⬆️ UPGRADE: Autoupdate pre-commit config

.pre-commit-config.yaml

@@ -3,12 +3,12 @@ repos:
   #    FORMATTER    #
   ###################
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "2.1.4"
+    rev: "v2.11.1"
     hooks:
       - id: pyproject-fmt
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-ast
       - id: check-builtin-literals
@@ -20,7 +20,7 @@ repos:
         args: [--fix=lf]
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: 06907d0
+    rev: v1.7.7
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]
@@ -43,7 +43,7 @@ repos:
   ###################
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.1
+    rev: v0.14.9
     hooks:
       - id: ruff
         name: "ruff sort imports"
@@ -58,7 +58,7 @@ repos:
         name: "ruff lint"
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v1.19.0
     hooks:
       - id: mypy
         exclude: "docs"
@@ -68,7 +68,7 @@ repos:
   #   LINTER DOCS   #
   ###################
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.1.0
+    rev: 7.3.0
     hooks:
       - id: flake8
         alias: flake8-docs
@@ -91,7 +91,7 @@ repos:
         pass_filenames: false
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         types: [file]
@@ -100,6 +100,6 @@ repos:
         exclude: ^examples/
 
   - repo: https://github.com/rhysd/actionlint
-    rev: "v1.7.1"
+    rev: "v1.7.9"
     hooks:
       - id: actionlint

pyparamgui/generator.py

@@ -38,8 +38,8 @@ def _generate_decay_model(
     dict[str, Any]
         The generated model dictionary.
     """
-    compartments = [f"species_{i+1}" for i in range(nr_compartments)]
-    rates = [f"rates.species_{i+1}" for i in range(nr_compartments)]
+    compartments = [f"species_{i + 1}" for i in range(nr_compartments)]
+    rates = [f"rates.species_{i + 1}" for i in range(nr_compartments)]
 
     model: dict[str, Any] = {
         "megacomplex": {
@@ -56,18 +56,18 @@ def _generate_decay_model(
             "megacomplex_spectral": {
                 "type": "spectral",
                 "shape": {
-                    compartment: f"shape_species_{i+1}"
+                    compartment: f"shape_species_{i + 1}"
                     for i, compartment in enumerate(compartments)
                 },
             }
         }
         model["shape"] = {
-            f"shape_species_{i+1}": {
+            f"shape_species_{i + 1}": {
                 "type": "skewed-gaussian",
-                "amplitude": f"shapes.species_{i+1}.amplitude",
-                "location": f"shapes.species_{i+1}.location",
-                "width": f"shapes.species_{i+1}.width",
-                "skewness": f"shapes.species_{i+1}.skewness",
+                "amplitude": f"shapes.species_{i + 1}.amplitude",
+                "location": f"shapes.species_{i + 1}.location",
+                "width": f"shapes.species_{i + 1}.width",
+                "skewness": f"shapes.species_{i + 1}.skewness",
             }
             for i in range(nr_compartments)
         }

pyparamgui/schema.py

@@ -13,9 +13,7 @@
 class KineticParameters(BaseModel):
     """Kinetic parameters for the simulation.
 
-    Attributes
-    ----------
-        decay_rates (list[float]): List of decay rates.
+    Attributes ----------     decay_rates (list[float]): List of decay rates.
     """
 
     decay_rates: list[float]
@@ -24,12 +22,9 @@ class KineticParameters(BaseModel):
 class SpectralParameters(BaseModel):
     """Spectral parameters for the simulation.
 
-    Attributes
-    ----------
-        amplitude (list[float]): List of amplitudes.
-        location (list[float]): List of locations.
-        width (list[float]): List of widths.
-        skewness (list[float]): List of skewness values.
+    Attributes ----------     amplitude (list[float]): List of amplitudes.     location
+    (list[float]): List of locations.     width (list[float]): List of widths.     skewness
+    (list[float]): List of skewness values.
     """
 
     amplitude: list[float]
@@ -41,10 +36,8 @@ class SpectralParameters(BaseModel):
 class TimeCoordinates(BaseModel):
     """Time coordinates for the simulation.
 
-    Attributes
-    ----------
-        timepoints_max (int): Maximum number of time points.
-        timepoints_stepsize (float): Step size between time points.
+    Attributes ----------     timepoints_max (int): Maximum number of time points.
+    timepoints_stepsize (float): Step size between time points.
     """
 
     timepoints_max: int
@@ -54,11 +47,8 @@ class TimeCoordinates(BaseModel):
 class SpectralCoordinates(BaseModel):
     """Spectral coordinates for the simulation.
 
-    Attributes
-    ----------
-        wavelength_min (int): Minimum wavelength.
-        wavelength_max (int): Maximum wavelength.
-        wavelength_stepsize (float): Step size between wavelengths.
+    Attributes ----------     wavelength_min (int): Minimum wavelength.     wavelength_max (int):
+    Maximum wavelength.     wavelength_stepsize (float): Step size between wavelengths.
     """
 
     wavelength_min: int
@@ -98,14 +88,11 @@ def generate_simulation_coordinates(
 class Settings(BaseModel):
     """Other settings for the simulation.
 
-    Attributes
-    ----------
-        stdev_noise (float): Standard deviation of the noise to be added to the simulation data.
-        seed (int): Seed for the random number generator to ensure reproducibility.
-        add_gaussian_irf (bool): Whether to add a Gaussian IRF to the simulation.
-            Default is False.
-        use_sequential_scheme (bool): Whether to use a sequential scheme in the simulation.
-            Default is False.
+    Attributes ----------     stdev_noise (float): Standard deviation of the noise to be added to
+    the simulation data.     seed (int): Seed for the random number generator to ensure
+    reproducibility.     add_gaussian_irf (bool): Whether to add a Gaussian IRF to the simulation.
+    Default is False.     use_sequential_scheme (bool): Whether to use a sequential scheme in the
+    simulation.         Default is False.
     """
 
     stdev_noise: float
@@ -117,10 +104,8 @@ class Settings(BaseModel):
 class IRF(BaseModel):
     """Instrument Response Function (IRF) settings for the simulation.
 
-    Attributes
-    ----------
-        center (float): The center position of the IRF.
-        width (float): The width of the IRF.
+    Attributes ----------     center (float): The center position of the IRF.     width (float):
+    The width of the IRF.
     """
 
     center: float
@@ -130,15 +115,13 @@ class IRF(BaseModel):
 class SimulationConfig(BaseModel):
     """Configuration for the simulation, combining various parameters and settings.
 
-    Attributes
-    ----------
-        kinetic_parameters (KineticParameters): Kinetic parameters for the simulation.
-        spectral_parameters (SpectralParameters): Spectral parameters for the simulation.
-        coordinates (Dict[str, np.ndarray]): Dictionary containing the time and spectral axes as
-            numpy arrays.
-        settings (Settings): Other settings for the simulation, including noise standard deviation,
-            random seed, and flags for adding Gaussian IRF and using a sequential scheme.
-        irf (IRF): Instrument Response Function (IRF) settings, e.g. center position and width.
+    Attributes ----------     kinetic_parameters (KineticParameters): Kinetic parameters for the
+    simulation.     spectral_parameters (SpectralParameters): Spectral parameters for the
+    simulation.     coordinates (Dict[str, np.ndarray]): Dictionary containing the time and
+    spectral axes as         numpy arrays.     settings (Settings): Other settings for the
+    simulation, including noise standard deviation,         random seed, and flags for adding
+    Gaussian IRF and using a sequential scheme.     irf (IRF): Instrument Response Function (IRF)
+    settings, e.g. center position and width.
     """
 
     kinetic_parameters: KineticParameters

pyparamgui/widget.py

@@ -23,31 +23,24 @@
 class Widget(anywidget.AnyWidget):
     """A widget class for handling simulation parameters, coordinates and settings.
 
-    Attributes
-    ----------
-        _esm (pathlib.Path): Path to the JavaScript file for the widget.
-        _css (pathlib.Path): Path to the CSS file for the widget.
-        decay_rates_input (traitlets.List): List of decay rates as floats.
-        amplitude_input (traitlets.List): List of amplitudes as floats.
-        location_input (traitlets.List): List of locations as floats.
-        width_input (traitlets.List): List of widths as floats.
-        skewness_input (traitlets.List): List of skewness values as floats.
-        timepoints_max_input (traitlets.Int): Maximum number of timepoints.
-        timepoints_stepsize_input (traitlets.Float): Step size for timepoints.
-        wavelength_min_input (traitlets.Float): Minimum wavelength value.
-        wavelength_max_input (traitlets.Float): Maximum wavelength value.
-        wavelength_stepsize_input (traitlets.Float): Step size for wavelength.
-        stdev_noise_input (traitlets.Float): Standard deviation of noise.
-        seed_input (traitlets.Int): Seed for random number generation.
-        add_gaussian_irf_input (traitlets.Bool): Flag to add Gaussian IRF.
-        irf_location_input (traitlets.Float): Location of the IRF center.
-        irf_width_input (traitlets.Float): Width of the IRF.
-        use_sequential_scheme_input (traitlets.Bool): Flag to use sequential scheme.
-        model_file_name_input (traitlets.Unicode): Name of the model file.
-        parameter_file_name_input (traitlets.Unicode): Name of the parameter file.
-        data_file_name_input (traitlets.Unicode): Name of the data file.
-        simulate (traitlets.Unicode): Trigger for simulation.
-        visualize_data (traitlets.Bool): Flag to visualize data.
+    Attributes ----------     _esm (pathlib.Path): Path to the JavaScript file for the widget. _css
+    (pathlib.Path): Path to the CSS file for the widget.     decay_rates_input (traitlets.List):
+    List of decay rates as floats.     amplitude_input (traitlets.List): List of amplitudes as
+    floats.     location_input (traitlets.List): List of locations as floats. width_input
+    (traitlets.List): List of widths as floats.     skewness_input (traitlets.List): List of
+    skewness values as floats.     timepoints_max_input (traitlets.Int): Maximum number of
+    timepoints.     timepoints_stepsize_input (traitlets.Float): Step size for timepoints.
+    wavelength_min_input (traitlets.Float): Minimum wavelength value.     wavelength_max_input
+    (traitlets.Float): Maximum wavelength value.     wavelength_stepsize_input (traitlets.Float):
+    Step size for wavelength.     stdev_noise_input (traitlets.Float): Standard deviation of noise.
+    seed_input (traitlets.Int): Seed for random number generation.     add_gaussian_irf_input
+    (traitlets.Bool): Flag to add Gaussian IRF.     irf_location_input (traitlets.Float): Location
+    of the IRF center.     irf_width_input (traitlets.Float): Width of the IRF.
+    use_sequential_scheme_input (traitlets.Bool): Flag to use sequential scheme.
+    model_file_name_input (traitlets.Unicode): Name of the model file. parameter_file_name_input
+    (traitlets.Unicode): Name of the parameter file. data_file_name_input (traitlets.Unicode): Name
+    of the data file.     simulate (traitlets.Unicode): Trigger for simulation.     visualize_data
+    (traitlets.Bool): Flag to visualize data.
     """
 
     _esm: pathlib.Path = pathlib.Path(__file__).parent / "static" / "form.js"

pyproject.toml

@@ -27,6 +27,7 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
 ]
 dynamic = [
   "version",

tests/test_simulate.py

@@ -36,13 +36,13 @@ def _create_mock_widget():
     return widget
 
 
-@pytest.fixture()
+@pytest.fixture
 def mock_widget():
     """Return a mock Widget for testing."""
     return _create_mock_widget()
 
 
-@pytest.fixture()
+@pytest.fixture
 def temp_dir():
     """Create a temporary directory for testing."""
     with tempfile.TemporaryDirectory() as tmpdirname: