diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index 608b87d150a31c4a7839459d5767c5a8a051ee40..b17e50295ff6e3b622cefb4027f0c27b31aadd6f 100644
Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ
diff --git a/docs/build/doctrees/population_extensions/HPC.doctree b/docs/build/doctrees/population_extensions/HPC.doctree
index 4cb333230a9af5af239e1762e04560dbaa7792e5..9f32f75abf63d27e39312a4e644dfc5bb905217e 100644
Binary files a/docs/build/doctrees/population_extensions/HPC.doctree and b/docs/build/doctrees/population_extensions/HPC.doctree differ
diff --git a/docs/build/doctrees/population_extensions/gridcode.doctree b/docs/build/doctrees/population_extensions/gridcode.doctree
index b15ef530e4f7ca5f5602657124ccf3a57a52270f..7a5f57ded599d4d3c5c9e0b4c0d9a6e7b3c80fe2 100644
Binary files a/docs/build/doctrees/population_extensions/gridcode.doctree and b/docs/build/doctrees/population_extensions/gridcode.doctree differ
diff --git a/docs/build/html/_images/test_coverage.svg b/docs/build/html/_images/test_coverage.svg
index 6d68f472b0f880260c3f22f1fc057e768f16f432..012a8497e3c9a2a79933b6a7062337837907a8d7 100644
--- a/docs/build/html/_images/test_coverage.svg
+++ b/docs/build/html/_images/test_coverage.svg
@@ -15,7 +15,7 @@
<g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11">
<text x="31.5" y="15" fill="#010101" fill-opacity=".3">coverage</text>
<text x="31.5" y="14">coverage</text>
- <text x="80" y="15" fill="#010101" fill-opacity=".3">64%</text>
- <text x="80" y="14">64%</text>
+ <text x="80" y="15" fill="#010101" fill-opacity=".3">70%</text>
+ <text x="80" y="14">70%</text>
</g>
</svg>
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 22c46847393726f26d3ccea2852211a25d7e1166..801f29ba3e2db99c6a8b63077a31330e56f067a0 100644
--- a/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/custom_logging_functions.html
@@ -551,7 +551,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/dicts.html b/docs/build/html/_modules/binarycpython/utils/dicts.html
index 906af63f2471ede6025bfec434c8f2abff796526..75d64e6ee175d858447420b06554dde2d7244649 100644
--- a/docs/build/html/_modules/binarycpython/utils/dicts.html
+++ b/docs/build/html/_modules/binarycpython/utils/dicts.html
@@ -86,13 +86,14 @@
<span class="n">ALLOWED_NUMERICAL_TYPES</span> <span class="o">=</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="nb">complex</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="n">UNION_ALLOWED_NUMERICAL_TYPES</span> <span class="o">=</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="nb">complex</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">number</span><span class="p">]</span>
+
<div class="viewcode-block" id="keys_to_floats"><a class="viewcode-back" href="../../../dicts.html#binarycpython.utils.dicts.keys_to_floats">[docs]</a><span class="k">def</span> <span class="nf">keys_to_floats</span><span class="p">(</span><span class="n">input_dict</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="nb">dict</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Function to convert all the keys of the dictionary to float to float</span>
<span class="sd"> we need to convert keys to floats:</span>
<span class="sd"> this is ~ a factor 10 faster than David's ``recursive_change_key_to_float`` routine, probably because this version only does the float conversion, nothing else.</span>
-<span class="sd"> </span>
+
<span class="sd"> Args:</span>
<span class="sd"> input_dict: dict of which we want to turn all the keys to float types if possible</span>
@@ -191,7 +192,9 @@
<span class="c1"># If dictionary type, call function again</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">)):</span>
- <span class="n">new_dict</span><span class="p">[</span><span class="n">string_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span><span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">custom_format</span><span class="p">)</span>
+ <span class="n">new_dict</span><span class="p">[</span><span class="n">string_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">recursive_change_key_to_string</span><span class="p">(</span>
+ <span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">custom_format</span>
+ <span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">string_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">input_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
@@ -274,7 +277,9 @@
<span class="sd"> """</span>
<span class="n">path</span> <span class="o">=</span> <span class="p">[]</span>
- <span class="n">_recursive_normalize_floats</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">input_dict</span><span class="p">,</span> <span class="n">factor</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">input_dict</span><span class="p">,</span> <span class="n">ignore</span><span class="o">=</span><span class="n">ignore</span><span class="p">)</span></div>
+ <span class="n">_recursive_normalize_floats</span><span class="p">(</span>
+ <span class="n">path</span><span class="p">,</span> <span class="n">input_dict</span><span class="p">,</span> <span class="n">factor</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">input_dict</span><span class="p">,</span> <span class="n">ignore</span><span class="o">=</span><span class="n">ignore</span>
+ <span class="p">)</span></div>
<div class="viewcode-block" id="subtract_dicts"><a class="viewcode-back" href="../../../dicts.html#binarycpython.utils.dicts.subtract_dicts">[docs]</a><span class="k">def</span> <span class="nf">subtract_dicts</span><span class="p">(</span><span class="n">dict_1</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">dict_2</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="nb">dict</span><span class="p">:</span>
@@ -580,7 +585,9 @@
<span class="k">try</span><span class="p">:</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">])</span> <span class="o">+</span> <span class="nb">int</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
<span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
- <span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">: Failed to convert string (either '</span><span class="si">{}</span><span class="s2">' or '</span><span class="si">{}</span><span class="s2">') to an int"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">: Failed to convert string (either '</span><span class="si">{}</span><span class="s2">' or '</span><span class="si">{}</span><span class="s2">') to an int"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">key</span><span class="p">,</span> <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+ <span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">e</span>
<span class="c1"># string-float clash : convert both to floats and save</span>
@@ -593,7 +600,9 @@
<span class="k">try</span><span class="p">:</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">])</span> <span class="o">+</span> <span class="nb">float</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
<span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
- <span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">: Failed to convert string (either '</span><span class="si">{}</span><span class="s2">' or '</span><span class="si">{}</span><span class="s2">') to an float"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">: Failed to convert string (either '</span><span class="si">{}</span><span class="s2">' or '</span><span class="si">{}</span><span class="s2">') to an float"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">key</span><span class="p">,</span> <span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+ <span class="p">)</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">e</span>
<span class="c1"># If the above cases have not dealt with it, then we should raise an error</span>
@@ -710,7 +719,9 @@
<span class="c1"># See whether the types are actually the same</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">type</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">type</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]):</span>
<span class="c1"># Exceptions:</span>
- <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">ALLOWED_NUMERICAL_TYPES</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">ALLOWED_NUMERICAL_TYPES</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_1</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">ALLOWED_NUMERICAL_TYPES</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span>
+ <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">ALLOWED_NUMERICAL_TYPES</span>
+ <span class="p">):</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">dict_2</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
@@ -943,7 +954,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/ensemble.html b/docs/build/html/_modules/binarycpython/utils/ensemble.html
index 23e5c2120989ba551be806abecf091e3e79626cb..d7be6d9a70e0d4892d9a5ea74a8b07952529dd5f 100644
--- a/docs/build/html/_modules/binarycpython/utils/ensemble.html
+++ b/docs/build/html/_modules/binarycpython/utils/ensemble.html
@@ -241,6 +241,7 @@
<span class="c1"># simplejson is faster than standard json and "just works"</span>
<span class="c1"># on the big Moe set in 37s</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">simplejson</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">file_object</span><span class="p">,</span> <span class="n">object_hook</span><span class="o">=</span><span class="n">_hook</span><span class="p">)</span>
+ <span class="n">file_object</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="c1"># standard json module</span>
<span class="c1"># on the big Moe set takes 42s</span>
@@ -248,6 +249,7 @@
<span class="c1"># object_hook=_hook)</span>
<span class="k">elif</span> <span class="n">filetype</span> <span class="o">==</span> <span class="s2">"msgpack"</span><span class="p">:</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">msgpack</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">file_object</span><span class="p">,</span> <span class="n">object_hook</span><span class="o">=</span><span class="n">_hook</span><span class="p">)</span>
+ <span class="n">file_object</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">if</span> <span class="n">timing</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span>
@@ -468,7 +470,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/functions.html b/docs/build/html/_modules/binarycpython/utils/functions.html
index 2c2a85d905b3464b278d90ae4ab9ba6bd16a4383..230b323d9a3630a1d9eddfc30a2147cf4fc5fbde 100644
--- a/docs/build/html/_modules/binarycpython/utils/functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/functions.html
@@ -222,7 +222,7 @@
<div class="viewcode-block" id="mem_use"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.mem_use">[docs]</a><span class="k">def</span> <span class="nf">mem_use</span><span class="p">():</span>
<span class="sd">"""</span>
-<span class="sd"> Return current process memory use in MB. (Takes no arguments) </span>
+<span class="sd"> Return current process memory use in MB. (Takes no arguments)</span>
<span class="sd"> Note: this is per-thread only.</span>
<span class="sd"> """</span>
@@ -344,6 +344,7 @@
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">False</span></div>
+
<div class="viewcode-block" id="isint"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.isint">[docs]</a><span class="k">def</span> <span class="nf">isint</span><span class="p">(</span><span class="n">x</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="nb">int</span><span class="p">]):</span>
<span class="sd">"""</span>
<span class="sd"> Function to return `True` if the "number" x, which could be a string, is an int, otherwise return `False`.</span>
@@ -411,7 +412,7 @@
<span class="k">return</span> <span class="n">dist</span></div>
-<div class="viewcode-block" id="catchtime"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.catchtime">[docs]</a><span class="k">class</span> <span class="nc">catchtime</span><span class="p">():</span>
+<div class="viewcode-block" id="catchtime"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.catchtime">[docs]</a><span class="k">class</span> <span class="nc">catchtime</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Context manager to calculate time spent</span>
<span class="sd"> """</span>
@@ -488,6 +489,7 @@
<span class="c1"># utility functions</span>
<span class="c1">########################################################</span>
+
<div class="viewcode-block" id="verbose_print"><a class="viewcode-back" href="../../../functions.html#binarycpython.utils.functions.verbose_print">[docs]</a><span class="k">def</span> <span class="nf">verbose_print</span><span class="p">(</span>
<span class="n">message</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">verbosity</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">minimal_verbosity</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">newline</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
<span class="p">)</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span>
@@ -1177,7 +1179,11 @@
<span class="n">build_info</span> <span class="o">=</span> <span class="n">make_build_text</span><span class="p">()</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">output_file</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">".rst"</span><span class="p">):</span>
- <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Filename (</span><span class="si">{}</span><span class="s2">) doesn't end with .rst, please provide a proper filename."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">output_file</span><span class="p">))</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+ <span class="s2">"Filename (</span><span class="si">{}</span><span class="s2">) doesn't end with .rst, please provide a proper filename."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">output_file</span>
+ <span class="p">)</span>
+ <span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="s2">"utf-8"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
@@ -1199,7 +1205,14 @@
<span class="n">argdict</span> <span class="o">=</span> <span class="n">arguments_dict</span><span class="p">[</span><span class="n">el</span><span class="p">][</span><span class="s2">"parameters"</span><span class="p">][</span><span class="n">arg</span><span class="p">]</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"| **Parameter**: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">argdict</span><span class="p">[</span><span class="s2">"param_name"</span><span class="p">]),</span> <span class="n">file</span><span class="o">=</span><span class="n">f</span><span class="p">)</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"| **Description**: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">argdict</span><span class="p">[</span><span class="s2">"description"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"|Rout/Rin-1|"</span><span class="p">,</span> <span class="s2">"abs(Rout/Rin-1)"</span><span class="p">)),</span> <span class="n">file</span><span class="o">=</span><span class="n">f</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span>
+ <span class="s2">"| **Description**: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">argdict</span><span class="p">[</span><span class="s2">"description"</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+ <span class="s2">"|Rout/Rin-1|"</span><span class="p">,</span> <span class="s2">"abs(Rout/Rin-1)"</span>
+ <span class="p">)</span>
+ <span class="p">),</span>
+ <span class="n">file</span><span class="o">=</span><span class="n">f</span><span class="p">,</span>
+ <span class="p">)</span>
<span class="k">if</span> <span class="s2">"parameter_value_input_type"</span> <span class="ow">in</span> <span class="n">argdict</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span>
<span class="s2">"| **Parameter input type**: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
@@ -1287,7 +1300,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/grid.html b/docs/build/html/_modules/binarycpython/utils/grid.html
index 16be3244bfc164866c17de3a7bc0424ef23389ef..9308263452be711f26b84790bb0f52208ba852ca 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid.html
@@ -127,7 +127,7 @@
<span class="n">get_help_all</span><span class="p">,</span>
<span class="n">mem_use</span><span class="p">,</span>
<span class="n">timedelta</span><span class="p">,</span>
- <span class="n">now</span>
+ <span class="n">now</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.ensemble</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">binaryc_json_serializer</span><span class="p">,</span>
@@ -143,14 +143,22 @@
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.analytics</span> <span class="kn">import</span> <span class="n">analytics</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.cache</span> <span class="kn">import</span> <span class="n">cache</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.dataIO</span> <span class="kn">import</span> <span class="n">dataIO</span>
-<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.distribution_functions</span> <span class="kn">import</span> <span class="n">distribution_functions</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.distribution_functions</span> <span class="kn">import</span> <span class="p">(</span>
+ <span class="n">distribution_functions</span><span class="p">,</span>
+<span class="p">)</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.grid_logging</span> <span class="kn">import</span> <span class="n">grid_logging</span>
-<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.grid_options_defaults</span> <span class="kn">import</span> <span class="n">grid_options_defaults</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.grid_options_defaults</span> <span class="kn">import</span> <span class="p">(</span>
+ <span class="n">grid_options_defaults</span><span class="p">,</span>
+<span class="p">)</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.gridcode</span> <span class="kn">import</span> <span class="n">gridcode</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.HPC</span> <span class="kn">import</span> <span class="n">HPC</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.metadata</span> <span class="kn">import</span> <span class="n">metadata</span>
-<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.Moe_di_Stefano_2017</span> <span class="kn">import</span> <span class="n">Moe_di_Stefano_2017</span>
-<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.spacing_functions</span> <span class="kn">import</span> <span class="n">spacing_functions</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.Moe_di_Stefano_2017</span> <span class="kn">import</span> <span class="p">(</span>
+ <span class="n">Moe_di_Stefano_2017</span><span class="p">,</span>
+<span class="p">)</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.spacing_functions</span> <span class="kn">import</span> <span class="p">(</span>
+ <span class="n">spacing_functions</span><span class="p">,</span>
+<span class="p">)</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.version_info</span> <span class="kn">import</span> <span class="n">version_info</span>
<span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
@@ -2469,7 +2477,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/plot_functions.html b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
index edac88deb1bc0100573eca4cd3fc51e1ae26f770..96edc10e3464cb14e55f9a5831790885cac8d2db 100644
--- a/docs/build/html/_modules/binarycpython/utils/plot_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
@@ -475,6 +475,7 @@
<span class="k">return</span> <span class="kc">None</span></div>
+
<div class="viewcode-block" id="parse_function_hr_diagram"><a class="viewcode-back" href="../../../plot_functions.html#binarycpython.utils.plot_functions.parse_function_hr_diagram">[docs]</a><span class="k">def</span> <span class="nf">parse_function_hr_diagram</span><span class="p">(</span><span class="n">output</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Parsing function for the HR plotting routine</span>
@@ -713,7 +714,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/HPC.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/HPC.html
index 8208ba4e006f4ab626f3f8648984a46cee90d788..2943539202a2743a283a017882d3d4cdd1c4cc05 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/HPC.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/HPC.html
@@ -125,7 +125,12 @@
<span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">n</span><span class="p">)</span></div>
<div class="viewcode-block" id="HPC.HPC_make_joiningfile"><a class="viewcode-back" href="../../../../population_extensions/HPC.html#binarycpython.utils.population_extensions.HPC.HPC.HPC_make_joiningfile">[docs]</a> <span class="k">def</span> <span class="nf">HPC_make_joiningfile</span><span class="p">(</span>
- <span class="bp">self</span><span class="p">,</span> <span class="n">hpc_jobid</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">hpc_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">n</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">overwrite</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">error_on_overwrite</span><span class="o">=</span><span class="kc">False</span>
+ <span class="bp">self</span><span class="p">,</span>
+ <span class="n">hpc_jobid</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">hpc_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">n</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">overwrite</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+ <span class="n">error_on_overwrite</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to make the joiningfile file that contains the filenames of results from each job. When all these exist, we can join.</span>
@@ -160,7 +165,11 @@
<span class="c1"># this to remove any asynchronicity</span>
<span class="n">lines</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n</span><span class="p">):</span>
- <span class="n">lines</span> <span class="o">+=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="s2">"</span><span class="si">{hpc_jobid}</span><span class="s2">.</span><span class="si">{i}</span><span class="s2">.gz</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">hpc_jobid</span><span class="o">=</span><span class="n">hpc_jobid</span><span class="p">,</span> <span class="n">i</span><span class="o">=</span><span class="n">i</span><span class="p">))]</span>
+ <span class="n">lines</span> <span class="o">+=</span> <span class="p">[</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">prefix</span><span class="p">,</span> <span class="s2">"</span><span class="si">{hpc_jobid}</span><span class="s2">.</span><span class="si">{i}</span><span class="s2">.gz</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">hpc_jobid</span><span class="o">=</span><span class="n">hpc_jobid</span><span class="p">,</span> <span class="n">i</span><span class="o">=</span><span class="n">i</span><span class="p">)</span>
+ <span class="p">)</span>
+ <span class="p">]</span>
<span class="n">string</span> <span class="o">=</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">lines</span><span class="p">)</span>
<span class="c1"># check the joiningfile doesn't exist</span>
@@ -250,7 +259,11 @@
<span class="p">)</span>
<span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"Failed to open joinlist at </span><span class="si">{joinlist}</span><span class="s2"> : </span><span class="si">{e}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">joinlist</span><span class="o">=</span><span class="n">joinlist</span><span class="p">,</span> <span class="n">e</span><span class="o">=</span><span class="n">e</span><span class="p">))</span>
+ <span class="nb">print</span><span class="p">(</span>
+ <span class="s2">"Failed to open joinlist at </span><span class="si">{joinlist}</span><span class="s2"> : </span><span class="si">{e}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">joinlist</span><span class="o">=</span><span class="n">joinlist</span><span class="p">,</span> <span class="n">e</span><span class="o">=</span><span class="n">e</span>
+ <span class="p">)</span>
+ <span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">return</span> <span class="n">joinlist</span></div>
@@ -366,31 +379,33 @@
<span class="sd">"""</span>
<span class="sd"> Function to return an HPC (Slurm or Condor) job id in the form x.y. Returns None if not an HPC job.</span>
<span class="sd"> """</span>
+
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">hpc_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">slurmID</span><span class="p">()</span>
+ <span class="n">hpc_jobid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">slurmID</span><span class="p">()</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">hpc_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">condorID</span><span class="p">()</span>
+ <span class="n">hpc_jobid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">condorID</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="c1"># not an HPC job</span>
- <span class="n">hpc_id</span> <span class="o">=</span> <span class="kc">None</span>
- <span class="k">return</span> <span class="n">hpc_id</span></div>
+ <span class="n">hpc_jobid</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="k">return</span> <span class="n">hpc_jobid</span></div>
<div class="viewcode-block" id="HPC.HPC_jobID_tuple"><a class="viewcode-back" href="../../../../population_extensions/HPC.html#binarycpython.utils.population_extensions.HPC.HPC.HPC_jobID_tuple">[docs]</a> <span class="k">def</span> <span class="nf">HPC_jobID_tuple</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Return the job ID as a tuple of ints, (x,y), or (None,None) on failure</span>
<span class="sd"> """</span>
+
<span class="n">hpc_jobid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">HPC_jobID</span><span class="p">()</span>
- <span class="k">if</span> <span class="n">hpc_jobid</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">id</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"None"</span><span class="p">):</span>
- <span class="n">t</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span>
- <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">HPC_job</span><span class="p">():</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"JOBID"</span><span class="p">,</span> <span class="nb">id</span><span class="p">)</span>
- <span class="n">t</span> <span class="o">=</span> <span class="nb">id</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
- <span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">t</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
- <span class="n">t</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
- <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">t</span><span class="p">)</span></div>
+ <span class="k">if</span> <span class="n">hpc_jobid</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">hpc_jobid</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"None"</span><span class="p">):</span>
+ <span class="n">split_hpc_jobid</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">split_hpc_jobid</span> <span class="o">=</span> <span class="n">hpc_jobid</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">split_hpc_jobid</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
+ <span class="n">split_hpc_jobid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">split_hpc_jobid</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
+ <span class="n">split_hpc_jobid</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">split_hpc_jobid</span><span class="p">)</span></div>
<div class="viewcode-block" id="HPC.HPC_set_status"><a class="viewcode-back" href="../../../../population_extensions/HPC.html#binarycpython.utils.population_extensions.HPC.HPC.HPC_set_status">[docs]</a> <span class="k">def</span> <span class="nf">HPC_set_status</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">string</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -398,20 +413,14 @@
<span class="sd"> Arguments:</span>
<span class="sd"> string : the new contents of the status file</span>
-
-<span class="sd"> Returns:</span>
-<span class="sd"> True if the status was set, False otherwise.</span>
-<span class="sd"> (As returned by either the appropriate Condor or Slurm function)</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">status</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">set_slurm_status</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">set_slurm_status</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">status</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">set_condor_status</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">set_condor_status</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">status</span> <span class="o">=</span> <span class="kc">None</span>
-
- <span class="k">return</span> <span class="n">status</span></div>
+ <span class="k">pass</span></div>
<div class="viewcode-block" id="HPC.HPC_get_status"><a class="viewcode-back" href="../../../../population_extensions/HPC.html#binarycpython.utils.population_extensions.HPC.HPC.HPC_get_status">[docs]</a> <span class="k">def</span> <span class="nf">HPC_get_status</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_id</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">job_index</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">hpc_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -802,7 +811,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/Moe_di_Stefano_2017.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/Moe_di_Stefano_2017.html
index b89f2b9791c239d8249c4fee8eb01cb3edec5735..2e8a6a6d848119d04f2570cdbd39795a9c51edcb 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/Moe_di_Stefano_2017.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/Moe_di_Stefano_2017.html
@@ -100,7 +100,6 @@
<span class="kn">from</span> <span class="nn">binarycpython.utils</span> <span class="kn">import</span> <span class="n">moe_di_stefano_2017_data</span>
-
<div class="viewcode-block" id="Moe_di_Stefano_2017"><a class="viewcode-back" href="../../../../population_extensions/Moe_di_Stefano_2017.html#binarycpython.utils.population_extensions.Moe_di_Stefano_2017.Moe_di_Stefano_2017">[docs]</a><span class="k">class</span> <span class="nc">Moe_di_Stefano_2017</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Extension to the population grid object that contains functionality to handle handle the Moe & distefano distributions</span>
@@ -384,7 +383,8 @@
<span class="n">Moecache</span><span class="p">[</span><span class="s2">"period_distributions"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
<span class="p">[</span>
<span class="nb">float</span><span class="p">(</span><span class="n">logmass</span><span class="p">),</span>
- <span class="nb">float</span><span class="p">(</span><span class="n">logperiods</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span> <span class="o">+</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="n">dlog10P</span><span class="p">,</span> <span class="c1"># TODO: why this shift? to center it?</span>
+ <span class="nb">float</span><span class="p">(</span><span class="n">logperiods</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+ <span class="o">+</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="n">dlog10P</span><span class="p">,</span> <span class="c1"># TODO: why this shift? to center it?</span>
<span class="n">json_data</span><span class="p">[</span><span class="s2">"log10M1"</span><span class="p">][</span><span class="n">logmass</span><span class="p">][</span><span class="s2">"logP"</span><span class="p">][</span><span class="n">logperiods</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]][</span>
<span class="s2">"normed_bin_frac_p_dist"</span>
<span class="p">]</span>
@@ -1317,7 +1317,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/analytics.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/analytics.html
index 9b3e860045b7631074f69bb1d1e58fe0f2f3ced4..f493aec9f6aa1a5389798f9febb34f7f8b1c94bf 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/analytics.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/analytics.html
@@ -79,6 +79,7 @@
<span class="kn">import</span> <span class="nn">time</span>
+
<div class="viewcode-block" id="analytics"><a class="viewcode-back" href="../../../../population_extensions/analytics.html#binarycpython.utils.population_extensions.analytics.analytics">[docs]</a><span class="k">class</span> <span class="nc">analytics</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Extension for the Population class containing the functions for analytics</span>
@@ -205,7 +206,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/cache.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/cache.html
index c102d48a570df3fafed6c1070049aa35f5be9aa2..f4d7c98ea76feb1c6bfd09fd9ba8daf3cece7e02 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/cache.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/cache.html
@@ -128,7 +128,7 @@
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Init function for the spacing_functions class</span>
-<span class="sd"> </span>
+
<span class="sd"> TODO: is this class necesarry to be defined *within* the cache class? can't it just be outside?</span>
<span class="sd"> """</span>
@@ -221,7 +221,9 @@
<span class="n">x</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
<span class="n">modulename</span> <span class="o">=</span> <span class="s2">"binarycpython.utils.population_extensions."</span> <span class="o">+</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">module</span> <span class="o">=</span> <span class="n">importlib</span><span class="o">.</span><span class="n">import_module</span><span class="p">(</span><span class="n">modulename</span><span class="p">)</span>
- <span class="n">_method</span> <span class="o">=</span> <span class="nb">eval</span><span class="p">(</span><span class="s2">"module.</span><span class="si">{}</span><span class="s2">.</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span> <span class="c1"># TODO: we can do this differently with some .get call instead of eval</span>
+ <span class="n">_method</span> <span class="o">=</span> <span class="nb">eval</span><span class="p">(</span>
+ <span class="s2">"module.</span><span class="si">{}</span><span class="s2">.</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="p">)</span> <span class="c1"># TODO: we can do this differently with some .get call instead of eval</span>
<span class="n">_wrapped</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">_method</span><span class="p">,</span> <span class="s2">"__wrapped__"</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
<span class="c1"># if function is wrapped...</span>
@@ -323,10 +325,11 @@
<span class="n">_method</span> <span class="o">=</span> <span class="nb">eval</span><span class="p">(</span><span class="s2">"module.</span><span class="si">{}</span><span class="s2">.</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">if</span> <span class="n">testargs</span><span class="p">:</span>
+
<span class="k">def</span> <span class="nf">_func_wrap</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> wrap to return args and kwargs</span>
-<span class="sd"> </span>
+
<span class="sd"> TODO: i think this function can be defined elsewhere</span>
<span class="sd"> """</span>
@@ -369,7 +372,6 @@
<span class="p">)</span>
<span class="p">)</span></div>
-
<span class="sd">"""</span>
<span class="sd">Cache speed test of function distribution_functions.powerlaw_constant</span>
<span class="sd"> 0 1 2 4 8 16 32 64 128 256</span>
@@ -451,7 +453,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/condor.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/condor.html
index 2da637e8e5f15199ac47f4754256cb433b228cbc..498e332c74a824cf6acc3992324c2025cd66b22d 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/condor.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/condor.html
@@ -91,6 +91,7 @@
<span class="kn">import</span> <span class="nn">datasize</span>
<span class="kn">import</span> <span class="nn">lib_programname</span>
+
<div class="viewcode-block" id="condor"><a class="viewcode-back" href="../../../../population_extensions/condor.html#binarycpython.utils.population_extensions.condor.condor">[docs]</a><span class="k">class</span> <span class="nc">condor</span><span class="p">:</span>
<span class="sd">"""</span>
<span class="sd"> Extension for the Population class containing the code for Condor grid runs</span>
@@ -127,17 +128,21 @@
<span class="sd"> Return the condor status file corresponding to the ClusterID and Process, which default to grid_options condor_ClusterID and condor_Process, respectively.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">condorpath</span><span class="p">(</span><span class="s2">"status"</span><span class="p">,</span> <span class="n">condor_dir</span><span class="o">=</span><span class="n">condor_dir</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">condorID</span><span class="p">(</span><span class="n">ClusterID</span><span class="p">,</span> <span class="n">Process</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">condorpath</span><span class="p">(</span><span class="s2">"status"</span><span class="p">,</span> <span class="n">condor_dir</span><span class="o">=</span><span class="n">condor_dir</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">condorID</span><span class="p">(</span><span class="n">ClusterID</span><span class="p">,</span> <span class="n">Process</span><span class="p">),</span>
<span class="p">)</span></div>
<div class="viewcode-block" id="condor.condor_check_requirements"><a class="viewcode-back" href="../../../../population_extensions/condor.html#binarycpython.utils.population_extensions.condor.condor.condor_check_requirements">[docs]</a> <span class="k">def</span> <span class="nf">condor_check_requirements</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to check whether the condor parameters in grid_options have been set appropriately.</span>
<span class="sd"> """</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor_dir"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor_dir"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span>
+ <span class="ow">or</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor_dir"</span><span class="p">])</span>
+ <span class="p">):</span>
<span class="k">return</span> <span class="p">(</span>
<span class="kc">False</span><span class="p">,</span>
- <span class="s2">"You have set condor=</span><span class="si">{condor}</span><span class="s2"> but not set condor_dir (which is </span><span class="si">{condor_dir}</span><span class="s2">). Please set it and try again."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"You have set condor=</span><span class="si">{condor}</span><span class="s2"> but not set condor_dir (</span><span class="si">{condor_dir}</span><span class="s2">) correctly. Please set it and try again."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">condor</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor"</span><span class="p">],</span>
<span class="n">condor_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"condor_dir"</span><span class="p">],</span>
<span class="p">),</span>
@@ -197,7 +202,9 @@
<span class="k">try</span><span class="p">:</span>
<span class="n">path</span> <span class="o">=</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span><span class="p">(</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">condor_status_file</span><span class="p">(</span><span class="n">condor_dir</span><span class="o">=</span><span class="n">condor_dir</span><span class="p">,</span> <span class="n">ClusterID</span><span class="o">=</span><span class="n">ClusterID</span><span class="p">,</span> <span class="n">Process</span><span class="o">=</span><span class="n">Process</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">condor_status_file</span><span class="p">(</span>
+ <span class="n">condor_dir</span><span class="o">=</span><span class="n">condor_dir</span><span class="p">,</span> <span class="n">ClusterID</span><span class="o">=</span><span class="n">ClusterID</span><span class="p">,</span> <span class="n">Process</span><span class="o">=</span><span class="n">Process</span>
+ <span class="p">)</span>
<span class="p">)</span>
<span class="c1"># print("path={}".format(path))</span>
<span class="c1"># print("size={}".format(path.stat().st_size))</span>
@@ -546,7 +553,6 @@
<span class="p">)</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="n">err_msg</span><span class="p">)</span>
-
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">std_err</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span>
<span class="s2">"</span><span class="si">{red}{err}{reset}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
@@ -641,7 +647,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/dataIO.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/dataIO.html
index a816bf532181c2f8398d9f648c165268b97edbbd..8e3c8d6ab4cbe3b6155c107d6e0b7a6f625b69f1 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/dataIO.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/dataIO.html
@@ -91,10 +91,7 @@
<span class="kn">import</span> <span class="nn">flufl.lock</span>
<span class="kn">import</span> <span class="nn">compress_pickle</span>
-<span class="kn">from</span> <span class="nn">binarycpython.utils.ensemble</span> <span class="kn">import</span> <span class="p">(</span>
- <span class="n">ensemble_file_type</span><span class="p">,</span>
- <span class="n">ensemble_compression</span>
-<span class="p">)</span>
+<span class="kn">from</span> <span class="nn">binarycpython.utils.ensemble</span> <span class="kn">import</span> <span class="n">ensemble_file_type</span><span class="p">,</span> <span class="n">ensemble_compression</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.dicts</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">merge_dicts</span><span class="p">,</span>
<span class="p">)</span>
@@ -124,7 +121,11 @@
<span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">directory</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">F_OK</span><span class="p">)</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">directory</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">R_OK</span> <span class="o">|</span> <span class="n">os</span><span class="o">.</span><span class="n">W_OK</span><span class="p">)</span></div>
<div class="viewcode-block" id="dataIO.save_population_object"><a class="viewcode-back" href="../../../../population_extensions/dataIO.html#binarycpython.utils.population_extensions.dataIO.dataIO.save_population_object">[docs]</a> <span class="k">def</span> <span class="nf">save_population_object</span><span class="p">(</span>
- <span class="bp">self</span><span class="p">,</span> <span class="n">population_object</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">confirmation</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">compression</span><span class="o">=</span><span class="s2">"gzip"</span>
+ <span class="bp">self</span><span class="p">,</span>
+ <span class="n">population_object</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">confirmation</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">compression</span><span class="o">=</span><span class="s2">"gzip"</span><span class="p">,</span>
<span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Save pickled Population object to file at filename or, if filename is None, whatever is set at self.grid_options['save_population_object']</span>
@@ -205,7 +206,9 @@
<span class="c1"># restore data</span>
<span class="n">population_object</span><span class="o">.</span><span class="n">shared_memory</span> <span class="o">=</span> <span class="n">shared_memory</span>
<span class="n">population_object</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_system_generator"</span><span class="p">]</span> <span class="o">=</span> <span class="n">system_generator</span>
- <span class="k">del</span> <span class="n">population_object</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"save_population_time"</span><span class="p">]</span>
+ <span class="k">del</span> <span class="n">population_object</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
+ <span class="s2">"save_population_time"</span>
+ <span class="p">]</span>
<span class="n">population_object</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"store_memaddr"</span><span class="p">]</span> <span class="o">=</span> <span class="n">_store_memaddr</span>
<span class="n">population_object</span><span class="o">.</span><span class="n">persistent_data_memory_dict</span> <span class="o">=</span> <span class="n">persistent_data_memory_dict</span>
@@ -252,7 +255,9 @@
<span class="c1"># special cases</span>
<span class="n">maxmem</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="k">if</span> <span class="s2">"max_memory_use"</span> <span class="ow">in</span> <span class="n">refpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"metadata"</span><span class="p">,</span> <span class="p">{})</span> <span class="ow">and</span> <span class="s2">"max_memory_use"</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"metadata"</span><span class="p">,</span> <span class="p">{}):</span>
+ <span class="k">if</span> <span class="s2">"max_memory_use"</span> <span class="ow">in</span> <span class="n">refpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"metadata"</span><span class="p">,</span> <span class="p">{}</span>
+ <span class="p">)</span> <span class="ow">and</span> <span class="s2">"max_memory_use"</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"metadata"</span><span class="p">,</span> <span class="p">{}):</span>
<span class="n">maxmem</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span>
<span class="n">refpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"max_memory_use"</span><span class="p">],</span>
<span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"max_memory_use"</span><span class="p">],</span>
@@ -318,11 +323,14 @@
<span class="n">newpop</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_population_object</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
- <span class="k">if</span> <span class="s1">'total_count'</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_options</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s2">"total_count"</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_options</span><span class="p">:</span>
<span class="n">n</span> <span class="o">=</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"total_count"</span><span class="p">]</span>
<span class="k">elif</span> <span class="s2">"_count"</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_options</span><span class="p">:</span>
<span class="n">n</span> <span class="o">=</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"_count"</span><span class="p">]</span>
- <span class="k">elif</span> <span class="s1">'metadata'</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span> <span class="ow">and</span> <span class="s2">"_count"</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">]:</span>
+ <span class="k">elif</span> <span class="p">(</span>
+ <span class="s2">"metadata"</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span>
+ <span class="ow">and</span> <span class="s2">"_count"</span> <span class="ow">in</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">]</span>
+ <span class="p">):</span>
<span class="n">n</span> <span class="o">=</span> <span class="n">newpop</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"_count"</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">n</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
@@ -428,7 +436,9 @@
<span class="k">if</span> <span class="ow">not</span> <span class="n">file_type</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span>
- <span class="s2">"Unable to determine file type from ensemble filename </span><span class="si">{}</span><span class="s2"> : it should be .json or .msgpack."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">output_file</span><span class="p">)</span>
+ <span class="s2">"Unable to determine file type from ensemble filename </span><span class="si">{}</span><span class="s2"> : it should be .json or .msgpack."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">output_file</span>
+ <span class="p">)</span>
<span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
@@ -444,7 +454,9 @@
<span class="p">)</span>
<span class="p">)</span>
<span class="k">elif</span> <span class="n">file_type</span> <span class="o">==</span> <span class="s2">"msgpack"</span><span class="p">:</span>
- <span class="n">f</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="c1"># TODO: i think something is going wrong here. not sure but doing msgpack and .gz e.g gives an error about str input rather than bytes. i think this is because the self.open does not take into account that the msgpack stream requires different properties.</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">open</span><span class="p">(</span>
+ <span class="n">output_file</span><span class="p">,</span> <span class="s2">"w"</span>
+ <span class="p">)</span> <span class="c1"># TODO: i think something is going wrong here. not sure but doing msgpack and .gz e.g gives an error about str input rather than bytes. i think this is because the self.open does not take into account that the msgpack stream requires different properties.</span>
<span class="c1"># msgpack output</span>
<span class="n">msgpack</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span>
@@ -887,7 +899,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/distribution_functions.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/distribution_functions.html
index 3e30a26ef4529b6db8f330916d90adb09940ef3d..aece0e4ed64ce8b0f449f542fcc1388f33acdb6c 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/distribution_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/distribution_functions.html
@@ -213,7 +213,9 @@
<span class="k">return</span> <span class="n">powerlaw_const</span></div>
<div class="viewcode-block" id="distribution_functions.powerlaw_constant"><a class="viewcode-back" href="../../../../population_extensions/distribution_functions.html#binarycpython.utils.population_extensions.distribution_functions.distribution_functions.powerlaw_constant">[docs]</a> <span class="nd">@cachetools</span><span class="o">.</span><span class="n">cachedmethod</span><span class="p">(</span>
- <span class="k">lambda</span> <span class="bp">self</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">caches</span><span class="p">[</span><span class="s2">"population_extensions._distribution_functions.powerlaw_constant"</span><span class="p">]</span>
+ <span class="k">lambda</span> <span class="bp">self</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">caches</span><span class="p">[</span>
+ <span class="s2">"population_extensions._distribution_functions.powerlaw_constant"</span>
+ <span class="p">]</span>
<span class="p">)</span>
<span class="k">def</span> <span class="nf">powerlaw_constant</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
@@ -1294,7 +1296,7 @@
<span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">for</span> <span class="n">q</span> <span class="ow">in</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mf">0.15</span><span class="p">,</span> <span class="mf">0.950001</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">):</span>
- <span class="k">if</span> <span class="n">qmin</span><span class="o"><=</span> <span class="n">q</span> <span class="o"><=</span> <span class="n">qmax</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">qmin</span> <span class="o"><=</span> <span class="n">q</span> <span class="o"><=</span> <span class="n">qmax</span><span class="p">:</span>
<span class="n">qdata</span><span class="p">[</span><span class="n">q</span><span class="p">]</span> <span class="o">=</span> <span class="n">Moecache</span><span class="p">[</span><span class="s2">"rinterpolator_q"</span><span class="p">]</span><span class="o">.</span><span class="n">interpolate</span><span class="p">(</span>
<span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="n">m</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">options</span><span class="p">[</span><span class="n">p</span><span class="p">]),</span> <span class="n">q</span><span class="p">]</span>
<span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
@@ -2400,7 +2402,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_logging.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_logging.html
index 054e1c6619f9a626519b1818525ebff9018bf309..3058d93464a5138a042692167b1abedee490e8a6 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_logging.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_logging.html
@@ -89,15 +89,14 @@
<span class="n">format_number</span><span class="p">,</span>
<span class="n">trem</span><span class="p">,</span>
<span class="n">remove_file</span><span class="p">,</span>
- <span class="n">verbose_print</span>
+ <span class="n">verbose_print</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.population_extensions.grid_options_defaults</span> <span class="kn">import</span> <span class="n">secs_per_day</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.custom_logging_functions</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">binary_c_log_code</span><span class="p">,</span>
<span class="n">create_and_load_logging_function</span><span class="p">,</span>
- <span class="n">autogen_C_logging_code</span>
-
+ <span class="n">autogen_C_logging_code</span><span class="p">,</span>
<span class="p">)</span>
@@ -105,6 +104,7 @@
<span class="sd">"""</span>
<span class="sd"> The class extension for the population object that contains logging functionality</span>
<span class="sd"> """</span>
+
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Init function for the grid_logging class</span>
@@ -399,7 +399,7 @@
<span class="n">blue</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"blue"</span><span class="p">],</span>
<span class="n">cmdline</span><span class="o">=</span><span class="n">cmdline_string</span><span class="p">,</span>
<span class="n">reset</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ANSI_colours</span><span class="p">[</span><span class="s2">"reset"</span><span class="p">],</span>
- <span class="n">system_dict</span><span class="o">=</span><span class="n">system_dict</span>
+ <span class="n">system_dict</span><span class="o">=</span><span class="n">system_dict</span><span class="p">,</span>
<span class="p">)</span>
<span class="p">)</span></div>
@@ -419,7 +419,9 @@
<span class="c1"># Pass the rest to the original verbose print</span>
<span class="n">verbose_print</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
- <span class="k">def</span> <span class="nf">_boxed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">stringlist</span><span class="p">,</span> <span class="n">colour</span><span class="o">=</span><span class="s2">"yellow on black"</span><span class="p">,</span> <span class="n">boxchar</span><span class="o">=</span><span class="s2">"*"</span><span class="p">,</span> <span class="n">separator</span><span class="o">=</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">):</span>
+ <span class="k">def</span> <span class="nf">_boxed</span><span class="p">(</span>
+ <span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">stringlist</span><span class="p">,</span> <span class="n">colour</span><span class="o">=</span><span class="s2">"yellow on black"</span><span class="p">,</span> <span class="n">boxchar</span><span class="o">=</span><span class="s2">"*"</span><span class="p">,</span> <span class="n">separator</span><span class="o">=</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to output a list of strings in a single box.</span>
@@ -552,7 +554,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_options_defaults.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_options_defaults.html
index 226ea280d1bd72f4e19297d5a63677ae062d3001..ff7f85380844ad3695ad4c4d18bbaa0841408ae5 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_options_defaults.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/grid_options_defaults.html
@@ -177,9 +177,7 @@
<span class="c1">##########################</span>
<span class="c1"># binary_c files</span>
<span class="c1">##########################</span>
- <span class="s2">"_binary_c_executable"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
- <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s2">"BINARY_C"</span><span class="p">],</span> <span class="s2">"binary_c"</span>
- <span class="p">),</span>
+ <span class="s2">"_binary_c_executable"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s2">"BINARY_C"</span><span class="p">],</span> <span class="s2">"binary_c"</span><span class="p">),</span>
<span class="s2">"_binary_c_shared_library"</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
<span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s2">"BINARY_C"</span><span class="p">],</span> <span class="s2">"src"</span><span class="p">,</span> <span class="s2">"libbinary_c.so"</span>
<span class="p">),</span>
@@ -609,12 +607,14 @@
<span class="c1"># Check input</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">output_file</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">".rst"</span><span class="p">):</span>
- <span class="n">msg</span><span class="o">=</span><span class="s2">"Filename doesn't end with .rst, please provide a proper filename"</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"Filename doesn't end with .rst, please provide a proper filename"</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
<span class="c1"># M&S options</span>
<span class="n">moe_di_stefano_default_options</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_Moe_di_Stefano_2017_default_options</span><span class="p">()</span>
- <span class="n">moe_di_stefano_default_options_description</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_Moe_di_Stefano_2017_default_options_description</span><span class="p">()</span>
+ <span class="n">moe_di_stefano_default_options_description</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">get_Moe_di_Stefano_2017_default_options_description</span><span class="p">()</span>
+ <span class="p">)</span>
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"Population grid code options"</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">f</span><span class="p">)</span>
@@ -658,7 +658,9 @@
<span class="s2">"The following options are not meant to be changed by the user, as these options are used and set internally by the object itself. The description still is provided, but just for documentation purposes."</span><span class="p">,</span>
<span class="p">)</span></div>
-<div class="viewcode-block" id="grid_options_defaults.print_option_descriptions"><a class="viewcode-back" href="../../../../population_extensions/grid_options_defaults.html#binarycpython.utils.population_extensions.grid_options_defaults.grid_options_defaults.print_option_descriptions">[docs]</a> <span class="k">def</span> <span class="nf">print_option_descriptions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filehandle</span><span class="p">,</span> <span class="n">options</span><span class="p">,</span> <span class="n">descriptions</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="n">extra_text</span><span class="p">):</span>
+<div class="viewcode-block" id="grid_options_defaults.print_option_descriptions"><a class="viewcode-back" href="../../../../population_extensions/grid_options_defaults.html#binarycpython.utils.population_extensions.grid_options_defaults.grid_options_defaults.print_option_descriptions">[docs]</a> <span class="k">def</span> <span class="nf">print_option_descriptions</span><span class="p">(</span>
+ <span class="bp">self</span><span class="p">,</span> <span class="n">filehandle</span><span class="p">,</span> <span class="n">options</span><span class="p">,</span> <span class="n">descriptions</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="n">extra_text</span>
+ <span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Function to print the description of an option</span>
<span class="sd"> """</span>
@@ -713,7 +715,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/gridcode.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/gridcode.html
index 2575ae26381f1033b3971140a91ff03c475e4b9f..ec70c2e5f7732cb05d58e2a69adef962b5413595 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/gridcode.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/gridcode.html
@@ -169,7 +169,7 @@
<span class="sd"> Results in a generated file that contains a system_generator function.</span>
<span class="sd"> # TODO: make sure running systems with multiplicity 3+ is also possible.</span>
-<span class="sd"> # TODO: there is a lot of things going on in this function. Make sure to describe clearly what happens here. </span>
+<span class="sd"> # TODO: there is a lot of things going on in this function. Make sure to describe clearly what happens here.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">verbose_print</span><span class="p">(</span><span class="s2">"Generating grid code"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"verbosity"</span><span class="p">],</span> <span class="mi">1</span><span class="p">)</span>
@@ -895,7 +895,8 @@
<span class="c1"># run the hook function, only if given</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"dry_run_hook"</span><span class="p">]:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_add_code</span><span class="p">(</span>
- <span class="s2">"self.grid_options['dry_run_hook'](self, parameter_dict)</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">1</span>
+ <span class="s2">"self.grid_options['dry_run_hook'](self, parameter_dict)</span><span class="se">\n</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="c1"># or pass</span>
@@ -1074,6 +1075,7 @@
<span class="sd"> the rest of the function</span>
<span class="sd"> Examples::</span>
+
<span class="sd"> name = 'lnM_1'</span>
<span class="sd"> parameter_name:</span>
@@ -1089,7 +1091,8 @@
<span class="sd"> longname:</span>
<span class="sd"> Long name of parameter</span>
-<span class="sd"> Examples:</span>
+<span class="sd"> Examples::</span>
+
<span class="sd"> longname = 'Primary mass'</span>
<span class="sd"> range:</span>
@@ -1097,6 +1100,7 @@
<span class="sd"> get the values from</span>
<span class="sd"> Examples::</span>
+
<span class="sd"> range = [math.log(m_min), math.log(m_max)]</span>
<span class="sd"> samplerfunc:</span>
@@ -1104,6 +1108,7 @@
<span class="sd"> You can either use a real function, or a string representation of a function call.</span>
<span class="sd"> Examples::</span>
+
<span class="sd"> samplerfunc = "self.const_linear(math.log(m_min), math.log(m_max), {})".format(resolution['M_1'])</span>
<span class="sd"> precode:</span>
@@ -1111,6 +1116,7 @@
<span class="sd"> sampling function (i.e. a value for lnM_1 is chosen already)</span>
<span class="sd"> Examples::</span>
+
<span class="sd"> precode = 'M_1=math.exp(lnM_1);'</span>
<span class="sd"> postcode:</span>
@@ -1119,21 +1125,24 @@
<span class="sd"> probdist:</span>
<span class="sd"> Function determining the probability that gets assigned to the sampled parameter</span>
-<span class="sd"> Examples:</span>
+<span class="sd"> Examples::</span>
+
<span class="sd"> probdist = 'self.Kroupa2001(M_1)*M_1'</span>
<span class="sd"> dphasevol:</span>
<span class="sd"> part of the parameter space that the total probability is calculated with. Put to -1</span>
<span class="sd"> if you want to ignore any dphasevol calculations and set the value to 1</span>
-<span class="sd"> Examples::"</span>
+<span class="sd"> Examples::</span>
+
<span class="sd"> dphasevol = 'dlnM_1'</span>
<span class="sd"> condition:</span>
<span class="sd"> condition that has to be met in order for the grid generation to continue</span>
<span class="sd"> Examples::</span>
-<span class="sd"> condition = 'self.grid_options['binary']==1'</span>
+
+<span class="sd"> condition = "self.grid_options['binary']==1"</span>
<span class="sd"> gridtype:</span>
<span class="sd"> Method on how the value range is sampled. Can be either 'edge' (steps starting at</span>
@@ -1226,7 +1235,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/metadata.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/metadata.html
index fa4785533b3d3106581302a542e87bd6641c35d3..c62057f470a70f90a5e7da7fc66fcca83c243fee 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/metadata.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/metadata.html
@@ -122,16 +122,10 @@
<span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"platform_uname"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
<span class="n">platform</span><span class="o">.</span><span class="n">uname</span><span class="p">()</span>
<span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
- <span class="s2">"platform_machine"</span>
- <span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">machine</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"platform_machine"</span><span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">machine</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"platform_node"</span><span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">node</span><span class="p">()</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
- <span class="s2">"platform_release"</span>
- <span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">release</span><span class="p">()</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
- <span class="s2">"platform_version"</span>
- <span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">version</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"platform_release"</span><span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">release</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span><span class="s2">"platform_version"</span><span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">version</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">grid_ensemble_results</span><span class="p">[</span><span class="s2">"metadata"</span><span class="p">][</span>
<span class="s2">"platform_processor"</span>
<span class="p">]</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">processor</span><span class="p">()</span>
@@ -234,7 +228,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/slurm.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/slurm.html
index 3e649ba79c268aa7c029b36607e21b5ea365b65c..62162547a66400fd4304a7d47f459c27e0d3a537 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/slurm.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/slurm.html
@@ -136,10 +136,14 @@
<span class="sd">"""</span>
<span class="sd"> Function to check whether the slurm parameters in grid_options have been set appropriately.</span>
<span class="sd"> """</span>
- <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm_dir"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm"</span><span class="p">]</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm_dir"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span>
+ <span class="ow">or</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm_dir"</span><span class="p">])</span>
+ <span class="p">):</span>
<span class="k">return</span> <span class="p">(</span>
<span class="kc">False</span><span class="p">,</span>
- <span class="s2">"You have set slurm=</span><span class="si">{slurm}</span><span class="s2"> but not set slurm_dir (which is </span><span class="si">{slurm_dir}</span><span class="s2">). Please set it and try again."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="s2">"You have set slurm=</span><span class="si">{slurm}</span><span class="s2"> but not set slurm_dir (</span><span class="si">{slurm_dir}</span><span class="s2">) correctly. Please set it and try again."</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">slurm</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm"</span><span class="p">],</span>
<span class="n">slurm_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm_dir"</span><span class="p">],</span>
<span class="p">),</span>
@@ -169,15 +173,15 @@
<span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">idfile</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="s2">"utf-8"</span><span class="p">)</span> <span class="k">as</span> <span class="n">fjobid</span><span class="p">:</span>
<span class="n">fjobid</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{jobid}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">jobid</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">grid_options</span><span class="p">[</span><span class="s2">"slurm_jobid"</span><span class="p">]))</span>
<span class="n">fjobid</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">NFS_flush_hach</span><span class="p">(</span><span class="n">idfile</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">NFS_flush_hack</span><span class="p">(</span><span class="n">idfile</span><span class="p">)</span>
<span class="c1"># save slurm status</span>
- <span class="n">file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">slurm_status_file</span><span class="p">(</span><span class="n">slurm_dir</span><span class="o">=</span><span class="n">slurm_dir</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">file</span><span class="p">:</span>
- <span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">file</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="s2">"utf-8"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">status_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">slurm_status_file</span><span class="p">(</span><span class="n">slurm_dir</span><span class="o">=</span><span class="n">slurm_dir</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">status_file</span><span class="p">:</span>
+ <span class="k">with</span> <span class="bp">self</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">status_file</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="s2">"utf-8"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">NFS_fluch_hack</span><span class="p">(</span><span class="n">file</span><span class="p">)</span></div>
+ <span class="bp">self</span><span class="o">.</span><span class="n">NFS_flush_hack</span><span class="p">(</span><span class="n">status_file</span><span class="p">)</span></div>
<div class="viewcode-block" id="slurm.get_slurm_status"><a class="viewcode-back" href="../../../../population_extensions/slurm.html#binarycpython.utils.population_extensions.slurm.slurm.get_slurm_status">[docs]</a> <span class="k">def</span> <span class="nf">get_slurm_status</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">jobid</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">jobarrayindex</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">slurm_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -535,7 +539,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/spacing_functions.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/spacing_functions.html
index 385bee8e9c14863446b2543172ef33279bb4fa7f..2578d44ee9cdb6109b0cb6fd2f58fd1d90b3256e 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/spacing_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/spacing_functions.html
@@ -450,12 +450,12 @@
<span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> first thing to do is make a stellar lifetime table</span>
-<span class="sd"> </span>
+
<span class="sd"> we should use the bse_options_json passed in</span>
<span class="sd"> so our lifetime_population uses the same physics</span>
<span class="sd"> as the main grid</span>
-<span class="sd"> TODO: Describe this function better with arguments and </span>
+<span class="sd"> TODO: Describe this function better with arguments and</span>
<span class="sd"> """</span>
<span class="c1"># convert bse_options to dict</span>
@@ -595,7 +595,7 @@
<span class="sd">"""</span>
<span class="sd"> Function to get a mass given a time, calculated by using the interpolator_time_mass</span>
<span class="sd"> """</span>
-
+
<span class="k">return</span> <span class="p">(</span>
<span class="mf">10.0</span>
<span class="o">**</span> <span class="n">interpolator_time_mass</span><span class="o">.</span><span class="n">interpolate</span><span class="p">([</span><span class="n">math</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">linear_time</span><span class="p">)])[</span><span class="mi">0</span><span class="p">]</span>
@@ -773,7 +773,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/population_extensions/version_info.html b/docs/build/html/_modules/binarycpython/utils/population_extensions/version_info.html
index 44d4d8d9b45dffcdc56f95ae690cc57ed5cad030..83900937634217154a78eac762e46c498aea3a1c 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/version_info.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/version_info.html
@@ -521,7 +521,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
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 6d93e5bf57d2e94ea3bbcc85950b97576b4e275f..25d796272e3c1a7bfc2f95d3303fba6f9b83c8f2 100644
--- a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
+++ b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
@@ -205,7 +205,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
index 64b1bc526081405e877c3183dae0db3531d686e9..5ea3a2451dcb964c9843bc89120d3146b5edb921 100644
--- a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
+++ b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
@@ -471,7 +471,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
index d10dce7beb6d33f5e807e7e1becdbd6e1ff6e1f1..4b5447f811b9eb7382b6eb5db124820f7c060503 100644
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@@ -109,7 +109,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/binary_c_parameters.html b/docs/build/html/binary_c_parameters.html
index f03f2b7888dc9bd45a004de7eeb2afaa97a709a6..2cacf0b649be8a94dde9857af72183c49ed04261 100644
--- a/docs/build/html/binary_c_parameters.html
+++ b/docs/build/html/binary_c_parameters.html
@@ -3506,7 +3506,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/custom_logging_functions.html b/docs/build/html/custom_logging_functions.html
index 1c2e6f7411b1bc69370a04731081974bb4216075..3fafba53d37536e05111b1a95a2a4f9c522cdd86 100644
--- a/docs/build/html/custom_logging_functions.html
+++ b/docs/build/html/custom_logging_functions.html
@@ -329,7 +329,7 @@ I recommend using this in function in combination with a function that generates
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/dicts.html b/docs/build/html/dicts.html
index 7399197fb8b71807f23053046d9c68f2107a8cbd..6deff5bf1231925008b569ae427a2fd47330d388 100644
--- a/docs/build/html/dicts.html
+++ b/docs/build/html/dicts.html
@@ -524,7 +524,7 @@ so that they don’t have to be calculated each time.</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/ensemble.html b/docs/build/html/ensemble.html
index 925edc168a70e2db51d07e60c1d3dbc01c193299..b93997b71499142056999852f0b940cae082f736 100644
--- a/docs/build/html/ensemble.html
+++ b/docs/build/html/ensemble.html
@@ -275,7 +275,7 @@ and return its contents to as a Python dictionary.</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/example_notebooks.html b/docs/build/html/example_notebooks.html
index 14115fec60fe872deb58be35ab7140cd267494aa..068921e20c6d165ea3c1fd4d984ba2c393e087bd 100644
--- a/docs/build/html/example_notebooks.html
+++ b/docs/build/html/example_notebooks.html
@@ -215,7 +215,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_BHBH.html b/docs/build/html/examples/notebook_BHBH.html
index 40d2eb5c806d12e072b8c5ad352c7fecd8775d20..6a16d20a62e64556737f4f32a188fa7ce08a01d5 100644
--- a/docs/build/html/examples/notebook_BHBH.html
+++ b/docs/build/html/examples/notebook_BHBH.html
@@ -5574,7 +5574,7 @@ system 2 / 100
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_HRD.html b/docs/build/html/examples/notebook_HRD.html
index 0be8b2b43d58990601d5b7108256486d04444402..3c946dbfffdffd70d2988f7f717c4f667622861d 100644
--- a/docs/build/html/examples/notebook_HRD.html
+++ b/docs/build/html/examples/notebook_HRD.html
@@ -1366,7 +1366,7 @@ very start.</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_api_functionality.html b/docs/build/html/examples/notebook_api_functionality.html
index 0f40b7a4b4935d6fa8af1583ff54e36016585f9e..014647c40bee0a958d50ff886077ee4549d278dc 100644
--- a/docs/build/html/examples/notebook_api_functionality.html
+++ b/docs/build/html/examples/notebook_api_functionality.html
@@ -1291,7 +1291,7 @@ MAXIMUM MASS RATIO 0.0141
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_common_envelope_evolution.html b/docs/build/html/examples/notebook_common_envelope_evolution.html
index 857d8658b8f2fc42c75772c7ac373f7416750fe8..46f389cb63b530e9a1bcea6d9ea57269aed9ac06 100644
--- a/docs/build/html/examples/notebook_common_envelope_evolution.html
+++ b/docs/build/html/examples/notebook_common_envelope_evolution.html
@@ -1131,7 +1131,7 @@ Text(0, 0.5, 'Number of stars')
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_custom_logging.html b/docs/build/html/examples/notebook_custom_logging.html
index ed1c723bc3bd1e9b3b24a2726c3b682226c22396..3d78a5f307cbb1e3fcafb5e74ef035996c3347e9 100644
--- a/docs/build/html/examples/notebook_custom_logging.html
+++ b/docs/build/html/examples/notebook_custom_logging.html
@@ -785,7 +785,7 @@ EXAMPLE_SN 1.050651207308e+01 1.59452 9.34213 20 12 13 5 1 6.55458 4
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_extra_features.html b/docs/build/html/examples/notebook_extra_features.html
index 844a5b0b538132e3b8b7b8429d2c615bde4fea88..8ef0676684bb42c8f96dfecfa5f255990c55915d 100644
--- a/docs/build/html/examples/notebook_extra_features.html
+++ b/docs/build/html/examples/notebook_extra_features.html
@@ -537,7 +537,7 @@ dict_keys(['networks', 'isotopes', 'argpairs', 'ense
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_individual_systems.html b/docs/build/html/examples/notebook_individual_systems.html
index e167d4e9b968b7f78f69b1f28ce020fb0532625f..b810bc3b9c0ae5833368a47a4b5e38551043e441 100644
--- a/docs/build/html/examples/notebook_individual_systems.html
+++ b/docs/build/html/examples/notebook_individual_systems.html
@@ -839,7 +839,7 @@ SINGLE_STAR_LIFETIME 15 14.9927
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_luminosity_function_binaries.html b/docs/build/html/examples/notebook_luminosity_function_binaries.html
index a6fad454e68e09d0264e49b2747a7e6ae747fad8..ceceef794152a84b6d165b2a644cb612483ab0fc 100644
--- a/docs/build/html/examples/notebook_luminosity_function_binaries.html
+++ b/docs/build/html/examples/notebook_luminosity_function_binaries.html
@@ -1198,7 +1198,7 @@ Done population run!
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_luminosity_function_single.html b/docs/build/html/examples/notebook_luminosity_function_single.html
index 9e3c5a6b0365d7218c676b26624715757549e7f5..d6cd69b648c7e30087100a7c3f196714428e6beb 100644
--- a/docs/build/html/examples/notebook_luminosity_function_single.html
+++ b/docs/build/html/examples/notebook_luminosity_function_single.html
@@ -855,7 +855,7 @@ works perfectly well.</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_massive_remnants.html b/docs/build/html/examples/notebook_massive_remnants.html
index da6130b5ce8d89d5b13271c289e5e6d8e4c6a301..958cd632195d751ab655a9de293b152514c046ef 100644
--- a/docs/build/html/examples/notebook_massive_remnants.html
+++ b/docs/build/html/examples/notebook_massive_remnants.html
@@ -960,7 +960,7 @@ There were no errors found in this run.
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_population.html b/docs/build/html/examples/notebook_population.html
index 0e8e6ad1da0cbd5523d153802f4c959299bac7d0..7aa2a669bcfd9a1122de36c75ce0d4ecbf772c4f 100644
--- a/docs/build/html/examples/notebook_population.html
+++ b/docs/build/html/examples/notebook_population.html
@@ -1414,7 +1414,7 @@ time mass_1 zams_mass_1 mass_2 zams_mass_2 stellar_type_1 prev_stellar_type_1 st
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/notebook_solar_system.html b/docs/build/html/examples/notebook_solar_system.html
index 48c1ae1517ad2d5817bfd4af1ebef0bde92fbc1c..4835683a9aa0175fd4680c2dbf6c3f1c0b9b611d 100644
--- a/docs/build/html/examples/notebook_solar_system.html
+++ b/docs/build/html/examples/notebook_solar_system.html
@@ -614,7 +614,7 @@ div.rendered_html tbody tr:hover {
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/old/basic_example.html b/docs/build/html/examples/old/basic_example.html
index cc749b54ade05badde63839211b440418c7cdfce..0785ce893e317492a378e63f199a80ebc6aec00b 100644
--- a/docs/build/html/examples/old/basic_example.html
+++ b/docs/build/html/examples/old/basic_example.html
@@ -453,7 +453,7 @@ div.rendered_html tbody tr:hover {
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/examples/old/workshop_example_notebook.html b/docs/build/html/examples/old/workshop_example_notebook.html
index eb52c1db3cd8b260773e4e529ca15d05225d22e3..ce732f9cd04144213a7378ec5a673ab48f96a35c 100644
--- a/docs/build/html/examples/old/workshop_example_notebook.html
+++ b/docs/build/html/examples/old/workshop_example_notebook.html
@@ -892,7 +892,7 @@ Took 14.214274644851685s
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/functions.html b/docs/build/html/functions.html
index f884d644214801446f36c4eca0227fd51e7593bc..49203d8492bbcb195ba9fe54b96d3042df243b7d 100644
--- a/docs/build/html/functions.html
+++ b/docs/build/html/functions.html
@@ -720,7 +720,7 @@ of all the binary_c parameters.</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 913f76a7eacbf9908468a6d536144e347f0b2aca..43f078a4c901b01f752f3225c0c388d37f31493e 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -1074,7 +1074,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/grid.html b/docs/build/html/grid.html
index 9b04bd91afa0be2d6c7e7cb5381905791f66edcf..7a86f17b60c33db93e3ae3582d62ef8b82c1a7a1 100644
--- a/docs/build/html/grid.html
+++ b/docs/build/html/grid.html
@@ -376,7 +376,7 @@ in the self.grid_options</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/grid_options_descriptions.html b/docs/build/html/grid_options_descriptions.html
index 45833b1676e0bf435df97a06dc43d4faeaa72f52..ad7536b60556d8cd13b33b502cbbe1bb5ceb8ffb 100644
--- a/docs/build/html/grid_options_descriptions.html
+++ b/docs/build/html/grid_options_descriptions.html
@@ -643,7 +643,7 @@ q extrapolation (below 0.15) method
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index 7fbbc9c5e789dfdf90163751917c8aa4666286c4..34d577daa2000482664f62eb279dd61e8e4e08a2 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -309,7 +309,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
index 893b741ecae385d657e89539ebafcede2f515e7e..1914f6ae5292e17bc78d9fcb4ec937ab2ecb07ee 100644
--- a/docs/build/html/modules.html
+++ b/docs/build/html/modules.html
@@ -173,7 +173,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/plot_functions.html b/docs/build/html/plot_functions.html
index 5121512fdc99288061117760b8f17e2b0ae33af8..78451a3f2eddd4170abc21ad358e3476b1011a66 100644
--- a/docs/build/html/plot_functions.html
+++ b/docs/build/html/plot_functions.html
@@ -377,7 +377,7 @@ This is not included in all the plotting routines.</p></li>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/HPC.html b/docs/build/html/population_extensions/HPC.html
index 1117c346f701ce1c57fb4fd451d568dbd63ccb41..696887e1d1fecb079688606c61c1ae8b3d8e5a76 100644
--- a/docs/build/html/population_extensions/HPC.html
+++ b/docs/build/html/population_extensions/HPC.html
@@ -322,10 +322,6 @@ the run-grid stage of the process.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>string</strong> – the new contents of the status file</p>
</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>True if the status was set, False otherwise.
-(As returned by either the appropriate Condor or Slurm function)</p>
-</dd>
</dl>
</dd></dl>
@@ -372,7 +368,7 @@ and (if given) the string passed in.</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/Moe_di_Stefano_2017.html b/docs/build/html/population_extensions/Moe_di_Stefano_2017.html
index 1cf74ec6010da6ed2dd1e14cf5665f44c660d65d..3d318c6f9e65b4b00289062f341c6f0d22d462cf 100644
--- a/docs/build/html/population_extensions/Moe_di_Stefano_2017.html
+++ b/docs/build/html/population_extensions/Moe_di_Stefano_2017.html
@@ -192,7 +192,7 @@ then set the distribution functions</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/analytics.html b/docs/build/html/population_extensions/analytics.html
index 9d1384b75bf643cd3e6dfc7fdb2c7c9449c4f176..2320938c5fd9cb33d3d6358150dd53126587ecf1 100644
--- a/docs/build/html/population_extensions/analytics.html
+++ b/docs/build/html/population_extensions/analytics.html
@@ -181,7 +181,7 @@ the time elapsed if otherwise or if force is True</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/cache.html b/docs/build/html/population_extensions/cache.html
index cb7e145c6cd47620792e043da0166fc1efee8e88..3e7c191cb65ff93f8fb5815c2eb6afc871112891 100644
--- a/docs/build/html/population_extensions/cache.html
+++ b/docs/build/html/population_extensions/cache.html
@@ -215,7 +215,7 @@ given caches of size self.grid_options[‘function_cache_size’][func]</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/condor.html b/docs/build/html/population_extensions/condor.html
index 404180eeee06a82fb7a751deef471b8749b82a1f..989e82da3b0d1f9acf5341b9f83744e5962f11f2 100644
--- a/docs/build/html/population_extensions/condor.html
+++ b/docs/build/html/population_extensions/condor.html
@@ -232,7 +232,7 @@ if grid_options[‘condor’]==3, we are being called from the jobs to run the g
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/dataIO.html b/docs/build/html/population_extensions/dataIO.html
index cc4b5fdfa0648d03430ec88469c25f1b076f81ec..d2964d6593b165e36af4bd6277877c1c07d2f28d 100644
--- a/docs/build/html/population_extensions/dataIO.html
+++ b/docs/build/html/population_extensions/dataIO.html
@@ -393,7 +393,7 @@ passed to json.dumps)</p></li>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/distribution_functions.html b/docs/build/html/population_extensions/distribution_functions.html
index f4898a794a01f6efb01f5f799b92affe7f221edb..2fb35dc9b2c6cace6844891b780b0b83e1383e48 100644
--- a/docs/build/html/population_extensions/distribution_functions.html
+++ b/docs/build/html/population_extensions/distribution_functions.html
@@ -833,7 +833,7 @@ and is be given by dp/dlogP ~ (logP)^p for all other binary configurations (defa
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/grid_logging.html b/docs/build/html/population_extensions/grid_logging.html
index 9221cf65a2b9c9ed226edcc2cd4aeab2477bd35d..dad3f8ebe59c45491f4331c64c0dde78b8cd99e6 100644
--- a/docs/build/html/population_extensions/grid_logging.html
+++ b/docs/build/html/population_extensions/grid_logging.html
@@ -179,7 +179,7 @@ system_number: the system number</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/grid_options_defaults.html b/docs/build/html/population_extensions/grid_options_defaults.html
index 9d073af621b13ad36395426849f6ba9e5418937c..4011bf4580a7b0e4a454122954f3b08db781a70b 100644
--- a/docs/build/html/population_extensions/grid_options_defaults.html
+++ b/docs/build/html/population_extensions/grid_options_defaults.html
@@ -242,7 +242,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/gridcode.html b/docs/build/html/population_extensions/gridcode.html
index e7144b6016c4633d5a2e8964759b646077f2267f..671b3dd3b5ff43d9bf8122c535577085c610dadf 100644
--- a/docs/build/html/population_extensions/gridcode.html
+++ b/docs/build/html/population_extensions/gridcode.html
@@ -148,10 +148,10 @@ Use at own risk.</p>
<li><p><strong>name</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>name of parameter used in the grid Python code.
This is evaluated as a parameter and you can use it throughout
the rest of the function</p>
-<dl class="simple">
-<dt>Examples::</dt><dd><p>name = ‘lnM_1’</p>
-</dd>
-</dl>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">name</span> <span class="o">=</span> <span class="s1">'lnM_1'</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>parameter_name</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>name of the parameter in binary_c</p>
<p>This name must correspond to a Python variable of the same name,
@@ -163,47 +163,51 @@ called parameter_name</p>
</dl>
</p></li>
<li><p><strong>longname</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>Long name of parameter</p>
-<p class="rubric">Examples</p>
-<p>longname = ‘Primary mass’</p>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">longname</span> <span class="o">=</span> <span class="s1">'Primary mass'</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>range</strong> – <p>Range of values to take. Does not get used really, the samplerfunc is used to
get the values from</p>
-<dl class="simple">
-<dt>Examples::</dt><dd><p>range = [math.log(m_min), math.log(m_max)]</p>
-</dd>
-</dl>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">range</span> <span class="o">=</span> <span class="p">[</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">m_min</span><span class="p">),</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">m_max</span><span class="p">)]</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>samplerfunc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>Function returning a list or numpy array of samples spaced appropriately.
You can either use a real function, or a string representation of a function call.</p>
-<dl class="simple">
-<dt>Examples::</dt><dd><p>samplerfunc = “self.const_linear(math.log(m_min), math.log(m_max), {})â€.format(resolution[‘M_1’])</p>
-</dd>
-</dl>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">samplerfunc</span> <span class="o">=</span> <span class="s2">"self.const_linear(math.log(m_min), math.log(m_max), </span><span class="si">{}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">resolution</span><span class="p">[</span><span class="s1">'M_1'</span><span class="p">])</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>precode</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>]) – <p>Extra room for some code. This code will be evaluated within the loop of the
sampling function (i.e. a value for lnM_1 is chosen already)</p>
-<dl class="simple">
-<dt>Examples::</dt><dd><p>precode = ‘M_1=math.exp(lnM_1);’</p>
-</dd>
-</dl>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">precode</span> <span class="o">=</span> <span class="s1">'M_1=math.exp(lnM_1);'</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>postcode</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>]) – Code executed after the probability is calculated.</p></li>
<li><p><strong>probdist</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – <p>Function determining the probability that gets assigned to the sampled parameter</p>
-<p class="rubric">Examples</p>
-<p>probdist = ‘self.Kroupa2001(M_1)*M_1’</p>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">probdist</span> <span class="o">=</span> <span class="s1">'self.Kroupa2001(M_1)*M_1'</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>dphasevol</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code>]) – <p>part of the parameter space that the total probability is calculated with. Put to -1
if you want to ignore any dphasevol calculations and set the value to 1</p>
-<dl class="simple">
-<dt>Examples::â€</dt><dd><p>dphasevol = ‘dlnM_1’</p>
-</dd>
-</dl>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">dphasevol</span> <span class="o">=</span> <span class="s1">'dlnM_1'</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>condition</strong> (<code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>]) – <p>condition that has to be met in order for the grid generation to continue</p>
-<dl class="simple">
-<dt>Examples::</dt><dd><p>condition = ‘self.grid_options[‘binary’]==1’</p>
-</dd>
-</dl>
+<p>Examples:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">condition</span> <span class="o">=</span> <span class="s2">"self.grid_options['binary']==1"</span>
+</pre></div>
+</div>
</p></li>
<li><p><strong>gridtype</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>) – Method on how the value range is sampled. Can be either ‘edge’ (steps starting at
the lower edge of the value range) or ‘centred’
@@ -294,7 +298,7 @@ of the self.grid_options[“_grid_variablesâ€] dictionary.</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/population_extensions/metadata.html b/docs/build/html/population_extensions/metadata.html
index 6188b029910d931f013d80a95e42ae16b61a4197..0a0fd4c2aabf9532b4651a986340b1bf8f746fa3 100644
--- a/docs/build/html/population_extensions/metadata.html
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d:37,zoom_mean:37,zoomfac_multiplier_decreas:[0,7],zoomfac_multiplier_increas:[0,7],zsolar:31,zytkow:[0,7]},titles:["Binary_c parameters","custom_logging_functions module","dicts module","ensemble module","Example notebooks","Example use case: Binary black hole systems","Example use case: Hertzsprung-Russell diagrams","Tutorial: Using the API functionality of binary_c-python","Example use case: Common-envelope evolution","Tutorial: Using custom logging routines with binary_c-python","Tutorial: Extra features and functionality of binary_c-python","Tutorial: Running individual systems with binary_c-python","Example use case: Zero-age stellar luminosity function in binaries","Example use case: Zero-age stellar luminosity function","Example use case: Massive star luminosity","Tutorial: Running populations with binary_c-python","Example use case: Solar system using the API functionality","Basic example","Binary_c and python example notebook","functions module","Population class module","Population grid code options","Welcome to binary_c-python\u2019s documentation!","Binarycpython code","plot_functions module","Population class extension: HPC module","Population class extension: Moe_di_Stefano_2017 module","Population class extension: analytics module","Population class extension: cache module","Population class extension: condor module","Population class extension: dataIO module","Population class extension: distribution_functions module","Population class extension: grid_logging module","Population class extension: grid_options_defaults module","Population class extension: gridcode module","Population class extension: metadata module","Population class extension: slurm module","Population class extension: spacing_functions module","Population class extension: version_info module","Python module for binary_c","run_system_wrapper module","stellar_types module","useful_funcs 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parameters","custom_logging_functions module","dicts module","ensemble module","Example notebooks","Example use case: Binary black hole systems","Example use case: Hertzsprung-Russell diagrams","Tutorial: Using the API functionality of binary_c-python","Example use case: Common-envelope evolution","Tutorial: Using custom logging routines with binary_c-python","Tutorial: Extra features and functionality of binary_c-python","Tutorial: Running individual systems with binary_c-python","Example use case: Zero-age stellar luminosity function in binaries","Example use case: Zero-age stellar luminosity function","Example use case: Massive star luminosity","Tutorial: Running populations with binary_c-python","Example use case: Solar system using the API functionality","Basic example","Binary_c and python example notebook","functions module","Population class module","Population grid code options","Welcome to binary_c-python\u2019s documentation!","Binarycpython code","plot_functions 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\ No newline at end of file
diff --git a/docs/build/html/stellar_types.html b/docs/build/html/stellar_types.html
index c14f0d2e58716615e94b044b63eec20913b8b620..9979794488ca28424f2901d2567e3f0385dab621 100644
--- a/docs/build/html/stellar_types.html
+++ b/docs/build/html/stellar_types.html
@@ -153,7 +153,7 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/useful_funcs.html b/docs/build/html/useful_funcs.html
index afe07d32be51b30a371b5780662746d9a6178184..d89a1b76a1c92164fcf1c66afd84e93f76d0c38f 100644
--- a/docs/build/html/useful_funcs.html
+++ b/docs/build/html/useful_funcs.html
@@ -350,7 +350,7 @@ determine if two stars collide on the ZAMS</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/source/_templates/footer.html b/docs/source/_templates/footer.html
index efaf1b9ad49ac60e5b3ad75dd00c2888f8cbb593..82662b9d4d4b453c318901f7b4869efb88e9b055 100644
--- a/docs/source/_templates/footer.html
+++ b/docs/source/_templates/footer.html
@@ -2,7 +2,7 @@
{%- block extrafooter %}
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7e2b822d04dcc5482eabcc79ac1fe76bc42a6ece url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 7569fb77696d8d4c8498755efaa1e2f5c869487f url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c-python/-/tree/development_0.9.3/2.2.1">git url</a>.
<br><br>
Using binary_c with bit branch branch_david: git revision: "5845:20220107:201620bd7" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/source/badges/test_coverage.svg b/docs/source/badges/test_coverage.svg
index 6d68f472b0f880260c3f22f1fc057e768f16f432..012a8497e3c9a2a79933b6a7062337837907a8d7 100644
--- a/docs/source/badges/test_coverage.svg
+++ b/docs/source/badges/test_coverage.svg
@@ -15,7 +15,7 @@
<g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11">
<text x="31.5" y="15" fill="#010101" fill-opacity=".3">coverage</text>
<text x="31.5" y="14">coverage</text>
- <text x="80" y="15" fill="#010101" fill-opacity=".3">64%</text>
- <text x="80" y="14">64%</text>
+ <text x="80" y="15" fill="#010101" fill-opacity=".3">70%</text>
+ <text x="80" y="14">70%</text>
</g>
</svg>