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<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
<li class="toctree-l1"><a class="reference internal" href="example_notebooks.html">Example notebooks</a></li>
<li class="toctree-l1"><a class="reference internal" href="binary_c_parameters.html">Binary_c parameters</a></li>
<li class="toctree-l1"><a class="reference internal" href="grid_options_descriptions.html">Population grid code options</a></li>
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python">Visit the GitLab repo</a></li>
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<div class="section" id="welcome-to-binary-c-python-s-documentation">
<h1>Welcome to binary_c-python’s documentation!<a class="headerlink" href="#welcome-to-binary-c-python-s-documentation" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="python-module-for-binary-c">
<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this headline">¶</a></h1>
<p>Docstring coverage:</p>
<a class="reference external image-reference" href="./badges/docstring_coverage.svg"><img alt="docstring coverage" src="_images/docstring_coverage.svg" /></a>
<p>Test coverage:</p>
<a class="reference external image-reference" href="./badges/test_coverage.svg"><img alt="test coverage" src="_images/test_coverage.svg" /></a>
<p>Binary population synthesis code that interfaces with binary_c. Based on a original work by Jeff Andrews. Updated and extended for Python3 by David Hendriks, Robert Izzard.</p>
<p>The current release is version <a class="reference external" href="VERSION">version</a>, make sure to use that version number when installing!</p>
<div class="section" id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h2>
<p>To run this code you need to at least have installations of:</p>
<ul class="simple">
<li><p>Python 3.6 or higher</p></li>
<li><p>binary_c version 2.1.7 or higher</p></li>
</ul>
<p>And the following python packages (which will get installed automatically when installing with pip):</p>
<ul class="simple">
<li><p>numpy</p></li>
<li><p>pytest</p></li>
<li><p>h5py</p></li>
<li><p>pathos</p></li>
<li><p>pandas</p></li>
<li><p>astropy</p></li>
<li><p>matplotlib</p></li>
<li><p>py_rinterpolate</p></li>
</ul></div>
<div class="section" id="environment-variables">
<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">¶</a></h2>
<p>Before compilation you need to have certain environment variables:</p>
<p>Required:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">BINARY_C</span></code> should point to the root directory of your binary_c installation</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">LD_LIBRARY_PATH</span></code> should include $BINARY_C/src and whatever directories are required to run binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">LIBRARY_PATH</span></code> should include whatever directories are required to build binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">GSL_DIR</span></code> should point to the root location where you installed GSL to. This root dir should contain <code class="docutils literal notranslate"><span class="pre">bin/</span></code>, <code class="docutils literal notranslate"><span class="pre">lib/</span></code> etc</p></li>
</ul>
</div>
<div class="section" id="build-instructions">
<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">¶</a></h2>
<p>First, make sure you have built binary_c (See <code class="docutils literal notranslate"><span class="pre">$BINARY_C/doc/binary_c2.pdf</span></code> section: installation for all the installation instructions for <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>)) and that it functions correctly.</p>
<div class="section" id="installation-via-pip">
<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this headline">¶</a></h3>
<p>To install this package via pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">binarycpython</span>
</pre></div>
</div>
<p>This will install the latest stable installation that is available on pip.</p>
</div>
<div class="section" id="installation-from-source">
<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">¶</a></h3>
<p>We can also install the package from source, which is useful for development versions and when you want to modify the code. It is recommended that you install this into a virtual environment. From within the root directory, run</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">install</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
<p>This will install the package, along with all the dependencies.</p>
<p>If this is not the first time you install the package, but rather rebuild it because you made changes in either binary_c or binarycpython, you can run</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">install_without_dependencies</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
<p>to reinstall just binarycpython.</p>
<div class="section" id="after-installation">
<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this headline">¶</a></h4>
<p>After installing the code via source it is useful to run the test suite before doing any programming with it. The test suite is stored in <code class="docutils literal notranslate"><span class="pre">binarycpython/tests</span></code> and running <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">main.py</span></code> in there will run all the tests.</p>
</div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<p>See the examples/ directory for example scripts and notebooks. The documentation contains example pages as well.</p>
</div>
<div class="section" id="usage-notes">
<h2>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this headline">¶</a></h2>
<p>Make sure that with every change/recompilation you make in <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>, you also rebuild this package. Whenever you change the sourcecode of this package, you need to reinstall it into your virtualenvironment as well</p>
</div>
<div class="section" id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h2>
<p>Look in the docs/ directory. Within the build/html/ there is the html version of the documentation. The</p>
</div>
<div class="section" id="development">
<h2>Development:<a class="headerlink" href="#development" title="Permalink to this headline">¶</a></h2>
<p>If you want to contribute to the code, then it is recommended that you install the packages in <code class="docutils literal notranslate"><span class="pre">development_requirements.txt</span></code>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">r</span> <span class="n">development_requirements</span><span class="o">.</span><span class="n">txt</span>
</pre></div>
</div>
</div>
<div class="section" id="faq-issues">
<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this headline">¶</a></h2>
<p>Building issues with binary_c itself:</p>
<ul class="simple">
<li><p>see the documentation of binary_c (in doc/).</p></li>
<li><p>If you have MESA installed, make sure that the <code class="docutils literal notranslate"><span class="pre">$MESASDK_ROOT/bin/mesasdk_init.sh</span></code> is not sourced. It comes with its own version of some programs, and those can interfere with installing.</p></li>
</ul>
<p>When Pip install fails:</p>
<ul class="simple">
<li><p>Run the installation with <code class="docutils literal notranslate"><span class="pre">-v</span></code> and/or <code class="docutils literal notranslate"><span class="pre">--log</span> <span class="pre"><logfile></span></code> to get some more info</p></li><li><p>If gcc throws errors like <code class="docutils literal notranslate"><span class="pre">gcc:</span> <span class="pre">error:</span> <span class="pre">unrecognized</span> <span class="pre">command</span> <span class="pre">line</span> <span class="pre">option</span> <span class="pre">‘-ftz’;</span> <span class="pre">did</span> <span class="pre">you</span> <span class="pre">mean</span> <span class="pre">‘-flto’?</span></code>, this might be due to that the python on that system was built with a different compiler. It then passes the python3.6-config –cflags to the binarycpython installation, which, if done with gcc, will not work. Try a different python3.6. I suggest using <code class="docutils literal notranslate"><span class="pre">pyenv</span></code> to manage python versions. If installing a version of python with pyenv is not possible, then try to use a python version that is avaible to the machine that is built with the same compiler as binary_c was built with.</p></li>
<li><p>if pip installation results in <code class="docutils literal notranslate"><span class="pre">No</span> <span class="pre">files/directories</span> <span class="pre">in</span> <span class="pre">/tmp/pip-1ckzg0p9-build/pip-egg-info</span> <span class="pre">(from</span> <span class="pre">PKG-INFO)</span></code>, try running it verbose (<code class="docutils literal notranslate"><span class="pre">-v</span></code>) to see what is actually going wrong.</p></li>
<li><p>If pip terminates with the error FileNotFoundError: [Errno 2] No such file or directory: ‘<…>/binary_c-config’ Then make sure that the path to your main $BINARY_C directory is set correctly.</p></li>
</ul>
<p>Other:</p>
<ul class="simple">
<li><p>When running jupyter notebooks, make sure you are running the jupyter installation from the same virtual environment.</p></li>
<li><p>When the output of binary_c seems to be different than expected, you might need to rebuild this python package. Everytime binary_c is compiled, this package needs to be rebuilt too.</p></li>
</ul>
<div class="toctree-wrapper compound">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a><ul>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#environment-variables">Environment variables</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#build-instructions">Build instructions</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#examples">Examples</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#usage-notes">Usage notes</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#documentation">Documentation</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#development">Development:</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#faq-issues">FAQ/Issues:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a><ul>
<li class="toctree-l2"><a class="reference internal" href="custom_logging_functions.html">custom_logging_functions module</a></li>
<li class="toctree-l2"><a class="reference internal" href="distribution_functions.html">distribution_functions module</a></li>
<li class="toctree-l2"><a class="reference internal" href="functions.html">functions module</a></li>
<li class="toctree-l2"><a class="reference internal" href="grid.html">grid_class module</a></li>
<li class="toctree-l2"><a class="reference internal" href="grid_options_defaults.html">Grid options and descriptions</a></li>
<li class="toctree-l2"><a class="reference internal" href="hpc_functions.html">hpc_functions module</a></li>
<li class="toctree-l2"><a class="reference internal" href="plot_functions.html">plot_functions module</a></li>
<li class="toctree-l2"><a class="reference internal" href="run_system_wrapper.html">run_system_wrapper module</a></li>
<li class="toctree-l2"><a class="reference internal" href="spacing_functions.html">spacing_functions module</a></li>
<li class="toctree-l2"><a class="reference internal" href="stellar_types.html">stellar_types module</a></li>
<li class="toctree-l2"><a class="reference internal" href="useful_funcs.html">useful_funcs module</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="example_notebooks.html">Example notebooks</a><ul>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_individual_systems.html">Tutorial: Running individual systems with binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_custom_logging.html">Tutorial: Using custom logging routines with binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_population.html">Tutorial: Running populations with binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_extra_features.html">Tutorial: Extra features and functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_api_functionality.html">Tutorial: Using the API functionality of binary_c-python</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_luminosity_function_single.html">Example use case: Zero-age stellar luminosity function</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_luminosity_function_binaries.html">Example use case: Zero-age stellar luminosity function in binaries</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_HRD.html">Example use case: Hertzsprung-Russell diagrams</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_common_envelope_evolution.html">Example use case: Common-envelope evolution</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_BHBH.html">Example use case: Binary black hole systems</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_massive_remnants.html">Example use case: Massive star luminosity</a></li>
<li class="toctree-l2"><a class="reference internal" href="examples/notebook_solar_system.html">Example use case: Solar system using the API functionality</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="binary_c_parameters.html">Binary_c parameters</a><ul>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-stars">Section: stars</a></li>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-binary">Section: binary</a></li>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-nucsyn">Section: nucsyn</a></li>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-output">Section: output</a></li>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-input">Section: input</a></li>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-i-o">Section: i/o</a></li>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-algorithms">Section: algorithms</a></li>
<li class="toctree-l2"><a class="reference internal" href="binary_c_parameters.html#section-misc">Section: misc</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="grid_options_descriptions.html">Population grid code options</a><ul>
<li class="toctree-l2"><a class="reference internal" href="grid_options_descriptions.html#public-options">Public options</a></li>
<li class="toctree-l2"><a class="reference internal" href="grid_options_descriptions.html#moe-di-stefano-sampler-options">Moe & di Stefano sampler options</a></li>
<li class="toctree-l2"><a class="reference internal" href="grid_options_descriptions.html#private-options">Private options</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python">Visit the GitLab repo</a></li><li class="toctree-l1"><a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/issues/new">Submit an issue</a></li>
</ul>
</div>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
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