Merge branch 'main' into executable-pages

jarrodmillman · web-flow · commit 270f3f21e7f7 · 2024-12-16T18:38:03.000-08:00
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu, macos]
-        python-version: ["3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -19,27 +19,27 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: 1463d990e0801964764a375260dca598513f3be5 # frozen: v3.3.3
+    rev: bc7af46104f0f5368b95878decf720f9f00c2559 # frozen: v3.4.2
     hooks:
       - id: prettier
         files: \.(md|rst|yml|yaml)
         args: [--prose-wrap=preserve]
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: 9247866fce7128f2c0eaf4a09f437880397d4689 # frozen: v0.16.2
+    rev: 1ac5158c1b0f405350517c218f03d3a21bbb381c # frozen: v0.16.6
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle, --max-line-length=88]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 75b98813cfb7e663870a28c74366a1e99d7bfe79 # frozen: v0.6.9
+    rev: 8b76f04e7e5a9cd259e9d1db7799599355f97cdf # frozen: v0.8.2
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes", "--exit-non-zero-on-fix"]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "d4911cfb7f1010759fde68da196036feeb25b99d" # frozen: v1.11.2
+    rev: "f56614daa94d5cd733d3b7004c5df9caad267b4a" # frozen: v1.13.0
     hooks:
       - id: mypy
         additional_dependencies:
@@ -68,6 +68,8 @@ repos:
             | advanced/interfacing_with_c/numpy_c_api/test_cos_module_np\.py$
             | intro/numpy/solutions/2_a_call_fortran\.py$
             | advanced/advanced_numpy/examples/mandelplot\.py$
+            | intro/numpy/solutions/2_5_markov_chain\.py$
+            | intro/matplotlib/examples/plot_bar\.py$
           )
 
   - repo: https://github.com/codespell-project/codespell
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -33,7 +33,7 @@ Design choices:
 
 * Each chapter should provide a useful basis for a 1‒2 h tutorial.
 * The code should be readable.
-* An idomatic style should be followed, e.g. ``import numpy as np``,
+* An idiomatic style should be followed, e.g. ``import numpy as np``,
   preference for array operations, PEP8 coding conventions.
 
 
diff --git a/advanced/advanced_numpy/examples/wavreader.py b/advanced/advanced_numpy/examples/wavreader.py
@@ -46,6 +46,5 @@
 f.close()
 
 print(
-    "Sample rate: %d, channels: %d"
-    % (wav_header["sample_rate"][0], wav_header["num_channels"][0])
+    f"Sample rate: {wav_header['sample_rate'][0]}, channels: {wav_header['num_channels'][0]}"
 )
diff --git a/advanced/debugging/to_debug.py b/advanced/debugging/to_debug.py
@@ -61,8 +61,7 @@ def compare_optimizers(optimizers):
     print("Benching 1D root-finder optimizers from scipy.optimize:")
     for optimizer in OPTIMIZERS:
         print(
-            "% 20s: % 8i total function calls"
-            % (optimizer.__name__, bench_optimizer(optimizer, param_grid))
+            f"{optimizer.__name__:>20s}: {bench_optimizer(optimizer, param_grid):>8d} total function calls"
         )
 
 
diff --git a/advanced/debugging/to_debug_solution.py b/advanced/debugging/to_debug_solution.py
@@ -61,8 +61,7 @@ def compare_optimizers(optimizers):
     print("Benching 1D root-finder optimizers from scipy.optimize:")
     for optimizer in OPTIMIZERS:
         print(
-            "% 20s: % 8i total function calls"
-            % (optimizer.__name__, bench_optimizer(optimizer, param_grid))
+            f"{optimizer.__name__:>20s}: {bench_optimizer(optimizer, param_grid):>8d} total function calls"
         )
 
 
diff --git a/advanced/mathematical_optimization/examples/helper/compare_optimizers.py b/advanced/mathematical_optimization/examples/helper/compare_optimizers.py
@@ -183,8 +183,8 @@ def mk_costs(ndim=2):
 
                 # Normalize across methods
                 x0_mean = np.mean(all_bench)
-                for method_name in function_bench:
-                    function_bench[method_name][-1] /= x0_mean
+                for _, values in function_bench.items():
+                    values[-1] /= x0_mean
             this_dim_benchs[cost_name] = function_bench
         gradient_less_benchs[ndim] = this_dim_benchs
         print(80 * "_")
diff --git a/advanced/mathematical_optimization/examples/plot_compare_optimizers.py b/advanced/mathematical_optimization/examples/plot_compare_optimizers.py
@@ -86,7 +86,7 @@
         ],
         "o",
         color=color,
-        label="# dim: %i" % n_dim,
+        label=f"# dim: {n_dim}",
     )
 plt.legend(
     loc=(0.47, 0.07),
diff --git a/advanced/optimizing/ica.py b/advanced/optimizing/ica.py
@@ -87,7 +87,7 @@ def _ica_par(X, tol, g, gprime, fun_args, maxit, w_init):
 
         W1 = _sym_decorrelation(W1)
 
-        lim = max(abs(abs(np.diag(W1 @ W.T)) - 1))
+        lim = np.max(np.abs(np.abs(np.diag(W1 @ W.T)) - 1))
         W = W1
         it = it + 1
 
diff --git a/advanced/scipy_sparse/examples/pyamg_with_lobpcg.py b/advanced/scipy_sparse/examples/pyamg_with_lobpcg.py
@@ -36,7 +36,7 @@
 
 for i in range(K):
     plt.subplot(3, 3, i + 1)
-    plt.title("Eigenvector %d" % i)
+    plt.title(f"Eigenvector {i}")
     plt.pcolor(V[:, i].reshape(N, N))
     plt.axis("equal")
     plt.axis("off")
diff --git a/intro/matplotlib/examples/plot_bar.py b/intro/matplotlib/examples/plot_bar.py
@@ -11,18 +11,18 @@
 n = 12
 X = np.arange(n)
 rng = np.random.default_rng()
-Y1 = (1 - X / float(n)) * rng.uniform(0.5, 1.0, n)
-Y2 = (1 - X / float(n)) * rng.uniform(0.5, 1.0, n)
+Y1 = (1 - X / n) * rng.uniform(0.5, 1.0, n)
+Y2 = (1 - X / n) * rng.uniform(0.5, 1.0, n)
 
 plt.axes((0.025, 0.025, 0.95, 0.95))
 plt.bar(X, +Y1, facecolor="#9999ff", edgecolor="white")
 plt.bar(X, -Y2, facecolor="#ff9999", edgecolor="white")
 
-for x, y in zip(X, Y1, strict=True):
-    plt.text(x + 0.4, y + 0.05, f"{y:.2f}", ha="center", va="bottom")
+for x, y in zip(X, Y1):
+    plt.text(x, y + 0.05, f"{y:.2f}", ha="center", va="bottom")
 
-for x, y in zip(X, Y2, strict=True):
-    plt.text(x + 0.4, -y - 0.05, f"{y:.2f}", ha="center", va="top")
+for x, y in zip(X, Y2):
+    plt.text(x, -y - 0.05, f"{y:.2f}", ha="center", va="top")
 
 plt.xlim(-0.5, n)
 plt.xticks([])
diff --git a/intro/matplotlib/examples/plot_plot3d.py b/intro/matplotlib/examples/plot_plot3d.py
@@ -10,9 +10,9 @@
 from mpl_toolkits.mplot3d import Axes3D
 
 ax: Axes3D = plt.figure().add_subplot(projection="3d")
-X = np.arange(-4, 4, 0.25)
-Y = np.arange(-4, 4, 0.25)
-X, Y = np.meshgrid(X, Y)
+x = np.arange(-4, 4, 0.25)
+y = np.arange(-4, 4, 0.25)
+X, Y = np.meshgrid(x, y)
 R = np.sqrt(X**2 + Y**2)
 Z = np.sin(R)
 
diff --git a/intro/matplotlib/examples/pretty_plots/plot_plot3d_ext.py b/intro/matplotlib/examples/pretty_plots/plot_plot3d_ext.py
@@ -9,16 +9,18 @@
 import matplotlib.pyplot as plt
 from mpl_toolkits.mplot3d import Axes3D
 
-fig = plt.figure()
-ax = Axes3D(fig)
-X = np.arange(-4, 4, 0.25)
-Y = np.arange(-4, 4, 0.25)
-X, Y = np.meshgrid(X, Y)
+x = np.arange(-4, 4, 0.25)
+y = np.arange(-4, 4, 0.25)
+X, Y = np.meshgrid(x, y)
 R = np.sqrt(X**2 + Y**2)
 Z = np.sin(R)
 
+fig = plt.figure()
+ax: Axes3D = fig.add_subplot(111, projection="3d")
+
 ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap="hot")
 ax.contourf(X, Y, Z, zdir="z", offset=-2, cmap="hot")
+
 ax.set_zlim(-2, 2)
 plt.xticks([])
 plt.yticks([])
diff --git a/intro/matplotlib/index.rst b/intro/matplotlib/index.rst
@@ -1126,7 +1126,7 @@ from within a python session:
 ::
 
    >>> import matplotlib.pyplot as plt
-   >>> help(plt.plot)
+   >>> help(plt.plot)  # doctest: +SKIP
    Help on function plot in module matplotlib.pyplot:
    <BLANKLINE>
    plot(*args: ...) -> 'list[Line2D]'
diff --git a/packages/scikit-learn/examples/plot_bias_variance.py b/packages/scikit-learn/examples/plot_bias_variance.py
@@ -139,7 +139,7 @@ def generating_func(x, rng=None, error=0.5):
     plt.legend(loc="best")
     plt.xlabel("number of train samples")
     plt.ylabel("explained variance")
-    plt.title("Learning curve (degree=%i)" % d)
+    plt.title(f"Learning curve (degree={d})")
     plt.tight_layout()
 
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,8 +23,12 @@ exclude = '''
   | advanced/interfacing_with_c/numpy_c_api/test_cos_module_np\.py$
   | intro/numpy/solutions/2_a_call_fortran\.py$
   | advanced/advanced_numpy/examples/mandelplot\.py$
+  | intro/numpy/solutions/2_5_markov_chain\.py$
+  | intro/matplotlib/examples/plot_bar\.py$
 )
 '''
+# intro/numpy/solutions/2_5_markov_chain.py -> https://github.com/numpy/numpy/issues/27957
+# intro/matplotliub/examples/plot_bar.py -> https://github.com/matplotlib/matplotlib/issues/29332
 
 # Can make these more strict over time
 allow_untyped_defs = true
@@ -109,6 +113,7 @@ ignore = [
   "B006",     # Do not use mutable data structures for argument defaults
   "B007",     # Loop control variable {name} not used within loop body
   "B018",     # Found useless expression. Either assign it to a variable or remove it.
+  "B905",     # Zip without explicit `strict` keyword
   "E402",     # Module level import not at top of file
   "E501",     # Line too long
   "E741",     # Ambiguous variable name
diff --git a/requirements.txt b/requirements.txt
@@ -1,13 +1,13 @@
-numpy==2.1.1
+numpy==2.2.0
 scipy==1.14.1
-matplotlib==3.9.2
+matplotlib==3.10.0
 pandas==2.2.3
-patsy==0.5.6
-pyarrow==17.0.0
+patsy==1.0.1
+pyarrow==18.1.0
 scikit-learn==1.5.2
-scikit-image==0.24.0
+scikit-image==0.25.0
 sympy==1.13.3
-statsmodels==0.14.3
+statsmodels==0.14.4
 seaborn==0.13.2
 pytest>=8.3
 sphinx>=8.0
@@ -18,7 +18,7 @@ Pillow
 pooch
 ipython
 pickleshare
-pre-commit==4.0
+pre-commit==4.0.1
 requests
 sphinxcontrib-jquery
 myst-nb

Original file line number	Diff line number	Diff line change
`@@ -46,6 +46,5 @@`
`46`	`46`	`f.close()`
`47`	`47`
`48`	`48`	`print(`
`49`		`- "Sample rate: %d, channels: %d"`
`50`		`- % (wav_header["sample_rate"][0], wav_header["num_channels"][0])`
	`49`	`+ f"Sample rate: {wav_header['sample_rate'][0]}, channels: {wav_header['num_channels'][0]}"`
`51`	`50`	`)`
Original file line number	Diff line number	Diff line change
`@@ -61,8 +61,7 @@ def compare_optimizers(optimizers):`
`61`	`61`	`print("Benching 1D root-finder optimizers from scipy.optimize:")`
`62`	`62`	`for optimizer in OPTIMIZERS:`
`63`	`63`	`print(`
`64`		`- "% 20s: % 8i total function calls"`
`65`		`- % (optimizer.__name__, bench_optimizer(optimizer, param_grid))`
	`64`	`+ f"{optimizer.__name__:>20s}: {bench_optimizer(optimizer, param_grid):>8d} total function calls"`
`66`	`65`	`)`
`67`	`66`
`68`	`67`
Original file line number	Diff line number	Diff line change
`@@ -86,7 +86,7 @@`
`86`	`86`	`],`
`87`	`87`	`"o",`
`88`	`88`	`color=color,`
`89`		`- label="# dim: %i" % n_dim,`
	`89`	`+ label=f"# dim: {n_dim}",`
`90`	`90`	`)`
`91`	`91`	`plt.legend(`
`92`	`92`	`loc=(0.47, 0.07),`