Merge pull request #245 from pybop-team/244-add-reorder-python-import…

…s-to-pre-commit

Adds import linting with ruff

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+- [#245](https://github.com/pybop-team/PyBOP/pull/245) - Updates ruff config for import linting.
 - [#198](https://github.com/pybop-team/PyBOP/pull/198) - Adds default subplot trace options, removes `[]` in axis plots as per SI standard, add varying signal length to quick_plot, restores design optimisation execption.
 - [#224](https://github.com/pybop-team/PyBOP/pull/224) - Updated prediction objects to dictionaries, cost class calculations, added `additional_variables` argument to problem class, updated scipy.minimize defualt method to Nelder-Mead, added gradient cost landscape plots with optional argument.
 - [#179](https://github.com/pybop-team/PyBOP/pull/203) - Adds `asv` configuration for benchmarking and initial benchmark suite.

benchmarks/benchmark_model.py

@@ -1,5 +1,7 @@
-import pybop
 import numpy as np
+
+import pybop
+
 from .benchmark_utils import set_random_seed
 
 

benchmarks/benchmark_optim_construction.py

@@ -1,5 +1,7 @@
-import pybop
 import numpy as np
+
+import pybop
+
 from .benchmark_utils import set_random_seed
 
 

benchmarks/benchmark_parameterisation.py

@@ -1,5 +1,7 @@
-import pybop
 import numpy as np
+
+import pybop
+
 from .benchmark_utils import set_random_seed
 
 

benchmarks/benchmark_track_parameterisation.py

@@ -1,5 +1,7 @@
-import pybop
 import numpy as np
+
+import pybop
+
 from .benchmark_utils import set_random_seed
 
 

conftest.py

@@ -1,6 +1,6 @@
-import pytest
 import matplotlib
 import plotly
+import pytest
 
 plotly.io.renderers.default = None
 matplotlib.use("Template")

examples/notebooks/equivalent_circuit_identification.ipynb

@@ -72,8 +72,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pybop\n",
-    "import numpy as np"
+    "import numpy as np\n",
+    "\n",
+    "import pybop"
    ]
   },
   {

examples/notebooks/spm_Adam.ipynb

@@ -82,8 +82,9 @@
    },
    "outputs": [],
    "source": [
-    "import pybop\n",
-    "import numpy as np"
+    "import numpy as np\n",
+    "\n",
+    "import pybop"
    ]
   },
   {

examples/notebooks/spm_CMAES.ipynb

@@ -80,8 +80,9 @@
    },
    "outputs": [],
    "source": [
-    "import pybop\n",
-    "import numpy as np"
+    "import numpy as np\n",
+    "\n",
+    "import pybop"
    ]
   },
   {

examples/notebooks/spm_scipy_DifferentialEvolution.ipynb

@@ -80,8 +80,9 @@
    },
    "outputs": [],
    "source": [
-    "import pybop\n",
-    "import numpy as np"
+    "import numpy as np\n",
+    "\n",
+    "import pybop"
    ]
   },
   {

examples/scripts/ecm_CMAES.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Import the ECM parameter set from JSON
 params = pybop.ParameterSet(
     json_path="examples/scripts/parameters/initial_ecm_parameters.json"

examples/scripts/exp_UKF.py

@@ -1,6 +1,7 @@
-import pybop
-import pybamm
 import numpy as np
+import pybamm
+
+import pybop
 from examples.standalone.model import ExponentialDecay
 
 # Parameter set and model definition

examples/scripts/spm_CMAES.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Define model
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPM(parameter_set=parameter_set)

examples/scripts/spm_IRPropMin.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Define model
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPM(parameter_set=parameter_set)

examples/scripts/spm_MLE.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Define model
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPM(parameter_set=parameter_set)

examples/scripts/spm_SNES.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Define model
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPM(parameter_set=parameter_set)

examples/scripts/spm_UKF.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Parameter set and model definition
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPM(parameter_set=parameter_set)

examples/scripts/spm_XNES.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Define model
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPM(parameter_set=parameter_set)

examples/scripts/spm_adam.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Parameter set and model definition
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPMe(parameter_set=parameter_set)

examples/scripts/spm_descent.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Parameter set and model definition
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPMe(parameter_set=parameter_set)

examples/scripts/spm_pso.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 # Define model
 parameter_set = pybop.ParameterSet.pybamm("Chen2020")
 model = pybop.lithium_ion.SPM(parameter_set=parameter_set)

examples/scripts/spm_scipymin.py

@@ -1,6 +1,7 @@
-import pybop
 import pandas as pd
 
+import pybop
+
 # Form dataset
 Measurements = pd.read_csv("examples/scripts/Chen_example.csv", comment="#").to_numpy()
 dataset = pybop.Dataset(

examples/scripts/spme_max_energy.py

@@ -1,6 +1,5 @@
 import pybop
 
-
 # A design optimisation example loosely based on work by L.D. Couto
 # available at https://doi.org/10.1016/j.energy.2022.125966.
 

examples/standalone/cost.py

@@ -1,6 +1,7 @@
-import pybop
 import numpy as np
 
+import pybop
+
 
 class StandaloneCost(pybop.BaseCost):
     """

examples/standalone/problem.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 from pybop._problem import BaseProblem
 
 

noxfile.py

@@ -1,6 +1,6 @@
 import os
-import nox
 
+import nox
 
 # nox options
 nox.options.reuse_existing_virtualenvs = True

pybop/_dataset.py

@@ -1,5 +1,5 @@
-import pybamm
 import numpy as np
+import pybamm
 
 
 class Dataset:

pybop/_optimisation.py

@@ -1,8 +1,10 @@
-import pybop
-import pints
-import numpy as np
 import warnings
 
+import numpy as np
+import pints
+
+import pybop
+
 
 class Optimisation:
     """

pybop/_problem.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 import pybop
 
 

pybop/costs/_likelihoods.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 from pybop.costs.base_cost import BaseCost
 
 

pybop/costs/base_cost.py

@@ -1,6 +1,7 @@
-from pybop import BaseProblem
 import numpy as np
 
+from pybop import BaseProblem
+
 
 class BaseCost:
     """

pybop/costs/design_costs.py

@@ -1,6 +1,7 @@
-import numpy as np
 import warnings
 
+import numpy as np
+
 from pybop import is_numeric
 from pybop.costs.base_cost import BaseCost
 

pybop/models/base_model.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
+
+import copy
 from dataclasses import dataclass
 from typing import Any, Dict, Optional
-import pybamm
-import copy
-import numpy as np
+
 import casadi
+import numpy as np
+import pybamm
 
 Inputs = Dict[str, float]
 

pybop/models/empirical/ecm.py

@@ -1,4 +1,5 @@
 import pybamm
+
 from .ecm_base import ECircuitModel
 
 

pybop/models/lithium_ion/echem.py

@@ -1,4 +1,5 @@
 import pybamm
+
 from .echem_base import EChemBaseModel
 
 

pybop/models/lithium_ion/echem_base.py

@@ -1,4 +1,5 @@
 import warnings
+
 from ..base_model import BaseModel
 
 

pybop/observers/observer.py

@@ -1,5 +1,7 @@
 from typing import List, Optional
+
 import numpy as np
+
 from pybop._problem import BaseProblem
 from pybop.models.base_model import BaseModel, Inputs, TimeSeriesState
 from pybop.parameters.parameter import Parameter

pybop/observers/unscented_kalman.py

@@ -1,7 +1,8 @@
 from dataclasses import dataclass
+from typing import List, Tuple, Union
+
 import numpy as np
 import scipy.linalg as linalg
-from typing import List, Tuple, Union
 
 from pybop.models.base_model import BaseModel, Inputs
 from pybop.observers.observer import Observer

pybop/optimisers/pints_optimisers.py

@@ -1,5 +1,5 @@
-import pints
 import numpy as np
+import pints
 
 
 class GradientDescent(pints.GradientDescent):

pybop/optimisers/scipy_optimisers.py

@@ -1,6 +1,7 @@
-from scipy.optimize import minimize, differential_evolution
-from .base_optimiser import BaseOptimiser
 import numpy as np
+from scipy.optimize import differential_evolution, minimize
+
+from .base_optimiser import BaseOptimiser
 
 
 class SciPyMinimize(BaseOptimiser):

pybop/parameters/parameter_set.py

@@ -1,6 +1,8 @@
 import json
 import types
+
 import pybamm
+
 import pybop
 
 

pybop/parameters/priors.py

@@ -1,5 +1,5 @@
-import scipy.stats as stats
 import numpy as np
+import scipy.stats as stats
 
 
 class Gaussian:

pybop/plotting/plot2d.py

@@ -1,7 +1,9 @@
 import sys
-import pybop
+
 import numpy as np
 
+import pybop
+
 
 def plot2d(
     cost_or_optim, gradient=False, bounds=None, steps=10, show=True, **layout_kwargs

pybop/plotting/plot_convergence.py

@@ -1,7 +1,9 @@
 import sys
-import pybop
+
 import numpy as np
 
+import pybop
+
 
 def plot_convergence(optim, show=True, **layout_kwargs):
     """