Lint - line length

mxcube3/__init__.py

@@ -66,7 +66,11 @@ def parse_args(argv):
         "-el",
         "--enabled-loggers",
         dest="enabled_logger_list",
-        help="Which loggers to use, default is to use all loggers ([exception_logger, hwr_logger, mx3_hwr_logger, user_logger, queue_logger])",
+        help=(
+            "Which loggers to use, default is to use all loggers"
+            " ([exception_logger, hwr_logger, mx3_hwr_logger,"
+            " user_logger, queue_logger])"
+        ),
         default=[
             "exception_logger",
             "hwr_logger",

mxcube3/app.py

@@ -20,7 +20,9 @@
 from mxcubecore.utils.conversion import make_table
 
 from mxcube3.logging_handler import MX3LoggingHandler
-from mxcube3.core.util.adapterutils import get_adapter_cls_from_hardware_object
+from mxcube3.core.util.adapterutils import (
+    get_adapter_cls_from_hardware_object,
+)
 from mxcube3.core.adapter.adapter_base import AdapterBase
 from mxcube3.core.components.component_base import import_component
 from mxcube3.core.components.lims import Lims
@@ -85,7 +87,9 @@ def init(app):
 
         :return: None
         """
-        from mxcube3.core.adapter.beamline_adapter import BeamlineAdapter
+        from mxcube3.core.adapter.beamline_adapter import (
+            BeamlineAdapter,
+        )
 
         fname = os.path.dirname(__file__)
         HWR.add_hardware_objects_dirs([os.path.join(fname, "HardwareObjects")])
@@ -256,7 +260,13 @@ def __init__(self):
 
     @staticmethod
     def init(
-        server, allow_remote, ra_timeout, log_fpath, log_level, enabled_logger_list, cfg
+        server,
+        allow_remote,
+        ra_timeout,
+        log_fpath,
+        log_level,
+        enabled_logger_list,
+        cfg,
     ):
         """
         Initializes application wide variables, sample video stream, and applies
@@ -438,16 +448,26 @@ def init_state_storage():
     def get_ui_properties():
         # Add type information to each component retrieved from the beamline adapter
         # (either via config or via mxcubecore.beamline)
-        for _item_name, item_data in MXCUBEApplication.CONFIG.app.ui_properties.items():
+        for (
+            _item_name,
+            item_data,
+        ) in MXCUBEApplication.CONFIG.app.ui_properties.items():
             for component_data in item_data.components:
                 try:
                     mxcore = MXCUBEApplication.mxcubecore
                     adapter = mxcore.get_adapter(component_data.attribute)
                     adapter_cls_name = type(adapter).__name__
                     value_type = adapter.adapter_type
                 except AttributeError:
-                    msg = f"{component_data.attribute} not accessible via Beamline object. "
-                    msg += f"Verify that beamline.{component_data.attribute} is valid and/or "
+                    msg = (
+                        f"{component_data.attribute} not accessible"
+                        " via Beamline object. "
+                    )
+                    msg += (
+                        "Verify that"
+                        f" beamline.{component_data.attribute} is"
+                        " valid and/or "
+                    )
                     msg += f"{component_data.attribute} accessible via get_role "
                     msg += "check ui.yaml configuration file. "
                     msg += "(attribute will NOT be avilable in UI)"
@@ -465,7 +485,10 @@ def get_ui_properties():
 
         return {
             key: value.dict()
-            for (key, value) in MXCUBEApplication.CONFIG.app.ui_properties.items()
+            for (
+                key,
+                value,
+            ) in MXCUBEApplication.CONFIG.app.ui_properties.items()
         }
 
     @staticmethod

mxcube3/core/adapter/adapter_base.py

@@ -8,7 +8,9 @@
 
 from typing import Any
 
-from mxcube3.core.util.adapterutils import get_adapter_cls_from_hardware_object
+from mxcube3.core.util.adapterutils import (
+    get_adapter_cls_from_hardware_object,
+)
 from mxcube3.core.models.adaptermodels import HOModel, HOActuatorModel
 
 
@@ -232,7 +234,9 @@ def attributes(self):
                     model["return"].validate({"return": value})
                 except pydantic.ValidationError:
                     logging.getLogger("MX3.HWR").exception(
-                        f"Return value of {self._name}.{attribute_name} is of wrong type"
+                        "Return value of"
+                        f" {self._name}.{attribute_name} is of wrong"
+                        " type"
                     )
                     _attributes[attribute_name] = {}
                 else:
@@ -425,7 +429,8 @@ def _dict_repr(self):
                 f"Could not get dictionary representation of {self._ho.name()}"
             )
             logging.getLogger("MX3.HWR").error(
-                f"Check status of {self._ho.name()}, object is offline, in fault or returns unexpected value !"
+                f"Check status of {self._ho.name()}, object is"
+                " offline, in fault or returns unexpected value !"
             )
 
             self._available = False

mxcube3/core/adapter/beam_adapter.py

@@ -1,6 +1,9 @@
 from mxcube3.core.adapter.adapter_base import ActuatorAdapterBase
 from mxcube3.core.util.adapterutils import export
-from mxcube3.core.models.adaptermodels import HOBeamModel, HOBeamValueModel
+from mxcube3.core.models.adaptermodels import (
+    HOBeamModel,
+    HOBeamValueModel,
+)
 
 
 class BeamAdapter(ActuatorAdapterBase):
@@ -29,7 +32,12 @@ def _get_aperture(self) -> tuple:
     def _get_value(self) -> HOBeamValueModel:
         beam_ho = self._ho
 
-        beam_info_dict = {"position": [], "shape": "", "size_x": 0, "size_y": 0}
+        beam_info_dict = {
+            "position": [],
+            "shape": "",
+            "size_x": 0,
+            "size_y": 0,
+        }
         sx, sy, shape, _label = beam_ho.get_value()
 
         if beam_ho is not None:
@@ -45,7 +53,10 @@ def _get_value(self) -> HOBeamValueModel:
         aperture_list, current_aperture = self._get_aperture()
 
         beam_info_dict.update(
-            {"apertureList": aperture_list, "currentAperture": current_aperture}
+            {
+                "apertureList": aperture_list,
+                "currentAperture": current_aperture,
+            }
         )
 
         return HOBeamValueModel(**{"value": beam_info_dict})

mxcube3/core/adapter/wavelength_adapter.py

@@ -59,8 +59,8 @@ def _get_value(self) -> FloatValueModel:
         """
         try:
             return FloatValueModel(**{"value": self._ho.get_wavelength()})
-        except (AttributeError, TypeError):
-            raise ValueError("Could not get value")
+        except (AttributeError, TypeError) as ex:
+            raise ValueError("Could not get value") from ex
 
     def state(self):
         """
@@ -87,8 +87,8 @@ def limits(self):
         """
         try:
             return self._ho.get_wavelength_limits()
-        except (AttributeError, TypeError):
-            raise ValueError("Could not get limits")
+        except (AttributeError, TypeError) as ex:
+            raise ValueError("Could not get limits") from ex
 
     def read_only(self):
         """

mxcube3/core/components/beamline.py

@@ -35,10 +35,19 @@ def init_signals(self):
                     + HWR.beamline.beamline_actions.get_annotated_commands()
                 )
                 for cmd in cmds:
-                    cmd.connect("commandBeginWaitReply", signals.beamline_action_start)
-                    cmd.connect("commandReplyArrived", signals.beamline_action_done)
+                    cmd.connect(
+                        "commandBeginWaitReply",
+                        signals.beamline_action_start,
+                    )
+                    cmd.connect(
+                        "commandReplyArrived",
+                        signals.beamline_action_done,
+                    )
                     cmd.connect("commandReady", signals.beamline_action_done)
-                    cmd.connect("commandFailed", signals.beamline_action_failed)
+                    cmd.connect(
+                        "commandFailed",
+                        signals.beamline_action_failed,
+                    )
             else:
                 logging.getLogger("MX3.HWR").error(
                     "beamline_actions hardware object is not defined"
@@ -269,18 +278,20 @@ def beamline_run_action(self, name, params):
                 try:
                     cmd.emit("commandBeginWaitReply", name)
                     logging.getLogger("user_level_log").info(
-                        "Starting %s(%s)", cmd.name(), ", ".join(map(str, params))
+                        "Starting %s(%s)",
+                        cmd.name(),
+                        ", ".join(map(str, params)),
                     )
                     cmd(*params)
-                except Exception:
+                except Exception as ex:
                     err = str(sys.exc_info()[1])
-                    raise Exception(str(err))
+                    raise Exception(str(err)) from ex
         # Annotated command
         try:
             HWR.beamline.beamline_actions.execute_command(name, params)
-        except Exception:
+        except Exception as ex:
             msg = "Action cannot run: command '%s' does not exist" % name
-            raise Exception(msg)
+            raise Exception(msg) from ex
 
     def get_beam_info(self):
         """
@@ -291,7 +302,12 @@ def get_beam_info(self):
         :rtype: dict
         """
         beam = HWR.beamline.beam
-        beam_info_dict = {"position": [], "shape": "", "size_x": 0, "size_y": 0}
+        beam_info_dict = {
+            "position": [],
+            "shape": "",
+            "size_x": 0,
+            "size_y": 0,
+        }
         sx, sy, shape, _label = beam.get_value()
 
         if beam is not None:
@@ -307,7 +323,10 @@ def get_beam_info(self):
         aperture_list, current_aperture = self.get_aperture()
 
         beam_info_dict.update(
-            {"apertureList": aperture_list, "currentAperture": current_aperture}
+            {
+                "apertureList": aperture_list,
+                "currentAperture": current_aperture,
+            }
         )
 
         return beam_info_dict

mxcube3/core/components/gphl_workflow.py

@@ -24,7 +24,11 @@ def submit_parameters(self, params):
     def test_workflow_dialog(self, wf):
         dialog = {
             "properties": {
-                "name": {"title": "Task name", "type": "string", "minLength": 2},
+                "name": {
+                    "title": "Task name",
+                    "type": "string",
+                    "minLength": 2,
+                },
                 "description": {
                     "title": "Description",
                     "type": "string",

mxcube3/core/components/lims.py

@@ -237,14 +237,18 @@ def lims_login(self, loginID, password, create_session):
                 session["proposal_list"].append(dummy)
 
             login_res["proposalList"] = session["proposal_list"]
-            login_res["status"] = {"code": "ok", "msg": "Successful login"}
+            login_res["status"] = {
+                "code": "ok",
+                "msg": "Successful login",
+            }
         else:
             try:
                 login_res = HWR.beamline.lims.login(
                     loginID, password, create_session=create_session
                 )
                 proposal = HWR.beamline.lims.get_proposal(
-                    login_res["Proposal"]["code"], login_res["Proposal"]["number"]
+                    login_res["Proposal"]["code"],
+                    login_res["Proposal"]["number"],
                 )
 
             except Exception:
@@ -430,7 +434,8 @@ def synch_with_lims(self):
                 ] + ":%02d" % int(sample_info["sampleLocation"])
             except Exception:
                 logging.getLogger("MX3.HWR").info(
-                    "[LIMS] Could not parse sample loaction from LIMS, (perhaps not set ?)"
+                    "[LIMS] Could not parse sample loaction from"
+                    " LIMS, (perhaps not set ?)"
                 )
             else:
                 sample_info["lims_location"] = lims_location