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geomstats · Jun 17, 2024 · 9ad403f · 9ad403f
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Showing 204 changed files with 345 additions and 251 deletions.
diff --git a/.doctrees/api/geomstats.geometry.doctree b/.doctrees/api/geomstats.geometry.doctree
diff --git a/.doctrees/api/geomstats.test.doctree b/.doctrees/api/geomstats.test.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/notebooks/00_foundations__introduction_to_geomstats.doctree b/.doctrees/notebooks/00_foundations__introduction_to_geomstats.doctree
diff --git a/.doctrees/notebooks/01_foundations__manifolds.doctree b/.doctrees/notebooks/01_foundations__manifolds.doctree
diff --git a/.doctrees/notebooks/02_foundations__connection_riemannian_metric.doctree b/.doctrees/notebooks/02_foundations__connection_riemannian_metric.doctree
diff --git a/.doctrees/notebooks/11_real_world_applications__cell_shapes_analysis.doctree b/.doctrees/notebooks/11_real_world_applications__cell_shapes_analysis.doctree
diff --git a/...ees/notebooks/12_real_world_applications__emg_sign_classification_in_spd_manifold.doctree b/...ees/notebooks/12_real_world_applications__emg_sign_classification_in_spd_manifold.doctree
diff --git a/...ks/13_real_world_applications__graph_embedding_and_clustering_in_hyperbolic_space.doctree b/...ks/13_real_world_applications__graph_embedding_and_clustering_in_hyperbolic_space.doctree
diff --git a/.../notebooks/14_real_world_applications__hand_poses_analysis_in_kendall_shape_space.doctree b/.../notebooks/14_real_world_applications__hand_poses_analysis_in_kendall_shape_space.doctree
diff --git a/...oks/15_real_world_applications__optic_nerve_heads_analysis_in_kendall_shape_space.doctree b/...oks/15_real_world_applications__optic_nerve_heads_analysis_in_kendall_shape_space.doctree
diff --git a/.doctrees/notebooks/17_foundations__stratified_spaces.doctree b/.doctrees/notebooks/17_foundations__stratified_spaces.doctree
diff --git a/.doctrees/notebooks/18_real_world_applications__sao_paulo_traffic_optimization.doctree b/.doctrees/notebooks/18_real_world_applications__sao_paulo_traffic_optimization.doctree
diff --git a/_modules/geomstats/algebra_utils.html b/_modules/geomstats/algebra_utils.html
@@ -45,7 +45,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/datasets/prepare_emg_data.html b/_modules/geomstats/datasets/prepare_emg_data.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/datasets/prepare_graph_data.html b/_modules/geomstats/datasets/prepare_graph_data.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/datasets/utils.html b/_modules/geomstats/datasets/utils.html
@@ -45,7 +45,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/distributions/brownian_motion.html b/_modules/geomstats/distributions/brownian_motion.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/distributions/lognormal.html b/_modules/geomstats/distributions/lognormal.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/errors.html b/_modules/geomstats/errors.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/exceptions.html b/_modules/geomstats/exceptions.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/base.html b/_modules/geomstats/geometry/base.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/complex_manifold.html b/_modules/geomstats/geometry/complex_manifold.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/complex_matrices.html b/_modules/geomstats/geometry/complex_matrices.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/complex_poincare_disk.html b/_modules/geomstats/geometry/complex_poincare_disk.html
@@ -45,7 +45,7 @@
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+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/complex_riemannian_metric.html b/_modules/geomstats/geometry/complex_riemannian_metric.html
@@ -45,7 +45,7 @@
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-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/connection.html b/_modules/geomstats/geometry/connection.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/diffeo.html b/_modules/geomstats/geometry/diffeo.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/discrete_curves.html b/_modules/geomstats/geometry/discrete_curves.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/discrete_surfaces.html b/_modules/geomstats/geometry/discrete_surfaces.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 
@@ -448,6 +448,7 @@ <h1>Source code for geomstats.geometry.discrete_surfaces</h1><div class="highlig
 <span class="kn">from</span> <span class="nn">geomstats.geometry.fiber_bundle</span> <span class="kn">import</span> <span class="n">AlignerAlgorithm</span><span class="p">,</span> <span class="n">FiberBundle</span>
 <span class="kn">from</span> <span class="nn">geomstats.geometry.manifold</span> <span class="kn">import</span> <span class="n">Manifold</span><span class="p">,</span> <span class="n">register_quotient</span>
 <span class="kn">from</span> <span class="nn">geomstats.geometry.matrices</span> <span class="kn">import</span> <span class="n">Matrices</span>
+<span class="kn">from</span> <span class="nn">geomstats.geometry.nfold_manifold</span> <span class="kn">import</span> <span class="n">NFoldMetric</span>
 <span class="kn">from</span> <span class="nn">geomstats.geometry.quotient_metric</span> <span class="kn">import</span> <span class="n">QuotientMetric</span>
 <span class="kn">from</span> <span class="nn">geomstats.geometry.riemannian_metric</span> <span class="kn">import</span> <span class="n">RiemannianMetric</span>
 <span class="kn">from</span> <span class="nn">geomstats.numerics.geodesic</span> <span class="kn">import</span> <span class="n">ExpSolver</span><span class="p">,</span> <span class="n">PathBasedLogSolver</span><span class="p">,</span> <span class="n">PathStraightening</span>
@@ -1319,13 +1320,13 @@ <h1>Source code for geomstats.geometry.discrete_surfaces</h1><div class="highlig
 <span class="sd">            Tangent vector at base point.</span>
 <span class="sd">        tangent_vec_b : array-like, shape=[..., n_vertices, 3]</span>
 <span class="sd">            Tangent vector at base point.</span>
-<span class="sd">        base_point : array-like, shape=[n_vertices, 3]</span>
+<span class="sd">        base_point : array-like, shape=[..., n_vertices, 3]</span>
 <span class="sd">            Surface, as the 3D coordinates of the vertices of its triangulation.</span>
 
 <span class="sd">        Returns</span>
 <span class="sd">        -------</span>
 <span class="sd">        inner_prod : array-like, shape=[...]</span>
-<span class="sd">            Inner-product.</span>
+<span class="sd">            Inner product.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">inner_prod_a0</span> <span class="o">=</span> <span class="mf">0.0</span>
         <span class="n">inner_prod_a1</span> <span class="o">=</span> <span class="mf">0.0</span>
@@ -1643,6 +1644,56 @@ <h1>Source code for geomstats.geometry.discrete_surfaces</h1><div class="highlig
 
 
 
+<div class="viewcode-block" id="L2SurfacesMetric">
+<a class="viewcode-back" href="../../../api/geomstats.geometry.html#geomstats.geometry.discrete_surfaces.L2SurfacesMetric">[docs]</a>
+<span class="k">class</span> <span class="nc">L2SurfacesMetric</span><span class="p">(</span><span class="n">NFoldMetric</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;L2 metric on the space of discrete surfaces.</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    Adds ``base_manifold`` (manifold that is repeated ``n_copies``</span>
+<span class="sd">    times) and ``n_copies`` to ``space`` as attribute if it does</span>
+<span class="sd">    not have them as their expected by ``NFoldMetric``.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">space</span><span class="p">):</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">space</span><span class="p">,</span> <span class="s2">&quot;base_manifold&quot;</span><span class="p">):</span>
+            <span class="n">space</span><span class="o">.</span><span class="n">base_manifold</span> <span class="o">=</span> <span class="n">Euclidean</span><span class="p">(</span><span class="n">dim</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
+            <span class="n">space</span><span class="o">.</span><span class="n">n_copies</span> <span class="o">=</span> <span class="n">space</span><span class="o">.</span><span class="n">n_vertices</span>
+
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">space</span><span class="o">=</span><span class="n">space</span><span class="p">)</span>
+
+<div class="viewcode-block" id="L2SurfacesMetric.inner_product">
+<a class="viewcode-back" href="../../../api/geomstats.geometry.html#geomstats.geometry.discrete_surfaces.L2SurfacesMetric.inner_product">[docs]</a>
+    <span class="k">def</span> <span class="nf">inner_product</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tangent_vec_a</span><span class="p">,</span> <span class="n">tangent_vec_b</span><span class="p">,</span> <span class="n">base_point</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Compute L2 inner product between two tangent vectors.</span>
+
+<span class="sd">        The inner product is the integral of the ambient space inner product,</span>
+<span class="sd">        approximated by a left Riemann sum.</span>
+
+<span class="sd">        Parameters</span>
+<span class="sd">        ----------</span>
+<span class="sd">        tangent_vec_a : array-like, shape=[..., n_vertices, 3]</span>
+<span class="sd">            Tangent vector at base point.</span>
+<span class="sd">        tangent_vec_b : array-like, shape=[..., n_vertices, 3]</span>
+<span class="sd">            Tangent vector at base point.</span>
+<span class="sd">        base_point : array-like, shape=[..., n_vertices, 3]</span>
+<span class="sd">            Surface, as the 3D coordinates of the vertices of its triangulation.</span>
+
+<span class="sd">        Return</span>
+<span class="sd">        ------</span>
+<span class="sd">        inner_prod : array_like, shape=[...]</span>
+<span class="sd">            Inner product.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">inner_products</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pointwise_inner_product</span><span class="p">(</span>
+            <span class="n">tangent_vec_a</span><span class="p">,</span> <span class="n">tangent_vec_b</span><span class="p">,</span> <span class="n">base_point</span>
+        <span class="p">)</span>
+        <span class="n">dt</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">_space</span><span class="o">.</span><span class="n">n_vertices</span>
+        <span class="k">return</span> <span class="n">dt</span> <span class="o">*</span> <span class="n">gs</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">inner_products</span><span class="p">,</span> <span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span></div>
+</div>
+
+
+
 <div class="viewcode-block" id="RelaxedPathStraightening">
 <a class="viewcode-back" href="../../../api/geomstats.geometry.html#geomstats.geometry.discrete_surfaces.RelaxedPathStraightening">[docs]</a>
 <span class="k">class</span> <span class="nc">RelaxedPathStraightening</span><span class="p">(</span><span class="n">PathBasedLogSolver</span><span class="p">,</span> <span class="n">AlignerAlgorithm</span><span class="p">):</span>

diff --git a/_modules/geomstats/geometry/euclidean.html b/_modules/geomstats/geometry/euclidean.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/fiber_bundle.html b/_modules/geomstats/geometry/fiber_bundle.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/full_rank_correlation_matrices.html b/_modules/geomstats/geometry/full_rank_correlation_matrices.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/full_rank_matrices.html b/_modules/geomstats/geometry/full_rank_matrices.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
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diff --git a/_modules/geomstats/geometry/functions.html b/_modules/geomstats/geometry/functions.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/general_linear.html b/_modules/geomstats/geometry/general_linear.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/grassmannian.html b/_modules/geomstats/geometry/grassmannian.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/group_action.html b/_modules/geomstats/geometry/group_action.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/heisenberg.html b/_modules/geomstats/geometry/heisenberg.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/hermitian.html b/_modules/geomstats/geometry/hermitian.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/hermitian_matrices.html b/_modules/geomstats/geometry/hermitian_matrices.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/hpd_matrices.html b/_modules/geomstats/geometry/hpd_matrices.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/hyperbolic.html b/_modules/geomstats/geometry/hyperbolic.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/hyperboloid.html b/_modules/geomstats/geometry/hyperboloid.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>
 
 

diff --git a/_modules/geomstats/geometry/hypersphere.html b/_modules/geomstats/geometry/hypersphere.html
@@ -45,7 +45,7 @@
     <link rel="search" title="Search" href="../../../search.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-    <meta name="docbuild:last-update" content="Jun 14, 2024, 7:46:07 AM"/>
+    <meta name="docbuild:last-update" content="Jun 17, 2024, 8:02:59 AM"/>
   </head>