Merge branch 'edge' into EXEC-281-volume-tracking

api-client/src/runs/types.ts

@@ -99,7 +99,7 @@ export interface RunsLinks {
 }
 
 export interface RunCommandLink {
-  current: CommandLinkNoMeta
+  lastCompleted: CommandLinkNoMeta
 }
 
 export interface CommandLinkNoMeta {

api/docs/v2/new_examples.rst

@@ -383,7 +383,7 @@ Opentrons electronic pipettes can do some things that a human cannot do with a p
                     location=3)
                 p300 = protocol.load_instrument(
                     instrument_name="p300_single", 
-                    mount="right",
+                    mount="left",
                     tip_racks=[tiprack_1])
 
                 p300.pick_up_tip()
@@ -442,13 +442,13 @@ This protocol dispenses diluent to all wells of a Corning 96-well plate. Next, i
                     source = reservoir.wells()[i]
                     row = plate.rows()[i]
 
-                # transfer 30 µL of source to first well in column
-                pipette.transfer(30, source, row[0], mix_after=(3, 25))
+                    # transfer 30 µL of source to first well in column
+                    pipette.transfer(30, source, row[0], mix_after=(3, 25))
 
-                # dilute the sample down the column
-                pipette.transfer(
-                    30, row[:11], row[1:],
-                    mix_after=(3, 25))
+                    # dilute the sample down the column
+                    pipette.transfer(
+                        30, row[:11], row[1:],
+                        mix_after=(3, 25))
     
     .. tab:: OT-2
 
@@ -474,7 +474,7 @@ This protocol dispenses diluent to all wells of a Corning 96-well plate. Next, i
                     location=4)
                 p300 = protocol.load_instrument(
                     instrument_name="p300_single",
-                    mount="right",
+                    mount="left",
                     tip_racks=[tiprack_1, tiprack_2])
                 # Dispense diluent
                 p300.distribute(50, reservoir["A12"], plate.wells())
@@ -483,16 +483,15 @@ This protocol dispenses diluent to all wells of a Corning 96-well plate. Next, i
                 for i in range(8):
                     # save the source well and destination column to variables
                     source = reservoir.wells()[i]
-                    source = reservoir.wells()[i]
                     row = plate.rows()[i]
 
-                # transfer 30 µL of source to first well in column
-                p300.transfer(30, source, row[0], mix_after=(3, 25))
+                    # transfer 30 µL of source to first well in column
+                    p300.transfer(30, source, row[0], mix_after=(3, 25))
 
-                # dilute the sample down the column
-                p300.transfer(
-                    30, row[:11], row[1:],
-                    mix_after=(3, 25))
+                    # dilute the sample down the column
+                    p300.transfer(
+                        30, row[:11], row[1:],
+                        mix_after=(3, 25))
 
 Notice here how the code sample loops through the rows and uses slicing to distribute the diluent. For information about these features, see the Loops and Air Gaps examples above. See also, the :ref:`tutorial-commands` section of the Tutorial.
 

api/src/opentrons/protocol_engine/state/frustum_helpers.py

@@ -11,6 +11,7 @@
     SphericalSegment,
     ConicalFrustum,
     CuboidalFrustum,
+    SquaredConeSegment,
 )
 
 
@@ -127,6 +128,15 @@ def _volume_from_height_spherical(
     return volume
 
 
+def _volume_from_height_squared_cone(
+    target_height: float, segment: SquaredConeSegment
+) -> float:
+    """Find the volume given a height within a squared cone segment."""
+    heights = segment.height_to_volume_table.keys()
+    best_fit_height = min(heights, key=lambda x: abs(x - target_height))
+    return segment.height_to_volume_table[best_fit_height]
+
+
 def _height_from_volume_circular(
     volume: float,
     total_frustum_height: float,
@@ -197,15 +207,24 @@ def _height_from_volume_spherical(
     return height
 
 
+def _height_from_volume_squared_cone(
+    target_volume: float, segment: SquaredConeSegment
+) -> float:
+    """Find the height given a volume within a squared cone segment."""
+    volumes = segment.volume_to_height_table.keys()
+    best_fit_volume = min(volumes, key=lambda x: abs(x - target_volume))
+    return segment.volume_to_height_table[best_fit_volume]
+
+
 def _get_segment_capacity(segment: WellSegment) -> float:
+    section_height = segment.topHeight - segment.bottomHeight
     match segment:
         case SphericalSegment():
             return _volume_from_height_spherical(
                 target_height=segment.topHeight,
                 radius_of_curvature=segment.radiusOfCurvature,
             )
         case CuboidalFrustum():
-            section_height = segment.topHeight - segment.bottomHeight
             return _volume_from_height_rectangular(
                 target_height=section_height,
                 bottom_length=segment.bottomYDimension,
@@ -215,13 +234,14 @@ def _get_segment_capacity(segment: WellSegment) -> float:
                 total_frustum_height=section_height,
             )
         case ConicalFrustum():
-            section_height = segment.topHeight - segment.bottomHeight
             return _volume_from_height_circular(
                 target_height=section_height,
                 total_frustum_height=section_height,
                 bottom_radius=(segment.bottomDiameter / 2),
                 top_radius=(segment.topDiameter / 2),
             )
+        case SquaredConeSegment():
+            return _volume_from_height_squared_cone(section_height, segment)
         case _:
             # TODO: implement volume calculations for truncated circular and rounded rectangular segments
             raise NotImplementedError(
@@ -275,6 +295,8 @@ def height_at_volume_within_section(
                 top_width=section.topXDimension,
                 top_length=section.topYDimension,
             )
+        case SquaredConeSegment():
+            return _height_from_volume_squared_cone(target_volume_relative, section)
         case _:
             raise NotImplementedError(
                 "Height from volume calculation not yet implemented for this well shape."
@@ -309,6 +331,8 @@ def volume_at_height_within_section(
                 top_width=section.topXDimension,
                 top_length=section.topYDimension,
             )
+        case SquaredConeSegment():
+            return _volume_from_height_squared_cone(target_height_relative, section)
         case _:
             # TODO(cm): this would be the NEST-96 2uL wells referenced in EXEC-712
             # we need to input the math attached to that issue

api/src/opentrons/protocol_runner/run_orchestrator.py

@@ -257,6 +257,22 @@ def get_current_command(self) -> Optional[CommandPointer]:
         """Get the "current" command, if any."""
         return self._protocol_engine.state_view.commands.get_current()
 
+    def get_most_recently_finalized_command(self) -> Optional[CommandPointer]:
+        """Get the most recently finalized command, if any."""
+        most_recently_finalized_command = (
+            self._protocol_engine.state_view.commands.get_most_recently_finalized_command()
+        )
+        return (
+            CommandPointer(
+                command_id=most_recently_finalized_command.command.id,
+                command_key=most_recently_finalized_command.command.key,
+                created_at=most_recently_finalized_command.command.createdAt,
+                index=most_recently_finalized_command.index,
+            )
+            if most_recently_finalized_command
+            else None
+        )
+
     def get_command_slice(
         self, cursor: Optional[int], length: int, include_fixit_commands: bool
     ) -> CommandSlice:

api/src/opentrons/util/logging_config.py

@@ -125,7 +125,7 @@ def _buildroot_config(level_value: int) -> Dict[str, Any]:
             },
             "sensor": {
                 "class": "logging.handlers.RotatingFileHandler",
-                "formatter": "basic",
+                "formatter": "message_only",
                 "filename": sensor_log_filename,
                 "maxBytes": 1000000,
                 "level": logging.DEBUG,

app/src/assets/localization/en/pipette_wizard_flows.json

@@ -49,7 +49,7 @@
   "install_probe": "Take the calibration probe from its storage location. Ensure its collar is unlocked. Push the pipette ejector up and press the probe firmly onto the <bold>{{location}}</bold> pipette nozzle. Twist the collar to lock the probe. Test that the probe is secure by gently pulling it back and forth.",
   "loose_detach": "Loosen screws and detach ",
   "move_gantry_to_front": "Move gantry to front",
-  "must_detach_mounting_plate": "You must detach the mounting plate and reattach the z-axis carraige before using other pipettes. We do not recommend exiting this process before completion.",
+  "must_detach_mounting_plate": "You must detach the mounting plate and reattach the z-axis carriage before using other pipettes. We do not recommend exiting this process before completion.",
   "name_and_volume_detected": "{{name}} Pipette Detected",
   "next": "next",
   "ninety_six_channel": "{{ninetySix}} pipette",

app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunHeader/RunHeaderContent/ActionButton/hooks/useActionButtonProperties.ts

@@ -1,5 +1,6 @@
 import { useTranslation } from 'react-i18next'
 import { useNavigate } from 'react-router-dom'
+import { useSelector } from 'react-redux'
 
 import {
   RUN_STATUS_IDLE,
@@ -14,6 +15,7 @@ import {
   useTrackEvent,
 } from '/app/redux/analytics'
 import { useTrackProtocolRunEvent } from '/app/redux-resources/analytics'
+import { getMissingSetupSteps } from '/app/redux/protocol-runs'
 import { useIsHeaterShakerInProtocol } from '/app/organisms/ModuleCard/hooks'
 import { isAnyHeaterShakerShaking } from '../../../RunHeaderModalContainer/modals'
 import {
@@ -24,6 +26,8 @@ import {
 
 import type { IconName } from '@opentrons/components'
 import type { BaseActionButtonProps } from '..'
+import type { State } from '/app/redux/types'
+import type { StepKey } from '/app/redux/protocol-runs'
 
 interface UseButtonPropertiesProps extends BaseActionButtonProps {
   isProtocolNotReady: boolean
@@ -42,7 +46,6 @@ interface UseButtonPropertiesProps extends BaseActionButtonProps {
 export function useActionButtonProperties({
   isProtocolNotReady,
   runStatus,
-  missingSetupSteps,
   robotName,
   runId,
   confirmAttachment,
@@ -66,6 +69,9 @@ export function useActionButtonProperties({
   const isHeaterShakerInProtocol = useIsHeaterShakerInProtocol()
   const isHeaterShakerShaking = isAnyHeaterShakerShaking(attachedModules)
   const trackEvent = useTrackEvent()
+  const missingSetupSteps = useSelector<State, StepKey[]>((state: State) =>
+    getMissingSetupSteps(state, runId)
+  )
 
   let buttonText = ''
   let handleButtonClick = (): void => {}

app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunHeader/RunHeaderModalContainer/hooks/useMissingStepsModal.ts

@@ -1,17 +1,21 @@
+import { useSelector } from 'react-redux'
 import { RUN_STATUS_IDLE, RUN_STATUS_STOPPED } from '@opentrons/api-client'
 import { useConditionalConfirm } from '@opentrons/components'
 
 import { useIsHeaterShakerInProtocol } from '/app/organisms/ModuleCard/hooks'
 import { isAnyHeaterShakerShaking } from '../modals'
+import { getMissingSetupSteps } from '/app/redux/protocol-runs'
 
 import type { UseConditionalConfirmResult } from '@opentrons/components'
 import type { RunStatus, AttachedModule } from '@opentrons/api-client'
 import type { ConfirmMissingStepsModalProps } from '../modals'
+import type { State } from '/app/redux/types'
+import type { StepKey } from '/app/redux/protocol-runs'
 
 interface UseMissingStepsModalProps {
   runStatus: RunStatus | null
   attachedModules: AttachedModule[]
-  missingSetupSteps: string[]
+  runId: string
   handleProceedToRunClick: () => void
 }
 
@@ -30,12 +34,14 @@ export type UseMissingStepsModalResult =
 export function useMissingStepsModal({
   attachedModules,
   runStatus,
-  missingSetupSteps,
+  runId,
   handleProceedToRunClick,
 }: UseMissingStepsModalProps): UseMissingStepsModalResult {
   const isHeaterShakerInProtocol = useIsHeaterShakerInProtocol()
   const isHeaterShakerShaking = isAnyHeaterShakerShaking(attachedModules)
-
+  const missingSetupSteps = useSelector<State, StepKey[]>((state: State) =>
+    getMissingSetupSteps(state, runId)
+  )
   const shouldShowHSConfirm =
     isHeaterShakerInProtocol &&
     !isHeaterShakerShaking &&

app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunHeader/RunHeaderModalContainer/modals/ConfirmMissingStepsModal.tsx

@@ -12,11 +12,27 @@ import {
   TYPOGRAPHY,
   Modal,
 } from '@opentrons/components'
+import {
+  LPC_STEP_KEY,
+  LABWARE_SETUP_STEP_KEY,
+  LIQUID_SETUP_STEP_KEY,
+  MODULE_SETUP_STEP_KEY,
+  ROBOT_CALIBRATION_STEP_KEY,
+} from '/app/redux/protocol-runs'
+import type { StepKey } from '/app/redux/protocol-runs'
+
+const STEP_KEY_TO_I18N_KEY = {
+  [LPC_STEP_KEY]: 'applied_labware_offsets',
+  [LABWARE_SETUP_STEP_KEY]: 'labware_placement',
+  [LIQUID_SETUP_STEP_KEY]: 'liquids',
+  [MODULE_SETUP_STEP_KEY]: 'module_setup',
+  [ROBOT_CALIBRATION_STEP_KEY]: 'robot_calibration',
+}
 
 export interface ConfirmMissingStepsModalProps {
   onCloseClick: () => void
   onConfirmClick: () => void
-  missingSteps: string[]
+  missingSteps: StepKey[]
 }
 export const ConfirmMissingStepsModal = (
   props: ConfirmMissingStepsModalProps
@@ -41,7 +57,7 @@ export const ConfirmMissingStepsModal = (
             missingSteps: new Intl.ListFormat('en', {
               style: 'short',
               type: 'conjunction',
-            }).format(missingSteps.map(step => t(step))),
+            }).format(missingSteps.map(step => t(STEP_KEY_TO_I18N_KEY[step]))),
           })}
         </LegacyStyledText>
       </Flex>

app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunHeader/RunHeaderModalContainer/useRunHeaderModalContainer.ts

@@ -62,7 +62,6 @@ export function useRunHeaderModalContainer({
   runStatus,
   runRecord,
   attachedModules,
-  missingSetupSteps,
   protocolRunControls,
   runErrors,
 }: UseRunHeaderModalContainerProps): UseRunHeaderModalContainerResult {
@@ -102,7 +101,7 @@ export function useRunHeaderModalContainer({
   const missingStepsModalUtils = useMissingStepsModal({
     attachedModules,
     runStatus,
-    missingSetupSteps,
+    runId,
     handleProceedToRunClick,
   })
 

app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunHeader/__tests__/ProtocolRunHeader.test.tsx

@@ -30,6 +30,7 @@ vi.mock('react-router-dom')
 vi.mock('@opentrons/react-api-client')
 vi.mock('/app/redux-resources/robots')
 vi.mock('/app/resources/runs')
+vi.mock('/app/redux/protocol-runs')
 vi.mock('../RunHeaderModalContainer')
 vi.mock('../RunHeaderBannerContainer')
 vi.mock('../RunHeaderContent')
@@ -51,7 +52,6 @@ describe('ProtocolRunHeader', () => {
       robotName: MOCK_ROBOT,
       runId: MOCK_RUN_ID,
       makeHandleJumpToStep: vi.fn(),
-      missingSetupSteps: [],
     }
 
     vi.mocked(useNavigate).mockReturnValue(mockNavigate)

app/src/organisms/Desktop/Devices/ProtocolRun/ProtocolRunHeader/index.tsx

@@ -35,7 +35,6 @@ export interface ProtocolRunHeaderProps {
   robotName: string
   runId: string
   makeHandleJumpToStep: (index: number) => () => void
-  missingSetupSteps: string[]
 }
 
 export function ProtocolRunHeader(