chore: release->edge or 7.2.0

api-client/src/calibration/types.ts

@@ -8,7 +8,7 @@ export interface PipOffsetDeletionParams {
 
 export interface TipLengthDeletionParams {
   calType: 'tipLength'
-  tiprack_hash: string
+  tiprack_uri: string
   pipette_id: string
 }
 export type DeleteCalRequestParams =
@@ -93,7 +93,7 @@ export interface TipLengthCalibration {
   source: CalibrationSourceType
   status: IndividualCalibrationHealthStatus
   id: string
-  uri?: string | null
+  uri: string
 }
 
 export interface AllTipLengthCalibrations {

api/docs/v2/versioning.rst

@@ -147,10 +147,6 @@ This version introduces new features for Flex and adds and improves methods for
 
   - :py:obj:`.ProtocolContext.fixed_trash` and :py:obj:`.InstrumentContext.trash_container` now return :py:class:`.TrashBin` objects instead of :py:class:`.Labware` objects.
   - Flex will no longer automatically drop tips in the trash at the end of a protocol. You can add a :py:meth:`.drop_tip()` command to your protocol or use the Opentrons App to drop the tips.
-
-- Known issues
-
-  - It's possible to load a Thermocycler and then load another item in slot A1. Don't do this, as it could lead to unexpected pipetting behavior and crashes.
 
 Version 2.15
 ------------

api/release-notes.md

@@ -6,23 +6,34 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
-## Opentrons Robot Software Changes in [!!EDIT ME WITH THE ACTUAL NUMBER OF THE NEXT RELEASE!!]
+## Opentrons Robot Software Changes in 7.2.0
 
-### HTTP API
+Welcome to the v7.2.0 release of the Opentrons robot software!
 
-- In the `/runs/commands`, `/maintenance_runs/commands`, and `/protocols` endpoints, the `dispense` command will now return an error if you try to dispense more than you've aspirated, instead of silently clamping.
-- The `/notifications/subscribe` WebSocket endpoint has been removed. See https://github.com/Opentrons/opentrons/pull/14280 for details.
-- The `/runs/commands` endpoints are significantly faster when you request a small number of commands from a stored run.
+This update may take longer than usual if your robot has a lot of long protocols and runs stored on it. Allow *approximately 20 minutes* for your robot to restart. This delay will only happen once.
 
-### Other Changes
+If you don't care about preserving your labware offsets and run history, you can avoid the delay by clearing your runs and protocols before starting this update. Go to **Robot Settings** > **Device Reset** and select **Clear protocol run history**.
+
+### Improved Features
+
+- The robot software now runs Python 3.10. Many built-in Python packages were updated to match. If you have installed your own Python packages on the robot, re-install them to ensure compatibility.
+- Added error handling when dispensing. The `/runs/commands`, `/maintenance_runs/commands`, and `/protocols` HTTP API endpoints now return an error if you try to dispense more than you've aspirated.
+- Improved performance of the `/runs/commands` endpoints. They are now significantly faster when requesting a small number of commands from a stored run.
 
-- The `notify_server` Python package has been removed. See https://github.com/Opentrons/opentrons/pull/14280 for details.
+### Bug Fixes
+
+- The OT-2 now consistently applies tip length calibration. There used to be a height discrepancy between Labware Position Check and protocol runs. If you previously compensated for the inconsistent pipette height with labware offsets, re-run Labware Position Check to avoid pipette crashes.
+- The OT-2 now accurately calculates the position of the Thermocycler. If you previously compensated for the incorrect position with labware offsets, re-run Labware Position Check to avoid pipette crashes.
+- The Flex Gripper will no longer pick up large labware that could collide with tips held by an adjoining pipette.
+- Flex now properly configures itself when connected by Ethernet directly to a computer.
 
-### Upgrade Notes
+### Removals
 
-This update may take longer than usual if your robot has a lot of long protocols and runs stored on it. Allow **approximately 25 minutes** for your robot to restart. This delay will only happen once.
+- Removed the `notify_server` Python package and `/notifications/subscribe` WebSocket endpoint, as they were never fully used. (See pull request [#14280](https://github.com/Opentrons/opentrons/pull/14280) for details.)
+
+### Known Issues
 
-If you don't care about preserving your labware offsets and run history, you can avoid the delay. Clear your runs and protocols before starting this update. Go to **Robot Settings** > **Device Reset** and select **Clear protocol run history**.
+- Downgrading an OT-2 to an earlier software version will delete tip length calibrations created with version 7.2.0. If you need to downgrade, re-run all pipette calibrations afterward.
 
 ---
 

api/src/opentrons/calibration_storage/ot2/models/v1.py

@@ -32,8 +32,12 @@ class TipLengthModel(BaseModel):
         default_factory=CalibrationStatus,
         description="The status of the calibration data.",
     )
-    uri: typing.Union[LabwareUri, Literal[""]] = Field(
-        ..., description="The tiprack URI associated with the tip length data."
+    # Old data may have a `uri` field, replaced later by `definitionHash`.
+    # uri: typing.Union[LabwareUri, Literal[""]] = Field(
+    #    ..., description="The tiprack URI associated with the tip length data."
+    # )
+    definitionHash: str = Field(
+        ..., description="The tiprack hash associated with the tip length data."
     )
 
     @validator("tipLength")

api/src/opentrons/calibration_storage/ot2/tip_length.py

@@ -7,6 +7,7 @@
 from opentrons import config
 
 from .. import file_operators as io, helpers, types as local_types
+from opentrons_shared_data.pipette.dev_types import LabwareUri
 
 from opentrons.protocols.api_support.constants import OPENTRONS_NAMESPACE
 from opentrons.util.helpers import utc_now
@@ -22,9 +23,9 @@
 # Get Tip Length Calibration
 
 
-def _conver_tip_length_model_to_dict(
-    to_dict: typing.Dict[str, v1.TipLengthModel]
-) -> typing.Dict[str, typing.Any]:
+def _convert_tip_length_model_to_dict(
+    to_dict: typing.Dict[LabwareUri, v1.TipLengthModel]
+) -> typing.Dict[LabwareUri, typing.Any]:
     # This is a workaround since pydantic doesn't have a nice way to
     # add encoders when converting to a dict.
     dict_of_tip_lengths = {}
@@ -35,17 +36,23 @@ def _conver_tip_length_model_to_dict(
 
 def tip_lengths_for_pipette(
     pipette_id: str,
-) -> typing.Dict[str, v1.TipLengthModel]:
+) -> typing.Dict[LabwareUri, v1.TipLengthModel]:
     tip_lengths = {}
     try:
         tip_length_filepath = config.get_tip_length_cal_path() / f"{pipette_id}.json"
         all_tip_lengths_for_pipette = io.read_cal_file(tip_length_filepath)
-        for tiprack, data in all_tip_lengths_for_pipette.items():
+        for tiprack_identifier, data in all_tip_lengths_for_pipette.items():
+            # We normally key these calibrations by their tip rack URI,
+            # but older software had them keyed by their tip rack hash.
+            # Migrate from the old format, if necessary.
+            if "/" not in tiprack_identifier:
+                data["definitionHash"] = tiprack_identifier
+                tiprack_identifier = data.pop("uri")
             try:
-                tip_lengths[tiprack] = v1.TipLengthModel(**data)
+                tip_lengths[LabwareUri(tiprack_identifier)] = v1.TipLengthModel(**data)
             except (json.JSONDecodeError, ValidationError):
                 log.warning(
-                    f"Tip length calibration is malformed for {tiprack} on {pipette_id}"
+                    f"Tip length calibration is malformed for {tiprack_identifier} on {pipette_id}"
                 )
                 pass
         return tip_lengths
@@ -64,10 +71,10 @@ def load_tip_length_calibration(
     :param pip_id: pipette you are using
     :param definition: full definition of the tiprack
     """
-    labware_hash = helpers.hash_labware_def(definition)
+    labware_uri = helpers.uri_from_definition(definition)
     load_name = definition["parameters"]["loadName"]
     try:
-        return tip_lengths_for_pipette(pip_id)[labware_hash]
+        return tip_lengths_for_pipette(pip_id)[labware_uri]
     except KeyError as e:
         raise local_types.TipLengthCalNotFound(
             f"Tip length of {load_name} has not been "
@@ -89,16 +96,16 @@ def get_all_tip_length_calibrations() -> typing.List[v1.TipLengthCalibration]:
         if filepath.stem == "index":
             continue
         tip_lengths = tip_lengths_for_pipette(filepath.stem)
-        for tiprack_hash, tip_length in tip_lengths.items():
+        for tiprack_uri, tip_length in tip_lengths.items():
             all_tip_lengths_available.append(
                 v1.TipLengthCalibration(
                     pipette=filepath.stem,
-                    tiprack=tiprack_hash,
+                    tiprack=tip_length.definitionHash,
                     tipLength=tip_length.tipLength,
                     lastModified=tip_length.lastModified,
                     source=tip_length.source,
                     status=tip_length.status,
-                    uri=tip_length.uri,
+                    uri=tiprack_uri,
                 )
             )
     return all_tip_lengths_available
@@ -129,28 +136,45 @@ def get_custom_tiprack_definition_for_tlc(labware_uri: str) -> "LabwareDefinitio
 # Delete Tip Length Calibration
 
 
-def delete_tip_length_calibration(tiprack: str, pipette_id: str) -> None:
+def delete_tip_length_calibration(
+    pipette_id: str,
+    tiprack_uri: typing.Optional[LabwareUri] = None,
+    tiprack_hash: typing.Optional[str] = None,
+) -> None:
     """
-    Delete tip length calibration based on tiprack hash and
-    pipette serial number
+    Delete tip length calibration based on an optional tiprack uri or
+    tiprack hash and pipette serial number.
 
-    :param tiprack: tiprack hash
+    :param tiprack_uri: tiprack uri
+    :param tiprack_hash: tiprack uri
     :param pipette: pipette serial number
     """
     tip_lengths = tip_lengths_for_pipette(pipette_id)
-
-    if tiprack in tip_lengths:
+    tip_length_dir = config.get_tip_length_cal_path()
+    if tiprack_uri in tip_lengths:
         # maybe make modify and delete same file?
-        del tip_lengths[tiprack]
-        tip_length_dir = config.get_tip_length_cal_path()
+        del tip_lengths[tiprack_uri]
+
+        if tip_lengths:
+            dict_of_tip_lengths = _convert_tip_length_model_to_dict(tip_lengths)
+            io.save_to_file(tip_length_dir, pipette_id, dict_of_tip_lengths)
+        else:
+            io.delete_file(tip_length_dir / f"{pipette_id}.json")
+    elif tiprack_hash and any(tiprack_hash in v.dict() for v in tip_lengths.values()):
+        # NOTE this is for backwards compatibilty only
+        # TODO delete this check once the tip_length DELETE router
+        # no longer depends on a tiprack hash
+        for k, v in tip_lengths.items():
+            if tiprack_hash in v.dict():
+                tip_lengths.pop(k)
         if tip_lengths:
-            dict_of_tip_lengths = _conver_tip_length_model_to_dict(tip_lengths)
+            dict_of_tip_lengths = _convert_tip_length_model_to_dict(tip_lengths)
             io.save_to_file(tip_length_dir, pipette_id, dict_of_tip_lengths)
         else:
             io.delete_file(tip_length_dir / f"{pipette_id}.json")
     else:
         raise local_types.TipLengthCalNotFound(
-            f"Tip length for hash {tiprack} has not been "
+            f"Tip length for uri {tiprack_uri} and hash {tiprack_hash} has not been "
             f"calibrated for this pipette: {pipette_id} and cannot"
             "be loaded"
         )
@@ -176,7 +200,7 @@ def create_tip_length_data(
     cal_status: typing.Optional[
         typing.Union[local_types.CalibrationStatus, v1.CalibrationStatus]
     ] = None,
-) -> typing.Dict[str, v1.TipLengthModel]:
+) -> typing.Dict[LabwareUri, v1.TipLengthModel]:
     """
     Function to correctly format tip length data.
 
@@ -197,13 +221,13 @@ def create_tip_length_data(
         lastModified=utc_now(),
         source=local_types.SourceType.user,
         status=cal_status_model,
-        uri=labware_uri,
+        definitionHash=labware_hash,
     )
 
     if not definition.get("namespace") == OPENTRONS_NAMESPACE:
         _save_custom_tiprack_definition(labware_uri, definition)
 
-    data = {labware_hash: tip_length_data}
+    data = {labware_uri: tip_length_data}
     return data
 
 
@@ -220,7 +244,7 @@ def _save_custom_tiprack_definition(
 
 def save_tip_length_calibration(
     pip_id: str,
-    tip_length_cal: typing.Dict[str, v1.TipLengthModel],
+    tip_length_cal: typing.Dict[LabwareUri, v1.TipLengthModel],
 ) -> None:
     """
     Function used to save tip length calibration to file.
@@ -235,5 +259,5 @@ def save_tip_length_calibration(
 
     all_tip_lengths.update(tip_length_cal)
 
-    dict_of_tip_lengths = _conver_tip_length_model_to_dict(all_tip_lengths)
+    dict_of_tip_lengths = _convert_tip_length_model_to_dict(all_tip_lengths)
     io.save_to_file(tip_length_dir_path, pip_id, dict_of_tip_lengths)

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

@@ -1157,7 +1157,7 @@ async def watch(self, loop: asyncio.AbstractEventLoop) -> None:
     def axis_bounds(self) -> OT3AxisMap[Tuple[float, float]]:
         """Get the axis bounds."""
         # TODO (AL, 2021-11-18): The bounds need to be defined
-        phony_bounds = (0, 10000)
+        phony_bounds = (0, 500)
         return {
             Axis.Z_L: phony_bounds,
             Axis.Z_R: phony_bounds,

api/src/opentrons/hardware_control/dev_types.py

@@ -19,6 +19,7 @@
 from opentrons_shared_data.pipette.pipette_definition import (
     PipetteConfigurations,
     SupportedTipsDefinition,
+    PipetteBoundingBoxOffsetDefinition,
 )
 from opentrons_shared_data.gripper import (
     GripperModel,
@@ -95,7 +96,8 @@ class PipetteDict(InstrumentDict):
     has_tip: bool
     default_push_out_volume: Optional[float]
     supported_tips: Dict[PipetteTipType, SupportedTipsDefinition]
-    current_nozzle_map: NozzleMap  # spp: why was this Optional?
+    pipette_bounding_box_offsets: PipetteBoundingBoxOffsetDefinition
+    current_nozzle_map: NozzleMap
 
 
 class PipetteStateDict(TypedDict):

api/src/opentrons/hardware_control/instruments/ot2/instrument_calibration.py

@@ -130,18 +130,15 @@ def load_tip_length_for_pipette(
         pipette_id, tiprack
     )
 
-    # TODO (lc 09-26-2022) We shouldn't have to do a hash twice. We should figure out what
-    # information we actually need from the labware definition and pass it into
-    # the `load_tip_length_calibration` function.
-    tiprack_hash = helpers.hash_labware_def(tiprack)
+    tiprack_uri = helpers.uri_from_definition(tiprack)
 
     return TipLengthCalibration(
         tip_length=tip_length_data.tipLength,
         source=tip_length_data.source,
         pipette=pipette_id,
-        tiprack=tiprack_hash,
+        tiprack=tip_length_data.definitionHash,
         last_modified=tip_length_data.lastModified,
-        uri=tip_length_data.uri,
+        uri=tiprack_uri,
         status=types.CalibrationStatus(
             markedAt=tip_length_data.status.markedAt,
             markedBad=tip_length_data.status.markedBad,

api/src/opentrons/hardware_control/instruments/ot2/pipette.py

@@ -75,7 +75,9 @@ class Pipette(AbstractInstrument[PipetteConfigurations]):
     control API. Its only purpose is to gather state.
     """
 
-    DictType = Dict[str, Union[str, float, bool]]
+    DictType = Dict[
+        str, Union[str, float, bool]
+    ]  # spp: as_dict() has value items that aren't Union[str, float, bool]..
     #: The type of this data class as a dict
 
     def __init__(

api/src/opentrons/hardware_control/instruments/ot2/pipette_handler.py

@@ -242,8 +242,6 @@ def get_attached_instrument(self, mount: MountType) -> PipetteDict:
                 instr, instr.blow_out_flow_rate, "dispense"
             )
             result["ready_to_aspirate"] = instr.ready_to_aspirate
-            # TODO (12-5-2022) figure out why this is using default aspirate flow rate
-            # rather than default dispense flow rate.
             result["default_blow_out_speeds"] = {
                 alvl: self.plunger_speed(instr, fr, "blowout")
                 for alvl, fr in instr.blow_out_flow_rates_lookup.items()
@@ -257,6 +255,9 @@ def get_attached_instrument(self, mount: MountType) -> PipetteDict:
                 alvl: self.plunger_speed(instr, fr, "aspirate")
                 for alvl, fr in instr.aspirate_flow_rates_lookup.items()
             }
+            result[
+                "pipette_bounding_box_offsets"
+            ] = instr.config.pipette_bounding_box_offsets
         return cast(PipetteDict, result)
 
     @property

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

@@ -276,6 +276,9 @@ def get_attached_instrument(self, mount: OT3Mount) -> PipetteDict:
             result[
                 "default_push_out_volume"
             ] = instr.active_tip_settings.default_push_out_volume
+            result[
+                "pipette_bounding_box_offsets"
+            ] = instr.config.pipette_bounding_box_offsets
         return cast(PipetteDict, result)
 
     @property

api/src/opentrons/hardware_control/modules/update.py

@@ -34,7 +34,6 @@ async def update_firmware(
         kwargs: Dict[str, Any] = {
             "stdout": asyncio.subprocess.PIPE,
             "stderr": asyncio.subprocess.PIPE,
-            "loop": loop,
         }
         successful, res = await module.bootloader()(
             flash_port_or_dfu_serial, str(firmware_file), kwargs