Use ruff as Python code formatter and linter

Use `ruff` to replace:

* `autoflake`
* `black`
* `flake8`
* `isort`

Also reorganize the `pre-commit` hooks in a more logical order.

.pre-commit-config.yaml

@@ -1,41 +1,10 @@
----
-
-repos:
-
-  - repo: https://github.com/adrienverge/yamllint
-    rev: v1.35.1
-    hooks:
-      - id: yamllint
-        args:
-          - --strict
+%YAML 1.2
 
-  - repo: https://github.com/python-poetry/poetry
-    rev: 2.0.1
-    hooks:
-      - id: poetry-check
+---
 
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.3.1
-    hooks:
-      - id: autoflake
-        name: Autoflake
-        args:
-          - --expand-star-imports
-          - --ignore-init-module-imports
-          - --in-place
-          - --remove-duplicate-keys
-          - --ignore-pass-after-docstring
 
-  - repo: https://github.com/pycqa/isort
-    rev: 6.0.0
-    hooks:
-      - id: isort
+repos:
 
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.1.0
-    hooks:
-      - id: black
-        name: Black
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
@@ -46,17 +15,14 @@ repos:
         exclude: |
             (?x)^(
                 mxcubecore/configuration/.*|
-                mxcubecore/HardwareObjects/(MotorsNPosition|PlateManipulator|TangoMotor)\.py|
-                mxcubecore/HardwareObjects/(PlateManipulatorMaintenance|TangoLimaMpegVideo)\.py|
-                mxcubecore/HardwareObjects/DESY/P11(EDNACharacterisation|BackLight|Shutter|Collect|DetectorCover)\.py|
-                mxcubecore/HardwareObjects/LNLS/LNLS(PilatusDet|Energy|Diffractometer)\.py|
+                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|DoorInterlock|OnlineProcessing)\.py|
-                mxcubecore/HardwareObjects/mockup/(ISPyBClient|Motor|PlateManipulator)Mockup\.py|
-                mxcubecore/HardwareObjects/abstract/(AbstractXRFSpectrum|sample_changer/Crims)\.py|
+                mxcubecore/HardwareObjects/EMBL/EMBL(Energy|OnlineProcessing)\.py|
+                mxcubecore/HardwareObjects/mockup/MotorMockup\.py|
                 mxcubecore/HardwareObjects/SOLEIL/PX2/PX2Resolution\.py|
-                mxcubecore/HardwareObjects/ESRF/ID29XRFSpectrum\.py
             )$
       - id: end-of-file-fixer
         # Exclude files from end-of-file-fixer checks until we get around fixing them.
@@ -75,6 +41,30 @@ repos:
       - id: check-symlinks
       - id: check-xml
       - id: check-yaml
-        exclude: ^.drone\.yml
       - id: mixed-line-ending
         args: ["--fix=lf"]
+
+
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        args:
+          - --strict
+
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.6
+    hooks:
+      - id: ruff
+      # TODO: args: [--fix]
+      - id: ruff-format
+
+
+  - repo: https://github.com/python-poetry/poetry
+    rev: 2.0.1
+    hooks:
+      - id: poetry-check
+
+
+...

CONTRIBUTING.md

@@ -268,15 +268,15 @@ def function_with_types_in_docstring(param1, param2):
 
   ```
 
+The Python code is to be formatted and checked for lint with
+[*ruff*](https://astral.sh/ruff).
+This repository uses [*pre-commit*](https://pre-commit.com/) hooks
+to check the code quality automatically.
+These checks are done for each pull request on GitHub.
+It is also recommended to do these checks locally by enabling the git pre-commit hooks.
+For example with a one-time command like this: `pre-commit install`.
 
 
-You can use [autopep8](https://pypi.org/project/autopep8/) and [black](https://pypi.org/project/autopep8/) to format your code:
-
-  ```bash
-  autopep8 -a -r -j 0 -i --max-line-length 88 ./
-  black --safe ./
-  ```
-
 ### Continuous integration (CI)
 
 GitHub Action are used for continues integration

deprecated/HardwareObjects/Camera.py

@@ -922,7 +922,6 @@ def getBpmState(self):
                 def setROI(self, startx, endx, starty, endy):
                     """taco"""
                     if self.is_ready():
-
                         self.getBpmValues()
                         if self.res["live"]:
                             self.set_live(False)
@@ -937,7 +936,6 @@ def setROI(self, startx, endx, starty, endy):
                 def setExposure(self, exposure):
                     """taco"""
                     if self.is_ready():
-
                         self.getBpmValues()
                         if self.res["live"]:
                             self.set_live(False)
@@ -952,7 +950,6 @@ def setExposure(self, exposure):
                 def setGain(self, gain):
                     """taco"""
                     if self.is_ready():
-
                         self.getBpmValues()
                         if self.res["live"]:
                             self.set_live(False)
@@ -967,7 +964,6 @@ def setGain(self, gain):
                 def setThreshold(self, threshold):
                     """taco"""
                     if self.is_ready():
-
                         self.getBpmValues()
                         if self.res["live"]:
                             self.set_live(False)

deprecated/HardwareObjects/NamedState.py

@@ -130,7 +130,6 @@ def get_state(self):
             return "unknown"
 
     def setState(self, statename):
-
         self.emit("hardwareStateChanged", ("STANDBY",))
         logging.getLogger().exception(
             ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..............changing state for %s to ws: %s."

mxcubecore/Command/Sardana.py

@@ -76,9 +76,7 @@
 
 
 def processSardanaEvents():
-
     while not SardanaObject._eventsQueue.empty():
-
         try:
             ev = SardanaObject._eventsQueue.get_nowait()
         except queue.Empty:
@@ -181,7 +179,6 @@ def result_callback(self, received_event):
             self.emit("macroResultUpdated", received_event.attr_value.value)
 
     def __call__(self, *args, **kwargs):
-
         self._reply_arrived_event.clear()
         self.result = None
 
@@ -348,7 +345,6 @@ def __init__(self, name, command, taurusname=None, username=None, **kwargs):
         self.device = None
 
     def init_device(self):
-
         try:
             self.device = Device(self.taurusname)
         except DevFailed as traceback:
@@ -365,7 +361,6 @@ def init_device(self):
                 raise ConnectionError
 
     def __call__(self, *args, **kwargs):
-
         self.emit("commandBeginWaitReply", (str(self.name()),))
 
         if self.device is None:
@@ -422,7 +417,6 @@ def __init__(self):
         self.init_device()
 
     def init_device(self):
-
         try:
             self.attribute = Attribute(self.model)
             #
@@ -496,7 +490,6 @@ def get_info(self):
         return self.info
 
     def update(self, event):
-
         data = event.event[2]
 
         try:

mxcubecore/Command/Tango.py

@@ -325,7 +325,6 @@ def get_info(self):
         return self.device.get_attribute_config(self.attribute_name)
 
     def update(self, value=Poller.NotInitializedValue):
-
         # start with checking if we have a numpy array, as comparing
         # numpy.ndarray to Poller.NotInitializedValue raises a ValueError exception
         if isinstance(value, numpy.ndarray):

mxcubecore/Command/Tine.py

@@ -232,7 +232,6 @@ def tineEventCallback(self, id, cc, data_list):
             """
 
     def update(self, value=None):
-
         # if self.tineName.split("/")[2] == 'ics':
         #   print '>>>>>>>>>>>>>>>>>>', self.attributeName, value, self.value, self.oldvalue
 

mxcubecore/Command/exporter/StandardClient.py

@@ -19,6 +19,7 @@
 #  along with MXCuBE. If not, see <http://www.gnu.org/licenses/>.
 
 """ProtocolError and StandardClient implementation"""
+
 import socket
 import sys
 

mxcubecore/CommandContainer.py

@@ -492,7 +492,6 @@ def add_channel(
                 )
 
         elif channel_type.lower() == "sardana":
-
             if "taurusname" not in attributes_dict:
                 try:
                     attributes_dict["taurusname"] = self.taurusname
@@ -762,7 +761,6 @@ def add_command(
                 )
 
         elif cmd_type.lower() == "sardana":
-
             doorname = None
             taurusname = None
             cmd_type = None

mxcubecore/HardwareObjects/ALBA/ALBAAutoProcessing.py

@@ -37,7 +37,6 @@ def init(self):
 
     # input files for standard collection auto processing
     def create_input_files(self, xds_dir, mosflm_dir, dc_pars):
-
         fileinfo = dc_pars["fileinfo"]
         osc_seq = dc_pars["oscillation_sequence"][0]
 

mxcubecore/HardwareObjects/ALBA/ALBABackLight.py

@@ -21,7 +21,6 @@ def __init__(self, *args):
         self.default_minimum_level = 7.0
 
     def init(self):
-
         self.backlightin_channel = self.get_channel_object("backlightin")
         self.level_channel = self.get_channel_object("light_level")
 
@@ -65,7 +64,6 @@ def state_changed(self, value):
                 self.emit("stateChanged", "off")
 
     def _current_state(self):
-
         state = None
 
         if self.actuator_status:

mxcubecore/HardwareObjects/ALBA/ALBACalibration.py

@@ -57,7 +57,6 @@ def __init__(self, name):
         super().__init__(name)
 
     def init(self):
-
         self.calibx = self.get_channel_object("calibx")
         self.caliby = self.get_channel_object("caliby")
 

mxcubecore/HardwareObjects/ALBA/ALBAClusterJob.py

@@ -20,7 +20,6 @@ def run(self, *args):
         pass
 
     def wait_done(self, wait=True):
-
         if not self.job:
             return
 
@@ -47,7 +46,6 @@ class ALBAAutoprocJob(ALBAClusterJob):
     sls_script = os.path.join(root, "edna-mx/autoproc/edna-mx.autoproc.sl")
 
     def run(self, *args):
-
         jobname = os.path.basename(os.path.dirname(edna_directory))
         self.job = XalocJob(
             "edna-autoproc", jobname, self.sls_script, input_file, edna_directory
@@ -67,11 +65,9 @@ def run(self, *args):
 
 
 class ALBAStrategyJob(ALBAClusterJob):
-
     sls_script = os.path.join(root, "edna-mx/strategy/edna-mx.strategy.sl")
 
     def run(self, *args):
-
         logging.getLogger("HWR").debug("Starting StrategyJob - ")
 
         input_file, results_file, edna_directory = args

mxcubecore/HardwareObjects/ALBA/ALBADataAnalysis.py

@@ -26,7 +26,6 @@ def init(self):
         EDNACharacterisation.init(self)
 
     def prepare_input(self, edna_input):
-
         # used for strategy calculation (characterization) using data analysis cluster
         # ALBA specific
 
@@ -119,7 +118,6 @@ def fix_path(self, path):
         return outpath
 
     def wait_done(self):
-
         logging.getLogger("HWR").debug("Polling for Job state")
         time.sleep(0.5)
         logging.getLogger("HWR").debug("Polling for Job state 2")
@@ -145,7 +143,6 @@ def wait_done(self):
         return state
 
     def get_result(self):
-
         jobstatus = self.job.status
 
         # outname = self.input_file.replace("Input", "Output")

mxcubecore/HardwareObjects/ALBA/ALBAEnergy.py

@@ -64,7 +64,6 @@ def get_wavelength_limits(self):
 
 
 def test_hwo(hwo):
-
     print("Wavelength is: ", hwo.get_wavelength())
     print("Energy limits are: ", hwo.get_limits())
     print("Wavelength limits are: ", hwo.get_wavelength_limits())

mxcubecore/HardwareObjects/ALBA/ALBAFrontLight.py

@@ -20,7 +20,6 @@ def __init__(self, *args):
         self.off_threshold = None
 
     def init(self):
-
         self.level_channel = self.get_channel_object("light_level")
         self.state_channel = self.get_channel_object("state")
         threshold = self.get_property("off_threshold")

mxcubecore/HardwareObjects/ALBA/ALBAMiniDiff.py

@@ -75,7 +75,6 @@ def __init__(self, *args):
         self.super_hwobj = None
 
     def init(self):
-
         self.calibration = self.get_object_by_role("calibration")
 
         self.centring_hwobj = self.get_object_by_role("centring")