Use nbqa and ruff to check style of notebooks (#34)

Add `nbqa` and `ruff` to the `environment.yml` file. Add a `Makefile` to
the repo to easily run regular tasks like building the website, running
the notebooks, checking style and autoformatting the notebooks. Add a
`check.yml` GitHub Action to check style of notebooks in PRs.

Author: santisoler

.github/workflows/check.yml

@@ -0,0 +1,31 @@
+name: Check style
+
+on:
+  # Check style after every push to main
+  push:
+    branches:
+      - main
+  # Check style on every PR
+  pull_request:
+
+jobs:
+
+  style:
+    runs-on: ubuntu-latest
+    env:
+      PYTHON: "3.12"
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON }}
+
+      - name: Install required packages
+        run: pip install ruff nbqa
+
+      - name: Check style of notebooks
+        run: make check

Makefile

@@ -0,0 +1,29 @@
+NOTEBOOKS_DIR=notebooks
+
+.PHONY: build run clean check format
+
+help:
+	@echo "Commands:"
+	@echo ""
+	@echo "  build   build Myst website (without running notebooks)"
+	@echo "  clean   clean output of Myst website"
+	@echo "  run     run all notebooks"
+	@echo "  check   lint notebooks with nbqa and ruff"
+	@echo "  format  autoformat notebooks with nbqa and ruff"
+	@echo ""
+
+
+build:
+	msyt build --html
+
+clean:
+	msyt clean --all
+
+run:
+	jupyter nbconvert --to notebook --execute --inplace "${NOTEBOOKS_DIR}/**/*.ipynb"
+
+check:
+	nbqa ruff "${NOTEBOOKS_DIR}"
+
+format:
+	nbqa ruff --fix "${NOTEBOOKS_DIR}"

README.md

@@ -113,6 +113,26 @@ jupyter nbconvert --to notebook --execute --inplace notebooks/**/*.ipynb
 [mystmd.org]: https://mystmd.org
 
 
+## Check style of notebooks
+
+We can check the code style of our notebooks using [`ruff`][ruff] and
+[`nbqa`][nbqa]. Simply run the following command to check the style of the
+notebooks:
+
+```bash
+nbqa ruff notebooks
+```
+
+And run this to autoformat them:
+
+```bash
+nbqa ruff --fix notebooks
+```
+
+Alternatively, you can use the targets we have in the `Makefile`, like `make
+check` and `make format`. Read more information about the available targets
+by running `make help`.
+
 ## License
 
 All text and figures are licensed under a

environment.yml

@@ -13,3 +13,6 @@ dependencies:
   - simpeg==0.22.*
   - discretize==0.10.*
   - pymatsolver
+  # Code quality
+  - nbqa
+  - ruff