CircleCI update of dev docs (388).

TorchDR · Jul 15, 2024 · 28e996b · 28e996b
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diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
diff --git a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
diff --git a/dev/_images/sphx_glr_demo_tsne_swiss_roll_003.png b/dev/_images/sphx_glr_demo_tsne_swiss_roll_003.png
diff --git a/dev/_modules/torchdr/neighbor_embedding/base.html b/dev/_modules/torchdr/neighbor_embedding/base.html
@@ -98,8 +98,8 @@ <h1>Source code for torchdr.neighbor_embedding.base</h1><div class="highlight"><
 
 <span class="kn">from</span> <span class="nn">torchdr.affinity</span> <span class="kn">import</span> <span class="p">(</span>
     <span class="n">Affinity</span><span class="p">,</span>
-    <span class="n">LogAffinity</span><span class="p">,</span>
     <span class="n">UnnormalizedAffinity</span><span class="p">,</span>
+    <span class="n">UnnormalizedLogAffinity</span><span class="p">,</span>
     <span class="n">SparseLogAffinity</span><span class="p">,</span>
 <span class="p">)</span>
 <span class="kn">from</span> <span class="nn">torchdr.affinity_matcher</span> <span class="kn">import</span> <span class="n">AffinityMatcher</span>
@@ -427,7 +427,7 @@ <h1>Source code for torchdr.neighbor_embedding.base</h1><div class="highlight"><
         <span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">_attractive_loss</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">affinity_out</span><span class="p">,</span> <span class="n">LogAffinity</span><span class="p">):</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">affinity_out</span><span class="p">,</span> <span class="n">UnnormalizedLogAffinity</span><span class="p">):</span>
             <span class="n">log_Q</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">affinity_out</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">embedding_</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">indices</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">indices_</span><span class="p">)</span>
             <span class="k">return</span> <span class="n">cross_entropy_loss</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">PX_</span><span class="p">,</span> <span class="n">log_Q</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>

diff --git a/dev/_sources/auto_examples/affinities/demo_ea_adaptivity.rst.txt b/dev/_sources/auto_examples/affinities/demo_ea_adaptivity.rst.txt
@@ -214,7 +214,7 @@ This affinity is an important component of the **TSNE** algorithm.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 2.890 seconds)
+   **Total running time of the script:** (0 minutes 2.629 seconds)
 
 
 .. _sphx_glr_download_auto_examples_affinities_demo_ea_adaptivity.py:

diff --git a/dev/_sources/auto_examples/affinities/sg_execution_times.rst.txt b/dev/_sources/auto_examples/affinities/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:02.890** total execution time for 1 file **from auto_examples/affinities**:
+**00:02.629** total execution time for 1 file **from auto_examples/affinities**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_affinities_demo_ea_adaptivity.py` (``demo_ea_adaptivity.py``)
-     - 00:02.890
+     - 00:02.629
      - 0.0
diff --git a/dev/_sources/auto_examples/basics/demo_pca_via_affinity_matcher.rst.txt b/dev/_sources/auto_examples/basics/demo_pca_via_affinity_matcher.rst.txt
@@ -160,7 +160,7 @@ both methods.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 7.542 seconds)
+   **Total running time of the script:** (0 minutes 3.341 seconds)
 
 
 .. _sphx_glr_download_auto_examples_basics_demo_pca_via_affinity_matcher.py:

diff --git a/dev/_sources/auto_examples/basics/demo_tsne_swiss_roll.rst.txt b/dev/_sources/auto_examples/basics/demo_tsne_swiss_roll.rst.txt
@@ -228,7 +228,7 @@ mistakenly considered neighbors.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (1 minutes 58.208 seconds)
+   **Total running time of the script:** (1 minutes 19.401 seconds)
 
 
 .. _sphx_glr_download_auto_examples_basics_demo_tsne_swiss_roll.py:

diff --git a/dev/_sources/auto_examples/basics/sg_execution_times.rst.txt b/dev/_sources/auto_examples/basics/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**02:05.749** total execution time for 2 files **from auto_examples/basics**:
+**01:22.742** total execution time for 2 files **from auto_examples/basics**:
 
 .. container::
 
@@ -33,8 +33,8 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_basics_demo_tsne_swiss_roll.py` (``demo_tsne_swiss_roll.py``)
-     - 01:58.208
+     - 01:19.401
      - 0.0
    * - :ref:`sphx_glr_auto_examples_basics_demo_pca_via_affinity_matcher.py` (``demo_pca_via_affinity_matcher.py``)
-     - 00:07.542
+     - 00:03.341
      - 0.0
diff --git a/dev/_sources/sg_execution_times.rst.txt b/dev/_sources/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**02:08.639** total execution time for 3 files **from all galleries**:
+**01:25.371** total execution time for 3 files **from all galleries**:
 
 .. container::
 
@@ -33,11 +33,11 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_basics_demo_tsne_swiss_roll.py` (``../../examples/basics/demo_tsne_swiss_roll.py``)
-     - 01:58.208
+     - 01:19.401
      - 0.0
    * - :ref:`sphx_glr_auto_examples_basics_demo_pca_via_affinity_matcher.py` (``../../examples/basics/demo_pca_via_affinity_matcher.py``)
-     - 00:07.542
+     - 00:03.341
      - 0.0
    * - :ref:`sphx_glr_auto_examples_affinities_demo_ea_adaptivity.py` (``../../examples/affinities/demo_ea_adaptivity.py``)
-     - 00:02.890
+     - 00:02.629
      - 0.0
diff --git a/dev/auto_examples/affinities/demo_ea_adaptivity.html b/dev/auto_examples/affinities/demo_ea_adaptivity.html
@@ -220,7 +220,7 @@ <h2>Entropic affinity (adaptive bandwidth)<a class="headerlink" href="#entropic-
 <img src="../../_images/sphx_glr_demo_ea_adaptivity_002.png" srcset="../../_images/sphx_glr_demo_ea_adaptivity_002.png" alt="Entropic Affinity Matrix, Entropic Affinity Graph" class = "sphx-glr-single-img"/><p>We can now observe a <strong>homogeneous density of connections</strong> across clusters.
 Thus, the entropic affinity effectively filters out the various noise levels.</p>
 <p>This affinity is an important component of the <strong>TSNE</strong> algorithm.</p>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.890 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.629 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-affinities-demo-ea-adaptivity-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../../_downloads/17d429f11ca029172465ca0d7bb1879e/demo_ea_adaptivity.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">demo_ea_adaptivity.ipynb</span></code></a></p>

diff --git a/dev/auto_examples/affinities/sg_execution_times.html b/dev/auto_examples/affinities/sg_execution_times.html
@@ -85,7 +85,7 @@
 
   <section id="computation-times">
 <span id="sphx-glr-auto-examples-affinities-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading"></a></h1>
-<p><strong>00:02.890</strong> total execution time for 1 file <strong>from auto_examples/affinities</strong>:</p>
+<p><strong>00:02.629</strong> total execution time for 1 file <strong>from auto_examples/affinities</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -107,7 +107,7 @@
 </thead>
 <tbody>
 <tr class="row-even"><td><p><a class="reference internal" href="demo_ea_adaptivity.html#sphx-glr-auto-examples-affinities-demo-ea-adaptivity-py"><span class="std std-ref">Entropic Affinities can adapt to varying noise levels</span></a> (<code class="docutils literal notranslate"><span class="pre">demo_ea_adaptivity.py</span></code>)</p></td>
-<td><p>00:02.890</p></td>
+<td><p>00:02.629</p></td>
 <td><p>0.0</p></td>
 </tr>
 </tbody>

diff --git a/dev/auto_examples/basics/demo_pca_via_affinity_matcher.html b/dev/auto_examples/basics/demo_pca_via_affinity_matcher.html
@@ -169,7 +169,7 @@ <h2>PCA via AffinityMatcher<a class="headerlink" href="#pca-via-affinitymatcher"
 </div>
 <img src="../../_images/sphx_glr_demo_pca_via_affinity_matcher_002.png" srcset="../../_images/sphx_glr_demo_pca_via_affinity_matcher_002.png" alt="PCA via AffinityMatcher" class = "sphx-glr-single-img"/><p>We can see that we obtain the same PCA embedding (up to a rotation) using
 both methods.</p>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 7.542 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 3.341 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-basics-demo-pca-via-affinity-matcher-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../../_downloads/01119b09b904483a657e921d21bc15d1/demo_pca_via_affinity_matcher.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">demo_pca_via_affinity_matcher.ipynb</span></code></a></p>

diff --git a/dev/auto_examples/basics/demo_tsne_swiss_roll.html b/dev/auto_examples/basics/demo_tsne_swiss_roll.html
@@ -193,7 +193,7 @@ <h2>See the impact of perplexity<a class="headerlink" href="#see-the-impact-of-p
 and fails to capture the manifold’s geometry. Conversely, when the perplexity is too
 high, points that are distant on the manifold but close in the ambient space are
 mistakenly considered neighbors.</p>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (1 minutes 58.208 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (1 minutes 19.401 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-basics-demo-tsne-swiss-roll-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../../_downloads/d07a5a618e87545c420604821fa60541/demo_tsne_swiss_roll.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">demo_tsne_swiss_roll.ipynb</span></code></a></p>

diff --git a/dev/auto_examples/basics/sg_execution_times.html b/dev/auto_examples/basics/sg_execution_times.html
@@ -85,7 +85,7 @@
 
   <section id="computation-times">
 <span id="sphx-glr-auto-examples-basics-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading"></a></h1>
-<p><strong>02:05.749</strong> total execution time for 2 files <strong>from auto_examples/basics</strong>:</p>
+<p><strong>01:22.742</strong> total execution time for 2 files <strong>from auto_examples/basics</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -107,11 +107,11 @@
 </thead>
 <tbody>
 <tr class="row-even"><td><p><a class="reference internal" href="demo_tsne_swiss_roll.html#sphx-glr-auto-examples-basics-demo-tsne-swiss-roll-py"><span class="std std-ref">TSNE embedding of the swiss roll dataset</span></a> (<code class="docutils literal notranslate"><span class="pre">demo_tsne_swiss_roll.py</span></code>)</p></td>
-<td><p>01:58.208</p></td>
+<td><p>01:19.401</p></td>
 <td><p>0.0</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="demo_pca_via_affinity_matcher.html#sphx-glr-auto-examples-basics-demo-pca-via-affinity-matcher-py"><span class="std std-ref">PCA via SVD and via AffinityMatcher</span></a> (<code class="docutils literal notranslate"><span class="pre">demo_pca_via_affinity_matcher.py</span></code>)</p></td>
-<td><p>00:07.542</p></td>
+<td><p>00:03.341</p></td>
 <td><p>0.0</p></td>
 </tr>
 </tbody>

diff --git a/dev/searchindex.js b/dev/searchindex.js
diff --git a/dev/sg_execution_times.html b/dev/sg_execution_times.html
@@ -85,7 +85,7 @@
 
   <section id="computation-times">
 <span id="sphx-glr-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading"></a></h1>
-<p><strong>02:08.639</strong> total execution time for 3 files <strong>from all galleries</strong>:</p>
+<p><strong>01:25.371</strong> total execution time for 3 files <strong>from all galleries</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -107,15 +107,15 @@
 </thead>
 <tbody>
 <tr class="row-even"><td><p><a class="reference internal" href="auto_examples/basics/demo_tsne_swiss_roll.html#sphx-glr-auto-examples-basics-demo-tsne-swiss-roll-py"><span class="std std-ref">TSNE embedding of the swiss roll dataset</span></a> (<code class="docutils literal notranslate"><span class="pre">../../examples/basics/demo_tsne_swiss_roll.py</span></code>)</p></td>
-<td><p>01:58.208</p></td>
+<td><p>01:19.401</p></td>
 <td><p>0.0</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="auto_examples/basics/demo_pca_via_affinity_matcher.html#sphx-glr-auto-examples-basics-demo-pca-via-affinity-matcher-py"><span class="std std-ref">PCA via SVD and via AffinityMatcher</span></a> (<code class="docutils literal notranslate"><span class="pre">../../examples/basics/demo_pca_via_affinity_matcher.py</span></code>)</p></td>
-<td><p>00:07.542</p></td>
+<td><p>00:03.341</p></td>
 <td><p>0.0</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="auto_examples/affinities/demo_ea_adaptivity.html#sphx-glr-auto-examples-affinities-demo-ea-adaptivity-py"><span class="std std-ref">Entropic Affinities can adapt to varying noise levels</span></a> (<code class="docutils literal notranslate"><span class="pre">../../examples/affinities/demo_ea_adaptivity.py</span></code>)</p></td>
-<td><p>00:02.890</p></td>
+<td><p>00:02.629</p></td>
 <td><p>0.0</p></td>
 </tr>
 </tbody>