Enforce import order with isort

.isort.cfg

@@ -0,0 +1,4 @@
+[settings]
+profile=black
+py_version=38
+force_grid_wrap=2

.pre-commit-config.yaml

@@ -48,6 +48,11 @@ repos:
           - --remove-duplicate-keys
           - --ignore-pass-after-docstring
 
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+
   - repo: https://github.com/psf/black
     rev: 22.8.0
     hooks:

mxcubeweb-server

@@ -2,6 +2,5 @@
 
 from mxcubeweb import main
 
-
 if __name__ == "__main__":
     main()

mxcubeweb/__init__.py

@@ -5,15 +5,17 @@
 # Disabling E402 (module level import not at top of file)
 # for the lines below as we are monkey patching
 import argparse  # noqa: E402
-import mock  # noqa: E402
 import os  # noqa: E402
 import sys  # noqa: E402
 import traceback  # noqa: E402
 from pathlib import Path  # noqa: E402
-from mxcubeweb.server import Server as server  # noqa: E402
+
+import mock  # noqa: E402
+from mxcubecore import HardwareRepository as HWR  # noqa: E402
+
 from mxcubeweb.app import MXCUBEApplication as mxcube  # noqa: E402
 from mxcubeweb.config import Config  # noqa: E402
-from mxcubecore import HardwareRepository as HWR  # noqa: E402
+from mxcubeweb.server import Server as server  # noqa: E402
 
 sys.modules["Qub"] = mock.Mock()
 sys.modules["Qub.CTools"] = mock.Mock()

mxcubeweb/__version__.py

@@ -6,10 +6,8 @@
     )
 except ImportError:
     # Python3.7 module backport
-    from importlib_metadata import (
-        PackageNotFoundError,
-        version,  # pyright: ignore[reportMissingImports]
-    )
+    from importlib_metadata import version  # pyright: ignore[reportMissingImports]
+    from importlib_metadata import PackageNotFoundError
 
 __version__: str
 try:

mxcubeweb/app.py

@@ -3,38 +3,37 @@
 for accessing and manipulating those.
 """
 
+import json
+import logging
 import os
 import sys
-import logging
-import traceback
-import json
 import time
-
-from pathlib import Path
+import traceback
 from logging import StreamHandler
 from logging.handlers import TimedRotatingFileHandler
+from pathlib import Path
 
+from mxcubecore import ColorFormatter
 from mxcubecore import HardwareRepository as HWR
-from mxcubecore import removeLoggingHandlers, ColorFormatter
-from mxcubecore import queue_entry
+from mxcubecore import (
+    queue_entry,
+    removeLoggingHandlers,
+)
 from mxcubecore.utils.conversion import make_table
 
-from mxcubeweb.logging_handler import MX3LoggingHandler
-from mxcubeweb.core.util.adapterutils import (
-    get_adapter_cls_from_hardware_object,
-)
 from mxcubeweb.core.adapter.adapter_base import AdapterBase
+from mxcubeweb.core.components.beamline import Beamline
+from mxcubeweb.core.components.chat import Chat
 from mxcubeweb.core.components.component_base import import_component
+from mxcubeweb.core.components.harvester import Harvester
 from mxcubeweb.core.components.lims import Lims
-from mxcubeweb.core.components.chat import Chat
+from mxcubeweb.core.components.queue import Queue
 from mxcubeweb.core.components.samplechanger import SampleChanger
-from mxcubeweb.core.components.beamline import Beamline
 from mxcubeweb.core.components.sampleview import SampleView
-from mxcubeweb.core.components.queue import Queue
 from mxcubeweb.core.components.workflow import Workflow
 from mxcubeweb.core.models.configmodels import UIComponentModel
-from mxcubeweb.core.components.harvester import Harvester
-
+from mxcubeweb.core.util.adapterutils import get_adapter_cls_from_hardware_object
+from mxcubeweb.logging_handler import MX3LoggingHandler
 
 removeLoggingHandlers()
 
@@ -88,9 +87,7 @@ def init(app):
 
         :return: None
         """
-        from mxcubeweb.core.adapter.beamline_adapter import (
-            BeamlineAdapter,
-        )
+        from mxcubeweb.core.adapter.beamline_adapter import BeamlineAdapter
 
         fname = os.path.dirname(__file__)
         HWR.add_hardware_objects_dirs([os.path.join(fname, "HardwareObjects")])

mxcubeweb/config.py

@@ -1,15 +1,18 @@
+import logging
 import os
 import sys
-import logging
-import ruamel.yaml
 
-from pydantic.v1 import BaseModel, ValidationError
+import ruamel.yaml
+from pydantic.v1 import (
+    BaseModel,
+    ValidationError,
+)
 
 from mxcubeweb.core.models.configmodels import (
-    UIPropertiesListModel,
     AppConfigModel,
     FlaskConfigModel,
     MXCUBEAppConfigModel,
+    UIPropertiesListModel,
 )
 
 

mxcubeweb/core/adapter/actuator_adapter.py

@@ -1,11 +1,10 @@
 from mxcubeweb.core.adapter.adapter_base import ActuatorAdapterBase
-from mxcubeweb.core.util.adapterutils import export
-from mxcubeweb.core.util.networkutils import RateLimited
-
 from mxcubeweb.core.models.adaptermodels import (
-    HOActuatorValueChangeModel,
     FloatValueModel,
+    HOActuatorValueChangeModel,
 )
+from mxcubeweb.core.util.adapterutils import export
+from mxcubeweb.core.util.networkutils import RateLimited
 
 
 class ActuatorAdapter(ActuatorAdapterBase):

mxcubeweb/core/adapter/adapter_base.py

@@ -1,17 +1,21 @@
 import inspect
+import logging
 import traceback
 import typing
-import logging
+from typing import Any
 
-from pydantic.v1 import ValidationError, Field, create_model
 import gevent
+from pydantic.v1 import (
+    Field,
+    ValidationError,
+    create_model,
+)
 
-from typing import Any
-
-from mxcubeweb.core.util.adapterutils import (
-    get_adapter_cls_from_hardware_object,
+from mxcubeweb.core.models.adaptermodels import (
+    HOActuatorModel,
+    HOModel,
 )
-from mxcubeweb.core.models.adaptermodels import HOModel, HOActuatorModel
+from mxcubeweb.core.util.adapterutils import get_adapter_cls_from_hardware_object
 
 
 class AdapterBase:

mxcubeweb/core/adapter/beam_adapter.py

@@ -1,9 +1,9 @@
 from mxcubeweb.core.adapter.adapter_base import ActuatorAdapterBase
-from mxcubeweb.core.util.adapterutils import export
 from mxcubeweb.core.models.adaptermodels import (
     HOBeamModel,
     HOBeamValueModel,
 )
+from mxcubeweb.core.util.adapterutils import export
 
 
 class BeamAdapter(ActuatorAdapterBase):

mxcubeweb/core/adapter/beamline_action_adapter.py

@@ -1,11 +1,10 @@
 import logging
-
 from enum import Enum
 
 from mxcubeweb.core.adapter.adapter_base import ActuatorAdapterBase
 from mxcubeweb.core.models.adaptermodels import (
-    NStateModel,
     HOActuatorValueChangeModel,
+    NStateModel,
     StrValueModel,
 )
 

mxcubeweb/core/adapter/energy_adapter.py

@@ -1,6 +1,7 @@
+from mxcubecore import HardwareRepository as HWR
+
 from mxcubeweb.core.adapter.actuator_adapter import ActuatorAdapter
 from mxcubeweb.core.adapter.wavelength_adapter import WavelengthAdapter
-from mxcubecore import HardwareRepository as HWR
 
 
 class EnergyAdapter(ActuatorAdapter):

mxcubeweb/core/adapter/motor_adapter.py

@@ -1,10 +1,9 @@
 from mxcubeweb.core.adapter.adapter_base import ActuatorAdapterBase
-from mxcubeweb.core.util.networkutils import RateLimited
-
 from mxcubeweb.core.models.adaptermodels import (
-    HOActuatorValueChangeModel,
     FloatValueModel,
+    HOActuatorValueChangeModel,
 )
+from mxcubeweb.core.util.networkutils import RateLimited
 
 
 class MotorAdapter(ActuatorAdapterBase):

mxcubeweb/core/adapter/nstate_adapter.py

@@ -1,10 +1,10 @@
-from enum import Enum
 import logging
+from enum import Enum
 
 from mxcubeweb.core.adapter.adapter_base import ActuatorAdapterBase
 from mxcubeweb.core.models.adaptermodels import (
-    NStateModel,
     HOActuatorValueChangeModel,
+    NStateModel,
     StrValueModel,
 )
 

mxcubeweb/core/adapter/wavelength_adapter.py

@@ -1,10 +1,9 @@
 from mxcubeweb.core.adapter.adapter_base import ActuatorAdapterBase
-from mxcubeweb.core.util.networkutils import RateLimited
-
 from mxcubeweb.core.models.adaptermodels import (
     FloatValueModel,
     HOActuatorValueChangeModel,
 )
+from mxcubeweb.core.util.networkutils import RateLimited
 
 
 class WavelengthAdapter(ActuatorAdapterBase):

mxcubeweb/core/components/harvester.py

@@ -1,13 +1,16 @@
 # -*- coding: utf-8 -*-
 from __future__ import annotations
+
 import logging
 
 from mxcubecore import HardwareRepository as HWR
+from mxcubecore.HardwareObjects.abstract.sample_changer import Crims
 
 from mxcubeweb.core.components.component_base import ComponentBase
-from mxcubeweb.core.components.queue import COLLECTED, UNCOLLECTED
-
-from mxcubecore.HardwareObjects.abstract.sample_changer import Crims
+from mxcubeweb.core.components.queue import (
+    COLLECTED,
+    UNCOLLECTED,
+)
 
 
 # TO CONSIDER:

mxcubeweb/core/components/lims.py

@@ -1,22 +1,20 @@
 # -*- coding: utf-8 -*-
-import sys
-import logging
 import copy
 import io
+import json
+import logging
 import math
 import re
-import json
+import sys
 
+from flask import session
+from flask_login import current_user
 from mxcubecore import HardwareRepository as HWR
 from mxcubecore.model import queue_model_objects as qmo
 
 from mxcubeweb.core.components.component_base import ComponentBase
 from mxcubeweb.core.util import fsutils
 
-from flask import session
-from flask_login import current_user
-
-
 VALID_SAMPLE_NAME_REGEXP = re.compile("^[a-zA-Z0-9:+_-]+$")
 
 

mxcubeweb/core/components/queue.py

@@ -1,27 +1,25 @@
 # -*- coding: utf-8 -*-
-import os
-import json
 import itertools
+import json
 import logging
+import os
 import re
+from functools import reduce
 
 from mock import Mock
-
 from mxcubecore import HardwareRepository as HWR
-
-from mxcubecore.model import queue_model_objects as qmo
-from mxcubecore.model import queue_model_enumerables as qme
-
 from mxcubecore import queue_entry as qe
-from mxcubecore.queue_entry.base_queue_entry import QUEUE_ENTRY_STATUS
-
 from mxcubecore.HardwareObjects.Gphl import GphlQueueEntry
+from mxcubecore.model import queue_model_enumerables as qme
+from mxcubecore.model import queue_model_objects as qmo
+from mxcubecore.queue_entry.base_queue_entry import QUEUE_ENTRY_STATUS
 
 from mxcubeweb.core.components.component_base import ComponentBase
-from mxcubeweb.core.util.convertutils import str_to_camel, str_to_snake
 from mxcubeweb.core.models.generic import SimpleNameValue
-
-from functools import reduce
+from mxcubeweb.core.util.convertutils import (
+    str_to_camel,
+    str_to_snake,
+)
 
 # Important: same constants as in constants.js
 QUEUE_PAUSED = "QueuePaused"

mxcubeweb/core/components/samplechanger.py

@@ -1,13 +1,16 @@
 # -*- coding: utf-8 -*-
 import logging
 import time
-import gevent
 
-from mxcubecore import queue_entry
+import gevent
 from mxcubecore import HardwareRepository as HWR
+from mxcubecore import queue_entry
 
 from mxcubeweb.core.components.component_base import ComponentBase
-from mxcubeweb.core.components.queue import COLLECTED, UNCOLLECTED
+from mxcubeweb.core.components.queue import (
+    COLLECTED,
+    UNCOLLECTED,
+)
 
 
 # TO CONSIDER:
@@ -414,8 +417,8 @@ def _gripper_changed(self):
 
 # Disabling C901 function is too complex (19)
 def queue_mount_sample(view, data_model, centring_done_cb, async_result):  # noqa: C901
-    from mxcubeweb.routes import signals
     from mxcubeweb.app import MXCUBEApplication as mxcube
+    from mxcubeweb.routes import signals
 
     HWR.beamline.sample_view.clear_all()
     logging.getLogger("user_level_log").info("Loading sample ...")