Fix ruff issues (ISISNeutronMuon#653)

Add to workflows

.github/workflows/black.yml → .github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Black
+name: Lint
 
 on:
   push:
@@ -16,11 +16,20 @@ jobs:
           options: "--check --verbose"
           src: "MDANSE/Src"
 
-  lint-mdanse-gui:
+  lint_check_ruff_gui:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: psf/black@stable
+      - uses: astral-sh/ruff-action@v3
         with:
-          options: "--check --verbose"
-          src: "MDANSE_GUI/Src"
+          src: "./MDANSE_GUI/Src"
+          args: "format --check"
+
+  lint_check_ruff_gui:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+        with:
+          src: "./MDANSE_GUI/Src"
+          args: "check"

MDANSE_GUI/Src/MDANSE_GUI/ElementsDatabaseEditor.py

@@ -146,7 +146,7 @@ def new_line_dialog(self):
         ne_dialog = InputDialog(fields=dialog_variables)
         ne_dialog.got_values.connect(self.add_new_line)
         ne_dialog.show()
-        result = ne_dialog.exec()
+        _result = ne_dialog.exec()
 
     @Slot()
     def new_column_dialog(self):
@@ -173,7 +173,7 @@ def new_column_dialog(self):
         ne_dialog = InputDialog(fields=dialog_variables)
         ne_dialog.got_values.connect(self.add_new_column)
         ne_dialog.show()
-        result = ne_dialog.exec()
+        _result = ne_dialog.exec()
 
     @Slot(dict)
     def add_new_line(self, input_variables: dict):
@@ -182,7 +182,7 @@ def add_new_line(self, input_variables: dict):
             new_label = input_variables["atom_name"]
         except KeyError:
             return None
-        if not new_label in self.database.atoms:
+        if new_label not in self.database.atoms:
             self.database.add_atom(new_label)
             row = []
             for key in self.all_column_names:
@@ -209,7 +209,7 @@ def add_new_column(self, input_variables: dict):
             new_type = input_variables["property_type"]
         except KeyError:
             return None
-        if not new_label in self.database.atoms:
+        if new_label not in self.database.atoms:
             self.database.add_property(new_label, new_type)
             column = []
             for key in self.all_row_names:

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AseInputFileWidget.py

@@ -87,7 +87,7 @@ def valueFromDialog(self):
             self.updateValue()
             try:
                 type_guess = filetype(new_value[0])
-            except:
+            except Exception:
                 type_guess = "guess"
             self._type_combo.setCurrentText(type_guess)
 

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py

@@ -190,7 +190,6 @@ def left_widgets(self) -> list[QWidget]:
         self.combo_boxes = []
 
         for k, v in self.settings.items():
-
             if isinstance(v, bool):
                 check_layout = QHBoxLayout()
                 checkbox = QCheckBox()

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/BackupWidget.py

@@ -21,7 +21,7 @@
 class BackupWidget(WidgetBase):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        source_object = kwargs.get("source_object", None)
+        _source_object = kwargs.get("source_object", None)
         self._field = QLineEdit(str(self._configurator.default))
         self._field.setPlaceholderText(str(self._configurator.default))
         self._layout.addWidget(self._field)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CorrelationFramesWidget.py

@@ -22,7 +22,6 @@
 
 
 class CorrelationFramesWidget(FramesWidget):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DerivativeOrderWidget.py

@@ -29,7 +29,6 @@
 
 
 class DerivativeOrderWidget(WidgetBase):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, layout_type="QHBoxLayout", **kwargs)
         self._field = QSpinBox(self._base)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DistHistCutoffWidget.py

@@ -18,7 +18,6 @@
 
 
 class DistHistCutoffWidget(RangeWidget):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DummyWidget.py

@@ -21,7 +21,7 @@
 class DummyWidget(WidgetBase):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        source_object = kwargs.get("source_object", None)
+        _source_object = kwargs.get("source_object", None)
         self._layout.addWidget(QLabel("content is missing here", self._base))
         self._configurator = {"value": "Oops!"}
         self.default_labels()

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/FramesWidget.py

@@ -28,7 +28,7 @@ def __init__(self, *args, **kwargs):
         if trajectory_configurator is not None:
             try:
                 self._last_frame = trajectory_configurator["length"]
-            except:
+            except Exception:
                 self._last_frame = -1
         else:
             self._last_frame = -1
@@ -93,7 +93,7 @@ def get_widget_value(self):
             strval = field.text()
             try:
                 val = int(strval)
-            except:
+            except Exception:
                 val = int(self._default_values[n])
             result.append(val)
         return result

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/HDFTrajectoryWidget.py

@@ -22,7 +22,6 @@
 
 
 class HDFTrajectoryWidget(WidgetBase):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         source_object = kwargs.get("source_object", None)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/InputFileWidget.py

@@ -25,7 +25,6 @@
 
 
 class InputFileWidget(WidgetBase):
-
     def __init__(self, *args, file_dialog=QFileDialog.getOpenFileName, **kwargs):
         super().__init__(*args, **kwargs)
         configurator = kwargs.get("configurator", None)
@@ -103,7 +102,7 @@ def valueFromDialog(self):
                     self._parent._default_path = str(
                         PurePath(os.path.split(new_value[0])[0])
                     )
-            except:
+            except Exception:
                 LOG.error(
                     f"session.set_path failed for {self._job_name}, {os.path.split(new_value[0])[0]}"
                 )

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/InterpolationOrderWidget.py

@@ -33,7 +33,7 @@
 class InterpolationOrderWidget(WidgetBase):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, layout_type="QHBoxLayout", **kwargs)
-        source_object = kwargs.get("source_object", None)
+        _source_object = kwargs.get("source_object", None)
 
         self._field = QSpinBox(self._base)
         self._field.setMaximum(5)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisCoordinateFileWidget.py

@@ -23,7 +23,6 @@
 class MDAnalysisCoordinateFileWidget(
     MultiInputFileWidget, MDAnalysisTopologyFileWidget
 ):
-
     def __init__(self, *args, file_dialog=QFileDialog.getOpenFileNames, **kwargs):
         super().__init__(
             *args,

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py

@@ -17,7 +17,6 @@
 
 
 class MDAnalysisMDTrajTimeStepWidget(FloatWidget):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTopologyFileWidget.py

@@ -21,7 +21,6 @@
 
 
 class MDAnalysisTopologyFileWidget(InputFileWidget):
-
     def __init__(self, *args, format_options=sorted(mda._PARSERS.keys()), **kwargs):
         self.format_options = ["AUTO"] + list(format_options)
         super().__init__(*args, **kwargs)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py

@@ -17,7 +17,6 @@
 
 
 class MDTrajTopologyFileWidget(InputFileWidget):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py

@@ -24,7 +24,6 @@
 
 
 class MultiInputFileWidget(InputFileWidget):
-
     def __init__(self, *args, file_dialog=QFileDialog.getOpenFileNames, **kwargs):
         super().__init__(
             *args,
@@ -37,7 +36,7 @@ def valueFromDialog(self):
         paths_group = self._settings.group("paths")
         try:
             self.default_path = paths_group.get(self._job_name)
-        except:
+        except Exception:
             LOG.warning(f"session.get_path failed for {self._job_name}")
         new_value = self._file_dialog(
             self.parent(),
@@ -57,7 +56,7 @@ def valueFromDialog(self):
                 paths_group.set(
                     self._job_name, str(PurePath(os.path.split(new_value[0][0])[0]))
                 )
-            except:
+            except Exception:
                 LOG.error(
                     f"session.set_path failed for {self._job_name}, {os.path.split(new_value[0][0])[0]}"
                 )

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OptionalFloatWidget.py

@@ -22,7 +22,6 @@
 
 
 class OptionalFloatWidget(WidgetBase):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         try:

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputFilesWidget.py

@@ -50,7 +50,7 @@ def __init__(self, *args, **kwargs):
             guess_name = str(
                 PurePath(os.path.join(self.default_path, jobname + "_result1"))
             )
-        except:
+        except Exception:
             guess_name = str(PurePath(default_value[0]))
             LOG.error("It was not possible to get the job name from the parent")
         while os.path.exists(guess_name + ".mda"):

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputStructureWidget.py

@@ -46,7 +46,7 @@ def __init__(self, *args, **kwargs):
         try:
             parent = kwargs.get("parent", None)
             guess_name = str(PurePath(os.path.join(self.default_path, "POSCAR")))
-        except:
+        except Exception:
             guess_name = str(PurePath(default_value[0]))
             LOG.error("It was not possible to get the job name from the parent")
         else:

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputTrajectoryWidget.py

@@ -39,7 +39,6 @@
 
 
 class OutputTrajectoryWidget(WidgetBase):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, layout_type="QGridLayout", **kwargs)
         default_value = self._configurator.default
@@ -62,7 +61,7 @@ def __init__(self, *args, **kwargs):
             guess_name = str(
                 PurePath(os.path.join(self.default_path, jobname + "_trajectory1"))
             )
-        except:
+        except Exception:
             guess_name = str(PurePath(default_value[0]))
             LOG.error("It was not possible to get the job name from the parent")
         while os.path.exists(guess_name + ".mdt"):

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/PartialChargeWidget.py

@@ -131,7 +131,7 @@ def update_charge_textbox(self) -> None:
         """
         map = self.mapper.get_full_setting()
 
-        text = [f"Partial charge mapping:\n"]
+        text = ["Partial charge mapping:\n"]
         atoms = self.selector.system.atom_list
         for idx, charge in map.items():
             text.append(f"{idx}  ({atoms[idx]}) -> {charge}\n")

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/ProjectionWidget.py

@@ -23,7 +23,7 @@
 class ProjectionWidget(WidgetBase):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        source_object = kwargs.get("source_object", None)
+        _source_object = kwargs.get("source_object", None)
         bgroup = QButtonGroup(self._base)
         for id, blabel in enumerate(["None", "Axial", "Planar"]):
             rbutton = QRadioButton(blabel, parent=self._base)

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/QVectorsWidget.py

@@ -24,7 +24,6 @@
 
 
 class VectorModel(QStandardItemModel):
-
     type_changed = Signal()
     input_is_valid = Signal(bool)
 

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/RangeWidget.py

@@ -22,7 +22,6 @@
 
 
 class RangeWidget(WidgetBase):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, layout_type="QGridLayout", **kwargs)
         self.setup_fields(*args, **kwargs)
@@ -95,7 +94,7 @@ def get_widget_value(self):
             strval = field.text()
             try:
                 val = self._num_type(strval)
-            except:
+            except Exception:
                 val = self._num_type(self._default_values[n])
             result.append(val)
         return result

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/UnitCellWidget.py

@@ -22,7 +22,6 @@
 
 
 class UnitCellWidget(WidgetBase):
-
     def __init__(self, *args, **kwargs):
         super().__init__(*args, layout_type="grid", **kwargs)
         self._changing_label = QLabel("Unit cell", parent=self._base)
@@ -81,7 +80,7 @@ def get_widget_value(self):
             for key, value in self._array_fields.items():
                 try:
                     array[key[0]][key[1]] = float(value.text())
-                except:
+                except Exception:
                     LOG.error(
                         f"Could not set value ({key[0]}, {key[1]}) to {value.text()}"
                     )

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/VectorWidget.py

@@ -45,6 +45,6 @@ def get_widget_value(self):
         """Collect the results from the input widgets and return the value."""
         try:
             vector = [float(x.text()) for x in self._vector_fields]
-        except:
+        except Exception:
             vector = [0, 0, 0]
         return vector

MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/WidgetBase.py

@@ -29,7 +29,6 @@
 
 
 class WidgetBase(QObject):
-
     valid_changed = Signal()
     value_updated = Signal()
     value_changed = Signal()
@@ -126,7 +125,7 @@ def updateValue(self):
             self.configure_using_default()
         try:
             self._configurator.configure(current_value)
-        except:
+        except Exception:
             self.mark_error(
                 "COULD NOT SET THIS VALUE - you may need to change the values in other widgets"
             )

MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/Contents.py

@@ -63,8 +63,8 @@ def parseInformation(self, unique=True):
         atom_ids = self._reader.atom_ids
         grouped_by_type = {}
         name_by_type = {}
-        colour_by_type = {}
-        radius_by_type = {}
+        _colour_by_type = {}
+        _radius_by_type = {}
         unique_types = np.unique(atom_types)
         for type in unique_types:
             crit = np.where(atom_types == type)

MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/Controls.py

@@ -96,7 +96,7 @@
 class ViewerControls(QWidget):
     def __init__(self, *args, **kwargs):
         super(QWidget, self).__init__(*args, **kwargs)
-        layout = QGridLayout(self)
+        _layout = QGridLayout(self)
         self._viewer = None
         self._buttons = {}
         self._delegates = {}