Ditch nbqa and use ruff only to lint and format notebooks (#51)

Since `ruff` can run in either scripts and notebooks, we don't need to
rely on `nbqa` to run style checks and autoformats to notebooks. Ditch
`nbqa` from the `environment.yml` and update the Makefile and the
Action.

Author: santisoler

.github/workflows/check.yml

@@ -25,7 +25,7 @@ jobs:
           python-version: ${{ env.PYTHON }}
 
       - name: Install required packages
-        run: pip install ruff nbqa
+        run: pip install ruff
 
       - name: Check style of notebooks
         run: make check

Makefile

@@ -1,15 +1,17 @@
 NOTEBOOKS_DIR=notebooks
 
-.PHONY: build run clean check format
+.PHONY: build run clean check check-style check-format 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        build Myst website (without running notebooks)"
+	@echo "  clean        clean output of Myst website"
+	@echo "  run          run all notebooks"
+	@echo "  check        check notebooks style and format with ruff"
+	@echo "  check-style  check notebooks style with ruff"
+	@echo "  check-format check notebooks format with ruff"
+	@echo "  format       autoformat notebooks with ruff"
 	@echo ""
 
 
@@ -22,8 +24,13 @@ clean:
 run:
 	jupyter nbconvert --to notebook --execute --inplace "${NOTEBOOKS_DIR}/**/*.ipynb"
 
-check:
-	nbqa ruff "${NOTEBOOKS_DIR}"
+check: check-format check-style
+
+check-style:
+	ruff check "${NOTEBOOKS_DIR}"
+
+check-format:
+	ruff format --check "${NOTEBOOKS_DIR}"
 
 format:
-	nbqa ruff --fix "${NOTEBOOKS_DIR}"
+	ruff format "${NOTEBOOKS_DIR}"

README.md

@@ -115,24 +115,31 @@ jupyter nbconvert --to notebook --execute --inplace notebooks/**/*.ipynb
 
 ## 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:
+We can check the code style of our notebooks using [`ruff`][ruff].
+Simply run the following command to check the style of the notebooks:
 
 ```bash
-nbqa ruff notebooks
+ruff check notebooks
+```
+
+You can run the following that the notebooks are correctly formatted:
+
+```bash
+ruff format --check notebooks
 ```
 
 And run this to autoformat them:
 
 ```bash
-nbqa ruff --fix notebooks
+ruff format --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`.
 
+[ruff]: https://astral.sh/ruff
+
 ## License
 
 All text and figures are licensed under a

environment.yml

@@ -15,6 +15,5 @@ dependencies:
   - choclo==0.3.*
   - scikit-learn
   - pymatsolver
-  # Code quality
-  - nbqa
+  # Code style
   - ruff

notebooks/03-gravity/weighting_strategies.ipynb

@@ -354,7 +354,7 @@
    },
    "outputs": [],
    "source": [
-    "data_object = data.Data(survey, dobs=dobs, standard_deviation=uncertainties)\n"
+    "data_object = data.Data(survey, dobs=dobs, standard_deviation=uncertainties)"
    ]
   },
   {
@@ -430,7 +430,7 @@
     "model_map = maps.IdentityMap(nP=nC)  # model consists of a value for each active cell\n",
     "\n",
     "# Define and plot starting model\n",
-    "starting_model = np.zeros(nC)\n"
+    "starting_model = np.zeros(nC)"
    ]
   },
   {
@@ -469,7 +469,7 @@
     "# residual between the observed data and the data predicted for a given model.\n",
     "# Within the data misfit, the residual between predicted and observed data are\n",
     "# normalized by the data's standard deviation.\n",
-    "dmis = data_misfit.L2DataMisfit(data=data_object, simulation=simulation)\n"
+    "dmis = data_misfit.L2DataMisfit(data=data_object, simulation=simulation)"
    ]
   },
   {
@@ -1636,7 +1636,7 @@
     "    np.r_[35.0, 0.0, -40.0], 15.0, mesh.gridCC\n",
     ")\n",
     "ind_sphere = ind_sphere[ind_active]\n",
-    "true_model[ind_sphere] = sphere_density\n"
+    "true_model[ind_sphere] = sphere_density"
    ]
   },
   {

notebooks/04-magnetics/fwd_magnetics_induced_3d.ipynb

@@ -245,15 +245,15 @@
     "receiver_list = [receiver_list]\n",
     "\n",
     "# Define the inducing field\n",
-    "inclination = 90   # inclination [deg]\n",
-    "declination = 0    # declination [deg]\n",
+    "inclination = 90  # inclination [deg]\n",
+    "declination = 0  # declination [deg]\n",
     "amplitude = 50000  # amplitude [nT]\n",
     "\n",
     "source_field = magnetics.sources.UniformBackgroundField(\n",
     "    receiver_list=receiver_list,\n",
     "    amplitude=amplitude,\n",
     "    inclination=inclination,\n",
-    "    declination=declination\n",
+    "    declination=declination,\n",
     ")\n",
     "\n",
     "# Define the survey\n",

notebooks/04-magnetics/fwd_magnetics_mvi_3d.ipynb

@@ -247,15 +247,15 @@
     "receiver_list = [receiver_list]\n",
     "\n",
     "# Define the inducing field\n",
-    "field_inclination = 90   # inclination [deg]\n",
-    "field_declination = 0    # declination [deg]\n",
+    "field_inclination = 90  # inclination [deg]\n",
+    "field_declination = 0  # declination [deg]\n",
     "field_amplitude = 50000  # amplitude [nT]\n",
     "\n",
     "source_field = magnetics.sources.UniformBackgroundField(\n",
     "    receiver_list=receiver_list,\n",
     "    amplitude=field_amplitude,\n",
     "    inclination=field_inclination,\n",
-    "    declination=field_declination\n",
+    "    declination=field_declination,\n",
     ")\n",
     "\n",
     "# Define the survey\n",

notebooks/04-magnetics/inv_magnetics_induced_3d.ipynb

@@ -367,15 +367,15 @@
     "receiver_list = [receiver_list]\n",
     "\n",
     "# Define the inducing field\n",
-    "inclination = 90   # inclination [deg]\n",
-    "declination = 0    # declination [deg]\n",
+    "inclination = 90  # inclination [deg]\n",
+    "declination = 0  # declination [deg]\n",
     "amplitude = 50000  # amplitude [nT]\n",
     "\n",
     "source_field = magnetics.sources.UniformBackgroundField(\n",
     "    receiver_list=receiver_list,\n",
     "    amplitude=amplitude,\n",
     "    inclination=inclination,\n",
-    "    declination=declination\n",
+    "    declination=declination,\n",
     ")\n",
     "\n",
     "# Define the survey\n",