Add nbQA for notebook and docs linting (#361)

* Add NBQA for notebook and docs linting

This is now possible after nbQA-dev/nbQA#745 which solved this issue (nbQA-dev/nbQA#668) I opened a year ago.

* Run pre-commit filters on all files

* Lint

* bump

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update os

* Fix all nbqa issues

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -11,9 +11,17 @@ repos:
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
-      - id: black
+      - id: black-jupyter
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: "v0.0.261"
     hooks:
       - id: ruff
         args: ["--fix"]
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-black
+        additional_dependencies: [jupytext, black]
+      - id: nbqa
+        args: ["ruff", "--fix", "--ignore=E402,B018,F704"]
+        additional_dependencies: [jupytext, ruff]

docs/source/algorithms_and_examples.md

@@ -1,15 +1,13 @@
 ---
-kernelspec:
-  name: python3
-  display_name: python3
 jupytext:
   text_representation:
     extension: .md
     format_name: myst
-    format_version: '0.13'
-    jupytext_version: 1.13.8
-execution:
-  timeout: 300
+    format_version: 0.13
+    jupytext_version: 1.14.5
+kernelspec:
+  display_name: python3
+  name: python3
 ---
 
 ```{include} ../../README.md
@@ -101,16 +99,17 @@ def plot_loss_interval(learner):
     return hv.Scatter((x, y)).opts(size=6, color="r")
 
 
-def plot(learner, npoints):
-    adaptive.runner.simple(learner, npoints_goal= npoints)
+def plot_interval(learner, npoints):
+    adaptive.runner.simple(learner, npoints_goal=npoints)
     return (learner.plot() * plot_loss_interval(learner))[:, -1.1:1.1]
 
 
 def get_hm(loss_per_interval, N=101):
     learner = adaptive.Learner1D(f, bounds=(-1, 1), loss_per_interval=loss_per_interval)
-    plots = {n: plot(learner, n) for n in range(N)}
+    plots = {n: plot_interval(learner, n) for n in range(N)}
     return hv.HoloMap(plots, kdims=["npoints"])
 
+
 plot_homo = get_hm(uniform_loss).relabel("homogeneous sampling")
 plot_adaptive = get_hm(default_loss).relabel("with adaptive")
 layout = plot_homo + plot_adaptive
@@ -122,7 +121,6 @@ layout.opts(toolbar=None)
 ```{code-cell} ipython3
 :tags: [hide-input]
 
-
 def ring(xy):
     import numpy as np
 
@@ -131,7 +129,7 @@ def ring(xy):
     return x + np.exp(-((x**2 + y**2 - 0.75**2) ** 2) / a**4)
 
 
-def plot(learner, npoints):
+def plot_compare(learner, npoints):
     adaptive.runner.simple(learner, npoints_goal=npoints)
     learner2 = adaptive.Learner2D(ring, bounds=learner.bounds)
     xs = ys = np.linspace(*learner.bounds[0], int(learner.npoints**0.5))
@@ -146,7 +144,7 @@ def plot(learner, npoints):
 
 
 learner = adaptive.Learner2D(ring, bounds=[(-1, 1), (-1, 1)])
-plots = {n: plot(learner, n) for n in range(4, 1010, 20)}
+plots = {n: plot_compare(learner, n) for n in range(4, 1010, 20)}
 hv.HoloMap(plots, kdims=["npoints"]).collate()
 ```
 
@@ -155,7 +153,6 @@ hv.HoloMap(plots, kdims=["npoints"]).collate()
 ```{code-cell} ipython3
 :tags: [hide-input]
 
-
 def g(n):
     import random
 
@@ -167,12 +164,12 @@ def g(n):
 learner = adaptive.AverageLearner(g, atol=None, rtol=0.01)
 
 
-def plot(learner, npoints):
+def plot_avg(learner, npoints):
     adaptive.runner.simple(learner, npoints_goal=npoints)
     return learner.plot().relabel(f"loss={learner.loss():.2f}")
 
 
-plots = {n: plot(learner, n) for n in range(10, 10000, 200)}
+plots = {n: plot_avg(learner, n) for n in range(10, 10000, 200)}
 hv.HoloMap(plots, kdims=["npoints"])
 ```
 
@@ -181,7 +178,6 @@ hv.HoloMap(plots, kdims=["npoints"])
 ```{code-cell} ipython3
 :tags: [hide-input]
 
-
 def sphere(xyz):
     import numpy as np
 

docs/source/logo.md

@@ -4,19 +4,16 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.14.1
+    jupytext_version: 1.14.5
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
   name: python3
-execution:
-  timeout: 300
 ---
 
 ```{code-cell} ipython3
 :tags: [remove-input]
 
-import os
 import functools
 import subprocess
 import tempfile
@@ -75,7 +72,7 @@ def remove_rounded_corners(fname):
 
 def learner_till(till, learner, data):
     new_learner = adaptive.Learner2D(None, bounds=learner.bounds)
-    new_learner.data = {k: v for k, v in data[:till]}
+    new_learner.data = dict(data[:till])
     for x, y in learner._bounds_points:
         # always include the bounds
         new_learner.tell((x, y), learner.data[x, y])

docs/source/tutorial/tutorial.BalancingLearner.md

@@ -1,14 +1,15 @@
 ---
-kernelspec:
-  name: python3
-  display_name: python3
 jupytext:
   text_representation:
     extension: .md
     format_name: myst
-    format_version: '0.13'
-    jupytext_version: 1.13.8
+    format_version: 0.13
+    jupytext_version: 1.14.5
+kernelspec:
+  display_name: python3
+  name: python3
 ---
+
 # Tutorial {class}`~adaptive.BalancingLearner`
 
 ```{note}
@@ -60,7 +61,10 @@ runner.live_info()
 ```
 
 ```{code-cell} ipython3
-plotter = lambda learner: hv.Overlay([L.plot() for L in learner.learners])
+def plotter(learner):
+    return hv.Overlay([L.plot() for L in learner.learners])
+
+
 runner.live_plot(plotter=plotter, update_interval=0.1)
 ```
 
@@ -83,7 +87,7 @@ combos = {
 }
 
 learner = adaptive.BalancingLearner.from_product(
-    jacobi, adaptive.Learner1D, dict(bounds=(0, 1)), combos
+    jacobi, adaptive.Learner1D, {"bounds": (0, 1)}, combos
 )
 
 runner = adaptive.BlockingRunner(learner, loss_goal=0.01)

docs/source/tutorial/tutorial.DataSaver.md

@@ -69,7 +69,7 @@ runner.live_info()
 ```
 
 ```{code-cell} ipython3
-runner.live_plot(plotter=lambda l: l.learner.plot(), update_interval=0.1)
+runner.live_plot(plotter=lambda lrn: lrn.learner.plot(), update_interval=0.1)
 ```
 
 Now the `DataSavingLearner` will have an dictionary attribute `extra_data` that has `x` as key and the data that was returned by `learner.function` as values.

docs/source/tutorial/tutorial.IntegratorLearner.md

@@ -1,14 +1,15 @@
 ---
-kernelspec:
-  name: python3
-  display_name: python3
 jupytext:
   text_representation:
     extension: .md
     format_name: myst
-    format_version: '0.13'
-    jupytext_version: 1.13.8
+    format_version: 0.13
+    jupytext_version: 1.14.5
+kernelspec:
+  display_name: python3
+  name: python3
 ---
+
 # Tutorial {class}`~adaptive.IntegratorLearner`
 
 ```{note}
@@ -60,9 +61,7 @@ learner = adaptive.IntegratorLearner(f24, bounds=(0, 3), tol=1e-8)
 # We use a SequentialExecutor, which runs the function to be learned in
 # *this* process only. This means we don't pay
 # the overhead of evaluating the function in another process.
-runner = adaptive.Runner(
-    learner, executor=SequentialExecutor()
-)
+runner = adaptive.Runner(learner, executor=SequentialExecutor())
 ```
 
 ```{code-cell} ipython3

docs/source/tutorial/tutorial.Learner1D.md

@@ -1,14 +1,15 @@
 ---
-kernelspec:
-  name: python3
-  display_name: python3
 jupytext:
   text_representation:
     extension: .md
     format_name: myst
-    format_version: '0.13'
-    jupytext_version: 1.13.8
+    format_version: 0.13
+    jupytext_version: 1.14.5
+kernelspec:
+  display_name: python3
+  name: python3
 ---
+
 (TutorialLearner1D)=
 # Tutorial {class}`~adaptive.Learner1D`
 
@@ -112,6 +113,8 @@ random.seed(0)
 offsets = [random.uniform(-0.8, 0.8) for _ in range(3)]
 
 # sharp peaks at random locations in the domain
+
+
 def f_levels(x, offsets=offsets):
     a = 0.01
     return np.array(
@@ -124,7 +127,9 @@ The `Learner1D` can be used for such functions:
 
 ```{code-cell} ipython3
 learner = adaptive.Learner1D(f_levels, bounds=(-1, 1))
-runner = adaptive.Runner(learner, loss_goal=0.01)  # continue until `learner.loss()<=0.01`
+runner = adaptive.Runner(
+    learner, loss_goal=0.01
+)  # continue until `learner.loss()<=0.01`
 ```
 
 ```{code-cell} ipython3
@@ -211,12 +216,14 @@ learner.to_numpy()
 ```
 
 If Pandas is installed (optional dependency), you can also run
+
 ```{code-cell} ipython3
 df = learner.to_dataframe()
 df
 ```
 
 and load that data into a new learner with
+
 ```{code-cell} ipython3
 new_learner = adaptive.Learner1D(learner.function, (-1, 1))  # create an empty learner
 new_learner.load_dataframe(df)  # load the pandas.DataFrame's data

docs/source/tutorial/tutorial.Learner2D.md

@@ -1,14 +1,15 @@
 ---
-kernelspec:
-  name: python3
-  display_name: python3
 jupytext:
   text_representation:
     extension: .md
     format_name: myst
-    format_version: '0.13'
-    jupytext_version: 1.13.8
+    format_version: 0.13
+    jupytext_version: 1.14.5
+kernelspec:
+  display_name: python3
+  name: python3
 ---
+
 # Tutorial {class}`~adaptive.Learner2D`
 
 ```{note}
@@ -24,6 +25,7 @@ import holoviews as hv
 import numpy as np
 
 from functools import partial
+
 adaptive.notebook_extension()
 ```
 

docs/source/tutorial/tutorial.LearnerND.md

@@ -1,16 +1,15 @@
 ---
-kernelspec:
-  name: python3
-  display_name: python3
 jupytext:
   text_representation:
     extension: .md
     format_name: myst
-    format_version: '0.13'
-    jupytext_version: 1.13.8
-execution:
-  timeout: 300
+    format_version: 0.13
+    jupytext_version: 1.14.5
+kernelspec:
+  display_name: python3
+  name: python3
 ---
+
 # Tutorial {class}`~adaptive.LearnerND`
 
 ```{note}
@@ -111,6 +110,7 @@ You could use the following code as an example:
 ```{code-cell} ipython3
 import scipy
 
+
 def f(xyz):
     x, y, z = xyz
     return x**4 + y**4 + z**4 - (x**2 + y**2 + z**2) ** 2