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346 changes: 195 additions & 151 deletions GITIM.html
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356 changes: 201 additions & 155 deletions ITIM.html
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140 changes: 73 additions & 67 deletions install.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>How to Install Pytim &#8212; Pytim 0.7.0 documentation</title>
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<title>How to Install Pytim &#8212; Pytim 1.0.0 documentation</title>
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Expand All @@ -43,7 +38,8 @@ <h3>Navigation</h3>
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<a href="quick.html" title="Pytim: Quick Tour"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">Pytim 0.7.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">Pytim 1.0.0 documentation</a> &#187;</li>
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Expand All @@ -52,37 +48,40 @@ <h3>Navigation</h3>
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<div class="body" role="main">

<div class="section" id="how-to-install-pytim">
<h1>How to Install Pytim<a class="headerlink" href="#how-to-install-pytim" title="Permalink to this headline"></a></h1>
<p><strong>IMPORTANT:</strong> Pytim (mainly because of its dependency on MDAnalysis) is compatible with <strong>Python 2.7 only</strong>. Python 3.x is not supported.</p>
<p>There are three ways to install Pytim:</p>
<div class="section" id="download-the-source-from-github">
<h2>Download the source from github<a class="headerlink" href="#download-the-source-from-github" title="Permalink to this headline"></a></h2>
<p>The package will download all the dependencies which are needed. Prerequisites for running the setup.py script are <cite>setuptools</cite> and <cite>cython</cite>.</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>pip install setuptools --user --upgrade
pip install cython --user --upgrade

git clone https://github.com/Marcello-Sega/pytim.git
<section id="how-to-install-pytim">
<h1>How to Install Pytim<a class="headerlink" href="#how-to-install-pytim" title="Permalink to this heading"></a></h1>
<p><strong>IMPORTANT:</strong> <a class="reference internal" href="quick.html"><span class="doc">Pytim</span></a> (mainly because of its dependency on MDAnalysis) is compatible with <strong>Python 2.7 only</strong>. Python 3.x is not supported.</p>
<p>There are three ways to install <a class="reference internal" href="quick.html"><span class="doc">Pytim</span></a>:</p>
<section id="download-the-source-from-github">
<h2>Download the source from github<a class="headerlink" href="#download-the-source-from-github" title="Permalink to this heading"></a></h2>
<p>The package will download all the dependencies which are needed. Prerequisites for running the setup.py script are <a class="reference external" href="https://pypi.python.org/pypi/setuptools">setuptools</a>, <a class="reference external" href="http://www.numpy.org">numpy</a> and <a class="reference external" href="http://www.cython.org">cython</a>.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone https://github.com/Marcello-Sega/pytim.git
<span class="nb">cd</span> pytim
python setup.py install --user
</pre></div>
</div>
<p>Note that on os-x it is usually better not to install Pytim system-wide using <cite>sudo</cite>, unless you know what you are doing, as newer versions of the operating system are protecting some system files to be overwritten even being super user.</p>
</div>
<div class="section" id="using-pip-to-access-the-python-package-index">
<h2>Using pip to access the Python Package Index<a class="headerlink" href="#using-pip-to-access-the-python-package-index" title="Permalink to this headline"></a></h2>
<p>The package can also be installed directly from the Python Package Index, along with the prerequisites <cite>setuptools</cite> and <cite>cython</cite>.</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>pip install setuptools --user --upgrade
pip install cython --user --upgrade

pip install pytim --user --upgrade
<p>Note that on os-x it is usually better not to install <a class="reference internal" href="quick.html"><span class="doc">Pytim</span></a> system-wide using <cite>sudo</cite>, unless you know what you are doing, as newer versions of the operating system are protecting some system files to be overwritten even being super user.</p>
</section>
<section id="using-pip-to-access-the-python-package-index">
<h2>Using pip to access the Python Package Index<a class="headerlink" href="#using-pip-to-access-the-python-package-index" title="Permalink to this heading"></a></h2>
<p>The package can also be installed directly from the Python Package Index, along with all the prerequisites.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone https://github.com/Marcello-Sega/pytim.git
<span class="nb">cd</span> pytim
pip install pytim --user --upgrade
</pre></div>
</div>
<p>Alternatively, you can use pip (directly or as a module) to install pytim, possibly in developer/editable mode:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone https://github.com/Marcello-Sega/pytim.git
<span class="nb">cd</span> pytim
python -m pip install -e .
</pre></div>
</div>
<div class="section" id="using-anaconda">
<h2>Using Anaconda<a class="headerlink" href="#using-anaconda" title="Permalink to this headline"></a></h2>
<p>Finally, Pytim is also available in the Anaconda Package Manager.</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>conda install -c conda-forge pytim
<p>This way the changes in the source will be reflected immediately after restarting a python shell, avoiding the need to reinstall every time.</p>
</section>
<section id="using-anaconda">
<h2>Using Anaconda<a class="headerlink" href="#using-anaconda" title="Permalink to this heading"></a></h2>
<p>Finally, <a class="reference internal" href="quick.html"><span class="doc">Pytim</span></a> is also available in the Anaconda Package Manager.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda install -c conda-forge pytim
</pre></div>
</div>
<hr class="docutils" />
Expand All @@ -99,10 +98,11 @@ <h2>Using Anaconda<a class="headerlink" href="#using-anaconda" title="Permalink

</script>

</div>
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</section>
</section>


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Expand All @@ -111,8 +111,8 @@ <h2>Using Anaconda<a class="headerlink" href="#using-anaconda" title="Permalink
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<img class="logo" src="_static/logo.png" alt="Logo"/>
</a></p>
<h3><a href="index.html">Table Of Contents</a></h3>
<p class="caption"><span class="caption-text">Tutorials</span></p>
<h3><a href="index.html">Table of Contents</a></h3>
<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
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<li class="toctree-l1"><a class="reference internal" href="quick.html">Pytim: Quick Tour</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">How to Install Pytim</a><ul>
Expand All @@ -128,23 +128,28 @@ <h3><a href="index.html">Table Of Contents</a></h3>
<li class="toctree-l1"><a class="reference internal" href="guessing_radii.html">Choosing the atomic radii</a></li>
<li class="toctree-l1"><a class="reference internal" href="newproperties.html">New properties of Atoms</a></li>
</ul>
<p class="caption"><span class="caption-text">Modules</span></p>
<p class="caption" role="heading"><span class="caption-text">Modules</span></p>
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<li class="toctree-l1"><a class="reference internal" href="ITIM.html">ITIM</a></li>
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title="previous chapter">Pytim: Quick Tour</a></p>
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Expand All @@ -153,15 +158,15 @@ <h3>This Page</h3>
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Expand All @@ -181,12 +186,13 @@ <h3>Navigation</h3>
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>previous</a> |</li>
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<li class="nav-item nav-item-0"><a href="index.html">Pytim 1.0.0 documentation</a> &#187;</li>
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