From 19db8997c408c0f615d80813dd875920171991d8 Mon Sep 17 00:00:00 2001 From: fabcor Date: Fri, 18 Oct 2024 09:13:51 +0200 Subject: [PATCH] Update pre-commit hooks --- .pre-commit-config.yaml | 10 ++- deprecated/HardwareObjects/Camera.py | 1 + .../SpecMotorWSpecPositions.py | 1 + .../HardwareObjects/mockup/CameraMockup.py | 1 + .../HardwareObjects/mockup/VideoMockup.py | 1 + .../HardwareObjects/ALBA/XalocCalibration.py | 1 + mxcubecore/HardwareObjects/BlissActuator.py | 1 + mxcubecore/HardwareObjects/Camera.py | 1 + mxcubecore/HardwareObjects/CatsMaint.py | 1 + .../HardwareObjects/DESY/P11BeamStop.py | 6 +- .../HardwareObjects/DESY/P11Collimator.py | 12 +-- .../HardwareObjects/ESRF/BM14EnergyScan.py | 6 +- mxcubecore/HardwareObjects/ESRF/ESRFMD2SC3.py | 1 + mxcubecore/HardwareObjects/ESRF/ESRFSC3.py | 1 + .../HardwareObjects/ESRF/ID231EnergyScan.py | 6 +- .../HardwareObjects/ESRF/ID30BEnergyScan.py | 6 +- .../HardwareObjects/ESRF/ID30BXRFSpectrum.py | 6 +- mxcubecore/HardwareObjects/ESRF/ID30SC3.py | 1 + .../HardwareObjects/Gphl/CollectEmulator.py | 2 +- .../Gphl/GphlWorkflowConnection.py | 12 +-- .../HardwareObjects/GrobSampleChanger.py | 1 + mxcubecore/HardwareObjects/ISPyBRestClient.py | 1 + .../HardwareObjects/LimaEigerDetector.py | 1 + .../HardwareObjects/MAXIV/BIOMAXKafka.py | 1 + .../HardwareObjects/MAXIV/MaxIVSession.py | 1 + mxcubecore/HardwareObjects/MiniDiff.py | 6 +- mxcubecore/HardwareObjects/MotorWPositions.py | 2 +- mxcubecore/HardwareObjects/PyISPyBClient.py | 1 + .../HardwareObjects/QtGraphicsManager.py | 6 +- mxcubecore/HardwareObjects/QueueManager.py | 1 + .../SOLEIL/PX1/PX1EnergyScan.py | 1 + .../HardwareObjects/SOLEIL/SOLEILCatsMaint.py | 1 + mxcubecore/HardwareObjects/Session.py | 1 + .../SpecMotorWSpecPositions.py | 1 + mxcubecore/HardwareObjects/TangoLimaVideo.py | 1 + .../HardwareObjects/TangoLimaVideoLoopback.py | 1 + mxcubecore/HardwareObjects/VaporyVideo.py | 1 - mxcubecore/HardwareObjects/XRFSpectrum.py | 12 +-- .../abstract/AbstractMultiCollect.py | 78 +++++++++---------- .../abstract/AbstractOnlineProcessing.py | 20 ++--- .../abstract/AbstractXRFSpectrum.py | 6 +- .../HardwareObjects/mockup/CatsMaintMockup.py | 1 + .../mockup/EnergyScanMockup.py | 6 +- .../mockup/ISPyBRestClientMockup.py | 1 + .../mockup/MachineInfoMockup.py | 1 + .../mockup/MicrodiffZoomMockup.py | 1 + mxcubecore/HardwareObjects/sample_centring.py | 32 +++++--- mxcubecore/model/queue_model_objects.py | 6 +- mxcubecore/queue_entry/advanced_connector.py | 6 +- mxcubecore/queue_entry/base_queue_entry.py | 6 +- 50 files changed, 159 insertions(+), 122 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 322a8429fd..8a360004dd 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,12 +10,12 @@ repos: - --strict - repo: https://github.com/python-poetry/poetry - rev: 1.5.0 + rev: 1.8.0 hooks: - id: poetry-check - repo: https://github.com/myint/autoflake - rev: v1.6.0 + rev: v2.3.1 hooks: - id: autoflake name: Autoflake @@ -27,13 +27,15 @@ repos: - --ignore-pass-after-docstring - repo: https://github.com/psf/black - rev: 22.8.0 + rev: 24.8.0 # The following version (`24.10.0`) dropped support for Python 3.8. hooks: - id: black name: Black - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.3.0 + rev: v4.6.0 + # The following version (pre-commit-hooks 5.0.0) requires pre-commit 3.2.0 + # which does not support Python 3.8 (dropped in pre-commit 3.0.0). hooks: - id: trailing-whitespace # Exclude files from trailing-whitespace checks until we get around fixing them. diff --git a/deprecated/HardwareObjects/Camera.py b/deprecated/HardwareObjects/Camera.py index d062b6e277..25f1a9c4dc 100644 --- a/deprecated/HardwareObjects/Camera.py +++ b/deprecated/HardwareObjects/Camera.py @@ -15,6 +15,7 @@ --> """ + from mxcubecore import BaseHardwareObjects from mxcubecore import CommandContainer import gevent diff --git a/deprecated/HardwareObjects/SpecMotorWSpecPositions.py b/deprecated/HardwareObjects/SpecMotorWSpecPositions.py index 3614fbc868..763f510634 100644 --- a/deprecated/HardwareObjects/SpecMotorWSpecPositions.py +++ b/deprecated/HardwareObjects/SpecMotorWSpecPositions.py @@ -11,6 +11,7 @@ tolerance allowed between real motor position and defined position --> """ + import logging from mxcubecore.HardwareObjects import SpecMotor diff --git a/deprecated/HardwareObjects/mockup/CameraMockup.py b/deprecated/HardwareObjects/mockup/CameraMockup.py index fbeb17ae57..8ca6852157 100644 --- a/deprecated/HardwareObjects/mockup/CameraMockup.py +++ b/deprecated/HardwareObjects/mockup/CameraMockup.py @@ -1,5 +1,6 @@ """Class for cameras connected to framegrabbers run by Taco Device Servers """ + from mxcubecore import BaseHardwareObjects import logging import os diff --git a/deprecated/HardwareObjects/mockup/VideoMockup.py b/deprecated/HardwareObjects/mockup/VideoMockup.py index b1a3e57230..54fdb399cc 100755 --- a/deprecated/HardwareObjects/mockup/VideoMockup.py +++ b/deprecated/HardwareObjects/mockup/VideoMockup.py @@ -1,6 +1,7 @@ """ Descript. : """ + import os import time import gevent diff --git a/mxcubecore/HardwareObjects/ALBA/XalocCalibration.py b/mxcubecore/HardwareObjects/ALBA/XalocCalibration.py index 19bf3d143f..10aef0434e 100644 --- a/mxcubecore/HardwareObjects/ALBA/XalocCalibration.py +++ b/mxcubecore/HardwareObjects/ALBA/XalocCalibration.py @@ -1,6 +1,7 @@ """ Class for reading images from Falcon camera OAV """ + from mxcubecore import HardwareRepository as HWR from mxcubecore import BaseHardwareObjects diff --git a/mxcubecore/HardwareObjects/BlissActuator.py b/mxcubecore/HardwareObjects/BlissActuator.py index 0110abb54b..fcaf3a2d5d 100644 --- a/mxcubecore/HardwareObjects/BlissActuator.py +++ b/mxcubecore/HardwareObjects/BlissActuator.py @@ -7,6 +7,7 @@ """ + import logging from warnings import warn diff --git a/mxcubecore/HardwareObjects/Camera.py b/mxcubecore/HardwareObjects/Camera.py index 075e965dde..34e9ce03ef 100644 --- a/mxcubecore/HardwareObjects/Camera.py +++ b/mxcubecore/HardwareObjects/Camera.py @@ -15,6 +15,7 @@ --> """ + from mxcubecore import BaseHardwareObjects from mxcubecore import CommandContainer import gevent diff --git a/mxcubecore/HardwareObjects/CatsMaint.py b/mxcubecore/HardwareObjects/CatsMaint.py index 9d1fdc3644..fe5c19d8a3 100644 --- a/mxcubecore/HardwareObjects/CatsMaint.py +++ b/mxcubecore/HardwareObjects/CatsMaint.py @@ -11,6 +11,7 @@ Vicente Rey - add support for ISARA Model """ + import logging from mxcubecore.TaskUtils import task diff --git a/mxcubecore/HardwareObjects/DESY/P11BeamStop.py b/mxcubecore/HardwareObjects/DESY/P11BeamStop.py index 0e73c67084..24e4c9ee13 100644 --- a/mxcubecore/HardwareObjects/DESY/P11BeamStop.py +++ b/mxcubecore/HardwareObjects/DESY/P11BeamStop.py @@ -74,9 +74,9 @@ def load_deltas(self): # If a delta is not specified, fallback to a default delta value self.deltas = { - "bstopx": float(delta_bstopx) - if delta_bstopx is not None - else self.default_delta, + "bstopx": ( + float(delta_bstopx) if delta_bstopx is not None else self.default_delta + ), } # Log the deltas for each motor diff --git a/mxcubecore/HardwareObjects/DESY/P11Collimator.py b/mxcubecore/HardwareObjects/DESY/P11Collimator.py index 7bc0a676b3..7a7bcf4460 100644 --- a/mxcubecore/HardwareObjects/DESY/P11Collimator.py +++ b/mxcubecore/HardwareObjects/DESY/P11Collimator.py @@ -79,12 +79,12 @@ def load_deltas(self): # If a delta is not specified, fallback to a default delta value self.deltas = { - "collimatory": float(delta_y) - if delta_y is not None - else self.default_delta, - "collimatorz": float(delta_z) - if delta_z is not None - else self.default_delta, + "collimatory": ( + float(delta_y) if delta_y is not None else self.default_delta + ), + "collimatorz": ( + float(delta_z) if delta_z is not None else self.default_delta + ), } # Log the deltas for each motor diff --git a/mxcubecore/HardwareObjects/ESRF/BM14EnergyScan.py b/mxcubecore/HardwareObjects/ESRF/BM14EnergyScan.py index af9c0a1f83..f4320964d5 100644 --- a/mxcubecore/HardwareObjects/ESRF/BM14EnergyScan.py +++ b/mxcubecore/HardwareObjects/ESRF/BM14EnergyScan.py @@ -28,9 +28,9 @@ def choose_attenuation(self): "Cannot find appropriate attenuation" ) raise RuntimeError("Cannot find appropriate attenuation") - self.energy_scan_parameters[ - "transmissionFactor" - ] = self.transmission.get_value() + self.energy_scan_parameters["transmissionFactor"] = ( + self.transmission.get_value() + ) @task def execute_energy_scan(self, energy_scan_parameters): diff --git a/mxcubecore/HardwareObjects/ESRF/ESRFMD2SC3.py b/mxcubecore/HardwareObjects/ESRF/ESRFMD2SC3.py index 12d388bd93..6c687f7e6b 100644 --- a/mxcubecore/HardwareObjects/ESRF/ESRFMD2SC3.py +++ b/mxcubecore/HardwareObjects/ESRF/ESRFMD2SC3.py @@ -1,5 +1,6 @@ """ESRF SC3 Sample Changer Hardware Object """ + from mxcubecore.TaskUtils import task import SC3 import ESRF.ESRFSC3 as ESRFSC3 diff --git a/mxcubecore/HardwareObjects/ESRF/ESRFSC3.py b/mxcubecore/HardwareObjects/ESRF/ESRFSC3.py index fc2bd37f52..424639fc65 100644 --- a/mxcubecore/HardwareObjects/ESRF/ESRFSC3.py +++ b/mxcubecore/HardwareObjects/ESRF/ESRFSC3.py @@ -1,5 +1,6 @@ """ESRF SC3 Sample Changer Hardware Object """ + import functools import logging from mxcubecore.TaskUtils import task, cleanup, error_cleanup diff --git a/mxcubecore/HardwareObjects/ESRF/ID231EnergyScan.py b/mxcubecore/HardwareObjects/ESRF/ID231EnergyScan.py index b31ec1036a..26218e13bb 100644 --- a/mxcubecore/HardwareObjects/ESRF/ID231EnergyScan.py +++ b/mxcubecore/HardwareObjects/ESRF/ID231EnergyScan.py @@ -27,9 +27,9 @@ def set_mca_roi(self, eroi_min, eroi_max): @task def choose_attenuation(self): self.execute_command("chooseAttenuation") - self.energy_scan_parameters[ - "transmissionFactor" - ] = self.transmission.get_value() + self.energy_scan_parameters["transmissionFactor"] = ( + self.transmission.get_value() + ) @task def execute_energy_scan(self, energy_scan_parameters): diff --git a/mxcubecore/HardwareObjects/ESRF/ID30BEnergyScan.py b/mxcubecore/HardwareObjects/ESRF/ID30BEnergyScan.py index c04d788a7a..9ee711a236 100644 --- a/mxcubecore/HardwareObjects/ESRF/ID30BEnergyScan.py +++ b/mxcubecore/HardwareObjects/ESRF/ID30BEnergyScan.py @@ -45,9 +45,9 @@ def choose_attenuation(self): eroi_max = self.energy_scan_parameters["eroi_max"] self.ctrl.detcover.set_in() self.ctrl.find_max_attenuation(ctime=2, roi=[eroi_min, eroi_max]) - self.energy_scan_parameters[ - "transmissionFactor" - ] = self.transmission.get_value() + self.energy_scan_parameters["transmissionFactor"] = ( + self.transmission.get_value() + ) @task def execute_energy_scan(self, energy_scan_parameters): diff --git a/mxcubecore/HardwareObjects/ESRF/ID30BXRFSpectrum.py b/mxcubecore/HardwareObjects/ESRF/ID30BXRFSpectrum.py index b4725cd016..b956624aba 100644 --- a/mxcubecore/HardwareObjects/ESRF/ID30BXRFSpectrum.py +++ b/mxcubecore/HardwareObjects/ESRF/ID30BXRFSpectrum.py @@ -409,9 +409,9 @@ def _findAttenuation(self, ct): print(ic) if ic > min_cnt: self.ctrl_hwobj.diffractometer.msclose() - self.spectrumInfo[ - "beamTransmission" - ] = HWR.beamline.transmission.get_value() + self.spectrumInfo["beamTransmission"] = ( + HWR.beamline.transmission.get_value() + ) logging.getLogger("user_level_log").info( "Transmission used for spectra: %g" % self.spectrumInfo["beamTransmission"] diff --git a/mxcubecore/HardwareObjects/ESRF/ID30SC3.py b/mxcubecore/HardwareObjects/ESRF/ID30SC3.py index 96abc49d43..c88ccd7110 100644 --- a/mxcubecore/HardwareObjects/ESRF/ID30SC3.py +++ b/mxcubecore/HardwareObjects/ESRF/ID30SC3.py @@ -1,5 +1,6 @@ """ESRF SC3 Sample Changer Hardware Object """ + from mxcubecore.TaskUtils import task import SC3 import ESRFSC3 diff --git a/mxcubecore/HardwareObjects/Gphl/CollectEmulator.py b/mxcubecore/HardwareObjects/Gphl/CollectEmulator.py index 6e1ce9a2f8..3626b0ec00 100644 --- a/mxcubecore/HardwareObjects/Gphl/CollectEmulator.py +++ b/mxcubecore/HardwareObjects/Gphl/CollectEmulator.py @@ -229,7 +229,7 @@ def _get_simcal_input(self, data_collect_parameters, crystal_data): template = template.replace(ss0, "?" * int(ss0[1:-1])) name_template = os.path.join( text_type(data_collect_parameters["fileinfo"]["directory"]), - template + template, # data_collect_parameters['fileinfo']['template'] ) # We still use the normal name template for compressed data diff --git a/mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py b/mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py index fc12ec4e57..793568a005 100644 --- a/mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py +++ b/mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py @@ -289,9 +289,9 @@ def start_workflow(self, workflow_queue, workflow_model_obj): # Set the workflow root subdirectory parameter from the base image directory image_root = os.path.abspath(HWR.beamline.session.get_base_image_directory()) if strategy_settings["wftype"] != "transcal": - workflow_options[ - "appdir" - ] = HWR.beamline.session.get_base_process_directory() + workflow_options["appdir"] = ( + HWR.beamline.session.get_base_process_directory() + ) rootsubdir = path_template.directory[len(image_root) :] if rootsubdir.startswith(os.path.sep): rootsubdir = rootsubdir[1:] @@ -1065,9 +1065,9 @@ def _CollectionDone_to_java(self, collectionDone): ) scanIdMap = {} for item in collectionDone.scanIdMap.items(): - scanIdMap[ - jvm.java.util.UUID.fromString(conversion.text_type(item[0])) - ] = jvm.java.util.UUID.fromString(conversion.text_type(item[1])) + scanIdMap[jvm.java.util.UUID.fromString(conversion.text_type(item[0]))] = ( + jvm.java.util.UUID.fromString(conversion.text_type(item[1])) + ) return jvm.astra.messagebus.messages.information.CollectionDoneImpl( proposalId, collectionDone.status, diff --git a/mxcubecore/HardwareObjects/GrobSampleChanger.py b/mxcubecore/HardwareObjects/GrobSampleChanger.py index d91df18876..6938468f84 100644 --- a/mxcubecore/HardwareObjects/GrobSampleChanger.py +++ b/mxcubecore/HardwareObjects/GrobSampleChanger.py @@ -1,5 +1,6 @@ """Sample Changer Hardware Object """ + import logging from mxcubecore.BaseHardwareObjects import HardwareObject import gevent diff --git a/mxcubecore/HardwareObjects/ISPyBRestClient.py b/mxcubecore/HardwareObjects/ISPyBRestClient.py index 1ea47ecb29..7b2bb43075 100644 --- a/mxcubecore/HardwareObjects/ISPyBRestClient.py +++ b/mxcubecore/HardwareObjects/ISPyBRestClient.py @@ -1,6 +1,7 @@ """ A client for ISPyB Webservices. """ + import logging import json import cgi diff --git a/mxcubecore/HardwareObjects/LimaEigerDetector.py b/mxcubecore/HardwareObjects/LimaEigerDetector.py index 189e0d53f8..442e175255 100644 --- a/mxcubecore/HardwareObjects/LimaEigerDetector.py +++ b/mxcubecore/HardwareObjects/LimaEigerDetector.py @@ -1,6 +1,7 @@ """LimaEigerDetector Class Lima Tango Device Server implementation of the Dectris Eiger2 Detector. """ + import gevent import time import os diff --git a/mxcubecore/HardwareObjects/MAXIV/BIOMAXKafka.py b/mxcubecore/HardwareObjects/MAXIV/BIOMAXKafka.py index e65d9ff30e..4c410fbada 100644 --- a/mxcubecore/HardwareObjects/MAXIV/BIOMAXKafka.py +++ b/mxcubecore/HardwareObjects/MAXIV/BIOMAXKafka.py @@ -1,6 +1,7 @@ """ A client for Biomax Kafka services. """ + import logging import time import json diff --git a/mxcubecore/HardwareObjects/MAXIV/MaxIVSession.py b/mxcubecore/HardwareObjects/MAXIV/MaxIVSession.py index 2f8b9ea7eb..c6cdbed28a 100644 --- a/mxcubecore/HardwareObjects/MAXIV/MaxIVSession.py +++ b/mxcubecore/HardwareObjects/MAXIV/MaxIVSession.py @@ -3,6 +3,7 @@ Adapting from original Session.py to adapt the names of data directories """ + import os import time import socket diff --git a/mxcubecore/HardwareObjects/MiniDiff.py b/mxcubecore/HardwareObjects/MiniDiff.py index 3ae5e7fe92..1b8a553802 100644 --- a/mxcubecore/HardwareObjects/MiniDiff.py +++ b/mxcubecore/HardwareObjects/MiniDiff.py @@ -993,9 +993,9 @@ def get_positions(self): "sampx": float(self.sampleXMotor.get_value()), "sampy": float(self.sampleYMotor.get_value()), "kappa": float(self.kappaMotor.get_value()) if self.kappaMotor else None, - "kappa_phi": float(self.kappaPhiMotor.get_value()) - if self.kappaPhiMotor - else None, + "kappa_phi": ( + float(self.kappaPhiMotor.get_value()) if self.kappaPhiMotor else None + ), "zoom": float(self.zoomMotor.get_value()), } diff --git a/mxcubecore/HardwareObjects/MotorWPositions.py b/mxcubecore/HardwareObjects/MotorWPositions.py index db5bf0ce28..6a0bc3f010 100644 --- a/mxcubecore/HardwareObjects/MotorWPositions.py +++ b/mxcubecore/HardwareObjects/MotorWPositions.py @@ -97,7 +97,7 @@ def get_predefined_positions_list(self): def get_current_position_name(self, pos=None): if pos is None: pos = self.motor.get_value() - for (position_name, position) in self.predefined_positions.items(): + for position_name, position in self.predefined_positions.items(): if self.delta >= abs(pos - position): return position_name return "" diff --git a/mxcubecore/HardwareObjects/PyISPyBClient.py b/mxcubecore/HardwareObjects/PyISPyBClient.py index 954f231d11..648e71730b 100644 --- a/mxcubecore/HardwareObjects/PyISPyBClient.py +++ b/mxcubecore/HardwareObjects/PyISPyBClient.py @@ -1,6 +1,7 @@ """ A client for PyISPyB Webservices. """ + import os import json import logging diff --git a/mxcubecore/HardwareObjects/QtGraphicsManager.py b/mxcubecore/HardwareObjects/QtGraphicsManager.py index 3737fe312a..7c71c06779 100644 --- a/mxcubecore/HardwareObjects/QtGraphicsManager.py +++ b/mxcubecore/HardwareObjects/QtGraphicsManager.py @@ -976,9 +976,9 @@ def mouse_released(self, pos_x, pos_y): # self._shapes.add_shape(self.graphics_grid_draw_item.get_display_name(), # self.graphics_grid_draw_item # ) - self.shape_dict[ - self.graphics_grid_draw_item.get_display_name() - ] = self.graphics_grid_draw_item + self.shape_dict[self.graphics_grid_draw_item.get_display_name()] = ( + self.graphics_grid_draw_item + ) elif self.in_beam_define_state: self.stop_beam_define() elif self.in_select_items_state: diff --git a/mxcubecore/HardwareObjects/QueueManager.py b/mxcubecore/HardwareObjects/QueueManager.py index 368b5384b4..bf4dc51dcc 100644 --- a/mxcubecore/HardwareObjects/QueueManager.py +++ b/mxcubecore/HardwareObjects/QueueManager.py @@ -7,6 +7,7 @@ container of the queue, note the inheritance from QueueEntryContainer. See the documentation for the queue_entry module for more information. """ + import logging import gevent import traceback diff --git a/mxcubecore/HardwareObjects/SOLEIL/PX1/PX1EnergyScan.py b/mxcubecore/HardwareObjects/SOLEIL/PX1/PX1EnergyScan.py index 1617bc6a43..e1165a6770 100644 --- a/mxcubecore/HardwareObjects/SOLEIL/PX1/PX1EnergyScan.py +++ b/mxcubecore/HardwareObjects/SOLEIL/PX1/PX1EnergyScan.py @@ -10,6 +10,7 @@ This has been modified to follow the AbstractEnergyScan method """ + import logging import os import time diff --git a/mxcubecore/HardwareObjects/SOLEIL/SOLEILCatsMaint.py b/mxcubecore/HardwareObjects/SOLEIL/SOLEILCatsMaint.py index 4ada5bb2cb..39e9749cce 100644 --- a/mxcubecore/HardwareObjects/SOLEIL/SOLEILCatsMaint.py +++ b/mxcubecore/HardwareObjects/SOLEIL/SOLEILCatsMaint.py @@ -4,6 +4,7 @@ Functionality in addition to sample-transfer functionality: power control, lid control, error-recovery commands, ... """ + import logging from mxcubecore.TaskUtils import task from mxcubecore.BaseHardwareObjects import HardwareObject diff --git a/mxcubecore/HardwareObjects/Session.py b/mxcubecore/HardwareObjects/Session.py index dd80bc2d6f..4dec423be4 100644 --- a/mxcubecore/HardwareObjects/Session.py +++ b/mxcubecore/HardwareObjects/Session.py @@ -4,6 +4,7 @@ Contains information regarding the current session and methods to access and manipulate this information. """ + import os import time import socket diff --git a/mxcubecore/HardwareObjects/SpecMotorWSpecPositions.py b/mxcubecore/HardwareObjects/SpecMotorWSpecPositions.py index 3614fbc868..763f510634 100644 --- a/mxcubecore/HardwareObjects/SpecMotorWSpecPositions.py +++ b/mxcubecore/HardwareObjects/SpecMotorWSpecPositions.py @@ -11,6 +11,7 @@ tolerance allowed between real motor position and defined position --> """ + import logging from mxcubecore.HardwareObjects import SpecMotor diff --git a/mxcubecore/HardwareObjects/TangoLimaVideo.py b/mxcubecore/HardwareObjects/TangoLimaVideo.py index 15ee24c988..439212cf68 100755 --- a/mxcubecore/HardwareObjects/TangoLimaVideo.py +++ b/mxcubecore/HardwareObjects/TangoLimaVideo.py @@ -12,6 +12,7 @@ If video mode is not specified, BAYER_RG16 is used by default. """ + import logging import time import struct diff --git a/mxcubecore/HardwareObjects/TangoLimaVideoLoopback.py b/mxcubecore/HardwareObjects/TangoLimaVideoLoopback.py index 9aafc29084..583c88196c 100644 --- a/mxcubecore/HardwareObjects/TangoLimaVideoLoopback.py +++ b/mxcubecore/HardwareObjects/TangoLimaVideoLoopback.py @@ -12,6 +12,7 @@ If video mode is not specified, BAYER_RG16 is used by default. """ + import logging import v4l2 import gipc diff --git a/mxcubecore/HardwareObjects/VaporyVideo.py b/mxcubecore/HardwareObjects/VaporyVideo.py index f9787221bf..d09445d4ff 100755 --- a/mxcubecore/HardwareObjects/VaporyVideo.py +++ b/mxcubecore/HardwareObjects/VaporyVideo.py @@ -19,7 +19,6 @@ [Included Hardware Objects] """ - import time import gevent import vapory diff --git a/mxcubecore/HardwareObjects/XRFSpectrum.py b/mxcubecore/HardwareObjects/XRFSpectrum.py index de862b8fb5..046a126afb 100644 --- a/mxcubecore/HardwareObjects/XRFSpectrum.py +++ b/mxcubecore/HardwareObjects/XRFSpectrum.py @@ -226,9 +226,9 @@ def spectrumCommandFinished(self, result): mcaData = self.mca_hwobj.read_data(save_data=True) mcaCalib = self.mca_hwobj.get_calibration() mcaConfig = {} - self.spectrumInfo[ - "beamTransmission" - ] = HWR.beamline.transmission.get_value() + self.spectrumInfo["beamTransmission"] = ( + HWR.beamline.transmission.get_value() + ) self.spectrumInfo["energy"] = HWR.beamline.energy.get_value() if HWR.beamline.flux: self.spectrumInfo["flux"] = HWR.beamline.flux.get_value() @@ -404,9 +404,9 @@ def _findAttenuation(self, ct): print(ic) if ic > min_cnt: self.ctrl_hwobj.diffractometer.msclose() - self.spectrumInfo[ - "beamTransmission" - ] = HWR.beamline.transmission.get_value() + self.spectrumInfo["beamTransmission"] = ( + HWR.beamline.transmission.get_value() + ) logging.getLogger("user_level_log").info( "Transmission used for spectra: %g" % self.spectrumInfo["beamTransmission"] diff --git a/mxcubecore/HardwareObjects/abstract/AbstractMultiCollect.py b/mxcubecore/HardwareObjects/abstract/AbstractMultiCollect.py index ce2ac41c30..378fd12970 100644 --- a/mxcubecore/HardwareObjects/abstract/AbstractMultiCollect.py +++ b/mxcubecore/HardwareObjects/abstract/AbstractMultiCollect.py @@ -445,9 +445,9 @@ def do_collect(self, owner, data_collect_parameters): logging.getLogger("user_level_log").info( "Getting synchrotron filling mode" ) - data_collect_parameters[ - "synchrotronMode" - ] = self.get_machine_fill_mode() + data_collect_parameters["synchrotronMode"] = ( + self.get_machine_fill_mode() + ) data_collect_parameters["status"] = "failed" logging.getLogger("user_level_log").info("Storing data collection in LIMS") @@ -487,9 +487,9 @@ def do_collect(self, owner, data_collect_parameters): if HWR.beamline.sample_changer is not None: try: - data_collect_parameters[ - "actualSampleBarcode" - ] = HWR.beamline.sample_changer.get_loaded_sample().get_id() + data_collect_parameters["actualSampleBarcode"] = ( + HWR.beamline.sample_changer.get_loaded_sample().get_id() + ) data_collect_parameters["actualContainerBarcode"] = ( HWR.beamline.sample_changer.get_loaded_sample() .get_container() @@ -573,9 +573,9 @@ def do_collect(self, owner, data_collect_parameters): if HWR.beamline.lims: try: if self.current_lims_sample: - self.current_lims_sample[ - "lastKnownCentringPosition" - ] = positions_str + self.current_lims_sample["lastKnownCentringPosition"] = ( + positions_str + ) logging.getLogger("user_level_log").info( "Updating sample information in LIMS" ) @@ -624,9 +624,9 @@ def do_collect(self, owner, data_collect_parameters): except Exception: pass - data_collect_parameters[ - "xtalSnapshotFullPath%i" % snapshot_i - ] = full_snapshot + data_collect_parameters["xtalSnapshotFullPath%i" % snapshot_i] = ( + full_snapshot + ) snapshots.append(full_snapshot) snapshot_i += 1 @@ -642,12 +642,12 @@ def do_collect(self, owner, data_collect_parameters): "Updating data collection in LIMS" ) if "kappa" in data_collect_parameters["actualCenteringPosition"]: - data_collect_parameters["oscillation_sequence"][0][ - "kappaStart" - ] = current_diffractometer_position["kappa"] - data_collect_parameters["oscillation_sequence"][0][ - "phiStart" - ] = current_diffractometer_position["kappa_phi"] + data_collect_parameters["oscillation_sequence"][0]["kappaStart"] = ( + current_diffractometer_position["kappa"] + ) + data_collect_parameters["oscillation_sequence"][0]["phiStart"] = ( + current_diffractometer_position["kappa_phi"] + ) HWR.beamline.lims.update_data_collection(data_collect_parameters) except Exception: logging.getLogger("HWR").exception( @@ -808,18 +808,18 @@ def do_collect(self, owner, data_collect_parameters): data_collect_parameters["flux_end"] = data_collect_parameters[ "flux" ] - data_collect_parameters[ - "wavelength" - ] = HWR.beamline.energy.get_wavelength() - data_collect_parameters[ - "detectorDistance" - ] = HWR.beamline.detector.distance.get_value() - data_collect_parameters[ - "resolution" - ] = HWR.beamline.resolution.get_value() - data_collect_parameters[ - "transmission" - ] = HWR.beamline.transmission.get_value() + data_collect_parameters["wavelength"] = ( + HWR.beamline.energy.get_wavelength() + ) + data_collect_parameters["detectorDistance"] = ( + HWR.beamline.detector.distance.get_value() + ) + data_collect_parameters["resolution"] = ( + HWR.beamline.resolution.get_value() + ) + data_collect_parameters["transmission"] = ( + HWR.beamline.transmission.get_value() + ) beam_centre_x, beam_centre_y = self.get_beam_centre() data_collect_parameters["xBeam"] = beam_centre_x data_collect_parameters["yBeam"] = beam_centre_y @@ -831,9 +831,9 @@ def do_collect(self, owner, data_collect_parameters): if key in und: data_collect_parameters["undulatorGap%d" % (i)] = und[key] i += 1 - data_collect_parameters[ - "resolutionAtCorner" - ] = self.get_resolution_at_corner() + data_collect_parameters["resolutionAtCorner"] = ( + self.get_resolution_at_corner() + ) beam_size_x, beam_size_y = self.get_beam_size() data_collect_parameters["beamSizeAtSampleX"] = beam_size_x data_collect_parameters["beamSizeAtSampleY"] = beam_size_y @@ -971,9 +971,9 @@ def do_collect(self, owner, data_collect_parameters): if archive_directory: lims_image["jpegFileFullPath"] = jpeg_full_path - lims_image[ - "jpegThumbnailFileFullPath" - ] = jpeg_thumbnail_full_path + lims_image["jpegThumbnailFileFullPath"] = ( + jpeg_thumbnail_full_path + ) try: HWR.beamline.lims.store_image(lims_image) @@ -1103,9 +1103,9 @@ def loop(self, owner, data_collect_parameters_list): logging.getLogger("user_level_log").info( "Data collection failed %s" % exc_value ) - data_collect_parameters[ - "status" - ] = "Data collection failed!" # Message to be stored in LIMS + data_collect_parameters["status"] = ( + "Data collection failed!" # Message to be stored in LIMS + ) failed_msg = "Data collection failed!\n%s" % exc_value self.emit( "collectOscillationFailed", diff --git a/mxcubecore/HardwareObjects/abstract/AbstractOnlineProcessing.py b/mxcubecore/HardwareObjects/abstract/AbstractOnlineProcessing.py index 595368a034..ce061784c1 100644 --- a/mxcubecore/HardwareObjects/abstract/AbstractOnlineProcessing.py +++ b/mxcubecore/HardwareObjects/abstract/AbstractOnlineProcessing.py @@ -224,9 +224,9 @@ def prepare_processing(self): if not acq_params.num_images_per_trigger: self.params_dict["num_images_per_trigger"] = 1 else: - self.params_dict[ - "num_images_per_trigger" - ] = acq_params.num_images_per_trigger + self.params_dict["num_images_per_trigger"] = ( + acq_params.num_images_per_trigger + ) self.params_dict["status"] = "Started" self.params_dict["title"] = "%s_%d_#####.cbf (%d - %d)" % ( @@ -770,13 +770,13 @@ def align_processing_results(self, start_index, end_index): center_x = ndimage.measurements.center_of_mass( self.results_aligned["score"] )[0] - self.results_aligned[ - "center_mass" - ] = HWR.beamline.diffractometer.get_point_from_line( - centred_positions[0], - centred_positions[1], - center_x, - self.params_dict["images_num"], + self.results_aligned["center_mass"] = ( + HWR.beamline.diffractometer.get_point_from_line( + centred_positions[0], + centred_positions[1], + center_x, + self.params_dict["images_num"], + ) ) else: self.results_aligned["center_mass"] = centred_positions[0] diff --git a/mxcubecore/HardwareObjects/abstract/AbstractXRFSpectrum.py b/mxcubecore/HardwareObjects/abstract/AbstractXRFSpectrum.py index 0ceab69ad9..b8c8d99304 100644 --- a/mxcubecore/HardwareObjects/abstract/AbstractXRFSpectrum.py +++ b/mxcubecore/HardwareObjects/abstract/AbstractXRFSpectrum.py @@ -204,9 +204,9 @@ def spectrum_command_finished(self): """Actions to do if spectrum acquired.""" self.spectrum_info_dict["endTime"] = time.strftime("%Y-%m-%d %H:%M:%S") if HWR.beamline.transmission: - self.spectrum_info_dict[ - "beamTransmission" - ] = HWR.beamline.transmission.get_value() + self.spectrum_info_dict["beamTransmission"] = ( + HWR.beamline.transmission.get_value() + ) if HWR.beamline.energy: self.spectrum_info_dict["energy"] = HWR.beamline.energy.get_value() if HWR.beamline.flux: diff --git a/mxcubecore/HardwareObjects/mockup/CatsMaintMockup.py b/mxcubecore/HardwareObjects/mockup/CatsMaintMockup.py index df613409c2..f85b50439b 100644 --- a/mxcubecore/HardwareObjects/mockup/CatsMaintMockup.py +++ b/mxcubecore/HardwareObjects/mockup/CatsMaintMockup.py @@ -1,6 +1,7 @@ """ CATS maintenance mockup. """ + import logging from mxcubecore.TaskUtils import task diff --git a/mxcubecore/HardwareObjects/mockup/EnergyScanMockup.py b/mxcubecore/HardwareObjects/mockup/EnergyScanMockup.py index 2f57f60135..fadbbd6e87 100644 --- a/mxcubecore/HardwareObjects/mockup/EnergyScanMockup.py +++ b/mxcubecore/HardwareObjects/mockup/EnergyScanMockup.py @@ -198,9 +198,9 @@ def execute_energy_scan(self, energy_scan_parameters): self.energy_scan_parameters["exposureTime"] = 0.01 print(self.cpos) if HWR.beamline.transmission is not None: - self.energy_scan_parameters[ - "transmissionFactor" - ] = HWR.beamline.transmission.get_value() + self.energy_scan_parameters["transmissionFactor"] = ( + HWR.beamline.transmission.get_value() + ) else: self.energy_scan_parameters["transmissionFactor"] = None size_hor = None diff --git a/mxcubecore/HardwareObjects/mockup/ISPyBRestClientMockup.py b/mxcubecore/HardwareObjects/mockup/ISPyBRestClientMockup.py index 16d93649ce..72bb047533 100644 --- a/mxcubecore/HardwareObjects/mockup/ISPyBRestClientMockup.py +++ b/mxcubecore/HardwareObjects/mockup/ISPyBRestClientMockup.py @@ -1,6 +1,7 @@ """ A client for ISPyB Webservices. """ + from __future__ import print_function import logging from datetime import datetime diff --git a/mxcubecore/HardwareObjects/mockup/MachineInfoMockup.py b/mxcubecore/HardwareObjects/mockup/MachineInfoMockup.py index 3f019fc053..152dd89afa 100644 --- a/mxcubecore/HardwareObjects/mockup/MachineInfoMockup.py +++ b/mxcubecore/HardwareObjects/mockup/MachineInfoMockup.py @@ -31,6 +31,7 @@ values['lifetime'] values['topup_remaining'] """ + import time import gevent diff --git a/mxcubecore/HardwareObjects/mockup/MicrodiffZoomMockup.py b/mxcubecore/HardwareObjects/mockup/MicrodiffZoomMockup.py index 5e6c27274c..2333d6bdcf 100644 --- a/mxcubecore/HardwareObjects/mockup/MicrodiffZoomMockup.py +++ b/mxcubecore/HardwareObjects/mockup/MicrodiffZoomMockup.py @@ -8,6 +8,7 @@ EL6": 6} """ + from enum import Enum import gevent diff --git a/mxcubecore/HardwareObjects/sample_centring.py b/mxcubecore/HardwareObjects/sample_centring.py index 9610814deb..e900367170 100644 --- a/mxcubecore/HardwareObjects/sample_centring.py +++ b/mxcubecore/HardwareObjects/sample_centring.py @@ -356,12 +356,16 @@ def centre_plate( { sampx.motor: float(sampx.get_value() + sampx.direction * dx), sampy.motor: float(sampy.get_value() + sampy.direction * dy), - phiz.motor: float(phiz.get_value() + phiz.direction * d_vertical[0, 0]) - if phiz.__dict__.get("reference_position") is None - else phiz.reference_position, - phiy.motor: float(phiy.get_value() + phiy.direction * d_horizontal[0, 0]) - if phiy.__dict__.get("reference_position") is None - else phiy.reference_position, + phiz.motor: ( + float(phiz.get_value() + phiz.direction * d_vertical[0, 0]) + if phiz.__dict__.get("reference_position") is None + else phiz.reference_position + ), + phiy.motor: ( + float(phiy.get_value() + phiy.direction * d_horizontal[0, 0]) + if phiy.__dict__.get("reference_position") is None + else phiy.reference_position + ), } ) @@ -477,12 +481,16 @@ def center( { sampx.motor: float(sampx.get_value() + sampx.direction * dx), sampy.motor: float(sampy.get_value() + sampy.direction * dy), - phiz.motor: float(phiz.get_value() + phiz.direction * d_vertical[0, 0]) - if phiz.__dict__.get("reference_position") is None - else phiz.reference_position, - phiy.motor: float(phiy.get_value() + phiy.direction * d_horizontal[0, 0]) - if phiy.__dict__.get("reference_position") is None - else phiy.reference_position, + phiz.motor: ( + float(phiz.get_value() + phiz.direction * d_vertical[0, 0]) + if phiz.__dict__.get("reference_position") is None + else phiz.reference_position + ), + phiy.motor: ( + float(phiy.get_value() + phiy.direction * d_horizontal[0, 0]) + if phiy.__dict__.get("reference_position") is None + else phiy.reference_position + ), } ) diff --git a/mxcubecore/model/queue_model_objects.py b/mxcubecore/model/queue_model_objects.py index 359c6e283a..fac0562481 100644 --- a/mxcubecore/model/queue_model_objects.py +++ b/mxcubecore/model/queue_model_objects.py @@ -793,9 +793,9 @@ def get_online_processing_results(self): return self.online_processing_results def set_snapshot(self, snapshot): - self.acquisitions[ - 0 - ].acquisition_parameters.centred_position.snapshot_image = snapshot + self.acquisitions[0].acquisition_parameters.centred_position.snapshot_image = ( + snapshot + ) def add_processing_msg(self, time, method, status, msg): self.processing_msg_list.append((time, method, status, msg)) diff --git a/mxcubecore/queue_entry/advanced_connector.py b/mxcubecore/queue_entry/advanced_connector.py index 15255b7f58..6c8bdeb7bf 100644 --- a/mxcubecore/queue_entry/advanced_connector.py +++ b/mxcubecore/queue_entry/advanced_connector.py @@ -68,9 +68,9 @@ def execute(self): cpos_one, cpos_two, ) = HWR.beamline.sample_view.create_auto_line() - helical_model.acquisitions[ - 0 - ].acquisition_parameters.osc_start = cpos_one.phi + helical_model.acquisitions[0].acquisition_parameters.osc_start = ( + cpos_one.phi + ) helical_model.acquisitions[ 0 ].acquisition_parameters.centred_position = cpos_one diff --git a/mxcubecore/queue_entry/base_queue_entry.py b/mxcubecore/queue_entry/base_queue_entry.py index cf57e98f62..e2d2e1f720 100644 --- a/mxcubecore/queue_entry/base_queue_entry.py +++ b/mxcubecore/queue_entry/base_queue_entry.py @@ -565,9 +565,9 @@ def execute_interleaved(self, ref_num_images, interleave_num_images): acq_first_image, acq_first_image + item["collect_num_images"] - 1, ) - self.interleave_items[item["collect_index"]][ - "queue_entry" - ].in_queue = item_index < (len(self.interleave_sw_list) - 1) + self.interleave_items[item["collect_index"]]["queue_entry"].in_queue = ( + item_index < (len(self.interleave_sw_list) - 1) + ) msg = "Executing %s collection (subwedge %d:%d, " % ( method_type,