Fix usage of deprecated ruamel.yaml API

Also formatted with `black`.
Also removed commented code.

mxcubecore/model/queue_model_objects.py

@@ -31,9 +31,11 @@
 
 try:
     from mxcubecore.model import crystal_symmetry
-    import ruamel.yaml as yaml
+    from ruamel.yaml import YAML
 except Exception:
-    logging.getLogger("HWR").warning("Cannot import dependenices needed for GPHL workflows - GPhL workflows might not work")
+    logging.getLogger("HWR").warning(
+        "Cannot import dependenices needed for GPHL workflows - GPhL workflows might not work"
+    )
 
 # This module is used as a self contained entity by the BES
 # workflows, so we need to make sure that this module can be
@@ -1609,7 +1611,6 @@ def get_archive_directory(self):
             logging.getLogger("HWR").debug(
                 "PathTemplate (DESY) - (to be defined) directory is %s" % self.directory
             )
-            #archive_directory = self.directory
             archive_directory = HWR.beamline.session.get_archive_directory()
         elif PathTemplate.synchrotron_name == "ALBA":
             logging.getLogger("HWR").debug(
@@ -2311,19 +2312,17 @@ def init_from_task_data(self, sample_model, params):
         """
 
         from mxcubecore.HardwareObjects.Gphl import GphlMessages
-        import ruamel.yaml as yaml
 
         if self.automation_mode == "TEST_FROM_FILE":
             fname = os.getenv("GPHL_TEST_INPUT")
             if os.path.isfile(fname):
-                with open(fname, "r") as fp0:
-                    task = yaml.load(fp0)["task"]
+                with open(fname, "r", encoding="utf-8") as fp0:
+                    task = YAML.load(fp0)["task"]
                     print(task)
                     params.update(task["parameters"])
             else:
                 print("WARNING no GPHL_TEST_INPUT found. test using default values")
 
-
         # Set attributes directly from params
         self.strategy_settings = HWR.beamline.gphl_workflow.workflow_strategies.get(
             params["strategy_name"]
@@ -2480,6 +2479,7 @@ def cell_parameters(self, value):
                 self._cell_parameters = tuple(float(x) for x in value)
             else:
                 raise ValueError("invalid value for cell_parameters: %s" % str(value))
+
     @property
     def total_strategy_length(self):
         """Total strategy length for a single repetition
@@ -2491,7 +2491,6 @@ def total_strategy_length(self):
         #
         return result
 
-
     def calc_maximum_dose(self, energy=None, exposure_time=None, image_width=None):
         """Dose at transmission=100 for given energy, exposure time and image width
 
@@ -2505,30 +2504,22 @@ def calc_maximum_dose(self, energy=None, exposure_time=None, image_width=None):
         Returns:
             float: Maximum dose in MGy
         """
-        energy = (
-            energy
-            or HWR.beamline.energy.calculate_energy(self.wavelengths[0].wavelength)
+        energy = energy or HWR.beamline.energy.calculate_energy(
+            self.wavelengths[0].wavelength
         )
         dose_rate = HWR.beamline.gphl_workflow.maximum_dose_rate(energy)
         exposure_time = exposure_time or self.exposure_time
-        image_width = image_width  or self.image_width
+        image_width = image_width or self.image_width
         total_strategy_length = self.strategy_length * len(self.wavelengths)
-        if (dose_rate and exposure_time and image_width and total_strategy_length):
-            return (dose_rate * total_strategy_length * exposure_time / image_width)
+        if dose_rate and exposure_time and image_width and total_strategy_length:
+            return dose_rate * total_strategy_length * exposure_time / image_width
         msg = (
             "WARNING: Dose could not be calculated from:\n"
             " energy:%s keV, total_strategy_length:%s deg, exposure_time:%s s, "
             "image_width:%s deg, dose_rate: %s"
         )
         raise UserWarning(
-            msg
-            % (
-                energy,
-                total_strategy_length,
-                exposure_time,
-                image_width,
-                dose_rate
-            )
+            msg % (energy, total_strategy_length, exposure_time, image_width, dose_rate)
         )
         return 0
 

pyproject.toml

@@ -240,7 +240,6 @@ force-exclude = '''
   | mxcubecore/HardwareObjects/mockup/PlateManipulatorMockup.py
   | mxcubecore/model/crystal_symmetry.py
   | mxcubecore/HardwareObjects/XSDataMXCuBEv1_4.py
-  | mxcubecore/model/queue_model_objects.py
   | mxcubecore/HardwareObjects/XSDataMXv1.py
 )
 '''