Add pre commit and migrate to ruff

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# activated pre-commit
+7fb3b8f437d608fbea8edab417d2bba10b58bcc0

.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

.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]

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):

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
+
+`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
+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.
@@ -44,14 +61,18 @@ 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 liionpack 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
 
@@ -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
 
@@ -173,7 +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:
@@ -198,7 +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.
 
@@ -214,7 +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
 

environment.yml

@@ -27,7 +27,7 @@ dependencies:
   - ipython
   - jupyter
   - sympy
-  - flake8
+  - ruff
   - pip
   - pip:
     - pybamm>=23.2

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)

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)

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)

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)
 

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")

examples/save_output.py

@@ -17,31 +17,36 @@
 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
 parameter_values = pybamm.ParameterValues(chemistry=chemistry)
 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)

examples/step_external_variable.py

@@ -53,7 +53,7 @@
     inputs=inputs,
     nproc=2,
     initial_soc=0.5,
-    setup_only=True
+    setup_only=True,
 )