Fix ruff

.github/workflows/pipeline.yml

@@ -43,7 +43,7 @@ jobs:
       - name: Install
         run: |
           python -m pip install --upgrade pip
-          pip install -e ./[testing]
+          pip install -e . --group testing
 
       - name: Test
         if: always()

.github/workflows/ruff.yml

@@ -1,17 +1,15 @@
 name: Ruff
-on: [ push, pull_request ]
+on:
+  push:
+    branches:
+      - master
+      - dev
+  pull_request:
 jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Install Python
-        uses: actions/setup-python@v5
+      - uses: astral-sh/ruff-action@v3
         with:
-          python-version: "3.11"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff
-        run: ruff check --output-format=github  .
+          args: check --output-format=github

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.11.7
+  hooks:
+    # Run the linter.
+    - id: ruff

CADETPythonSimulator/__init__.py

@@ -1,3 +1,4 @@
 """Version information."""
+
 name = "CADET-Python-Simulator"
 __version__ = "0.0.1"

CADETPythonSimulator/componentsystem.py

@@ -1,4 +1,4 @@
-from CADETProcess.processModel import ComponentSystem, Component, Species
+from CADETProcess.processModel import ComponentSystem, Component
 from CADETProcess.dataStructure import UnsignedFloat, String, Integer
 from CADETProcess.dataStructure import Structure
 
@@ -81,16 +81,18 @@ class CPSComponent(Component):
 
     """
 
-    def __init__(self,
-                 name=None,
-                 species=None,
-                 charge=None,
-                 molecular_weight=None,
-                 density=None,
-                 molecular_volume=None,
-                 viscosity=None,
-                 pure_density=None,
-                 specific_cake_resistance=None):
+    def __init__(
+        self,
+        name=None,
+        species=None,
+        charge=None,
+        molecular_weight=None,
+        density=None,
+        molecular_volume=None,
+        viscosity=None,
+        pure_density=None,
+        specific_cake_resistance=None,
+    ):
         """Construct CPSComponent."""
         self.name = name
         self._species = []
@@ -104,7 +106,7 @@ def __init__(self,
                 molecular_volume,
                 viscosity,
                 pure_density,
-                specific_cake_resistance
+                specific_cake_resistance,
             )
         elif isinstance(species, str):
             self.add_species(
@@ -115,7 +117,7 @@ def __init__(self,
                 molecular_volume,
                 viscosity,
                 pure_density,
-                specific_cake_resistance
+                specific_cake_resistance,
             )
         elif isinstance(species, list):
             if charge is None:
@@ -141,7 +143,7 @@ def __init__(self,
                     molecular_volume[i],
                     viscosity[i],
                     pure_density[i],
-                    specific_cake_resistance[i]
+                    specific_cake_resistance[i],
                 )
         else:
             raise CADETPythonSimError("Could not determine number of species")
@@ -182,6 +184,7 @@ def specific_cake_resistance(self):
         """List of float or None: specific cake resistance of the subspecies."""
         return [spec.specific_cake_resistance for spec in self.species]
 
+
 class CPSComponentSystem(ComponentSystem):
     """
     Component System Class.
@@ -228,16 +231,16 @@ class CPSComponentSystem(ComponentSystem):
     """
 
     def __init__(
-            self,
-            components=None,
-            name=None,
-            charges=None,
-            molecular_weights=None,
-            densities=None,
-            molecular_volume=None,
-            viscosities=None,
-            specific_cake_resistances=None
-        ):
+        self,
+        components=None,
+        name=None,
+        charges=None,
+        molecular_weights=None,
+        densities=None,
+        molecular_volume=None,
+        viscosities=None,
+        specific_cake_resistances=None,
+    ):
         """
         Initialize the ComponentSystem object.
 
@@ -295,7 +298,6 @@ def __init__(
         if specific_cake_resistances is None:
             specific_cake_resistances = n_comp * [None]
 
-
         for i, comp in enumerate(components):
             self.add_component(
                 comp,
@@ -304,7 +306,7 @@ def __init__(
                 density=densities[i],
                 molecular_volume=molecular_volume[i],
                 viscosity=viscosities[i],
-                specific_cake_resistance=specific_cake_resistances[i]
+                specific_cake_resistance=specific_cake_resistances[i],
             )
 
     @wraps(CPSComponent.__init__)
@@ -327,8 +329,7 @@ def add_component(self, component, *args, **kwargs):
 
         if component.name in self.names:
             raise CADETPythonSimError(
-                f"Component '{component.name}' "
-                "already exists in ComponentSystem."
+                f"Component '{component.name}' already exists in ComponentSystem."
             )
 
         self._components.append(component)
@@ -356,7 +357,7 @@ def viscosities(self):
         """list: List of species viscosity."""
         viscosities = []
         for comp in self.components:
-            viscosities +=comp.viscosity
+            viscosities += comp.viscosity
 
         return viscosities
 

CADETPythonSimulator/coupling_interface.py

@@ -1,6 +1,5 @@
 import abc
 import numpy as np
-from CADETPythonSimulator.unit_operation import UnitOperationBase
 
 
 class CouplingInterface(abc.ABC):
@@ -10,18 +9,19 @@ class CouplingInterface(abc.ABC):
     def get_coupled_state(
         self,
         origin_list: list[(dict, float)],
-        state: str
-        ) -> np.ndarray:
+        state: str,
+    ) -> np.ndarray:
         """Calculate new state for destination_unit."""
 
 
 class WeightedAverageCoupling(CouplingInterface):
     """Implements the Coupling Interface for average Coupling."""
 
-    def get_coupled_state(self,
-                          origin_list: list[(dict, float)],
-                          state: str
-                          ) -> np.ndarray:
+    def get_coupled_state(
+        self,
+        origin_list: list[(dict, float)],
+        state: str,
+    ) -> np.ndarray:
         """Calculate new state for destination_unit with average Coupling."""
         ret = np.zeros(origin_list[0][0][state].shape)
         rate_tot = 0

CADETPythonSimulator/distribution_base.py

@@ -3,13 +3,15 @@
 from CADETPythonSimulator.componentsystem import CPSComponentSystem
 from CADETPythonSimulator.exception import CADETPythonSimError
 
+
 class DistributionBase:
     """Small wrapper class for implementing Distributions for Boundary Conditions."""
 
-    def get_distribution(t: float, section_nr: int)->np.ndarray:
+    def get_distribution(t: float, section_nr: int) -> np.ndarray:
         """Abtract class to call."""
         pass
 
+
 class ConstantVolumeDistribution(DistributionBase):
     """Implements DistributionBase for a Constant Volume Distribution."""
 
@@ -29,26 +31,19 @@ def __init__(self, component_system: CPSComponentSystem, c: npt.ArrayLike):
 
         n = [i for i in self.c]
         m = [
-            n_i * self.component_system.molecular_weights[i]
-            for i, n_i in enumerate(n)
-        ]
-        V = [
-            m_i / self.component_system.densities[i]
-            for i, m_i in enumerate(m)
+            n_i * self.component_system.molecular_weights[i] for i, n_i in enumerate(n)
         ]
+        V = [m_i / self.component_system.densities[i] for i, m_i in enumerate(m)]
         V_solvent = 1 - sum(V)
 
-        if V_solvent<0:
+        if V_solvent < 0:
             raise CADETPythonSimError(
                 "Last species Volume is negative. Misconfigured Simulation"
-                )
+            )
 
         V.append(V_solvent)
 
-        self.V_dist = [
-            i / sum(V)
-            for i in V
-            ]
+        self.V_dist = [i / sum(V) for i in V]
 
     def get_distribution(self, t, sec) -> list[float]:
         """Return Constant Volume Distribution."""
@@ -72,27 +67,20 @@ def __init__(self, component_system: CPSComponentSystem, c: npt.ArrayLike):
         self.component_system = component_system
 
         n = [i for i in c]
-        m = [
-            n_i * component_system.molecular_weights[i]
-            for i, n_i in enumerate(n)
-        ]
-        V = [
-            m_i / component_system.densities[i]
-            for i, m_i in enumerate(m)
-        ]
+        m = [n_i * component_system.molecular_weights[i] for i, n_i in enumerate(n)]
+        V = [m_i / component_system.densities[i] for i, m_i in enumerate(m)]
         V_solvent = 1 - sum(V)
 
-        if V_solvent<0:
+        if V_solvent < 0:
             raise CADETPythonSimError(
                 "Last species Volume is negative. Misconfigured Simulation"
-                )
+            )
 
         m_solvent = component_system.densities[-1] * V_solvent
         n_solvent = m_solvent / component_system.molecular_weights[-1]
 
         self.c = [*c, n_solvent]
 
-
     def get_distribution(self, t, sec) -> list[float]:
         """Return Constant Concentrations."""
         return self.c

CADETPythonSimulator/field.py

@@ -1,9 +1,8 @@
-from typing import NoReturn, Optional, Union
+from typing import Optional, Union
 
 import numpy as np
 import numpy.typing as npt
 import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
 from scipy.interpolate import RegularGridInterpolator