Merge branch 'edge' into fix-hardware-testing-robot-assembly-qc-for-d…

…vt-2

api-client/src/protocols/getProtocolIds.ts

@@ -0,0 +1,11 @@
+import { GET, request } from '../request'
+
+import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+import type { ProtocolsIds } from './types'
+
+export function getProtocolIds(
+  config: HostConfig
+): ResponsePromise<ProtocolsIds> {
+  return request<ProtocolsIds>(GET, `/protocols/ids`, null, config)
+}

api-client/src/protocols/index.ts

@@ -3,6 +3,7 @@ export { getProtocolAnalyses } from './getProtocolAnalyses'
 export { deleteProtocol } from './deleteProtocol'
 export { createProtocol } from './createProtocol'
 export { getProtocols } from './getProtocols'
+export { getProtocolIds } from './getProtocolIds'
 
 export * from './types'
 export * from './utils'

api-client/src/protocols/types.ts

@@ -38,3 +38,8 @@ export interface Protocols {
   links?: ResourceLinks
   data: ProtocolResource[]
 }
+
+export interface ProtocolsIds {
+  links?: ResourceLinks
+  data: string[]
+}

api/release-notes-internal.md

@@ -16,37 +16,6 @@ Some things are known not to work, and are listed below. Specific compatibility
 
 For more details about this release, please see the full [technical change log][]. 
 
-# Internal Release 0.7.0
-
-This is internal release 0.7.0 for the Opentrons Flex robot software, involving both robot control and the on-device display.
-
-Some things are known not to work, and are listed below. Specific compatibility notes about peripheral hardware are also listed.
-
-## Big New Things
-### Robot Control
-- Updated python api version to 2.15
-- Added load Magnetic block as a module in python api and in PE. You can now load a magnetic block using `protocol_context.load_module("magneticBlockV1", <slot_name>)` with `apiLevel` of 2.15.
-
-For more details about this release, please see the full [technical change log][]. 
-
-[technical change log]: https://github.com/Opentrons/opentrons/releases
-
----
-
-# Internal Release 0.6.0
-
-This is internal release 0.6.0 for the Opentrons Flex robot software, involving both robot control and the on-device display.
-
-Some things are known not to work, and are listed below. Specific compatibility notes about peripheral hardware are also listed.
-
-## Hardware Revision Compatibility
-
-- This release will work best on a DVT robot frame with a programmed rear-panel board. If that doesn't apply, edit `/data/feature_flags.json` and turn `rearPanelIntegration` to `false` or the robot server won't start.
-- This release is compatible with EVT pipettes and gripper only if they have received the tool ID rework.
-- This release is compatible with DVT pipettes and gripper.
-- This release should be used with DVT module caddies. This might introduce a slight LPC offset change if the previous offsets for labware on modules were measured while using EVT caddies.
-- This release should be used with pipette bootloaders of at least v7.
-
 ## Big Things That Don't Work Yet So Don't Report Bugs About Them
 
 ### ODD
@@ -56,27 +25,10 @@ Some things are known not to work, and are listed below. Specific compatibility
 - It can take a while for the robot to start after installing an update (it's the firmware updates happening on boot). Allow 10 minutes after an update that has a firmware change.
 
 ### Robot Control
-- USB connectivity
 - Pipette/gripper firmware update on attach: if you need to attach a new instrument, attach it and then power-cycle the robot or restart the robot server
 - Pipette pressure sensing both for liquid-level sensing purposes and for clog-detection purposes
 - Labware pick up failure with gripper
 
-## Big New Things
-### Robot Control
-- All python protocol API functions that take deck slot names (like load_labware) now support deck slot "coordinates", e.g. specifying a deck slot as "A1" rather than 1. This feature requires a Python protocol to request API version 2.15.
-
-## Reasonably Sized New Things
-### ODD
-- Protocol result screens! No more do you have to stare at those big buttons forever
-
-### Robot Control
-- Python API `load_labware`, `load_module` and `move_labware` can accept location as deck coordinates (e.g. "A1", "D3") in addition to slot numbers
-- The `.parent` property for Module and Labware objects (loaded on the deck) will return a coordinate style deck location (e.g. "B2", "C3") for protocols with robotType "OT-3 Standard" instead of the slot number
-- Rerunning a protocol should no longer result in being on step ?
-- DVT gripper sets its force more accurately now
-- Fixed a couple more bugs with pipette calibration; it should no longer fail during the Z height calibration
-- Fixed a problem where the change-pipette process would crash after removing a pipette because it tried to home the now-not-present pipette
-
 ## Big Things That Do Work Please Do Report Bugs About Them
 ### Robot Control
 - Liquid handling protocols with 1 and 8 channel pipettes
@@ -86,6 +38,7 @@ Some things are known not to work, and are listed below. Specific compatibility
 - Network connectivity and discoverability
 - Firmware update for all devices attached when the robot turns on
 - Cancelling a protocol run. We're even more sure we fixed this so definitely tell us if it's not.
+- USB connectivity
 
 ### ODD
 - Protocol execution including end-of-protocol screen

api/src/opentrons/config/advanced_settings.py

@@ -181,6 +181,11 @@ class Setting(NamedTuple):
         title="Enable robots with the new usb connected rear-panel board.",
         description="This is an Opentrons-internal setting to test new rear-panel.",
     ),
+    SettingDefinition(
+        _id="disableStallDetection",
+        title="Disable stall detection on the Flex.",
+        description="This is an Opentrons-internal setting for hardware-testing.",
+    ),
 ]
 
 if ARCHITECTURE == SystemArchitecture.BUILDROOT:
@@ -547,6 +552,16 @@ def _migrate23to24(previous: SettingsMap) -> SettingsMap:
     return newmap
 
 
+def _migrate24to25(previous: SettingsMap) -> SettingsMap:
+    """Migrate to version 25 of the feature flags file.
+
+    - Adds the disableStallDetection config element.
+    """
+    newmap = {k: v for k, v in previous.items()}
+    newmap["disableStallDetection"] = None
+    return newmap
+
+
 _MIGRATIONS = [
     _migrate0to1,
     _migrate1to2,
@@ -572,6 +587,7 @@ def _migrate23to24(previous: SettingsMap) -> SettingsMap:
     _migrate21to22,
     _migrate22to23,
     _migrate23to24,
+    _migrate24to25,
 ]
 """
 List of all migrations to apply, indexed by (version - 1). See _migrate below

api/src/opentrons/config/feature_flags.py

@@ -35,3 +35,7 @@ def rear_panel_integration() -> bool:
     """Whether to enable usb connected rear_panel for the OT-3."""
 
     return advs.get_setting_with_env_overload("rearPanelIntegration")
+
+
+def stall_detection_enabled() -> bool:
+    return not advs.get_setting_with_env_overload("disableStallDetection")

api/src/opentrons/hardware_control/backends/ot3controller.py

@@ -25,7 +25,7 @@
     Union,
 )
 from opentrons.config.types import OT3Config, GantryLoad
-from opentrons.config import ot3_pipette_config, gripper_config
+from opentrons.config import ot3_pipette_config, gripper_config, feature_flags as ff
 from .ot3utils import (
     UpdateProgress,
     axis_convert,
@@ -124,7 +124,6 @@
     OT3SubSystem,
 )
 from opentrons.hardware_control.errors import (
-    MustHomeError,
     InvalidPipetteName,
     InvalidPipetteModel,
     FirmwareUpdateRequired,
@@ -414,12 +413,6 @@ async def update_motor_status(self) -> None:
     async def update_motor_estimation(self, axes: Sequence[OT3Axis]) -> None:
         """Update motor position estimation for commanded nodes, and update cache of data."""
         nodes = set([axis_to_node(a) for a in axes])
-        for node in nodes:
-            if not (
-                node in self._motor_status.keys()
-                and self._motor_status[node].encoder_ok
-            ):
-                raise MustHomeError(f"Axis {node} has invalid encoder position")
         response = await update_motor_position_estimation(self._messenger, nodes)
         self._handle_motor_status_response(response)
 
@@ -501,16 +494,8 @@ def _handle_motor_status_response(
         for axis, pos in response.items():
             self._position.update({axis: pos[0]})
             self._encoder_position.update({axis: pos[1]})
-            # if an axis has already been homed, we're not clearing the motor ok status flag
-            # TODO: (2023-01-10) This is just a temp fix so we're not blocking hardware testing,
-            # we should port the encoder position over to use as motor position if encoder status is ok
-            already_homed = (
-                self._motor_status[axis].motor_ok
-                if axis in self._motor_status.keys()
-                else False
-            )
             self._motor_status.update(
-                {axis: MotorStatus(motor_ok=pos[2] or already_homed, encoder_ok=pos[3])}
+                {axis: MotorStatus(motor_ok=pos[2], encoder_ok=pos[3])}
             )
 
     @requires_update
@@ -532,7 +517,10 @@ async def move(
         """
         group = create_move_group(origin, moves, self._motor_nodes(), stop_condition)
         move_group, _ = group
-        runner = MoveGroupRunner(move_groups=[move_group])
+        runner = MoveGroupRunner(
+            move_groups=[move_group],
+            ignore_stalls=True if not ff.stall_detection_enabled() else False,
+        )
         positions = await runner.run(can_messenger=self._messenger)
         self._handle_motor_status_response(positions)
 

api/src/opentrons/hardware_control/instruments/ot3/pipette_handler.py

@@ -79,6 +79,9 @@ class TipMotorPickUpTipSpec:
     pick_up_distance: float
     speed: float
     currents: Dict[OT3Axis, float]
+    # FIXME we should throw this in a config
+    # file of some sort
+    home_buffer: float = 0
 
 
 @dataclass(frozen=True)
@@ -100,6 +103,9 @@ class DropTipMove:
     home_after_safety_margin: float = 0
     home_axes: Sequence[OT3Axis] = tuple()
     is_ht_tip_action: bool = False
+    # FIXME we should throw this in a config
+    # file of some sort
+    home_buffer: float = 0
 
 
 @dataclass(frozen=True)
@@ -691,6 +697,7 @@ def build_presses() -> Iterator[Tuple[float, float]]:
                         pick_up_distance=instrument.pick_up_configurations.distance,
                         speed=instrument.pick_up_configurations.speed,
                         currents={OT3Axis.Q: instrument.pick_up_configurations.current},
+                        home_buffer=10,
                     ),
                 ),
                 add_tip_to_instr,
@@ -769,6 +776,7 @@ def build() -> List[DropTipMove]:
                     home_after_safety_margin=abs(bottom_pos - droptip_pos),
                     home_axes=home_axes,
                     is_ht_tip_action=is_ht_pipette,
+                    home_buffer=10 if is_ht_pipette else 0,
                 ),
                 DropTipMove(  # always finish drop-tip at a known safe plunger position
                     target_position=bottom_pos, current=plunger_currents, speed=None

api/src/opentrons/hardware_control/ot3_calibration.py

@@ -47,6 +47,11 @@ class CalibrationMethod(Enum):
     NONCONTACT_PASS = "noncontact pass"
 
 
+class CalibrationTarget(Enum):
+    DECK_OBJECT = "deck_object"
+    GANTRY_INSTRUMENT = "gantry_instrument"
+
+
 class CalibrationStructureNotFoundError(RuntimeError):
     def __init__(self, structure_height: float, lower_limit: float) -> None:
         super().__init__(
@@ -546,7 +551,11 @@ async def _calibrate_mount(
     try:
         # find the center of the calibration sqaure
         offset = await find_calibration_structure_position(
-            hcapi, mount, nominal_center, method, raise_verify_error
+            hcapi,
+            mount,
+            nominal_center,
+            method=method,
+            raise_verify_error=raise_verify_error,
         )
         # update center with values obtained during calibration
         LOG.info(f"Found calibration value {offset} for mount {mount.name}")
@@ -570,6 +579,7 @@ async def find_calibration_structure_position(
     mount: OT3Mount,
     nominal_center: Point,
     method: CalibrationMethod = CalibrationMethod.BINARY_SEARCH,
+    target: CalibrationTarget = CalibrationTarget.GANTRY_INSTRUMENT,
     raise_verify_error: bool = True,
 ) -> Point:
     """Find the calibration square offset given an arbitry postition on the deck."""
@@ -582,7 +592,15 @@ async def find_calibration_structure_position(
     found_center = await find_calibration_structure_center(
         hcapi, mount, initial_center, method, raise_verify_error
     )
-    return nominal_center - found_center
+
+    offset = nominal_center - found_center
+    # NOTE: If the calibration target is a deck object the polarity of the calibrated
+    #  offset needs to be reversed. This is because we are using the gantry instrument
+    #  to calibrate a stationary object on the deck and need to find the offset of that
+    #  deck object relative to the deck and not the instrument which sits above the deck.
+    if target == CalibrationTarget.DECK_OBJECT:
+        return offset * -1
+    return offset
 
 
 async def find_slot_center_binary_from_nominal_center(
@@ -782,7 +800,11 @@ async def calibrate_module(
             # from the nominal position so we dont have to alter any other part of the system.
             nominal_position = nominal_position - PREP_OFFSET_DEPTH
             offset = await find_calibration_structure_position(
-                hcapi, mount, nominal_position, method=CalibrationMethod.BINARY_SEARCH
+                hcapi,
+                mount,
+                nominal_position,
+                method=CalibrationMethod.BINARY_SEARCH,
+                target=CalibrationTarget.DECK_OBJECT,
             )
             await hcapi.save_module_offset(module_id, mount, slot, offset)
             return offset