(DataModel):
     """Description of a olfactory stimulus"""
 
     stimulus_type: Literal["Olfactory Stimulation"] = "Olfactory Stimulation"
@@ -120,7 +120,7 @@ class OlfactoryStimulation(AindModel):
     notes: Optional[str] = Field(default=None, title="Notes")
 
 
-class AuditoryStimulation(AindModel):
+class AuditoryStimulation(DataModel):
     """Description of an auditory stimulus"""
 
     stimulus_type: Literal["Auditory Stimulation"] = "Auditory Stimulation"