👌 Update dependencies and fix compatibility newer python versions

.github/workflows/test.yml

@@ -66,7 +66,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - name: Check out repo

.pre-commit-config.yaml

@@ -3,12 +3,12 @@ repos:
   #    FORMATTER    #
   ###################
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "2.1.4"
+    rev: "v2.20.0"
     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: v0.15.7
     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: v1.19.1
     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: v2.4.2
     hooks:
       - id: codespell
         types: [file]
@@ -100,6 +100,6 @@ repos:
         exclude: ^examples/
 
   - repo: https://github.com/rhysd/actionlint
-    rev: "v1.7.1"
+    rev: "v1.7.11"
     hooks:
       - id: actionlint

README.md

@@ -16,6 +16,38 @@
 
 A pyglotaran based jupyter notebook widget for teaching parameter estimation examples. It can simulate data, visualize it and create related model.yml, parameters.csv and dataset.nc files. It is supposed to help students learn about the basics of the pyglotaran ecosystem.
 
+## Usage
+
+### Option 1: Run directly from GitHub with uv
+
+Install and run PyParamGUI directly from the repository without cloning:
+
+```bash
+uv run --with "pyparamgui @ git+https://github.com/glotaran/pyparamgui" --with jupyter jupyter lab
+```
+
+### Option 2: Run from a local clone
+
+Clone the repository and run with the local source:
+
+```bash
+uv run --with . --with jupyter jupyter lab
+```
+
+### Option 3: Add to an existing uv project
+
+Add PyParamGUI as a dependency to your project:
+
+```bash
+uv add "pyparamgui @ git+https://github.com/glotaran/pyparamgui"
+```
+
+Then run Jupyter Lab in your project environment:
+
+```bash
+uv run jupyter lab
+```
+
 ## Contributors ✨
 
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
@@ -26,7 +58,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 <table>
   <tbody>
     <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/anmolbhatia05"><img src="https://avatars.githubusercontent.com/u/34206963?v=4?s=100" width="100px;" alt="Anmol Bhatia"/><br /><sub><b>Anmol Bhatia</b></sub></a><br /><a href="https://github.com/glotaran/PyParamGUI/commits?author=anmolbhatia05" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/anmolbhatia05"><img src="https://avatars.githubusercontent.com/u/34206963?v=4?s=100" width="100px;" alt="Anmol Bhatia"/><br /><sub><b>Anmol Bhatia</b></sub></a><br /><a href="https://github.com/glotaran/pyparamgui/commits?author=anmolbhatia05" title="Code">💻</a></td>
     </tr>
   </tbody>
 </table>

pyparamgui/__init__.py

@@ -11,7 +11,6 @@
 __all__ = ["Widget"]
 """
 Package Usage:
-    %env ANYWIDGET_HMR=1
     from pyparamgui import Widget
 
     widget = Widget()

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)
         }
@@ -275,4 +275,4 @@ def generate_model_yml(*, generator_name: str, generator_arguments: GeneratorArg
         )
         raise ValueError(msg)
     model = generators[generator_name](**generator_arguments)
-    return cast(str, write_dict(model))
+    return cast("str", write_dict(model))

pyparamgui/schema.py

@@ -15,7 +15,8 @@ class KineticParameters(BaseModel):
 
     Attributes
     ----------
-        decay_rates (list[float]): List of decay rates.
+    decay_rates : list[float]
+        List of decay rates.
     """
 
     decay_rates: list[float]
@@ -26,10 +27,14 @@ class SpectralParameters(BaseModel):
 
     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]
+        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]
@@ -43,8 +48,10 @@ class TimeCoordinates(BaseModel):
 
     Attributes
     ----------
-        timepoints_max (int): Maximum number of time points.
-        timepoints_stepsize (float): Step size between time points.
+    timepoints_max : int
+        Maximum number of time points.
+    timepoints_stepsize : float
+        Step size between time points.
     """
 
     timepoints_max: int
@@ -56,9 +63,12 @@ class SpectralCoordinates(BaseModel):
 
     Attributes
     ----------
-        wavelength_min (int): Minimum wavelength.
-        wavelength_max (int): Maximum wavelength.
-        wavelength_stepsize (float): Step size between wavelengths.
+    wavelength_min : int
+        Minimum wavelength.
+    wavelength_max : int
+        Maximum wavelength.
+    wavelength_stepsize : float
+        Step size between wavelengths.
     """
 
     wavelength_min: int
@@ -100,12 +110,14 @@ class Settings(BaseModel):
 
     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
+        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
@@ -119,8 +131,10 @@ class IRF(BaseModel):
 
     Attributes
     ----------
-        center (float): The center position of the IRF.
-        width (float): The width of the IRF.
+    center : float
+        The center position of the IRF.
+    width : float
+        The width of the IRF.
     """
 
     center: float
@@ -132,13 +146,17 @@ class SimulationConfig(BaseModel):
 
     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
+        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