From 22bbd454f5af32d5f63928b702ae470ce77fe0f4 Mon Sep 17 00:00:00 2001 From: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com> Date: Mon, 10 Feb 2025 13:27:28 +0000 Subject: [PATCH 1/2] - Add ruff format linting to workflows - Run ruff format --- .github/workflows/lint.yml | 8 ++++---- .../Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py | 1 - .../MDANSE_GUI/InputWidgets/CorrelationFramesWidget.py | 1 - .../Src/MDANSE_GUI/InputWidgets/DerivativeOrderWidget.py | 1 - .../Src/MDANSE_GUI/InputWidgets/DistHistCutoffWidget.py | 1 - .../Src/MDANSE_GUI/InputWidgets/HDFTrajectoryWidget.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/InputFileWidget.py | 1 - .../InputWidgets/MDAnalysisCoordinateFileWidget.py | 1 - .../InputWidgets/MDAnalysisMDTrajTimeStepWidget.py | 1 - .../InputWidgets/MDAnalysisTopologyFileWidget.py | 1 - .../MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py | 1 - .../Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py | 1 - .../Src/MDANSE_GUI/InputWidgets/OptionalFloatWidget.py | 1 - .../Src/MDANSE_GUI/InputWidgets/OutputTrajectoryWidget.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/QVectorsWidget.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/RangeWidget.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/UnitCellWidget.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/WidgetBase.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Session/StructuredSession.py | 4 ---- MDANSE_GUI/Src/MDANSE_GUI/Subprocess/JobState.py | 7 ------- MDANSE_GUI/Src/MDANSE_GUI/Subprocess/Subprocess.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/InstrumentTab.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/LoggingTab.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobHolder.py | 2 -- MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlotDataModel.py | 3 --- MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlottingContext.py | 3 --- .../Src/MDANSE_GUI/Tabs/PlotModifiers/AxesWrapper.py | 1 - .../Src/MDANSE_GUI/Tabs/PlotModifiers/NormGenerator.py | 1 - .../Src/MDANSE_GUI/Tabs/PlotModifiers/WeightGenerator.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotSelectionTab.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotTab.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Grid.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Heatmap.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Plotter.py | 1 - .../Src/MDANSE_GUI/Tabs/Plotters/PlotterTemplate.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Single.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/ActionsTree.py | 3 +-- MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/Delegates.py | 5 ----- MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/PlotDataView.py | 3 +-- MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/RunTable.py | 3 +-- MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py | 3 +-- MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/DataWidget.py | 3 +-- .../Src/MDANSE_GUI/Tabs/Visualisers/InstrumentDetails.py | 1 - .../Src/MDANSE_GUI/Tabs/Visualisers/InstrumentInfo.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/JobLogInfo.py | 1 - .../Src/MDANSE_GUI/Tabs/Visualisers/PlotSettings.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotWidget.py | 2 -- MDANSE_GUI/Src/MDANSE_GUI/UserSettingsEditor.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Widgets/DataDialog.py | 2 +- MDANSE_GUI/Src/MDANSE_GUI/Widgets/DelayedButton.py | 1 - .../Src/MDANSE_GUI/Widgets/NotificationTabWidget.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionDialog.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionWidget.py | 2 -- MDANSE_GUI/Src/MDANSE_GUI/Widgets/RestrictedSlider.py | 1 - MDANSE_GUI/Src/MDANSE_GUI/Widgets/VectorWidget.py | 1 - 56 files changed, 10 insertions(+), 84 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 4641bae389..13a52b9d2f 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -25,14 +25,14 @@ jobs: src: "./MDANSE/Src" args: "check" - lint-mdanse-gui: + lint_format_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 diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py index c7c6c784dc..64285f7197 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomSelectionWidget.py +++ b/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() diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CorrelationFramesWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CorrelationFramesWidget.py index 475a577ebc..ef2a5b63f9 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CorrelationFramesWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CorrelationFramesWidget.py @@ -22,7 +22,6 @@ class CorrelationFramesWidget(FramesWidget): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DerivativeOrderWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DerivativeOrderWidget.py index 55d76721eb..9d270296a2 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DerivativeOrderWidget.py +++ b/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) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DistHistCutoffWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DistHistCutoffWidget.py index 0edcf66527..1a9d59069b 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DistHistCutoffWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/DistHistCutoffWidget.py @@ -18,7 +18,6 @@ class DistHistCutoffWidget(RangeWidget): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/HDFTrajectoryWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/HDFTrajectoryWidget.py index 46de7aa1e5..df93080dcc 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/HDFTrajectoryWidget.py +++ b/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) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/InputFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/InputFileWidget.py index ad51830f1c..b7f126a046 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/InputFileWidget.py +++ b/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) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisCoordinateFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisCoordinateFileWidget.py index 699ff6c460..6e32209d0d 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisCoordinateFileWidget.py +++ b/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, diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py index 0457e089c2..b8215386a4 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py @@ -17,7 +17,6 @@ class MDAnalysisMDTrajTimeStepWidget(FloatWidget): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTopologyFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTopologyFileWidget.py index 2f3ea88807..d6c832b704 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTopologyFileWidget.py +++ b/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) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py index a85634f9f1..893b97534f 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py @@ -17,7 +17,6 @@ class MDTrajTopologyFileWidget(InputFileWidget): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py index 0aea3a9721..cc94abbeff 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py +++ b/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, diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OptionalFloatWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OptionalFloatWidget.py index 5dfba5784f..07804849b8 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OptionalFloatWidget.py +++ b/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: diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputTrajectoryWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputTrajectoryWidget.py index 3854c9a64c..059d2a350d 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/OutputTrajectoryWidget.py +++ b/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 diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/QVectorsWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/QVectorsWidget.py index b61d868b58..f2722755a7 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/QVectorsWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/QVectorsWidget.py @@ -24,7 +24,6 @@ class VectorModel(QStandardItemModel): - type_changed = Signal() input_is_valid = Signal(bool) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/RangeWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/RangeWidget.py index fb9bb03dda..0fc198860c 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/RangeWidget.py +++ b/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) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/UnitCellWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/UnitCellWidget.py index 99f64febc3..3232d8ef65 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/UnitCellWidget.py +++ b/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) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/WidgetBase.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/WidgetBase.py index 8591de9f53..86be1bc077 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/WidgetBase.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/WidgetBase.py @@ -29,7 +29,6 @@ class WidgetBase(QObject): - valid_changed = Signal() value_updated = Signal() value_changed = Signal() diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Session/StructuredSession.py b/MDANSE_GUI/Src/MDANSE_GUI/Session/StructuredSession.py index be8536e4b9..94af2a50a3 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Session/StructuredSession.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Session/StructuredSession.py @@ -29,7 +29,6 @@ class UserSettingsModel(QStandardItemModel): - file_loaded = Signal(str) def __init__(self, *args, settings_filename: str = "", **kwargs): @@ -187,7 +186,6 @@ def writeout_settings(self): class SettingsGroup: - def __init__(self, group_name: str) -> None: self._name = group_name self._settings = {} @@ -261,9 +259,7 @@ def as_dict(self): class SettingsFile: - def __init__(self, name, settings_path: str = None): - if settings_path is None: settings_path = PLATFORM.application_directory() self._top_name = name diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/JobState.py b/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/JobState.py index 9a220476c0..84f812349e 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/JobState.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/JobState.py @@ -17,7 +17,6 @@ class JobState(ABC): - _label = "JobState" _allowed_actions = [] @@ -54,7 +53,6 @@ def fail(self): class Running(JobState): - _label = "Running" _allowed_actions = [ "Pause", @@ -92,7 +90,6 @@ def fail(self): class Aborted(JobState): - _label = "Aborted" _allowed_actions = ["Delete"] @@ -119,7 +116,6 @@ def fail(self): class Failed(JobState): - _label = "Failed" _allowed_actions = ["Delete"] @@ -146,7 +142,6 @@ def fail(self): class Finished(JobState): - _label = "Finished" _allowed_actions = ["Delete"] @@ -173,7 +168,6 @@ def fail(self): class Starting(JobState): - _label = "Starting" _allowed_actions = [ "Pause", @@ -206,7 +200,6 @@ def fail(self): class Paused(JobState): - _label = "Paused" _allowed_actions = [ "Resume", diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/Subprocess.py b/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/Subprocess.py index 3056ab7b33..d321946827 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/Subprocess.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Subprocess/Subprocess.py @@ -26,7 +26,6 @@ class Subprocess(Process): - def __init__(self, *args, **kwargs): super().__init__() job_name = kwargs.get("job_name") diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/InstrumentTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/InstrumentTab.py index 0406482504..28ab525b58 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/InstrumentTab.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/InstrumentTab.py @@ -42,7 +42,6 @@ class InstrumentTab(GeneralTab): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._core.add_button("Create Instrument", self._view.add_instrument) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/LoggingTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/LoggingTab.py index 2f5df8ea16..9d2f41bfc4 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/LoggingTab.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/LoggingTab.py @@ -36,7 +36,6 @@ class GuiLogHandler(Handler): - def __init__(self, *args, **kwargs): self._visualiser = None super().__init__(*args, **kwargs) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobHolder.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobHolder.py index 42329dc4ac..be126de2b6 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobHolder.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/JobHolder.py @@ -38,7 +38,6 @@ class JobThread(QThread): - def __init__( self, job_comm: "JobCommunicator", @@ -90,7 +89,6 @@ def run(self): class JobLogHandler(Handler): - def __init__(self): super().__init__() self.records = [] diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlotDataModel.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlotDataModel.py index ce58df9ba6..43e43be239 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlotDataModel.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlotDataModel.py @@ -64,7 +64,6 @@ def populate(self, file): class DataSetItem(BasicPlotDataItem): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._item_type = "dataset" @@ -79,7 +78,6 @@ def file_number(self) -> int: class DataFileItem(BasicPlotDataItem): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._item_type = "file" @@ -92,7 +90,6 @@ def file_number(self) -> int: class MDADataStructure: - def __init__(self, filename: str): self._file = h5py.File(filename) self.check_metadata() diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlottingContext.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlottingContext.py index d31ce8368f..7280973915 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlottingContext.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Models/PlottingContext.py @@ -56,7 +56,6 @@ def get_mpl_colours(): class SingleDataset: - def __init__(self, name: str, source: "h5py.File"): self._name = name self._filename = source.filename @@ -228,7 +227,6 @@ def planes_vs_axis(self, axis_number: int) -> List[np.ndarray]: class SingleCurve: - def __init__(self, data_name: str, file_name: str, *args, **kwargs): self._name = data_name self._filename = file_name @@ -289,7 +287,6 @@ def standard_items(self, key: int) -> List["QStandardItem"]: class PlottingContext(QStandardItemModel): - needs_an_update = Signal() def __init__(self, *args, unit_lookup=None, **kwargs): diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/AxesWrapper.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/AxesWrapper.py index 7b8ae58d89..b5ba9c5f4d 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/AxesWrapper.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/AxesWrapper.py @@ -24,7 +24,6 @@ class AxesWrapper: - def __init__(self, *args, **kwargs): self._axes = kwargs.pop("axes", None) self._plot_elements = [] diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/NormGenerator.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/NormGenerator.py index 9e86e0a6a1..2f6ba2bf31 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/NormGenerator.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/NormGenerator.py @@ -18,6 +18,5 @@ class NullNorms: - def __call__(self, *args, **kwds) -> float: return 1.0 diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/WeightGenerator.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/WeightGenerator.py index c0ac7a1054..c4f3d4ad1f 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/WeightGenerator.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotModifiers/WeightGenerator.py @@ -18,6 +18,5 @@ class NullWeights: - def __call__(self, *args, **kwds) -> float: return 1.0 diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotSelectionTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotSelectionTab.py index 3d798ac448..ab0d60d6ad 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotSelectionTab.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotSelectionTab.py @@ -37,7 +37,6 @@ class PlotSelectionTab(GeneralTab): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._core.add_button("Load .MDA results", self.load_files) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotTab.py index d3fb6dde4b..6b3ca87290 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotTab.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/PlotTab.py @@ -36,7 +36,6 @@ class PlotTab(GeneralTab): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._visualiser._unit_lookup = self diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Grid.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Grid.py index 57526ba5d7..d94ded0577 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Grid.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Grid.py @@ -27,7 +27,6 @@ class Grid(Plotter): - def __init__(self) -> None: super().__init__() self._figure = None diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Heatmap.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Heatmap.py index 2feeb3139e..fea0751b6c 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Heatmap.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Heatmap.py @@ -31,7 +31,6 @@ class Heatmap(Plotter): - def __init__(self) -> None: super().__init__() self._figure = None diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Plotter.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Plotter.py index 564cf42fc4..652cc03043 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Plotter.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Plotter.py @@ -27,7 +27,6 @@ class Plotter(metaclass=SubclassFactory): - def __init__(self) -> None: self._figure = None self._axes = [] diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/PlotterTemplate.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/PlotterTemplate.py index c0334df2a5..8d7ad49328 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/PlotterTemplate.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/PlotterTemplate.py @@ -31,7 +31,6 @@ class PlotterTemplate(metaclass=SubclassFactory): - def __init__(self) -> None: self._figure = None self._axes = {} diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Single.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Single.py index 307d3ad083..df9edd373b 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Single.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Plotters/Single.py @@ -26,7 +26,6 @@ class Single(Plotter): - def __init__(self) -> None: super().__init__() self._figure = None diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py index 7a2a79e661..14c8210242 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py @@ -44,7 +44,6 @@ class TrajectoryTab(GeneralTab): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._core.add_button("Load .MDT Trajectories", self.load_trajectories) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/ActionsTree.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/ActionsTree.py index 06827b9a63..a463cb5818 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/ActionsTree.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/ActionsTree.py @@ -100,6 +100,5 @@ def connect_to_visualiser(self, visualiser: Union[Action, TextInfo]) -> None: self.item_details.connect(visualiser.update_panel) else: raise NotImplementedError( - f"Unable to connect view {type(self)} to visualiser " - f"{type(visualiser)}" + f"Unable to connect view {type(self)} to visualiser {type(visualiser)}" ) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/Delegates.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/Delegates.py index 83df1d672c..66c85b1131 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/Delegates.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/Delegates.py @@ -29,7 +29,6 @@ class ColourPicker(QStyledItemDelegate): - def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) @@ -51,7 +50,6 @@ def setModelData(self, editor, model, index): class MainAxisCombo(QItemDelegate): - def __init__(self, *args, **kwargs) -> None: self._items = [] super().__init__(*args, **kwargs) @@ -85,7 +83,6 @@ def currentIndexChanged(self): class MplStyleCombo(QItemDelegate): - def __init__(self, *args, mpl_items=None, **kwargs) -> None: self._items = list([str(x) for x in mpl_items.keys()]) super().__init__(*args, **kwargs) @@ -118,7 +115,6 @@ def currentIndexChanged(self): class RadiusSpinBox(QItemDelegate): - def __init__(self, *args, mpl_items=None, **kwargs) -> None: self._minimum = 0.0 self._step = 0.01 @@ -144,7 +140,6 @@ def valueChanged(self): class ProgressDelegate(QItemDelegate): - progress_role = Qt.UserRole + 1000 def paint(self, painter, option, index): diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/PlotDataView.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/PlotDataView.py index bf1ae6f8d3..d4db9f2428 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/PlotDataView.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/PlotDataView.py @@ -148,6 +148,5 @@ def connect_to_visualiser( self.item_details.connect(visualiser.update_panel) else: raise NotImplementedError( - f"Unable to connect view {type(self)} to visualiser " - f"{type(visualiser)}" + f"Unable to connect view {type(self)} to visualiser {type(visualiser)}" ) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/RunTable.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/RunTable.py index 592613c16e..e5a4e7b612 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/RunTable.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/RunTable.py @@ -163,6 +163,5 @@ def connect_to_visualiser(self, visualiser: TextInfo) -> None: self.jobs_logs.connect(visualiser.update_panel) else: raise NotImplementedError( - f"Unable to connect view {type(self)} to visualiser " - f"{type(visualiser)}" + f"Unable to connect view {type(self)} to visualiser {type(visualiser)}" ) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py index a97932e770..411c932fb7 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py @@ -80,6 +80,5 @@ def connect_to_visualiser(self, visualiser: Union[View3D, TrajectoryInfo]) -> No self.item_details.connect(visualiser.update_panel) else: raise NotImplementedError( - f"Unable to connect view {type(self)} to visualiser " - f"{type(visualiser)}" + f"Unable to connect view {type(self)} to visualiser {type(visualiser)}" ) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/DataWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/DataWidget.py index 4ce6f53f7a..8c5c8c4fbf 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/DataWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/DataWidget.py @@ -46,7 +46,6 @@ class DataWidget(QWidget): - change_slider_labels = Signal(object) change_slider_limits = Signal(object) reset_slider_values = Signal(bool) @@ -257,7 +256,7 @@ def plot_data(self, update_only=False): self._current_path = PurePath(os.path.split(dataset._filename)[0]) break except Exception as e: - LOG.error(f"DataWidget error: {e}" f"traceback {format_exc()}") + LOG.error(f"DataWidget error: {e}traceback {format_exc()}") def make_canvas(self): """Creates a matplotlib figure for plotting diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentDetails.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentDetails.py index 3d575cda84..a4be4badcc 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentDetails.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentDetails.py @@ -32,7 +32,6 @@ class InstrumentDetails(QWidget): - instrument_details_changed = Signal(int) def __init__(self, *args, **kwargs): diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentInfo.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentInfo.py index 935d30acb2..52738487d5 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentInfo.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/InstrumentInfo.py @@ -24,7 +24,6 @@ class SimpleInstrument: - sample_options = ["isotropic", "crystal"] technique_options = ["QENS", "INS"] resolution_options = [str(x) for x in widget_text_map.keys()] diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/JobLogInfo.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/JobLogInfo.py index a150649dad..c96b9c7f3b 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/JobLogInfo.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/JobLogInfo.py @@ -18,7 +18,6 @@ class JobLogInfo(TextInfo): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.setStyleSheet("font-family: Courier New;") diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotSettings.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotSettings.py index dc135778bb..9d61bce750 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotSettings.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotSettings.py @@ -28,7 +28,6 @@ class PlotSettings(QWidget): - plot_settings_changed = Signal() def __init__(self, *args, settings=None, **kwargs) -> None: diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotWidget.py index 7dfca46ab5..0405269828 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/PlotWidget.py @@ -41,7 +41,6 @@ class SliderPack(QWidget): - new_values = Signal(object) def __init__(self, *args, n_sliders=2, **kwargs) -> None: @@ -152,7 +151,6 @@ def collect_values(self): class PlotWidget(QWidget): - change_slider_labels = Signal(object) change_slider_limits = Signal(object) reset_slider_values = Signal(bool) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/UserSettingsEditor.py b/MDANSE_GUI/Src/MDANSE_GUI/UserSettingsEditor.py index 8054ab6462..8b9edaccfc 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/UserSettingsEditor.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/UserSettingsEditor.py @@ -30,7 +30,6 @@ class SettingsView(QTreeView): - def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DataDialog.py b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DataDialog.py index aeb594daf1..5cb857433b 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DataDialog.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DataDialog.py @@ -39,7 +39,7 @@ def __init__( input_data: List[np.ndarray], input_units: List[str], is_input=False, - **kwargs + **kwargs, ): super().__init__(*args, **kwargs) diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DelayedButton.py b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DelayedButton.py index aaceda17e6..e3228cda7d 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DelayedButton.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/DelayedButton.py @@ -19,7 +19,6 @@ class DelayedButton(QPushButton): - needs_updating = Signal() def __init__(self, *args, **kwargs): diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/NotificationTabWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/NotificationTabWidget.py index fa8e386c61..3a13453e35 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/NotificationTabWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/NotificationTabWidget.py @@ -20,7 +20,6 @@ class NotificationTabWidget(QTabWidget): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._normal_colours = {} diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionDialog.py b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionDialog.py index db6c67ea52..680b3fed11 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionDialog.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionDialog.py @@ -25,7 +25,6 @@ class ResolutionDialog(QDialog): - parameters_changed = Signal(dict) def __init__(self, *args, **kwargs): diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionWidget.py index 7f895eba92..c019a441e6 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/ResolutionWidget.py @@ -139,7 +139,6 @@ def revert_parameters(values: dict, peak_type: str) -> List[float]: class ResolutionCalculator: - def __init__(self) -> None: self._valid = False self._fwhm_value = 1.0 @@ -251,7 +250,6 @@ def summarise_results(self, rounding_precision=3): class ResolutionWidget(QWidget): - parameters_changed = Signal(dict) def __init__(self, *args, **kwargs): diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/RestrictedSlider.py b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/RestrictedSlider.py index ed9ddef3f8..587fdd6c41 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/RestrictedSlider.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/RestrictedSlider.py @@ -19,7 +19,6 @@ class RestrictedSlider(QSlider): - new_limit = Signal(object) def __init__(self, *args, **kwargs): diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/VectorWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/VectorWidget.py index 568af83f2a..a822822915 100644 --- a/MDANSE_GUI/Src/MDANSE_GUI/Widgets/VectorWidget.py +++ b/MDANSE_GUI/Src/MDANSE_GUI/Widgets/VectorWidget.py @@ -26,7 +26,6 @@ class VectorWidget(QWidget): - value_changed = Signal(list) def __init__(self, *args, dtype=None, **kwargs) -> None: From 128b78b0a46b4ed1dbdc43cbcd7fbd05b0a4bc2f Mon Sep 17 00:00:00 2001 From: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:15:32 +0000 Subject: [PATCH 2/2] Run ruff format (#666) --- .github/workflows/lint.yml | 6 +++--- MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py | 1 - MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py | 1 - MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py | 3 --- .../Framework/Configurators/ASEFileConfigurator.py | 1 - .../Configurators/AtomTransmutationConfigurator.py | 1 - .../Framework/Configurators/ConfigFileConfigurator.py | 2 -- .../Configurators/CorrelationFramesConfigurator.py | 4 +--- .../Configurators/DistHistCutoffConfigurator.py | 1 - .../Configurators/FileWithAtomDataConfigurator.py | 1 - .../Framework/Configurators/GroupingLevelConfigurator.py | 2 +- .../MDAnalysisCoordinateFileConfigurator.py | 1 - .../Configurators/MDAnalysisTimeStepConfigurator.py | 1 - .../Configurators/MDAnalysisTopologyFileConfigurator.py | 1 - .../Configurators/MDTrajTimeStepConfigurator.py | 1 - .../Configurators/MDTrajTopologyFileConfigurator.py | 1 - .../Configurators/MDTrajTrajectoryFileConfigurator.py | 1 - .../Configurators/MultiInputFileConfigurator.py | 1 - .../MDANSE/Framework/Configurators/RangeConfigurator.py | 1 - .../Framework/Configurators/XDATCARFileConfigurator.py | 2 -- .../Framework/Configurators/XTDFileConfigurator.py | 1 - MDANSE/Src/MDANSE/Framework/Converters/CP2K.py | 2 +- MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py | 1 - MDANSE/Src/MDANSE/Framework/Converters/Forcite.py | 4 ++-- MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py | 7 ++++--- MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py | 9 --------- MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py | 4 ++-- MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py | 2 +- MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py | 3 +-- .../Framework/Jobs/DipoleAutoCorrelationFunction.py | 1 - MDANSE/Src/MDANSE/Framework/Jobs/IJob.py | 1 - MDANSE/Src/MDANSE/Framework/Jobs/Infrared.py | 1 - .../MDANSE/Framework/Jobs/SolventAccessibleSurface.py | 5 +---- .../Framework/QVectors/ApproximateDispersionQVectors.py | 6 +++--- MDANSE/Src/MDANSE/IO/FortranFormat.py | 1 + MDANSE/Src/MDANSE/IO/MinimalPDBReader.py | 2 -- MDANSE/Src/MDANSE/MolecularDynamics/Configuration.py | 2 -- MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py | 1 - MDANSE/Src/MDANSE/NeutronInstruments/Method/__init__.py | 1 - MDANSE/Src/MDANSE/Scripts/mdanse.py | 4 +++- MDANSE/pyproject.toml | 2 +- 41 files changed, 25 insertions(+), 68 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 13a52b9d2f..b636f84a92 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -11,10 +11,10 @@ jobs: 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/Src" + src: "./MDANSE/Src" + args: "format --check" lint_check_ruff: runs-on: ubuntu-latest diff --git a/MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py b/MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py index 9b8348f913..7cf476dde8 100644 --- a/MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py +++ b/MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py @@ -28,7 +28,6 @@ class ChemicalSystem: - def __init__(self, name: str = "", trajectory=None): """ diff --git a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py b/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py index b2ee2ca975..e7e3deb63a 100644 --- a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py +++ b/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py @@ -21,7 +21,6 @@ class AtomLabel: - def __init__(self, atm_label: str, **kwargs): """Creates an atom label object which is used for atom mapping and atom type guessing. diff --git a/MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py b/MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py index 3562149e70..b721f7db32 100644 --- a/MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py +++ b/MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py @@ -202,7 +202,6 @@ def get_idxs(self) -> set[int]: idxs = set([]) for k, v in self.settings.items(): - if isinstance(v, dict): args = [{self._kwarg_keys[k]: i} for i in v.keys()] switches = v.values() @@ -234,7 +233,6 @@ def update_with_idxs(self, idxs: set[int]) -> None: added = set([]) for k, v in self.settings.items(): - if k == "index": continue @@ -338,7 +336,6 @@ def check_valid_setting(self, settings: dict[str, Union[bool, dict]]) -> bool: setting_keys = self._default.keys() dict_setting_keys = self._kwarg_keys.keys() for k0, v0 in settings.items(): - if k0 not in setting_keys: return False diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py index 8f57aa1e20..e3fdab1532 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py @@ -28,7 +28,6 @@ class ASEFileConfigurator(FileWithAtomDataConfigurator): """ def parse(self): - try: self._input = ASETrajectory(self["filename"]) except Exception: diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py index ddd2ce27d2..af8eee2abe 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py @@ -142,7 +142,6 @@ def configure(self, value: str): self._nTransmutedAtoms = 0 for idx, element in value.items(): - try: idx = int(idx) except ValueError: diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py index 1af42d6711..afe5710c85 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py @@ -29,7 +29,6 @@ class LAMMPSConfigFileError(Error): def parse_unit_cell(inputs): - unit_cell = np.zeros(9) xlo, xhi, xy = inputs[0], inputs[1], inputs[2] @@ -53,7 +52,6 @@ def parse_unit_cell(inputs): class ConfigFileConfigurator(FileWithAtomDataConfigurator): - def parse(self): self._filename = self["filename"] diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py index 4de5aa93c3..bc341933d1 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py @@ -19,7 +19,6 @@ class CorrelationFramesConfigurator(FramesConfigurator): - def configure(self, value: tuple[int, int, int, int]): """Configure the correlation and set the number of correlation frames to use. @@ -50,8 +49,7 @@ def configure(self, value: tuple[int, int, int, int]): if c_frames < 2: self.error_status = ( - "Number of frames used for the correlation " - "should be greater then zero." + "Number of frames used for the correlation should be greater then zero." ) return diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py index dee9d13c9d..ad99cc9ee0 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py @@ -6,7 +6,6 @@ class DistHistCutoffConfigurator(RangeConfigurator): - def __init__(self, name, **kwargs): super().__init__(name, **kwargs) self._max_value = kwargs.get("max_value", True) diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py index 8f3c8d5407..1858f379c4 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py @@ -22,7 +22,6 @@ class FileWithAtomDataConfigurator(InputFileConfigurator): - def configure(self, filepath: str) -> None: """ Parameters diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/GroupingLevelConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/GroupingLevelConfigurator.py index 1b635682bd..7babdc9544 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/GroupingLevelConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/GroupingLevelConfigurator.py @@ -90,7 +90,7 @@ def configure(self, value): ): indices.append(cluster) elements.append([chemical_system.atom_list[x] for x in cluster]) - names.append(f"{mol_name}_mol{mol_number+1}") + names.append(f"{mol_name}_mol{mol_number + 1}") masses.append([mass_lookup[x] for x in cluster]) elif value == "group": for group_name, group_indices in chemical_system._labels.items(): diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py index ce9d17c174..6b4f907283 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py @@ -22,7 +22,6 @@ class MDAnalysisCoordinateFileConfigurator(MultiInputFileConfigurator): - _default = ("", "AUTO") def __init__(self, name, wildcard="All files (*)", **kwargs): diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py index eab8d125a1..1bfe8bfd54 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py @@ -19,7 +19,6 @@ class MDAnalysisTimeStepConfigurator(FloatConfigurator): - _default = 0.0 def configure(self, value): diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py index 50b0c4e9ab..02c73ac057 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py @@ -22,7 +22,6 @@ class MDAnalysisTopologyFileConfigurator(FileWithAtomDataConfigurator): - _default = ("", "AUTO") def configure(self, setting: str) -> None: diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py index dea06a4d9b..36e9503387 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py @@ -19,7 +19,6 @@ class MDTrajTimeStepConfigurator(FloatConfigurator): - _default = 0.0 def configure(self, value): diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py index ee3e6fe221..a8519714f8 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py @@ -25,7 +25,6 @@ class MDTrajTopologyFileConfigurator(FileWithAtomDataConfigurator): - def configure(self, value: Optional[str]): """ Parameters diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py index 41df11c7ad..367a429c54 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py @@ -21,7 +21,6 @@ class MDTrajTrajectoryFileConfigurator(MultiInputFileConfigurator): - def configure(self, value): super().configure(value) diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py index 772c64efb3..863e50114c 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py @@ -21,7 +21,6 @@ class MultiInputFileConfigurator(IConfigurator): - _default = "" def __init__(self, name, wildcard="All files (*)", **kwargs): diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py index 477524ac49..dd332d510e 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py @@ -211,7 +211,6 @@ def get_information(self): """ if self._valid: - info = f"{self['number']:d} values from {self['first']} to {self['last']}" if self._includeLast: diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py index 85d889e3e3..5eb79cabfb 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py @@ -74,7 +74,6 @@ def check_trajectory(filename: str): class XDATCARFileConfigurator(FileWithAtomDataConfigurator): - def parse(self): filename = self["filename"] with open(filename, "r") as source: @@ -107,7 +106,6 @@ def parse(self): self._coordinates = np.empty((self["n_atoms"], 3)) def read_step(self, step): - if step > 0 and not self._has_fixed_cell: unit_cell, atoms, atom_numbers, system_name = read_modern_header( self["instance"] diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py index eb46ff7ab9..d5a4864023 100644 --- a/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py +++ b/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py @@ -33,7 +33,6 @@ class XTDFileConfigurator(FileWithAtomDataConfigurator): - def __init__(self, name, **kwargs): super().__init__(name, **kwargs) self._atoms = None diff --git a/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py b/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py index b334f7407f..10f2bc9a0d 100644 --- a/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py +++ b/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py @@ -184,7 +184,7 @@ def initialize(self): self._cellFile = CellFile(self.configuration["cell_file"]["filename"]) if abs(self._cellFile["time_step"] - self._xyzFile["time_step"]) > 1.0e-09: - LOG.error(f'{self._cellFile["time_step"]}, {self._xyzFile["time_step"]}') + LOG.error(f"{self._cellFile['time_step']}, {self._xyzFile['time_step']}") raise CP2KConverterError( "Inconsistent time step between pos and cell files" ) diff --git a/MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py b/MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py index ed643e4162..541286bc43 100644 --- a/MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py +++ b/MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py @@ -37,7 +37,6 @@ class DL_POLYConverterError(Error): class HistoryFile(dict): - def __init__(self, filename): super().__init__() self._dist_conversion = measure(1.0, "ang").toval("nm") diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Forcite.py b/MDANSE/Src/MDANSE/Framework/Converters/Forcite.py index 75f1f80a4c..2f7e6d0e22 100644 --- a/MDANSE/Src/MDANSE/Framework/Converters/Forcite.py +++ b/MDANSE/Src/MDANSE/Framework/Converters/Forcite.py @@ -55,7 +55,7 @@ def parse_header(self): rec = "!i" recSize = struct.calcsize(rec) (NTRJTI,) = struct.unpack(rec, trjfile.read(recSize)) - rec = f"!{80*NTRJTI}s8x" + rec = f"!{80 * NTRJTI}s8x" recSize = struct.calcsize(rec) self["title"] = struct.unpack(rec, trjfile.read(recSize)) self["title"] = "\n".join([t.decode("utf-8") for t in self["title"]]) @@ -82,7 +82,7 @@ def parse_header(self): recSize = struct.calcsize(rec) NFLUSD = struct.unpack(rec, trjfile.read(recSize))[0] - rec = f"!{NFLUSD}i{NFLUSD}i{8*NFLUSD}s8x" + rec = f"!{NFLUSD}i{NFLUSD}i{8 * NFLUSD}s8x" recSize = struct.calcsize(rec) trjfile.read(recSize) diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py b/MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py index bf956d3a86..bdd4d8b7bb 100644 --- a/MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py +++ b/MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py @@ -102,9 +102,10 @@ def initialize(self): ) # The TRRTrajectoryFile object returns ints for these values, so turn them into bools - self._read_velocities, self._read_forces = bool( - self._read_velocities - ), bool(self._read_forces) + self._read_velocities, self._read_forces = ( + bool(self._read_velocities), + bool(self._read_forces), + ) if self._read_velocities: data_to_be_written.append("velocities") diff --git a/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py b/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py index 06557f1713..b4d1032222 100644 --- a/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py +++ b/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py @@ -40,7 +40,6 @@ class LAMMPSTrajectoryFileError(Error): class LAMMPSReader: - def __init__(self, *args, **kwargs): self._units = kwargs.get("lammps_units", "real") self._timestep = kwargs.get("timestep", 1.0) @@ -116,7 +115,6 @@ def set_units(self, lammps_units): class LAMMPScustom(LAMMPSReader): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) @@ -135,7 +133,6 @@ def open_file(self, filename: str): self._start = 0 def parse_first_step(self, aliases, config): - self._itemsPosition = collections.OrderedDict() comp = -1 @@ -387,7 +384,6 @@ def run_step(self, index): class LAMMPSxyz(LAMMPSReader): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._full_cell = None @@ -406,7 +402,6 @@ def open_file(self, filename: str): self._file = open(filename, "r") def read_any_step(self): - line = self._file.readline() number_of_atoms = int(line) line = self._file.readline() @@ -416,7 +411,6 @@ def read_any_step(self): atom_types = np.empty(number_of_atoms, dtype=int) for at_num in range(number_of_atoms): - line = self._file.readline() if not line: @@ -433,7 +427,6 @@ def read_any_step(self): return timestep, atom_types, positions def parse_first_step(self, aliases, config): - _, atom_types, positions = self.read_any_step() self._nAtoms = len(atom_types) @@ -527,7 +520,6 @@ def run_step(self, index): class LAMMPSh5md(LAMMPSReader): - def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._charges_fixed = None @@ -544,7 +536,6 @@ def open_file(self, filename: str): self._file = h5py.File(filename, "r") def parse_first_step(self, aliases, config): - try: atom_types = self._file["/particles/all/species/value"][0] except KeyError: diff --git a/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py b/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py index 6a567fc46e..f602029115 100644 --- a/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py +++ b/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py @@ -108,7 +108,7 @@ def initialize(self): *coord_files, continuous=self.configuration["continuous"]["value"], format=coord_format, - topology_format=self.configuration["topology_file"]["format"] + topology_format=self.configuration["topology_file"]["format"], ) else: coord_files = [(i, coord_format) for i in coord_files] @@ -176,7 +176,7 @@ def initialize(self): self.configuration["output_files"]["file"], self._chemical_system, self.numberOfSteps, - **kwargs + **kwargs, ) super().initialize() diff --git a/MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py b/MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py index 4d838454a4..23cc86b3c7 100644 --- a/MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py +++ b/MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py @@ -156,7 +156,7 @@ def initialize(self): self.configuration["output_files"]["file"], self._chemical_system, self.numberOfSteps, - **kwargs + **kwargs, ) super().initialize() diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py b/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py index f507a4b399..2c439dbd94 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py +++ b/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py @@ -98,8 +98,7 @@ def initialize(self): ) if self._nMolecules == 0: raise AreaPerMoleculeError( - "No molecule matches " - f"{self.configuration['molecule_name']['value']!r} name." + f"No molecule matches {self.configuration['molecule_name']['value']!r} name." ) self._outputData.add( diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py b/MDANSE/Src/MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py index b48d0e99e5..5f8c498d21 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py +++ b/MDANSE/Src/MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py @@ -23,7 +23,6 @@ class DipoleAutoCorrelationFunction(IJob): - enabled = True label = "Dipole AutoCorrelation Function" diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py b/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py index e0fc7ba377..e39881e448 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py +++ b/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py @@ -257,7 +257,6 @@ def _run_singlecore(self): LOG.info("Single-core job completed all the steps") def process_tasks_queue(self, tasks, outputs, log_queues): - queue_handlers = [] for log_queue in log_queues: queue_handler = QueueHandler(log_queue) diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Infrared.py b/MDANSE/Src/MDANSE/Framework/Jobs/Infrared.py index 81e11d3558..222486a875 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/Infrared.py +++ b/MDANSE/Src/MDANSE/Framework/Jobs/Infrared.py @@ -24,7 +24,6 @@ class Infrared(IJob): - enabled = True label = "Infrared Spectrum" diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py b/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py index 79e1b22859..e7570a597c 100644 --- a/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py +++ b/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py @@ -32,7 +32,6 @@ def solvent_accessible_surface( sphere_points: np.ndarray, probe_radius_value: float, ): - # Computes the Solvent Accessible Surface Based on the algorithm published by Shrake, A., and J. A. Rupley. JMB (1973) 79:351-371. sas = 0.0 @@ -161,9 +160,7 @@ def initialize(self): # A mapping between the atom indices and covalent_radius radius for the whole universe. self.vdwRadii = self.configuration["trajectory"][ "instance" - ].chemical_system.atom_property( - "vdw_radius" - ) # should it be covalent? + ].chemical_system.atom_property("vdw_radius") # should it be covalent? self._indices = [ idx diff --git a/MDANSE/Src/MDANSE/Framework/QVectors/ApproximateDispersionQVectors.py b/MDANSE/Src/MDANSE/Framework/QVectors/ApproximateDispersionQVectors.py index cdb223921f..891203e473 100644 --- a/MDANSE/Src/MDANSE/Framework/QVectors/ApproximateDispersionQVectors.py +++ b/MDANSE/Src/MDANSE/Framework/QVectors/ApproximateDispersionQVectors.py @@ -59,9 +59,9 @@ def _generate(self): try: n = (qEnd - qStart).normal() except ZeroDivisionError: - self._configuration["q_end"].error_status = ( - "Zero-length vector cannot be used here" - ) + self._configuration[ + "q_end" + ].error_status = "Zero-length vector cannot be used here" return nSteps = int(d / qStep) + 1 diff --git a/MDANSE/Src/MDANSE/IO/FortranFormat.py b/MDANSE/Src/MDANSE/IO/FortranFormat.py index 350b0c6fb3..425df01f52 100644 --- a/MDANSE/Src/MDANSE/IO/FortranFormat.py +++ b/MDANSE/Src/MDANSE/IO/FortranFormat.py @@ -46,6 +46,7 @@ '3.14159D+00 2.71828D+00' """ + import string from MDANSE.MLogging import LOG diff --git a/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py b/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py index 0baab13af8..a2cb8e3edf 100644 --- a/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py +++ b/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py @@ -58,9 +58,7 @@ def atom_line_slice(keyword: str) -> slice: class MinimalPDBReader: - def __init__(self, filename: str): - self._unit_cell = None cell_params = self.find_unit_cell(filename) if len(cell_params) == 0: diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/Configuration.py b/MDANSE/Src/MDANSE/MolecularDynamics/Configuration.py index f34c2f21f0..efdba38f45 100644 --- a/MDANSE/Src/MDANSE/MolecularDynamics/Configuration.py +++ b/MDANSE/Src/MDANSE/MolecularDynamics/Configuration.py @@ -95,7 +95,6 @@ def contiguous_coordinates_real( scaleconfig = np.matmul(coords, rcell) for idxs in indices: - if len(idxs) < 2: continue if bring_to_centre: @@ -146,7 +145,6 @@ def contiguous_coordinates_box( contiguous_coords = frac_coords.copy() for tupleidxs in indices: - if len(tupleidxs) < 2: continue diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py b/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py index 3f27c1519b..b0e82d7e5b 100644 --- a/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py +++ b/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py @@ -77,7 +77,6 @@ def find_atoms_in_molecule( atom_names: list[str], indices: bool = False, ) -> list[list[int]]: - if entity_name not in chemical_system._clusters: return [] diff --git a/MDANSE/Src/MDANSE/NeutronInstruments/Method/__init__.py b/MDANSE/Src/MDANSE/NeutronInstruments/Method/__init__.py index 30a570b634..4739e13452 100644 --- a/MDANSE/Src/MDANSE/NeutronInstruments/Method/__init__.py +++ b/MDANSE/Src/MDANSE/NeutronInstruments/Method/__init__.py @@ -25,7 +25,6 @@ performed. Initially, the plan is to start with time-of-flight diffraction, direct and indirect spectrometry.""" - import importlib from pathlib import Path diff --git a/MDANSE/Src/MDANSE/Scripts/mdanse.py b/MDANSE/Src/MDANSE/Scripts/mdanse.py index d77b09b30d..bab6464170 100644 --- a/MDANSE/Src/MDANSE/Scripts/mdanse.py +++ b/MDANSE/Src/MDANSE/Scripts/mdanse.py @@ -74,7 +74,9 @@ def format_option(self, option): # Everything is the same after here result += f"{indent_first}{help_lines[0]}\n" result += ( - "\n".join(f"{' '*self.help_position}{line}" for line in help_lines[1:]) + "\n".join( + f"{' ' * self.help_position}{line}" for line in help_lines[1:] + ) + "\n" ) elif not opts.endswith("\n"): diff --git a/MDANSE/pyproject.toml b/MDANSE/pyproject.toml index 434f12b335..cfcfbc62f2 100644 --- a/MDANSE/pyproject.toml +++ b/MDANSE/pyproject.toml @@ -59,7 +59,7 @@ MDANSE = ["Chemistry/*.json", mdanse = "MDANSE.Scripts.mdanse:main" [tool.ruff] -line-length = 100 +line-length = 88 indent-width = 4 target-version = "py39" extend-exclude = [