Remove trailing empty spaces with pre-commit hook

Use the `trailing-whitespace` pre-commit hook
to remove trailing empty spaces in files.
Only the following file extensions are excluded from this rule:
* `.hkli`
* `.nml`
* `.XDS`

.pre-commit-config.yaml

@@ -10,20 +10,7 @@ repos:
     rev: v5.0.0
     hooks:
       - id: trailing-whitespace
-        # Exclude files from trailing-whitespace checks until we get around fixing them.
-        # This way we can check that other files are trailing-whitespace clean in CI.
-        exclude: |
-            (?x)^(
-                mxcubecore/configuration/.*|
-                mxcubecore/HardwareObjects/(PlateManipulatorMaintenance|TangoMotor)\.py|
-                mxcubecore/HardwareObjects/DESY/P11(BackLight|Collect|DetectorCover|Shutter)\.py|
-                mxcubecore/HardwareObjects/LNLS/LNLS(Diffractometer|Energy|PilatusDet)\.py|
-                mxcubecore/HardwareObjects/LNLS/EPICS(Actuator|Motor|NState)\.py|
-                mxcubecore/HardwareObjects/LNLS/set_transmission_mnc.py|
-                mxcubecore/HardwareObjects/EMBL/EMBL(Energy|OnlineProcessing)\.py|
-                mxcubecore/HardwareObjects/mockup/MotorMockup\.py|
-                mxcubecore/HardwareObjects/SOLEIL/PX2/PX2Resolution\.py|
-            )$
+        exclude: \.(hkli|nml|XDS)$
       - id: end-of-file-fixer
         exclude: \.(hkli|nml)$
       - id: check-case-conflict

mxcubecore/HardwareObjects/DESY/P11BackLight.py

@@ -114,7 +114,7 @@ def _set_value(self, value):
             self.cmd_started = time.time()
 
     def update_light_state(self, value=None):
-        """Updates light state 
+        """Updates light state
 
         :return: light state as str
         """

mxcubecore/HardwareObjects/DESY/P11Collect.py

@@ -863,7 +863,7 @@ def get_filter_transmission(self):
 
     def xdsapp_maxwell(self):
         """Starts XDSAPP auto-processing on the Maxwell cluster."""
-        
+
         if HWR.beamline.session.get_beamtime_metadata() != None:
 
             self.log.debug("==== XDSAPP AUTOPROCESSING IS STARTED ==========")
@@ -933,7 +933,7 @@ def xdsapp_maxwell(self):
 
     def autoproc_maxwell(self):
         """Starts AutoProc auto-processing on the Maxwell cluster."""
-            
+
         if HWR.beamline.session.get_beamtime_metadata() != None:
 
             self.log.debug("==== AUTOPROC AUTOPROCESSING IS STARTED ==========")

mxcubecore/HardwareObjects/DESY/P11DetectorCover.py

@@ -167,7 +167,7 @@ def state_closed_changed(self, value):
         self.update_cover_state()
 
     def update_cover_state(self):
-        """Updates cover state 
+        """Updates cover state
 
         :return: cover state as str
         """

mxcubecore/HardwareObjects/DESY/P11Shutter.py

@@ -159,7 +159,7 @@ def do_finish_exc(self, exc=None):
         self.log.debug("### simulated finished with exception")
 
     def update_shutter_state(self, state=None):
-        """Updates shutter state 
+        """Updates shutter state
 
         :return: shutter state as str
         """

mxcubecore/HardwareObjects/EMBL/EMBLEnergy.py

@@ -288,7 +288,7 @@ def energy_position_changed(self, pos):
             pos = pos[0]
         value = pos / 1000
 
-        if self._nominal_value is None or abs(value - self._nominal_value) > 1e-3: 
+        if self._nominal_value is None or abs(value - self._nominal_value) > 1e-3:
             self.update_value(value)
 
     def energy_limits_changed(self, limits):

mxcubecore/HardwareObjects/EMBL/EMBLOnlineProcessing.py

@@ -492,7 +492,7 @@ def finish_processing(self):
            self.all_frames_dozor_is = False
            self.all_frames_batch_processed = False
            self.is_count = 0
-           self.batch_count = 0 
+           self.batch_count = 0
 
     def dozor_average_i_changed(self, average_i_value):
         if self.started:
@@ -730,7 +730,7 @@ def start_crystfel_autoproc_launchjob(self, proc_params, all_file_filename):
         acq_params = self.data_collection.acquisitions[0].acquisition_parameters
 
         sample_basename   = self.params_dict["template"].split("/")[-1].split("_%d_%0")[0]
-        # stream_filename   = sample_basename + "_crystfel_xgandalf.stream" 
+        # stream_filename   = sample_basename + "_crystfel_xgandalf.stream"
         stream_filename   = sample_basename + cell_name_tag + "_crystfel.stream"
         geom_filename     = "crystfel_detector.geom"
         cell_filename     = "crystfel_cell" + cell_name_tag + ".cell"

mxcubecore/HardwareObjects/LNLS/EPICSActuator.py

@@ -73,7 +73,7 @@ def abort(self):
         if self.__wait_actuator_task is not None:
             self.__wait_actuator_task.kill()
         self.update_state(self.STATES.READY)
-        
+
     def _set_value(self, value):
         """ Override AbstractActuator method."""
         self.set_channel_value(self.ACTUATOR_VAL, value)

mxcubecore/HardwareObjects/LNLS/EPICSMotor.py

@@ -50,7 +50,7 @@ def init(self):
         self.get_velocity()
         self.__watch_task = gevent.spawn(self._watch)
         self.update_state(self.STATES.READY)
-    
+
     def _watch(self):
         """ Watch motor current value and update it on the UI."""
         while True:
@@ -85,7 +85,7 @@ def get_limits(self):
         if self._nominal_limits in [(0, 0), (float('-inf'), float('inf'))]:
             # Treat infinite limits
             self._nominal_limits = (None, None)
-        
+
         logging.getLogger("HWR").info('Motor %s limits: %s' % (self.motor_name, self._nominal_limits))
         return self._nominal_limits
 
@@ -97,7 +97,7 @@ def get_velocity(self):
     def set_velocity(self, value):
         """Override AbstractMotor method."""
         self.__velocity = self.set_channel_value(self.MOTOR_VELO, value)
-    
+
     def done_movement(self):
         """ Return whether motor finished movement or not."""
         dmov = self.get_channel_value(self.MOTOR_DMOV)

mxcubecore/HardwareObjects/LNLS/EPICSNState.py

@@ -69,7 +69,7 @@ def valueChanged(self, value):
         self.set_value(enum_val)
         self.actuatorState = self.states.get(value, "unknown")
         self.emit("actuatorStateChanged", (self.actuatorState,))
-    
+
     def actuatorIn(self, wait=True, timeout=None):
         try:
             self.state_attr = self.moves["in"]

mxcubecore/HardwareObjects/LNLS/LNLSDiffractometer.py

@@ -358,7 +358,7 @@ def calculate_move_to_beam_pos(self, x, y):
         if y <= (- x + 1152):
             dir_goniox = 1
         else:
-            dir_goniox = -1         
+            dir_goniox = -1
         move_goniox = dir_goniox * drx_goniox
         # mm to move
         move_goniox = move_goniox / self.pixels_per_mm_x

mxcubecore/HardwareObjects/LNLS/LNLSEnergy.py

@@ -48,13 +48,13 @@ def get_value(self):
         #if abs(self._nominal_value - value) < 0.001:
         #    logging.getLogger("HWR").info("Pilatus threshold is still okay.")
         #    return value
-        
+
         threshold_ok = self.check_threshold_energy(value)
         if threshold_ok:
             self._nominal_value = value
         else:
            value = None  # Invalid energy because threshold is invalid
-        
+
         return value
 
     def check_threshold_energy(self, energy):

mxcubecore/HardwareObjects/LNLS/LNLSPilatusDet.py

@@ -192,13 +192,13 @@ def set_wavelength(self, wavelength):
         #        "Pilatus wavelength still okay."
         #    )
         #    return True
-        
+
         # As the set of Pilatus wavelength, det dist and beam xy is fast,
         # there is no need to compare the target value with the current one.
         logging.getLogger("HWR").info("Setting Pilatus wavelength...")
         self.set_channel_value(self.DET_WAVELENGTH, wavelength)
         time.sleep(0.6)
-        
+
         print('WAVELENGHT WAS SET: ' + str(wavelength))
         self.wavelength = self.get_wavelength()
         print('WAVELENGHT GOT: ' + str(self.wavelength))
@@ -277,7 +277,7 @@ def set_beam_x(self, from_user=False, beam_x=None):
         """
         Set detector beam_x and returns whether it was successful or not.
 
-        Beam X value can come from different sources. The priority (from 
+        Beam X value can come from different sources. The priority (from
         high to low) is:
         * from_user
         * beam_x argument
@@ -339,7 +339,7 @@ def set_beam_y(self, from_user=False, beam_y=None):
         """
         Set detector beam_y and returns whether it was successful or not.
 
-        Beam Y value can come from different sources. The priority (from 
+        Beam Y value can come from different sources. The priority (from
         high to low) is:
         * from_user
         * beam_y argument
@@ -380,7 +380,7 @@ def set_beam_y(self, from_user=False, beam_y=None):
             "Error while setting Pilatus beam Y. Please, check the detector."
         )
         return False
-    
+
     def get_transmission(self):
         """
         Returns:
@@ -417,7 +417,7 @@ def set_transmission(self, transmission):
             "Error while setting Pilatus transmission. Please, check the detector."
         )
         return False
-    
+
     def get_start_angle(self):
         """
         Returns:
@@ -454,7 +454,7 @@ def set_start_angle(self, start_angle):
             "Error while setting Pilatus start angle. Please, check the detector."
         )
         return False
-    
+
     def get_angle_incr(self):
         """
         Returns:

mxcubecore/HardwareObjects/LNLS/set_transmission_mnc.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
- 
+
 """Transmission control for MANACA.
    Attenuator: ABS-300-12-C-DN-DN40 Flanges.
    Foils: #1, 8 um Al;
@@ -37,7 +37,7 @@ def read_input():
 
 def get_transmission(energy, transmission):
     transmission = transmission/100
-    # Expressions (interpolation) for calculations of MU (linear attenuation coeficient [cm^-1]) for each material in function of the beam energy. 
+    # Expressions (interpolation) for calculations of MU (linear attenuation coeficient [cm^-1]) for each material in function of the beam energy.
     # The data used to obtain the expressions (curve fitting) are from  "https://physics.nist.gov/PhysRefData/FFast/html/form.html"
     # This attenuation coeficients can be verified and optimised after experimental validation at the beamline.
     MU_Al = (78657.01011 * math.exp(-energy/0.65969)) + (6406.36151 * math.exp(-energy/1.63268)) + (492.29999 * math.exp(-energy/4.42554)) + (3.2588)
@@ -47,7 +47,7 @@ def get_transmission(energy, transmission):
     MU_Zr = (11143.28458 * math.exp(-energy/5.87029)) + (102.27474)
     MU_EMPTY = 0.0
     # Foils in ABS-attenuator. The dictionary gives the foil position and material in the key (e.g. 'F1_Al', position 1 occuped by an aluminium foil),
-    # and the thickness [um] in the value. The list gives the positions and materials, similar to the dictionary, and it is used in the combination. 
+    # and the thickness [um] in the value. The list gives the positions and materials, similar to the dictionary, and it is used in the combination.
     foils_dict = {'F0_EMPTY':0, 'F1_Al':8, 'F2_Al':10, 'F3_Al':20, 'F4_Al':80, 'F5_Al':160, 'F6_Al':320, 'F7_Al':800,
                   'F8_Al':1500, 'F9_Ti':8, 'F10_Cu':10, 'F11_Au':5, 'F12_Zr':25}
 
@@ -64,18 +64,18 @@ def get_transmission(energy, transmission):
         attenuator_position = attenuator_position[0:12]
     elif energy >= 18.5:
         attenuator_position = attenuator_position[0:13]
-    
+
     foils_comb = []
     atten_coef_sum = []
-    
+
     # calculate the all possible unique combinations
     for i in range(1, len(attenuator_position)+1):
         product = itertools.combinations(attenuator_position, i)
         for item in product:
             foils_comb.append(list(item))
     # calculate the product of MU (cm^-1) * thickness (cm) for each material (MU * d)
     # and sum the products to obtain the total (final) attenuation for each possible combination.
-    # and put the results (total attenuation) in a list. 
+    # and put the results (total attenuation) in a list.
     comb_sum = []
     for item in foils_comb:
         comb_tmp = []
@@ -114,11 +114,11 @@ def get_transmission(energy, transmission):
 
 
 def set_foils(filter_combination):
-    
+
     # declare a list with available foils and a dictionary with epics PV class (FOIL ACT, FOIL IN, FOIL OUT) for each foil
     attenuator_position = ['F1_Al', 'F2_Al', 'F3_Al', 'F4_Al', 'F5_Al', 'F6_Al', 'F7_Al', 'F8_Al',
                            'F9_Ti', 'F10_Cu', 'F11_Au', 'F12_Zr']
-    
+
     foils_pv = {'F1_Al':(PV('MNC:B:RIO01:9474C:bo0'), PV('MNC:B:RIO01:9425A:bi11'), PV('MNC:B:RIO01:9425A:bi12')),
                  'F2_Al':(PV('MNC:B:RIO01:9474C:bo1'), PV('MNC:B:RIO01:9425A:bi10'), PV('MNC:B:RIO01:9425A:bi13')),
                  'F3_Al':(PV('MNC:B:RIO01:9474C:bo2'), PV('MNC:B:RIO01:9425A:bi9'), PV('MNC:B:RIO01:9425A:bi14')),
@@ -133,9 +133,9 @@ def set_foils(filter_combination):
                  'F12_Zr':(PV('MNC:B:RIO01:9474D:bo3'), PV('MNC:B:RIO01:9425A:bi0'), PV('MNC:B:RIO01:9425A:bi23'))}
 
     # setup the foils: check foil status, put the foils in the 'filter_combination' and remove the others
-    
+
     wt = 0.1
-    
+
     # the commented lines bellow works for the attenuator expected logic (0 for foil out and 1 for foil in).
     # as the current logic is inverted (1 is foil out and 0 is foil in) use the uncommented lines.
 
@@ -166,7 +166,7 @@ def set_foils(filter_combination):
             elif foils_pv[foil][1].get() == foils_pv[foil][2].get():
                 status = 1
                 break
-    
+
     return status
 
 
@@ -176,7 +176,7 @@ def main():
     transmission_setup = get_transmission(energy, transmission)
     # transmission required by the user
     user_transmission = transmission_setup[0] * 100
-    # real transmission got with calculated foil combination 
+    # real transmission got with calculated foil combination
     actual_transmission = round(transmission_setup[1] * 100, 2)
     # calculated foil combination to get the required transmission
     filter_combination = transmission_setup[2]

mxcubecore/HardwareObjects/PlateManipulatorMaintenance.py

@@ -15,7 +15,7 @@ class PlateManipulatorMaintenance(HardwareObject):
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-    
+
     def init(self):
         self._sc = self.get_object_by_role("sample_changer")
         self._scan_limits = ''
@@ -28,7 +28,7 @@ def _do_abort(self):
         :rtype: None
         """
         return self._sc._do_abort()
-    
+
     def _move_to_crystal_position(self, args):
         """
         command to move MD head to x, y crystal position
@@ -38,7 +38,7 @@ def _move_to_crystal_position(self, args):
         :rtype: None
         """
         return self._sc.move_to_crystal_position(args)
-    
+
 
     def _do_change_mode(self, args):
         self._sc._do_change_mode(args)
@@ -66,7 +66,7 @@ def _get_scan_limits(self, args):
     def _update_global_state(self):
         state_dict, cmd_state, message = self.get_global_state()
         self.emit("globalStateChanged", (state_dict, cmd_state, message))
-    
+
     def get_global_state(self):
         """
         """
@@ -90,7 +90,7 @@ def get_global_state(self):
 
         return state_dict, cmd_state, message
 
-    
+
 
     def get_cmd_info(self):
         """ return information about existing commands for this object
@@ -121,5 +121,5 @@ def send_command(self, cmdname, args=None):
         if cmdname == "setPlateBarcode":
             self.set_plate_barcode(args)
         # if cmdname == "change_mode":
-        #     self._do_change_mode(args)      
+        #     self._do_change_mode(args)
         return True

mxcubecore/HardwareObjects/SOLEIL/PX2/PX2Resolution.py

@@ -12,15 +12,15 @@ def __init__(self, name):
         super(PX2Resolution, self).__init__(name)
         self.resolution_motor = resolution()
         self.beam_center = beam_center()
-        
+
     def connect_notify(self, signal):
         if signal == "stateChanged":
             self.update_state(self.get_state())
 
     def get_value(self):
         self._nominal_value = self.resolution_motor.get_resolution()
         return self._nominal_value
-    
+
     def _set_value(self, value):
         self.resolution_motor.set_resolution(value)