Fix ruff issues

Add to workflows

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

@@ -1,4 +1,4 @@
-name: Black
+name: Lint
 
 on:
   push:
@@ -24,3 +24,12 @@ jobs:
         with:
           options: "--check --verbose"
           src: "MDANSE_GUI/Src"
+
+  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/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/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/InputFileWidget.py

@@ -103,7 +103,7 @@ 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/MultiInputFileWidget.py

@@ -37,7 +37,7 @@ 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 +57,7 @@ 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/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

@@ -62,7 +62,7 @@ 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/RangeWidget.py

@@ -95,7 +95,7 @@ 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

@@ -81,7 +81,7 @@ 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

@@ -126,7 +126,7 @@ 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 = {}

MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py

@@ -13,6 +13,7 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+
 from typing import List
 
 import numpy as np
@@ -199,9 +200,9 @@ def _draw_isosurface(self, index):
 
         LOG.info("Computing isosurface ...")
 
-        initial_coords = self._reader.read_frame(0)
+        _initial_coords = self._reader.read_frame(0)
         coords, lower_bounds, upper_bounds = self._reader.read_atom_trajectory(index)
-        spacing, self._atomic_trace_histogram = histogram_3d(
+        spacing, self._atomic_trace_histogram = histogram_3d(  # noqa
             coords, lower_bounds, upper_bounds, 100, 100, 100
         )
 
@@ -548,7 +549,7 @@ def on_open_atomic_trace_settings_dialog(self):
         hist_max = self._atomic_trace_histogram.max()
         hist_mean = self._atomic_trace_histogram.mean()
 
-        dlg = AtomicTraceSettingsDialog(hist_min, hist_max, hist_mean, self)
+        dlg = AtomicTraceSettingsDialog(hist_min, hist_max, hist_mean, self)  # noqa
 
         dlg.rendering_type_changed.connect(self.on_change_atomic_trace_rendering_type)
         dlg.opacity_changed.connect(self.on_change_atomic_trace_opacity)

MDANSE_GUI/Src/MDANSE_GUI/Session/LocalSession.py

@@ -111,7 +111,7 @@ def save(self, fname: str = None):
         try:
             with open(fname, "w") as target:
                 target.write(output)
-        except:
+        except Exception:
             return
         else:
             self._filename = fname
@@ -122,7 +122,7 @@ def load(self, fname: str = None):
         try:
             with open(fname, "r") as source:
                 all_items_text = source.readline()
-        except:
+        except Exception:
             LOG.warning(f"Failed to read session settings from {fname}")
         else:
             all_items = json_decoder.decode(all_items_text)

MDANSE_GUI/Src/MDANSE_GUI/Session/StructuredSession.py

@@ -135,7 +135,7 @@ def save_new_value(self, item_index: QModelIndex):
                     group.set(item_key, new_value)
                 elif column_number == 2:
                     group.set_comment(item_key, new_value)
-        except:
+        except Exception:
             LOG.warning(
                 f"Could not store {new_value} in group[{group_key}]->[{item_key}]"
             )

MDANSE_GUI/Src/MDANSE_GUI/Subprocess/JobStatusProcess.py

@@ -53,12 +53,12 @@ def terminate_the_process(self):
         LOG.info(f"JobCommunicator PID: {os.getpid()} started 'terminate_the_process")
         try:
             self._process.terminate()
-        except:
+        except Exception:
             return
         else:
             try:
                 self._process.close()
-            except:
+            except Exception:
                 return
 
 
@@ -91,7 +91,7 @@ def start_status(self):
         LOG.info(f"JobStatusProcess PID: {os.getpid()} started 'start_status")
         try:
             temp = int(self._nSteps)
-        except:
+        except Exception:
             self._pipe.send(("STARTED", None))
         else:
             self._pipe.send(("STARTED", temp))

MDANSE_GUI/Src/MDANSE_GUI/TabbedWindow.py

@@ -177,7 +177,7 @@ def version_information(self):
         version = ""
         version += f"MDANSE version: {metadata.version('MDANSE')}\n"
         version += f"MDANSE_GUI version: {metadata.version('MDANSE_GUI')}\n"
-        popup = QMessageBox.about(self, "MDANSE Version Information", version)
+        _popup = QMessageBox.about(self, "MDANSE Version Information", version)
 
     def setupToolbar(self):
         self._toolBar = QToolBar("Main MDANSE toolbar", self)

MDANSE_GUI/Src/MDANSE_GUI/Tabs/GeneralTab.py

@@ -154,7 +154,7 @@ def conversion_factor(self, input_unit: str) -> Tuple[float, str]:
             conversion_factor = measure(1.0, input_unit, equivalent=True).toval(
                 target_unit
             )
-        except:
+        except Exception:
             target_unit = self._settings.default_value("units", property)
             conversion_factor = measure(1.0, input_unit, equivalent=True).toval(
                 target_unit

MDANSE_GUI/Src/MDANSE_GUI/Tabs/LoggingTab.py

@@ -78,7 +78,7 @@ def change_log_level(self, new_level: str):
             return
         try:
             self._extra_handler.setLevel(new_level)
-        except:
+        except Exception:
             LOG.error(f"Could not set GuiLogHandler to log level {new_level}")
         else:
             self._visualiser.append_text(
@@ -88,7 +88,7 @@ def change_log_level(self, new_level: str):
     def add_handler(self, new_handler):
         try:
             current_level = self._loglevel_combo.currentText()
-        except:
+        except Exception:
             current_level = "INFO"
         self._extra_handler = new_handler
         self._extra_handler.add_visualiser(self._visualiser)

MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobHolder.py

@@ -83,7 +83,7 @@ def run(self):
         while self._keep_running:
             try:
                 status_update = self._pipe_end.recv()
-            except:
+            except Exception:
                 self.fail()
             else:
                 self._job_comm.status_update(status_update)
@@ -329,7 +329,7 @@ def startProcess(self, job_vars: list, load_afterwards=False):
             else:
                 try:
                     int(job_vars[1]["output_files"][1])
-                except:
+                except Exception:
                     item_th.for_loading.connect(self.results_for_loading)
                 else:
                     item_th.for_loading.connect(self.trajectory_for_loading)
@@ -341,7 +341,7 @@ def startProcess(self, job_vars: list, load_afterwards=False):
         watcher_thread.start()
         try:
             task_name = str(job_vars[0])
-        except:
+        except Exception:
             task_name = str("This should have been a job name")
         name_item = QStandardItem(task_name)
         name_item.setData(entry_number, role=Qt.ItemDataRole.UserRole)

MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobTree.py

@@ -112,7 +112,7 @@ def parentsFromCategories(self, category_tuple):
         """
         parent = self.invisibleRootItem()
         for cat_string in category_tuple:
-            if not cat_string in self._categories.keys():
+            if cat_string not in self._categories:
                 current_node = QStandardItem(cat_string)
                 parent.appendRow(current_node)
                 parent = current_node

MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlotDataModel.py

@@ -58,7 +58,7 @@ def populate(self, file):
                 child.setData(key, role=Qt.ItemDataRole.UserRole)
                 try:
                     file[key][:]
-                except:
+                except Exception:
                     child._item_type = "group"
                 self.appendRow(child)