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<div class="section" id="documentation">
<span id="sec-documentation"></span><h1>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h1>
<p><span class="sc">Psi4</span>‘s documentation is generated by <a class="reference external" href="http://sphinx.pocoo.org/">Sphinx</a>
and lives in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman">psi4/doc/sphinxman</a>. It is available online at
<a class="reference external" href="http://psicode.org/psi4manual/master/index.html">http://psicode.org/psi4manual/master/index.html</a>
for the latest development branch.</p>
<div class="section" id="installing-sphinx">
<h2>Installing Sphinx<a class="headerlink" href="#installing-sphinx" title="Permalink to this headline">¶</a></h2>
<p>Installing Sphinx is only necessary to build the documentation
yourself, locally. The docs are served from
from psicode, so most users/developers won’t need Sphinx
installed. Nevertheless, installation is easy.</p>
<p>On Mac:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">U</span> <span class="n">Sphinx</span>
<span class="go"># or</span>
<span class="gp">>>> </span><span class="n">conda</span> <span class="n">install</span> <span class="n">sphinx</span>
</pre></div>
</div>
<p>On Linux:</p>
<ul>
<li><p class="first">Download</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">curl</span> <span class="o">-</span><span class="n">O</span> <span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">pypi</span><span class="o">.</span><span class="n">python</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">packages</span><span class="o">/</span><span class="n">source</span><span class="o">/</span><span class="n">S</span><span class="o">/</span><span class="n">Sphinx</span><span class="o">/</span><span class="n">Sphinx</span><span class="o">-</span><span class="mf">1.3</span><span class="o">.</span><span class="mf">1.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
</li>
<li><p class="first">Unpack, etc.</p>
</li>
<li><p class="first">Build and Install</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span>
<span class="gp">>>> </span><span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
</pre></div>
</div>
</li>
<li><p class="first">Check the path</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">which</span> <span class="n">sphinx</span><span class="o">-</span><span class="n">build</span>
<span class="gp">>>> </span><span class="n">which</span> <span class="n">latex</span>
<span class="gp">>>> </span><span class="n">which</span> <span class="n">dvipng</span>
</pre></div>
</div>
</li>
<li><p class="first">LaTeX and dvipng are needed to render math. If the latter is missing,
the following may work.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">sudo</span> <span class="n">yum</span> <span class="n">install</span> <span class="n">dvipng</span>
</pre></div>
</div>
</li>
</ul>
</div>
<div class="section" id="documentation-structure">
<h2>Documentation Structure<a class="headerlink" href="#documentation-structure" title="Permalink to this headline">¶</a></h2>
<p>Sphinx has nice capabilities for extracting docstrings from python files,
presenting both auto-generated and narrative documentation in the same
format, hyperlinking within and to trac/external websites, and generating
documentation in different formats from the same source. <span class="sc">Psi4</span>‘s
documentation is a unified document covering information for both users
and programmers in separate sections. From the top-level object directory,
build the following target (note that a working version of the <span class="sc">Psi4</span>
executable in <code class="docutils literal"><span class="pre">bin/psi4</span></code> is a requirement for building the
documentation).:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">make</span> <span class="n">sphinxman</span>
</pre></div>
</div>
<p>This will build a full set of documentation in the <code class="docutils literal"><span class="pre">html</span></code> directory that can be viewed offline through any browser.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">doc</span><span class="o">/</span><span class="n">sphinxman</span><span class="o">/</span><span class="n">html</span><span class="o">/</span><span class="n">index</span><span class="o">.</span><span class="n">html</span>
</pre></div>
</div>
<p>Much of the documentation is auto-generated from the source. At present,
this covers:</p>
<ul class="simple">
<li>Physical Constants: <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/include/physconst.h">psi4/include/physconst.h</a></li>
<li>Python Driver: docstrings from *.py files in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/python">psi4/lib/python</a></li>
<li>Databases: docstrings from *.py files in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/databases">psi4/lib/databases</a></li>
<li>Basis Sets: *.gbs files in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/basis">psi4/lib/basis</a></li>
<li>C++ Keywords: <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/src/bin/psi4/read_options.cc">psi4/src/bin/psi4/read_options.cc</a></li>
<li>Sample Inputs: input.dat files in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples">psi4/samples</a></li>
<li>PSI Variables: <code class="docutils literal"><span class="pre">Process::environment.globals</span></code> lines and comments in the C++ code</li>
<li>Plugins: <code class="docutils literal"><span class="pre">doc.rst</span></code> text, *.py modules, and C++ keywords in <code class="docutils literal"><span class="pre">psi4/tests/plugin_*</span></code> plugin directories (disabled at the moment)</li>
<li>PSI Files: scratch file names and numbers in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/include/psifiles.h">psi4/include/psifiles.h</a></li>
</ul>
<p>Some documentation is even extracted from Psi4 objects at runtime.</p>
<ul class="simple">
<li>psi4: docstrings for the psi4 built-in module constructed in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/src/bin/psi4">psi4/src/bin/psi4</a></li>
<li>DFT: functional availibility and characteristics as encoded in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/python/functional.py">psi4/lib/python/functional.py</a></li>
<li>BasisFamily: fitting basis sets for each orbital basis as encoded in <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/python/basislistdunning.py">psi4/lib/python/basislistdunning.py</a> and <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/lib/python/basislistother.py">psi4/lib/python/basislistother.py</a></li>
</ul>
<p>Building all the documentation takes ~10 minutes. There is now good
dependency structure built into the <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman/CMakeLists.txt">psi4/doc/sphinxman/CMakeLists.txt</a>
, so very long builds should be infrequent (unless you’re touching
<a class="reference external" href="https://github.com/psi4/psi4public/blob/master/src/bin/psi4/read_options.cc">psi4/src/bin/psi4/read_options.cc</a>. Note that not all dependencies are
encoded (PSI variables, for instance, depend on every .cc file in the
source tree), so for a definitive doc build, remove (in the object
directory) <code class="docutils literal"><span class="pre">doc/sphinxman</span></code> and start from scratch.</p>
<p>Even ~10 minutes of build time can be annoying when developing
documentation and testing <code class="docutils literal"><span class="pre">rst</span></code> files. In that situation, use the target
below which builds only the written docs (not autodocs) in
<code class="docutils literal"><span class="pre">psi4/doc/sphinxman/source</span></code> quickly, though with a lot of warnings for
unresolved links:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">make</span> <span class="n">sphinxmini</span>
</pre></div>
</div>
</div>
<div class="section" id="restructuredtext">
<h2>reStructuredText<a class="headerlink" href="#restructuredtext" title="Permalink to this headline">¶</a></h2>
<p>Sphinx files are written in reStructuredText (*.rst). In the html
documentation, source code is available from the sidebar. Here’re a
few resources on Sphinx formatting.</p>
<ul class="simple">
<li><a class="reference external" href="http://docutils.sourceforge.net/docs/user/rst/quickref.html">reStructuredText</a></li>
<li><a class="reference external" href="http://docutils.sourceforge.net/test/functional/expected/standalone_rst_html4css1.html">rendered test document</a>
<em>vs.</em> <a class="reference external" href="http://svn.python.org/projects/external/docutils-0.5/docs/user/rst/demo.txt">source test document</a></li>
<li><a class="reference external" href="http://people.ee.ethz.ch/~creller/web/tricks/reST.html">Another reStructuredText</a></li>
<li><a class="reference external" href="http://openalea.gforge.inria.fr/doc/openalea/doc/_build/html/source/sphinx/rest_syntax.html">A third reStructuredText and Sphinx</a></li>
<li><a class="reference external" href="ftp://ftp.ams.org/ams/doc/amsmath/short-math-guide.pdf">LaTeX that Sphinx can handle</a></li>
<li><a class="reference external" href="http://sphinx.pocoo.org/contents.html">Sphinx Docs</a></li>
</ul>
</div>
<div class="section" id="math-in-the-codebase">
<h2>Math in the Codebase<a class="headerlink" href="#math-in-the-codebase" title="Permalink to this headline">¶</a></h2>
<p>It is often useful to have mathematical expressions in docstrings or
comments in the code that are auto-documented into the manual. Such
locations include the <code class="docutils literal"><span class="pre">#!</span> <span class="pre">comment</span></code> comments at the top of test case
input files, the <code class="docutils literal"><span class="pre">/*-</span> <span class="pre">comment</span> <span class="pre">-*/</span></code> comments in
<a class="reference external" href="https://github.com/psi4/psi4public/blob/master/src/bin/psi4/read_options.cc">psi4/src/bin/psi4/read_options.cc</a>, and the <code class="docutils literal"><span class="pre">r"""</span> <span class="pre">comment</span> <span class="pre">"""</span></code>
docstrings in python modules. (That <code class="docutils literal"><span class="pre">r"""</span></code> makes the string read
literally, so your LaTeX symbols aren’t confused with escape characters.)
For the two former, math has traditionally
been written in LaTeX (with the special substitution <code class="docutils literal"><span class="pre">@@</span></code> for
subscripting underscore). The autodoc script has been trained to convert
inline LaTeX math to reST math, provided the expression within dollar
signs is offset from other text. That is, expressions of the form
<code class="regexp docutils literal"><span class="pre">^</span> <span class="pre">$latex</span> <span class="pre">math$[.,</span> <span class="pre">]$</span></code> (pseudo-regex) are good, while <code class="docutils literal"><span class="pre">H$_2$O</span></code> and LaTeX tables
are not translated correctly. Python docstrings are absorbed as-is, so
please use reST math formatting (essentially <code class="docutils literal"><span class="pre">$latex</span> <span class="pre">math$</span></code> <img class="math" src="_images/math/fcb47d177e58f83257e03078e39b830ee90caec8.png" alt="\Rightarrow" style="vertical-align: -1px"/>
<code class="docutils literal"><span class="pre">:math:`latex</span> <span class="pre">math`</span></code>).</p>
</div>
<div class="section" id="the-map-of-the-sphinx">
<h2>The Map of the Sphinx<a class="headerlink" href="#the-map-of-the-sphinx" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Adding a new Appendix or First-TOC-Level page</p>
<p>Create your reST file and fill it with information. Add the name of your
file to <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman/source/appendices.rst">psi4/doc/sphinxman/source/appendices.rst</a> for an appendix or
to <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman/source/index.rst">psi4/doc/sphinxman/source/index.rst</a> for a first-TOC-level.
Finally, add your file to the <code class="docutils literal"><span class="pre">STATICDOC</span></code> variable in
<a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman/CMakeLists.txt">psi4/doc/sphinxman/CMakeLists.txt</a>. Sphinx will now build with your
new page.</p>
</li>
<li><p class="first">Adding a new module to “Theoretical Methods”</p>
<p>Copy the file of a well-established module, like
<a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman/source/sapt.rst">psi4/doc/sphinxman/source/sapt.rst</a>. Change the title, author, sec
label, ref, and source labels at the top of the file to point instead to
your code. Edit <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman/source/methods.rst">psi4/doc/sphinxman/source/methods.rst</a> to add the
name of your file so that it will appear in the TOC tree. Add your file
to the <code class="docutils literal"><span class="pre">STATICDOC</span></code> variable in
<a class="reference external" href="https://github.com/psi4/psi4public/blob/master/doc/sphinxman/CMakeLists.txt">psi4/doc/sphinxman/CMakeLists.txt</a>. Sphinx will now build with your new
file. Follow the models in existing methods pages to write your
documentation. If you don’t get all the keyword links, bibliography
links, sample inputs, math, tables, etc. working in Sphinx, don’t worry
about it. A genie will probably come through and tidy up all your
source.</p>
</li>
</ul>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Documentation</a><ul>
<li><a class="reference internal" href="#installing-sphinx">Installing Sphinx</a></li>
<li><a class="reference internal" href="#documentation-structure">Documentation Structure</a></li>
<li><a class="reference internal" href="#restructuredtext">reStructuredText</a></li>
<li><a class="reference internal" href="#math-in-the-codebase">Math in the Codebase</a></li>
<li><a class="reference internal" href="#the-map-of-the-sphinx">The Map of the Sphinx</a></li>
</ul>
</li>
</ul>
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