Pushing the docs to dev/ for branch: main, commit e838429839f4d11b63380f0ac810db853955a0aa

Author: sklearn-ci

dev/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 2ccc2acf4828f3ca83cd5004e280d200
+config: d33342b06755304fde4cac8e35421a5a
 tags: 645f666f9bcd5a90fca523b33c5a78b7

dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip

@@ -87,7 +87,7 @@
       },
       "outputs": [],
       "source": [
-        "from sklearn.decomposition import TruncatedSVD\nfrom sklearn.discriminant_analysis import LinearDiscriminantAnalysis\nfrom sklearn.ensemble import RandomTreesEmbedding\nfrom sklearn.manifold import (\n    MDS,\n    TSNE,\n    Isomap,\n    LocallyLinearEmbedding,\n    SpectralEmbedding,\n)\nfrom sklearn.neighbors import NeighborhoodComponentsAnalysis\nfrom sklearn.pipeline import make_pipeline\nfrom sklearn.random_projection import SparseRandomProjection\n\nembeddings = {\n    \"Random projection embedding\": SparseRandomProjection(\n        n_components=2, random_state=42\n    ),\n    \"Truncated SVD embedding\": TruncatedSVD(n_components=2),\n    \"Linear Discriminant Analysis embedding\": LinearDiscriminantAnalysis(\n        n_components=2\n    ),\n    \"Isomap embedding\": Isomap(n_neighbors=n_neighbors, n_components=2),\n    \"Standard LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"standard\"\n    ),\n    \"Modified LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"modified\"\n    ),\n    \"Hessian LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"hessian\"\n    ),\n    \"LTSA LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"ltsa\"\n    ),\n    \"MDS embedding\": MDS(\n        n_components=2, n_init=1, max_iter=120, n_jobs=2, normalized_stress=\"auto\"\n    ),\n    \"Random Trees embedding\": make_pipeline(\n        RandomTreesEmbedding(n_estimators=200, max_depth=5, random_state=0),\n        TruncatedSVD(n_components=2),\n    ),\n    \"Spectral embedding\": SpectralEmbedding(\n        n_components=2, random_state=0, eigen_solver=\"arpack\"\n    ),\n    \"t-SNE embedding\": TSNE(\n        n_components=2,\n        n_iter=500,\n        n_iter_without_progress=150,\n        n_jobs=2,\n        random_state=0,\n    ),\n    \"NCA embedding\": NeighborhoodComponentsAnalysis(\n        n_components=2, init=\"pca\", random_state=0\n    ),\n}"
+        "from sklearn.decomposition import TruncatedSVD\nfrom sklearn.discriminant_analysis import LinearDiscriminantAnalysis\nfrom sklearn.ensemble import RandomTreesEmbedding\nfrom sklearn.manifold import (\n    MDS,\n    TSNE,\n    Isomap,\n    LocallyLinearEmbedding,\n    SpectralEmbedding,\n)\nfrom sklearn.neighbors import NeighborhoodComponentsAnalysis\nfrom sklearn.pipeline import make_pipeline\nfrom sklearn.random_projection import SparseRandomProjection\n\nembeddings = {\n    \"Random projection embedding\": SparseRandomProjection(\n        n_components=2, random_state=42\n    ),\n    \"Truncated SVD embedding\": TruncatedSVD(n_components=2),\n    \"Linear Discriminant Analysis embedding\": LinearDiscriminantAnalysis(\n        n_components=2\n    ),\n    \"Isomap embedding\": Isomap(n_neighbors=n_neighbors, n_components=2),\n    \"Standard LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"standard\"\n    ),\n    \"Modified LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"modified\"\n    ),\n    \"Hessian LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"hessian\"\n    ),\n    \"LTSA LLE embedding\": LocallyLinearEmbedding(\n        n_neighbors=n_neighbors, n_components=2, method=\"ltsa\"\n    ),\n    \"MDS embedding\": MDS(n_components=2, n_init=1, max_iter=120, n_jobs=2),\n    \"Random Trees embedding\": make_pipeline(\n        RandomTreesEmbedding(n_estimators=200, max_depth=5, random_state=0),\n        TruncatedSVD(n_components=2),\n    ),\n    \"Spectral embedding\": SpectralEmbedding(\n        n_components=2, random_state=0, eigen_solver=\"arpack\"\n    ),\n    \"t-SNE embedding\": TSNE(\n        n_components=2,\n        n_iter=500,\n        n_iter_without_progress=150,\n        n_jobs=2,\n        random_state=0,\n    ),\n    \"NCA embedding\": NeighborhoodComponentsAnalysis(\n        n_components=2, init=\"pca\", random_state=0\n    ),\n}"
       ]
     },
     {

dev/_downloads/1e0968da80ca868bbdf21c1d0547f68c/plot_lle_digits.ipynb

@@ -15,7 +15,7 @@
       },
       "outputs": [],
       "source": [
-        "# Author: Jaques Grobler <[email protected]>\n# License: BSD 3 clause\n\nfrom time import time\n\nimport matplotlib.pyplot as plt\n\n# Unused but required import for doing 3d projections with matplotlib < 3.2\nimport mpl_toolkits.mplot3d  # noqa: F401\nimport numpy as np\nfrom matplotlib.ticker import NullFormatter\n\nfrom sklearn import manifold\nfrom sklearn.utils import check_random_state\n\n# Variables for manifold learning.\nn_neighbors = 10\nn_samples = 1000\n\n# Create our sphere.\nrandom_state = check_random_state(0)\np = random_state.rand(n_samples) * (2 * np.pi - 0.55)\nt = random_state.rand(n_samples) * np.pi\n\n# Sever the poles from the sphere.\nindices = (t < (np.pi - (np.pi / 8))) & (t > ((np.pi / 8)))\ncolors = p[indices]\nx, y, z = (\n    np.sin(t[indices]) * np.cos(p[indices]),\n    np.sin(t[indices]) * np.sin(p[indices]),\n    np.cos(t[indices]),\n)\n\n# Plot our dataset.\nfig = plt.figure(figsize=(15, 8))\nplt.suptitle(\n    \"Manifold Learning with %i points, %i neighbors\" % (1000, n_neighbors), fontsize=14\n)\n\nax = fig.add_subplot(251, projection=\"3d\")\nax.scatter(x, y, z, c=p[indices], cmap=plt.cm.rainbow)\nax.view_init(40, -10)\n\nsphere_data = np.array([x, y, z]).T\n\n# Perform Locally Linear Embedding Manifold learning\nmethods = [\"standard\", \"ltsa\", \"hessian\", \"modified\"]\nlabels = [\"LLE\", \"LTSA\", \"Hessian LLE\", \"Modified LLE\"]\n\nfor i, method in enumerate(methods):\n    t0 = time()\n    trans_data = (\n        manifold.LocallyLinearEmbedding(\n            n_neighbors=n_neighbors, n_components=2, method=method, random_state=42\n        )\n        .fit_transform(sphere_data)\n        .T\n    )\n    t1 = time()\n    print(\"%s: %.2g sec\" % (methods[i], t1 - t0))\n\n    ax = fig.add_subplot(252 + i)\n    plt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\n    plt.title(\"%s (%.2g sec)\" % (labels[i], t1 - t0))\n    ax.xaxis.set_major_formatter(NullFormatter())\n    ax.yaxis.set_major_formatter(NullFormatter())\n    plt.axis(\"tight\")\n\n# Perform Isomap Manifold learning.\nt0 = time()\ntrans_data = (\n    manifold.Isomap(n_neighbors=n_neighbors, n_components=2)\n    .fit_transform(sphere_data)\n    .T\n)\nt1 = time()\nprint(\"%s: %.2g sec\" % (\"ISO\", t1 - t0))\n\nax = fig.add_subplot(257)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"%s (%.2g sec)\" % (\"Isomap\", t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\n# Perform Multi-dimensional scaling.\nt0 = time()\nmds = manifold.MDS(2, max_iter=100, n_init=1, normalized_stress=\"auto\", random_state=42)\ntrans_data = mds.fit_transform(sphere_data).T\nt1 = time()\nprint(\"MDS: %.2g sec\" % (t1 - t0))\n\nax = fig.add_subplot(258)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"MDS (%.2g sec)\" % (t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\n# Perform Spectral Embedding.\nt0 = time()\nse = manifold.SpectralEmbedding(\n    n_components=2, n_neighbors=n_neighbors, random_state=42\n)\ntrans_data = se.fit_transform(sphere_data).T\nt1 = time()\nprint(\"Spectral Embedding: %.2g sec\" % (t1 - t0))\n\nax = fig.add_subplot(259)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"Spectral Embedding (%.2g sec)\" % (t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\n# Perform t-distributed stochastic neighbor embedding.\nt0 = time()\ntsne = manifold.TSNE(n_components=2, random_state=0)\ntrans_data = tsne.fit_transform(sphere_data).T\nt1 = time()\nprint(\"t-SNE: %.2g sec\" % (t1 - t0))\n\nax = fig.add_subplot(2, 5, 10)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"t-SNE (%.2g sec)\" % (t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\nplt.show()"
+        "# Author: Jaques Grobler <[email protected]>\n# License: BSD 3 clause\n\nfrom time import time\n\nimport matplotlib.pyplot as plt\n\n# Unused but required import for doing 3d projections with matplotlib < 3.2\nimport mpl_toolkits.mplot3d  # noqa: F401\nimport numpy as np\nfrom matplotlib.ticker import NullFormatter\n\nfrom sklearn import manifold\nfrom sklearn.utils import check_random_state\n\n# Variables for manifold learning.\nn_neighbors = 10\nn_samples = 1000\n\n# Create our sphere.\nrandom_state = check_random_state(0)\np = random_state.rand(n_samples) * (2 * np.pi - 0.55)\nt = random_state.rand(n_samples) * np.pi\n\n# Sever the poles from the sphere.\nindices = (t < (np.pi - (np.pi / 8))) & (t > ((np.pi / 8)))\ncolors = p[indices]\nx, y, z = (\n    np.sin(t[indices]) * np.cos(p[indices]),\n    np.sin(t[indices]) * np.sin(p[indices]),\n    np.cos(t[indices]),\n)\n\n# Plot our dataset.\nfig = plt.figure(figsize=(15, 8))\nplt.suptitle(\n    \"Manifold Learning with %i points, %i neighbors\" % (1000, n_neighbors), fontsize=14\n)\n\nax = fig.add_subplot(251, projection=\"3d\")\nax.scatter(x, y, z, c=p[indices], cmap=plt.cm.rainbow)\nax.view_init(40, -10)\n\nsphere_data = np.array([x, y, z]).T\n\n# Perform Locally Linear Embedding Manifold learning\nmethods = [\"standard\", \"ltsa\", \"hessian\", \"modified\"]\nlabels = [\"LLE\", \"LTSA\", \"Hessian LLE\", \"Modified LLE\"]\n\nfor i, method in enumerate(methods):\n    t0 = time()\n    trans_data = (\n        manifold.LocallyLinearEmbedding(\n            n_neighbors=n_neighbors, n_components=2, method=method, random_state=42\n        )\n        .fit_transform(sphere_data)\n        .T\n    )\n    t1 = time()\n    print(\"%s: %.2g sec\" % (methods[i], t1 - t0))\n\n    ax = fig.add_subplot(252 + i)\n    plt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\n    plt.title(\"%s (%.2g sec)\" % (labels[i], t1 - t0))\n    ax.xaxis.set_major_formatter(NullFormatter())\n    ax.yaxis.set_major_formatter(NullFormatter())\n    plt.axis(\"tight\")\n\n# Perform Isomap Manifold learning.\nt0 = time()\ntrans_data = (\n    manifold.Isomap(n_neighbors=n_neighbors, n_components=2)\n    .fit_transform(sphere_data)\n    .T\n)\nt1 = time()\nprint(\"%s: %.2g sec\" % (\"ISO\", t1 - t0))\n\nax = fig.add_subplot(257)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"%s (%.2g sec)\" % (\"Isomap\", t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\n# Perform Multi-dimensional scaling.\nt0 = time()\nmds = manifold.MDS(2, max_iter=100, n_init=1, random_state=42)\ntrans_data = mds.fit_transform(sphere_data).T\nt1 = time()\nprint(\"MDS: %.2g sec\" % (t1 - t0))\n\nax = fig.add_subplot(258)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"MDS (%.2g sec)\" % (t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\n# Perform Spectral Embedding.\nt0 = time()\nse = manifold.SpectralEmbedding(\n    n_components=2, n_neighbors=n_neighbors, random_state=42\n)\ntrans_data = se.fit_transform(sphere_data).T\nt1 = time()\nprint(\"Spectral Embedding: %.2g sec\" % (t1 - t0))\n\nax = fig.add_subplot(259)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"Spectral Embedding (%.2g sec)\" % (t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\n# Perform t-distributed stochastic neighbor embedding.\nt0 = time()\ntsne = manifold.TSNE(n_components=2, random_state=0)\ntrans_data = tsne.fit_transform(sphere_data).T\nt1 = time()\nprint(\"t-SNE: %.2g sec\" % (t1 - t0))\n\nax = fig.add_subplot(2, 5, 10)\nplt.scatter(trans_data[0], trans_data[1], c=colors, cmap=plt.cm.rainbow)\nplt.title(\"t-SNE (%.2g sec)\" % (t1 - t0))\nax.xaxis.set_major_formatter(NullFormatter())\nax.yaxis.set_major_formatter(NullFormatter())\nplt.axis(\"tight\")\n\nplt.show()"
       ]
     }
   ],

dev/_downloads/604c0a9de0e1b80dae9e6754fdb27014/plot_manifold_sphere.ipynb

@@ -112,7 +112,7 @@
 
 # Perform Multi-dimensional scaling.
 t0 = time()
-mds = manifold.MDS(2, max_iter=100, n_init=1, normalized_stress="auto", random_state=42)
+mds = manifold.MDS(2, max_iter=100, n_init=1, random_state=42)
 trans_data = mds.fit_transform(sphere_data).T
 t1 = time()
 print("MDS: %.2g sec" % (t1 - t0))

dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip

@@ -135,9 +135,7 @@ def plot_embedding(X, title):
     "LTSA LLE embedding": LocallyLinearEmbedding(
         n_neighbors=n_neighbors, n_components=2, method="ltsa"
     ),
-    "MDS embedding": MDS(
-        n_components=2, n_init=1, max_iter=120, n_jobs=2, normalized_stress="auto"
-    ),
+    "MDS embedding": MDS(n_components=2, n_init=1, max_iter=120, n_jobs=2),
     "Random Trees embedding": make_pipeline(
         RandomTreesEmbedding(n_estimators=200, max_depth=5, random_state=0),
         TruncatedSVD(n_components=2),