changes from pre-commit

pyparamgui/__init__.py

@@ -6,6 +6,7 @@
 __email__ = "[email protected]"
 __version__ = "0.0.1"
 
-from .widget import widget, setup_widget_observer
+from pyparamgui.widget import setup_widget_observer
+from pyparamgui.widget import widget
 
-__all__ = ['widget', 'setup_widget_observer']
+__all__ = ["widget", "setup_widget_observer"]

pyparamgui/generator.py

@@ -1,4 +1,4 @@
-"""The glotaran generator module."""     
+"""The glotaran generator module."""
 
 from __future__ import annotations
 
@@ -60,15 +60,15 @@ def _generate_decay_model(
                 "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"
+                "skewness": f"shapes.species_{i+1}.skewness",
             }
             for i in range(nr_compartments)
         }
         model["dataset"]["dataset_1"]["global_megacomplex"] = [  # type:ignore[index]
             "megacomplex_spectral"
         ]
         model["dataset"]["dataset_1"]["spectral_axis_inverted"] = True
-        model["dataset"]["dataset_1"]["spectral_axis_scale"] = 1E7
+        model["dataset"]["dataset_1"]["spectral_axis_scale"] = 1e7
     if irf:
         model["dataset"]["dataset_1"]["irf"] = "gaussian_irf"  # type:ignore[index]
         model["irf"] = {
@@ -193,7 +193,7 @@ class GeneratorArguments(TypedDict, total=False):
     irf: bool
 
 
-def generate_model(*, generator_name: str, generator_arguments: GeneratorArguments) -> Model:  
+def generate_model(*, generator_name: str, generator_arguments: GeneratorArguments) -> Model:
     """Generate a model.
 
     Parameters

pyparamgui/schema.py

@@ -1,20 +1,25 @@
-"""This module has the different model classes representing different parameters, coordinates, and settings for simulation."""
+"""This module has the different model classes representing different parameters, coordinates, and
+settings for simulation."""
 
 from __future__ import annotations
 
 from typing import Dict
 
 import numpy as np
-from pydantic import BaseModel, ConfigDict
+from pydantic import BaseModel
+from pydantic import ConfigDict
+
 
 class KineticParameters(BaseModel):
     """Kinetic parameters for the simulation.
 
     Attributes:
         decay_rates (list[float]): List of decay rates.
     """
+
     decay_rates: list[float]
 
+
 class SpectralParameters(BaseModel):
     """Spectral parameters for the simulation.
 
@@ -24,38 +29,43 @@ class SpectralParameters(BaseModel):
         width (list[float]): List of widths.
         skewness (list[float]): List of skewness values.
     """
+
     amplitude: list[float]
     location: list[float]
     width: list[float]
     skewness: list[float]
 
+
 class TimeCoordinates(BaseModel):
-    """
-    Time coordinates for the simulation.
+    """Time coordinates for the simulation.
 
     Attributes:
         timepoints_max (int): Maximum number of time points.
         timepoints_stepsize (float): Step size between time points.
     """
+
     timepoints_max: int
     timepoints_stepsize: float
 
+
 class SpectralCoordinates(BaseModel):
-    """
-    Spectral coordinates for the simulation.
+    """Spectral coordinates for the simulation.
 
     Attributes:
         wavelength_min (int): Minimum wavelength.
         wavelength_max (int): Maximum wavelength.
         wavelength_stepsize (float): Step size between wavelengths.
     """
+
     wavelength_min: int
     wavelength_max: int
     wavelength_stepsize: float
-
-def generate_simulation_coordinates(time_coordinates: TimeCoordinates, spectral_coordinates: SpectralCoordinates) -> Dict[str, np.ndarray]:
-    """
-    Generate simulation coordinates based on time and spectral coordinates.
+
+
+def generate_simulation_coordinates(
+    time_coordinates: TimeCoordinates, spectral_coordinates: SpectralCoordinates
+) -> Dict[str, np.ndarray]:
+    """Generate simulation coordinates based on time and spectral coordinates.
 
     Args:
         time_coordinates (TimeCoordinates): The time coordinates for the simulation.
@@ -64,39 +74,49 @@ def generate_simulation_coordinates(time_coordinates: TimeCoordinates, spectral_
     Returns:
         Dict[str, np.ndarray]: A dictionary containing the time and spectral axes as numpy arrays.
     """
-    time_axis = np.arange(0, time_coordinates.timepoints_max * time_coordinates.timepoints_stepsize, time_coordinates.timepoints_stepsize)
-    spectral_axis = np.arange(spectral_coordinates.wavelength_min, spectral_coordinates.wavelength_max, spectral_coordinates.wavelength_stepsize)
+    time_axis = np.arange(
+        0,
+        time_coordinates.timepoints_max * time_coordinates.timepoints_stepsize,
+        time_coordinates.timepoints_stepsize,
+    )
+    spectral_axis = np.arange(
+        spectral_coordinates.wavelength_min,
+        spectral_coordinates.wavelength_max,
+        spectral_coordinates.wavelength_stepsize,
+    )
     return {"time": time_axis, "spectral": spectral_axis}
 
+
 class Settings(BaseModel):
-    """
-    Other settings for the simulation.
+    """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): Flag to indicate whether to add a Gaussian Instrument Response Function (IRF) to the simulation. Default is False.
         use_sequential_scheme (bool): Flag to indicate whether to use a sequential scheme in the simulation. Default is False.
     """
+
     stdev_noise: float
     seed: int
     add_gaussian_irf: bool = False
     use_sequential_scheme: bool = False
 
+
 class IRF(BaseModel):
-    """
-    Instrument Response Function (IRF) settings for the simulation.
+    """Instrument Response Function (IRF) settings for the simulation.
 
     Attributes:
         center (float): The center position of the IRF.
         width (float): The width of the IRF.
     """
+
     center: float
     width: float
 
+
 class SimulationConfig(BaseModel):
-    """
-    Configuration for the simulation, combining various parameters and settings.
+    """Configuration for the simulation, combining various parameters and settings.
 
     Attributes:
         kinetic_parameters (KineticParameters): Kinetic parameters for the simulation.
@@ -105,6 +125,7 @@ class SimulationConfig(BaseModel):
         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, including center position and width.
     """
+
     kinetic_parameters: KineticParameters
     spectral_parameters: SpectralParameters
     coordinates: Dict[str, np.ndarray]

pyparamgui/static/form.css

@@ -1,26 +1,26 @@
 form {
-    display: flex;
-    flex-direction: column;
+  display: flex;
+  flex-direction: column;
 }
 .form-group {
-    display: flex;
-    align-items: center;
-    margin-bottom: 10px;
+  display: flex;
+  align-items: center;
+  margin-bottom: 10px;
 }
 label {
-    margin-right: 10px;
-    color: black;
-    width: 150px; 
+  margin-right: 10px;
+  color: black;
+  width: 150px;
 }
 input {
-    flex: 1;
-    margin: 5px 0;
+  flex: 1;
+  margin: 5px 0;
 }
 hr {
-    margin: 20px 0;
-    border: none;
-    border-top: 1px solid #ccc;
+  margin: 20px 0;
+  border: none;
+  border-top: 1px solid #ccc;
 }
 button {
-    margin-top: 10px;
-}
+  margin-top: 10px;
+}