@opentrons/shared-data 0.0.1-alpha.1 → 0.0.1-alpha.17

package/python/build/lib/opentrons_shared_data/protocol/models/protocol_schema_v6.py

@@ -1,145 +0,0 @@
-from pydantic import BaseModel, Field, validator
-from typing import Any, List, Optional, Dict, Union
-from typing_extensions import Literal
-from opentrons_shared_data.labware.labware_definition import LabwareDefinition
-
-from .shared_models import (
-    Liquid,
-    Labware,
-    CommandAnnotation,
-    Location,
-    ProfileStep,
-    WellLocation,
-    OffsetVector,
-    Metadata,
-    Module,
-    Pipette,
-    Robot,
-    DesignerApplication,
-)
-
-
-# TODO (tamar 3/15/22): split apart all the command payloads when we tackle #9583
-class Params(BaseModel):
-    slotName: Optional[str]
-    axes: Optional[List[str]]
-    pipetteId: Optional[str]
-    mount: Optional[str]
-    moduleId: Optional[str]
-    location: Optional[Union[Location, Literal["offDeck"]]]
-    labwareId: Optional[str]
-    displayName: Optional[str]
-    liquidId: Optional[str]
-    volumeByWell: Optional[Dict[str, Any]]
-    wellName: Optional[str]
-    volume: Optional[float]
-    flowRate: Optional[float]
-    wellLocation: Optional[Union[WellLocation]]
-    waitForResume: Optional[Literal[True]]
-    seconds: Optional[float]
-    minimumZHeight: Optional[float]
-    forceDirect: Optional[bool]
-    speed: Optional[float]
-    message: Optional[str]
-    coordinates: Optional[OffsetVector]
-    axis: Optional[str]
-    distance: Optional[float]
-    positionId: Optional[str]
-    temperature: Optional[float]
-    celsius: Optional[float]
-    blockMaxVolumeUl: Optional[float]
-    rpm: Optional[float]
-    height: Optional[float]
-    offset: Optional[OffsetVector]
-    profile: Optional[List[ProfileStep]]
-    radius: Optional[float]
-
-
-class Command(BaseModel):
-    commandType: str
-    params: Params
-    key: Optional[str]
-
-
-class ProtocolSchemaV6(BaseModel):
-    otSharedSchema: Literal["#/protocol/schemas/6"] = Field(
-        ...,
-        alias="$otSharedSchema",
-        description="The path to a valid Opentrons shared schema relative to "
-        "the shared-data directory, without its extension.",
-    )
-    schemaVersion: Literal[6]
-    metadata: Metadata
-    robot: Robot
-    pipettes: Dict[str, Pipette]
-    labware: Dict[str, Labware]
-    modules: Optional[Dict[str, Module]]
-    liquids: Optional[Dict[str, Liquid]]
-    labwareDefinitions: Dict[str, LabwareDefinition]
-    # commands must be after pipettes, labware, etc. for its @validator to work.
-    commands: List[Command]
-    commandAnnotations: Optional[List[CommandAnnotation]]
-    designerApplication: Optional[DesignerApplication]
-
-    class Config:
-        # added for constructing the class with field name instead of alias
-        allow_population_by_field_name = True
-
-    @validator("commands")
-    def _validate_commands(
-        cls,
-        value: List[Command],
-        values: Dict[str, Any],
-    ) -> List[Command]:
-        pipette_ids = set(values["pipettes"].keys()) if "pipettes" in values else set()
-        labware_ids = set(values["labware"].keys()) if "labware" in values else set()
-        module_ids = (
-            set(values["modules"].keys())
-            if "modules" in values and values["modules"]
-            else set()
-        )
-        liquid_ids = (
-            set(values["liquids"].keys())
-            if "liquids" in values and values["liquids"]
-            else set()
-        )
-
-        for index, command in enumerate(value):
-            if (
-                command.params.pipetteId is not None
-                and command.params.pipetteId not in pipette_ids
-            ):
-                raise ValueError(
-                    f"{command.commandType} command at index {index}"
-                    f" references ID {command.params.pipetteId},"
-                    f" which doesn't exist."
-                )
-            if (
-                command.params.labwareId is not None
-                and command.params.labwareId not in labware_ids
-            ):
-                raise ValueError(
-                    f"{command.commandType} command at index {index}"
-                    f" references ID {command.params.labwareId},"
-                    f" which doesn't exist."
-                )
-            if (
-                command.params.moduleId is not None
-                and command.params.moduleId not in module_ids
-            ):
-                raise ValueError(
-                    f"{command.commandType} command at index {index}"
-                    f" references ID {command.params.moduleId},"
-                    f" which doesn't exist."
-                )
-            if (
-                command.params.liquidId is not None
-                and command.params.liquidId not in liquid_ids
-            ):
-                raise ValueError(
-                    f"{command.commandType} command at index {index}"
-                    f" references ID {command.params.liquidId},"
-                    f" which doesn't exist."
-                )
-
-        return value

package/python/build/lib/opentrons_shared_data/protocol/models/protocol_schema_v7.py

@@ -1,93 +0,0 @@
-from pydantic import BaseModel, Field
-from typing import Any, List, Optional, Dict, Union
-from typing_extensions import Literal
-
-from opentrons_shared_data.labware.labware_definition import LabwareDefinition
-
-from .shared_models import (
-    Liquid,
-    CommandAnnotation,
-    Location,
-    ProfileStep,
-    WellLocation,
-    OffsetVector,
-    Metadata,
-    Robot,
-    DesignerApplication,
-)
-
-
-# TODO (tamar 3/15/22): split apart all the command payloads when we tackle #9583
-class Params(BaseModel):
-    slotName: Optional[str]
-    axes: Optional[List[str]]
-    pipetteId: Optional[str]
-    mount: Optional[str]
-    moduleId: Optional[str]
-    location: Optional[Union[Location, Literal["offDeck"]]]
-    labwareId: Optional[str]
-    displayName: Optional[str]
-    liquidId: Optional[str]
-    volumeByWell: Optional[Dict[str, Any]]
-    wellName: Optional[str]
-    volume: Optional[float]
-    flowRate: Optional[float]
-    wellLocation: Optional[WellLocation]
-    waitForResume: Optional[Literal[True]]
-    seconds: Optional[float]
-    minimumZHeight: Optional[float]
-    forceDirect: Optional[bool]
-    speed: Optional[float]
-    message: Optional[str]
-    coordinates: Optional[OffsetVector]
-    axis: Optional[str]
-    distance: Optional[float]
-    positionId: Optional[str]
-    temperature: Optional[float]
-    celsius: Optional[float]
-    blockMaxVolumeUl: Optional[float]
-    rpm: Optional[float]
-    height: Optional[float]
-    offset: Optional[OffsetVector]
-    profile: Optional[List[ProfileStep]]
-    radius: Optional[float]
-    newLocation: Optional[Union[Location, Literal["offDeck"]]]
-    strategy: Optional[str]
-    # schema v7 add-ons
-    homeAfter: Optional[bool]
-    alternateDropLocation: Optional[bool]
-    holdTimeSeconds: Optional[float]
-    maintenancePosition: Optional[str]
-    pipetteName: Optional[str]
-    model: Optional[str]
-    loadName: Optional[str]
-    namespace: Optional[str]
-    version: Optional[int]
-    pushOut: Optional[float]
-
-
-class Command(BaseModel):
-    commandType: str
-    params: Params
-    key: Optional[str]
-
-
-class ProtocolSchemaV7(BaseModel):
-    otSharedSchema: Literal["#/protocol/schemas/7"] = Field(
-        ...,
-        alias="$otSharedSchema",
-        description="The path to a valid Opentrons shared schema relative to "
-        "the shared-data directory, without its extension.",
-    )
-    schemaVersion: Literal[7]
-    metadata: Metadata
-    robot: Robot
-    liquids: Optional[Dict[str, Liquid]]
-    labwareDefinitions: Dict[str, LabwareDefinition]
-    commands: List[Command]
-    commandAnnotations: Optional[List[CommandAnnotation]]
-    designerApplication: Optional[DesignerApplication]
-
-    class Config:
-        # added for constructing the class with field name instead of alias
-        allow_population_by_field_name = True

package/python/build/lib/opentrons_shared_data/protocol/models/shared_models.py

@@ -1,104 +0,0 @@
-from typing import Optional, List, Dict, Any
-from typing_extensions import Literal
-from enum import Enum
-from pydantic import BaseModel
-
-
-class Dimensions(BaseModel):
-    xDimension: float
-    yDimension: float
-    zDimension: float
-
-
-class GroupMetadata(BaseModel):
-    pass
-
-
-class Group(BaseModel):
-    metadata: GroupMetadata
-    wells: List[str]
-
-
-class Shape(Enum):
-    circular = "circular"
-    rectangular = "rectangular"
-
-
-class WellDefinition(BaseModel):
-    depth: float
-    totalLiquidVolume: int
-    shape: Shape
-    x: float
-    y: float
-    z: float
-    diameter: Optional[float]
-    yDimension: Optional[float]
-    xDimension: Optional[float]
-
-
-class Metadata(BaseModel):
-    protocolName: Optional[str]
-    author: Optional[str]
-    description: Optional[str]
-    created: Optional[int]
-    lastModified: Optional[int]
-    category: Optional[str]
-    subcategory: Optional[str]
-    tags: Optional[List[str]]
-
-
-class Module(BaseModel):
-    model: str
-
-
-class Pipette(BaseModel):
-    name: str
-
-
-class Robot(BaseModel):
-    model: Literal["OT-2 Standard", "OT-3 Standard"]
-    deckId: str
-
-
-class DesignerApplication(BaseModel):
-    name: Optional[str]
-    version: Optional[str]
-    data: Optional[Dict[str, Any]]
-
-
-class CommandAnnotation(BaseModel):
-    commandIds: List[str]
-    annotationType: str
-
-
-class OffsetVector(BaseModel):
-    x: Optional[float]
-    y: Optional[float]
-    z: Optional[float]
-
-
-class Location(BaseModel):
-    slotName: Optional[str]
-    moduleId: Optional[str]
-    labwareId: Optional[str]
-
-
-class ProfileStep(BaseModel):
-    celsius: float
-    holdSeconds: float
-
-
-class WellLocation(BaseModel):
-    origin: Optional[str]
-    offset: Optional[OffsetVector]
-
-
-class Liquid(BaseModel):
-    displayName: str
-    description: str
-    displayColor: Optional[str]
-
-
-class Labware(BaseModel):
-    displayName: Optional[str]
-    definitionId: str

package/python/build/lib/opentrons_shared_data/robot/__init__.py

@@ -1,25 +0,0 @@
-"""opentrons_shared_data.robot: Submodule for handling robot definition data."""
-from pathlib import Path
-from typing import cast
-from typing_extensions import Final
-
-import json
-
-from .. import get_shared_data_root
-
-from .dev_types import RobotDefinition, RobotType
-
-DEFAULT_ROBOT_DEFINITION_VERSION: Final = 1
-
-
-def load(
-    robot_type: RobotType, version: int = DEFAULT_ROBOT_DEFINITION_VERSION
-) -> RobotDefinition:
-    """Load the definition for the specified robot id."""
-    for fi in Path(
-        get_shared_data_root() / "robot" / "definitions" / f"{version}"
-    ).iterdir():
-        defn = json.load(fi.open("r"))
-        if defn["robotType"] == robot_type:
-            return cast(RobotDefinition, defn)
-    raise KeyError(robot_type)

package/python/build/lib/opentrons_shared_data/robot/dev_types.py

@@ -1,37 +0,0 @@
-"""opentrons_shared_data.robot.dev_types: types for robot def."""
-import enum
-from typing import NewType, List, Dict, Any
-from typing_extensions import Literal, TypedDict
-
-RobotSchemaVersion1 = Literal[1]
-
-RobotSchema = NewType("RobotSchema", Dict[str, Any])
-
-RobotType = Literal["OT-2 Standard", "OT-3 Standard"]
-
-
-class RobotTypeEnum(enum.Enum):
-    """An enum representing the active robot type."""
-
-    # TODO we should switch over to using Enums fully (if possible)
-    # to represent our robot types in code -- rather than having
-    # to string match everywhere.
-    OT2 = enum.auto()
-    FLEX = enum.auto()
-
-    @classmethod
-    def robot_literal_to_enum(cls, robot_type: RobotType) -> "RobotTypeEnum":
-        """Convert Robot Type Literal to Robot Type Enum."""
-        if robot_type == "OT-2 Standard":
-            return cls.OT2
-        elif robot_type == "OT-3 Standard":
-            return cls.FLEX
-        # No final `else` statement, depend on mypy exhaustiveness checking
-
-
-class RobotDefinition(TypedDict):
-    """A python version of the robot definition type."""
-
-    displayName: str
-    robotType: RobotType
-    models: List[str]

package/python/build/lib/tests/deck/__init__.py

@@ -1,18 +0,0 @@
-from typing import List
-from pathlib import Path
-
-
-def list_deck_def_paths(version: int) -> List[str]:
-    loadnames = [
-        deffile
-        for deffile in (
-            Path(__file__).parent
-            / ".."
-            / ".."
-            / ".."
-            / "deck"
-            / "definitions"
-            / f"{version}"
-        ).iterdir()
-    ]
-    return [loadname.stem for loadname in loadnames]

package/python/build/lib/tests/deck/test_typechecks.py

@@ -1,21 +0,0 @@
-import sys
-
-import pytest
-import typeguard
-
-from opentrons_shared_data.deck import load as load_deck_definition
-from opentrons_shared_data.deck.dev_types import DeckDefinitionV3
-
-from . import list_deck_def_paths
-
-
-pytestmark = pytest.mark.xfail(
-    condition=sys.version_info >= (3, 10),
-    reason="https://github.com/agronholm/typeguard/issues/242",
-)
-
-
-@pytest.mark.parametrize("defname", list_deck_def_paths(version=3))
-def test_v3_defs(defname):
-    defn = load_deck_definition(name=defname, version=3)
-    typeguard.check_type("defn", defn, DeckDefinitionV3)

package/python/build/lib/tests/errors/__init__.py

@@ -1 +0,0 @@
-"""Tests for shared-data global errors."""

package/python/build/lib/tests/errors/test_error_completeness.py

@@ -1,19 +0,0 @@
-"""Tests that we have all errors in our python bindings."""
-
-import json
-
-import pytest
-
-from opentrons_shared_data.load import load_shared_data
-from opentrons_shared_data.errors.codes import ErrorCodes
-
-
-error_json = json.loads(load_shared_data("errors/definitions/1/errors.json"))
-
-
-@pytest.mark.parametrize("code", list(error_json["codes"].keys()))
-def check_error_present_and_correct(code: str) -> None:
-    """Test that each error in json is retrievable."""
-    error = ErrorCodes.by_error_code(code)
-    assert error.value.code == code
-    assert error.value.category.value.name == error_json["code"]["category"]

package/python/build/lib/tests/errors/test_exceptions.py

@@ -1,74 +0,0 @@
-"""Test exception handling."""
-from opentrons_shared_data.errors.exceptions import PythonException
-
-
-def test_exception_wrapping_single_level() -> None:
-    """When we make a PythonException it should capture details of an exception."""
-    try:
-        raise RuntimeError("oh no!")
-    except RuntimeError as e:
-        captured_exc = e
-
-    wrapped = PythonException(captured_exc)
-    assert wrapped.detail["class"] == "RuntimeError"
-    assert wrapped.detail["traceback"]
-    assert wrapped.detail["args"] == "('oh no!',)"
-
-
-def test_exception_wrapping_multi_level() -> None:
-    """We can wrap all exceptions in a raise-from chain."""
-
-    def _raise_inner() -> None:
-        raise KeyError("oh no!")
-
-    try:
-        try:
-            _raise_inner()
-        except KeyError as e:
-            raise RuntimeError("uh oh!") from e
-    except RuntimeError as e:
-        captured_exc = e
-
-    wrapped = PythonException(captured_exc)
-    assert wrapped.detail["class"] == "RuntimeError"
-    assert wrapped.detail["traceback"]
-    assert wrapped.detail["args"] == "('uh oh!',)"
-    second = wrapped.wrapping[0]
-    assert isinstance(second, PythonException)
-    assert second.detail["class"] == "KeyError"
-    assert second.detail["args"] == "('oh no!',)"
-    assert not second.wrapping
-
-
-def test_exception_wrapping_rethrow() -> None:
-    """We can wrap raise-froms."""
-    try:
-        try:
-            raise RuntimeError("oh no!")
-        except RuntimeError as e:
-            raise PythonException(e) from e
-    except PythonException as pe:
-        wrapped = pe
-
-    assert wrapped.detail["class"] == "RuntimeError"
-    assert wrapped.detail["traceback"]
-    assert wrapped.detail["args"] == "('oh no!',)"
-
-
-def test_exception_wrapping_error_in_except() -> None:
-    """We can even wrap exceptions in exception handlers."""
-    try:
-        try:
-            raise RuntimeError("oh no!")
-        except RuntimeError:
-            raise KeyError("uh oh")
-    except BaseException as e:
-        wrapped = PythonException(e)
-
-    # when we have an exception-during-handler, the originally-handled
-    # exception is what's bubbled up:
-    assert wrapped.detail["class"] == "KeyError"
-    assert len(wrapped.wrapping) == 1
-    assert wrapped.wrapping[0].detail["class"] == "RuntimeError"
-    assert wrapped.wrapping[0].detail["traceback"]
-    assert wrapped.wrapping[0].detail["args"] == "('oh no!',)"

package/python/build/lib/tests/gripper/test_definition.py

@@ -1,30 +0,0 @@
-import pytest
-from pydantic import ValidationError
-import json
-from opentrons_shared_data import gripper, load_shared_data
-from opentrons_shared_data.gripper import (
-    GripperDefinition,
-    GripperModel,
-)
-
-GRIPPER_DEF = json.loads(load_shared_data("gripper/definitions/1/gripperV1.json"))
-
-
-def test_gripper_definition() -> None:
-    gripper_def = gripper.load_definition(GripperModel.v1)
-    assert isinstance(gripper_def, GripperDefinition)
-    assert gripper_def.schema_version == 1
-
-
-def test_gripper_definition_type() -> None:
-    assert GripperDefinition.parse_obj(GRIPPER_DEF)
-
-    # missing key
-    del GRIPPER_DEF["gripForceProfile"]
-    with pytest.raises(ValidationError):
-        assert GripperDefinition.parse_obj(GRIPPER_DEF)
-
-    # no missing key but with incorrect value
-    GRIPPER_DEF["geometry"]["gripForceProfile"] = {"min": 1.0, "max": "0.0"}
-    with pytest.raises(ValidationError):
-        assert GripperDefinition.parse_obj(GRIPPER_DEF)

package/python/build/lib/tests/gripper/test_load.py

@@ -1,16 +0,0 @@
-import json
-from opentrons_shared_data.gripper import load_definition, load_schema
-from opentrons_shared_data.gripper.gripper_definition import (
-    GripperModel,
-)
-from opentrons_shared_data import load_shared_data
-
-
-def test_load_schema() -> None:
-    assert load_schema(1) == json.loads(load_shared_data("gripper/schemas/1.json"))
-
-
-def test_load_definition() -> None:
-    load_definition(GripperModel.v1, 1) == json.loads(
-        load_shared_data("gripper/definitions/1/gripperV1.json")
-    )

package/python/build/lib/tests/labware/__init__.py

@@ -1,13 +0,0 @@
-from typing import List, Tuple
-
-from pathlib import Path
-
-
-def get_ot_defs() -> List[Tuple[str, int]]:
-    def_files = (
-        Path(__file__).parent / ".." / ".." / ".." / "labware" / "definitions" / "2"
-    ).glob("**/*.json")
-
-    # example filename
-    # shared-data/labware/definitions/2/opentrons_96_tiprack_300ul/1.json
-    return [(f.parent.name, int(f.stem)) for f in def_files]

package/python/build/lib/tests/labware/test_typechecks.py

@@ -1,21 +0,0 @@
-import sys
-
-import pytest
-import typeguard
-
-from opentrons_shared_data.labware import load_definition
-from opentrons_shared_data.labware.dev_types import LabwareDefinition
-
-from . import get_ot_defs
-
-
-pytestmark = pytest.mark.xfail(
-    condition=sys.version_info >= (3, 10),
-    reason="https://github.com/agronholm/typeguard/issues/242",
-)
-
-
-@pytest.mark.parametrize("loadname,version", get_ot_defs())
-def test_opentrons_definition_types(loadname, version):
-    defdict = load_definition(loadname, version)
-    typeguard.check_type("defdict", defdict, LabwareDefinition)

package/python/build/lib/tests/module/__init__.py

@@ -1,20 +0,0 @@
-from pathlib import Path
-from typing import List
-
-
-def list_v2_defs() -> List[str]:
-    return [
-        deffile.stem
-        for deffile in (
-            Path(__file__).parent / ".." / ".." / ".." / "module" / "definitions" / "2"
-        ).iterdir()
-    ]
-
-
-def list_v3_defs() -> List[str]:
-    return [
-        deffile.stem
-        for deffile in (
-            Path(__file__).parent / ".." / ".." / ".." / "module" / "definitions" / "3"
-        ).iterdir()
-    ]