Merge branch 'edge' into EXEC-504-provide-a-list-of-all-errors-encoun…

…tered
Opentrons · Jul 31, 2024 · bcec2ec · bcec2ec
2 parents ce6dc63 + 36a7501
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diff --git a/api-client/src/protocols/getCsvFiles.ts b/api-client/src/protocols/getCsvFiles.ts
@@ -1,43 +1,17 @@
-// import { GET, request } from '../request'
+import { GET, request } from '../request'
 
-// import type { ResponsePromise } from '../request'
+import type { ResponsePromise } from '../request'
 import type { HostConfig } from '../types'
 import type { UploadedCsvFilesResponse } from '../dataFiles/types'
 
-/**
 export function getCsvFiles(
   config: HostConfig,
   protocolId: string
-): ResponsePromise<UploadCsvFilesResponse> {
-  return request<UploadCsvFilesResponse>(
+): ResponsePromise<UploadedCsvFilesResponse> {
+  return request<UploadedCsvFilesResponse>(
     GET,
     `/protocols/${protocolId}/dataFiles`,
     null,
     config
   )
-}
-   */
-
-// ToDo (kk:06/14/2024) remove when activate the above code
-export function getCsvFiles(
-  config: HostConfig,
-  protocolId: string
-): Promise<{ data: UploadedCsvFilesResponse }> {
-  const stub = {
-    data: {
-      files: [
-        {
-          id: '1',
-          createdAt: '2024-06-07T19:19:56.268029+00:00',
-          name: 'rtp_mock_file1.csv',
-        },
-        {
-          id: '2',
-          createdAt: '2024-06-17T19:19:56.268029+00:00',
-          name: 'rtp_mock_file2.csv',
-        },
-      ],
-    },
-  }
-  return Promise.resolve({ data: stub })
 }
diff --git a/api/release-notes-internal.md b/api/release-notes-internal.md
@@ -2,15 +2,31 @@ For more details about this release, please see the full [technical change log][
 
 [technical change log]: https://github.com/Opentrons/opentrons/releases
 
+## Internal Release 2.0.0-alpha.3
+
+This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only.
+
+- [Opentrons changes since the latest stable release](https://github.com/Opentrons/opentrons/compare/[email protected])
+- [Opentrons changes since the last internal release](https://github.com/Opentrons/opentrons/compare/[email protected]@2.0.0-alpha.3)
+- [Flex changes](https://github.com/Opentrons/oe-core/compare/[email protected]@2.0.0-alpha.3)
+- [Flex firmware changes](https://github.com/Opentrons/ot3-firmware/compare/[email protected]@v10)
+- [OT2 changes](https://github.com/Opentrons/buildroot/compare/[email protected])
+
+## Internal Release 2.0.0-alpha.2
+
+This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only.
+
+<https://github.com/Opentrons/opentrons/compare/[email protected]@2.0.0-alpha.2>
+
 ## Internal Release 2.0.0-alpha.1
 
-This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only. Usage may require a robot factory reset to restore robot stability.
+This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only.
 
 <https://github.com/Opentrons/opentrons/compare/[email protected]@2.0.0-alpha.1>
 
 ## Internal Release 2.0.0-alpha.0
 
-This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only. Usage may require a robot factory reset to restore robot stability.
+This internal release, pulled from the `edge` branch, contains features being developed for 8.0.0. It's for internal testing only.
 
 <https://github.com/Opentrons/opentrons/compare/[email protected]@2.0.0-alpha.0>
 

diff --git a/api/release-notes.md b/api/release-notes.md
@@ -6,15 +6,23 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
-## Opentrons Robot Software Changes in 7.4.0
+## Opentrons Robot Software Changes in 7.5.0
 
-Welcome to the v7.4.0 release of the Opentrons robot software!
+Welcome to the v7.5.0 release of the Opentrons robot software!
 
-This release adds support for the [Opentrons Flex HEPA/UV Module](https://opentrons.com/products/opentrons-flex-hepa-uv-module).
+### Hardware Support
+
+- [Opentrons Flex HEPA/UV Module](https://opentrons.com/products/opentrons-flex-hepa-uv-module)
+- Latest Flex Gripper model (serial numbers beginning `GRPV13`)
 
 ### Bug Fixes
 
 - Fixed certain string runtime parameter values being misinterpreted as an incorrect type.
+
+### Known Issue
+
+- The HEPA/UV Module's buttons may not respond properly after its safety shutoff is activated. This happens when the module is removed from the top of Flex while its lights are on. Power cycle the module to restore normal behavior. The module is safe to use even if you do not power cycle it.
+
 ---
 
 ## Opentrons Robot Software Changes in 7.3.1

diff --git a/api/src/opentrons/cli/analyze.py b/api/src/opentrons/cli/analyze.py
@@ -248,6 +248,7 @@ async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
             protocol_source=protocol_source,
             parse_mode=ParseMode.NORMAL,
             run_time_param_values=None,
+            run_time_param_files=None,
         )
     except Exception as error:
         err_id = "analysis-setup-error"

diff --git a/api/src/opentrons/hardware_control/ot3api.py b/api/src/opentrons/hardware_control/ot3api.py
@@ -761,7 +761,7 @@ async def reset_tip_detectors(
 
     @ExecutionManagerProvider.wait_for_running
     async def _update_position_estimation(
-        self, axes: Optional[List[Axis]] = None
+        self, axes: Optional[Sequence[Axis]] = None
     ) -> None:
         """
         Function to update motor estimation for a set of axes
@@ -1141,6 +1141,12 @@ async def gantry_position(
             z=cur_pos[Axis.by_mount(realmount)],
         )
 
+    async def update_axis_position_estimations(self, axes: Sequence[Axis]) -> None:
+        """Update specified axes position estimators from their encoders."""
+        await self._update_position_estimation(axes)
+        await self._cache_current_position()
+        await self._cache_encoder_position()
+
     async def move_to(
         self,
         mount: Union[top_types.Mount, OT3Mount],

diff --git a/api/src/opentrons/hardware_control/protocols/__init__.py b/api/src/opentrons/hardware_control/protocols/__init__.py
@@ -1,8 +1,6 @@
 """Typing protocols describing a hardware controller."""
 from typing_extensions import Protocol, Type
 
-from opentrons.hardware_control.types import Axis
-
 from .module_provider import ModuleProvider
 from .hardware_manager import HardwareManager
 from .chassis_accessory_manager import ChassisAccessoryManager
@@ -20,6 +18,7 @@
 from .gripper_controller import GripperController
 from .flex_calibratable import FlexCalibratable
 from .flex_instrument_configurer import FlexInstrumentConfigurer
+from .position_estimator import PositionEstimator
 
 from .types import (
     CalibrationType,
@@ -64,6 +63,7 @@ def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
 
 
 class FlexHardwareControlInterface(
+    PositionEstimator,
     ModuleProvider,
     ExecutionControllable,
     LiquidHandler[CalibrationType, MountArgType, ConfigType],
@@ -87,12 +87,6 @@ class FlexHardwareControlInterface(
     def get_robot_type(self) -> Type[FlexRobotType]:
         return FlexRobotType
 
-    def motor_status_ok(self, axis: Axis) -> bool:
-        ...
-
-    def encoder_status_ok(self, axis: Axis) -> bool:
-        ...
-
     def cache_tip(self, mount: MountArgType, tip_length: float) -> None:
         ...
 

diff --git a/api/src/opentrons/hardware_control/protocols/position_estimator.py b/api/src/opentrons/hardware_control/protocols/position_estimator.py
@@ -0,0 +1,43 @@
+from typing import Protocol, Sequence
+
+from ..types import Axis
+
+
+class PositionEstimator(Protocol):
+    """Position-control extensions for harwdare with encoders."""
+
+    async def update_axis_position_estimations(self, axes: Sequence[Axis]) -> None:
+        """Update the specified axes' position estimators from their encoders.
+
+        This will allow these axes to make a non-home move even if they do not currently have
+        a position estimation (unless there is no tracked poition from the encoders, as would be
+        true immediately after boot).
+
+        Axis encoders have less precision than their position estimators. Calling this function will
+        cause absolute position drift. After this function is called, the axis should be homed before
+        it is relied upon for accurate motion.
+
+        This function updates only the requested axes. If other axes have bad position estimation,
+        moves that require those axes or attempts to get the position of those axes will still fail.
+        """
+        ...
+
+    def motor_status_ok(self, axis: Axis) -> bool:
+        """Return whether an axis' position estimator is healthy.
+
+        The position estimator is healthy if the axis has
+        1) been homed
+        2) not suffered a loss-of-positioning (from a cancel or stall, for instance) since being homed
+
+        If this function returns false, getting the position of this axis or asking it to move will fail.
+        """
+        ...
+
+    def encoder_status_ok(self, axis: Axis) -> bool:
+        """Return whether an axis' position encoder tracking is healthy.
+
+        The encoder status is healthy if the axis has been homed since booting up.
+
+        If this function returns false, updating the estimator from the encoder will fail.
+        """
+        ...
diff --git a/api/src/opentrons/protocol_api/_parameter_context.py b/api/src/opentrons/protocol_api/_parameter_context.py
@@ -12,10 +12,15 @@
     ParameterChoice,
     UserFacingTypes,
 )
-from opentrons.protocols.parameters.exceptions import ParameterDefinitionError
+from opentrons.protocols.parameters.exceptions import (
+    ParameterDefinitionError,
+    ParameterValueError,
+)
 from opentrons.protocol_engine.types import (
     RunTimeParameter,
     PrimitiveRunTimeParamValuesType,
+    CSVRunTimeParamFilesType,
+    FileInfo,
 )
 
 from ._parameters import Parameters
@@ -202,13 +207,45 @@ def set_parameters(
                     f"Parameter {variable_name} is not defined as a parameter for this protocol."
                 )
             if isinstance(parameter, csv_parameter_definition.CSVParameterDefinition):
-                pass
+                raise ParameterValueError(
+                    f"A primitive param value was provided for the parameter '{variable_name}',"
+                    f" but '{variable_name}' is a CSV parameter that can only accept file IDs."
+                )
             else:
                 validated_value = validation.ensure_value_type(
                     override_value, parameter.parameter_type
                 )
                 parameter.value = validated_value
 
+    def initialize_csv_files(
+        self, run_time_param_file_overrides: CSVRunTimeParamFilesType
+    ) -> None:
+        """Initializes the files for CSV parameters.
+
+        :meta private:
+
+        This is intended for Opentrons internal use only and is not a guaranteed API.
+        """
+        for variable_name, file_id in run_time_param_file_overrides.items():
+            try:
+                parameter = self._parameters[variable_name]
+            except KeyError:
+                raise ParameterDefinitionError(
+                    f"Parameter {variable_name} is not defined as a parameter for this protocol."
+                )
+            if not isinstance(
+                parameter, csv_parameter_definition.CSVParameterDefinition
+            ):
+                raise ParameterValueError(
+                    f"File Id was provided for the parameter '{variable_name}',"
+                    f" but '{variable_name}' is not a CSV parameter."
+                )
+
+            parameter.file_info = FileInfo(id=file_id, name="")
+            # TODO (spp, 2024-07-16): set the file name and assign the file as parameter.value.
+            #  Most likely, we will be creating a temporary file copy of the original
+            #  to pass onto the protocol context
+
     def export_parameters_for_analysis(self) -> List[RunTimeParameter]:
         """Exports all parameters into a protocol engine models for reporting in analysis.
 

diff --git a/api/src/opentrons/protocol_engine/actions/actions.py b/api/src/opentrons/protocol_engine/actions/actions.py
@@ -20,7 +20,7 @@
     CommandDefinedErrorData,
     CommandPrivateResult,
 )
-from ..error_recovery_policy import ErrorRecoveryType
+from ..error_recovery_policy import ErrorRecoveryPolicy, ErrorRecoveryType
 from ..notes.notes import CommandNote
 from ..types import (
     LabwareOffsetCreate,
@@ -266,6 +266,13 @@ class SetPipetteMovementSpeedAction:
     speed: Optional[float]
 
 
+@dataclass(frozen=True)
+class SetErrorRecoveryPolicyAction:
+    """See `ProtocolEngine.set_error_recovery_policy()`."""
+
+    error_recovery_policy: ErrorRecoveryPolicy
+
+
 Action = Union[
     PlayAction,
     PauseAction,
@@ -286,4 +293,5 @@ class SetPipetteMovementSpeedAction:
     AddLiquidAction,
     ResetTipsAction,
     SetPipetteMovementSpeedAction,
+    SetErrorRecoveryPolicyAction,
 ]
diff --git a/api/src/opentrons/protocol_engine/commands/__init__.py b/api/src/opentrons/protocol_engine/commands/__init__.py
@@ -19,6 +19,7 @@
 from . import temperature_module
 from . import thermocycler
 from . import calibration
+from . import unsafe
 
 from .hash_command_params import hash_protocol_command_params
 from .generate_command_schema import generate_command_schema
@@ -548,6 +549,8 @@
     "thermocycler",
     # calibration command bundle
     "calibration",
+    # unsafe command bundle
+    "unsafe",
     # configure pipette volume command bundle
     "ConfigureForVolume",
     "ConfigureForVolumeCreate",

diff --git a/api/src/opentrons/protocol_engine/commands/command_unions.py b/api/src/opentrons/protocol_engine/commands/command_unions.py
@@ -22,6 +22,7 @@
 from . import thermocycler
 
 from . import calibration
+from . import unsafe
 
 from .set_rail_lights import (
     SetRailLights,
@@ -387,6 +388,9 @@
         calibration.CalibratePipette,
         calibration.CalibrateModule,
         calibration.MoveToMaintenancePosition,
+        unsafe.UnsafeBlowOutInPlace,
+        unsafe.UnsafeDropTipInPlace,
+        unsafe.UpdatePositionEstimators,
     ],
     Field(discriminator="commandType"),
 ]
@@ -456,6 +460,9 @@
     calibration.CalibratePipetteParams,
     calibration.CalibrateModuleParams,
     calibration.MoveToMaintenancePositionParams,
+    unsafe.UnsafeBlowOutInPlaceParams,
+    unsafe.UnsafeDropTipInPlaceParams,
+    unsafe.UpdatePositionEstimatorsParams,
 ]
 
 CommandType = Union[
@@ -523,6 +530,9 @@
     calibration.CalibratePipetteCommandType,
     calibration.CalibrateModuleCommandType,
     calibration.MoveToMaintenancePositionCommandType,
+    unsafe.UnsafeBlowOutInPlaceCommandType,
+    unsafe.UnsafeDropTipInPlaceCommandType,
+    unsafe.UpdatePositionEstimatorsCommandType,
 ]
 
 CommandCreate = Annotated[
@@ -591,6 +601,9 @@
         calibration.CalibratePipetteCreate,
         calibration.CalibrateModuleCreate,
         calibration.MoveToMaintenancePositionCreate,
+        unsafe.UnsafeBlowOutInPlaceCreate,
+        unsafe.UnsafeDropTipInPlaceCreate,
+        unsafe.UpdatePositionEstimatorsCreate,
     ],
     Field(discriminator="commandType"),
 ]
@@ -660,6 +673,9 @@
     calibration.CalibratePipetteResult,
     calibration.CalibrateModuleResult,
     calibration.MoveToMaintenancePositionResult,
+    unsafe.UnsafeBlowOutInPlaceResult,
+    unsafe.UnsafeDropTipInPlaceResult,
+    unsafe.UpdatePositionEstimatorsResult,
 ]
 
 # todo(mm, 2024-06-12): Ideally, command return types would have specific