mxcubecore 1.329.0__py3-none-any.whl → 1.331.0__py3-none-any.whl

mxcubecore/HardwareObjects/abstract/AbstractLims.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractMachineInfo.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube.
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractMotor.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractNState.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractOnlineProcessing.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractProcedure.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractResolution.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractSampleChanger.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractSampleView.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractShutter.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractSlits.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractTransmission.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractVideoDevice.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/abstract/AbstractXRFSpectrum.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.
@@ -22,8 +22,8 @@
 
 import abc
 import logging
-import os
 import time
+from pathlib import Path
 
 import gevent
 
@@ -73,29 +73,31 @@ class AbstractXRFSpectrum(HardwareObject):
 
     def start_spectrum(
         self,
-        integration_time=None,
-        data_dir=None,
-        prefix=None,
-        archive_dir=None,
-        session_id=None,
-        blsample_id=None,
-        cpos=None,
+        integration_time: float | None = None,
+        data_dir: str | None = None,
+        prefix: str | None = None,
+        archive_dir: str | None = None,
+        session_id: int | None = None,
+        blsample_id: int | None = None,
+        cpos: dict | None = None,
     ):
         """Start the procedure. Called by the queue_model.
 
         Args:
-            integration_time (float): Inregration time [s].
-            data_dir (str): Directory to save the data (full path).
-            archive_dir (str): Directory to save the archive data (full path).
-            prefix (str): File prefix
-            session_id (int): Session ID number (from ISpyB)
-            blsample_id (int): Sample ID number (from ISpyB)
+            integration_time: Inregration time [s].
+            data_dir: Directory to save the data (full path).
+            archive_dir: Directory to save the archive data (full path).
+            prefix: File prefix
+            session_id: Session ID number (from ISpyB)
+            blsample_id: Sample ID number (from ISpyB)
+            cpos: The centred position motors and their values.
         """
         self.cpos = cpos
         self.spectrum_info_dict = {"sessionId": session_id, "blSampleId": blsample_id}
         integration_time = integration_time or self.default_integration_time
         self.spectrum_info_dict["exposureTime"] = integration_time
         self.spectrum_info_dict["filename"] = ""
+
         # Create the data and the archive directory (if needed) and files
         if data_dir:
             if not self.create_directory(data_dir):
@@ -125,12 +127,16 @@ class AbstractXRFSpectrum(HardwareObject):
         )
         return True
 
-    def execute_spectrum(self, integration_time=None, filename=None):
+    def execute_spectrum(
+        self,
+        integration_time: float | None = None,
+        filename: str | None = None,
+    ):
         """Do the acquisition.
 
         Args:
-            integration_time (float): MCA integration time [s].
-            filename (str): Data file (full path).
+            integration_time: MCA integration time [s].
+            filename: Data file (full path).
         Raises:
             RuntimeError: Cannot acquire data.
         """
@@ -149,23 +155,27 @@ class AbstractXRFSpectrum(HardwareObject):
             self.update_state(self.STATES.FAULT)
 
     @abc.abstractmethod
-    def _execute_spectrum(self, integration_time=None, filename=None):
+    def _execute_spectrum(
+        self,
+        integration_time: float | None = None,
+        filename: str | None = None,
+    ) -> bool:
         """Specific XRF acquisition procedure"""
         return True
 
-    def create_directory(self, directory):
+    def create_directory(self, directory: str) -> bool:
         """Create a directory, if needed.
         Args:
-            directory (str): Directory to save the data (full path).
+            directory: Directory to save the data (full path).
         Returns:
-           (bool): Tue if directory created or already exists, False if error.
+           ``True`` if directory created or already exists, ``False`` if error.
         """
-        if not os.path.isdir(directory):
+        if not Path(directory).is_dir():
             msg = f"XRFSpectrum: directory creating {directory}"
             try:
-                if not os.path.exists(directory):
+                if not Path(directory).exists():
                     logging.getLogger("user_level_log").debug(msg)
-                    os.makedirs(directory)
+                    Path(directory).mkdir(parents=True)
                 return True
             except OSError as err:
                 msg += f": {err}"
@@ -175,7 +185,7 @@ class AbstractXRFSpectrum(HardwareObject):
                 return False
         return True
 
-    def get_filename(self, directory, prefix):
+    def get_filename(self, directory: str, prefix: str) -> str:
         """Create file template.
         Args:
             directory(str): directory name (full path)
@@ -183,19 +193,16 @@ class AbstractXRFSpectrum(HardwareObject):
             (str): File template
         """
         _pattern = f"{prefix}_{time.strftime('%d_%b_%Y')}_%02d_xrf"
-        filename_pattern = os.path.join(directory, _pattern)
-        filename = filename_pattern % 1
-        # fileprefix = _pattern % 1
+        filename = Path(directory) / (_pattern % 1)
 
         i = 2
-        while os.path.isfile(filename):
-            filename = filename_pattern % i
-            # fileprefix = _pattern % i
-            i = i + 1
+        while Path(filename).is_file():
+            filename = Path(directory) / (_pattern % i)
+            i += 1
 
-        return filename
+        return str(filename)
 
-    def spectrum_status_change(self, status_msg):
+    def spectrum_status_change(self, status_msg: str):
         """Emit the signal xrfSpectrumStatusChanged with appropriate message.
         Args:
             status_msg(str): Message to send.
@@ -224,7 +231,8 @@ class AbstractXRFSpectrum(HardwareObject):
 
     def spectrum_analyse(self):
         """Get the spectrum data. Do analysis and save fitted data.
-        The method has to be implemented as specific for each site.
+        The method has to be implemented as specific for each site, but
+        is only optional.
         """
 
     def spectrum_command_aborted(self):

mxcubecore/HardwareObjects/mockup/ActuatorMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/ApertureMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/BeamDefinerMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/BeamMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/BeamlineTestMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/BeamstopMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/CollectMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/DoorInterlockMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/EDNACharacterisationMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/EnergyMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/ExporterNStateMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube.
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/FluxMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/HarvesterMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/MotorMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/MotorMockupBis.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/OfflineProcessingMockup.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/OnlineProcessingMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/PlateManipulatorMockup.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/QtVideoMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/ScanMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/ShutterMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/SlitsMockup.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/TransmissionMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareObjects/mockup/XRFSpectrumMockup.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/HardwareRepository.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/model/queue_model_enumerables.py

@@ -1,5 +1,5 @@
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/model/queue_model_objects.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 #
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/__init__.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/advanced_connector.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/base_queue_entry.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/characterisation.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/data_collection.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/energy_scan.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/generic_workflow.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/import_helper.py

@@ -1,6 +1,6 @@
 # encoding: utf-8
 
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/optical_centring.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/sample_centring.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/xray_centering.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/xray_centering2.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.

mxcubecore/queue_entry/xrf_spectrum.py

@@ -1,4 +1,4 @@
-#  Project: MXCuBE
+#  Project name: MXCuBE
 #  https://github.com/mxcube
 #
 #  This file is part of MXCuBE software.
@@ -43,12 +43,12 @@ class XrfSpectrumQueueEntry(BaseQueueEntry):
         super().__init__(view, data_model)
         self._failed = False
 
-    def __getstate__(self):
+    def __getstate__(self) -> dict:
         d = dict(self.__dict__)
         d["xrf_spectrum_task"] = None
         return d
 
-    def __setstate__(self, d):
+    def __setstate__(self, d: dict):
         self.__dict__.update(d)
 
     def execute(self):
@@ -67,7 +67,7 @@ class XrfSpectrumQueueEntry(BaseQueueEntry):
                 archive_dir=xrf_spectrum.path_template.get_archive_directory(),
                 prefix=f"{path_template.get_prefix()}_{path_template.run_number}",
                 session_id=HWR.beamline.session.session_id,
-                blsample_id=xrf_spectrum._node_id,
+                blsample_id=xrf_spectrum.sample.lims_id,
                 cpos=xrf_spectrum.centred_position,
             )
             HWR.beamline.xrf_spectrum._ready_event.wait()
@@ -108,10 +108,10 @@ class XrfSpectrumQueueEntry(BaseQueueEntry):
         self.get_view().set_checkable(False)
         super().post_execute()
 
-    def xrf_spectrum_status_changed(self, msg):
+    def xrf_spectrum_status_changed(self, msg: str):
         """xrfSpectrumStatusChanged handler.
         Args:
-            msg (str): Message when xrfSpectrumStatusChanged emitted.
+            msg: Message when ``xrfSpectrumStatusChanged`` emitted.
         """
         logging.getLogger("user_level_log").info(msg)
 
@@ -136,5 +136,5 @@ class XrfSpectrumQueueEntry(BaseQueueEntry):
             logging.getLogger("user_level_log").error("XRF spectrum failed.")
             raise QueueExecutionException("XRF spectrum failed", self)
 
-    def get_type_str(self):
+    def get_type_str(self) -> str:
         return "XRF spectrum"