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<div class="section" id="development">
<h1>Development<a class="headerlink" href="#development" title="Permalink to this headline">¶</a></h1>
<div class="section" id="basic-instructions">
<h2>Basic instructions<a class="headerlink" href="#basic-instructions" title="Permalink to this headline">¶</a></h2>
<p>The default cclib files distributed with a release, as described in the <a class="reference external" href="tutorial.html">tutorial</a>, do not include any unit tests and logfiles necessary to run those tests. This section covers how to download the full source along with all test data and scripts, and how to use these for development and testing.</p>
<div class="section" id="cloning-cclib-from-github">
<h3>Cloning cclib from GitHub<a class="headerlink" href="#cloning-cclib-from-github" title="Permalink to this headline">¶</a></h3>
<p>cclib is hosted by the fantastic people at <a class="reference external" href="https://github.com">GitHub</a> (previously at <a class="reference external" href="https://sourceforge.net">Sourceforge</a>) in a <a class="reference external" href="http://git-scm.com">git</a> repository. You can download a <a class="reference external" href="https://github.com/cclib/cclib/archive/master.zip">zipped archive</a> of the current development version (called <cite>master</cite>) for installation and testing or browse the available <a class="reference external" href="https://github.com/cclib/cclib/releases">releases</a>. In order to contribute any changes, however, you will need to create a local copy of the repository:</p>
<div class="highlight-bash"><div class="highlight"><pre>git clone https://github.com/cclib/cclib.git cclib
</pre></div>
</div>
</div>
<div class="section" id="guidelines">
<h3>Guidelines<a class="headerlink" href="#guidelines" title="Permalink to this headline">¶</a></h3>
<p>We follow a typical GitHub collaborative model, relying on <a class="reference external" href="https://help.github.com/articles/using-pull-requests">forks and pull requests</a>. In short, the development process consists of:</p>
<ul class="simple">
<li><a class="reference external" href="https://help.github.com/articles/fork-a-repo">Creating your own fork</a> of cclib in order to develop</li>
<li><a class="reference external" href="https://help.github.com/articles/creating-a-pull-request">Creating a pull request</a> to contribute your changes</li>
<li>Reviewing and merging open pull requests (by someone else)</li>
<li>Using <a class="reference external" href="https://github.com/cclib/cclib/issues">issues</a> to plan and prioritize future work</li>
</ul>
<p>Here are some general guidelines for developers who are contributing code:</p>
<ul class="simple">
<li>Run and review the unit tests (see below) before submitting a pull request</li>
<li>There should normally not be more failed tests than before your changes</li>
<li>For larger changes or features that take some time to implement, <a class="reference external" href="https://help.github.com/articles/branching-out">using branches</a> is recommended</li>
</ul>
</div>
<div class="section" id="releasing-a-new-version">
<h3>Releasing a new version<a class="headerlink" href="#releasing-a-new-version" title="Permalink to this headline">¶</a></h3>
<p>The release cycle of cclib is irregular, with new versions being created as deemed necessary after significant changes or new features. We roughly follow semantic versioning with respect to the <a class="reference external" href="data.html">parsed attributes</a>.</p>
<p>When creating a new release on GitHub, the typical procedure might include the following steps:</p>
<ul class="simple">
<li>Update the <a class="reference external" href="https://github.com/cclib/cclib/blob/master/CHANGELOG">CHANGELOG</a>, <a class="reference external" href="https://github.com/cclib/cclib/blob/master/ANNOUNCE">ANNOUNCE</a> and any other files that might change content with the new version</li>
<li>Make sure that <a class="reference external" href="https://github.com/cclib/cclib/blob/master/setup.py">setup.py</a> has the right version number, as well as __version__ in <a class="reference external" href="https://github.com/cclib/cclib/blob/master/src/cclib/__init__.py">__init__.py</a> and any other relevant files</li>
<li>Update the download and install instructions in the documentation, if appropriate</li>
<li>Create a branch for the release, so that development can continue</li>
<li>Run all tests for a final time and fix any remaining issues</li>
<li>Tag the release (make sure to use an annotated tag using <tt class="docutils literal"><span class="pre">git</span> <span class="pre">-a</span></tt>) and upload it (<tt class="docutils literal"><span class="pre">git</span> <span class="pre">push</span> <span class="pre">--tags</span></tt>)</li>
<li>Run <a class="reference external" href="https://github.com/cclib/cclib/blob/master/manifest.py">manifest.py</a> to update the MANIFEST file</li>
<li>Create the source distributions (<tt class="docutils literal"><span class="pre">python</span> <span class="pre">setup.py</span> <span class="pre">sdist</span> <span class="pre">--formats=gztar,zip</span></tt>) and Windows binary installers (<tt class="docutils literal"><span class="pre">python</span> <span class="pre">setup.py</span> <span class="pre">bdist_wininst</span></tt>)</li>
<li>Create a release on Github using the created tag (see <a class="reference external" href="https://help.github.com/articles/creating-releases">Creating releases</a>) and upload the source distribiuions and Windows binaries</li>
<li>Email the users and developers mailing list with the message in <a class="reference external" href="https://github.com/cclib/cclib/blob/master/ANNOUNCE">ANNOUNCE</a></li>
<li>Update the Python package index (<a class="reference external" href="https://pypi.python.org/pypi/cclib">https://pypi.python.org/pypi/cclib</a>), normally done by <tt class="docutils literal"><span class="pre">python</span> <span class="pre">setup.py</span> <span class="pre">register</span></tt></li>
<li>For significant releases, if appropriate, send an email to the <a class="reference external" href="http://www.ccl.net">CCL list</a> and any mailing lists for computational chemistry packages supported by cclib</li>
</ul>
</div>
</div>
<div class="section" id="testing">
<h2>Testing<a class="headerlink" href="#testing" title="Permalink to this headline">¶</a></h2>
<p id="index-0">The <a class="reference external" href="https://github.com/cclib/cclib/tree/master/test">test directory</a>, which is not included in the default download, contains the test scripts that keep cclib reliable, and keep the developers sane. With any new commit or pull request to cclib on GitHub the tests are triggered and run with <a class="reference external" href="https://travis-ci.org/cclib/cclib">Travis CI</a>, for both the current production version 1.3.1 (<img alt="travis_prod" src="https://travis-ci.org/cclib/cclib.svg?branch=v1.3.1" />) as well as master (<img alt="travis_master" src="https://travis-ci.org/cclib/cclib.svg?branch=master" />).</p>
<p>The input files for tests, which are logfiles from computational chemistry programs, are located in the <a class="reference external" href="https://github.com/cclib/cclib/tree/master/test">data directory</a>. These are a central part of cclib, and any progress should always be supported by corresponding tests. When a user opens an issue or reports a bug, it is prudent to write a test that reproduces the bug as well as fixing it. This ensures it will remain fixed in the future. Likewise, extending the coverage of data attributes to more programs should proceed in parallel with the growth of unit tests.</p>
<div class="section" id="unit-tests">
<span id="index-1"></span><h3>Unit tests<a class="headerlink" href="#unit-tests" title="Permalink to this headline">¶</a></h3>
<p>Unit tests check that the parsers work correctly for typical calculation types on small molecules, usually water or 1,4-divinylbenzene (dvb) with C2h symmetry. The corresponding logfiles stored in folders like <tt class="docutils literal"><span class="pre">data/NWChem/basicNWChem6.0</span></tt> are intended to test logfiles for an approximate major version of a program, and are standardized for all supported programs to the extent possible. They are located alongside the code in the repository, but are not normally distributed with the source. Two different recent versions are often used in the unit tests, with older versions being moved to the regression suite (see below). Attributes are considered supported only if they are checked by at least one test, and the <a class="reference external" href="data_dev.html#details-of-current-implementation">table of attribute coverage</a> is generated automatically using this criterion.</p>
<p>The job types currently included as unit tests:</p>
<ul class="simple">
<li>restricted and unrestricted single point energies for dvb (RHF/STO-3G <strong>and</strong> B3LYP/STO-3G)</li>
<li>geometry optimization and scan for dvb (RHF/STO-3G and/or B3LYP/STO-3G)</li>
<li>frequency calculation with IR and Raman intensities for dvb (RHF/STO-3G or B3LYP/STO-3G)</li>
<li>single point energy for carbon atom using a large basis set such as aug-cc-pCVQZ</li>
<li>Møller–Plesset and coupled cluster energies for water (STO-3G or 6-31G basis set)</li>
</ul>
</div>
<div class="section" id="regression-tests">
<span id="index-2"></span><h3>Regression tests<a class="headerlink" href="#regression-tests" title="Permalink to this headline">¶</a></h3>
<p>Regression tests ensure that bugs, once fixed, stay fixed. These are real-life files that at some point broke a cclib parser, and are stored in folders like <tt class="docutils literal"><span class="pre">data/regression/Jaguar/Jaguar6.4</span></tt>. The files associated with regression tests are not stored stored together with the source code as they are often quite large. A separate repository on github, <a class="reference external" href="https://github.com/cclib/cclib-data">cclib-data</a>, is used to track these files, and we do not distribute them with any releases.</p>
<p>For every bug found in the parsers, there should be a corresponding regression test that tests this bug stays fixed. The process is automated by <a class="reference external" href="https://github.com/cclib/cclib/blob/master/test/regression.py">regression.py</a>, which runs through all of our test data, both the basic data and regression files, opens them, tries to parse, and runs any relevant regression tests defined for that file. New regression tests are added by creating a function <tt class="docutils literal"><span class="pre">testMyFileName_out</span></tt> according to the examples at the start of <a class="reference external" href="https://github.com/cclib/cclib/blob/master/test/regression.py">regression.py</a>.</p>
</div>
<div class="section" id="doctests">
<h3>Doctests<a class="headerlink" href="#doctests" title="Permalink to this headline">¶</a></h3>
<p>Doctests are a useful Python feature for unit testing individual functions. To run the doctests in a particular file, you need to run the script. For example, <tt class="docutils literal"><span class="pre">python</span> <span class="pre">gaussianparser.py</span></tt> runs the doctests contained in <a class="reference external" href="https://github.com/cclib/cclib/blob/master/src/cclib/parser/gaussianparser.py">gaussianparser.py</a>. To run all of the doctests at once, you need to install a testing tool such as <a class="reference external" href="https://nose.readthedocs.org/en/latest/">nose</a>, and then use the following command (note that many errors may be due to missing libraries like <a class="reference external" href="http://biopython.org/wiki/Main_Page">biopython</a>):</p>
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>nose cclib --with-doctest -e <span class="nb">test</span>* -v
ERROR
ERROR
Doctest: cclib.bridge.cclib2openbabel.makeopenbabel ... ok
ERROR
ERROR
Doctest: cclib.parser.adfparser.ADF.normalisesym ... ok
Doctest: cclib.parser.gamessparser.GAMESS.normalise_aonames ... ok
Doctest: cclib.parser.gamessparser.GAMESS.normalisesym ... ok
Doctest: cclib.parser.gamessukparser.GAMESSUK.normalisesym ... ok
Doctest: cclib.parser.gaussianparser.Gaussian.normalisesym ... ok
Doctest: cclib.parser.jaguarparser.Jaguar.normalisesym ... ok
Doctest: cclib.parser.logfileparser.Logfile.float ... ok
Doctest: cclib.parser.utils.PeriodicTable ... ok
Doctest: cclib.parser.utils.convertor ... ok
ERROR
ERROR
......
</pre></div>
</div>
</div>
</div>
<div class="section" id="websites-related-to-cclib">
<h2>Websites related to cclib<a class="headerlink" href="#websites-related-to-cclib" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>The official <a class="reference external" href="https://github.com/cclib">cclib organization on github</a></li>
<li>The <a class="reference external" href="http://sourceforge.net/projects/cclib/">cclib project page on Sourceforge</a> (inactive now)</li>
<li>The <a class="reference external" href="https://travis-ci.org/cclib/cclib">cclib page for Travis CI</a></li>
<li>The <a class="reference external" href="http://www.python.org/pypi/cclib">cclib entry on PyPI</a></li>
<li>The <a class="reference external" href="https://www.ohloh.net/p/cclib">cclib entry on Ohloh</a></li>
</ul>
</div>
<div class="section" id="developers">
<h2>Developers<a class="headerlink" href="#developers" title="Permalink to this headline">¶</a></h2>
<p>Besides input from a number of people <a class="reference external" href="https://github.com/cclib/cclib/blob/master/THANKS">listed in the repository</a>, the following developers have contributed code to cclib (in alphabetical order):</p>
<ul class="simple">
<li>Eric Berquist</li>
<li><a class="reference external" href="https://github.com/langner">Karol M. Langner</a></li>
<li><a class="reference external" href="http://www.redbrick.dcu.ie/~noel">Noel O’Boyle</a></li>
<li>Christopher Rowley</li>
<li>Adam Tenderholt</li>
</ul>
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