refactor: applied isort to repo

ophyd_devices/epics/DeviceFactory.py

@@ -6,10 +6,10 @@ Created on Wed Oct 13 17:06:51 2021
 """
 
 import os
-import yaml
-from ophyd.ophydobj import OphydObject
 
+import yaml
 from devices import *
+from ophyd.ophydobj import OphydObject
 
 # ####################################################
 # Test connection to beamline devices

ophyd_devices/epics/devices/InsertionDevice.py

@@ -1,4 +1,4 @@
-from ophyd import PVPositioner, Component, EpicsSignal, EpicsSignalRO, Kind
+from ophyd import Component, EpicsSignal, EpicsSignalRO, Kind, PVPositioner
 
 
 class InsertionDevice(PVPositioner):

ophyd_devices/epics/devices/__init__.py

@@ -3,14 +3,23 @@ from ophyd import EpicsMotor, EpicsSignal, EpicsSignalRO
 from ophyd.quadem import QuadEM
 from ophyd.sim import SynAxis, SynPeriodicSignal, SynSignal
 
+from .aerotech.AerotechAutomation1 import (
+    EpicsMotorX,
+    aa1AxisDriveDataCollection,
+    aa1AxisPsoDistance,
+    aa1Controller,
+    aa1GlobalVariableBindings,
+    aa1GlobalVariables,
+    aa1Tasks,
+)
 from .delay_generator_csaxs import DelayGeneratorcSAXS
 from .eiger9m_csaxs import Eiger9McSAXS
-from .grashopper_tomcat import GrashopperTOMCAT
 
 # cSAXS
 from .epics_motor_ex import EpicsMotorEx
 from .falcon_csaxs import FalconcSAXS
 from .flomni_sample_storage import FlomniSampleStorage
+from .grashopper_tomcat import GrashopperTOMCAT
 from .InsertionDevice import InsertionDevice
 from .mcs_csaxs import MCScSAXS
 from .pilatus_csaxs import PilatuscSAXS
@@ -29,24 +38,4 @@ from .specMotors import (
     PmDetectorRotation,
     PmMonoBender,
 )
-
-from .aerotech.AerotechAutomation1 import (
-    aa1Controller,
-    aa1Tasks,
-    aa1GlobalVariables,
-    aa1GlobalVariableBindings,
-    aa1AxisPsoDistance,
-    aa1AxisDriveDataCollection,
-    EpicsMotorX,
-)
-
 from .SpmBase import SpmBase
-from .aerotech.AerotechAutomation1 import (
-    aa1Controller,
-    aa1Tasks,
-    aa1GlobalVariables,
-    aa1GlobalVariableBindings,
-    aa1AxisPsoDistance,
-    aa1AxisDriveDataCollection,
-    EpicsMotorX,
-)

ophyd_devices/epics/devices/aerotech/AerotechAutomation1.py

@@ -63,12 +63,7 @@ class EpicsMotorX(EpicsMotor):
     def _progress_update(self, value, **kwargs) -> None:
         """Progress update on the scan"""
         if (self._startPosition is None) or (self._targetPosition is None) or (not self.moving):
-            self._run_subs(
+            self._run_subs(sub_type=self.SUB_PROGRESS, value=1, max_value=1, done=1)
-                sub_type=self.SUB_PROGRESS,
-                value=1,
-                max_value=1,
-                done=1,
-            )
             return
 
         progress = np.abs(
@@ -214,12 +209,7 @@ class aa1Tasks(Device):
     def _progress_update(self, value, **kwargs) -> None:
         """Progress update on the scan"""
         value = self.progress()
-        self._run_subs(
+        self._run_subs(sub_type=self.SUB_PROGRESS, value=value, max_value=1, done=1)
-            sub_type=self.SUB_PROGRESS,
-            value=value,
-            max_value=1,
-            done=1,
-        )
 
     def _progress(self) -> None:
         """Progress update on the scan"""
@@ -1007,12 +997,7 @@ class aa1AxisPsoDistance(aa1AxisPsoBase):
         """Progress update on the scan"""
         if self.dstArrayDepleted.value:
             print("PSO array depleted")
-            self._run_subs(
+            self._run_subs(sub_type=self.SUB_PROGRESS, value=1, max_value=1, done=1)
-                sub_type=self.SUB_PROGRESS,
-                value=1,
-                max_value=1,
-                done=1,
-            )
             return
 
         progress = 1
@@ -1375,12 +1360,7 @@ class aa1AxisDriveDataCollection(Device):
     def _progress_update(self, value, **kwargs) -> None:
         """Progress update on the scan"""
         if self.state.value not in (2, "Acquiring"):
-            self._run_subs(
+            self._run_subs(sub_type=self.SUB_PROGRESS, value=1, max_value=1, done=1)
-                sub_type=self.SUB_PROGRESS,
-                value=1,
-                max_value=1,
-                done=1,
-            )
             return
 
         progress = 1

ophyd_devices/epics/devices/epics_motor_ex.py

@@ -1,4 +1,5 @@
-from ophyd import Component as Cpt, EpicsSignal, EpicsMotor
+from ophyd import Component as Cpt
+from ophyd import EpicsMotor, EpicsSignal
 
 
 class EpicsMotorEx(EpicsMotor):

ophyd_devices/epics/devices/grashopper_tomcat.py

@@ -3,20 +3,23 @@ import os
 import threading
 import time as ttime
 
+from bec_lib.logger import bec_logger
+
+# from typing import Any
+from ophyd import ADComponent as ADCpt
+from ophyd import Component as Cpt
+from ophyd import Device, EpicsSignal, EpicsSignalRO, EpicsSignalWithRBV
+
 # import numpy as np
 from ophyd.ophydobj import Kind
 
+from ophyd_devices.epics.devices.psi_detector_base import CustomDetectorMixin, PSIDetectorBase
+
 # os.environ["EPICS_CA_AUTO_ADDR_LIST"] = "No"
 # os.environ["EPICS_CA_ADDR_LIST"] = "129.129.208.143"
 
-# from typing import Any
-from ophyd import EpicsSignal, EpicsSignalRO, EpicsSignalWithRBV
-from ophyd import Device
-from ophyd import Component as Cpt, ADComponent as ADCpt
 
-from bec_lib.logger import bec_logger
 
-from ophyd_devices.epics.devices.psi_detector_base import PSIDetectorBase, CustomDetectorMixin
 
 logger = bec_logger.logger
 

ophyd_devices/epics/devices/mono_dccm.py

@@ -7,20 +7,21 @@ Created on Wed Oct 13 18:06:15 2021
 IMPORTANT: Virtual monochromator axes should be implemented already in EPICS!!!
 """
 
-import numpy as np
 from math import isclose
+
+import numpy as np
 from ophyd import (
+    Component,
+    Device,
+    EpicsMotor,
     EpicsSignal,
     EpicsSignalRO,
-    EpicsMotor,
+    Kind,
     PseudoPositioner,
     PseudoSingle,
-    Device,
-    Component,
-    Kind,
 )
 from ophyd.pseudopos import pseudo_position_argument, real_position_argument
-from ophyd.sim import SynAxis, Syn2DGauss
+from ophyd.sim import Syn2DGauss, SynAxis
 
 LN_CORR = 2e-4
 

ophyd_devices/epics/devices/sequencer_x12sa.py

@@ -1,4 +1,5 @@
-from ophyd import Component as Cpt, EpicsSignal, EpicsSignalRO, Device
+from ophyd import Component as Cpt
+from ophyd import Device, EpicsSignal, EpicsSignalRO
 
 
 class SequencerX12SA(Device):

ophyd_devices/epics/devices/slits.py

@@ -1,4 +1,4 @@
-from ophyd import Device, Component, EpicsMotor, PseudoPositioner, PseudoSingle
+from ophyd import Component, Device, EpicsMotor, PseudoPositioner, PseudoSingle
 from ophyd.pseudopos import pseudo_position_argument, real_position_argument
 
 

ophyd_devices/epics/devices/slsDetector.py

@@ -1,6 +1,5 @@
-from ophyd import EpicsSignal, EpicsSignalRO, EpicsSignalWithRBV
-from ophyd import CamBase, DetectorBase
 from ophyd import ADComponent as ADCpt
+from ophyd import CamBase, DetectorBase, EpicsSignal, EpicsSignalRO, EpicsSignalWithRBV
 from ophyd.areadetector.plugins import FileBase
 
 

ophyd_devices/epics/devices/specMotors.py

@@ -7,20 +7,21 @@ Created on Wed Oct 13 18:06:15 2021
 IMPORTANT: Virtual monochromator axes should be implemented already in EPICS!!!
 """
 
-import numpy as np
 import time
-from math import isclose, tan, atan, sqrt, sin, asin
+from math import asin, atan, isclose, sin, sqrt, tan
+
+import numpy as np
 from ophyd import (
+    Component,
+    Device,
+    EpicsMotor,
     EpicsSignal,
     EpicsSignalRO,
-    EpicsMotor,
+    Kind,
     PseudoPositioner,
     PseudoSingle,
     PVPositioner,
-    Device,
     Signal,
-    Component,
-    Kind,
 )
 from ophyd.pseudopos import pseudo_position_argument, real_position_argument
 

ophyd_devices/galil/sgalil_ophyd.py

@@ -4,13 +4,14 @@ import time
 
 import numpy as np
 from bec_lib import bec_logger
-from ophyd import Component as Cpt, DeviceStatus
+from ophyd import Component as Cpt
-from ophyd import Device, PositionerBase, Signal
+from ophyd import Device, DeviceStatus, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError, ReadOnlyError
+from prettytable import PrettyTable
+
 from ophyd_devices.utils.controller import Controller, threadlocked
 from ophyd_devices.utils.socket import SocketIO, SocketSignal, raise_if_disconnected
-from prettytable import PrettyTable
 
 logger = bec_logger.logger
 

ophyd_devices/npoint/__init__.py

@@ -1 +1 @@
-from .npoint import NPointController, NPointAxis
+from .npoint import NPointAxis, NPointController

ophyd_devices/ophyd_patch.py

@@ -1,10 +1,10 @@
 import inspect
 import threading
 import types
+from unittest.mock import Mock, patch
 
 from ophyd import status as ophyd_status_module
 from ophyd.status import StatusBase
-from unittest.mock import patch, Mock
 
 dummy_thread = Mock(spec=threading.Thread)
 

ophyd_devices/sim/__init__.py

@@ -1,12 +1,7 @@
-from .sim import (
+from .sim import SimCamera
-    SimPositioner,
+from .sim import SimFlyer
-    SimMonitor,
+from .sim import SimFlyer as SynFlyer
-    SimCamera,
+from .sim import SimMonitor, SimPositioner
-    SimFlyer,
-    SimFlyer as SynFlyer,
-)
-from .sim_xtreme import SynXtremeOtf
-
-from .sim_signals import SetableSignal, ReadOnlySignal
-
 from .sim_frameworks import SlitProxy
+from .sim_signals import ReadOnlySignal, SetableSignal
+from .sim_xtreme import SynXtremeOtf

ophyd_devices/sim/sim_data.py

@@ -1,17 +1,15 @@
 from __future__ import annotations
 
-from collections import defaultdict
-from abc import ABC, abstractmethod
-
-from prettytable import PrettyTable
-
 import enum
 import inspect
 import time as ttime
-import numpy as np
+from abc import ABC, abstractmethod
-from lmfit import models, Model
+from collections import defaultdict
 
+import numpy as np
 from bec_lib import bec_logger
+from lmfit import Model, models
+from prettytable import PrettyTable
 
 logger = bec_logger.logger
 

ophyd_devices/sim/sim_frameworks.py

@@ -1,13 +1,12 @@
-import numpy as np
-from scipy.ndimage import gaussian_filter
 from abc import ABC, abstractmethod
+from collections import defaultdict
 
 import h5py
 import hdf5plugin
+import numpy as np
+from ophyd import Kind, Staged
+from scipy.ndimage import gaussian_filter
 
-from ophyd import Staged, Kind
-
-from collections import defaultdict
 from ophyd_devices.sim.sim_data import NoiseType
 from ophyd_devices.sim.sim_signals import CustomSetableSignal
 from ophyd_devices.utils.bec_device_base import BECDeviceBase

ophyd_devices/sim/sim_signals.py

@@ -1,8 +1,8 @@
 import time
-import numpy as np
 
+import numpy as np
 from bec_lib import bec_logger
-from ophyd import Signal, Kind
+from ophyd import Kind, Signal
 from ophyd.utils import ReadOnlyError
 
 from ophyd_devices.utils.bec_device_base import BECDeviceBase

ophyd_devices/sim/sim_xtreme.py

@@ -2,7 +2,7 @@ import threading
 import time
 
 import numpy as np
-from bec_lib import messages, MessageEndpoints
+from bec_lib import MessageEndpoints, messages
 from ophyd import Component as Cpt
 from ophyd import Device, Kind, Signal
 from ophyd.flyers import FlyerInterface

ophyd_devices/sim/test.py

@@ -1,6 +1,7 @@
-import lmfit
 import inspect
 
+import lmfit
+
 
 class LmfitModelMixin:
 

ophyd_devices/smaract/__init__.py

@@ -1,2 +1,2 @@
-from .smaract_ophyd import SmaractMotor
 from .smaract_controller import SmaractController
+from .smaract_ophyd import SmaractMotor

ophyd_devices/smaract/serializer.py

@@ -3,6 +3,7 @@ import json
 from ophyd import Component as Cpt
 from ophyd import Device, PositionerBase, Signal
 from ophyd.ophydobj import OphydObject
+
 from ophyd_devices.utils.socket import SocketMock
 
 

ophyd_devices/utils/bec_device_base.py

@@ -1,4 +1,5 @@
 from typing import Protocol, runtime_checkable
+
 from ophyd import Kind
 
 

ophyd_devices/utils/dynamic_pseudo.py

@@ -2,12 +2,11 @@
 This module provides a class for creating a pseudo signal that is computed from other signals.
 """
 
-import numpy as np
-import scipy as sp
-
 from functools import reduce
 from typing import Callable
 
+import numpy as np
+import scipy as sp
 from bec_lib import bec_logger
 from ophyd import SignalRO
 from ophyd.ophydobj import Kind

tests/test_npoint_piezo.py

@@ -1,6 +1,6 @@
 import pytest
 
-from ophyd_devices.npoint import NPointController, NPointAxis
+from ophyd_devices.npoint import NPointAxis, NPointController
 
 
 class SocketMock:

tests/test_ophyd_status_obj.py

@@ -1,12 +1,12 @@
-import pytest
 import threading
 import time
-
 from unittest.mock import Mock
 
-import ophyd_devices  # ensure we are patched
+import pytest
 from ophyd.status import StatusBase, StatusTimeoutError
 
+import ophyd_devices  # ensure we are patched
+
 
 def test_ophyd_status_patch():
     cb = Mock()