Merge branch 'chore_release-8.0.0' into invalid_liquid_class_bug_pipe…

…tte_mismatch_fix

api-client/src/dataFiles/getCsvFile.ts

@@ -0,0 +1,12 @@
+import { GET, request } from '../request'
+
+import type { CsvFileDataResponse } from './types'
+import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+
+export function getCsvFile(
+  config: HostConfig,
+  fileId: string
+): ResponsePromise<CsvFileDataResponse> {
+  return request<CsvFileDataResponse>(GET, `/dataFiles/${fileId}`, null, config)
+}

api-client/src/dataFiles/index.ts

@@ -1,3 +1,4 @@
+export { getCsvFile } from './getCsvFile'
 export { getCsvFileRaw } from './getCsvFileRaw'
 export { uploadCsvFile } from './uploadCsvFile'
 

api-client/src/dataFiles/types.ts

@@ -13,10 +13,12 @@ export interface CsvFileData {
   name: string
 }
 
-export interface UploadedCsvFileResponse {
+export interface CsvFileDataResponse {
   data: CsvFileData
 }
 
+export type UploadedCsvFileResponse = CsvFileDataResponse
+
 export interface UploadedCsvFilesResponse {
   data: CsvFileData[]
 }

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

@@ -0,0 +1,19 @@
+import { GET, request } from '../../request'
+
+import type { ResponsePromise } from '../../request'
+import type { HostConfig } from '../../types'
+import type { GetCommandsParams, RunCommandErrors } from '../types'
+
+export function getRunCommandErrors(
+  config: HostConfig,
+  runId: string,
+  params: GetCommandsParams
+): ResponsePromise<RunCommandErrors> {
+  return request<RunCommandErrors>(
+    GET,
+    `/runs/${runId}/commandErrors`,
+    null,
+    config,
+    params
+  )
+}

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

@@ -1,10 +1,15 @@
-import type { RunTimeCommand } from '@opentrons/shared-data'
+import type { RunTimeCommand, RunCommandError } from '@opentrons/shared-data'
 
 export interface GetCommandsParams {
   cursor: number | null // the index of the command at the center of the window
   pageLength: number // the number of items to include
 }
 
+export interface RunCommandErrors {
+  data: RunCommandError[]
+  meta: GetCommandsParams & { totalLength: number }
+}
+
 // NOTE: this incantation allows us to omit a key from each item in a union distributively
 // this means we can, for example, maintain the associated commandType and params after the Omit is applied
 type DistributiveOmit<T, K extends keyof T> = T extends any ? Omit<T, K> : never

api-client/src/runs/index.ts

@@ -9,6 +9,7 @@ export { getCommand } from './commands/getCommand'
 export { getCommands } from './commands/getCommands'
 export { getCommandsAsPreSerializedList } from './commands/getCommandsAsPreSerializedList'
 export { createRunAction } from './createRunAction'
+export { getRunCommandErrors } from './commands/getRunCommandErrors'
 export * from './createLabwareOffset'
 export * from './createLabwareDefinition'
 export * from './constants'

api-client/src/runs/types.ts

@@ -54,11 +54,11 @@ export interface LegacyGoodRunData {
   modules: LoadedModule[]
   protocolId?: string
   labwareOffsets?: LabwareOffset[]
-  runTimeParameters: RunTimeParameter[]
 }
 
 export interface KnownGoodRunData extends LegacyGoodRunData {
   ok: true
+  runTimeParameters: RunTimeParameter[]
 }
 
 export interface KnownInvalidRunData extends LegacyGoodRunData {

api/docs/v2/versioning.rst

@@ -132,6 +132,11 @@ This table lists the correspondence between Protocol API versions and robot soft
 Changes in API Versions
 =======================
 
+Version 2.20
+------------
+
+- You can now call :py:obj:`.ProtocolContext.define_liquid()` without supplying a ``description`` or ``display_color``.
+
 Version 2.19
 ------------
 

api/release-notes.md

@@ -4,6 +4,26 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 [technical change log]: https://github.com/Opentrons/opentrons/releases
 [opentrons issue tracker]: https://github.com/Opentrons/opentrons/issues?q=is%3Aopen+is%3Aissue+label%3Abug
 
+By installing and using Opentrons software, you agree to the Opentrons End-User License Agreement (EULA). You can view the EULA at [opentrons.com/eula](https://opentrons.com/eula).
+
+---
+
+## Opentrons Robot Software Changes in 8.0.0
+
+Welcome to the v8.0.0 release of the Opentrons robot software!
+
+### New Features
+
+- Create, store, and run quick transfers on Flex.
+- Define and use CSV runtime parameters in Python protocols.
+- Detect the presence or absence of liquid in a well (Flex pipettes only), and continue or pause the protocol based on the result.
+- Automatically pause Flex protocol runs when detecting overpressure, allowing for error recovery and run resumption.
+
+### Improved Features
+
+- Provides more partial tip pickup configurations. All multi-channel pipettes now support single and partial column pickup, and the Flex 96-channel pipette now supports row pickup.
+- Improves homing behavior when a Flex protocol completes or is canceled with liquid-filled tips attached to the pipette.
+
 ---
 
 ## Opentrons Robot Software Changes in 7.5.0

api/src/opentrons/execute.py

@@ -142,23 +142,23 @@ def get_protocol_api(
     When this function is called, modules and instruments will be recached.
 
     :param version: The API version to use. This must be lower than
-                    ``opentrons.protocol_api.MAX_SUPPORTED_VERSION``.
-                    It may be specified either as a string (``'2.0'``) or
-                    as a ``protocols.types.APIVersion``
-                    (``APIVersion(2, 0)``).
+        ``opentrons.protocol_api.MAX_SUPPORTED_VERSION``.
+        It may be specified either as a string (``'2.0'``) or
+        as a ``protocols.types.APIVersion``
+        (``APIVersion(2, 0)``).
     :param bundled_labware: If specified, a mapping from labware names to
-                            labware definitions for labware to consider in the
-                            protocol. Note that if you specify this, _only_
-                            labware in this argument will be allowed in the
-                            protocol. This is preparation for a beta feature
-                            and is best not used.
+        labware definitions for labware to consider in the
+        protocol. Note that if you specify this, *only*
+        labware in this argument will be allowed in the
+        protocol. This is preparation for a beta feature
+        and is best not used.
     :param bundled_data: If specified, a mapping from filenames to contents
-                         for data to be available in the protocol from
-                         :py:obj:`opentrons.protocol_api.ProtocolContext.bundled_data`.
+        for data to be available in the protocol from
+        :py:obj:`opentrons.protocol_api.ProtocolContext.bundled_data`.
     :param extra_labware: A mapping from labware load names to custom labware definitions.
-                          If this is ``None`` (the default), and this function is called on a robot,
-                          it will look for labware in the ``labware`` subdirectory of the Jupyter
-                          data directory.
+        If this is ``None`` (the default), and this function is called on a robot,
+        it will look for labware in the ``labware`` subdirectory of the Jupyter
+        data directory.
     :return: The protocol context.
     """
     if isinstance(version, str):
@@ -313,18 +313,18 @@ def execute(
 
     :param protocol_file: The protocol file to execute
     :param protocol_name: The name of the protocol file. This is required
-                          internally, but it may not be a thing we can get
-                          from the protocol_file argument.
+        internally, but it may not be a thing we can get
+        from the ``protocol_file`` argument.
     :param propagate_logs: Whether this function should allow logs from the
-                           Opentrons stack to propagate up to the root handler.
-                           This can be useful if you're integrating this
-                           function in a larger application, but most logs that
-                           occur during protocol simulation are best associated
-                           with the actions in the protocol that cause them.
-                           Default: ``False``
+        Opentrons stack to propagate up to the root handler.
+        This can be useful if you're integrating this
+        function in a larger application, but most logs that
+        occur during protocol simulation are best associated
+        with the actions in the protocol that cause them.
+        Default: ``False``
     :param log_level: The level of logs to emit on the command line:
-                      ``"debug"``, ``"info"``, ``"warning"``, or ``"error"``.
-                      Defaults to ``"warning"``.
+        ``"debug"``, ``"info"``, ``"warning"``, or ``"error"``.
+        Defaults to ``"warning"``.
     :param emit_runlog: A callback for printing the run log. If specified, this
         will be called whenever a command adds an entry to the
         run log, which can be used for display and progress
@@ -353,17 +353,17 @@ def execute(
           ``KeyError``.
 
     :param custom_labware_paths: A list of directories to search for custom labware.
-                                 Loads valid labware from these paths and makes them available
-                                 to the protocol context. If this is ``None`` (the default), and
-                                 this function is called on a robot, it will look in the ``labware``
-                                 subdirectory of the Jupyter data directory.
+        Loads valid labware from these paths and makes them available
+        to the protocol context. If this is ``None`` (the default), and
+        this function is called on a robot, it will look in the ``labware``
+        subdirectory of the Jupyter data directory.
     :param custom_data_paths: A list of directories or files to load custom
-                              data files from. Ignored if the apiv2 feature
-                              flag if not set. Entries may be either files or
-                              directories. Specified files and the
-                              non-recursive contents of specified directories
-                              are presented by the protocol context in
-                              ``ProtocolContext.bundled_data``.
+        data files from. Ignored if the apiv2 feature
+        flag if not set. Entries may be either files or
+        directories. Specified files and the
+        non-recursive contents of specified directories
+        are presented by the protocol context in
+        ``ProtocolContext.bundled_data``.
     """
     stack_logger = logging.getLogger("opentrons")
     stack_logger.propagate = propagate_logs
@@ -457,10 +457,10 @@ def main() -> int:
     """Handler for command line invocation to run a protocol.
 
     :param argv: The arguments the program was invoked with; this is usually
-                 :py:obj:`sys.argv` but if you want to override that you can.
+        :py:obj:`sys.argv` but if you want to override that you can.
     :returns int: A success or failure value suitable for use as a shell
-                  return code passed to :py:obj:`sys.exit` (0 means success,
-                  anything else is a kind of failure).
+        return code passed to :py:obj:`sys.exit` (0 means success,
+        anything else is a kind of failure).
     """
     parser = argparse.ArgumentParser(
         prog="opentrons_execute", description="Run an OT-2 protocol"

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

@@ -48,6 +48,11 @@ async def _status_bar_software_error(self) -> None:
         if self._enabled:
             await self._controller.static_color(status_bar.YELLOW)
 
+    async def _status_bar_error_recovery(self) -> None:
+        self._status_bar_state = StatusBarState.ERROR_RECOVERY
+        if self._enabled:
+            await self._controller.pulse_color(status_bar.YELLOW)
+
     async def _status_bar_confirm(self) -> None:
         # Confirm should revert to IDLE
         self._status_bar_state = StatusBarState.IDLE
@@ -163,6 +168,7 @@ async def set_status_bar_state(self, state: StatusBarState) -> None:
             StatusBarState.PAUSED: self._status_bar_paused,
             StatusBarState.HARDWARE_ERROR: self._status_bar_hardware_error,
             StatusBarState.SOFTWARE_ERROR: self._status_bar_software_error,
+            StatusBarState.ERROR_RECOVERY: self._status_bar_error_recovery,
             StatusBarState.CONFIRMATION: self._status_bar_confirm,
             StatusBarState.RUN_COMPLETED: self._status_bar_run_complete,
             StatusBarState.UPDATING: self._status_bar_updating,

api/src/opentrons/hardware_control/ot3api.py

@@ -2629,7 +2629,7 @@ async def _liquid_probe_pass(
         force_both_sensors: bool = False,
     ) -> float:
         plunger_direction = -1 if probe_settings.aspirate_while_sensing else 1
-        await self._backend.liquid_probe(
+        end_z = await self._backend.liquid_probe(
             mount,
             p_travel,
             probe_settings.mount_speed,
@@ -2641,8 +2641,17 @@ async def _liquid_probe_pass(
             probe=probe,
             force_both_sensors=force_both_sensors,
         )
-        end_pos = await self.gantry_position(mount, refresh=True)
-        return end_pos.z
+        machine_pos = await self._backend.update_position()
+        machine_pos[Axis.by_mount(mount)] = end_z
+        deck_end_z = self._deck_from_machine(machine_pos)[Axis.by_mount(mount)]
+        offset = offset_for_mount(
+            mount,
+            top_types.Point(*self._config.left_mount_offset),
+            top_types.Point(*self._config.right_mount_offset),
+            top_types.Point(*self._config.gripper_mount_offset),
+        )
+        cp = self.critical_point_for(mount, None)
+        return deck_end_z + offset.z + cp.z
 
     async def liquid_probe(
         self,
@@ -2714,7 +2723,10 @@ async def liquid_probe(
 
         error: Optional[PipetteLiquidNotFoundError] = None
         pos = await self.gantry_position(checked_mount, refresh=True)
-        while (probe_start_pos.z - pos.z) < max_z_dist:
+        #  probe_start_pos.z + z_distance of pass - pos.z should be < max_z_dist
+        # due to rounding errors this can get caught in an infinite loop when the distance is almost equal
+        # so we check to see if they're within 0.01 which is 1/5th the minimum movement distance from move_utils.py
+        while (probe_start_pos.z - pos.z) < (max_z_dist - 0.01):
             # safe distance so we don't accidentally aspirate liquid if we're already close to liquid
             safe_plunger_pos = top_types.Point(
                 pos.x, pos.y, pos.z + probe_safe_reset_mm
@@ -2724,7 +2736,7 @@ async def liquid_probe(
                 pos.x, pos.y, pos.z + probe_pass_z_offset_mm
             )
             max_z_time = (
-                max_z_dist - (probe_start_pos.z - safe_plunger_pos.z)
+                max_z_dist - probe_start_pos.z + pass_start_pos.z
             ) / probe_settings.mount_speed
             p_travel_required_for_z = max_z_time * probe_settings.plunger_speed
             p_pass_travel = min(p_travel_required_for_z, p_working_mm)

api/src/opentrons/hardware_control/types.py

@@ -572,17 +572,23 @@ class PauseType(enum.Enum):
 
 
 class StatusBarState(enum.Enum):
-    IDLE = 0
-    RUNNING = 1
-    PAUSED = 2
-    HARDWARE_ERROR = 3
-    SOFTWARE_ERROR = 4
-    CONFIRMATION = 5
-    RUN_COMPLETED = 6
-    UPDATING = 7
-    ACTIVATION = 8
-    DISCO = 9
-    OFF = 10
+    """Semantic status bar states.
+
+    These mostly correspond to cases listed out in the Flex manual.
+    """
+
+    IDLE = enum.auto()
+    RUNNING = enum.auto()
+    PAUSED = enum.auto()
+    HARDWARE_ERROR = enum.auto()
+    SOFTWARE_ERROR = enum.auto()
+    ERROR_RECOVERY = enum.auto()
+    CONFIRMATION = enum.auto()
+    RUN_COMPLETED = enum.auto()
+    UPDATING = enum.auto()
+    ACTIVATION = enum.auto()
+    DISCO = enum.auto()
+    OFF = enum.auto()
 
     def transient(self) -> bool:
         return self.value in {

api/src/opentrons/protocol_api/__init__.py

@@ -12,7 +12,7 @@
 from opentrons.protocols.parameters.exceptions import (
     RuntimeParameterRequired as RuntimeParameterRequiredError,
 )
-from opentrons.protocols.parameters.types import CSVParameter
+from opentrons.protocols.parameters.csv_parameter_interface import CSVParameter
 
 from .protocol_context import ProtocolContext
 from .deck import Deck