From 7fb3b8f437d608fbea8edab417d2bba10b58bcc0 Mon Sep 17 00:00:00 2001
From: Saransh Chopra <saransh0701@gmail.com>
Date: Tue, 7 Mar 2023 23:15:00 +0530
Subject: [PATCH 1/3] Add pre-commit and ruff

---
 .flake8                               |  3 --
 .pre-commit-config.yaml               | 15 ++++++++++
 benchmarks/benchmarks.py              |  3 --
 examples/basic_16p2s.py               | 40 +++++++++++++++------------
 examples/big_circuit.py               |  4 +--
 examples/drive_cycle.py               |  6 ++--
 examples/drive_cycle_comparison.py    |  8 ++++--
 examples/paper_example.py             | 31 ++++++++++++---------
 examples/save_output.py               | 37 ++++++++++++++-----------
 examples/step_external_variable.py    |  2 +-
 examples/thermal_external.py          | 25 +++++++++--------
 liionpack/netlist_utils.py            |  4 +--
 liionpack/protocols.py                |  2 --
 liionpack/solvers.py                  | 10 ++-----
 liionpack/utils.py                    | 14 +++++-----
 tests/integration/test_1p1s.py        | 22 ++++++++-------
 tests/integration/test_all_solvers.py |  4 +--
 tests/unit/test_netlist_utils.py      |  2 +-
 tests/unit/test_notebooks.py          |  1 -
 tests/unit/test_simulations.py        |  5 ++--
 tests/unit/test_utils.py              | 37 ++++++++++++-------------
 21 files changed, 149 insertions(+), 126 deletions(-)
 delete mode 100644 .flake8
 create mode 100644 .pre-commit-config.yaml

diff --git a/.flake8 b/.flake8
deleted file mode 100644
index 5c1a3fb8..00000000
--- a/.flake8
+++ /dev/null
@@ -1,3 +0,0 @@
-[flake8]
-max-line-length = 89
-ignore = F403 F401 W503 E741 E203 W605
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..d35257c9
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,15 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.0.254"
+    hooks:
+      - id: ruff
+        args: [--ignore=E741, --exclude=__init__.py]
diff --git a/benchmarks/benchmarks.py b/benchmarks/benchmarks.py
index b9f02b2a..3139ffd5 100644
--- a/benchmarks/benchmarks.py
+++ b/benchmarks/benchmarks.py
@@ -14,7 +14,6 @@ def time_solve_model(self):
 
 
 class SmallPack:
-
     timeout = 60
 
     def setup(self):
@@ -47,7 +46,6 @@ def time_discharge_2cpu(self):
 
 
 class MediumPack:
-
     timeout = 120
 
     def setup(self):
@@ -80,7 +78,6 @@ def time_discharge_2cpu(self):
 
 
 class LargePack:
-
     timeout = 600
 
     def setup(self):
diff --git a/examples/basic_16p2s.py b/examples/basic_16p2s.py
index de25cb9c..5199d827 100644
--- a/examples/basic_16p2s.py
+++ b/examples/basic_16p2s.py
@@ -8,7 +8,7 @@
 import numpy as np
 import os
 
-lp.set_logging_level('NOTICE')
+lp.set_logging_level("NOTICE")
 
 # Define parameters
 Np = 16
@@ -19,31 +19,35 @@
 netlist = lp.setup_circuit(Np=Np, Ns=Ns)
 
 # Define additional output variables
-output_variables = [
-    'Volume-averaged cell temperature [K]']
+output_variables = ["Volume-averaged cell temperature [K]"]
 
 # Define a cycling experiment using PyBaMM
-experiment = pybamm.Experiment([
-    f'Charge at {Iapp} A for 30 minutes',
-    'Rest for 15 minutes',
-    f'Discharge at {Iapp} A for 30 minutes',
-    'Rest for 30 minutes'],
-    period='10 seconds')
+experiment = pybamm.Experiment(
+    [
+        f"Charge at {Iapp} A for 30 minutes",
+        "Rest for 15 minutes",
+        f"Discharge at {Iapp} A for 30 minutes",
+        "Rest for 30 minutes",
+    ],
+    period="10 seconds",
+)
 
 # Define the PyBaMM parameters
 parameter_values = pybamm.ParameterValues("Chen2020")
 inputs = {"Total heat transfer coefficient [W.m-2.K-1]": np.ones(Np * Ns) * 10}
 
 # Solve the pack
-output = lp.solve(netlist=netlist,
-                  sim_func=lp.thermal_simulation,
-                  parameter_values=parameter_values,
-                  experiment=experiment,
-                  output_variables=output_variables,
-                  initial_soc=0.5,
-                  inputs=inputs,
-                  nproc=os.cpu_count(),
-                  manager='casadi')
+output = lp.solve(
+    netlist=netlist,
+    sim_func=lp.thermal_simulation,
+    parameter_values=parameter_values,
+    experiment=experiment,
+    output_variables=output_variables,
+    initial_soc=0.5,
+    inputs=inputs,
+    nproc=os.cpu_count(),
+    manager="casadi",
+)
 
 # Plot the pack and individual cell results
 lp.plot_pack(output)
diff --git a/examples/big_circuit.py b/examples/big_circuit.py
index d6917136..6c9a0d36 100644
--- a/examples/big_circuit.py
+++ b/examples/big_circuit.py
@@ -7,7 +7,7 @@
 import os
 import pickle
 
-lp.log_to_file('logger_info')
+lp.log_to_file("logger_info")
 
 
 if __name__ == "__main__":
@@ -41,5 +41,5 @@
         nproc=os.cpu_count(),
     )
 
-    with open('output.pickle', 'wb') as handle:
+    with open("output.pickle", "wb") as handle:
         pickle.dump(output, handle, protocol=pickle.HIGHEST_PROTOCOL)
diff --git a/examples/drive_cycle.py b/examples/drive_cycle.py
index 166fed35..d419d8ca 100644
--- a/examples/drive_cycle.py
+++ b/examples/drive_cycle.py
@@ -27,7 +27,8 @@
 experiment = pybamm.Experiment(
     operating_conditions=["Run US06 (A)"],
     period="1 minute",
-    drive_cycles={"US06": drive_cycle})
+    drive_cycles={"US06": drive_cycle},
+)
 
 # PyBaMM parameters
 parameter_values = pybamm.ParameterValues("Chen2020")
@@ -37,7 +38,8 @@
     netlist=netlist,
     parameter_values=parameter_values,
     experiment=experiment,
-    initial_soc=0.5)
+    initial_soc=0.5,
+)
 
 # Plot results
 lp.plot_output(output)
diff --git a/examples/drive_cycle_comparison.py b/examples/drive_cycle_comparison.py
index 03bb4642..6b5a9d6f 100644
--- a/examples/drive_cycle_comparison.py
+++ b/examples/drive_cycle_comparison.py
@@ -48,15 +48,17 @@
         experiment=experiment,
         output_variables=output_variables,
         initial_soc=init_SoC,
-        manager='casadi',
-        nproc=8)
+        manager="casadi",
+        nproc=8,
+    )
 
     parameter_values = pybamm.ParameterValues("Chen2020")
 
     sim = pybamm.Simulation(
         model=pybamm.lithium_ion.SPM(),
         experiment=experiment,
-        parameter_values=parameter_values)
+        parameter_values=parameter_values,
+    )
 
     sol = sim.solve(initial_soc=init_SoC)
 
diff --git a/examples/paper_example.py b/examples/paper_example.py
index 09521962..31b8b998 100644
--- a/examples/paper_example.py
+++ b/examples/paper_example.py
@@ -10,27 +10,32 @@
 
 # Define some additional variables to output
 output_variables = [
-    'X-averaged negative particle surface concentration [mol.m-3]',
-    'X-averaged positive particle surface concentration [mol.m-3]',
+    "X-averaged negative particle surface concentration [mol.m-3]",
+    "X-averaged positive particle surface concentration [mol.m-3]",
 ]
 
 # Cycling experiment, using PyBaMM
-experiment = pybamm.Experiment([
-    "Charge at 5 A for 30 minutes",
-    "Rest for 15 minutes",
-    "Discharge at 5 A for 30 minutes",
-    "Rest for 30 minutes"],
-    period="10 seconds")
+experiment = pybamm.Experiment(
+    [
+        "Charge at 5 A for 30 minutes",
+        "Rest for 15 minutes",
+        "Discharge at 5 A for 30 minutes",
+        "Rest for 30 minutes",
+    ],
+    period="10 seconds",
+)
 
 # PyBaMM battery parameters
 parameter_values = pybamm.ParameterValues("Chen2020")
 
 # Solve the pack problem
-output = lp.solve(netlist=netlist,
-                  parameter_values=parameter_values,
-                  experiment=experiment,
-                  output_variables=output_variables,
-                  initial_soc=0.5)
+output = lp.solve(
+    netlist=netlist,
+    parameter_values=parameter_values,
+    experiment=experiment,
+    output_variables=output_variables,
+    initial_soc=0.5,
+)
 
 # Display the results
 lp.plot_output(output, color="white")
diff --git a/examples/save_output.py b/examples/save_output.py
index 414d8f32..8647a4f4 100644
--- a/examples/save_output.py
+++ b/examples/save_output.py
@@ -17,15 +17,18 @@
 netlist = lp.setup_circuit(Np=Np, Ns=Ns)
 
 # Define additional output variables
-output_variables = ['Volume-averaged cell temperature [K]']
+output_variables = ["Volume-averaged cell temperature [K]"]
 
 # Define a cycling experiment using PyBaMM
-experiment = pybamm.Experiment([
-    f'Charge at {Iapp} A for 30 minutes',
-    'Rest for 15 minutes',
-    f'Discharge at {Iapp} A for 30 minutes',
-    'Rest for 30 minutes'],
-    period='10 seconds')
+experiment = pybamm.Experiment(
+    [
+        f"Charge at {Iapp} A for 30 minutes",
+        "Rest for 15 minutes",
+        f"Discharge at {Iapp} A for 30 minutes",
+        "Rest for 30 minutes",
+    ],
+    period="10 seconds",
+)
 
 # Define the PyBaMM parameters
 chemistry = pybamm.parameter_sets.Chen2020
@@ -33,15 +36,17 @@
 inputs = {"Total heat transfer coefficient [W.m-2.K-1]": np.ones(Np * Ns) * 10}
 
 # Solve the pack
-output = lp.solve(netlist=netlist,
-                  sim_func=lp.thermal_simulation,
-                  parameter_values=parameter_values,
-                  experiment=experiment,
-                  output_variables=output_variables,
-                  initial_soc=0.5,
-                  inputs=inputs,
-                  nproc=os.cpu_count(),
-                  manager='casadi')
+output = lp.solve(
+    netlist=netlist,
+    sim_func=lp.thermal_simulation,
+    parameter_values=parameter_values,
+    experiment=experiment,
+    output_variables=output_variables,
+    initial_soc=0.5,
+    inputs=inputs,
+    nproc=os.cpu_count(),
+    manager="casadi",
+)
 
 # Save simulation output to CSV files
 lp.save_to_csv(output)
diff --git a/examples/step_external_variable.py b/examples/step_external_variable.py
index 229d6eaa..8bb4c8ca 100644
--- a/examples/step_external_variable.py
+++ b/examples/step_external_variable.py
@@ -53,7 +53,7 @@
     inputs=inputs,
     nproc=2,
     initial_soc=0.5,
-    setup_only=True
+    setup_only=True,
 )
 
 
diff --git a/examples/thermal_external.py b/examples/thermal_external.py
index 79c6b703..0ae9f644 100644
--- a/examples/thermal_external.py
+++ b/examples/thermal_external.py
@@ -6,7 +6,8 @@
 import pybamm
 import numpy as np
 import matplotlib.pyplot as plt
-plt.close('all')
+
+plt.close("all")
 
 
 # Generate the netlist
@@ -15,13 +16,11 @@
 # Define some additional variables to output
 output_variables = [
     "Volume-averaged cell temperature [K]",
-    "Volume-averaged total heating [W.m-3]"
+    "Volume-averaged total heating [W.m-3]",
 ]
 
 # Cycling experiment, using PyBaMM
-experiment = pybamm.Experiment([
-    "Discharge at 5 A for 5 minutes"],
-    period="10 seconds")
+experiment = pybamm.Experiment(["Discharge at 5 A for 5 minutes"], period="10 seconds")
 
 # PyBaMM battery parameters
 parameter_values = pybamm.ParameterValues("Chen2020")
@@ -29,13 +28,15 @@
 # Solve the pack problem
 temps = np.ones(4) * 300 + np.arange(4) * 10
 inputs = {"Input temperature [K]": temps}
-output = lp.solve(netlist=netlist,
-                  sim_func=lp.thermal_external,
-                  inputs=inputs,
-                  parameter_values=parameter_values,
-                  experiment=experiment,
-                  output_variables=output_variables,
-                  initial_soc=0.5)
+output = lp.solve(
+    netlist=netlist,
+    sim_func=lp.thermal_external,
+    inputs=inputs,
+    parameter_values=parameter_values,
+    experiment=experiment,
+    output_variables=output_variables,
+    initial_soc=0.5,
+)
 
 # Display the results
 lp.plot_output(output, color="white")
diff --git a/liionpack/netlist_utils.py b/liionpack/netlist_utils.py
index 3cb2a6fe..63f2ea9a 100644
--- a/liionpack/netlist_utils.py
+++ b/liionpack/netlist_utils.py
@@ -114,7 +114,7 @@ def setup_circuit(
     V=4.2,
     plot=False,
     terminals="left",
-    configuration="parallel-strings"
+    configuration="parallel-strings",
 ):
     """
     Define a netlist from a number of batteries in parallel and series
@@ -757,7 +757,7 @@ def write_netlist(netlist, filename):
 
     """
     lines = ["* " + filename]
-    for (i, r) in netlist.iterrows():
+    for i, r in netlist.iterrows():
         line = r.desc + " " + _fn(r.node1) + " " + _fn(r.node2) + " " + str(r.value)
         lines.append(line)
     lines.append(".op")
diff --git a/liionpack/protocols.py b/liionpack/protocols.py
index fe7bfbe9..a9df22c6 100644
--- a/liionpack/protocols.py
+++ b/liionpack/protocols.py
@@ -2,8 +2,6 @@
 # Experimental protocol
 #
 
-import numpy as np
-
 
 def generate_protocol_from_experiment(experiment, flatten=True):
     """
diff --git a/liionpack/solvers.py b/liionpack/solvers.py
index b2f79c27..976a2470 100644
--- a/liionpack/solvers.py
+++ b/liionpack/solvers.py
@@ -282,7 +282,7 @@ def __init__(
     #         "Total stepping time " + str(np.around(toc - sim_start_time, 3)) + "s"
     #     )
     #     lp.logger.notice(
-    #         "Time per step " + str(np.around((toc - sim_start_time) / Nsteps, 3)) + "s"
+    #        "Time per step " + str(np.around((toc - sim_start_time) / Nsteps, 3)) + "s"
     #     )
     #     return self.all_output
 
@@ -351,9 +351,7 @@ def solve(
 
         # Handle the inputs
         self.inputs = inputs
-        self.inputs_dict = lp.build_inputs_dict(
-            self.shm_i_app[0, :], self.inputs, None
-        )
+        self.inputs_dict = lp.build_inputs_dict(self.shm_i_app[0, :], self.inputs, None)
         # Solver specific setup
         self.setup_actors(nproc, self.inputs_dict, initial_soc)
         # Get the initial state of the system
@@ -434,9 +432,7 @@ def _step(self, step, updated_inputs):
             # for the next step
             I_app = I_batt[:] * -1
             self.shm_i_app[step + 1, :] = I_app
-            self.inputs_dict = lp.build_inputs_dict(
-                I_app, self.inputs, updated_inputs
-            )
+            self.inputs_dict = lp.build_inputs_dict(I_app, self.inputs, updated_inputs)
         # 06 Check if voltage limits are reached and terminate
         if np.any(temp_v < self.v_cut_lower):
             lp.logger.warning("Low voltage limit reached")
diff --git a/liionpack/utils.py b/liionpack/utils.py
index a7e88494..4e637502 100644
--- a/liionpack/utils.py
+++ b/liionpack/utils.py
@@ -102,7 +102,7 @@ def add_events_to_model(model):
     return model
 
 
-def save_to_csv(output, path='./csv-results'):
+def save_to_csv(output, path="./csv-results"):
     """
     Save simulation output to a CSV file for each output variable.
 
@@ -126,11 +126,11 @@ def save_to_csv(output, path='./csv-results'):
 
     # Save simulation output to CSV files
     for k, v in output.items():
-        filename = k.replace(' ', '_') + '.csv'
-        np.savetxt(path / filename, v, delimiter=', ')
+        filename = k.replace(" ", "_") + ".csv"
+        np.savetxt(path / filename, v, delimiter=", ")
 
 
-def save_to_npy(output, path='./npy-results'):
+def save_to_npy(output, path="./npy-results"):
     """
     Save simulation output to NumPy `.npy` files where each file represents an
     output variable.
@@ -155,11 +155,11 @@ def save_to_npy(output, path='./npy-results'):
 
     # Save simulation output to npy files
     for k, v in output.items():
-        filename = k.replace(' ', '_') + '.npy'
+        filename = k.replace(" ", "_") + ".npy"
         np.save(path / filename, v)
 
 
-def save_to_npzcomp(output, path='.'):
+def save_to_npzcomp(output, path="."):
     """
     Save simulation output to a compressed NumPy `output.npz` file. The saved
     file is a dictionary-like object where each key represents a simulation
@@ -185,5 +185,5 @@ def save_to_npzcomp(output, path='.'):
     path.mkdir(exist_ok=True)
 
     # Save simulation output to a compressed npz file
-    filename = 'output.npz'
+    filename = "output.npz"
     np.savez_compressed(path / filename, **output)
diff --git a/tests/integration/test_1p1s.py b/tests/integration/test_1p1s.py
index b87d9b5b..e00ae423 100644
--- a/tests/integration/test_1p1s.py
+++ b/tests/integration/test_1p1s.py
@@ -21,15 +21,15 @@ def test_consistent_results_1_step(self):
         )
         # Solve pack
         output = lp.solve(
-            netlist=netlist,
-            parameter_values=parameter_values,
-            experiment=experiment
+            netlist=netlist, parameter_values=parameter_values, experiment=experiment
         )
 
         parameter_values = pybamm.ParameterValues("Chen2020")
-        sim = pybamm.Simulation(model=pybamm.lithium_ion.SPM(),
-                                parameter_values=parameter_values,
-                                experiment=experiment)
+        sim = pybamm.Simulation(
+            model=pybamm.lithium_ion.SPM(),
+            parameter_values=parameter_values,
+            experiment=experiment,
+        )
 
         sol = sim.solve()
         a = output["Terminal voltage [V]"].flatten()
@@ -61,13 +61,15 @@ def test_consistent_results_2_step(self):
             netlist=netlist,
             parameter_values=parameter_values,
             experiment=experiment,
-            initial_soc=SoC
+            initial_soc=SoC,
         )
 
         parameter_values = pybamm.ParameterValues("Chen2020")
-        sim = pybamm.Simulation(model=pybamm.lithium_ion.SPM(),
-                                parameter_values=parameter_values,
-                                experiment=experiment)
+        sim = pybamm.Simulation(
+            model=pybamm.lithium_ion.SPM(),
+            parameter_values=parameter_values,
+            experiment=experiment,
+        )
 
         sol = sim.solve(initial_soc=SoC)
         a = output["Terminal voltage [V]"].flatten()
diff --git a/tests/integration/test_all_solvers.py b/tests/integration/test_all_solvers.py
index 3b55e1f3..a0e29b7e 100644
--- a/tests/integration/test_all_solvers.py
+++ b/tests/integration/test_all_solvers.py
@@ -27,7 +27,7 @@ def test_consistent_results_1_step(self):
             experiment=experiment,
             inputs=None,
             nproc=1,
-            manager="casadi"
+            manager="casadi",
         )
         # Solve pack with ray
         b = lp.solve(
@@ -36,7 +36,7 @@ def test_consistent_results_1_step(self):
             experiment=experiment,
             inputs=None,
             nproc=1,
-            manager="ray"
+            manager="ray",
         )
 
         v_a = a["Terminal voltage [V]"]
diff --git a/tests/unit/test_netlist_utils.py b/tests/unit/test_netlist_utils.py
index a33d6df4..24aad9ac 100644
--- a/tests/unit/test_netlist_utils.py
+++ b/tests/unit/test_netlist_utils.py
@@ -137,7 +137,7 @@ def test_lcapy_circuit(self):
     def test_write_netlist(self):
         net = lp.setup_circuit(Np=1, Ns=2, Rb=1e-4, Rc=1e-2, Ri=1e-3, V=2.0, I=10.0)
         cwd = os.getcwd()
-        temp = os.path.join(cwd, 'temp.txt')
+        temp = os.path.join(cwd, "temp.txt")
         lp.write_netlist(net, temp)
         assert os.path.isfile(temp)
         os.remove(temp)
diff --git a/tests/unit/test_notebooks.py b/tests/unit/test_notebooks.py
index ef7deba5..287fbc76 100644
--- a/tests/unit/test_notebooks.py
+++ b/tests/unit/test_notebooks.py
@@ -14,7 +14,6 @@ class TestNotebooks(unittest.TestCase):
     def test_notebooks(self):
         examples_folder = os.path.join(lp.ROOT_DIR, "docs", "examples")
         for filename in os.listdir(examples_folder):
-
             if os.path.splitext(filename)[1] == ".ipynb":
                 print("-" * 80)
                 print("Testing notebook:", filename)
diff --git a/tests/unit/test_simulations.py b/tests/unit/test_simulations.py
index c4234bf7..cadb4255 100644
--- a/tests/unit/test_simulations.py
+++ b/tests/unit/test_simulations.py
@@ -11,8 +11,9 @@ def test_basic_simulation(self):
 
     def test_thermal_simulation(self):
         sim = lp.thermal_simulation()
-        sim.solve([0, 1800],
-                  inputs={"Total heat transfer coefficient [W.m-2.K-1]": 1.0})
+        sim.solve(
+            [0, 1800], inputs={"Total heat transfer coefficient [W.m-2.K-1]": 1.0}
+        )
         assert sim.__class__ == pybamm.Simulation
 
     # def test_thermal_external(self):
diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py
index 76daa70a..e94746de 100644
--- a/tests/unit/test_utils.py
+++ b/tests/unit/test_utils.py
@@ -7,11 +7,10 @@
 
 
 class utilsTest(unittest.TestCase):
-
     def setUp(self):
         currents = [4, 5.2, 8, 10]
         volts = np.array([[3.5, 3.6], [3.54, 3.58]])
-        output = {'currents': currents, 'volts': volts}
+        output = {"currents": currents, "volts": volts}
 
         self.currents = currents
         self.volts = volts
@@ -41,50 +40,50 @@ def test_build_inputs_dict(self):
         assert len(in_dict) == 2
 
     def test_save_to_csv(self):
-        lp.save_to_csv(self.output, path='.')
+        lp.save_to_csv(self.output, path=".")
 
-        with open('currents.csv', 'r') as f:
+        with open("currents.csv", "r") as f:
             current = float(f.readline())
         self.assertEqual(self.currents[0], current)
 
-        with open('volts.csv', 'r') as f:
-            volts = list(map(float, f.readline().split(', ')))
+        with open("volts.csv", "r") as f:
+            volts = list(map(float, f.readline().split(", ")))
         self.assertEqual(self.volts[0][0], volts[0])
 
     def test_save_to_npy(self):
-        lp.save_to_npy(self.output, path='.')
+        lp.save_to_npy(self.output, path=".")
 
-        currents = np.load('currents.npy')
+        currents = np.load("currents.npy")
         self.assertEqual(self.currents[0], currents[0])
 
-        volts = np.load('volts.npy')
+        volts = np.load("volts.npy")
         self.assertEqual(self.volts[0, 0], volts[0, 0])
 
     def test_save_to_npz(self):
-        lp.save_to_npzcomp(self.output, path='.')
+        lp.save_to_npzcomp(self.output, path=".")
 
-        output = np.load('output.npz')
-        currents = output['currents']
+        output = np.load("output.npz")
+        currents = output["currents"]
         self.assertEqual(self.currents[0], currents[0])
 
-        output = np.load('output.npz')
-        volts = output['volts']
+        output = np.load("output.npz")
+        volts = output["volts"]
         self.assertEqual(self.volts[0, 0], volts[0, 0])
 
     def tearDown(self):
-        path = pathlib.Path('currents.csv')
+        path = pathlib.Path("currents.csv")
         path.unlink(missing_ok=True)
 
-        path = pathlib.Path('volts.csv')
+        path = pathlib.Path("volts.csv")
         path.unlink(missing_ok=True)
 
-        path = pathlib.Path('currents.npy')
+        path = pathlib.Path("currents.npy")
         path.unlink(missing_ok=True)
 
-        path = pathlib.Path('volts.npy')
+        path = pathlib.Path("volts.npy")
         path.unlink(missing_ok=True)
 
-        path = pathlib.Path('output.npz')
+        path = pathlib.Path("output.npz")
         path.unlink(missing_ok=True)
 
 

From f8c03ee1594e0134522bbd0fbb1321359d449735 Mon Sep 17 00:00:00 2001
From: Saransh Chopra <saransh0701@gmail.com>
Date: Tue, 7 Mar 2023 23:18:19 +0530
Subject: [PATCH 2/3] Update docs + preserve git blame

---
 .git-blame-ignore-revs             |  2 ++
 .github/workflows/test_on_push.yml |  7 +++----
 docs/contributing.md               | 31 +++++++++++++++++++++++++-----
 environment.yml                    |  2 +-
 4 files changed, 32 insertions(+), 10 deletions(-)
 create mode 100644 .git-blame-ignore-revs

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
new file mode 100644
index 00000000..2afd1142
--- /dev/null
+++ b/.git-blame-ignore-revs
@@ -0,0 +1,2 @@
+# activated pre-commit
+7fb3b8f437d608fbea8edab417d2bba10b58bcc0
diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
index c08d1c58..221f852a 100644
--- a/.github/workflows/test_on_push.yml
+++ b/.github/workflows/test_on_push.yml
@@ -28,11 +28,10 @@ jobs:
       with:
         python-version: 3.8
 
-    - name: Lint with flake8
+    - name: Lint with ruff
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8
-        flake8
+        python -m pip install --upgrade pip pre-commit
+        pre-commit run ruff
 
   pip-build:
     needs: style
diff --git a/docs/contributing.md b/docs/contributing.md
index 419a3592..19b9051c 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -8,6 +8,23 @@ If you're already familiar with our workflow, maybe have a quick look at the [pr
 
 Fork the repository and create a pull request. Github actions should check that tests are passing.
 
+### Installing and using pre-commit
+
+`PyBaMM` uses a set of `pre-commit` hooks and the `pre-commit` bot to format and prettify the codebase. The hooks can be installed locally using -
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+This would run the checks every time a commit is created locally. The checks will only run on the files modified by that commit, but the checks can be triggered for all the files using -
+
+```bash
+pre-commit run --all-files
+```
+
+If you would like to skip the failing checks and push the code for further discussion, use the `--no-verify` option with `git commit`.
+
 ## Workflow
 
 We use [GIT](https://en.wikipedia.org/wiki/Git) and [GitHub](https://en.wikipedia.org/wiki/GitHub) to coordinate our work. When making any kind of update, we try to follow the procedure below.
@@ -44,20 +61,24 @@ You now have everything you need to start making changes!
 
 liionpack follows the [PEP8 recommendations](https://www.python.org/dev/peps/pep-0008/) for coding style. These are very common guidelines, and community tools have been developed to check how well projects implement them.
 
-### Flake8
+### Ruff
 
-We use [flake8](http://flake8.pycqa.org/en/latest/) to check our PEP8 adherence. To try this on your system, navigate to the liionpack directory in a console and type
+We use [ruff](https://github.com/charliermarsh/ruff) to check our PEP8 adherence. To try this on your system, navigate to the PyBaMM directory in a console and type
 
 ```bash
-flake8
+python -m pip install pre-commit
+pre-commit run ruff
 ```
 
+ruff is configured inside the file `pre-commit-config.yaml`, allowing us to ignore some errors. If you think this should be added or removed, please submit an [issue](#issues)
+
+When you commit your changes they will be checked against ruff automatically (see [infrastructure](#infrastructure)).
 
 ### Black
 
 We use [black](https://black.readthedocs.io/en/stable/) to automatically configure our code to adhere to PEP8. Black can be used in two ways:
 
-1. Command line: navigate to the liionpack directory in a console and type
+1. Command line: navigate to the PyBaMM directory in a console and type
 
 ```bash
 black {source_file_or_directory}
@@ -67,7 +88,7 @@ black {source_file_or_directory}
 
 If you want to use black in your editor, you may need to change the max line length in your editor settings.
 
-Even when code has been formatted by black, you should still make sure that it adheres to the PEP8 standard set by [Flake8](#flake8).
+Even when code has been formatted by black, you should still make sure that it adheres to the PEP8 standard set by [Ruff](#ruff).
 
 ### Naming
 
diff --git a/environment.yml b/environment.yml
index 938fdb0b..93bb2a6f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -27,7 +27,7 @@ dependencies:
   - ipython
   - jupyter
   - sympy
-  - flake8
+  - ruff
   - pip
   - pip:
     - pybamm>=23.2

From c574babafee3d79f45ad4dd66c728bd08cf3d51f Mon Sep 17 00:00:00 2001
From: Saransh Chopra <saransh0701@gmail.com>
Date: Wed, 8 Mar 2023 00:05:17 +0530
Subject: [PATCH 3/3] PyBaMM -> liionpack

---
 docs/contributing.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/contributing.md b/docs/contributing.md
index 19b9051c..afd6ffce 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -10,7 +10,7 @@ Fork the repository and create a pull request. Github actions should check that
 
 ### Installing and using pre-commit
 
-`PyBaMM` uses a set of `pre-commit` hooks and the `pre-commit` bot to format and prettify the codebase. The hooks can be installed locally using -
+`liionpack` uses a set of `pre-commit` hooks and the `pre-commit` bot to format and prettify the codebase. The hooks can be installed locally using -
 
 ```bash
 pip install pre-commit
@@ -63,7 +63,7 @@ liionpack follows the [PEP8 recommendations](https://www.python.org/dev/peps/pep
 
 ### Ruff
 
-We use [ruff](https://github.com/charliermarsh/ruff) to check our PEP8 adherence. To try this on your system, navigate to the PyBaMM directory in a console and type
+We use [ruff](https://github.com/charliermarsh/ruff) to check our PEP8 adherence. To try this on your system, navigate to the liionpack directory in a console and type
 
 ```bash
 python -m pip install pre-commit
@@ -78,7 +78,7 @@ When you commit your changes they will be checked against ruff automatically (se
 
 We use [black](https://black.readthedocs.io/en/stable/) to automatically configure our code to adhere to PEP8. Black can be used in two ways:
 
-1. Command line: navigate to the PyBaMM directory in a console and type
+1. Command line: navigate to the liionpack directory in a console and type
 
 ```bash
 black {source_file_or_directory}
@@ -194,7 +194,7 @@ wherever code is called that uses that citation (for example, in functions or in
 
 ## Benchmarks
 
-A benchmark suite is located in the `benchmarks` directory at the root of the PyBaMM project. These benchmarks can be run using [airspeed velocity](https://asv.readthedocs.io/en/stable/) (`asv`).
+A benchmark suite is located in the `benchmarks` directory at the root of the liionpack project. These benchmarks can be run using [airspeed velocity](https://asv.readthedocs.io/en/stable/) (`asv`).
 
 ### Running the benchmarks
 First of all, you'll need `asv` installed:
@@ -219,7 +219,7 @@ asv run commit_ID..develop
 ```
 Further information on how to run benchmarks with `asv` can be found in the documentation at [Using airspeed velocity](https://asv.readthedocs.io/en/stable/using.html).
 
-`asv` is configured using a file `asv.conf.json` located at the root of the PyBaMM repository. See the [asv reference](https://asv.readthedocs.io/en/stable/reference.html) for details on available settings and options.
+`asv` is configured using a file `asv.conf.json` located at the root of the liionpack repository. See the [asv reference](https://asv.readthedocs.io/en/stable/reference.html) for details on available settings and options.
 
 Benchmark results are stored in a directory `results/` at the location of the configuration file. There is one result file per commit, per machine.
 
@@ -235,7 +235,7 @@ then, to view the website:
 asv preview
 ```
 
-Current benchmarks over PyBaMM's history can be viewed at https://pybamm-team.github.io/liionpack-bench/
+Current benchmarks over liionpack's history can be viewed at https://pybamm-team.github.io/liionpack-bench/
 
 ### Adding benchmarks