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Merge pull request #15 from MunchLab/Fixing-folder-structure
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Hopefully fixed file structure now
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@lizliz
lizliz authored May 29, 2024
2 parents 4a22817 + 308351b commit 19e55d3
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2 changes: 1 addition & 1 deletion doc_source/conf.py
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author = 'MunchLab'

# The full version, including alpha/beta/rc tags
release = '0.1.4'
release = '0.1.5'


# -- General configuration ---------------------------------------------------
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2 changes: 1 addition & 1 deletion doc_source/ect_on_graphs.md
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# ECT on Graphs

```{eval-rst}
.. automodule:: ect_graph
.. automodule:: ect.ect_graph
:members:
```
2 changes: 1 addition & 1 deletion doc_source/embed_cw.md
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# Embedded CW complex

```{eval-rst}
.. automodule:: embed_cw
.. automodule:: ect.embed_cw
:members:
```
2 changes: 1 addition & 1 deletion doc_source/embed_graph.md
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# Embedded graphs

```{eval-rst}
.. automodule:: embed_graph
.. automodule:: ect.embed_graph
:members:
```
2 changes: 1 addition & 1 deletion docs/.buildinfo
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# 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: bb6f22dc7c43546dfebc85d9c3362e8b
config: 1dadfd971d70ecf359ab515ba8084b45
tags: 645f666f9bcd5a90fca523b33c5a78b7
82 changes: 41 additions & 41 deletions docs/_modules/ect_graph.html → docs/_modules/ect/ect_graph.html
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74 changes: 37 additions & 37 deletions docs/_modules/embed_cw.html → docs/_modules/ect/embed_cw.html
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<!DOCTYPE html>
<html class="writer-html5" lang="en" data-content_root="../">
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<head>
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<title>embed_cw &mdash; ect 0.1.4 documentation</title>
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<title>ect.embed_cw &mdash; ect 0.1.5 documentation</title>
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<a href="../index.html" class="icon icon-home">
<a href="../../index.html" class="icon icon-home">
ect
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../installation.html">1. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="../modules.html">2. Modules</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../license.html">5. License</a></li>
<li class="toctree-l1"><a class="reference internal" href="../citing.html">6. Citing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../installation.html">1. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../modules.html">2. Modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../tutorials.html">3. Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../contributing.html">4. Contributing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../license.html">5. License</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../citing.html">6. Citing</a></li>
</ul>

</div>
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<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="../index.html">ect</a>
<a href="../../index.html">ect</a>
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<li class="breadcrumb-item active">embed_cw</li>
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<li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
<li class="breadcrumb-item active">ect.embed_cw</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">

<h1>Source code for embed_cw</h1><div class="highlight"><pre>
<h1>Source code for ect.embed_cw</h1><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">itertools</span> <span class="kn">import</span> <span class="n">compress</span><span class="p">,</span> <span class="n">combinations</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
<span class="kn">from</span> <span class="nn">ect.ect_on_graphs.embed_graph</span> <span class="kn">import</span> <span class="n">EmbeddedGraph</span><span class="p">,</span> <span class="n">create_example_graph</span>
<span class="kn">from</span> <span class="nn">ect.embed_graph</span> <span class="kn">import</span> <span class="n">EmbeddedGraph</span><span class="p">,</span> <span class="n">create_example_graph</span>
<span class="kn">from</span> <span class="nn">scipy.optimize</span> <span class="kn">import</span> <span class="n">linprog</span>


<div class="viewcode-block" id="EmbeddedCW">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW">[docs]</a>
<span class="k">class</span> <span class="nc">EmbeddedCW</span><span class="p">(</span><span class="n">EmbeddedGraph</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> A class to represent a straight-line-embedded CW complex. We assume that the coordinates for the embedding of the vertices are given, the 1-skeleton is in fact a graph (so not as general as a full CW complex) with straight line embeddings, and 2-Cells are the interior of the shape outlined by its boundary edges. </span>
Expand All @@ -97,7 +97,7 @@ <h1>Source code for embed_cw</h1><div class="highlight"><pre>
<span class="sd"> &quot;&quot;&quot;</span>

<div class="viewcode-block" id="EmbeddedCW.__init__">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW.__init__">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW.__init__">[docs]</a>
<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="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Initializes an empty EmbeddedCW object.</span>
Expand All @@ -109,7 +109,7 @@ <h1>Source code for embed_cw</h1><div class="highlight"><pre>


<div class="viewcode-block" id="EmbeddedCW.add_from_embedded_graph">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW.add_from_embedded_graph">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW.add_from_embedded_graph">[docs]</a>
<span class="k">def</span> <span class="nf">add_from_embedded_graph</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">G</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Adds the edges and coordinates from an EmbeddedGraph object to the EmbeddedCW object.</span>
Expand All @@ -123,7 +123,7 @@ <h1>Source code for embed_cw</h1><div class="highlight"><pre>


<div class="viewcode-block" id="EmbeddedCW.add_face">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW.add_face">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW.add_face">[docs]</a>
<span class="k">def</span> <span class="nf">add_face</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">face</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Adds a face to the list of faces.</span>
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<div class="viewcode-block" id="EmbeddedCW.g_omega_faces">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW.g_omega_faces">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW.g_omega_faces">[docs]</a>
<span class="k">def</span> <span class="nf">g_omega_faces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">theta</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Calculates the function value of the faces of the graph by making the value equal to the max vertex value </span>
Expand All @@ -194,7 +194,7 @@ <h1>Source code for embed_cw</h1><div class="highlight"><pre>


<div class="viewcode-block" id="EmbeddedCW.sort_faces">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW.sort_faces">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW.sort_faces">[docs]</a>
<span class="k">def</span> <span class="nf">sort_faces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">theta</span><span class="p">,</span> <span class="n">return_g</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Function to sort the faces of the graph according to the function</span>
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<div class="viewcode-block" id="EmbeddedCW.plot_faces">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW.plot_faces">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW.plot_faces">[docs]</a>
<span class="k">def</span> <span class="nf">plot_faces</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">theta</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Plots the faces of the graph in the direction of theta.</span>
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<div class="viewcode-block" id="EmbeddedCW.plot">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.EmbeddedCW.plot">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.EmbeddedCW.plot">[docs]</a>
<span class="k">def</span> <span class="nf">plot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bounding_circle</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">color_nodes_theta</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Plots the graph with the faces filled in.</span>
Expand All @@ -280,7 +280,7 @@ <h1>Source code for embed_cw</h1><div class="highlight"><pre>


<div class="viewcode-block" id="create_example_cw">
<a class="viewcode-back" href="../embed_cw.html#embed_cw.create_example_cw">[docs]</a>
<a class="viewcode-back" href="../../embed_cw.html#ect.embed_cw.create_example_cw">[docs]</a>
<span class="k">def</span> <span class="nf">create_example_cw</span><span class="p">(</span><span class="n">mean_centered</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Creates an example EmbeddedCW object with a simple CW complex.</span>
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