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peekxc committed Aug 22, 2023
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">


<title>simplextree – index</title>
<title>index</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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<header id="quarto-header" class="headroom fixed-top">
<nav class="navbar navbar-expand-lg navbar-dark ">
<div class="navbar-container container-fluid">
<div class="navbar-brand-container">
<a class="navbar-brand" href="../index.html">
<span class="navbar-title">simplextree</span>
</a>
</div>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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<span class="menu-text">simplextree</span></a>
</li>
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<li class="nav-item compact">
<a class="nav-link" href="https://github.com/peekxc/simplextree-py" rel="" target=""><i class="bi bi-github" role="img">
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<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item">Installation</li></ol></nav>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item">simplextree</li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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<ul class="list-unstyled mt-1">
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../pages/quickstart.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Quick start</span></a>
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<span class="menu-text">Overview</span></a>
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<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
<!-- margin-sidebar -->
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">

<nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="3">
<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#install" id="toc-install" class="nav-link active" data-scroll-target="#install">Install</a></li>
<li><a href="#building-developing" id="toc-building-developing" class="nav-link" data-scroll-target="#building-developing">Building &amp; Developing</a></li>
<li><a href="#native-extensions" id="toc-native-extensions" class="nav-link" data-scroll-target="#native-extensions">Native Extensions</a></li>
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<main class="content" id="quarto-document-content">

<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Installation</h1>
<h1 class="title">simplextree</h1>
</div>


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</header>

<p><a href="https://github.com/peekxc/splex/actions/workflows/package.yml"><img src="https://github.com/peekxc/splex/actions/workflows/package.yml/badge.svg" class="img-fluid" alt="Tests"></a> <a href="https://coveralls.io/github/peekxc/splex"><img src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/peekxc/ef42349965f40edf4232737026690c5f/raw/coverage_info.json" class="img-fluid" alt="coverage_badge"></a> <a href="https://github.com/peekxc/splex/actions/workflows/python-package.yml"><img src="https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11-blue" class="img-fluid" alt="python_badge"></a> <a href="https://github.com/peekxc/splex/actions/workflows/build-macos.yml"><img src="https://img.shields.io/github/actions/workflow/status/peekxc/simplextree-py/build-macos.yml?logo=apple&amp;logoColor=white" class="img-fluid" alt="coverage_badge"></a> <a href="https://github.com/peekxc/splex/actions/workflows/build-windows.yml"><img src="https://img.shields.io/github/actions/workflow/status/peekxc/simplextree-py/build-windows.yml?logo=windows&amp;logoColor=white" class="img-fluid" alt="coverage_badge"></a> <a href="https://github.com/peekxc/splex/actions/workflows/build-linux.yml"><img src="https://img.shields.io/github/actions/workflow/status/peekxc/simplextree-py/build-linux.yml?logo=linux&amp;logoColor=white" class="img-fluid" alt="coverage_badge"></a></p>
<p><code>simplextree</code> is a Python package aimed at simplifying computation for general simplicial complexes of any dimension. This package facilitates this aim by providing bindings to a Simplex Tree data structure implemented using modern C++ and exported an <a href="https://docs.python.org/3/extending/extending.html">extension module</a>. <!-- The underlying library implementation also exports a C++ header, which can be specified as a dependency and used in other packages. --></p>
<p>The Simplex Tree was originally introduced in the following paper:</p>
<blockquote class="blockquote">
<p>Boissonnat, Jean-Daniel, and Clément Maria. “The simplex tree: An efficient data structure for general simplicial complexes.” Algorithmica 70.3 (2014): 406-427.</p>
</blockquote>
<p>A Simplex Tree is an ordered, trie-like structure whose nodes are in bijection with the faces of the complex. Here’s a picture (taken from the paper) of a simplicial 3-complex (left) and its corresponding Simplex Tree (right):</p>
<p><a href="https://coveralls.io/github/peekxc/simplextree-py"><img src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/peekxc/ef42349965f40edf4232737026690c5f/raw/coverage_info.json" class="img-fluid" alt="coverage_badge"></a> <a href="https://github.com/peekxc/simplextree-py/actions/workflows/build-macos.yml"><img src="https://img.shields.io/github/actions/workflow/status/peekxc/simplextree-py/build_macos.yml?logo=apple&amp;logoColor=white" class="img-fluid" alt="build_macos"></a> <a href="https://github.com/peekxc/simplextree-py/actions/workflows/build-windows.yml"><img src="https://img.shields.io/github/actions/workflow/status/peekxc/simplextree-py/build_windows.yml?logo=windows&amp;logoColor=white" class="img-fluid" alt="build_windows"></a> <a href="https://github.com/peekxc/simplextree-py/actions/workflows/build-linux.yml"><img src="https://img.shields.io/github/actions/workflow/status/peekxc/simplextree-py/build_linux.yml?logo=linux&amp;logoColor=white" class="img-fluid" alt="build_linux"></a></p>
<p><code>simplextree</code> is an Python package that simplifies computation for general <a href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complexes</a> of any dimension by providing <a href="https://github.com/pybind/pybind11">pybind11</a> bindings to a <em>Simplex Tree</em> data structure implemented in modern C++17.</p>
<p>A <em>Simplex Tree</em> is an ordered, <a href="https://en.wikipedia.org/wiki/Trie">trie</a>-like structure whose nodes are in bijection with the faces of the complex. Here’s a picture of a simplicial 3-complex (left) and its corresponding Simplex Tree (right):</p>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="static/simplextree_pic.png" class="preview-image img-fluid figure-img"></p>
<figcaption class="figure-caption">simplextree</figcaption>
<p><img src="./static/simplextree_pic.png" class="preview-image img-fluid figure-img"></p>
<figcaption class="figure-caption">Picture taken from Boissonnat et al: “The simplex tree: An efficient data structure for general simplicial complexes”</figcaption>
</figure>
</div>
<p>TODO</p>
<p>The <em>Simplex Tree</em> was originally introduced in the following paper:</p>
<blockquote class="blockquote">
<p>Boissonnat, Jean-Daniel, and Clément Maria. “The simplex tree: An efficient data structure for general simplicial complexes.” Algorithmica 70.3 (2014): 406-427.</p>
</blockquote>
<p>The <code>SimplexTree</code> class exported by the package includes support for many tree operations, e.g.&nbsp;insertions, removals, expansions, collapses, star/link enumerations, and other traversals.</p>
<section id="install" class="level2">
<h2 class="anchored" data-anchor-id="install">Install</h2>
<p>The easiest way to install the package is via the platform-specific <a href="https://pythonwheels.com/">wheels</a> on <a href="https://pypi.org/project/simplextree/">pypi</a>.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> pip install simplextree </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>You can also <code>pip install</code> the package manually by downloading the appropriate wheel (or sdist) from the <a href="https://github.com/peekxc/simplextree-py/releases/">releases</a>.</p>
<p>For installation instructions for developers looking to extend the package, see <a href="#building--developing">Building &amp; Developing</a>.</p>
</section>
<section id="building-developing" class="level2">
<h2 class="anchored" data-anchor-id="building-developing">Building &amp; Developing</h2>
<p>If you would like to build the package yourself for development reasons, a typical workflow is to install the <a href="https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/#build-time-dependencies">build-time dependencies</a> first:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> pip install meson-python ninja pybind11 numpy</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Then, build and install the package in <a href="https://peps.python.org/pep-0660/">editable mode</a> (see also <a href="https://meson-python.readthedocs.io/en/latest/how-to-guides/editable-installs.html">meson-python notes</a>), optionally without build isolation for speed:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> pip install <span class="at">--no-build-isolation</span> <span class="at">--editable</span> .</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Unit testing is handled with <a href="https://docs.pytest.org/en/7.4.x/">pytest</a>. See the <a href="https://github.com/peekxc/simplextree-py/actions">gh-workflows</a> for platform-specific configuration.</p>
</section>
<section id="native-extensions" class="level2">
<h2 class="anchored" data-anchor-id="native-extensions">Native Extensions</h2>
<p>The underlying C++ library is <a href="https://en.wikipedia.org/wiki/Header-only">header-only</a> and may be included as a dependency by <a href="https://docs.python.org/3/extending/extending.html">extension modules</a> in other Python packages.</p>
<p>Thus, to modify or extending the complex in C++, it is sufficient to add the package as a build-time dependency and append the include directory to the compilation target.</p>


</section>

</main> <!-- /main -->
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