Merge branch 'edge' into EXEC-663-refactor-non-responsive-z-distance

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -383,8 +383,11 @@ def get_run_error_info_from_robot(
                 errored_labware_dict["Slot"] = labware["location"].get("slotName", "")
                 errored_labware_dict["Labware Type"] = labware.get("definitionUri", "")
                 offset_id = labware.get("offsetId", "")
-                if offset_id == "":
-                    labware_slot = errored_labware_dict["Slot"]
+                labware_slot = errored_labware_dict["Slot"]
+                if str(labware_slot) == "":
+                    lpc_message = "No labware slot was associated with this error. \
+Please manually check LPC data."
+                elif offset_id == "":
                     lpc_message = f"The current LPC coords found at {labware_slot} are (0, 0, 0). \
 Please confirm with the ABR-LPC sheet and re-LPC."
                 else:

api/src/opentrons/config/defaults_ot3.py

@@ -29,6 +29,7 @@
     sensor_threshold_pascals=15,
     output_option=OutputOptions.sync_buffer_to_csv,
     aspirate_while_sensing=False,
+    z_overlap_between_passes_mm=0.1,
     samples_for_baselining=20,
     sample_time_sec=0.004,
     data_files={InstrumentProbeType.PRIMARY: "/data/pressure_sensor_data.csv"},
@@ -345,6 +346,9 @@ def _build_default_liquid_probe(
         aspirate_while_sensing=from_conf.get(
             "aspirate_while_sensing", default.aspirate_while_sensing
         ),
+        z_overlap_between_passes_mm=from_conf.get(
+            "z_overlap_between_passes_mm", default.z_overlap_between_passes_mm
+        ),
         samples_for_baselining=from_conf.get(
             "samples_for_baselining", default.samples_for_baselining
         ),

api/src/opentrons/config/types.py

@@ -137,6 +137,7 @@ class LiquidProbeSettings:
     sensor_threshold_pascals: float
     output_option: OutputOptions
     aspirate_while_sensing: bool
+    z_overlap_between_passes_mm: float
     samples_for_baselining: int
     sample_time_sec: float
     data_files: Optional[Dict[InstrumentProbeType, str]]

api/src/opentrons/hardware_control/ot3api.py

@@ -2707,14 +2707,14 @@ async def liquid_probe(
             instrument.backlash_distance + sensor_baseline_plunger_move_mm
         )
         # height where probe action will begin
-        # TODO: (sigler) add this to pipette's liquid def (per tip)
-        z_overlap_between_passes_mm = 0.1
         sensor_baseline_z_move_mm = OT3API.liquid_probe_non_responsive_z_distance(
             probe_settings.mount_speed,
             probe_settings.samples_for_baselining,
             probe_settings.sample_time_sec,
         )
-        z_offset_per_pass = sensor_baseline_z_move_mm + z_overlap_between_passes_mm
+        z_offset_per_pass = (
+            sensor_baseline_z_move_mm + probe_settings.z_overlap_between_passes_mm
+        )
 
         # height that is considered safe to reset the plunger without disturbing liquid
         # this usually needs to at least 1-2mm from liquid, to avoid splashes from air

api/tests/opentrons/config/ot3_settings.py

@@ -124,6 +124,7 @@
         "sensor_threshold_pascals": 17,
         "output_option": OutputOptions.stream_to_csv,
         "aspirate_while_sensing": False,
+        "z_overlap_between_passes_mm": 0.1,
         "samples_for_baselining": 20,
         "sample_time_sec": 0.004,
         "data_files": {"PRIMARY": "/data/pressure_sensor_data.csv"},

api/tests/opentrons/hardware_control/backends/test_ot3_controller.py

@@ -182,6 +182,7 @@ def fake_liquid_settings() -> LiquidProbeSettings:
         sensor_threshold_pascals=15,
         output_option=OutputOptions.can_bus_only,
         aspirate_while_sensing=False,
+        z_overlap_between_passes_mm=0.1,
         samples_for_baselining=20,
         sample_time_sec=0.004,
         data_files={InstrumentProbeType.PRIMARY: "fake_file_name"},

api/tests/opentrons/hardware_control/test_ot3_api.py

@@ -122,6 +122,7 @@ def fake_liquid_settings() -> LiquidProbeSettings:
         sensor_threshold_pascals=15,
         output_option=OutputOptions.can_bus_only,
         aspirate_while_sensing=False,
+        z_overlap_between_passes_mm=0.1,
         samples_for_baselining=20,
         sample_time_sec=0.004,
         data_files={InstrumentProbeType.PRIMARY: "fake_file_name"},
@@ -827,6 +828,7 @@ async def test_liquid_probe(
             sensor_threshold_pascals=15,
             output_option=OutputOptions.can_bus_only,
             aspirate_while_sensing=True,
+            z_overlap_between_passes_mm=0.1,
             samples_for_baselining=20,
             sample_time_sec=0.004,
             data_files={InstrumentProbeType.PRIMARY: "fake_file_name"},
@@ -913,7 +915,7 @@ async def test_liquid_probe_plunger_moves(
             sample_time_sec,
         )
 
-        probe_pass_overlap = 0.1
+        probe_pass_overlap = config.z_overlap_between_passes_mm
         probe_pass_z_offset_mm = non_responsive_z_mm + probe_pass_overlap
         probe_safe_reset_mm = max(2.0, probe_pass_z_offset_mm)
 
@@ -1011,7 +1013,7 @@ async def test_liquid_probe_mount_moves(
             sample_time_sec,
         )
 
-        probe_pass_overlap = 0.1
+        probe_pass_overlap = config.z_overlap_between_passes_mm
         probe_pass_z_offset_mm = non_responsive_z_mm + probe_pass_overlap
         probe_safe_reset_mm = max(2.0, probe_pass_z_offset_mm)
 
@@ -1080,6 +1082,7 @@ async def test_multi_liquid_probe(
             sensor_threshold_pascals=15,
             output_option=OutputOptions.can_bus_only,
             aspirate_while_sensing=True,
+            z_overlap_between_passes_mm=0.1,
             samples_for_baselining=20,
             sample_time_sec=0.004,
             data_files={InstrumentProbeType.PRIMARY: "fake_file_name"},
@@ -1154,6 +1157,7 @@ async def _fake_pos_update_and_raise(
         sensor_threshold_pascals=15,
         output_option=OutputOptions.can_bus_only,
         aspirate_while_sensing=True,
+        z_overlap_between_passes_mm=0.1,
         samples_for_baselining=20,
         sample_time_sec=0.004,
         data_files={InstrumentProbeType.PRIMARY: "fake_file_name"},

hardware-testing/hardware_testing/gravimetric/config.py

@@ -172,6 +172,7 @@ def _get_liquid_probe_settings(
         sensor_threshold_pascals=lqid_cfg["sensor_threshold_pascals"],
         output_option=OutputOptions.sync_only,
         aspirate_while_sensing=False,
+        z_overlap_between_passes_mm=0.1,
         samples_for_baselining=20,
         sample_time_sec=0.004,
         data_files={InstrumentProbeType.PRIMARY: "/data/testing_data/pressure.csv"},

hardware-testing/hardware_testing/liquid_sense/execute.py

@@ -447,6 +447,7 @@ def _run_trial(
         sensor_threshold_pascals=lqid_cfg["sensor_threshold_pascals"],
         output_option=OutputOptions.sync_buffer_to_csv,
         aspirate_while_sensing=run_args.aspirate,
+        z_overlap_between_passes_mm=0.1,
         samples_for_baselining=20,
         sample_time_sec=0.004,
         data_files=data_files,

hardware-testing/hardware_testing/production_qc/pipette_assembly_qc_ot3/__main__.py

@@ -1380,6 +1380,7 @@ async def _test_liquid_probe(
                 sensor_threshold_pascals=probe_cfg.sensor_threshold_pascals,
                 output_option=OutputOptions.can_bus_only,  # FIXME: remove
                 aspirate_while_sensing=False,
+                z_overlap_between_passes_mm=0.1,
                 samples_for_baselining=20,
                 sample_time_sec=0.004,
                 data_files=None,

protocol-designer/src/NavigationBar.tsx

@@ -79,7 +79,6 @@ export function NavigationBar({
           padding={`${SPACING.spacing12} ${SPACING.spacing40}`}
           gridGap={SPACING.spacing40}
         >
-          TODO add breadcrumbs here
           {navRoutes.map(({ name, navLinkTo }: RouteProps) => (
             <NavbarLink key={name} to={navLinkTo}>
               <StyledText desktopStyle="bodyDefaultRegular">{name}</StyledText>

protocol-designer/src/ProtocolRoutes.tsx

@@ -4,8 +4,7 @@ import { Box } from '@opentrons/components'
 import { Landing } from './pages/Landing'
 import { ProtocolOverview } from './pages/ProtocolOverview'
 import { Liquids } from './pages/Liquids'
-import { StartingDeckState } from './pages/StartingDeckState'
-import { ProtocolSteps } from './pages/ProtocolSteps'
+import { Designer } from './pages/Designer'
 import { CreateNewProtocolWizard } from './pages/CreateNewProtocolWizard'
 import { NavigationBar } from './NavigationBar'
 
@@ -26,16 +25,10 @@ const pdRoutes: RouteProps[] = [
     path: '/liquids',
   },
   {
-    Component: StartingDeckState,
-    name: 'Starting deck state',
-    navLinkTo: '/startingDeckState',
-    path: '/startingDeckState',
-  },
-  {
-    Component: ProtocolSteps,
-    name: 'Protocol steps',
-    navLinkTo: '/steps',
-    path: '/steps',
+    Component: Designer,
+    name: 'Edit protocol',
+    navLinkTo: '/designer',
+    path: '/designer',
   },
   {
     Component: CreateNewProtocolWizard,

protocol-designer/src/assets/localization/en/starting_deck_state.json

@@ -13,6 +13,7 @@
   "done": "Done",
   "edit": "Edit",
   "labware": "Labware",
+  "protocol_starting_deck": "Protocol starting deck",
   "reservoir": "Reservoir",
   "starting_deck_state": "Starting deck state",
   "tipRack": "Tip rack",

protocol-designer/src/pages/StartingDeckState/ControlSelect.tsx → protocol-designer/src/pages/Designer/DeckSetup/ControlSelect.tsx

@@ -8,11 +8,11 @@ import {
   LegacyStyledText,
   RobotCoordsForeignDiv,
 } from '@opentrons/components'
-import { START_TERMINAL_ITEM_ID } from '../../steplist'
-import { getDeckSetupForActiveItem } from '../../top-selectors/labware-locations'
+import { START_TERMINAL_ITEM_ID } from '../../../steplist'
+import { getDeckSetupForActiveItem } from '../../../top-selectors/labware-locations'
 
 import type { CoordinateTuple, Dimensions } from '@opentrons/shared-data'
-import type { TerminalItemId } from '../../steplist'
+import type { TerminalItemId } from '../../../steplist'
 
 import styles from './DeckSetup.module.css'
 

protocol-designer/src/pages/StartingDeckState/index.tsx → protocol-designer/src/pages/Designer/DeckSetup/DeckSetupContainer.tsx

@@ -23,11 +23,11 @@ import {
   TRASH_BIN_ADAPTER_FIXTURE,
   WASTE_CHUTE_CUTOUT,
 } from '@opentrons/shared-data'
-import { getSelectedTerminalItemId } from '../../ui/steps'
-import { getDeckSetupForActiveItem } from '../../top-selectors/labware-locations'
-import { getDisableModuleRestrictions } from '../../feature-flags/selectors'
-import { getRobotType } from '../../file-data/selectors'
-import { getHasGen1MultiChannelPipette } from '../../step-forms'
+import { getSelectedTerminalItemId } from '../../../ui/steps'
+import { getDeckSetupForActiveItem } from '../../../top-selectors/labware-locations'
+import { getDisableModuleRestrictions } from '../../../feature-flags/selectors'
+import { getRobotType } from '../../../file-data/selectors'
+import { getHasGen1MultiChannelPipette } from '../../../step-forms'
 import { SlotDetailsContainer } from './SlotDetailsContainer'
 import { DeckSetupDetails } from './DeckSetupDetails'
 import { getCutoutIdForAddressableArea } from './utils'
@@ -60,7 +60,7 @@ const OT2_STANDARD_DECK_VIEW_LAYER_BLOCK_LIST: string[] = [
 const lightFill = COLORS.grey35
 const darkFill = COLORS.grey60
 
-export function StartingDeckState(): JSX.Element {
+export function DeckSetupContainer(): JSX.Element {
   const selectedTerminalItemId = useSelector(getSelectedTerminalItemId)
   const activeDeckSetup = useSelector(getDeckSetupForActiveItem)
   const _disableCollisionWarnings = useSelector(getDisableModuleRestrictions)

protocol-designer/src/pages/StartingDeckState/DeckSetupDetails.tsx → protocol-designer/src/pages/Designer/DeckSetup/DeckSetupDetails.tsx

@@ -15,10 +15,13 @@ import {
   SPAN7_8_10_11_SLOT,
   THERMOCYCLER_MODULE_TYPE,
 } from '@opentrons/shared-data'
-import { getSlotIdsBlockedBySpanning, getSlotIsEmpty } from '../../step-forms'
-import { LabwareOnDeck } from '../../components/DeckSetup/LabwareOnDeck'
-import { SlotWarning } from '../../components/DeckSetup/SlotWarning'
-import { getStagingAreaAddressableAreas } from '../../utils'
+import {
+  getSlotIdsBlockedBySpanning,
+  getSlotIsEmpty,
+} from '../../../step-forms'
+import { LabwareOnDeck } from '../../../components/DeckSetup/LabwareOnDeck'
+import { SlotWarning } from '../../../components/DeckSetup/SlotWarning'
+import { getStagingAreaAddressableAreas } from '../../../utils'
 import { ControlSelect } from './ControlSelect'
 
 import type { ModuleTemporalProperties } from '@opentrons/step-generation'
@@ -32,8 +35,8 @@ import type {
   InitialDeckSetup,
   LabwareOnDeck as LabwareOnDeckType,
   ModuleOnDeck,
-} from '../../step-forms'
-import type { TerminalItemId } from '../../steplist'
+} from '../../../step-forms'
+import type { TerminalItemId } from '../../../steplist'
 
 interface DeckSetupDetailsProps {
   activeDeckSetup: InitialDeckSetup

protocol-designer/src/pages/StartingDeckState/DeckSetupTools.tsx → protocol-designer/src/pages/Designer/DeckSetup/DeckSetupTools.tsx

@@ -18,19 +18,22 @@ import {
   getModuleType,
 } from '@opentrons/shared-data'
 
-import { getRobotType } from '../../file-data/selectors'
+import { getRobotType } from '../../../file-data/selectors'
 import {
   createDeckFixture,
   deleteDeckFixture,
-} from '../../step-forms/actions/additionalItems'
-import { createModule, deleteModule } from '../../step-forms/actions'
-import { getDeckSetupForActiveItem } from '../../top-selectors/labware-locations'
-import { createContainer, deleteContainer } from '../../labware-ingred/actions'
+} from '../../../step-forms/actions/additionalItems'
+import { createModule, deleteModule } from '../../../step-forms/actions'
+import { getDeckSetupForActiveItem } from '../../../top-selectors/labware-locations'
+import {
+  createContainer,
+  deleteContainer,
+} from '../../../labware-ingred/actions'
 import {
   getEnableAbsorbanceReader,
   getEnableMoam,
-} from '../../feature-flags/selectors'
-import { createContainerAboveModule } from '../../step-forms/actions/thunks'
+} from '../../../feature-flags/selectors'
+import { createContainerAboveModule } from '../../../step-forms/actions/thunks'
 import {
   FIXTURES,
   MAX_MAGNETIC_BLOCKS,
@@ -42,8 +45,8 @@ import { getModuleModelsBySlot } from './utils'
 import { LabwareTools } from './LabwareTools'
 
 import type { CutoutId, DeckSlotId, ModuleModel } from '@opentrons/shared-data'
-import type { DeckFixture } from '../../step-forms/actions/additionalItems'
-import type { ThunkDispatch } from '../../types'
+import type { DeckFixture } from '../../../step-forms/actions/additionalItems'
+import type { ThunkDispatch } from '../../../types'
 import type { Fixture } from './constants'
 
 interface DeckSetupToolsProps {

protocol-designer/src/pages/StartingDeckState/LabwareTools.tsx → protocol-designer/src/pages/Designer/DeckSetup/LabwareTools.tsx

@@ -28,17 +28,17 @@ import {
   getModuleType,
 } from '@opentrons/shared-data'
 
-import { selectors as stepFormSelectors } from '../../step-forms'
-import { getOnlyLatestDefs } from '../../labware-defs'
+import { selectors as stepFormSelectors } from '../../../step-forms'
+import { getOnlyLatestDefs } from '../../../labware-defs'
 import {
   ADAPTER_96_CHANNEL,
   getLabwareIsCompatible as _getLabwareIsCompatible,
-} from '../../utils/labwareModuleCompatibility'
-import { getHas96Channel } from '../../utils'
-import { createCustomLabwareDef } from '../../labware-defs/actions'
-import { getRobotType } from '../../file-data/selectors'
-import { getCustomLabwareDefsByURI } from '../../labware-defs/selectors'
-import { getPipetteEntities } from '../../step-forms/selectors'
+} from '../../../utils/labwareModuleCompatibility'
+import { getHas96Channel } from '../../../utils'
+import { createCustomLabwareDef } from '../../../labware-defs/actions'
+import { getRobotType } from '../../../file-data/selectors'
+import { getCustomLabwareDefsByURI } from '../../../labware-defs/selectors'
+import { getPipetteEntities } from '../../../step-forms/selectors'
 import { ORDERED_CATEGORIES } from './constants'
 import {
   getLabwareIsRecommended,
@@ -50,9 +50,9 @@ import type {
   LabwareDefinition2,
   ModuleModel,
 } from '@opentrons/shared-data'
-import type { ModuleOnDeck } from '../../step-forms'
-import type { ThunkDispatch } from '../../types'
-import type { LabwareDefByDefURI } from '../../labware-defs'
+import type { ModuleOnDeck } from '../../../step-forms'
+import type { ThunkDispatch } from '../../../types'
+import type { LabwareDefByDefURI } from '../../../labware-defs'
 import type { Fixture } from './constants'
 
 const CUSTOM_CATEGORY = 'custom'

protocol-designer/src/pages/Designer/DeckSetup/__tests__/DeckSetupContainer.test.tsx

@@ -0,0 +1,3 @@
+import { it } from 'vitest'
+
+it.todo('write test for DeckSetupContainer')

protocol-designer/src/pages/StartingDeckState/__tests__/DeckSetupTools.test.tsx → protocol-designer/src/pages/Designer/DeckSetup/__tests__/DeckSetupTools.test.tsx

@@ -3,32 +3,32 @@ import { describe, it, expect, vi, beforeEach } from 'vitest'
 import '@testing-library/jest-dom/vitest'
 import { fireEvent, screen } from '@testing-library/react'
 import { FLEX_ROBOT_TYPE, fixture96Plate } from '@opentrons/shared-data'
-import { i18n } from '../../../assets/localization'
-import { renderWithProviders } from '../../../__testing-utils__'
-import { deleteContainer } from '../../../labware-ingred/actions'
-import { createModule, deleteModule } from '../../../step-forms/actions'
-import { getRobotType } from '../../../file-data/selectors'
+import { i18n } from '../../../../assets/localization'
+import { renderWithProviders } from '../../../../__testing-utils__'
+import { deleteContainer } from '../../../../labware-ingred/actions'
+import { createModule, deleteModule } from '../../../../step-forms/actions'
+import { getRobotType } from '../../../../file-data/selectors'
 import {
   getEnableAbsorbanceReader,
   getEnableMoam,
-} from '../../../feature-flags/selectors'
+} from '../../../../feature-flags/selectors'
 import {
   createDeckFixture,
   deleteDeckFixture,
-} from '../../../step-forms/actions/additionalItems'
-import { getDeckSetupForActiveItem } from '../../../top-selectors/labware-locations'
+} from '../../../../step-forms/actions/additionalItems'
+import { getDeckSetupForActiveItem } from '../../../../top-selectors/labware-locations'
 import { DeckSetupTools } from '../DeckSetupTools'
 import { LabwareTools } from '../LabwareTools'
 
 import type { LabwareDefinition2 } from '@opentrons/shared-data'
 
-vi.mock('../../../feature-flags/selectors')
-vi.mock('../../../file-data/selectors')
-vi.mock('../../../top-selectors/labware-locations')
+vi.mock('../../../../feature-flags/selectors')
+vi.mock('../../../../file-data/selectors')
+vi.mock('../../../../top-selectors/labware-locations')
 vi.mock('../LabwareTools')
-vi.mock('../../../labware-ingred/actions')
-vi.mock('../../../step-forms/actions')
-vi.mock('../../../step-forms/actions/additionalItems')
+vi.mock('../../../../labware-ingred/actions')
+vi.mock('../../../../step-forms/actions')
+vi.mock('../../../../step-forms/actions/additionalItems')
 
 const render = (props: React.ComponentProps<typeof DeckSetupTools>) => {
   return renderWithProviders(<DeckSetupTools {...props} />, {