Merge branch 'chore_release-7.0.0' into copy-review-aug17

CONTRIBUTING.md

@@ -380,10 +380,10 @@ ssh-keygen # note the path you save the key to
 make -C robot-server install-key br_ssh_pubkey=/path/to/pubkey host=${some_other_ip_address}
 ```
 
-and subsequently, when you do `make term`, add the `br_ssh_key=/path/to/key` option:
+and subsequently, when you do `make term`, add the `ssh_key=/path/to/key` option:
 
 ```shell
-make term br_ssh_key=/path/to/privkey
+make term ssh_key=/path/to/privkey
 ```
 
 If you create the key as `~/.ssh/robot_key` and `~/.ssh/robot_key.pub` then `make term` and `make install-key` will work without arguments.

api-client/src/instruments/types.ts

@@ -1,4 +1,11 @@
 export type InstrumentData = PipetteData | GripperData | BadPipette | BadGripper
+
+// pipettes module already exports type `Mount`
+type Mount = 'left' | 'right' | 'extension'
+
+export interface SharedInstrumentData {
+  mount: Mount
+}
 export interface GripperData {
   data: {
     jawState: string
@@ -11,7 +18,7 @@ export interface GripperData {
   firmwareVersion?: string
   instrumentModel: string
   instrumentType: 'gripper'
-  mount: string
+  mount: 'extension'
   serialNumber: string
   subsystem: 'gripper'
   ok: true
@@ -31,7 +38,7 @@ export interface PipetteData {
   instrumentName: string
   instrumentModel: string
   instrumentType: 'pipette'
-  mount: string
+  mount: 'left' | 'right'
   serialNumber: string
   subsystem: 'pipette_left' | 'pipette_right'
   ok: true

api-client/src/protocols/getProtocolAnalysisAsDocument.ts

@@ -0,0 +1,18 @@
+import { GET, request } from '../request'
+
+import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+import type { CompletedProtocolAnalysis } from '@opentrons/shared-data'
+
+export function getProtocolAnalysisAsDocument(
+  config: HostConfig,
+  protocolId: string,
+  analysisId: string
+): ResponsePromise<CompletedProtocolAnalysis> {
+  return request<CompletedProtocolAnalysis>(
+    GET,
+    `/protocols/${protocolId}/analyses/${analysisId}/asDocument`,
+    null,
+    config
+  )
+}

api-client/src/protocols/index.ts

@@ -1,5 +1,6 @@
 export { getProtocol } from './getProtocol'
 export { getProtocolAnalyses } from './getProtocolAnalyses'
+export { getProtocolAnalysisAsDocument } from './getProtocolAnalysisAsDocument'
 export { deleteProtocol } from './deleteProtocol'
 export { createProtocol } from './createProtocol'
 export { getProtocols } from './getProtocols'

api/Makefile

@@ -49,10 +49,12 @@ test_opts ?=
 pypi_username ?=
 pypi_password ?=
 
-# Host key location for buildroot robot
-br_ssh_key ?= $(default_ssh_key)
-# Other SSH args for buildroot robots
+# Host key location for robot
+ssh_key ?= $(default_ssh_key)
+# Other SSH args for robot
 ssh_opts ?= $(default_ssh_opts)
+# Helper to safely bundle ssh options
+ssh_helper = $(if $(ssh_key),-i $(ssh_key)) $(ssh_opts)
 
 twine_auth_args := --username $(pypi_username) --password $(pypi_password)
 twine_repository_url ?= $(pypi_test_upload_url)
@@ -171,24 +173,23 @@ local-shell:
 
 .PHONY: push-no-restart
 push-no-restart: wheel
-	$(call push-python-package,$(host),$(br_ssh_key),$(ssh_opts),$(wheel_file))
+	$(call push-python-package,$(host),$(ssh_key),$(ssh_opts),$(wheel_file))
 
 .PHONY: push
 push: push-no-restart
-	$(call restart-service,$(host),$(br_ssh_key),$(ssh_opts),"jupyter-notebook opentrons-robot-server")
+	$(call restart-service,$(host),$(ssh_key),$(ssh_opts),"jupyter-notebook opentrons-robot-server")
 
 .PHONY: push-no-restart-ot3
 push-no-restart-ot3: sdist
 	echo $(sdist_file)
-	$(call push-python-sdist,$(host),,$(ssh_opts),$(sdist_file),/opt/opentrons-robot-server,opentrons,src,,$(version_file))
-	ssh $(ssh_opts) root@$(host) "mount -o remount,rw / && mkdir -p /usr/local/bin"
-	scp $(ssh_opts) ./src/opentrons/hardware_control/scripts/ot3repl root@$(host):/usr/local/bin/ot3repl
-	scp $(ssh_opts) ./src/opentrons/hardware_control/scripts/ot3gripper root@$(host):/usr/local/bin/ot3gripper
-	ssh $(ssh_opts) root@$(host) "mount -o remount,ro /"
+	$(call push-python-sdist,$(host),$(ssh_key),$(ssh_opts),$(sdist_file),/opt/opentrons-robot-server,opentrons,src,,$(version_file))
+	ssh $(ssh_helper) root@$(host) "mount -o remount,rw / && mkdir -p /usr/local/bin"
+	scp $(ssh_helper) ./src/opentrons/hardware_control/scripts/{ot3repl,ot3gripper} root@$(host):/usr/local/bin/
+	ssh $(ssh_helper) root@$(host) "mount -o remount,ro /"
 
 .PHONY: push-ot3
 push-ot3: push-no-restart-ot3
-	$(call restart-server,$(host),,$(ssh_opts),"opentrons-robot-server")
+	$(call restart-server,$(host),$(host),$(ssh_opts),"opentrons-robot-server")
 
 .PHONY: simulate
 simulate:
@@ -206,7 +207,7 @@ deploy: wheel
 # User must currently specify host, e.g.: `make term host=169.254.202.176`
 .PHONY: term
 term:
-	ssh -i $(br_ssh_key) $(ssh_opts) root@$(host)
+	ssh $(ssh_helper) root@$(host)
 
 .PHONY: plot-session
 plot-session:

api/mypy.ini

@@ -14,8 +14,8 @@ warn_untyped_fields = True
 
 # TODO(mc, 2021-09-08): fix and remove any / all of the
 # overrides below whenever able
-# ~125 errors
-[mypy-opentrons.protocols.advanced_control.*,opentrons.protocols.api_support.*,opentrons.protocols.duration.*,opentrons.protocols.execution.*,opentrons.protocols.geometry.*,opentrons.protocols.models.*,opentrons.protocols.labware.*]
+# ~115 errors
+[mypy-opentrons.protocols.advanced_control.*,opentrons.protocols.api_support.*,opentrons.protocols.duration.*,opentrons.protocols.execution.dev_types,opentrons.protocols.execution.execute_json_v4,opentrons.protocols.execution.execute_python,opentrons.protocols.geometry.*,opentrons.protocols.models.*,opentrons.protocols.labware.*]
 disallow_any_generics = False
 disallow_untyped_defs = False
 disallow_untyped_calls = False

api/release-notes.md

@@ -10,6 +10,8 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 Welcome to the v7.0.0 release of the Opentrons robot software! This release adds support for the Opentrons Flex robot, instruments, modules, and labware.
 
+This update may take longer than usual. Allow **approximately 15 minutes** for your robot to restart. This delay will only happen once.
+
 ### New Features
 
 - Flex touchscreen

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

@@ -88,12 +88,13 @@ def get_pipette_offset(
             **io.read_cal_file(pipette_calibration_filepath)
         )
     except FileNotFoundError:
-        log.warning(f"Calibrations for {pipette_id} on {mount} does not exist.")
+        log.debug(f"Calibrations for {pipette_id} on {mount} does not exist.")
         return None
     except (json.JSONDecodeError, ValidationError):
         log.warning(
             f"Malformed calibrations for {pipette_id} on {mount}. Please factory reset your calibrations."
         )
+        # TODO: Delete the bad calibration here maybe?
         return None
 
 

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

@@ -50,7 +50,7 @@ def tip_lengths_for_pipette(
                 pass
         return tip_lengths
     except FileNotFoundError:
-        log.warning(f"Tip length calibrations not found for {pipette_id}")
+        log.debug(f"Tip length calibrations not found for {pipette_id}")
         return tip_lengths
 
 

api/src/opentrons/calibration_storage/ot3/pipette_offset.py

@@ -85,7 +85,7 @@ def get_pipette_offset(
             **io.read_cal_file(pipette_calibration_filepath)
         )
     except FileNotFoundError:
-        log.warning(f"Calibrations for {pipette_id} on {mount} does not exist.")
+        log.debug(f"Calibrations for {pipette_id} on {mount} does not exist.")
         return None
     except (json.JSONDecodeError, ValidationError):
         log.warning(

api/src/opentrons/calibration_storage/ot3/tip_length.py

@@ -37,19 +37,22 @@ def tip_lengths_for_pipette(
 ) -> typing.Dict[str, v1.TipLengthModel]:
     tip_lengths = {}
     try:
+        # While you technically could drop some data in for tip length calibration on the flex,
+        # it is not necessary and there is no UI frontend for it, so this code will mostly be
+        # taking the FileNotFoundError path.
         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():
             try:
                 tip_lengths[tiprack] = v1.TipLengthModel(**data)
             except (json.JSONDecodeError, ValidationError):
-                log.warning(
+                log.debug(
                     f"Tip length calibration is malformed for {tiprack} on {pipette_id}"
                 )
                 pass
         return tip_lengths
     except FileNotFoundError:
-        log.warning(f"Tip length calibrations not found for {pipette_id}")
+        # this is the overwhelmingly common case
         return tip_lengths
 
 

api/src/opentrons/config/advanced_settings.py

@@ -51,6 +51,7 @@ def __init__(
         restart_required: bool = False,
         show_if: Optional[Tuple[str, bool]] = None,
         internal_only: bool = False,
+        default_true_on_robot_types: Optional[List[RobotTypeEnum]] = None,
     ):
         self.id = _id
         #: The id of the setting for programmatic access through
@@ -70,6 +71,8 @@ def __init__(
         #: A list of RobotTypeEnums that are compatible with this feature flag.
         self.internal_only = internal_only
         #: A flag determining whether this setting is user-facing.
+        self.default_true_on_robot_types = default_true_on_robot_types or []
+        #: Robot types for which null/unset means the setting is activated
 
     def __repr__(self) -> str:
         return "{}: {}".format(self.__class__, self.id)
@@ -152,7 +155,7 @@ class Setting(NamedTuple):
         old_id="disable-home-on-boot",
         title="Disable home on boot",
         description="Prevent robot from homing motors on boot",
-        robot_type=[RobotTypeEnum.OT2],
+        robot_type=[RobotTypeEnum.OT2, RobotTypeEnum.FLEX],
     ),
     SettingDefinition(
         _id="useOldAspirationFunctions",
@@ -171,6 +174,7 @@ class Setting(NamedTuple):
         "pause your robot only after it has completed its "
         "current motion.",
         robot_type=[RobotTypeEnum.OT2],
+        default_true_on_robot_types=[RobotTypeEnum.FLEX],
     ),
     SettingDefinition(
         _id="disableFastProtocolUpload",
@@ -253,6 +257,14 @@ class Setting(NamedTuple):
 }
 
 
+def get_setting_definition(setting_id: str) -> Optional[SettingDefinition]:
+    clean = _clean_id(setting_id)
+    for setting in settings:
+        if setting.id == clean:
+            return setting
+    return None
+
+
 def get_adv_setting(setting: str, robot_type: RobotTypeEnum) -> Optional[Setting]:
     setting = _clean_id(setting)
     s = get_all_adv_settings(robot_type, include_internal=True)
@@ -749,11 +761,18 @@ def _ensure(data: Mapping[str, Any]) -> SettingsMap:
 
 def get_setting_with_env_overload(setting_name: str, robot_type: RobotTypeEnum) -> bool:
     env_name = "OT_API_FF_" + setting_name
+    defn = get_setting_definition(setting_name)
     if env_name in os.environ:
         return os.environ[env_name].lower() in {"1", "true", "on"}
     else:
         s = get_adv_setting(setting_name, robot_type)
-        return s.value is True if s is not None else False
+        if s is not None:
+            return s.value is True
+        if defn is None:
+            return False
+        if robot_type in defn.default_true_on_robot_types:
+            return True
+        return False
 
 
 _SETTINGS_RESTART_REQUIRED = False

api/src/opentrons/execute.py

@@ -41,6 +41,7 @@
     ThreadManagedHardware,
     ThreadManager,
 )
+from opentrons.protocol_engine.types import PostRunHardwareState
 
 from opentrons.protocols import parse
 from opentrons.protocols.api_support.deck_type import (
@@ -572,7 +573,8 @@ def _create_live_context_pe(
         create_protocol_engine_in_thread(
             hardware_api=hardware_api.wrapped(),
             config=_get_protocol_engine_config(),
-            drop_tips_and_home_after=False,
+            drop_tips_after_run=False,
+            post_run_hardware_state=PostRunHardwareState.STAY_ENGAGED_IN_PLACE,
         )
     )
 

api/src/opentrons/hardware_control/api.py

@@ -490,14 +490,15 @@ async def _chained_calls() -> None:
 
         asyncio.run_coroutine_threadsafe(_chained_calls(), self._loop)
 
-    async def halt(self) -> None:
+    async def halt(self, disengage_before_stopping: bool = False) -> None:
         """Immediately stop motion, cancel execution manager and cancel running tasks.
 
         After this call, the smoothie will be in a bad state until a call to
         :py:meth:`stop`.
         """
-        await self._backend.hard_halt()
-        await self._execution_manager.cancel()
+        if disengage_before_stopping:
+            await self._backend.hard_halt()
+        await self._backend.halt()
 
     async def stop(self, home_after: bool = True) -> None:
         """
@@ -508,6 +509,7 @@ async def stop(self, home_after: bool = True) -> None:
         robot. After this call, no further recovery is necessary.
         """
         await self._backend.halt()  # calls smoothie_driver.kill()
+        await self._execution_manager.cancel()
         self._log.info("Recovering from halt")
         await self.reset()
         await self.cache_instruments()
@@ -988,6 +990,7 @@ async def dispense(
         mount: top_types.Mount,
         volume: Optional[float] = None,
         rate: float = 1.0,
+        push_out: Optional[float] = None,
     ) -> None:
         """
         Dispense a volume of liquid in microliters(uL) using this pipette.

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

@@ -45,6 +45,7 @@
     LIMIT_SWITCH_OVERTRAVEL_DISTANCE,
     map_pipette_type_to_sensor_id,
     moving_axes_in_move_group,
+    gripper_jaw_state_from_fw,
 )
 
 try:
@@ -127,6 +128,7 @@
     TipStateType,
     FailedTipStateCheck,
     EstopState,
+    GripperJawState,
 )
 from opentrons.hardware_control.errors import (
     InvalidPipetteName,
@@ -152,6 +154,9 @@
     set_deck_light,
     get_deck_light_state,
 )
+from opentrons_hardware.hardware_control.gripper_settings import (
+    get_gripper_jaw_state,
+)
 
 from opentrons_hardware.drivers.gpio import OT3GPIO, RemoteOT3GPIO
 from opentrons_shared_data.pipette.dev_types import PipetteName
@@ -732,6 +737,10 @@ async def gripper_home_jaw(self, duty_cycle: float) -> None:
         positions = await runner.run(can_messenger=self._messenger)
         self._handle_motor_status_response(positions)
 
+    async def get_jaw_state(self) -> GripperJawState:
+        res = await get_gripper_jaw_state(self._messenger)
+        return gripper_jaw_state_from_fw(res)
+
     @staticmethod
     def _lookup_serial_key(pipette_name: FirmwarePipetteName) -> str:
         lookup_name = {