Switch to using ruff, re: python project template

.github/workflows/test-and-deploy.yml

@@ -23,8 +23,6 @@ jobs:
           auto-update-conda: true
           miniforge-version: latest
           environment-file: environment.yml
-      - name: flake8
-        run: flake8 --statistics RefRed test scripts
       - name: mypy type annotations
         run: mypy RefRed test scripts
       - name: dependencies synced

.pre-commit-config.yaml

@@ -16,15 +16,23 @@ repos:
       #  args: ['--maxkb=4096']
       - id: check-yaml
 
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.3
     hooks:
-      - id: black
-        exclude: test/data
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.1.1
-    hooks:
-    - id: flake8
-      exclude: dev-docs|docs|versioneer.py|RefRed/_version.py|create_graph.py|test/data
-      args: ['--extend-ignore=E999,F821,E402,E127']
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        exclude: |
+          dev-docs
+          docs
+          versioneer.py
+          RefRed/_version.py
+          create_graph.py
+          test/data
+      - id: ruff-format
+        exclude: |
+          dev-docs
+          docs
+          versioneer.py
+          RefRed/_version.py
+          create_graph.py
+          test/data

RefRed/__init__.py

@@ -1,9 +1,9 @@
 from ._version import get_versions
 
 # set by versioneer
-__version__ = get_versions()['version']
+__version__ = get_versions()["version"]
 del get_versions
 
-ORGANIZATION = 'neutrons'
-APPNAME = 'RefRed'
-WINDOW_TITLE = 'Liquids Reflectometer Reduction - '
+ORGANIZATION = "neutrons"
+APPNAME = "RefRed"
+WINDOW_TITLE = "Liquids Reflectometer Reduction - "

RefRed/_version.py

@@ -47,7 +47,7 @@ def get_config():
     return cfg
 
 
-class NotThisMethod(Exception):
+class NotThisMethod(Exception):  # noqa: N818
     """Exception raised if a method is not valid for the current scenario."""
 
 
@@ -192,7 +192,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
+        tags = set([r for r in refs if re.search(r"\d", r)])
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -273,7 +273,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
             pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
@@ -502,7 +502,7 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split('/'):
+        for i in cfg.versionfile_source.split("/"):
             root = os.path.dirname(root)
     except NameError:
         return {

RefRed/about_dialog.py

@@ -1,10 +1,12 @@
-from numpy.version import version as numpy_version_str
-from matplotlib import __version__ as matplotlib_version_str
-from RefRed import __version__ as RefRed_version_str
-from qtpy import QtWidgets, QT_VERSION, PYQT_VERSION
 import sys
-import mantid
+
 import lr_reduction
+import mantid
+from matplotlib import __version__ as matplotlib_version_str
+from numpy.version import version as numpy_version_str
+from qtpy import PYQT_VERSION, QT_VERSION, QtWidgets
+
+from RefRed import __version__ as refred_version_str
 
 
 class AboutDialog(object):
@@ -23,7 +25,7 @@ def display(self):
 
         message = f"""RefRed - Liquids Reflectrometry Reduction program
 
-        RefRed version {RefRed_version_str}
+        RefRed version {refred_version_str}
         Reduction version {lr_reduction.__version__}
 
         Library versions:

RefRed/autopopulatemaintable/auto_fill_widgets_handler.py

@@ -1,7 +1,8 @@
-from qtpy.QtWidgets import QApplication
-from qtpy import QtCore, QtGui
 import time
 
+from qtpy import QtCore, QtGui
+from qtpy.QtWidgets import QApplication
+
 
 class AutoFillWidgetsHandler(object):
     def __init__(self, parent=None):
@@ -14,7 +15,7 @@ def setup(self):
         self.parent.ui.progressBar_check5.setValue(0)
         self.parent.ui.progressBar_check2.setVisible(False)
         self.parent.ui.progressBar_check5.setVisible(False)
-        pixmap = QtGui.QPixmap(':/General/check_icon.png')
+        pixmap = QtGui.QPixmap(":/General/check_icon.png")
         self.parent.ui.check1.setPixmap(pixmap)
         self.parent.ui.check2.setPixmap(pixmap)
         self.parent.ui.check3.setPixmap(pixmap)
@@ -48,7 +49,7 @@ def step1(self):
         QApplication.processEvents()
 
     def error_step1(self):
-        pixmap = QtGui.QPixmap(':/General/clear_icon.png')
+        pixmap = QtGui.QPixmap(":/General/clear_icon.png")
         self.parent.ui.check1.setFixedWidth(25)
         self.parent.ui.check1.setFixedHeight(25)
         self.parent.ui.check1.setPixmap(pixmap)

RefRed/autopopulatemaintable/extract_lconfigdataset_runs.py

@@ -1,11 +1,11 @@
 class ExtractLConfigDataSetRuns(object):
-    '''This class get an array of LConfigDataSet and extract the data sets
+    """This class get an array of LConfigDataSet and extract the data sets
     and append them in a list that is returned
 
     #TODO: this doesn't need to be a class
-    '''
+    """
 
-    def __init__(self, lconfigdataset=None, data_type='data'):
+    def __init__(self, lconfigdataset=None, data_type="data"):
         self.lconfigdataset = lconfigdataset
         self.data_type = data_type
 
@@ -14,14 +14,14 @@ def list_runs(self):
 
         for _lconfig in self.lconfigdataset:
             if _lconfig is not None:
-                if self.data_type == 'data':
+                if self.data_type == "data":
                     _list_run = _lconfig.data_sets
                 else:
                     _list_run = _lconfig.norm_sets
 
-                if _list_run is not ['']:
+                if _list_run != [""]:
                     for _run in _list_run:
-                        if _run != '':
+                        if _run != "":
                             int_run = int(_run)
                             full_list_runs.append(int_run)
 

RefRed/autopopulatemaintable/populate_reduction_table_from_list_lrdata.py

@@ -10,7 +10,6 @@
 
 
 class PopulateReductionTableFromListLRData(object):
-
     list_lrdata_sorted = None
     list_wks_sorted = None
     list_runs_sorted = None
@@ -20,7 +19,6 @@ class PopulateReductionTableFromListLRData(object):
     THI_TOLERANCE = 0.015
 
     def __init__(self, parent=None, list_lrdata=None, list_wks=None, list_run=None, list_nexus=None, is_data=True):
-
         self.parent = parent
         self.list_run = list_run
         self.list_lrdata = list_lrdata

RefRed/autopopulatemaintable/reductiontable_auto_fill.py

@@ -1,25 +1,25 @@
 # import sys
 import time
-import numpy as np
 from itertools import chain
+
+import numpy as np
 from qtpy.QtWidgets import QApplication
 
-from RefRed.calculations.run_sequence_breaker import RunSequenceBreaker
+from RefRed.autopopulatemaintable.auto_fill_widgets_handler import AutoFillWidgetsHandler
 from RefRed.autopopulatemaintable.extract_lconfigdataset_runs import ExtractLConfigDataSetRuns
-from RefRed.thread.locate_run import LocateRunThread
-from RefRed.calculations.load_list_nexus import LoadListNexus
-from RefRed.calculations.sort_lrdata_list import SortLRDataList
-from RefRed.calculations.lr_data import LRData
 from RefRed.autopopulatemaintable.populate_reduction_table_from_list_lrdata import PopulateReductionTableFromListLRData
 from RefRed.calculations.check_list_run_compatibility_and_display import CheckListRunCompatibilityAndDisplay
+from RefRed.calculations.load_list_nexus import LoadListNexus
+from RefRed.calculations.lr_data import LRData
+from RefRed.calculations.run_sequence_breaker import RunSequenceBreaker
+from RefRed.calculations.sort_lrdata_list import SortLRDataList
 from RefRed.mantid_utility import MantidUtility
-from RefRed.utilities import format_to_list
-from RefRed.autopopulatemaintable.auto_fill_widgets_handler import AutoFillWidgetsHandler
 from RefRed.nexus_utilities import get_run_number
+from RefRed.thread.locate_run import LocateRunThread
+from RefRed.utilities import format_to_list
 
 
 class ReductionTableAutoFill(object):
-
     list_full_file_name = []
     list_nxs = []
     list_lrdata = []
@@ -29,14 +29,13 @@ class ReductionTableAutoFill(object):
     list_wks_sorted = []
     list_nexus_sorted = []
 
-    data_type_selected = 'data'
+    data_type_selected = "data"
     o_auto_fill_widgets_handler = None
 
-    def __init__(self, parent=None, list_of_run_from_input='', data_type_selected='data', reset_table=False):
-
+    def __init__(self, parent=None, list_of_run_from_input="", data_type_selected="data", reset_table=False):
         self.parent = parent
 
-        if data_type_selected == 'data':
+        if data_type_selected == "data":
             # add to norm box, previous loaded norm
             _str_old_runs = self.retrieve_list_norm_previously_loaded()
             if not _str_old_runs == "":
@@ -48,16 +47,16 @@ def __init__(self, parent=None, list_of_run_from_input='', data_type_selected='d
                 self.parent.ui.norm_sequence_lineEdit.setText(new_str)
 
         self.browsing_files_flag = False
-        if not (self.parent.browsed_files[data_type_selected] is None):
+        if self.parent.browsed_files[data_type_selected] is not None:
             self.browsing_files_flag = True
 
-        if list_of_run_from_input == '':
+        if list_of_run_from_input == "":
             self.sorted_list_of_runs = []
             if not self.browsing_files_flag:
                 return
 
-        if data_type_selected != 'data':
-            data_type_selected = 'norm'
+        if data_type_selected != "data":
+            data_type_selected = "norm"
         self.data_type_selected = data_type_selected
 
         self.init_variable()
@@ -85,13 +84,12 @@ def __init__(self, parent=None, list_of_run_from_input='', data_type_selected='d
         self.run()
 
     def merge_list_of_runs(self, new_runs=None):
-
         # manual entry of the runs
         self.raw_run_from_input = new_runs
         self.calculate_discrete_list_of_runs()  # step1 -> list_of_runs_from_input
 
         self.big_table_data = None
-        if (not self.reset_table) and (self.data_type_selected == 'data'):
+        if (not self.reset_table) and (self.data_type_selected == "data"):
             self.retrieve_bigtable_list_data_loaded()  # step2 -> list_of_runs_from_lconfig
 
         _full_list_of_runs = []
@@ -151,7 +149,7 @@ def loading_full_reductionTable(self):
         _list_nexus_sorted = self.list_nexus_sorted
         _list_runs_sorted = self.list_runs_sorted
         # _data_type_selected = self.data_type_selected
-        _is_working_with_data_column = True if self.data_type_selected == 'data' else False
+        _is_working_with_data_column = True if self.data_type_selected == "data" else False
 
         self.parent.ui.progressBar_check5.setMinimum(0)
         self.parent.ui.progressBar_check5.setValue(0)
@@ -275,7 +273,7 @@ def updating_reductionTable(self):
         list_runs_sorted = self.list_runs_sorted
         list_wks_sorted = self.list_wks_sorted
         list_nexus_sorted = self.list_nexus_sorted
-        is_data = True if self.data_type_selected == 'data' else False
+        is_data = True if self.data_type_selected == "data" else False
         o_pop_reduction_table = PopulateReductionTableFromListLRData(
             parent=self.parent,
             list_lrdata=list_lrdata_sorted,
@@ -297,7 +295,7 @@ def init_filename_thread_array(self, sz):
         _list_full_file_name = []
         for i in range(sz):
             _filename_thread_array.append(LocateRunThread())
-            _list_full_file_name.append('')
+            _list_full_file_name.append("")
         self.filename_thread_array = _filename_thread_array
         self.list_nxs = _list_full_file_name
 
@@ -320,7 +318,7 @@ def retrieve_list_norm_previously_loaded(self):
         if parent is None:
             return
         _big_table_data = parent.big_table_data
-        _extract_runs = ExtractLConfigDataSetRuns(_big_table_data[:, 2], data_type='norm')
+        _extract_runs = ExtractLConfigDataSetRuns(_big_table_data[:, 2], data_type="norm")
         _runs = _extract_runs.list_runs()
         _str_runs = ",".join([str(run) for run in _runs])
         return _str_runs
@@ -332,7 +330,7 @@ def remove_duplicate_runs(self):
 
     def check_minimum_requirements(self):
         _data_type_selected = self.data_type_selected
-        if _data_type_selected == 'data':
+        if _data_type_selected == "data":
             return True
 
         big_table_data = self.parent.big_table_data

RefRed/browsing_runs.py

@@ -1,10 +1,11 @@
 import os
+
 from qtpy import QtWidgets
+
 from RefRed import nexus_utilities
 
 
 class BrowsingRuns(object):
-
     list_files = None
     list_runs = None
 

RefRed/calculations/add_list_nexus.py

@@ -1,17 +1,17 @@
 from mantid.simpleapi import Plus
+
+from RefRed.calculations.check_if_same_nxs_property import CheckIfSameNxsProperty
 from RefRed.calculations.load_list_nexus import LoadListNexus
 from RefRed.calculations.load_nexus import LoadNexus
-from RefRed.calculations.check_if_same_nxs_property import CheckIfSameNxsProperty
 
 
 class AddListNexus(object):
-
     wks = None
     addition_worked = True
-    prefix = 'data'
+    prefix = "data"
 
     def __init__(
-        self, list_nexus=None, list_run=None, metadata_only=False, check_nexus_compatibility=True, prefix='data'
+        self, list_nexus=None, list_run=None, metadata_only=False, check_nexus_compatibility=True, prefix="data"
     ):
         if list_nexus is None:
             return
@@ -36,11 +36,10 @@ def __init__(
             if len(_list_wks) > 1:
                 is_same_property = False
                 if check_nexus_compatibility:
-                    check_same_property = CheckIfSameNxsProperty(list_wks=_list_wks, property_name='LambdaRequest')
+                    check_same_property = CheckIfSameNxsProperty(list_wks=_list_wks, property_name="LambdaRequest")
                     is_same_property = check_same_property.is_same_property
 
                 else:  # we force true
-
                     is_same_property = True
 
                 if is_same_property:

RefRed/calculations/check_if_same_nxs_property.py

@@ -2,9 +2,8 @@
 
 
 class CheckIfSameNxsProperty(object):
-
     is_same_property = False
-    property_name = ''
+    property_name = ""
 
     def __init__(self, list_wks=None, property_name=property_name):
         if list_wks is None: