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Deep-MI · Aug 30, 2024 · 89ff517 · 89ff517
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diff --git a/dev/.doctrees/api/generated/lapy.TriaMesh.doctree b/dev/.doctrees/api/generated/lapy.TriaMesh.doctree
diff --git a/dev/.doctrees/environment.pickle b/dev/.doctrees/environment.pickle
diff --git a/dev/.doctrees/nbsphinx/tutorials/examples/Test_Plot.ipynb b/dev/.doctrees/nbsphinx/tutorials/examples/Test_Plot.ipynb
diff --git a/dev/.doctrees/nbsphinx/tutorials/examples/Test_ShapeDNA.ipynb b/dev/.doctrees/nbsphinx/tutorials/examples/Test_ShapeDNA.ipynb
@@ -21,8 +21,7 @@
    "outputs": [],
    "source": [
     "# imports\n",
-    "from lapy import TriaMesh, TetMesh\n",
-    "from lapy import shapedna"
+    "from lapy import TetMesh, TriaMesh, shapedna"
    ]
   },
   {

diff --git a/dev/.doctrees/nbsphinx/tutorials/examples/Test_TetMesh_Geodesics.ipynb b/dev/.doctrees/nbsphinx/tutorials/examples/Test_TetMesh_Geodesics.ipynb
diff --git a/dev/.doctrees/nbsphinx/tutorials/examples/Test_TriaMesh.ipynb b/dev/.doctrees/nbsphinx/tutorials/examples/Test_TriaMesh.ipynb
@@ -14,6 +14,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
+    "\n",
     "from lapy import TriaMesh"
    ]
   },

diff --git a/dev/.doctrees/nbsphinx/tutorials/examples/Test_TriaMesh_Geodesics.ipynb b/dev/.doctrees/nbsphinx/tutorials/examples/Test_TriaMesh_Geodesics.ipynb
diff --git a/dev/.doctrees/tutorials/examples/Test_Plot.doctree b/dev/.doctrees/tutorials/examples/Test_Plot.doctree
diff --git a/dev/.doctrees/tutorials/examples/Test_ShapeDNA.doctree b/dev/.doctrees/tutorials/examples/Test_ShapeDNA.doctree
diff --git a/dev/.doctrees/tutorials/examples/Test_TetMesh_Geodesics.doctree b/dev/.doctrees/tutorials/examples/Test_TetMesh_Geodesics.doctree
diff --git a/dev/.doctrees/tutorials/examples/Test_TriaMesh.doctree b/dev/.doctrees/tutorials/examples/Test_TriaMesh.doctree
diff --git a/dev/.doctrees/tutorials/examples/Test_TriaMesh_Geodesics.doctree b/dev/.doctrees/tutorials/examples/Test_TriaMesh_Geodesics.doctree
diff --git a/dev/_sources/tutorials/examples/Test_Plot.ipynb.txt b/dev/_sources/tutorials/examples/Test_Plot.ipynb.txt
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# Visualization"
+    "# Visualization"
    ]
   },
   {
@@ -20,8 +20,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lapy import TriaMesh, TetMesh, Solver, plot, io\n",
     "import plotly.io as pio\n",
+    "\n",
+    "from lapy import Solver, TetMesh, TriaMesh, io, plot\n",
+    "\n",
     "pio.renderers.default = \"sphinx_gallery\""
    ]
   },

diff --git a/dev/_sources/tutorials/examples/Test_ShapeDNA.ipynb.txt b/dev/_sources/tutorials/examples/Test_ShapeDNA.ipynb.txt
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# ShapeDNA"
+    "# ShapeDNA"
    ]
   },
   {
@@ -21,8 +21,7 @@
    "outputs": [],
    "source": [
     "# imports\n",
-    "from lapy import TriaMesh, TetMesh\n",
-    "from lapy import shapedna"
+    "from lapy import TetMesh, TriaMesh, shapedna"
    ]
   },
   {

diff --git a/dev/_sources/tutorials/examples/Test_TetMesh_Geodesics.ipynb.txt b/dev/_sources/tutorials/examples/Test_TetMesh_Geodesics.ipynb.txt
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# TetMesh Geodesics"
+    "# TetMesh Geodesics"
    ]
   },
   {
@@ -39,11 +39,14 @@
    ],
    "source": [
     "import numpy as np\n",
-    "from lapy import TetMesh\n",
-    "from lapy.plot import plot_tet_mesh\n",
+    "\n",
     "# import plotly\n",
     "# plotly.offline.init_notebook_mode(connected=True)\n",
     "import plotly.io as pio\n",
+    "\n",
+    "from lapy import TetMesh\n",
+    "from lapy.plot import plot_tet_mesh\n",
+    "\n",
     "pio.renderers.default = \"sphinx_gallery\""
    ]
   },
@@ -116,6 +119,7 @@
    ],
    "source": [
     "from lapy import Solver\n",
+    "\n",
     "fem = Solver(T,lump=True)\n",
     "\n",
     "evals, evec = fem.eigs(10)\n"
@@ -168,8 +172,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lapy.diffgeo import compute_gradient\n",
-    "from lapy.diffgeo import compute_divergence\n",
+    "from lapy.diffgeo import compute_divergence, compute_gradient\n",
+    "\n",
     "grad = compute_gradient(T,evec[:,evnum])\n",
     "divx = -compute_divergence(T,grad)\n",
     "vfunc = Bi*divx\n"
@@ -299,6 +303,7 @@
    "source": [
     "# compute distance\n",
     "from scipy.sparse.linalg import splu\n",
+    "\n",
     "useCholmod = True\n",
     "try:\n",
     "    from sksparse.cholmod import cholesky\n",
@@ -373,8 +378,8 @@
     }
    ],
    "source": [
-    "from lapy.diffgeo import compute_geodesic_f\n",
     "from lapy import heat\n",
+    "from lapy.diffgeo import compute_geodesic_f\n",
     "\n",
     "tria = T.boundary_tria()\n",
     "bvert=np.unique(tria.t)\n",
@@ -473,7 +478,7 @@
    "version": "3"
   },
   "nbsphinx": {
-    "execute": "always"
+   "execute": "always"
   }
  },
  "nbformat": 4,

diff --git a/dev/_sources/tutorials/examples/Test_TriaMesh.ipynb.txt b/dev/_sources/tutorials/examples/Test_TriaMesh.ipynb.txt
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# Triangle Mesh"
+    "# Triangle Mesh"
    ]
   },
   {
@@ -14,6 +14,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
+    "\n",
     "from lapy import TriaMesh"
    ]
   },

diff --git a/dev/_sources/tutorials/examples/Test_TriaMesh_Geodesics.ipynb.txt b/dev/_sources/tutorials/examples/Test_TriaMesh_Geodesics.ipynb.txt
@@ -86,8 +86,10 @@
     "# import plotting functions\n",
     "# import plotly\n",
     "# plotly.offline.init_notebook_mode(connected=True)\n",
-    "from lapy.plot import plot_tria_mesh\n",
     "import plotly.io as pio\n",
+    "\n",
+    "from lapy.plot import plot_tria_mesh\n",
+    "\n",
     "pio.renderers.default = \"sphinx_gallery\""
    ]
   },
@@ -139,6 +141,7 @@
    "source": [
     "# compute first eigenfunction\n",
     "from lapy import Solver\n",
+    "\n",
     "fem = Solver(T,lump=True)\n",
     "eval, evec = fem.eigs()\n",
     "vfunc = evec[:,1]\n",
@@ -221,8 +224,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lapy.diffgeo import compute_gradient\n",
-    "from lapy.diffgeo import compute_divergence\n",
+    "from lapy.diffgeo import compute_divergence, compute_gradient\n",
+    "\n",
     "grad = compute_gradient(T,vfunc)\n",
     "divx = -compute_divergence(T,grad)\n",
     "plot_tria_mesh(T,Bi*divx,plot_edges=True)"
@@ -254,6 +257,7 @@
    ],
    "source": [
     "from lapy import heat\n",
+    "\n",
     "bvert = T.boundary_loops()\n",
     "u = heat.diffusion(T,bvert,m=1)"
    ]
@@ -338,6 +342,7 @@
    "source": [
     "# compute distance\n",
     "from scipy.sparse.linalg import splu\n",
+    "\n",
     "useCholmod = True\n",
     "try:\n",
     "    from sksparse.cholmod import cholesky\n",
@@ -488,6 +493,7 @@
    ],
    "source": [
     "from lapy.diffgeo import compute_geodesic_f\n",
+    "\n",
     "gf = compute_geodesic_f(T,u)\n",
     "plot_tria_mesh(T,gf,plot_edges=True,plot_levels=True)"
    ]
@@ -545,6 +551,7 @@
    "source": [
     "# testing if we can rotate the function\n",
     "from lapy.diffgeo import compute_rotated_f\n",
+    "\n",
     "gf = compute_rotated_f(T,vf)\n",
     "plot_tria_mesh(T,gf,plot_edges=True,plot_levels=True)"
    ]

diff --git a/dev/api/generated/lapy.TriaMesh.html b/dev/api/generated/lapy.TriaMesh.html
@@ -284,7 +284,7 @@
 <h1>lapy.TriaMesh<a class="headerlink" href="#lapy-triamesh" title="Link to this heading">¶</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="lapy.TriaMesh">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lapy.</span></span><span class="sig-name descname"><span class="pre">TriaMesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">v</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fsinfo</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L9-L1124"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lapy.</span></span><span class="sig-name descname"><span class="pre">TriaMesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">v</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fsinfo</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L9-L1122"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh" title="Link to this definition">¶</a></dt>
 <dd><p>Class representing a triangle mesh.</p>
 <p>This is an efficient implementation of a triangle mesh data structure
 with core functionality using sparse matrices internally (Scipy).</p>
@@ -699,7 +699,7 @@ <h1>lapy.TriaMesh<a class="headerlink" href="#lapy-triamesh" title="Link to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="lapy.TriaMesh.map_tfunc_to_vfunc">
-<span class="sig-name descname"><span class="pre">map_tfunc_to_vfunc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfunc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weighted</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1018-L1055"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.map_tfunc_to_vfunc" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">map_tfunc_to_vfunc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfunc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weighted</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1016-L1053"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.map_tfunc_to_vfunc" title="Link to this definition">¶</a></dt>
 <dd><p>Map tria function to vertices by attributing 1/3 to each vertex of triangle.</p>
 <p>Uses vertices and trias.</p>
 <dl class="field-list">
@@ -727,7 +727,7 @@ <h1>lapy.TriaMesh<a class="headerlink" href="#lapy-triamesh" title="Link to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="lapy.TriaMesh.map_vfunc_to_tfunc">
-<span class="sig-name descname"><span class="pre">map_vfunc_to_tfunc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vfunc</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1057-L1076"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.map_vfunc_to_tfunc" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">map_vfunc_to_tfunc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vfunc</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1055-L1074"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.map_vfunc_to_tfunc" title="Link to this definition">¶</a></dt>
 <dd><p>Map vertex function to triangles by attributing 1/3 to each.</p>
 <p>Uses number of vertices and trias</p>
 <dl class="field-list">
@@ -770,7 +770,7 @@ <h1>lapy.TriaMesh<a class="headerlink" href="#lapy-triamesh" title="Link to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="lapy.TriaMesh.orient_">
-<span class="sig-name descname"><span class="pre">orient_</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L913-L1016"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.orient_" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">orient_</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L913-L1014"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.orient_" title="Link to this definition">¶</a></dt>
 <dd><p>Re-orient triangles of manifold mesh to be consistent.</p>
 <p>Re-orients triangles of manifold mesh to be consistent, so that vertices are
 listed counter-clockwise, when looking from above (outside).</p>
@@ -892,7 +892,7 @@ <h1>lapy.TriaMesh<a class="headerlink" href="#lapy-triamesh" title="Link to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="lapy.TriaMesh.smooth_">
-<span class="sig-name descname"><span class="pre">smooth_</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1114-L1124"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.smooth_" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">smooth_</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1112-L1122"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.smooth_" title="Link to this definition">¶</a></dt>
 <dd><p>Smooth the mesh iteratively in-place.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -906,7 +906,7 @@ <h1>lapy.TriaMesh<a class="headerlink" href="#lapy-triamesh" title="Link to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="lapy.TriaMesh.smooth_vfunc">
-<span class="sig-name descname"><span class="pre">smooth_vfunc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vfunc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1078-L1112"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.smooth_vfunc" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">smooth_vfunc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vfunc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/Deep-MI/LaPy/blob/main/lapy/tria_mesh.py#L1076-L1110"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#lapy.TriaMesh.smooth_vfunc" title="Link to this definition">¶</a></dt>
 <dd><p>Smooth the mesh or a vertex function iteratively.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

diff --git a/dev/tutorials/examples/Test_Plot.html b/dev/tutorials/examples/Test_Plot.html
diff --git a/dev/tutorials/examples/Test_Plot.ipynb b/dev/tutorials/examples/Test_Plot.ipynb
diff --git a/dev/tutorials/examples/Test_ShapeDNA.html b/dev/tutorials/examples/Test_ShapeDNA.html
@@ -289,8 +289,7 @@ <h1>ShapeDNA<a class="headerlink" href="#ShapeDNA" title="Link to this heading">
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># imports</span>
-<span class="kn">from</span> <span class="nn">lapy</span> <span class="kn">import</span> <span class="n">TriaMesh</span><span class="p">,</span> <span class="n">TetMesh</span>
-<span class="kn">from</span> <span class="nn">lapy</span> <span class="kn">import</span> <span class="n">shapedna</span>
+<span class="kn">from</span> <span class="nn">lapy</span> <span class="kn">import</span> <span class="n">TetMesh</span><span class="p">,</span> <span class="n">TriaMesh</span><span class="p">,</span> <span class="n">shapedna</span>
 </pre></div>
 </div>
 </div>

diff --git a/dev/tutorials/examples/Test_ShapeDNA.ipynb b/dev/tutorials/examples/Test_ShapeDNA.ipynb
@@ -21,8 +21,7 @@
    "outputs": [],
    "source": [
     "# imports\n",
-    "from lapy import TriaMesh, TetMesh\n",
-    "from lapy import shapedna"
+    "from lapy import TetMesh, TriaMesh, shapedna"
    ]
   },
   {

diff --git a/dev/tutorials/examples/Test_TetMesh_Geodesics.html b/dev/tutorials/examples/Test_TetMesh_Geodesics.html
diff --git a/dev/tutorials/examples/Test_TetMesh_Geodesics.ipynb b/dev/tutorials/examples/Test_TetMesh_Geodesics.ipynb
diff --git a/dev/tutorials/examples/Test_TriaMesh.html b/dev/tutorials/examples/Test_TriaMesh.html
@@ -288,6 +288,7 @@ <h1>Triangle Mesh<a class="headerlink" href="#Triangle-Mesh" title="Link to this
 </pre></div>
 </div>
 <div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+
 <span class="kn">from</span> <span class="nn">lapy</span> <span class="kn">import</span> <span class="n">TriaMesh</span>
 </pre></div>
 </div>

diff --git a/dev/tutorials/examples/Test_TriaMesh.ipynb b/dev/tutorials/examples/Test_TriaMesh.ipynb
@@ -14,6 +14,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
+    "\n",
     "from lapy import TriaMesh"
    ]
   },

diff --git a/dev/tutorials/examples/Test_TriaMesh_Geodesics.html b/dev/tutorials/examples/Test_TriaMesh_Geodesics.html
diff --git a/dev/tutorials/examples/Test_TriaMesh_Geodesics.ipynb b/dev/tutorials/examples/Test_TriaMesh_Geodesics.ipynb