diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index a1c47f1cbca152a45b2ffa21300ef7ba6c48b24c..a55afdd521a7e085438117dc19577df0381194c4 100644
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diff --git a/docs/build/doctrees/grid_options_descriptions.doctree b/docs/build/doctrees/grid_options_descriptions.doctree
index 5aba912489ff05c0ec09862e425f4c8e0f74109d..cc9ffd870ff70d24ee5752c26ab67babc7654714 100644
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diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
index 22d2e370b6297ae4c7c2e6bc90ce11008f601f54..718a50346bbec6e764df22335dd992bdf73b095c 100644
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diff --git a/docs/build/doctrees/readme_link.doctree b/docs/build/doctrees/readme_link.doctree
index 44d8850ecc6026a410d1bd617360626979745a19..c4af319685ff890a89b27c4801b3ce7ae7da8e7f 100644
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diff --git a/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html b/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
index 4e934288308f3ab578cdd2f5cbba552e50231364..98ea493c5e771fc00f7fe273c9110db6e085917c 100644
--- a/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/distribution_functions.html b/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
index 57b7d0e499c418c39e1a1c007f0d729e5ba17542..cd4b2e23270282d3ed1f990bf92bccdfa0623131 100644
--- a/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/distribution_functions.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/functions.html b/docs/build/html/_modules/binarycpython/utils/functions.html
index 3f083c3256a1ccd9c95b561e397cf9ed5181bc85..9c27f1825f51b2da052c10a3eeff516fd7da797c 100644
--- a/docs/build/html/_modules/binarycpython/utils/functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/functions.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/grid.html b/docs/build/html/_modules/binarycpython/utils/grid.html
index 22e2ce4ca80215568065f514fce46637181c4ad8..2f1fc2d45c20d2645f36497098566055f9a44d5d 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html b/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
index 22629f991899b712cf6771625fe6db1273d928a8..9fe1f0d37aac25cdc226fc82cb57cf84092b460b 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid_options_defaults.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
@@ -239,8 +240,6 @@
<span class="s2">"_probtot"</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># total probability</span>
<span class="s2">"weight"</span><span class="p">:</span> <span class="mf">1.0</span><span class="p">,</span> <span class="c1"># weighting for the probability</span>
<span class="s2">"repeat"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># number of times to repeat each system (probability is adjusted to be 1/repeat)</span>
- <span class="s2">"results"</span><span class="p">:</span> <span class="p">{},</span> <span class="c1"># dict to store the results. Every process fills this on its own and then it will be joined later</span>
- <span class="s2">"ensemble_results"</span><span class="p">:</span> <span class="p">{},</span> <span class="c1"># Dict to store the ensemble results</span>
<span class="s2">"_start_time_evolution"</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># Start time of the grid</span>
<span class="s2">"_end_time_evolution"</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="c1"># end time of the grid</span>
<span class="s2">"_errors_found"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="c1"># Flag whether there are any errors from binary_c</span>
@@ -590,7 +589,6 @@
<span class="s2">"_errors_found"</span><span class="p">:</span> <span class="s2">"Variable storing a boolean flag whether errors by binary_c are encountered."</span><span class="p">,</span>
<span class="s2">"_errors_exceeded"</span><span class="p">:</span> <span class="s2">"Variable storing a boolean flag whether the amount of errors was higher than the set threshold (failed_systems_threshold). If True, then the commandline arguments of the failing systems will not be stored in the failed_system_log files."</span><span class="p">,</span>
<span class="s2">"source_file_filename"</span><span class="p">:</span> <span class="s2">"Variable containing the source file containing lines of binary_c commandline calls. These all have to start with binary_c."</span><span class="p">,</span> <span class="c1"># TODO: Expand</span>
- <span class="s2">"results"</span><span class="p">:</span> <span class="s2">"Dictionary in which the user can place their results. This dictionary gets merged at the end of a mulitprocessing simulation."</span><span class="p">,</span>
<span class="s2">"C_auto_logging"</span><span class="p">:</span> <span class="s2">"Dictionary containing parameters to be logged by binary_c. The structure of this dictionary is as follows: the key is used as the headline which the user can then catch. The value at that key is a list of binary_c system parameters (like star[0].mass)"</span><span class="p">,</span>
<span class="s2">"C_logging_code"</span><span class="p">:</span> <span class="s2">"Variable to store the exact code that is used for the custom_logging. In this way the user can do more complex logging, as well as putting these logging strings in files."</span><span class="p">,</span>
<span class="s2">"_failed_count"</span><span class="p">:</span> <span class="s2">"Variable storing the amount of failed systems."</span><span class="p">,</span>
@@ -618,7 +616,6 @@
<span class="s2">"repeat"</span><span class="p">:</span> <span class="s2">"Factor of how many times a system should be repeated. Consider the evolution splitting binary_c argument for supernovae kick repeating."</span><span class="p">,</span> <span class="c1"># TODO: make sure this is used.</span>
<span class="s2">"evolution_type"</span><span class="p">:</span> <span class="s2">"Variable containing the type of evolution used of the grid. Multiprocessing or linear processing"</span><span class="p">,</span>
<span class="s2">"combine_ensemble_with_thread_joining"</span><span class="p">:</span> <span class="s2">"BOolean flag on whether to combine everything and return it to the user or if false: write it to data_dir/ensemble_output_</span><span class="si">{popuation_id}</span><span class="s2">_</span><span class="si">{thread_id}</span><span class="s2">.json"</span><span class="p">,</span>
- <span class="s2">"ensemble_results"</span><span class="p">:</span> <span class="s2">"Dictinary that stores the ensemble results if combine_ensemble_with_thread_joining==True"</span><span class="p">,</span>
<span class="s2">"log_runtime_systems"</span><span class="p">:</span> <span class="s2">"Whether to log the runtime of the systems . Each systems run by the thread is logged to a file and is stored in the tmp_dir. (1 file per thread). Don't use this if you are planning to run alot of systems. This is mostly for debugging and finding systems that take long to run. Integer, default = 0. if value is 1 then the systems are logged"</span><span class="p">,</span>
<span class="p">}</span>
diff --git a/docs/build/html/_modules/binarycpython/utils/hpc_functions.html b/docs/build/html/_modules/binarycpython/utils/hpc_functions.html
index 24338e44ea77f361e3e82b567f41d1808bd0f93c..26343d65dc33a7a889e8aea6742dee86a6a2c590 100644
--- a/docs/build/html/_modules/binarycpython/utils/hpc_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/hpc_functions.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/plot_functions.html b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
index acfd39c1545acf75e6282c54bd8822bd16ac93e3..78320e491f44d65f2685c7c95b2fa2fa1743e81b 100644
--- a/docs/build/html/_modules/binarycpython/utils/plot_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
index fb0db0ee1323d8e88e7a47ddcaab1432a356dfd2..9025161f63123041999678a2031c0ab241331de5 100644
--- a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
+++ b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/spacing_functions.html b/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
index 87fe236fcbaca9f967067e6f03644d11a4c7c662..44e0ddf21742cb07096a6f33cccc86c9da49665d 100644
--- a/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/spacing_functions.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
index 31738128bd2382cd7026c887d8b4c18fdb9b771c..01c278d1968fd8cefbe657d3a55348b671d120ea 100644
--- a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
+++ b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
index a789af0843b21968bf2fb91f5c7fea80bd15f39f..8c749f2ce2073ac1abdd8b8c512b2754ced831ee 100644
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="../examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/_sources/grid_options_descriptions.rst.txt b/docs/build/html/_sources/grid_options_descriptions.rst.txt
index 0f948ea04cddcd472441000f45fd2de48011ee71..7c1c75c4f19882a77b78468b995bc5dd9594dac9 100644
--- a/docs/build/html/_sources/grid_options_descriptions.rst.txt
+++ b/docs/build/html/_sources/grid_options_descriptions.rst.txt
@@ -23,8 +23,6 @@ The following options are meant to be changed by the user.
| **custom_logging_func_memaddr**: Memory adress where the custom_logging_function is stored. Input: int
-| **ensemble_results**: Dictinary that stores the ensemble results if combine_ensemble_with_thread_joining==True
-
| **evolution_type**: Variable containing the type of evolution used of the grid. Multiprocessing or linear processing
| **failed_systems_threshold**: Variable storing the maximum amount of systems that are allowed to fail before logging their commandline arguments to failed_systems log files
@@ -45,8 +43,6 @@ The following options are meant to be changed by the user.
| **repeat**: Factor of how many times a system should be repeated. Consider the evolution splitting binary_c argument for supernovae kick repeating.
-| **results**: Dictionary in which the user can place their results. This dictionary gets merged at the end of a mulitprocessing simulation.
-
| **slurm**: Int flag whether to use a slurm type population evolution.
| **source_file_filename**: Variable containing the source file containing lines of binary_c commandline calls. These all have to start with binary_c.
diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
index bf0ccf76e20c9344a43d7345dd40a3d377bc2f68..d1f22839883a98a5815066ce6532ee7f488fc72e 100644
--- a/docs/build/html/_sources/index.rst.txt
+++ b/docs/build/html/_sources/index.rst.txt
@@ -5,6 +5,8 @@
Welcome to binary_c-python's documentation!
===========================================
+.. mdinclude:: ../../README.md
+
.. toctree::
:maxdepth: 2
@@ -15,11 +17,12 @@ Welcome to binary_c-python's documentation!
examples
binary_c_parameters
grid_options_descriptions
-
-
+ GitLab <https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python>
+
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
+
diff --git a/docs/build/html/binary_c_parameters.html b/docs/build/html/binary_c_parameters.html
index fadee75952a70b28799dfa0b17b5cf3f5f0e92a7..f49bcf2a64246f3317eb5649d6d25ea31842b4a6 100644
--- a/docs/build/html/binary_c_parameters.html
+++ b/docs/build/html/binary_c_parameters.html
@@ -99,6 +99,7 @@
</ul>
</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/custom_logging_functions.html b/docs/build/html/custom_logging_functions.html
index 24fb7ce334b87a930af40a6f711c21984b294e47..2ec6a003cf5c714053b7a6f124c0c037d440f535 100644
--- a/docs/build/html/custom_logging_functions.html
+++ b/docs/build/html/custom_logging_functions.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<li class="toctree-l2 current"><a class="current reference internal" href="#">custom_logging_functions module</a></li>
<li class="toctree-l2"><a class="reference internal" href="distribution_functions.html">distribution_functions module</a></li>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/distribution_functions.html b/docs/build/html/distribution_functions.html
index 24ab3090a372707eb5a272e075eed19bc3f6482a..828310cf1d1eff9a804f528bd3eba2e6e8bdf2a2 100644
--- a/docs/build/html/distribution_functions.html
+++ b/docs/build/html/distribution_functions.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="custom_logging_functions.html">custom_logging_functions module</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">distribution_functions module</a></li>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/examples.html b/docs/build/html/examples.html
index d94fdbd349546254cb6e17e9e8e0263c1eae4db4..bda1409f85990bcc71ca3e63051e830873b864a7 100644
--- a/docs/build/html/examples.html
+++ b/docs/build/html/examples.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Examples</a><ul>
<li class="toctree-l2"><a class="reference internal" href="general_examples.html">Examples</a></li>
@@ -93,6 +95,7 @@
</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/functions.html b/docs/build/html/functions.html
index 0b8698f3ef325ed40849dde447ef053806177b72..9184fde1e46441d41a45fb076088768dafb0f5fc 100644
--- a/docs/build/html/functions.html
+++ b/docs/build/html/functions.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/general_examples.html b/docs/build/html/general_examples.html
index 82aecdc2b570ec7d37f37139303bbb9ae38d0386..bfc9a31f245f1c2d0866fe6bc034eacdc366b223 100644
--- a/docs/build/html/general_examples.html
+++ b/docs/build/html/general_examples.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="examples.html">Examples</a><ul class="current">
<li class="toctree-l2 current"><a class="current reference internal" href="#">Examples</a></li>
@@ -93,6 +95,7 @@
</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index e9954b899a4e96fef83e739dab6e87ecd7338ace..e344e42eb5ce544e7843ed3e86a7b3e8bca0da41 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -87,6 +87,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/grid.html b/docs/build/html/grid.html
index 8ced97503a8ddaf708ab2e314b78d9bb496091c7..1e11f418ca0ecf32f9f67f209651d50b93bfc1b8 100644
--- a/docs/build/html/grid.html
+++ b/docs/build/html/grid.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/grid_options_defaults.html b/docs/build/html/grid_options_defaults.html
index 148ec390eb8387bb28eb85d726280d263da07bf8..37eea5bee7d7015dbc22489e3924a9d3893e80b0 100644
--- a/docs/build/html/grid_options_defaults.html
+++ b/docs/build/html/grid_options_defaults.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/grid_options_descriptions.html b/docs/build/html/grid_options_descriptions.html
index aef7e1c0c4f0583822bf0908c65a64d8a89b4417..99492f0b8df16760c67a65c05dfc595873272e7d 100644
--- a/docs/build/html/grid_options_descriptions.html
+++ b/docs/build/html/grid_options_descriptions.html
@@ -92,6 +92,7 @@
<li class="toctree-l2"><a class="reference internal" href="#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">GitLab</a></li>
</ul>
@@ -186,9 +187,6 @@ There are 1 options that are not described yet.</p>
<div class="line"><strong>custom_logging_func_memaddr</strong>: Memory adress where the custom_logging_function is stored. Input: int</div>
</div>
<div class="line-block">
-<div class="line"><strong>ensemble_results</strong>: Dictinary that stores the ensemble results if combine_ensemble_with_thread_joining==True</div>
-</div>
-<div class="line-block">
<div class="line"><strong>evolution_type</strong>: Variable containing the type of evolution used of the grid. Multiprocessing or linear processing</div>
</div>
<div class="line-block">
@@ -219,9 +217,6 @@ There are 1 options that are not described yet.</p>
<div class="line"><strong>repeat</strong>: Factor of how many times a system should be repeated. Consider the evolution splitting binary_c argument for supernovae kick repeating.</div>
</div>
<div class="line-block">
-<div class="line"><strong>results</strong>: Dictionary in which the user can place their results. This dictionary gets merged at the end of a mulitprocessing simulation.</div>
-</div>
-<div class="line-block">
<div class="line"><strong>slurm</strong>: Int flag whether to use a slurm type population evolution.</div>
</div>
<div class="line-block">
diff --git a/docs/build/html/hpc_functions.html b/docs/build/html/hpc_functions.html
index 627876c8f96a6fefdb5c1d5adcbf856a5b594d01..c1e1bf215502d6f186acfbd654991a2a4aa7f151 100644
--- a/docs/build/html/hpc_functions.html
+++ b/docs/build/html/hpc_functions.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index 7937e04943dba6d1afc70ff513cad7227b1a15d3..a7567522b55b45395ee333731e8922abd5118e18 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -88,6 +88,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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">GitLab</a></li>
</ul>
@@ -155,6 +156,102 @@
<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>Coverage:
+.. image:: coverage.svg</p>
+<blockquote>
+<div><dl class="field-list simple">
+<dt class="field-odd">target</dt>
+<dd class="field-odd"><p>coverage.svg</p>
+</dd>
+<dt class="field-even">alt</dt>
+<dd class="field-even"><p>alt text</p>
+</dd>
+</dl>
+</div></blockquote>
+<p>Based on a original work by Jeff Andrews (can be found in old_solution/ directory)
+updated and extended for Python3 by Robert Izzard, David hendriks</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>Python3</p></li>
+<li><p>binary_c version 2.1+</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>
+</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 $BINARY_C/src and whatever directories are required to run binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">LIBRARY_PATH</span></code> should include whatever directories are required to build binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
+</ul>
+</div>
+<div class="section" id="build-instructions">
+<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">¶</a></h2>
+<p>First, make sure you have built binary_c (See <code class="docutils literal notranslate"><span class="pre">$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>
+</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>For this it is best to set up a virtual environment for this. Activate the virtualenvironment and enter the downloaded version of the repo.</p>
+<p>Then run</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</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="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">ignore</span><span class="o">-</span><span class="n">installed</span> <span class="o">--</span><span class="n">no</span><span class="o">-</span><span class="n">dependencies</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
+</pre></div>
+</div>
+<p>This will install this package into the virtual environment. Making changes to the sourcecode can be “installed†into the virtual env with the same command.</p>
+</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 script. 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.</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 doc/ directory. Within the build/html/ there is the html version of the documentation.</p>
+</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"><span class="caption-text">Contents:</span></p>
<ul>
@@ -162,8 +259,10 @@
<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#faq">FAQ:</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#faq-issues">FAQ/Issues:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a><ul>
@@ -197,9 +296,11 @@
<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">GitLab</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">
diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
index aa5eb5e26efd91d79e10b479834dcd6295957375..6dc4b42e062fa90c6d5b93226122d1fd80d10a71 100644
--- a/docs/build/html/modules.html
+++ b/docs/build/html/modules.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index f64b02e86059822786cc5d39fb155ab3016694d5..73921d1fb3136eb65e2956afabe8464bdaa30722 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/plot_functions.html b/docs/build/html/plot_functions.html
index 308c870e7fc6e6eb40b16a5eb880c7e713b37bb4..275b33a6961deb042b2135a2ee7bc95415d73e45 100644
--- a/docs/build/html/plot_functions.html
+++ b/docs/build/html/plot_functions.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/population_example.html b/docs/build/html/population_example.html
index 3452450151bbf54692a145e148d5afeb399690a5..fdccaebaf24302af9f9fd50c0b82195ca67b67b8 100644
--- a/docs/build/html/population_example.html
+++ b/docs/build/html/population_example.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules.html">Binarycpython code</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="examples.html">Examples</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="general_examples.html">Examples</a></li>
@@ -93,6 +95,7 @@
</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 3a44ccaf316334b0c2cba68c95f003caf0842bff..895499d62d8e60ffe39df7f2ff3d702d8c67af3e 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -90,6 +90,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/readme_link.html b/docs/build/html/readme_link.html
index 0d318532938c6888bb3eeb3861f4d942b9478ae7..45cf9a2f9cd52e2e6d2f37e47544a13c25f44c14 100644
--- a/docs/build/html/readme_link.html
+++ b/docs/build/html/readme_link.html
@@ -87,15 +87,22 @@
<li class="toctree-l1 current"><a class="current reference internal" href="#">Python module for binary_c</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="#environment-variables">Environment variables</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions">Build instructions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#build-instructions">Build instructions</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#installation-from-source">Installation from source:</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l2"><a class="reference internal" href="#usage-notes">Usage notes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#faq">FAQ:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#documentation">Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#faq-issues">FAQ/Issues:</a></li>
</ul>
</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="examples.html">Examples</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">GitLab</a></li>
</ul>
@@ -177,65 +184,85 @@
</div></blockquote>
<p>Based on a original work by Jeff Andrews (can be found in old_solution/ directory)
updated and extended for Python3 by Robert Izzard, David hendriks</p>
-<p>Warning : THIS CODE IS EXPERIMENTAL!</p>
-<p><a class="reference external" href="mailto:r.izzard%40surrey.ac.uk">r<span>.</span>izzard<span>@</span>surrey<span>.</span>ac<span>.</span>uk</a>
-<a class="reference external" href="http://personal.ph.surrey.ac.uk/~ri0005/binary_c.html">http://personal.ph.surrey.ac.uk/~ri0005/binary_c.html</a>
-09/06/2019</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>Python3</p></li>
<li><p>binary_c version 2.1+</p></li>
-<li><p>requirements.txt (no?)</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>
</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 should set the following environment variables:</p>
+<p>Before compilation you need to have certain environment variables:</p>
+<p>Required:</p>
<ul class="simple">
-<li><p>required: <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>recommended: <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>recommended: <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">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 $BINARY_C/src and whatever directories are required to run binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">LIBRARY_PATH</span></code> should include whatever directories are required to build binary_c (e.g. locations of libgsl, libmemoize, librinterpolate, etc.)</p></li>
</ul>
</div>
<div class="section" id="build-instructions">
<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">¶</a></h2>
-<p>To build the module, make sure you have built binary_c (with <code class="docutils literal notranslate"><span class="pre">make</span></code> in the binary_c root directory), its shared library (with <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">libbinary_c.so</span></code> in the binary_c root directory), and set environment variables as described above, then run the following code in t:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">clean</span>
-<span class="n">make</span>
+<p>First, make sure you have built binary_c (See <code class="docutils literal notranslate"><span class="pre">$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>Then to test the Python module:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">./</span><span class="n">python_API_test</span><span class="o">.</span><span class="n">py</span>
-</pre></div>
</div>
-<p>You will require whatever libraries with which binary_c was compiled, as well as the compiler with which Python was built (usually gcc, which is easily installed on most systems).</p>
-<p>If you want to be able to import the binary_c module correctly for child directories (or anywhere for that matter), execute or put the following code in your .bashrc/.zshrc:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export LD_LIBRARY_PATH=<full path to root dir of repo>:$LD_LIBRARY_PATH
-export PYTHONPATH=<full path to root dir of repo>:$PYTHONPATH
+<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>For this it is best to set up a virtual environment for this. Activate the virtualenvironment and enter the downloaded version of the repo.</p>
+<p>Then run</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">clean</span> <span class="o">&&</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="o">--</span><span class="n">force</span> <span class="o">&&</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">sdist</span> <span class="o">&&</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">ignore</span><span class="o">-</span><span class="n">installed</span> <span class="o">--</span><span class="n">no</span><span class="o">-</span><span class="n">dependencies</span> <span class="o">-</span><span class="n">v</span> <span class="n">dist</span><span class="o">/</span><span class="n">binarycpython</span><span class="o">-<</span><span class="n">version</span> <span class="n">of</span> <span class="n">this</span> <span class="n">package</span><span class="o">>.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
+<p>This will install this package into the virtual environment. Making changes to the sourcecode can be “installed†into the virtual env with the same command.</p>
+</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 script. 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>When running a jupyter notebook and importing binary_c, it might happen that the module binary_c cannot be found. I experienced this when I executed Jupyter Notebook from a virtual environment which didnt use the same python (version/binary/shim) as the one I built this library with. Make sure jupyter does use the same underlying python version/binary/shim. That resolved the issue for me.</p>
-<p>Also: I figured that having binaryc output the log like “<span class="raw-html-m2r"><LOG HEADER></span> t=10e4 …†(i.e. printing the parameter names as well as their values) would be useful because in that way one can easily have python read that out automatically instead of having to manually copy the list of parameter names.</p>
-<p>See examples/ dir for some working examples</p>
-<p>When you try to <code class="docutils literal notranslate"><span class="pre">import</span> <span class="pre">binary_c_python_api</span></code> and python complains about it not existing, but you are sure that you correctly included the necessary pythonpaths, then you probably need to rebuild the package.</p>
+<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.</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 doc/ directory. Within the build/html/ there is the html version of the documentation.</p>
</div>
-<div class="section" id="faq">
-<h2>FAQ:<a class="headerlink" href="#faq" title="Permalink to this headline">¶</a></h2>
+<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>Pip install failed:</p>
+<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>
-<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>
</div>
</div>
diff --git a/docs/build/html/run_system_wrapper.html b/docs/build/html/run_system_wrapper.html
index 6a55ea25c60438e298258e2e7fc71285ea652c80..ee1b44108f78e7955a625d8fa6603daf09572205 100644
--- a/docs/build/html/run_system_wrapper.html
+++ b/docs/build/html/run_system_wrapper.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index 611aafb8d84bd3b75951ff9d0288a405cf408aee..07f1d222ebf4e636d738ba584e5aa0440c8544a8 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -89,6 +89,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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">GitLab</a></li>
</ul>
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 18e10d8649e817ea96646ad84173d62364080160..707bc22610eda7a47840ca865db1a007f14445e7 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/build/html/spacing_functions.html b/docs/build/html/spacing_functions.html
index 0aac247b138c0368c4ff7667efd99fc3f94224d1..413f97cc3711d94428c93f2b259c18b3220be459 100644
--- a/docs/build/html/spacing_functions.html
+++ b/docs/build/html/spacing_functions.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/stellar_types.html b/docs/build/html/stellar_types.html
index 51edae1c16d4afbf8d91ea328e5351ee23e0a1bb..8bad676f5f5901ff4224fff3907968874d2b0691 100644
--- a/docs/build/html/stellar_types.html
+++ b/docs/build/html/stellar_types.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/build/html/useful_funcs.html b/docs/build/html/useful_funcs.html
index aca941bd7dd59de07727620ec3a2e58f9a6b2787..00e6b4444d8bd0497c57b57ae1a495e8545045a4 100644
--- a/docs/build/html/useful_funcs.html
+++ b/docs/build/html/useful_funcs.html
@@ -85,6 +85,8 @@
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<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="readme_link.html#installation-via-pip">Installation via PIP:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="readme_link.html#installation-from-source">Installation from source:</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">Binarycpython code</a><ul class="current">
<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>
@@ -102,6 +104,7 @@
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</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="Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.">Test hyperlink: `Stack Overflow <http://stackoverflow.com/>`_.</a></li>
</ul>
diff --git a/docs/source/grid_options_descriptions.rst b/docs/source/grid_options_descriptions.rst
index 0f948ea04cddcd472441000f45fd2de48011ee71..7c1c75c4f19882a77b78468b995bc5dd9594dac9 100644
--- a/docs/source/grid_options_descriptions.rst
+++ b/docs/source/grid_options_descriptions.rst
@@ -23,8 +23,6 @@ The following options are meant to be changed by the user.
| **custom_logging_func_memaddr**: Memory adress where the custom_logging_function is stored. Input: int
-| **ensemble_results**: Dictinary that stores the ensemble results if combine_ensemble_with_thread_joining==True
-
| **evolution_type**: Variable containing the type of evolution used of the grid. Multiprocessing or linear processing
| **failed_systems_threshold**: Variable storing the maximum amount of systems that are allowed to fail before logging their commandline arguments to failed_systems log files
@@ -45,8 +43,6 @@ The following options are meant to be changed by the user.
| **repeat**: Factor of how many times a system should be repeated. Consider the evolution splitting binary_c argument for supernovae kick repeating.
-| **results**: Dictionary in which the user can place their results. This dictionary gets merged at the end of a mulitprocessing simulation.
-
| **slurm**: Int flag whether to use a slurm type population evolution.
| **source_file_filename**: Variable containing the source file containing lines of binary_c commandline calls. These all have to start with binary_c.
diff --git a/docs/source/index.rst b/docs/source/index.rst
index bf0ccf76e20c9344a43d7345dd40a3d377bc2f68..d1f22839883a98a5815066ce6532ee7f488fc72e 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -5,6 +5,8 @@
Welcome to binary_c-python's documentation!
===========================================
+.. mdinclude:: ../../README.md
+
.. toctree::
:maxdepth: 2
@@ -15,11 +17,12 @@ Welcome to binary_c-python's documentation!
examples
binary_c_parameters
grid_options_descriptions
-
-
+ GitLab <https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python>
+
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
+