Merge pull request #64 from pybop-team/58-pre-commit

Adds pre-commit

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -27,4 +27,4 @@ body:
     id: context
     attributes:
       label: Additional context
-      description: Add any additional context about the feature request.
+      description: Add any additional context about the feature request.

.github/workflows/release-action.yaml

@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/pybop 
+      url: https://pypi.org/p/pybop
     permissions:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
 
@@ -107,4 +107,4 @@ jobs:
     - name: Publish distribution 📦 to TestPyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        repository-url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/

.github/workflows/test_on_push.yaml

@@ -14,6 +14,21 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Check formatting with pre-commit
+        run: |
+          python -m pip install pre-commit
+          pre-commit run ruff
+
+
   build:
     runs-on: ubuntu-latest
     strategy:
@@ -61,4 +76,4 @@ jobs:
       - name: Upload coverage report
         uses: codecov/codecov-action@v3
         env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.0.292"
+    hooks:
+      - id: ruff
+        args: [--fix, --ignore=E741, --exclude=__init__.py]
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-ruff
+        additional_dependencies: [ruff==0.0.284]
+        args: ["--fix","--ignore=E501,E402"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+        - id: check-added-large-files
+        - id: check-case-conflict
+        - id: check-merge-conflict
+        - id: check-yaml
+        - id: debug-statements
+        - id: end-of-file-fixer
+        - id: mixed-line-ending
+        - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+        - id: python-check-blanket-type-ignore
+        - id: rst-backticks
+        - id: rst-directive-colons
+        - id: rst-inline-touching-normal

CONTRIBUTING.md

@@ -8,6 +8,22 @@ Before you commit any code, please perform the following checks:
 
 - [All tests pass](#testing): `$ nox -s unit_test`
 
+### Installing and using pre-commit
+
+`PyBOP` 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
 
@@ -279,4 +295,4 @@ GitHub does some magic with particular filenames. In particular:
 ## Acknowledgements
 
 This CONTRIBUTING.md file, along with large sections of the code infrastructure,
-was copied from the excellent [Pints repo](https://github.com/pints-team/pints), and [PyBaMM repo](https://github.com/pybamm-team/PyBaMM)
+was copied from the excellent [Pints repo](https://github.com/pints-team/pints), and [PyBaMM repo](https://github.com/pybamm-team/PyBaMM)

README.md

@@ -151,7 +151,7 @@ def getdata(x0):
 x0 = np.array([0.55, 0.63])
 solution = getdata(x0)
 ```
-Next, the observed variables are defined, with the model construction and parameter definitions following. Finally, the parameterisation class is constructed and parameter fitting is completed. 
+Next, the observed variables are defined, with the model construction and parameter definitions following. Finally, the parameterisation class is constructed and parameter fitting is completed.
 ```python
 observations = [
     pybop.Observed("Time [s]", solution["Time [s]"].data),
@@ -197,7 +197,7 @@ learning from the success of the [PyBaMM](https://pybamm.org/) community. Our va
 
 -   Inclusivity and fairness (those who want to contribute may do so, and their input is appropriately recognised)
 
--   Inter-operability (aiming for modularity to enable maximum impact and inclusivity)
+-   Interoperability (aiming for modularity to enable maximum impact and inclusivity)
 
 -   User-friendliness (putting user requirements first, thinking about user-assistance & workflows)
 
@@ -226,4 +226,4 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specifications. Contributions of any kind are welcome! See `contributing.md` for ways to get started.
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specifications. Contributions of any kind are welcome! See `contributing.md` for ways to get started.

examples/notebooks/rmse-estimisation.ipynb

@@ -220,7 +220,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, we define the targetted forward model parameters for estimation. Furthermore, PyBOP provides functionality to define a prior for the parameters. The initial parameters values used in the estimiation will be randomly drawn from the prior distribution."
+    "Next, we define the targeted forward model parameters for estimation. Furthermore, PyBOP provides functionality to define a prior for the parameters. The initial parameters values used in the estimiation will be randomly drawn from the prior distribution."
    ]
   },
   {

tests/unit/test_parameterisations.py

@@ -118,4 +118,34 @@ def getdata(self, model, x0):
         sim = model.predict(experiment=experiment)
         return sim
 
+    @pytest.mark.unit
+    def test_simulate_without_build_model(self):
+        # Define model
+        model = pybop.lithium_ion.SPM()
 
+        with pytest.raises(
+            ValueError, match="Model must be built before calling simulate"
+        ):
+            model.simulate(None, None)
+
+    @pytest.mark.unit
+    def test_priors(self):
+        # Tests priors
+        Gaussian = pybop.Gaussian(0.5, 1)
+        Uniform = pybop.Uniform(0, 1)
+        Exponential = pybop.Exponential(1)
+
+        np.testing.assert_allclose(Gaussian.pdf(0.5), 0.3989422804014327, atol=1e-4)
+        np.testing.assert_allclose(Uniform.pdf(0.5), 1, atol=1e-4)
+        np.testing.assert_allclose(Exponential.pdf(1), 0.36787944117144233, atol=1e-4)
+
+    @pytest.mark.unit
+    def test_parameter_set(self):
+        # Tests parameter set creation
+        with pytest.raises(ValueError):
+            pybop.ParameterSet("pybamms", "Chen2020")
+
+        parameter_test = pybop.ParameterSet("pybamm", "Chen2020")
+        np.testing.assert_allclose(
+            parameter_test["Negative electrode active material volume fraction"], 0.75
+        )