Merge branch 'edge' into chore_update-cypress

.eslintrc.js

@@ -52,6 +52,7 @@ module.exports = {
               'useLastRunCommandKey',
               'useCurrentMaintenanceRun',
               'useDeckConfigurationQuery',
+              'useAllCommandsAsPreSerializedList',
             ],
             message:
               'The HTTP hook is deprecated. Utilize the equivalent notification wrapper (useNotifyX) instead.',

abr-testing/abr_testing/data_collection/abr_calibration_logs.py

@@ -155,18 +155,10 @@ def upload_calibration_offsets(
     parser.add_argument(
         "email", metavar="EMAIL", type=str, nargs=1, help="opentrons gmail."
     )
-    parser.add_argument(
-        "ip_or_all",
-        metavar="IP_OR_ALL",
-        type=str,
-        nargs=1,
-        help="Enter 'ALL' to read IPs.json or type full IP address of 1 robot.",
-    )
     args = parser.parse_args()
     storage_directory = args.storage_directory[0]
     folder_name = args.folder_name[0]
     google_sheet_name = args.google_sheet_name[0]
-    ip_or_all = args.ip_or_all[0]
     email = args.email[0]
     # Connect to google drive.
     try:
@@ -191,6 +183,7 @@ def upload_calibration_offsets(
     except FileNotFoundError:
         print(f"Add .json file with robot IPs to: {storage_directory}.")
         sys.exit()
+    ip_or_all = input("IP Address or ALL: ")
 
     if ip_or_all == "ALL":
         ip_address_list = ip_file["ip_address_list"]

abr-testing/abr_testing/tools/abr_scale.py

@@ -25,25 +25,7 @@
         nargs=1,
         help="Name of google sheet and local csv to save data to.",
     )
-    parser.add_argument("robot", metavar="ROBOT", type=str, nargs=1, help="Robot name.")
-    parser.add_argument(
-        "labware_name",
-        metavar="LABWARE_NAME",
-        type=str,
-        nargs=1,
-        help="Name of labware.",
-    )
-    parser.add_argument(
-        "protocol_step",
-        metavar="PROTOCOL_STEP",
-        type=str,
-        nargs=1,
-        help="1 for empty plate, 2 for filled plate, 3 for end of protocol.",
-    )
     args = parser.parse_args()
-    robot = args.robot[0]
-    labware = args.labware_name[0]
-    protocol_step = args.protocol_step[0]
     storage_directory = args.storage_directory[0]
     file_name = args.file_name[0]
     file_name_csv = file_name + ".csv"
@@ -71,7 +53,9 @@
         print("Connected to google sheet.")
     except FileNotFoundError:
         print("No google sheets credentials. Add credentials to storage notebook.")
-
+    robot = input("Robot: ")
+    labware = input("Labware: ")
+    protocol_step = input("Measurement Step (1,2,3): ")
     # Scale Loop
     grams, is_stable = scale.read_mass()
     grams, is_stable = scale.read_mass()

api-client/src/runs/commands/getCommandsAsPreSerializedList.ts

@@ -0,0 +1,22 @@
+import { GET, request } from '../../request'
+
+import type { ResponsePromise } from '../../request'
+import type { HostConfig } from '../../types'
+import type {
+  CommandsAsPreSerializedListData,
+  GetCommandsParams,
+} from './types'
+
+export function getCommandsAsPreSerializedList(
+  config: HostConfig,
+  runId: string,
+  params: GetCommandsParams
+): ResponsePromise<CommandsAsPreSerializedListData> {
+  return request<CommandsAsPreSerializedListData>(
+    GET,
+    `/runs/${runId}/commandsAsPreSerializedList`,
+    null,
+    config,
+    params
+  )
+}

api-client/src/runs/commands/types.ts

@@ -34,6 +34,12 @@ export interface CommandsData {
   links: CommandsLinks
 }
 
+export interface CommandsAsPreSerializedListData {
+  data: string[]
+  meta: GetCommandsParams & { totalLength: number }
+  links: CommandsLinks
+}
+
 export interface CreateCommandParams {
   waitUntilComplete?: boolean
   timeout?: number

api-client/src/runs/index.ts

@@ -7,6 +7,7 @@ export { createCommand } from './commands/createCommand'
 export { createLiveCommand } from './commands/createLiveCommand'
 export { getCommand } from './commands/getCommand'
 export { getCommands } from './commands/getCommands'
+export { getCommandsAsPreSerializedList } from './commands/getCommandsAsPreSerializedList'
 export { createRunAction } from './createRunAction'
 export * from './createLabwareOffset'
 export * from './createLabwareDefinition'

api-client/src/system/__tests__/utils.test.ts

@@ -0,0 +1,20 @@
+import { describe, expect, it } from 'vitest'
+import { sanitizeFileName } from '../utils'
+
+describe('sanitizeFileName', () => {
+  it('returns original alphanumeric file name', () => {
+    expect(sanitizeFileName('an0ther_otie_logo.png')).toEqual(
+      'an0ther_otie_logo.png'
+    )
+  })
+
+  it('sanitizes a file name', () => {
+    expect(
+      sanitizeFileName(
+        `otie's birthday/party - (& the bouncy castle cost ~$100,000).jpeg`
+      )
+    ).toEqual(
+      'otie_s_birthday_party_-____the_bouncy_castle_cost___100_000_.jpeg'
+    )
+  })
+})

api-client/src/system/createSplash.ts

@@ -1,13 +1,15 @@
 import { POST, request } from '../request'
+import { sanitizeFileName } from './utils'
 import type { ResponsePromise } from '../request'
 import type { HostConfig } from '../types'
 
 export function createSplash(
   config: HostConfig,
   file: File
 ): ResponsePromise<void> {
-  // sanitize file name to ensure no spaces
-  const renamedFile = new File([file], file.name.replace(' ', '_'), {
+  // sanitize file name to ensure no spaces or special characters
+  const newFileName = sanitizeFileName(file.name)
+  const renamedFile = new File([file], newFileName, {
     type: 'image/png',
   })
 

api-client/src/system/index.ts

@@ -3,3 +3,4 @@ export { createRegistration } from './createRegistration'
 export { createSplash } from './createSplash'
 export { getConnections } from './getConnections'
 export * from './types'
+export * from './utils'

api-client/src/system/utils.ts

@@ -0,0 +1,3 @@
+export function sanitizeFileName(fileName: string): string {
+  return fileName.replace(/[^a-zA-Z0-9-.]/gi, '_')
+}

api/release-notes.md

@@ -6,6 +6,31 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
+## Opentrons Robot Software Changes in 7.3.0
+
+Welcome to the v7.3.0 release of the Opentrons robot software!
+
+### New Features
+
+- Runtime parameters: read, write, and use parameters in Python protocol runs.
+
+### Improved Features
+
+- Automatic tip tracking is now available for all nozzle configurations.
+- Flex no longer shows unnecessary pipette calibration warnings.
+- Python protocols can once again set labware offsets outside of Labware Position Check.
+
+### Changed Features
+
+- Calling `GET /runs/{id}/commands` for a JSON protocol no longer returns a full list of queued commands. Use protocol analysis to get a full list of commands.
+
+### Bug Fixes
+
+- Fixed an edge case where capitalizing part of a labware load name could cause unexpected behavior or collisions.
+- Fixed Python packages installed  on the OT-2 with `pip` not being found by `import` statements.
+
+---
+
 ## Opentrons Robot Software Changes in 7.2.2
 
 Welcome to the v7.2.2 release of the Opentrons robot software!

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

@@ -33,7 +33,7 @@
     Geometry,
 )
 
-RECONFIG_KEYS = {"quirks"}
+RECONFIG_KEYS = {"quirks", "grip_force_profile"}
 
 MAX_ACCEPTABLE_JAW_DISPLACEMENT: Final = 20
 
@@ -52,6 +52,7 @@ def __init__(
         config: GripperDefinition,
         gripper_cal_offset: GripperCalibrationOffset,
         gripper_id: str,
+        jaw_max_offset: Optional[float] = None,
     ) -> None:
         self._config = config
         self._model = config.model
@@ -83,7 +84,7 @@ def __init__(
         self._log.info(
             f"loaded: {self._model}, gripper offset: {self._calibration_offset}"
         )
-        self._jaw_max_offset: Optional[float] = None
+        self._jaw_max_offset = jaw_max_offset
 
     @property
     def grip_force_profile(self) -> GripForceProfile:
@@ -325,11 +326,13 @@ def _reload_gripper(
                 changed.add(k)
         if changed.intersection(RECONFIG_KEYS):
             # Something has changed that requires reconfig
+            # we shoud recalibrate the jaw as well
             return (
                 Gripper(
                     new_config,
                     cal_offset,
                     attached_instr._gripper_id,
+                    None,
                 ),
                 False,
             )

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

@@ -51,6 +51,7 @@ def reset_gripper(self) -> None:
             og_gripper.config,
             load_gripper_calibration_offset(og_gripper.gripper_id),
             og_gripper.gripper_id,
+            og_gripper._jaw_max_offset,
         )
         self._gripper = new_gripper
 

api/src/opentrons/protocol_api/instrument_context.py

@@ -60,6 +60,8 @@
 """The version after which a partial nozzle configuration became available for the 96 Channel Pipette."""
 _PARTIAL_NOZZLE_CONFIGURATION_AUTOMATIC_TIP_TRACKING_IN = APIVersion(2, 18)
 """The version after which automatic tip tracking supported partially configured nozzle layouts."""
+_DISPOSAL_LOCATION_OFFSET_ADDED_IN = APIVersion(2, 18)
+"""The version after which offsets for deck configured trash containers and changes to alternating tip drop behavior were introduced."""
 
 
 class InstrumentContext(publisher.CommandPublisher):
@@ -1086,16 +1088,22 @@ def drop_tip(
             well = maybe_well
 
         elif isinstance(location, (TrashBin, WasteChute)):
+            # In 2.16 and 2.17, we would always automatically use automatic alternate tip drop locations regardless
+            # of whether you explicitly passed the disposal location as a location or if none was provided. Now, in
+            # 2.18 and moving forward, passing it in will bypass the automatic behavior and instead go to the set
+            # offset or the XY center if none is provided.
+            if self.api_version < _DISPOSAL_LOCATION_OFFSET_ADDED_IN:
+                alternate_drop_location = True
             with publisher.publish_context(
                 broker=self.broker,
                 command=cmds.drop_tip_in_disposal_location(
                     instrument=self, location=location
                 ),
             ):
-                # TODO(jbl 2024-02-28) when adding 2.18 api version checks, set alternate_tip_drop
-                #   if below that version for compatability
                 self._core.drop_tip_in_disposal_location(
-                    location, home_after=home_after
+                    location,
+                    home_after=home_after,
+                    alternate_tip_drop=alternate_drop_location,
                 )
             self._last_tip_picked_up_from = None
             return self

api/src/opentrons/protocol_engine/commands/calibration/move_to_maintenance_position.py

@@ -80,46 +80,25 @@ async def execute(
         ot3_api = ensure_ot3_hardware(
             self._hardware_api,
         )
-        # the 96-channel mount is disengaged during gripper calibration and
-        #  must be homed before the gantry position can be called
+        max_height_z_tip = ot3_api.get_instrument_max_height(Mount.LEFT)
+        # disengage the gripper z mount if present and enabled
         await ot3_api.prepare_for_mount_movement(Mount.LEFT)
-        current_position_mount = await ot3_api.gantry_position(
+
+        await ot3_api.retract(Mount.LEFT)
+        current_pos = await ot3_api.gantry_position(
             Mount.LEFT, critical_point=CriticalPoint.MOUNT
         )
-        max_height_z_mount = ot3_api.get_instrument_max_height(
-            Mount.LEFT, critical_point=CriticalPoint.MOUNT
+        await ot3_api.move_to(
+            mount=Mount.LEFT,
+            abs_position=Point(x=_ATTACH_POINT.x, y=_ATTACH_POINT.y, z=current_pos.z),
+            critical_point=CriticalPoint.MOUNT,
         )
-        max_height_z_tip = ot3_api.get_instrument_max_height(Mount.LEFT)
-        # avoid using motion planning waypoints because we do not need to move the z at this moment
-        movement_points = [
-            # move the z to the highest position
-            Point(
-                x=current_position_mount.x,
-                y=current_position_mount.y,
-                z=max_height_z_mount,
-            ),
-            # move in x,y without going down the z
-            Point(x=_ATTACH_POINT.x, y=_ATTACH_POINT.y, z=max_height_z_mount),
-        ]
-
-        await ot3_api.prepare_for_mount_movement(Mount.LEFT)
-        for movement in movement_points:
-            await ot3_api.move_to(
-                mount=Mount.LEFT,
-                abs_position=movement,
-                critical_point=CriticalPoint.MOUNT,
-            )
 
         if params.mount != MountType.EXTENSION:
-
-            # disengage the gripper z to enable the e-brake, this prevents the gripper
-            # z from dropping when the right mount carriage gets released from the
-            # mount during 96-channel detach flow
-            if ot3_api.has_gripper():
-                await ot3_api.disengage_axes([Axis.Z_G])
-
             if params.maintenancePosition == MaintenancePosition.ATTACH_INSTRUMENT:
-                mount_to_axis = Axis.by_mount(params.mount.to_hw_mount())
+                mount = params.mount.to_hw_mount()
+                mount_to_axis = Axis.by_mount(mount)
+                await ot3_api.prepare_for_mount_movement(mount)
                 await ot3_api.move_axes(
                     {
                         mount_to_axis: _INSTRUMENT_ATTACH_Z_POINT,
@@ -134,6 +113,7 @@ async def execute(
                         Axis.Z_R: max_motion_range + _RIGHT_MOUNT_Z_MARGIN,
                     }
                 )
+                await ot3_api.disengage_axes([Axis.Z_L, Axis.Z_R])
 
         return MoveToMaintenancePositionResult()