feat(hardware-testing): collected work for upgrading scripts to PE (#…

…14245)

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# Overview
This upgrades our pipette QC scripts to using protocol engine interface,
this simplifies a lot of the code and lets us use new features:
  push out
  labware adapters
  using the normal ot3 deck definitions
  partial tip configuration

With the reduction in the amount of changes to the base repo required,
we now don't need to use patches before running the tests, this means we
only need the hardware-testing directory to be pushed to the bot with no
changes to the base software.

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# Test Plan

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Use this section to describe the steps that you took to test your Pull
Request.
If you did not perform any testing provide justification why.

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Once again, if you did not perform testing against hardware, justify
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Note: It can be helpful to write a test plan before doing development

Example Test Plan (HTTP API Change)

- Verified that new optional argument `dance-party` causes the robot to
flash its lights, move the pipettes,
then home.
- Verified that when you omit the `dance-party` option the robot homes
normally
- Added protocol that uses `dance-party` argument to G-Code Testing
Suite
- Ran protocol that did not use `dance-party` argument and everything
was successful
- Added unit tests to validate that changes to pydantic model are
correct

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# Changelog

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categorize your changes and describe what has changed and why.

Example changelog:
- Fixed app crash when trying to calibrate an illegal pipette
- Added state to API to track pipette usage
- Updated API docs to mention only two pipettes are supported

IMPORTANT: MAKE SURE ANY BREAKING CHANGES ARE PROPERLY COMMUNICATED
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# Risk assessment

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

@@ -1647,3 +1647,8 @@ async def get_hepa_uv_state(self) -> Optional[HepaUVState]:
             if res
             else None
         )
+
+    def _update_tip_state(self, mount: OT3Mount, status: bool) -> None:
+        """This is something we only use in the simulator.
+        It is required so that PE simulations using ot3api don't break."""
+        pass

api/src/opentrons/hardware_control/backends/ot3simulator.py

@@ -506,13 +506,20 @@ def _attached_pipette_to_mount(
                     ),
                     "id": None,
                 }
-        if found_model and expected_instr or found_model:
+        if found_model and init_instr["id"] is not None:
             # Instrument detected matches instrument expected (note:
             # "instrument detected" means passed as an argument to the
             # constructor of this class)
 
             # OR Instrument detected and no expected instrument specified
-            converted_name = pipette_load_name.convert_pipette_model(found_model)
+
+            found_model_version = ""
+            if found_model.find("flex") > -1:
+                found_model = found_model.replace("_flex", "")  # type: ignore
+                found_model_version = f"{init_instr['id'][4]}.{init_instr['id'][5]}"
+            converted_name = pipette_load_name.convert_pipette_model(
+                found_model, found_model_version
+            )
             return {
                 "config": load_pipette_data.load_definition(
                     converted_name.pipette_type,
@@ -843,3 +850,8 @@ async def set_hepa_uv_state(self, light_on: bool, timeout_s: int) -> bool:
 
     async def get_hepa_uv_state(self) -> Optional[HepaUVState]:
         return None
+
+    def _update_tip_state(self, mount: OT3Mount, status: bool) -> None:
+        """This is something we only use in the simulator.
+        It is required so that PE simulations using ot3api don't break."""
+        self._sim_tip_state[mount] = status

api/src/opentrons/hardware_control/ot3api.py

@@ -2133,6 +2133,8 @@ async def pick_up_tip(
         def add_tip_to_instr() -> None:
             instrument.add_tip(tip_length=tip_length)
             instrument.set_current_volume(0)
+            if isinstance(self._backend, OT3Simulator):
+                self._backend._update_tip_state(realmount, True)
 
         await self._move_to_plunger_bottom(realmount, rate=1.0)
         if (
@@ -2233,6 +2235,9 @@ def _remove_tips() -> None:
             await self._home([Axis.by_mount(mount)])
 
         _remove_tips()
+        # call this in case we're simulating
+        if isinstance(self._backend, OT3Simulator):
+            self._backend._update_tip_state(realmount, False)
 
     async def clean_up(self) -> None:
         """Get the API ready to stop cleanly."""

api/src/opentrons/protocol_api/core/engine/instrument.py

@@ -777,3 +777,8 @@ def configure_nozzle_layout(
         self._engine_client.configure_nozzle_layout(
             pipette_id=self._pipette_id, configuration_params=configuration_model
         )
+
+    def retract(self) -> None:
+        """Retract this instrument to the top of the gantry."""
+        z_axis = self._engine_client.state.pipettes.get_z_axis(self._pipette_id)
+        self._engine_client.home([z_axis])

api/src/opentrons/protocol_api/core/instrument.py

@@ -289,6 +289,9 @@ def configure_nozzle_layout(
     @abstractmethod
     def is_tip_tracking_available(self) -> bool:
         """Return whether auto tip tracking is available for the pipette's current nozzle configuration."""
+
+    def retract(self) -> None:
+        """Retract this instrument to the top of the gantry."""
         ...
 
 

api/src/opentrons/protocol_api/core/legacy/legacy_instrument_core.py

@@ -558,3 +558,7 @@ def get_nozzle_map(self) -> NozzleMap:
     def is_tip_tracking_available(self) -> bool:
         # Tip tracking is always available in legacy context
         return True
+
+    def retract(self) -> None:
+        """Retract this instrument to the top of the gantry."""
+        self._protocol_interface.get_hardware.retract(self._mount)  # type: ignore [attr-defined]

api/src/opentrons/protocol_api/core/legacy_simulator/legacy_instrument_core.py

@@ -476,3 +476,7 @@ def get_nozzle_map(self) -> NozzleMap:
     def is_tip_tracking_available(self) -> bool:
         # Tip tracking is always available in legacy context
         return True
+
+    def retract(self) -> None:
+        """Retract this instrument to the top of the gantry."""
+        self._protocol_interface.get_hardware.retract(self._mount)  # type: ignore [attr-defined]

api/src/opentrons/protocol_api/instrument_context.py

@@ -1532,6 +1532,12 @@ def move_to(
 
         return self
 
+    @requires_version(2, 18)
+    def _retract(
+        self,
+    ) -> None:
+        self._core.retract()
+
     @property
     @requires_version(2, 0)
     def mount(self) -> str:

api/src/opentrons/simulate.py

@@ -223,6 +223,7 @@ def get_protocol_api(
     # type checking, like Jupyter Notebook.
     *,
     robot_type: Optional[_UserSpecifiedRobotType] = None,
+    use_virtual_hardware: bool = True,
 ) -> protocol_api.ProtocolContext:
     """
     Build and return a ``protocol_api.ProtocolContext``
@@ -260,6 +261,7 @@ def get_protocol_api(
     :param robot_type: The type of robot to simulate: either ``"Flex"`` or ``"OT-2"``.
                        If you're running this function on a robot, the default is the type of that
                        robot. Otherwise, the default is ``"OT-2"``, for backwards compatibility.
+    :param use_virtual_hardware: If true, use the protocol engines virtual hardware, if false use the lower level hardware simulator.
     :return: The protocol context.
     """
     if isinstance(version, str):
@@ -317,6 +319,7 @@ def get_protocol_api(
             hardware_api=checked_hardware,
             bundled_data=bundled_data,
             extra_labware=extra_labware,
+            use_virtual_hardware=use_virtual_hardware,
         )
 
     # Intentional difference from execute.get_protocol_api():
@@ -790,6 +793,7 @@ def _create_live_context_pe(
     deck_type: str,
     extra_labware: Dict[str, "LabwareDefinitionDict"],
     bundled_data: Optional[Dict[str, bytes]],
+    use_virtual_hardware: bool = True,
 ) -> ProtocolContext:
     """Return a live ProtocolContext that controls the robot through ProtocolEngine."""
     assert api_version >= ENGINE_CORE_API_VERSION
@@ -798,7 +802,9 @@ def _create_live_context_pe(
     pe, loop = _LIVE_PROTOCOL_ENGINE_CONTEXTS.enter_context(
         create_protocol_engine_in_thread(
             hardware_api=hardware_api.wrapped(),
-            config=_get_protocol_engine_config(robot_type),
+            config=_get_protocol_engine_config(
+                robot_type, virtual=use_virtual_hardware
+            ),
             drop_tips_after_run=False,
             post_run_hardware_state=PostRunHardwareState.STAY_ENGAGED_IN_PLACE,
             load_fixed_trash=should_load_fixed_trash_labware_for_python_protocol(
@@ -899,7 +905,7 @@ def _run_file_pe(
     async def run(protocol_source: ProtocolSource) -> _SimulateResult:
         protocol_engine = await create_protocol_engine(
             hardware_api=hardware_api.wrapped(),
-            config=_get_protocol_engine_config(robot_type),
+            config=_get_protocol_engine_config(robot_type, virtual=True),
             load_fixed_trash=should_load_fixed_trash(protocol_source.config),
         )
 
@@ -934,15 +940,15 @@ async def run(protocol_source: ProtocolSource) -> _SimulateResult:
         return asyncio.run(run(protocol_source))
 
 
-def _get_protocol_engine_config(robot_type: RobotType) -> Config:
+def _get_protocol_engine_config(robot_type: RobotType, virtual: bool) -> Config:
     """Return a Protocol Engine config to execute protocols on this device."""
     return Config(
         robot_type=robot_type,
         deck_type=DeckType(deck_type_for_simulation(robot_type)),
         ignore_pause=True,
-        use_virtual_pipettes=True,
-        use_virtual_modules=True,
-        use_virtual_gripper=True,
+        use_virtual_pipettes=virtual,
+        use_virtual_modules=virtual,
+        use_virtual_gripper=virtual,
         use_simulated_deck_config=True,
     )
 

hardware-testing/Makefile

@@ -79,36 +79,26 @@ sdist:
 
 .PHONY: test
 test:
-	-$(MAKE) apply-patches-gravimetric
 	$(pytest) $(tests) $(test_opts)
-	-$(MAKE) remove-patches-gravimetric
 
 .PHONY: test-cov
 test-cov:
-	-$(MAKE) apply-patches-gravimetric
 	$(pytest) $(tests) $(test_opts) $(cov_opts)
-	-$(MAKE) remove-patches-gravimetric
 
 .PHONY: test-photometric-single
 test-photometric-single:
-	-$(MAKE) apply-patches-gravimetric
 	$(python) -m hardware_testing.gravimetric --photometric --simulate --pipette 50 --channels 1 --tip 50
 	$(python) -m hardware_testing.gravimetric --photometric --simulate --pipette 50 --channels 1 --tip 50 --photoplate-col-offset 3
 	$(python) -m hardware_testing.gravimetric --photometric --simulate --pipette 50 --channels 1 --tip 50 --dye-well-col-offset 3
-	-$(MAKE) remove-patches-gravimetric
 
 .PHONY: test-photometric-multi
 test-photometric-multi:
-	-$(MAKE) apply-patches-gravimetric
 	$(python) -m hardware_testing.gravimetric --photometric --simulate --pipette 50 --channels 8 --tip 50
-	-$(MAKE) remove-patches-gravimetric
 
 .PHONY: test-photometric
 test-photometric:
-	-$(MAKE) apply-patches-gravimetric
 	$(python) -m hardware_testing.gravimetric --photometric --simulate --pipette 1000 --channels 96 --tip 50 --trials 1
 	$(python) -m hardware_testing.gravimetric --photometric --simulate --pipette 1000 --channels 96 --tip 200 --trials 1
-	-$(MAKE) remove-patches-gravimetric
 
 .PHONY: test-gravimetric-single
 test-gravimetric-single:
@@ -134,14 +124,12 @@ test-gravimetric-96:
 
 .PHONY: test-gravimetric
 test-gravimetric:
-	-$(MAKE) apply-patches-gravimetric
 	$(python) -m hardware_testing.gravimetric.daily_setup --simulate
 	$(python) -m hardware_testing.gravimetric.daily_setup --simulate --calibrate
 	$(MAKE) test-gravimetric-single
 	$(MAKE) test-gravimetric-multi
 	$(MAKE) test-gravimetric-96
 	$(MAKE) test-photometric
-	-$(MAKE) remove-patches-gravimetric
 
 .PHONY: test-production-qc
 test-production-qc:
@@ -172,11 +160,9 @@ test-integration: test-production-qc test-examples test-scripts test-gravimetric
 
 .PHONY: lint
 lint:
-	-$(MAKE) apply-patches-gravimetric
 	$(python) -m mypy hardware_testing tests
 	$(python) -m black --check hardware_testing tests setup.py
 	$(python) -m flake8 hardware_testing tests setup.py
-	-$(MAKE) remove-patches-gravimetric
 
 .PHONY: format
 format:
@@ -297,9 +283,11 @@ sync-ot3: sync-sw-ot3 sync-fw-ot3
 
 .PHONY: push-ot3-gravimetric
 push-ot3-gravimetric:
+	$(MAKE) push-ot3
+	ssh $(ssh_helper_ot3) root@$(host) "mkdir -p /data/labware/v2/custom_definitions/custom_beta"
+	scp $(ssh_helper_ot3) -r hardware_testing/labware/* root@$(host):/data/labware/v2/custom_definitions/custom_beta/
 	$(MAKE) apply-patches-gravimetric
-	-$(MAKE) sync-sw-ot3
-	scp $(ssh_helper_ot3) -r hardware_testing/labware root@$(host):/data/labware/v2/custom_definitions/custom_beta/
+	cd ../ && $(MAKE) -C shared-data push-ot3
 	$(MAKE) remove-patches-gravimetric
 
 .PHONY: apply-patches-gravimetric

hardware-testing/hardware_testing/drivers/asair_sensor.py

@@ -92,7 +92,7 @@ def BuildAsairSensor(simulate: bool, autosearch: bool = True) -> AsairSensorBase
                     ui.print_info(f"Trying to connect to env sensor on port {port}")
                     sensor = AsairSensor.connect(port)
                     ser_id = sensor.get_serial()
-                    if len(ser_id) != 0:
+                    if ser_id == " ":
                         ui.print_info(f"Found env sensor {ser_id} on port {port}")
                         return sensor
                 except:  # noqa: E722