fix schema generation

This is in one commit so it's easy to diff vs the last sorted schema.

Minimal changes from the last one. Funny little trick from
https://skaaptjop.medium.com/how-i-use-pydantic-unrequired-fields-so-that-the-schema-works-0010d8758072
to make it express optional things in the same way as before.

Author: sfoster1

api/src/opentrons/protocol_engine/commands/absorbance_reader/initialize.py

@@ -1,9 +1,10 @@
 """Command models to initialize an Absorbance Reader."""
 from __future__ import annotations
-from typing import List, Optional, Literal, TYPE_CHECKING
+from typing import List, Optional, Literal, TYPE_CHECKING, Any
 from typing_extensions import Type
 
 from pydantic import BaseModel, Field
+from pydantic.json_schema import SkipJsonSchema
 
 from opentrons.drivers.types import ABSMeasurementMode
 from opentrons.protocol_engine.types import ABSMeasureMode
@@ -20,6 +21,10 @@
 InitializeCommandType = Literal["absorbanceReader/initialize"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class InitializeParams(BaseModel):
     """Input parameters to initialize an absorbance reading."""
 
@@ -28,8 +33,10 @@ class InitializeParams(BaseModel):
         ..., description="Initialize single or multi measurement mode."
     )
     sampleWavelengths: List[int] = Field(..., description="Sample wavelengths in nm.")
-    referenceWavelength: Optional[int] = Field(
-        None, description="Optional reference wavelength in nm."
+    referenceWavelength: int | SkipJsonSchema[None] = Field(
+        None,
+        description="Optional reference wavelength in nm.",
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/absorbance_reader/read.py

@@ -1,10 +1,11 @@
 """Command models to read absorbance."""
 from __future__ import annotations
 from datetime import datetime
-from typing import Optional, Dict, TYPE_CHECKING, List
-from typing_extensions import Literal, Type
+from typing import Optional, Dict, TYPE_CHECKING, List, Any
 
+from typing_extensions import Literal, Type
 from pydantic import BaseModel, Field
+from pydantic.json_schema import SkipJsonSchema
 
 from ..command import AbstractCommandImpl, BaseCommand, BaseCommandCreate, SuccessData
 from ...errors import CannotPerformModuleAction, StorageLimitReachedError
@@ -22,16 +23,21 @@
     from opentrons.protocol_engine.execution import EquipmentHandler
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 ReadAbsorbanceCommandType = Literal["absorbanceReader/read"]
 
 
 class ReadAbsorbanceParams(BaseModel):
     """Input parameters for an absorbance reading."""
 
     moduleId: str = Field(..., description="Unique ID of the Absorbance Reader.")
-    fileName: Optional[str] = Field(
+    fileName: str | SkipJsonSchema[None] = Field(
         None,
         description="Optional file name to use when storing the results of a measurement.",
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/calibration/calibrate_gripper.py

@@ -1,10 +1,11 @@
 """Models and implementation for the calibrateGripper command."""
 
 from enum import Enum
-from typing import Optional, Type
+from typing import Optional, Type, Any
 from typing_extensions import Literal
 
 from pydantic import BaseModel, Field
+from pydantic.json_schema import SkipJsonSchema
 
 from opentrons.types import Point
 from opentrons.hardware_control import HardwareControlAPI
@@ -22,6 +23,10 @@
 CalibrateGripperCommandType = Literal["calibration/calibrateGripper"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class CalibrateGripperParamsJaw(Enum):  # noqa: D101
     FRONT = "front"
     REAR = "rear"
@@ -39,7 +44,7 @@ class CalibrateGripperParams(BaseModel):
         ),
     )
 
-    otherJawOffset: Optional[Vec3f] = Field(
+    otherJawOffset: Vec3f | SkipJsonSchema[None] = Field(
         None,
         description=(
             "If an offset for the other probe is already found, then specifying it here"
@@ -48,6 +53,7 @@ class CalibrateGripperParams(BaseModel):
             " If this param is not specified then the command will only find and return"
             " the offset for the specified probe."
         ),
+        json_schema_extra=_remove_default,
     )
 
 
@@ -62,11 +68,12 @@ class CalibrateGripperResult(BaseModel):
         ),
     )
 
-    savedCalibration: Optional[GripperCalibrationOffset] = Field(
+    savedCalibration: GripperCalibrationOffset | SkipJsonSchema[None] = Field(
         None,
         description=(
             "Gripper calibration result data, when `otherJawOffset` is provided."
         ),
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/command.py

@@ -14,9 +14,12 @@
     List,
     Type,
     Union,
+    Any,
+    Dict,
 )
 
 from pydantic import BaseModel, Field
+from pydantic.json_schema import SkipJsonSchema
 
 from opentrons.hardware_control import HardwareControlAPI
 from opentrons.protocol_engine.state.update_types import StateUpdate
@@ -61,6 +64,10 @@ class CommandIntent(str, enum.Enum):
     FIXIT = "fixit"
 
 
+def _pop_default(s: Dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class BaseCommandCreate(
     BaseModel,
     # These type parameters need to be invariant because our fields are mutable.
@@ -80,7 +87,7 @@ class BaseCommandCreate(
         ),
     )
     params: _ParamsT = Field(..., description="Command execution data payload")
-    intent: Optional[CommandIntent] = Field(
+    intent: CommandIntent | SkipJsonSchema[None] = Field(
         None,
         description=(
             "The reason the command was added. If not specified or `protocol`,"
@@ -93,14 +100,16 @@ class BaseCommandCreate(
             "Use setup commands for activities like pre-run calibration checks"
             " and module setup, like pre-heating."
         ),
+        json_schema_extra=_pop_default,
     )
-    key: Optional[str] = Field(
+    key: str | SkipJsonSchema[None] = Field(
         None,
         description=(
             "A key value, unique in this run, that can be used to track"
             " the same logical command across multiple runs of the same protocol."
             " If a value is not provided, one will be generated."
         ),
+        json_schema_extra=_pop_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/configure_for_volume.py

@@ -1,7 +1,9 @@
 """Configure for volume command request, result, and implementation models."""
 from __future__ import annotations
+from typing import TYPE_CHECKING, Optional, Type, Any
+
 from pydantic import BaseModel, Field
-from typing import TYPE_CHECKING, Optional, Type
+from pydantic.json_schema import SkipJsonSchema
 from typing_extensions import Literal
 
 from .pipetting_common import PipetteIdMixin
@@ -16,6 +18,10 @@
 ConfigureForVolumeCommandType = Literal["configureForVolume"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class ConfigureForVolumeParams(PipetteIdMixin):
     """Parameters required to configure volume for a specific pipette."""
 
@@ -25,12 +31,13 @@ class ConfigureForVolumeParams(PipetteIdMixin):
         "than a pipette-specific maximum volume.",
         ge=0,
     )
-    tipOverlapNotAfterVersion: Optional[str] = Field(
+    tipOverlapNotAfterVersion: str | SkipJsonSchema[None] = Field(
         None,
         description="A version of tip overlap data to not exceed. The highest-versioned "
         "tip overlap data that does not exceed this version will be used. Versions are "
         "expressed as vN where N is an integer, counting up from v0. If None, the current "
         "highest version will be used.",
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/dispense.py

@@ -1,11 +1,12 @@
 """Dispense command request, result, and implementation models."""
 
 from __future__ import annotations
-from typing import TYPE_CHECKING, Optional, Type, Union
+from typing import TYPE_CHECKING, Optional, Type, Union, Any
 from typing_extensions import Literal
 
 
 from pydantic import Field
+from pydantic.json_schema import SkipJsonSchema
 
 from ..state.update_types import StateUpdate, CLEAR
 from .pipetting_common import (
@@ -39,14 +40,19 @@
 DispenseCommandType = Literal["dispense"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class DispenseParams(
     PipetteIdMixin, DispenseVolumeMixin, FlowRateMixin, LiquidHandlingWellLocationMixin
 ):
     """Payload required to dispense to a specific well."""
 
-    pushOut: Optional[float] = Field(
+    pushOut: float | SkipJsonSchema[None] = Field(
         None,
         description="push the plunger a small amount farther than necessary for accurate low-volume dispensing",
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/dispense_in_place.py

@@ -1,9 +1,10 @@
 """Dispense-in-place command request, result, and implementation models."""
 
 from __future__ import annotations
-from typing import TYPE_CHECKING, Optional, Type, Union
+from typing import TYPE_CHECKING, Optional, Type, Union, Any
 from typing_extensions import Literal
 from pydantic import Field
+from pydantic.json_schema import SkipJsonSchema
 
 from .pipetting_common import (
     PipetteIdMixin,
@@ -32,12 +33,17 @@
 DispenseInPlaceCommandType = Literal["dispenseInPlace"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class DispenseInPlaceParams(PipetteIdMixin, DispenseVolumeMixin, FlowRateMixin):
     """Payload required to dispense in place."""
 
-    pushOut: Optional[float] = Field(
+    pushOut: float | SkipJsonSchema[None] = Field(
         None,
         description="push the plunger a small amount farther than necessary for accurate low-volume dispensing",
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/drop_tip.py

@@ -1,9 +1,11 @@
 """Drop tip command request, result, and implementation models."""
 
 from __future__ import annotations
+from typing import TYPE_CHECKING, Optional, Type, Any
 
 from pydantic import Field
-from typing import TYPE_CHECKING, Optional, Type
+from pydantic.json_schema import SkipJsonSchema
+
 from typing_extensions import Literal
 
 from opentrons.protocol_engine.errors.exceptions import TipAttachedError
@@ -37,6 +39,10 @@
 DropTipCommandType = Literal["dropTip"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class DropTipParams(PipetteIdMixin):
     """Payload required to drop a tip in a specific well."""
 
@@ -46,15 +52,16 @@ class DropTipParams(PipetteIdMixin):
         default_factory=DropTipWellLocation,
         description="Relative well location at which to drop the tip.",
     )
-    homeAfter: Optional[bool] = Field(
+    homeAfter: bool | SkipJsonSchema[None] = Field(
         None,
         description=(
             "Whether to home this pipette's plunger after dropping the tip."
             " You should normally leave this unspecified to let the robot choose"
             " a safe default depending on its hardware."
         ),
+        json_schema_extra=_remove_default,
     )
-    alternateDropLocation: Optional[bool] = Field(
+    alternateDropLocation: bool | SkipJsonSchema[None] = Field(
         False,
         description=(
             "Whether to alternate location where tip is dropped within the labware."
@@ -63,6 +70,7 @@ class DropTipParams(PipetteIdMixin):
             " labware well."
             " If False, the tip will be dropped at the top center of the well."
         ),
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/drop_tip_in_place.py

@@ -1,7 +1,10 @@
 """Drop tip in place command request, result, and implementation models."""
 from __future__ import annotations
+
+from typing import TYPE_CHECKING, Optional, Type, Any
+
 from pydantic import Field, BaseModel
-from typing import TYPE_CHECKING, Optional, Type
+from pydantic.json_schema import SkipJsonSchema
 from typing_extensions import Literal
 
 from .command import (
@@ -24,16 +27,21 @@
 DropTipInPlaceCommandType = Literal["dropTipInPlace"]
 
 
+def _remove_default(s: dict[str, Any]) -> None:
+    s.pop("default")
+
+
 class DropTipInPlaceParams(PipetteIdMixin):
     """Payload required to drop a tip in place."""
 
-    homeAfter: Optional[bool] = Field(
+    homeAfter: bool | SkipJsonSchema[None] = Field(
         None,
         description=(
             "Whether to home this pipette's plunger after dropping the tip."
             " You should normally leave this unspecified to let the robot choose"
             " a safe default depending on its hardware."
         ),
+        json_schema_extra=_remove_default,
     )
 
 

api/src/opentrons/protocol_engine/commands/generate_command_schema.py

@@ -1,24 +1,17 @@
 """Generate a JSON schema against which all create commands statically validate."""
+
 import json
-import pydantic
 import argparse
 import sys
-from opentrons.protocol_engine.commands.command_unions import CommandCreate
-
-
-class CreateCommandUnion(pydantic.RootModel[CommandCreate]):
-    """Model that validates a union of all CommandCreate models."""
-
-    root: CommandCreate
+from opentrons.protocol_engine.commands.command_unions import CommandCreateAdapter
 
 
 def generate_command_schema(version: str) -> str:
     """Generate a JSON Schema that all valid create commands can validate against."""
-    raw_json_schema = CreateCommandUnion.schema_json()
-    schema_as_dict = json.loads(raw_json_schema)
+    schema_as_dict = CommandCreateAdapter.json_schema(mode="validation")
     schema_as_dict["$id"] = f"opentronsCommandSchemaV{version}"
     schema_as_dict["$schema"] = "http://json-schema.org/draft-07/schema#"
-    return json.dumps(schema_as_dict, indent=2)
+    return json.dumps(schema_as_dict, indent=2, sort_keys=True)
 
 
 if __name__ == "__main__":