style(python): remove line length limit from flake8 config

Closes #9931

api/.flake8

@@ -1,15 +1,14 @@
 [flake8]
 
-# set line-length for future black support
-# https://github.com/psf/black/blob/master/docs/compatible_configs.md
-max-line-length = 88
-
 # max cyclomatic complexity
 max-complexity = 9
 
 extend-ignore =
-    # ignore E203 because black might reformat it
+    # defer formatting concerns to black
+    # E203: space around `:` operator
+    # E501: maximum line length
     E203,
+    E501,
     # do not require type annotations for self nor cls
     ANN101,
     ANN102

api/setup.py

@@ -106,7 +106,7 @@ def read(*parts):
         },
         project_urls={
             "opentrons.com": "https://www.opentrons.com",
-            "Source Code On Github": "https://github.com/Opentrons/opentrons/tree/edge/api",  # noqa: E501
+            "Source Code On Github": "https://github.com/Opentrons/opentrons/tree/edge/api",
             "Documentation": "https://docs.opentrons.com",
         },
     )

api/src/opentrons/calibration_storage/modify.py

@@ -117,7 +117,7 @@ def create_tip_length_data(
         status = cal_status
     else:
         status = local_types.CalibrationStatus()
-    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]  # noqa: E501
+    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]
         status
     )
 
@@ -223,7 +223,7 @@ def save_robot_deck_attitude(
         status = cal_status
     else:
         status = local_types.CalibrationStatus()
-    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]  # noqa: E501
+    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]
         status
     )
 
@@ -268,7 +268,7 @@ def save_pipette_calibration(
         status = cal_status
     else:
         status = local_types.CalibrationStatus()
-    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]  # noqa: E501
+    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]
         status
     )
     offset_path = pip_dir / f"{pip_id}.json"
@@ -296,7 +296,7 @@ def save_gripper_calibration(
         status = cal_status
     else:
         status = local_types.CalibrationStatus()
-    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]  # noqa: E501
+    status_dict: "CalibrationStatusDict" = helpers.convert_to_dict(  # type: ignore[assignment]
         status
     )
 

api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py

@@ -1305,7 +1305,7 @@ def build_split(here: float, dest: float, split_distance: float) -> float:
             # - we have a split configuration
             and split
             # - it's been long enough since the last time it moved
-            and ((since_moved[ax] is None) or (split.after_time < since_moved[ax]))  # type: ignore[operator]  # noqa: E501
+            and ((since_moved[ax] is None) or (split.after_time < since_moved[ax]))  # type: ignore[operator]
         }
 
         split_command_string = create_coords_list(split_target)

api/src/opentrons/protocol_api/instrument_context.py

@@ -167,7 +167,7 @@ def aspirate(
             a location, specify it as a keyword argument:
             ``instr.aspirate(location=wellplate['A1'])``
 
-        """  # noqa: E501
+        """
         logger.debug(
             "aspirate {} from {} at {}".format(
                 volume, location if location else "current position", rate
@@ -282,7 +282,7 @@ def dispense(
             a location, specify it as a keyword argument:
             ``instr.dispense(location=wellplate['A1'])``
 
-        """  # noqa: E501
+        """
         logger.debug(
             "dispense {} from {} at {}".format(
                 volume, location if location else "current position", rate
@@ -1210,7 +1210,7 @@ def move_to(
                 broker=self.broker,
                 command=cmds.move_to(
                     instrument=self,
-                    location=location or self._ctx.location_cache,  # type: ignore[arg-type]  # noqa: E501
+                    location=location or self._ctx.location_cache,  # type: ignore[arg-type]
                 ),
             )
 

api/src/opentrons/protocol_api/labware.py

@@ -397,7 +397,7 @@ def wells(self, *args: Union[str, int]) -> List[Well]:
         if not args:
             res = self._implementation.get_wells()
         elif isinstance(args[0], int):
-            res = [self._implementation.get_wells()[idx] for idx in args]  # type: ignore[index]  # noqa: E501
+            res = [self._implementation.get_wells()[idx] for idx in args]  # type: ignore[index]
         elif isinstance(args[0], str):
             by_name = self._implementation.get_wells_by_name()
             res = [by_name[idx] for idx in args]  # type: ignore[index]

api/src/opentrons/protocol_engine/execution/command_executor.py

@@ -81,7 +81,7 @@ async def execute(self, command_id: str) -> None:
             log.debug(
                 f"Executing {command.id}, {command.commandType}, {command.params}"
             )
-            result = await command_impl.execute(command.params)  # type: ignore[arg-type]  # noqa: E501
+            result = await command_impl.execute(command.params)  # type: ignore[arg-type]
 
         except Exception as error:
             log.warning(f"Execution of {command.id} failed", exc_info=error)

api/src/opentrons/protocol_reader/file_reader_writer.py

@@ -63,7 +63,7 @@ async def _read_file(
 
             if filename.lower().endswith(".json"):
                 try:
-                    data = parse_raw_as(BufferedJsonFileData, contents)  # type: ignore[arg-type]  # noqa: E501
+                    data = parse_raw_as(BufferedJsonFileData, contents)  # type: ignore[arg-type]
 
                 # unlike other Pydantic functions/methods, `parse_raw_as` can
                 # raise both JSONDecodeError and ValidationError separately

api/src/opentrons/protocol_runner/legacy_command_mapper.py

@@ -44,10 +44,10 @@ class LegacyContextCommandError(ProtocolEngineError):
 _LEGACY_TO_PE_MODULE: Dict[LegacyModuleModel, pe_types.ModuleModel] = {
     LegacyMagneticModuleModel.MAGNETIC_V1: pe_types.ModuleModel.MAGNETIC_MODULE_V1,
     LegacyMagneticModuleModel.MAGNETIC_V2: pe_types.ModuleModel.MAGNETIC_MODULE_V2,
-    LegacyTemperatureModuleModel.TEMPERATURE_V1: pe_types.ModuleModel.TEMPERATURE_MODULE_V1,  # noqa: E501
-    LegacyTemperatureModuleModel.TEMPERATURE_V2: pe_types.ModuleModel.TEMPERATURE_MODULE_V2,  # noqa: E501
-    LegacyThermocyclerModuleModel.THERMOCYCLER_V1: pe_types.ModuleModel.THERMOCYCLER_MODULE_V1,  # noqa: E501
-    LegacyThermocyclerModuleModel.THERMOCYCLER_V2: pe_types.ModuleModel.THERMOCYCLER_MODULE_V2,  # noqa: E501
+    LegacyTemperatureModuleModel.TEMPERATURE_V1: pe_types.ModuleModel.TEMPERATURE_MODULE_V1,
+    LegacyTemperatureModuleModel.TEMPERATURE_V2: pe_types.ModuleModel.TEMPERATURE_MODULE_V2,
+    LegacyThermocyclerModuleModel.THERMOCYCLER_V1: pe_types.ModuleModel.THERMOCYCLER_MODULE_V1,
+    LegacyThermocyclerModuleModel.THERMOCYCLER_V2: pe_types.ModuleModel.THERMOCYCLER_MODULE_V2,
 }
 
 _HIGHER_ORDER_COMMAND_TYPES = {
@@ -203,7 +203,7 @@ def _build_initial_command(
             else:
                 raise Exception("Unknown pick_up_tip location.")
             mount = MountType(pipette.mount)
-            slot = DeckSlotName.from_primitive(well.parent.parent)  # type: ignore[arg-type] # noqa: E501
+            slot = DeckSlotName.from_primitive(well.parent.parent)  # type: ignore[arg-type]
             well_name = well.well_name
             labware_id = self._labware_id_by_slot[slot]
             pipette_id = self._pipette_id_by_mount[mount]
@@ -225,14 +225,14 @@ def _build_initial_command(
             and "instrument" in command["payload"]
             and "location" in command["payload"]
         ):
-            pipette: LegacyPipetteContext = command["payload"]["instrument"]  # type: ignore  # noqa: E501
+            pipette: LegacyPipetteContext = command["payload"]["instrument"]  # type: ignore
             location = command["payload"].get("location")
             if isinstance(location, Location):
                 well = location.labware.as_well()
             else:
                 raise Exception("Unknown drop_tip location.")
             mount = MountType(pipette.mount)
-            slot = DeckSlotName.from_primitive(well.parent.parent)  # type: ignore[arg-type] # noqa: E501
+            slot = DeckSlotName.from_primitive(well.parent.parent)  # type: ignore[arg-type]
             well_name = well.well_name
             labware_id = self._labware_id_by_slot[slot]
             pipette_id = self._pipette_id_by_mount[mount]

api/src/opentrons/protocols/api_support/instrument.py

@@ -149,4 +149,4 @@ def validate_can_dispense(location: types.Location) -> None:
 # things a `types.Location` can be (i.e. module, labware, well, etc.)
 def _is_tiprack(location: types.Location) -> bool:
     labware = location.labware.as_labware()
-    return labware.parent and labware.parent.is_tiprack  # type: ignore[return-value, union-attr]  # noqa: E501
+    return labware.parent and labware.parent.is_tiprack  # type: ignore[return-value, union-attr]

api/src/opentrons/protocols/context/protocol_api/protocol_context.py

@@ -199,7 +199,7 @@ def load_instrument(
 
         attached = {
             att_mount: instr.get("name", None)
-            for att_mount, instr in self._sync_hardware.attached_instruments.items()  # noqa: E501
+            for att_mount, instr in self._sync_hardware.attached_instruments.items()
             if instr
         }
         attached[mount] = instrument_name

api/src/opentrons/protocols/context/simulator/protocol_context.py

@@ -34,7 +34,7 @@ def load_instrument(
 
         attached = {
             att_mount: instr.get("name", None)
-            for att_mount, instr in self._sync_hardware.attached_instruments.items()  # noqa: E501
+            for att_mount, instr in self._sync_hardware.attached_instruments.items()
             if instr
         }
         attached[mount] = instrument_name

api/src/opentrons/protocols/execution/json_dispatchers.py

@@ -60,9 +60,9 @@
 }
 
 temperature_module_command_map: "JsonV4TemperatureModuleDispatch" = {
-    JsonTemperatureModuleCommand.temperatureModuleSetTargetTemperature.value: _temperature_module_set_temp,  # noqa: E501
-    JsonTemperatureModuleCommand.temperatureModuleDeactivate.value: _temperature_module_deactivate,  # noqa: E501
-    JsonTemperatureModuleCommand.temperatureModuleAwaitTemperature.value: _temperature_module_await_temp,  # noqa: E501
+    JsonTemperatureModuleCommand.temperatureModuleSetTargetTemperature.value: _temperature_module_set_temp,
+    JsonTemperatureModuleCommand.temperatureModuleDeactivate.value: _temperature_module_deactivate,
+    JsonTemperatureModuleCommand.temperatureModuleAwaitTemperature.value: _temperature_module_await_temp,
 }
 
 
@@ -73,10 +73,10 @@ def tc_do_nothing(module: ThermocyclerContext, params) -> None:
 thermocycler_module_command_map: "JsonV4ThermocyclerDispatch" = {
     JsonThermocyclerCommand.thermocyclerCloseLid.value: _thermocycler_close_lid,
     JsonThermocyclerCommand.thermocyclerOpenLid.value: _thermocycler_open_lid,
-    JsonThermocyclerCommand.thermocyclerDeactivateBlock.value: _thermocycler_deactivate_block,  # noqa: E501
-    JsonThermocyclerCommand.thermocyclerDeactivateLid.value: _thermocycler_deactivate_lid,  # noqa: E501
-    JsonThermocyclerCommand.thermocyclerSetTargetBlockTemperature.value: _thermocycler_set_block_temperature,  # noqa: E501
-    JsonThermocyclerCommand.thermocyclerSetTargetLidTemperature.value: _thermocycler_set_lid_temperature,  # noqa: E501
+    JsonThermocyclerCommand.thermocyclerDeactivateBlock.value: _thermocycler_deactivate_block,
+    JsonThermocyclerCommand.thermocyclerDeactivateLid.value: _thermocycler_deactivate_lid,
+    JsonThermocyclerCommand.thermocyclerSetTargetBlockTemperature.value: _thermocycler_set_block_temperature,
+    JsonThermocyclerCommand.thermocyclerSetTargetLidTemperature.value: _thermocycler_set_lid_temperature,
     JsonThermocyclerCommand.thermocyclerRunProfile.value: _thermocycler_run_profile,
     # NOTE: the thermocyclerAwaitX commands are expected to always
     # follow a corresponding SetX command, which is implemented as

api/src/opentrons/protocols/models/json_protocol.py

@@ -46,10 +46,10 @@
 CommandThermocyclerSetTargetLid: dev_types.ThermocyclerSetTargetLidCommandId = (
     "thermocycler/setTargetLidTemperature"
 )
-CommandThermocyclerAwaitLidTemperature: dev_types.ThermocyclerAwaitLidTemperatureCommandId = (  # noqa: E501
+CommandThermocyclerAwaitLidTemperature: dev_types.ThermocyclerAwaitLidTemperatureCommandId = (
     "thermocycler/awaitLidTemperature"
 )
-CommandThermocyclerAwaitBlockTemperature: dev_types.ThermocyclerAwaitBlockTemperatureCommandId = (  # noqa: E501
+CommandThermocyclerAwaitBlockTemperature: dev_types.ThermocyclerAwaitBlockTemperatureCommandId = (
     "thermocycler/awaitBlockTemperature"
 )
 CommandThermocyclerDeactivateBlock: dev_types.ThermocyclerDeactivateBlockCommandId = (

api/src/opentrons/protocols/types.py

@@ -78,7 +78,7 @@ def run(ctx):
 Please contact [email protected] to retrieve the previous software version and be guided
 through the downgrade process.
 
-"""  # noqa: E501
+"""
 
 
 class MalformedProtocolError(Exception):

api/src/opentrons/simulate.py

@@ -585,7 +585,7 @@ def main() -> int:
     args = parser.parse_args()
     # Try to migrate api v1 containers if needed
 
-    duration_estimator = DurationEstimator() if args.estimate_duration else None  # type: ignore[no-untyped-call]  # noqa: E501
+    duration_estimator = DurationEstimator() if args.estimate_duration else None  # type: ignore[no-untyped-call]
 
     runlog, maybe_bundle = simulate(
         args.protocol,

api/src/opentrons/system/camera.py

@@ -25,7 +25,7 @@ async def take_picture(filename: Path) -> None:
 
     if IS_OSX:
         # Purely for development on macos
-        cmd = 'ffmpeg -f avfoundation -framerate 1  -s 640x480  -i "0" -ss 0:0:1 -frames 1'  # noqa: E501
+        cmd = 'ffmpeg -f avfoundation -framerate 1  -s 640x480  -i "0" -ss 0:0:1 -frames 1'
 
     proc = await asyncio.create_subprocess_shell(
         f"{cmd} {filename}",

api/src/opentrons/util/linal.py

@@ -38,7 +38,7 @@ def solve_attitude(expected: SolvePoints, actual: SolvePoints) -> AttitudeMatrix
     mask_transform = np.array(
         [[True, True, False], [True, True, False], [False, False, False]]
     )
-    masked_array = np.ma.masked_array(t, ~mask_transform)  # type: ignore[var-annotated, no-untyped-call]  # noqa: E501
+    masked_array = np.ma.masked_array(t, ~mask_transform)  # type: ignore[var-annotated, no-untyped-call]
 
     no_z_component = np.zeros((3, 3))
     np.put(no_z_component, [8, 8], 1)

api/tests/opentrons/drivers/rpi_drivers/test_usb.py

@@ -17,7 +17,7 @@
     "/sys/bus/usb/devices/usb1/1-1/1-1.1/dev",
     "/sys/bus/usb/devices/usb1/1-1/dev",
     "/sys/bus/usb/devices/usb1/1-1/1-1.5/dev",
-    "/sys/bus/usb/devices/usb1/1-1/1-1.5/1-1.5:1.2/0003:046D:C52B.0017/hidraw/hidraw0/dev",  # noqa: E501
+    "/sys/bus/usb/devices/usb1/1-1/1-1.5/1-1.5:1.2/0003:046D:C52B.0017/hidraw/hidraw0/dev",
     "/sys/bus/usb/devices/usb1/1-1/1-1.5/1-1.5:1.2/usbmisc/hiddev0/dev",
 ]
 
@@ -57,7 +57,7 @@ def test_modify_module_list(revision: BoardRevision, usb_bus: USBBus):
     # TODO(mc, 2022-03-01): partial patching the class under test creates
     # a contaminated test subject that reduces the value of these tests
     # https://github.com/testdouble/contributing-tests/wiki/Partial-Mock
-    usb_bus._read_symlink = MagicMock(return_value="ttyACM1")  # type: ignore[assignment]  # noqa: E501
+    usb_bus._read_symlink = MagicMock(return_value="ttyACM1")  # type: ignore[assignment]
     mod_at_port_list = [
         ModuleAtPort(name="temperature module", port="dev/ot_module_temperature_module")
     ]
@@ -73,7 +73,7 @@ def test_modify_module_list(revision: BoardRevision, usb_bus: USBBus):
     # TODO(mc, 2022-03-01): figure out why this section of the test doesn't
     # work on using the OT-2R mocked port values
     if revision == BoardRevision.OG:
-        usb_bus._read_symlink = MagicMock(return_value="ttyACM2")  # type: ignore[assignment]  # noqa: E501
+        usb_bus._read_symlink = MagicMock(return_value="ttyACM2")  # type: ignore[assignment]
         mod_at_port_list = [
             ModuleAtPort(name="magnetic module", port="dev/ot_module_magnetic_module")
         ]

api/tests/opentrons/drivers/smoothie_drivers/test_connection.py

@@ -78,7 +78,7 @@ async def test_command_sender_sanitized_response(
         ["M3 R \r\n\r\n", "M3R:703130", "R:703130"],
         [
             "M369 L \r\n\r\n",
-            "M369 L \r\n\r\nL:5032304D56323032303230303432323036000000000000000000000000000000",  # noqa: E501
+            "M369 L \r\n\r\nL:5032304D56323032303230303432323036000000000000000000000000000000",
             "L:5032304D56323032303230303432323036000000000000000000000000000000",
         ],
     ],

api/tests/opentrons/hardware_control/modules/test_hc_thermocycler.py

@@ -200,7 +200,7 @@ async def test_set_temperature_fuzzy(
     # Test hold_time < _hold_time_fuzzy_seconds. Here we know
     # that wait_for_hold will be called with the direct hold
     # time rather than increments of 0.1
-    set_temperature_subject._wait_for_hold = mock.AsyncMock()  # type: ignore[assignment]  # noqa: E501
+    set_temperature_subject._wait_for_hold = mock.AsyncMock()  # type: ignore[assignment]
     await set_temperature_subject.set_temperature(40, hold_time_seconds=2)
     set_temperature_subject._wait_for_hold.assert_called_once_with(2)
     set_plate_temp_spy.assert_called_once_with(temp=40, hold_time=2, volume=None)

api/tests/opentrons/protocol_api/test_labware.py

@@ -82,7 +82,7 @@ def test_well_init() -> None:
             name="A1",
         ),
     )
-    assert well1.geometry.diameter == test_data[well_name]["diameter"]  # type: ignore[typeddict-item]  # noqa: E501
+    assert well1.geometry.diameter == test_data[well_name]["diameter"]  # type: ignore[typeddict-item]
     assert well1.geometry._length is None
     assert well1.geometry._width is None
 
@@ -101,8 +101,8 @@ def test_well_init() -> None:
         ),
     )
     assert well2.geometry.diameter is None
-    assert well2.geometry._length == test_data[well2_name]["xDimension"]  # type: ignore[typeddict-item]  # noqa: E501
-    assert well2.geometry._width == test_data[well2_name]["yDimension"]  # type: ignore[typeddict-item]  # noqa: E501
+    assert well2.geometry._length == test_data[well2_name]["xDimension"]  # type: ignore[typeddict-item]
+    assert well2.geometry._width == test_data[well2_name]["yDimension"]  # type: ignore[typeddict-item]
 
 
 def test_top() -> None: