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<br><br>
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+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 f455ac5366e8d052a8da83c68c32a0286869e190..d3bfcd0093190aa7cd92c8a878d8d3dfa3868994 100644
--- a/docs/build/html/_modules/binarycpython/utils/ensemble.html
+++ b/docs/build/html/_modules/binarycpython/utils/ensemble.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
+ <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../_static/js/theme.js"></script>
@@ -476,9 +477,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 6972ad96d6a7a148f37ad1c987201405f8211cdc..b456a0bb20af6fe43f4104bcd21f4b92adc680b9 100644
--- a/docs/build/html/_modules/binarycpython/utils/functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/functions.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
+ <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../_static/js/theme.js"></script>
@@ -1311,9 +1312,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 2c9765a3f562ae5da6dacba771aa0121a674dfad..51a7537a541da0041ea588c58e4bbaf2ef3e9ab1 100644
--- a/docs/build/html/_modules/binarycpython/utils/grid.html
+++ b/docs/build/html/_modules/binarycpython/utils/grid.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
+ <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../_static/js/theme.js"></script>
@@ -92,6 +93,8 @@
<span class="sd"> - TODO: fix the correct object types for the default values of the bse_options</span>
<span class="sd"> - TODO: think of a clean and nice way to unload and remove the custom_logging_info library from memory (and from disk)</span>
<span class="sd"> - TODO: think of a nice way to remove the loaded grid_code/ generator from memory.</span>
+
+<span class="sd">TODO: Some of the methods that we have defined in the (mixin) class are designed to be used as a portal to information (return_binary_c_version_info for example.) THe current design is that they are all instance methods, but that is not always necessary. We can decorate them with @staticmethod, or @classmethod to make it easier to use them (https://realpython.com/instance-class-and-static-methods-demystified/)</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">os</span>
@@ -2510,9 +2513,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 7ae04c55912cf9edf689c5f477ec4ac4848a9d61..9d2e8086a9782f519c89b50bc4fb2cc42efbd39e 100644
--- a/docs/build/html/_modules/binarycpython/utils/plot_functions.html
+++ b/docs/build/html/_modules/binarycpython/utils/plot_functions.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
+ <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../_static/js/theme.js"></script>
@@ -714,9 +715,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 643168fbe6b2b823f45a4fca81a01363777d938a..16984ce1d28903c4f52ed187ab3bb318bac05fa3 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/HPC.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/HPC.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -824,9 +825,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 65a11d7e10e22047674d9887c0a012808e281ab9..fd584fe1d610e1ffff908861b026fb152b7c9b77 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
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -1317,9 +1318,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 9182b9c8f41f1f796de492d7744f7f86f346b574..3e309fd6d829d307640034d761df99436d8d86d7 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/analytics.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/analytics.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -207,9 +208,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 4d0459caf15e0af65e567efebec4eae179f0fc2c..c39a167b44d73347a4630fd0d0fda3c8fd87cf7d 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/cache.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/cache.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -453,9 +454,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 54d9b3edf9518d6f8037d97e3cd31708c57cdb9d..10bdb9bfc26907afa6ffa86226f2935c68c75fc0 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/condor.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/condor.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -654,9 +655,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 38bfc648626ecdeaf533aa82f1e462ede4850646..4fbb43cd017fcf6f61036db75334cfa639616924 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/dataIO.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/dataIO.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -901,9 +902,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 1d74b3f801a9c6feac59dbb798959e6f718a6a7b..be502f563c9d9a3fab8904c15664b89bab891360 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
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -2402,9 +2403,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 676af2f6418b3429baf1831a5b9b79f31b5e8199..410f148356fa761e5f30c197f8c29c8543684a36 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
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -554,9 +555,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 eda3c579eeea1d11f24639158191f6bc3552b4f4..a5d68dad8a7564573790a839f55ad04ca04bc373 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
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -716,9 +717,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 dbdf11d8faef4294873b0d46745ac2968a50d6e4..690061d877dc088e364b76589d5d3fcfdd470e15 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/gridcode.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/gridcode.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -1235,9 +1236,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 6316c9ce4a346b6d5d4274d8030f71a9d3c7b638..6d977f8002188b94d76cdb8e50ea1406f5732bf9 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/metadata.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/metadata.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -228,9 +229,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 c49c344b5003982b6365268fa454413ebd2321ed..24d093b4f70846579c32a416aa26a1aaaa38e7b3 100644
--- a/docs/build/html/_modules/binarycpython/utils/population_extensions/slurm.html
+++ b/docs/build/html/_modules/binarycpython/utils/population_extensions/slurm.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -552,9 +553,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 2c758ddfed28a03897fa3c7dccbe716b9dad0391..7d536f438f13e0418657b75f25570f8b96d54f7c 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
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -775,9 +776,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 ca7256fc97b7b10084aa98e1603bdff4989105ca..7dd9c94b78a60c5b643565ce9ae634d8e0a015b2 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
@@ -13,6 +13,7 @@
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
+ <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../../_static/js/theme.js"></script>
@@ -521,9 +522,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 1c01f4a22872fe2cf71f545b6c26ad63e6644c2b..1e4907fd60a72eba32911d77df1cb0cd28093d56 100644
--- a/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
+++ b/docs/build/html/_modules/binarycpython/utils/run_system_wrapper.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
+ <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../_static/js/theme.js"></script>
@@ -205,9 +206,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 b6239a664d334026070db8ab2da4423ca5004789..e856554d3741cbfd3ccf2179c490121caa81f1f6 100644
--- a/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
+++ b/docs/build/html/_modules/binarycpython/utils/useful_funcs.html
@@ -13,6 +13,7 @@
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
+ <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../../../_static/js/theme.js"></script>
@@ -471,9 +472,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 29e1c56a4cb522738322db5e629cf671c5759f31..4a85dba1060e78793dea1a4ae0b79836e470239f 100644
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@@ -13,6 +13,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -109,9 +110,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/_sources/binary_c_parameters.rst.txt b/docs/build/html/_sources/binary_c_parameters.rst.txt
index 81bd07a9350f8d9aa75d828d9f5a0e2fe4e27520..1019b88d5098494448bf034ed2666e40cbd40cfa 100644
--- a/docs/build/html/_sources/binary_c_parameters.rst.txt
+++ b/docs/build/html/_sources/binary_c_parameters.rst.txt
@@ -4,7 +4,7 @@ The following chapter contains all the parameters that the current version of bi
This information was obtained by the following binary_c build:
- **binary_c git branch**: HEAD **binary_c git revision**: 5853:20220225:db09898b6 **Built on**: Feb 25 2022 19:21:31
+ **binary_c git branch**: branch_david **binary_c git revision**: 6072:20220603:69cdd3f72 **Built on**: Jun 3 2022 14:44:39
Section: stars
@@ -492,6 +492,12 @@ Section: stars
| **Default value**: 0
| **Extra**: Ignore
+| **Parameter**: PPISN_massloss_multiplier
+| **Description**: (Pulsational) Pair-Instability Supernova CO massloss multiplier: Value by which the (P)PISN massloss is multiplied. Currently only works with the new prescription. THe additional mass loss is not affected multiplied by this.
+| **Parameter input type**: Float
+| **Default value**: 1
+| **Extra**: Ignore
+
| **Parameter**: use_LWN_fallback
| **Description**: Flag whether to use the Nazehdin-Lovegrove-Woosley hydrogen envelope ejection at failed supernova.
| **Parameter input type**: Integer
@@ -2378,6 +2384,30 @@ Section: output
| **Parameter**: david_logging_function
| **Description**: Function to choose which kind of information gets logged Requires DAVID. Choices are: 0= None, >0 for custom logging functions
| **Parameter input type**: Integer
+| **Default value**: -1
+| **Extra**: Ignore
+
+| **Parameter**: david_tzo_logging
+| **Description**: Flag to enable logging for TZO project
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
+| **Parameter**: david_ppisn_logging
+| **Description**: Flag to enable logging for PPISN project
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
+| **Parameter**: david_rlof_episode_logging
+| **Description**: Flag to enable the RLOF episode logging
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
+| **Parameter**: david_rlof_ensemble_logging
+| **Description**: Flag to enable the RLOF ensemble logging
+| **Parameter input type**: Integer
| **Default value**: 0
| **Extra**: Ignore
diff --git a/docs/build/html/_static/_sphinx_javascript_frameworks_compat.js b/docs/build/html/_static/_sphinx_javascript_frameworks_compat.js
new file mode 100644
index 0000000000000000000000000000000000000000..8549469dc29fac0cbf16d10355e3313897cb3752
--- /dev/null
+++ b/docs/build/html/_static/_sphinx_javascript_frameworks_compat.js
@@ -0,0 +1,134 @@
+/*
+ * _sphinx_javascript_frameworks_compat.js
+ * ~~~~~~~~~~
+ *
+ * Compatability shim for jQuery and underscores.js.
+ *
+ * WILL BE REMOVED IN Sphinx 6.0
+ * xref RemovedInSphinx60Warning
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+ if (!x) {
+ return x
+ }
+ return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+ if (typeof s === 'undefined')
+ s = document.location.search;
+ var parts = s.substr(s.indexOf('?') + 1).split('&');
+ var result = {};
+ for (var i = 0; i < parts.length; i++) {
+ var tmp = parts[i].split('=', 2);
+ var key = jQuery.urldecode(tmp[0]);
+ var value = jQuery.urldecode(tmp[1]);
+ if (key in result)
+ result[key].push(value);
+ else
+ result[key] = [value];
+ }
+ return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+ function highlight(node, addItems) {
+ if (node.nodeType === 3) {
+ var val = node.nodeValue;
+ var pos = val.toLowerCase().indexOf(text);
+ if (pos >= 0 &&
+ !jQuery(node.parentNode).hasClass(className) &&
+ !jQuery(node.parentNode).hasClass("nohighlight")) {
+ var span;
+ var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+ if (isInSVG) {
+ span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+ } else {
+ span = document.createElement("span");
+ span.className = className;
+ }
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling));
+ node.nodeValue = val.substr(0, pos);
+ if (isInSVG) {
+ var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+ var bbox = node.parentElement.getBBox();
+ rect.x.baseVal.value = bbox.x;
+ rect.y.baseVal.value = bbox.y;
+ rect.width.baseVal.value = bbox.width;
+ rect.height.baseVal.value = bbox.height;
+ rect.setAttribute('class', className);
+ addItems.push({
+ "parent": node.parentNode,
+ "target": rect});
+ }
+ }
+ }
+ else if (!jQuery(node).is("button, select, textarea")) {
+ jQuery.each(node.childNodes, function() {
+ highlight(this, addItems);
+ });
+ }
+ }
+ var addItems = [];
+ var result = this.each(function() {
+ highlight(this, addItems);
+ });
+ for (var i = 0; i < addItems.length; ++i) {
+ jQuery(addItems[i].parent).before(addItems[i].target);
+ }
+ return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+ jQuery.uaMatch = function(ua) {
+ ua = ua.toLowerCase();
+
+ var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+ /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+ /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+ /(msie) ([\w.]+)/.exec(ua) ||
+ ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+ [];
+
+ return {
+ browser: match[ 1 ] || "",
+ version: match[ 2 ] || "0"
+ };
+ };
+ jQuery.browser = {};
+ jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
index 603f6a8798e7f7b07f32dfd1e0ad785b85bc7010..9039e027cdb56b0148480f7c3169cf776e6ecc97 100644
--- a/docs/build/html/_static/basic.css
+++ b/docs/build/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -222,7 +222,7 @@ table.modindextable td {
/* -- general body styles --------------------------------------------------- */
div.body {
- min-width: 450px;
+ min-width: 360px;
max-width: 800px;
}
@@ -335,13 +335,13 @@ p.sidebar-title {
font-weight: bold;
}
-div.admonition, div.topic, blockquote {
+div.admonition, div.topic, aside.topic, blockquote {
clear: left;
}
/* -- topics ---------------------------------------------------------------- */
-div.topic {
+div.topic, aside.topic {
border: 1px solid #ccc;
padding: 7px;
margin: 10px 0 10px 0;
@@ -380,6 +380,7 @@ div.body p.centered {
div.sidebar > :last-child,
aside.sidebar > :last-child,
div.topic > :last-child,
+aside.topic > :last-child,
div.admonition > :last-child {
margin-bottom: 0;
}
@@ -387,6 +388,7 @@ div.admonition > :last-child {
div.sidebar::after,
aside.sidebar::after,
div.topic::after,
+aside.topic::after,
div.admonition::after,
blockquote::after {
display: block;
@@ -428,10 +430,6 @@ table.docutils td, table.docutils th {
border-bottom: 1px solid #aaa;
}
-table.footnote td, table.footnote th {
- border: 0 !important;
-}
-
th {
text-align: left;
padding-right: 5px;
@@ -615,6 +613,7 @@ ul.simple p {
margin-bottom: 0;
}
+/* Docutils 0.17 and older (footnotes & citations) */
dl.footnote > dt,
dl.citation > dt {
float: left;
@@ -632,6 +631,33 @@ dl.citation > dd:after {
clear: both;
}
+/* Docutils 0.18+ (footnotes & citations) */
+aside.footnote > span,
+div.citation > span {
+ float: left;
+}
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+ padding-right: 0.5em;
+}
+aside.footnote > p {
+ margin-left: 2em;
+}
+div.citation > p {
+ margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
+ margin-bottom: 0em;
+}
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
+ content: "";
+ clear: both;
+}
+
+/* Footnotes & citations ends */
+
dl.field-list {
display: grid;
grid-template-columns: fit-content(30%) auto;
@@ -757,6 +783,7 @@ span.pre {
-ms-hyphens: none;
-webkit-hyphens: none;
hyphens: none;
+ white-space: nowrap;
}
div[class*="highlight-"] {
diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js
index 8cbf1b161a6527c8c6ad1c4f1fdc156e065ab262..c3db08d1c3896f616576ba6e6b96dc80fcfc50b9 100644
--- a/docs/build/html/_static/doctools.js
+++ b/docs/build/html/_static/doctools.js
@@ -2,322 +2,263 @@
* doctools.js
* ~~~~~~~~~~~
*
- * Sphinx JavaScript utilities for all documentation.
+ * Base JavaScript utilities for all Sphinx HTML documentation.
*
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
+"use strict";
-/**
- * select a different prefix for underscore
- */
-$u = _.noConflict();
-
-/**
- * make the code below compatible with browsers without
- * an installed firebug like debugger
-if (!window.console || !console.firebug) {
- var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
- "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
- "profile", "profileEnd"];
- window.console = {};
- for (var i = 0; i < names.length; ++i)
- window.console[names[i]] = function() {};
-}
- */
-
-/**
- * small helper function to urldecode strings
- *
- * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
- */
-jQuery.urldecode = function(x) {
- if (!x) {
- return x
+const _ready = (callback) => {
+ if (document.readyState !== "loading") {
+ callback();
+ } else {
+ document.addEventListener("DOMContentLoaded", callback);
}
- return decodeURIComponent(x.replace(/\+/g, ' '));
};
/**
- * small helper function to urlencode strings
+ * highlight a given string on a node by wrapping it in
+ * span elements with the given class name.
*/
-jQuery.urlencode = encodeURIComponent;
+const _highlight = (node, addItems, text, className) => {
+ if (node.nodeType === Node.TEXT_NODE) {
+ const val = node.nodeValue;
+ const parent = node.parentNode;
+ const pos = val.toLowerCase().indexOf(text);
+ if (
+ pos >= 0 &&
+ !parent.classList.contains(className) &&
+ !parent.classList.contains("nohighlight")
+ ) {
+ let span;
-/**
- * This function returns the parsed url parameters of the
- * current request. Multiple values per key are supported,
- * it will always return arrays of strings for the value parts.
- */
-jQuery.getQueryParameters = function(s) {
- if (typeof s === 'undefined')
- s = document.location.search;
- var parts = s.substr(s.indexOf('?') + 1).split('&');
- var result = {};
- for (var i = 0; i < parts.length; i++) {
- var tmp = parts[i].split('=', 2);
- var key = jQuery.urldecode(tmp[0]);
- var value = jQuery.urldecode(tmp[1]);
- if (key in result)
- result[key].push(value);
- else
- result[key] = [value];
- }
- return result;
-};
+ const closestNode = parent.closest("body, svg, foreignObject");
+ const isInSVG = closestNode && closestNode.matches("svg");
+ if (isInSVG) {
+ span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+ } else {
+ span = document.createElement("span");
+ span.classList.add(className);
+ }
-/**
- * highlight a given string on a jquery object by wrapping it in
- * span elements with the given class name.
- */
-jQuery.fn.highlightText = function(text, className) {
- function highlight(node, addItems) {
- if (node.nodeType === 3) {
- var val = node.nodeValue;
- var pos = val.toLowerCase().indexOf(text);
- if (pos >= 0 &&
- !jQuery(node.parentNode).hasClass(className) &&
- !jQuery(node.parentNode).hasClass("nohighlight")) {
- var span;
- var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
- if (isInSVG) {
- span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
- } else {
- span = document.createElement("span");
- span.className = className;
- }
- span.appendChild(document.createTextNode(val.substr(pos, text.length)));
- node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ parent.insertBefore(
+ span,
+ parent.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
- node.nextSibling));
- node.nodeValue = val.substr(0, pos);
- if (isInSVG) {
- var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
- var bbox = node.parentElement.getBBox();
- rect.x.baseVal.value = bbox.x;
- rect.y.baseVal.value = bbox.y;
- rect.width.baseVal.value = bbox.width;
- rect.height.baseVal.value = bbox.height;
- rect.setAttribute('class', className);
- addItems.push({
- "parent": node.parentNode,
- "target": rect});
- }
+ node.nextSibling
+ )
+ );
+ node.nodeValue = val.substr(0, pos);
+
+ if (isInSVG) {
+ const rect = document.createElementNS(
+ "http://www.w3.org/2000/svg",
+ "rect"
+ );
+ const bbox = parent.getBBox();
+ rect.x.baseVal.value = bbox.x;
+ rect.y.baseVal.value = bbox.y;
+ rect.width.baseVal.value = bbox.width;
+ rect.height.baseVal.value = bbox.height;
+ rect.setAttribute("class", className);
+ addItems.push({ parent: parent, target: rect });
}
}
- else if (!jQuery(node).is("button, select, textarea")) {
- jQuery.each(node.childNodes, function() {
- highlight(this, addItems);
- });
- }
+ } else if (node.matches && !node.matches("button, select, textarea")) {
+ node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
}
- var addItems = [];
- var result = this.each(function() {
- highlight(this, addItems);
- });
- for (var i = 0; i < addItems.length; ++i) {
- jQuery(addItems[i].parent).before(addItems[i].target);
- }
- return result;
};
-
-/*
- * backward compatibility for jQuery.browser
- * This will be supported until firefox bug is fixed.
- */
-if (!jQuery.browser) {
- jQuery.uaMatch = function(ua) {
- ua = ua.toLowerCase();
-
- var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
- /(webkit)[ \/]([\w.]+)/.exec(ua) ||
- /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
- /(msie) ([\w.]+)/.exec(ua) ||
- ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
- [];
-
- return {
- browser: match[ 1 ] || "",
- version: match[ 2 ] || "0"
- };
- };
- jQuery.browser = {};
- jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
-}
+const _highlightText = (thisNode, text, className) => {
+ let addItems = [];
+ _highlight(thisNode, addItems, text, className);
+ addItems.forEach((obj) =>
+ obj.parent.insertAdjacentElement("beforebegin", obj.target)
+ );
+};
/**
* Small JavaScript module for the documentation.
*/
-var Documentation = {
-
- init : function() {
- this.fixFirefoxAnchorBug();
- this.highlightSearchWords();
- this.initIndexTable();
- if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
- this.initOnKeyListeners();
- }
+const Documentation = {
+ init: () => {
+ Documentation.highlightSearchWords();
+ Documentation.initDomainIndexTable();
+ Documentation.initOnKeyListeners();
},
/**
* i18n support
*/
- TRANSLATIONS : {},
- PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
- LOCALE : 'unknown',
+ TRANSLATIONS: {},
+ PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
+ LOCALE: "unknown",
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
- gettext : function(string) {
- var translated = Documentation.TRANSLATIONS[string];
- if (typeof translated === 'undefined')
- return string;
- return (typeof translated === 'string') ? translated : translated[0];
- },
-
- ngettext : function(singular, plural, n) {
- var translated = Documentation.TRANSLATIONS[singular];
- if (typeof translated === 'undefined')
- return (n == 1) ? singular : plural;
- return translated[Documentation.PLURALEXPR(n)];
- },
-
- addTranslations : function(catalog) {
- for (var key in catalog.messages)
- this.TRANSLATIONS[key] = catalog.messages[key];
- this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
- this.LOCALE = catalog.locale;
+ gettext: (string) => {
+ const translated = Documentation.TRANSLATIONS[string];
+ switch (typeof translated) {
+ case "undefined":
+ return string; // no translation
+ case "string":
+ return translated; // translation exists
+ default:
+ return translated[0]; // (singular, plural) translation tuple exists
+ }
},
- /**
- * add context elements like header anchor links
- */
- addContextElements : function() {
- $('div[id] > :header:first').each(function() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
- attr('title', _('Permalink to this headline')).
- appendTo(this);
- });
- $('dt[id]').each(function() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
- attr('title', _('Permalink to this definition')).
- appendTo(this);
- });
+ ngettext: (singular, plural, n) => {
+ const translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated !== "undefined")
+ return translated[Documentation.PLURAL_EXPR(n)];
+ return n === 1 ? singular : plural;
},
- /**
- * workaround a firefox stupidity
- * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
- */
- fixFirefoxAnchorBug : function() {
- if (document.location.hash && $.browser.mozilla)
- window.setTimeout(function() {
- document.location.href += '';
- }, 10);
+ addTranslations: (catalog) => {
+ Object.assign(Documentation.TRANSLATIONS, catalog.messages);
+ Documentation.PLURAL_EXPR = new Function(
+ "n",
+ `return (${catalog.plural_expr})`
+ );
+ Documentation.LOCALE = catalog.locale;
},
/**
* highlight the search words provided in the url in the text
*/
- highlightSearchWords : function() {
- var params = $.getQueryParameters();
- var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
- if (terms.length) {
- var body = $('div.body');
- if (!body.length) {
- body = $('body');
- }
- window.setTimeout(function() {
- $.each(terms, function() {
- body.highlightText(this.toLowerCase(), 'highlighted');
- });
- }, 10);
- $('<p class="highlight-link"><a href="javascript:Documentation.' +
- 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
- .appendTo($('#searchbox'));
- }
- },
+ highlightSearchWords: () => {
+ const highlight =
+ new URLSearchParams(window.location.search).get("highlight") || "";
+ const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
+ if (terms.length === 0) return; // nothing to do
- /**
- * init the domain index toggle buttons
- */
- initIndexTable : function() {
- var togglers = $('img.toggler').click(function() {
- var src = $(this).attr('src');
- var idnum = $(this).attr('id').substr(7);
- $('tr.cg-' + idnum).toggle();
- if (src.substr(-9) === 'minus.png')
- $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
- else
- $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
- }).css('display', '');
- if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
- togglers.click();
- }
+ // There should never be more than one element matching "div.body"
+ const divBody = document.querySelectorAll("div.body");
+ const body = divBody.length ? divBody[0] : document.querySelector("body");
+ window.setTimeout(() => {
+ terms.forEach((term) => _highlightText(body, term, "highlighted"));
+ }, 10);
+
+ const searchBox = document.getElementById("searchbox");
+ if (searchBox === null) return;
+ searchBox.appendChild(
+ document
+ .createRange()
+ .createContextualFragment(
+ '<p class="highlight-link">' +
+ '<a href="javascript:Documentation.hideSearchWords()">' +
+ Documentation.gettext("Hide Search Matches") +
+ "</a></p>"
+ )
+ );
},
/**
* helper function to hide the search marks again
*/
- hideSearchWords : function() {
- $('#searchbox .highlight-link').fadeOut(300);
- $('span.highlighted').removeClass('highlighted');
+ hideSearchWords: () => {
+ document
+ .querySelectorAll("#searchbox .highlight-link")
+ .forEach((el) => el.remove());
+ document
+ .querySelectorAll("span.highlighted")
+ .forEach((el) => el.classList.remove("highlighted"));
+ const url = new URL(window.location);
+ url.searchParams.delete("highlight");
+ window.history.replaceState({}, "", url);
},
/**
- * make the url absolute
+ * helper function to focus on search bar
*/
- makeURL : function(relativeURL) {
- return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+ focusSearchBar: () => {
+ document.querySelectorAll("input[name=q]")[0]?.focus();
},
/**
- * get the current relative url
+ * Initialise the domain index toggle buttons
*/
- getCurrentURL : function() {
- var path = document.location.pathname;
- var parts = path.split(/\//);
- $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
- if (this === '..')
- parts.pop();
- });
- var url = parts.join('/');
- return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+ initDomainIndexTable: () => {
+ const toggler = (el) => {
+ const idNumber = el.id.substr(7);
+ const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
+ if (el.src.substr(-9) === "minus.png") {
+ el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
+ toggledRows.forEach((el) => (el.style.display = "none"));
+ } else {
+ el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
+ toggledRows.forEach((el) => (el.style.display = ""));
+ }
+ };
+
+ const togglerElements = document.querySelectorAll("img.toggler");
+ togglerElements.forEach((el) =>
+ el.addEventListener("click", (event) => toggler(event.currentTarget))
+ );
+ togglerElements.forEach((el) => (el.style.display = ""));
+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
},
- initOnKeyListeners: function() {
- $(document).keydown(function(event) {
- var activeElementType = document.activeElement.tagName;
- // don't navigate when in search box, textarea, dropdown or button
- if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
- && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
- && !event.shiftKey) {
- switch (event.keyCode) {
- case 37: // left
- var prevHref = $('link[rel="prev"]').prop('href');
- if (prevHref) {
- window.location.href = prevHref;
- return false;
+ initOnKeyListeners: () => {
+ // only install a listener if it is really needed
+ if (
+ !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+ !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
+ )
+ return;
+
+ const blacklistedElements = new Set([
+ "TEXTAREA",
+ "INPUT",
+ "SELECT",
+ "BUTTON",
+ ]);
+ document.addEventListener("keydown", (event) => {
+ if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements
+ if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys
+
+ if (!event.shiftKey) {
+ switch (event.key) {
+ case "ArrowLeft":
+ if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+ const prevLink = document.querySelector('link[rel="prev"]');
+ if (prevLink && prevLink.href) {
+ window.location.href = prevLink.href;
+ event.preventDefault();
}
break;
- case 39: // right
- var nextHref = $('link[rel="next"]').prop('href');
- if (nextHref) {
- window.location.href = nextHref;
- return false;
+ case "ArrowRight":
+ if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+ const nextLink = document.querySelector('link[rel="next"]');
+ if (nextLink && nextLink.href) {
+ window.location.href = nextLink.href;
+ event.preventDefault();
}
break;
+ case "Escape":
+ if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+ Documentation.hideSearchWords();
+ event.preventDefault();
}
}
+
+ // some keyboard layouts may need Shift to get /
+ switch (event.key) {
+ case "/":
+ if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+ Documentation.focusSearchBar();
+ event.preventDefault();
+ }
});
- }
+ },
};
// quick alias for translations
-_ = Documentation.gettext;
+const _ = Documentation.gettext;
-$(document).ready(function() {
- Documentation.init();
-});
+_ready(Documentation.init);
diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
index 2fa8c97fe42aebc1d50251eca054fdc6b40ed084..a750e4d5eefe934637d6f14b3647b6b084f924a5 100644
--- a/docs/build/html/_static/documentation_options.js
+++ b/docs/build/html/_static/documentation_options.js
@@ -1,12 +1,14 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '',
- LANGUAGE: 'None',
+ LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
FILE_SUFFIX: '.html',
LINK_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
- NAVIGATION_WITH_KEYS: false
+ NAVIGATION_WITH_KEYS: false,
+ SHOW_SEARCH_SUMMARY: true,
+ ENABLE_SEARCH_SHORTCUTS: false,
};
\ No newline at end of file
diff --git a/docs/build/html/_static/jquery-3.5.1.js b/docs/build/html/_static/jquery-3.6.0.js
similarity index 98%
rename from docs/build/html/_static/jquery-3.5.1.js
rename to docs/build/html/_static/jquery-3.6.0.js
index 50937333b99a5e168ac9e8292b22edd7e96c3e6a..fc6c299b73e792ef288e785c22393a5df9dded4b 100644
--- a/docs/build/html/_static/jquery-3.5.1.js
+++ b/docs/build/html/_static/jquery-3.6.0.js
@@ -1,15 +1,15 @@
/*!
- * jQuery JavaScript Library v3.5.1
+ * jQuery JavaScript Library v3.6.0
* https://jquery.com/
*
* Includes Sizzle.js
* https://sizzlejs.com/
*
- * Copyright JS Foundation and other contributors
+ * Copyright OpenJS Foundation and other contributors
* Released under the MIT license
* https://jquery.org/license
*
- * Date: 2020-05-04T22:49Z
+ * Date: 2021-03-02T17:08Z
*/
( function( global, factory ) {
@@ -76,12 +76,16 @@ var support = {};
var isFunction = function isFunction( obj ) {
- // Support: Chrome <=57, Firefox <=52
- // In some browsers, typeof returns "function" for HTML <object> elements
- // (i.e., `typeof document.createElement( "object" ) === "function"`).
- // We don't want to classify *any* DOM node as a function.
- return typeof obj === "function" && typeof obj.nodeType !== "number";
- };
+ // Support: Chrome <=57, Firefox <=52
+ // In some browsers, typeof returns "function" for HTML <object> elements
+ // (i.e., `typeof document.createElement( "object" ) === "function"`).
+ // We don't want to classify *any* DOM node as a function.
+ // Support: QtWeb <=3.8.5, WebKit <=534.34, wkhtmltopdf tool <=0.12.5
+ // Plus for old WebKit, typeof returns "function" for HTML collections
+ // (e.g., `typeof document.getElementsByTagName("div") === "function"`). (gh-4756)
+ return typeof obj === "function" && typeof obj.nodeType !== "number" &&
+ typeof obj.item !== "function";
+ };
var isWindow = function isWindow( obj ) {
@@ -147,7 +151,7 @@ function toType( obj ) {
var
- version = "3.5.1",
+ version = "3.6.0",
// Define a local copy of jQuery
jQuery = function( selector, context ) {
@@ -401,7 +405,7 @@ jQuery.extend( {
if ( isArrayLike( Object( arr ) ) ) {
jQuery.merge( ret,
typeof arr === "string" ?
- [ arr ] : arr
+ [ arr ] : arr
);
} else {
push.call( ret, arr );
@@ -496,9 +500,9 @@ if ( typeof Symbol === "function" ) {
// Populate the class2type map
jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ),
-function( _i, name ) {
- class2type[ "[object " + name + "]" ] = name.toLowerCase();
-} );
+ function( _i, name ) {
+ class2type[ "[object " + name + "]" ] = name.toLowerCase();
+ } );
function isArrayLike( obj ) {
@@ -518,14 +522,14 @@ function isArrayLike( obj ) {
}
var Sizzle =
/*!
- * Sizzle CSS Selector Engine v2.3.5
+ * Sizzle CSS Selector Engine v2.3.6
* https://sizzlejs.com/
*
* Copyright JS Foundation and other contributors
* Released under the MIT license
* https://js.foundation/
*
- * Date: 2020-03-14
+ * Date: 2021-02-16
*/
( function( window ) {
var i,
@@ -1108,8 +1112,8 @@ support = Sizzle.support = {};
* @returns {Boolean} True iff elem is a non-HTML XML node
*/
isXML = Sizzle.isXML = function( elem ) {
- var namespace = elem.namespaceURI,
- docElem = ( elem.ownerDocument || elem ).documentElement;
+ var namespace = elem && elem.namespaceURI,
+ docElem = elem && ( elem.ownerDocument || elem ).documentElement;
// Support: IE <=8
// Assume HTML when documentElement doesn't yet exist, such as inside loading iframes
@@ -3024,9 +3028,9 @@ var rneedsContext = jQuery.expr.match.needsContext;
function nodeName( elem, name ) {
- return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+ return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
-};
+}
var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i );
@@ -3997,8 +4001,8 @@ jQuery.extend( {
resolveContexts = Array( i ),
resolveValues = slice.call( arguments ),
- // the master Deferred
- master = jQuery.Deferred(),
+ // the primary Deferred
+ primary = jQuery.Deferred(),
// subordinate callback factory
updateFunc = function( i ) {
@@ -4006,30 +4010,30 @@ jQuery.extend( {
resolveContexts[ i ] = this;
resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
if ( !( --remaining ) ) {
- master.resolveWith( resolveContexts, resolveValues );
+ primary.resolveWith( resolveContexts, resolveValues );
}
};
};
// Single- and empty arguments are adopted like Promise.resolve
if ( remaining <= 1 ) {
- adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject,
+ adoptValue( singleValue, primary.done( updateFunc( i ) ).resolve, primary.reject,
!remaining );
// Use .then() to unwrap secondary thenables (cf. gh-3000)
- if ( master.state() === "pending" ||
+ if ( primary.state() === "pending" ||
isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) {
- return master.then();
+ return primary.then();
}
}
// Multiple arguments are aggregated like Promise.all array elements
while ( i-- ) {
- adoptValue( resolveValues[ i ], updateFunc( i ), master.reject );
+ adoptValue( resolveValues[ i ], updateFunc( i ), primary.reject );
}
- return master.promise();
+ return primary.promise();
}
} );
@@ -4180,8 +4184,8 @@ var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
for ( ; i < len; i++ ) {
fn(
elems[ i ], key, raw ?
- value :
- value.call( elems[ i ], i, fn( elems[ i ], key ) )
+ value :
+ value.call( elems[ i ], i, fn( elems[ i ], key ) )
);
}
}
@@ -5089,10 +5093,7 @@ function buildFragment( elems, context, scripts, selection, ignored ) {
}
-var
- rkeyEvent = /^key/,
- rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/,
- rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
+var rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
function returnTrue() {
return true;
@@ -5387,8 +5388,8 @@ jQuery.event = {
event = jQuery.event.fix( nativeEvent ),
handlers = (
- dataPriv.get( this, "events" ) || Object.create( null )
- )[ event.type ] || [],
+ dataPriv.get( this, "events" ) || Object.create( null )
+ )[ event.type ] || [],
special = jQuery.event.special[ event.type ] || {};
// Use the fix-ed jQuery.Event rather than the (read-only) native event
@@ -5512,12 +5513,12 @@ jQuery.event = {
get: isFunction( hook ) ?
function() {
if ( this.originalEvent ) {
- return hook( this.originalEvent );
+ return hook( this.originalEvent );
}
} :
function() {
if ( this.originalEvent ) {
- return this.originalEvent[ name ];
+ return this.originalEvent[ name ];
}
},
@@ -5656,7 +5657,13 @@ function leverageNative( el, type, expectSync ) {
// Cancel the outer synthetic event
event.stopImmediatePropagation();
event.preventDefault();
- return result.value;
+
+ // Support: Chrome 86+
+ // In Chrome, if an element having a focusout handler is blurred by
+ // clicking outside of it, it invokes the handler synchronously. If
+ // that handler calls `.remove()` on the element, the data is cleared,
+ // leaving `result` undefined. We need to guard against this.
+ return result && result.value;
}
// If this is an inner synthetic event for an event with a bubbling surrogate
@@ -5821,34 +5828,7 @@ jQuery.each( {
targetTouches: true,
toElement: true,
touches: true,
-
- which: function( event ) {
- var button = event.button;
-
- // Add which for key events
- if ( event.which == null && rkeyEvent.test( event.type ) ) {
- return event.charCode != null ? event.charCode : event.keyCode;
- }
-
- // Add which for click: 1 === left; 2 === middle; 3 === right
- if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) {
- if ( button & 1 ) {
- return 1;
- }
-
- if ( button & 2 ) {
- return 3;
- }
-
- if ( button & 4 ) {
- return 2;
- }
-
- return 0;
- }
-
- return event.which;
- }
+ which: true
}, jQuery.event.addProp );
jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) {
@@ -5874,6 +5854,12 @@ jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateTyp
return true;
},
+ // Suppress native focus or blur as it's already being fired
+ // in leverageNative.
+ _default: function() {
+ return true;
+ },
+
delegateType: delegateType
};
} );
@@ -6541,6 +6527,10 @@ var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" );
// set in CSS while `offset*` properties report correct values.
// Behavior in IE 9 is more subtle than in newer versions & it passes
// some versions of this test; make sure not to make it pass there!
+ //
+ // Support: Firefox 70+
+ // Only Firefox includes border widths
+ // in computed dimensions. (gh-4529)
reliableTrDimensions: function() {
var table, tr, trChild, trStyle;
if ( reliableTrDimensionsVal == null ) {
@@ -6548,17 +6538,32 @@ var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" );
tr = document.createElement( "tr" );
trChild = document.createElement( "div" );
- table.style.cssText = "position:absolute;left:-11111px";
+ table.style.cssText = "position:absolute;left:-11111px;border-collapse:separate";
+ tr.style.cssText = "border:1px solid";
+
+ // Support: Chrome 86+
+ // Height set through cssText does not get applied.
+ // Computed height then comes back as 0.
tr.style.height = "1px";
trChild.style.height = "9px";
+ // Support: Android 8 Chrome 86+
+ // In our bodyBackground.html iframe,
+ // display for all div elements is set to "inline",
+ // which causes a problem only in Android 8 Chrome 86.
+ // Ensuring the div is display: block
+ // gets around this issue.
+ trChild.style.display = "block";
+
documentElement
.appendChild( table )
.appendChild( tr )
.appendChild( trChild );
trStyle = window.getComputedStyle( tr );
- reliableTrDimensionsVal = parseInt( trStyle.height ) > 3;
+ reliableTrDimensionsVal = ( parseInt( trStyle.height, 10 ) +
+ parseInt( trStyle.borderTopWidth, 10 ) +
+ parseInt( trStyle.borderBottomWidth, 10 ) ) === tr.offsetHeight;
documentElement.removeChild( table );
}
@@ -7022,10 +7027,10 @@ jQuery.each( [ "height", "width" ], function( _i, dimension ) {
// Running getBoundingClientRect on a disconnected node
// in IE throws an error.
( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ?
- swap( elem, cssShow, function() {
- return getWidthOrHeight( elem, dimension, extra );
- } ) :
- getWidthOrHeight( elem, dimension, extra );
+ swap( elem, cssShow, function() {
+ return getWidthOrHeight( elem, dimension, extra );
+ } ) :
+ getWidthOrHeight( elem, dimension, extra );
}
},
@@ -7084,7 +7089,7 @@ jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft,
swap( elem, { marginLeft: 0 }, function() {
return elem.getBoundingClientRect().left;
} )
- ) + "px";
+ ) + "px";
}
}
);
@@ -7223,7 +7228,7 @@ Tween.propHooks = {
if ( jQuery.fx.step[ tween.prop ] ) {
jQuery.fx.step[ tween.prop ]( tween );
} else if ( tween.elem.nodeType === 1 && (
- jQuery.cssHooks[ tween.prop ] ||
+ jQuery.cssHooks[ tween.prop ] ||
tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) {
jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
} else {
@@ -7468,7 +7473,7 @@ function defaultPrefilter( elem, props, opts ) {
anim.done( function() {
- /* eslint-enable no-loop-func */
+ /* eslint-enable no-loop-func */
// The final step of a "hide" animation is actually hiding the element
if ( !hidden ) {
@@ -7588,7 +7593,7 @@ function Animation( elem, properties, options ) {
tweens: [],
createTween: function( prop, end ) {
var tween = jQuery.Tween( elem, animation.opts, prop, end,
- animation.opts.specialEasing[ prop ] || animation.opts.easing );
+ animation.opts.specialEasing[ prop ] || animation.opts.easing );
animation.tweens.push( tween );
return tween;
},
@@ -7761,7 +7766,8 @@ jQuery.fn.extend( {
anim.stop( true );
}
};
- doAnimation.finish = doAnimation;
+
+ doAnimation.finish = doAnimation;
return empty || optall.queue === false ?
this.each( doAnimation ) :
@@ -8401,8 +8407,8 @@ jQuery.fn.extend( {
if ( this.setAttribute ) {
this.setAttribute( "class",
className || value === false ?
- "" :
- dataPriv.get( this, "__className__" ) || ""
+ "" :
+ dataPriv.get( this, "__className__" ) || ""
);
}
}
@@ -8417,7 +8423,7 @@ jQuery.fn.extend( {
while ( ( elem = this[ i++ ] ) ) {
if ( elem.nodeType === 1 &&
( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) {
- return true;
+ return true;
}
}
@@ -8707,9 +8713,7 @@ jQuery.extend( jQuery.event, {
special.bindType || type;
// jQuery handler
- handle = (
- dataPriv.get( cur, "events" ) || Object.create( null )
- )[ event.type ] &&
+ handle = ( dataPriv.get( cur, "events" ) || Object.create( null ) )[ event.type ] &&
dataPriv.get( cur, "handle" );
if ( handle ) {
handle.apply( cur, data );
@@ -8856,7 +8860,7 @@ var rquery = ( /\?/ );
// Cross-browser xml parsing
jQuery.parseXML = function( data ) {
- var xml;
+ var xml, parserErrorElem;
if ( !data || typeof data !== "string" ) {
return null;
}
@@ -8865,12 +8869,17 @@ jQuery.parseXML = function( data ) {
// IE throws on parseFromString with invalid input.
try {
xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" );
- } catch ( e ) {
- xml = undefined;
- }
+ } catch ( e ) {}
- if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) {
- jQuery.error( "Invalid XML: " + data );
+ parserErrorElem = xml && xml.getElementsByTagName( "parsererror" )[ 0 ];
+ if ( !xml || parserErrorElem ) {
+ jQuery.error( "Invalid XML: " + (
+ parserErrorElem ?
+ jQuery.map( parserErrorElem.childNodes, function( el ) {
+ return el.textContent;
+ } ).join( "\n" ) :
+ data
+ ) );
}
return xml;
};
@@ -8971,16 +8980,14 @@ jQuery.fn.extend( {
// Can add propHook for "elements" to filter or add form elements
var elements = jQuery.prop( this, "elements" );
return elements ? jQuery.makeArray( elements ) : this;
- } )
- .filter( function() {
+ } ).filter( function() {
var type = this.type;
// Use .is( ":disabled" ) so that fieldset[disabled] works
return this.name && !jQuery( this ).is( ":disabled" ) &&
rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
( this.checked || !rcheckableType.test( type ) );
- } )
- .map( function( _i, elem ) {
+ } ).map( function( _i, elem ) {
var val = jQuery( this ).val();
if ( val == null ) {
@@ -9033,7 +9040,8 @@ var
// Anchor tag for parsing the document origin
originAnchor = document.createElement( "a" );
- originAnchor.href = location.href;
+
+originAnchor.href = location.href;
// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
function addToPrefiltersOrTransports( structure ) {
@@ -9414,8 +9422,8 @@ jQuery.extend( {
// Context for global events is callbackContext if it is a DOM node or jQuery collection
globalEventContext = s.context &&
( callbackContext.nodeType || callbackContext.jquery ) ?
- jQuery( callbackContext ) :
- jQuery.event,
+ jQuery( callbackContext ) :
+ jQuery.event,
// Deferreds
deferred = jQuery.Deferred(),
@@ -9727,8 +9735,10 @@ jQuery.extend( {
response = ajaxHandleResponses( s, jqXHR, responses );
}
- // Use a noop converter for missing script
- if ( !isSuccess && jQuery.inArray( "script", s.dataTypes ) > -1 ) {
+ // Use a noop converter for missing script but not if jsonp
+ if ( !isSuccess &&
+ jQuery.inArray( "script", s.dataTypes ) > -1 &&
+ jQuery.inArray( "json", s.dataTypes ) < 0 ) {
s.converters[ "text script" ] = function() {};
}
@@ -10466,12 +10476,6 @@ jQuery.offset = {
options.using.call( elem, props );
} else {
- if ( typeof props.top === "number" ) {
- props.top += "px";
- }
- if ( typeof props.left === "number" ) {
- props.left += "px";
- }
curElem.css( props );
}
}
@@ -10640,8 +10644,11 @@ jQuery.each( [ "top", "left" ], function( _i, prop ) {
// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
- jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name },
- function( defaultExtra, funcName ) {
+ jQuery.each( {
+ padding: "inner" + name,
+ content: type,
+ "": "outer" + name
+ }, function( defaultExtra, funcName ) {
// Margin is only for outerHeight, outerWidth
jQuery.fn[ funcName ] = function( margin, value ) {
@@ -10726,7 +10733,8 @@ jQuery.fn.extend( {
}
} );
-jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " +
+jQuery.each(
+ ( "blur focus focusin focusout resize scroll click dblclick " +
"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
"change select submit keydown keypress keyup contextmenu" ).split( " " ),
function( _i, name ) {
@@ -10737,7 +10745,8 @@ jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " +
this.on( name, null, data, fn ) :
this.trigger( name );
};
- } );
+ }
+);
diff --git a/docs/build/html/_static/jquery.js b/docs/build/html/_static/jquery.js
index b0614034ad3a95e4ae9f53c2b015eeb3e8d68bde..c4c6022f2982e8dae64cebd6b9a2b59f2547faad 100644
--- a/docs/build/html/_static/jquery.js
+++ b/docs/build/html/_static/jquery.js
@@ -1,2 +1,2 @@
-/*! jQuery v3.5.1 | (c) JS Foundation and other contributors | jquery.org/license */
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diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js
index 863704b310d1539241ef20e26ccce6af27f0ffce..2e22b06ab13bec689de4d1530b8b625bc6d69ae8 100644
--- a/docs/build/html/_static/language_data.js
+++ b/docs/build/html/_static/language_data.js
@@ -5,12 +5,12 @@
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
-var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
/* Non-minified version is copied as a separate JS file, is available */
@@ -197,101 +197,3 @@ var Stemmer = function() {
}
}
-
-
-
-var splitChars = (function() {
- var result = {};
- var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
- 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
- 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
- 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
- 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
- 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
- 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
- 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
- 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
- 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
- var i, j, start, end;
- for (i = 0; i < singles.length; i++) {
- result[singles[i]] = true;
- }
- var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
- [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
- [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
- [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
- [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
- [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
- [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
- [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
- [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
- [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
- [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
- [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
- [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
- [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
- [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
- [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
- [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
- [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
- [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
- [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
- [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
- [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
- [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
- [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
- [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
- [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
- [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
- [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
- [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
- [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
- [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
- [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
- [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
- [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
- [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
- [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
- [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
- [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
- [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
- [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
- [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
- [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
- [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
- [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
- [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
- [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
- [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
- [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
- [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
- for (i = 0; i < ranges.length; i++) {
- start = ranges[i][0];
- end = ranges[i][1];
- for (j = start; j <= end; j++) {
- result[j] = true;
- }
- }
- return result;
-})();
-
-function splitQuery(query) {
- var result = [];
- var start = -1;
- for (var i = 0; i < query.length; i++) {
- if (splitChars[query.charCodeAt(i)]) {
- if (start !== -1) {
- result.push(query.slice(start, i));
- start = -1;
- }
- } else if (start === -1) {
- start = i;
- }
- }
- if (start !== -1) {
- result.push(query.slice(start));
- }
- return result;
-}
-
-
diff --git a/docs/build/html/_static/pygments.css b/docs/build/html/_static/pygments.css
index 582d5c3adaddbab2178a4e1ea270afe51e5437d2..08bec689d3306e6c13d1973f61a01bee9a307e87 100644
--- a/docs/build/html/_static/pygments.css
+++ b/docs/build/html/_static/pygments.css
@@ -5,22 +5,22 @@ td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5
span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
-.highlight .c { color: #408080; font-style: italic } /* Comment */
+.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #008000; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
-.highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */
-.highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */
-.highlight .cp { color: #BC7A00 } /* Comment.Preproc */
-.highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */
-.highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */
-.highlight .cs { color: #408080; font-style: italic } /* Comment.Special */
+.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */
+.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #9C6500 } /* Comment.Preproc */
+.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */
+.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
.highlight .ge { font-style: italic } /* Generic.Emph */
-.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gr { color: #E40000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
-.highlight .gi { color: #00A000 } /* Generic.Inserted */
-.highlight .go { color: #888888 } /* Generic.Output */
+.highlight .gi { color: #008400 } /* Generic.Inserted */
+.highlight .go { color: #717171 } /* Generic.Output */
.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
@@ -33,15 +33,15 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
.highlight .kt { color: #B00040 } /* Keyword.Type */
.highlight .m { color: #666666 } /* Literal.Number */
.highlight .s { color: #BA2121 } /* Literal.String */
-.highlight .na { color: #7D9029 } /* Name.Attribute */
+.highlight .na { color: #687822 } /* Name.Attribute */
.highlight .nb { color: #008000 } /* Name.Builtin */
.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
.highlight .no { color: #880000 } /* Name.Constant */
.highlight .nd { color: #AA22FF } /* Name.Decorator */
-.highlight .ni { color: #999999; font-weight: bold } /* Name.Entity */
-.highlight .ne { color: #D2413A; font-weight: bold } /* Name.Exception */
+.highlight .ni { color: #717171; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #CB3F38; font-weight: bold } /* Name.Exception */
.highlight .nf { color: #0000FF } /* Name.Function */
-.highlight .nl { color: #A0A000 } /* Name.Label */
+.highlight .nl { color: #767600 } /* Name.Label */
.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #19177C } /* Name.Variable */
@@ -58,11 +58,11 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */
.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
-.highlight .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */
+.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */
.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
-.highlight .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */
+.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */
.highlight .sx { color: #008000 } /* Literal.String.Other */
-.highlight .sr { color: #BB6688 } /* Literal.String.Regex */
+.highlight .sr { color: #A45A77 } /* Literal.String.Regex */
.highlight .s1 { color: #BA2121 } /* Literal.String.Single */
.highlight .ss { color: #19177C } /* Literal.String.Symbol */
.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */
diff --git a/docs/build/html/_static/searchtools.js b/docs/build/html/_static/searchtools.js
index 002e9c4a20fb408e3cd2fd4edb11726364675c80..ac4d5861f95f5c6161b846522d572532725aa275 100644
--- a/docs/build/html/_static/searchtools.js
+++ b/docs/build/html/_static/searchtools.js
@@ -4,22 +4,24 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
+"use strict";
-if (!Scorer) {
- /**
- * Simple result scoring code.
- */
+/**
+ * Simple result scoring code.
+ */
+if (typeof Scorer === "undefined") {
var Scorer = {
// Implement the following function to further tweak the score for each result
- // The function takes a result array [filename, title, anchor, descr, score]
+ // The function takes a result array [docname, title, anchor, descr, score, filename]
// and returns the new score.
/*
- score: function(result) {
- return result[4];
+ score: result => {
+ const [docname, title, anchor, descr, score, filename] = result
+ return score
},
*/
@@ -28,9 +30,11 @@ if (!Scorer) {
// or matches in the last dotted part of the object name
objPartialMatch: 6,
// Additive scores depending on the priority of the object
- objPrio: {0: 15, // used to be importantResults
- 1: 5, // used to be objectResults
- 2: -5}, // used to be unimportantResults
+ objPrio: {
+ 0: 15, // used to be importantResults
+ 1: 5, // used to be objectResults
+ 2: -5, // used to be unimportantResults
+ },
// Used when the priority is not in the mapping.
objPrioDefault: 0,
@@ -39,456 +43,455 @@ if (!Scorer) {
partialTitle: 7,
// query found in terms
term: 5,
- partialTerm: 2
+ partialTerm: 2,
};
}
-if (!splitQuery) {
- function splitQuery(query) {
- return query.split(/\s+/);
+const _removeChildren = (element) => {
+ while (element && element.lastChild) element.removeChild(element.lastChild);
+};
+
+/**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
+ */
+const _escapeRegExp = (string) =>
+ string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+
+const _displayItem = (item, highlightTerms, searchTerms) => {
+ const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
+ const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
+ const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+ const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
+ const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+
+ const [docName, title, anchor, descr] = item;
+
+ let listItem = document.createElement("li");
+ let requestUrl;
+ let linkUrl;
+ if (docBuilder === "dirhtml") {
+ // dirhtml builder
+ let dirname = docName + "/";
+ if (dirname.match(/\/index\/$/))
+ dirname = dirname.substring(0, dirname.length - 6);
+ else if (dirname === "index/") dirname = "";
+ requestUrl = docUrlRoot + dirname;
+ linkUrl = requestUrl;
+ } else {
+ // normal html builders
+ requestUrl = docUrlRoot + docName + docFileSuffix;
+ linkUrl = docName + docLinkSuffix;
+ }
+ const params = new URLSearchParams();
+ params.set("highlight", [...highlightTerms].join(" "));
+ let linkEl = listItem.appendChild(document.createElement("a"));
+ linkEl.href = linkUrl + "?" + params.toString() + anchor;
+ linkEl.innerHTML = title;
+ if (descr)
+ listItem.appendChild(document.createElement("span")).innerText =
+ " (" + descr + ")";
+ else if (showSearchSummary)
+ fetch(requestUrl)
+ .then((responseData) => responseData.text())
+ .then((data) => {
+ if (data)
+ listItem.appendChild(
+ Search.makeSearchSummary(data, searchTerms, highlightTerms)
+ );
+ });
+ Search.output.appendChild(listItem);
+};
+const _finishSearch = (resultCount) => {
+ Search.stopPulse();
+ Search.title.innerText = _("Search Results");
+ if (!resultCount)
+ Search.status.innerText = Documentation.gettext(
+ "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
+ );
+ else
+ Search.status.innerText = _(
+ `Search finished, found ${resultCount} page(s) matching the search query.`
+ );
+};
+const _displayNextItem = (
+ results,
+ resultCount,
+ highlightTerms,
+ searchTerms
+) => {
+ // results left, load the summary and display it
+ // this is intended to be dynamic (don't sub resultsCount)
+ if (results.length) {
+ _displayItem(results.pop(), highlightTerms, searchTerms);
+ setTimeout(
+ () => _displayNextItem(results, resultCount, highlightTerms, searchTerms),
+ 5
+ );
}
+ // search finished, update title and status message
+ else _finishSearch(resultCount);
+};
+
+/**
+ * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
+ * custom function per language.
+ *
+ * The regular expression works by splitting the string on consecutive characters
+ * that are not Unicode letters, numbers, underscores, or emoji characters.
+ * This is the same as ``\W+`` in Python, preserving the surrogate pair area.
+ */
+if (typeof splitQuery === "undefined") {
+ var splitQuery = (query) => query
+ .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
+ .filter(term => term) // remove remaining empty strings
}
/**
* Search Module
*/
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- htmlToText : function(htmlString) {
- var virtualDocument = document.implementation.createHTMLDocument('virtual');
- var htmlElement = $(htmlString, virtualDocument);
- htmlElement.find('.headerlink').remove();
- docContent = htmlElement.find('[role=main]')[0];
- if(docContent === undefined) {
- console.warn("Content block not found. Sphinx search tries to obtain it " +
- "via '[role=main]'. Could you check your theme or template.");
- return "";
- }
- return docContent.textContent || docContent.innerText;
+const Search = {
+ _index: null,
+ _queued_query: null,
+ _pulse_status: -1,
+
+ htmlToText: (htmlString) => {
+ const htmlElement = document
+ .createRange()
+ .createContextualFragment(htmlString);
+ _removeChildren(htmlElement.querySelectorAll(".headerlink"));
+ const docContent = htmlElement.querySelector('[role="main"]');
+ if (docContent !== undefined) return docContent.textContent;
+ console.warn(
+ "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
+ );
+ return "";
},
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
+ init: () => {
+ const query = new URLSearchParams(window.location.search).get("q");
+ document
+ .querySelectorAll('input[name="q"]')
+ .forEach((el) => (el.value = query));
+ if (query) Search.performSearch(query);
},
- loadIndex : function(url) {
- $.ajax({type: "GET", url: url, data: null,
- dataType: "script", cache: true,
- complete: function(jqxhr, textstatus) {
- if (textstatus != "success") {
- document.getElementById("searchindexloader").src = url;
- }
- }});
- },
+ loadIndex: (url) =>
+ (document.body.appendChild(document.createElement("script")).src = url),
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
+ setIndex: (index) => {
+ Search._index = index;
+ if (Search._queued_query !== null) {
+ const query = Search._queued_query;
+ Search._queued_query = null;
+ Search.query(query);
}
},
- hasIndex : function() {
- return this._index !== null;
- },
+ hasIndex: () => Search._index !== null,
- deferQuery : function(query) {
- this._queued_query = query;
- },
+ deferQuery: (query) => (Search._queued_query = query),
- stopPulse : function() {
- this._pulse_status = 0;
- },
+ stopPulse: () => (Search._pulse_status = -1),
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- var i;
+ startPulse: () => {
+ if (Search._pulse_status >= 0) return;
+
+ const pulse = () => {
Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- }
+ Search.dots.innerText = ".".repeat(Search._pulse_status);
+ if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
+ };
pulse();
},
/**
* perform a search for something (or wait until index is loaded)
*/
- performSearch : function(query) {
+ performSearch: (query) => {
// create the required interface elements
- this.out = $('#search-results');
- this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
- this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p class="search-summary"> </p>').appendTo(this.out);
- this.output = $('<ul class="search"/>').appendTo(this.out);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
+ const searchText = document.createElement("h2");
+ searchText.textContent = _("Searching");
+ const searchSummary = document.createElement("p");
+ searchSummary.classList.add("search-summary");
+ searchSummary.innerText = "";
+ const searchList = document.createElement("ul");
+ searchList.classList.add("search");
+
+ const out = document.getElementById("search-results");
+ Search.title = out.appendChild(searchText);
+ Search.dots = Search.title.appendChild(document.createElement("span"));
+ Search.status = out.appendChild(searchSummary);
+ Search.output = out.appendChild(searchList);
+
+ const searchProgress = document.getElementById("search-progress");
+ // Some themes don't use the search progress node
+ if (searchProgress) {
+ searchProgress.innerText = _("Preparing search...");
+ }
+ Search.startPulse();
// index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
+ if (Search.hasIndex()) Search.query(query);
+ else Search.deferQuery(query);
},
/**
* execute search (requires search index to be loaded)
*/
- query : function(query) {
- var i;
-
- // stem the searchterms and add them to the correct list
- var stemmer = new Stemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = splitQuery(query);
- var objectterms = [];
- for (i = 0; i < tmp.length; i++) {
- if (tmp[i] !== "") {
- objectterms.push(tmp[i].toLowerCase());
- }
+ query: (query) => {
+ // stem the search terms and add them to the correct list
+ const stemmer = new Stemmer();
+ const searchTerms = new Set();
+ const excludedTerms = new Set();
+ const highlightTerms = new Set();
+ const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
+ splitQuery(query.trim()).forEach((queryTerm) => {
+ const queryTermLower = queryTerm.toLowerCase();
+
+ // maybe skip this "word"
+ // stopwords array is from language_data.js
+ if (
+ stopwords.indexOf(queryTermLower) !== -1 ||
+ queryTerm.match(/^\d+$/)
+ )
+ return;
- if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i] === "") {
- // skip this "word"
- continue;
- }
// stem the word
- var word = stemmer.stemWord(tmp[i].toLowerCase());
- // prevent stemmer from cutting word smaller than two chars
- if(word.length < 3 && tmp[i].length >= 3) {
- word = tmp[i];
- }
- var toAppend;
+ let word = stemmer.stemWord(queryTermLower);
// select the correct list
- if (word[0] == '-') {
- toAppend = excluded;
- word = word.substr(1);
- }
+ if (word[0] === "-") excludedTerms.add(word.substr(1));
else {
- toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
+ searchTerms.add(word);
+ highlightTerms.add(queryTermLower);
}
- // only add if not already in the list
- if (!$u.contains(toAppend, word))
- toAppend.push(word);
- }
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
- // console.debug('SEARCH: searching for:');
- // console.info('required: ', searchterms);
- // console.info('excluded: ', excluded);
+ });
- // prepare search
- var terms = this._index.terms;
- var titleterms = this._index.titleterms;
+ // console.debug("SEARCH: searching for:");
+ // console.info("required: ", [...searchTerms]);
+ // console.info("excluded: ", [...excludedTerms]);
- // array of [filename, title, anchor, descr, score]
- var results = [];
- $('#search-progress').empty();
+ // array of [docname, title, anchor, descr, score, filename]
+ let results = [];
+ _removeChildren(document.getElementById("search-progress"));
// lookup as object
- for (i = 0; i < objectterms.length; i++) {
- var others = [].concat(objectterms.slice(0, i),
- objectterms.slice(i+1, objectterms.length));
- results = results.concat(this.performObjectSearch(objectterms[i], others));
- }
+ objectTerms.forEach((term) =>
+ results.push(...Search.performObjectSearch(term, objectTerms))
+ );
// lookup as search terms in fulltext
- results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
+ results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
// let the scorer override scores with a custom scoring function
- if (Scorer.score) {
- for (i = 0; i < results.length; i++)
- results[i][4] = Scorer.score(results[i]);
- }
+ if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
// now sort the results by score (in opposite order of appearance, since the
// display function below uses pop() to retrieve items) and then
// alphabetically
- results.sort(function(a, b) {
- var left = a[4];
- var right = b[4];
- if (left > right) {
- return 1;
- } else if (left < right) {
- return -1;
- } else {
+ results.sort((a, b) => {
+ const leftScore = a[4];
+ const rightScore = b[4];
+ if (leftScore === rightScore) {
// same score: sort alphabetically
- left = a[1].toLowerCase();
- right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
+ const leftTitle = a[1].toLowerCase();
+ const rightTitle = b[1].toLowerCase();
+ if (leftTitle === rightTitle) return 0;
+ return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
}
+ return leftScore > rightScore ? 1 : -1;
});
+ // remove duplicate search results
+ // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
+ let seen = new Set();
+ results = results.reverse().reduce((acc, result) => {
+ let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
+ if (!seen.has(resultStr)) {
+ acc.push(result);
+ seen.add(resultStr);
+ }
+ return acc;
+ }, []);
+
+ results = results.reverse();
+
// for debugging
//Search.lastresults = results.slice(); // a copy
- //console.info('search results:', Search.lastresults);
+ // console.info("search results:", Search.lastresults);
// print the results
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li></li>');
- var requestUrl = "";
- var linkUrl = "";
- if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') {
- // dirhtml builder
- var dirname = item[0] + '/';
- if (dirname.match(/\/index\/$/)) {
- dirname = dirname.substring(0, dirname.length-6);
- } else if (dirname == 'index/') {
- dirname = '';
- }
- requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + dirname;
- linkUrl = requestUrl;
-
- } else {
- // normal html builders
- requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX;
- linkUrl = item[0] + DOCUMENTATION_OPTIONS.LINK_SUFFIX;
- }
- listItem.append($('<a/>').attr('href',
- linkUrl +
- highlightstring + item[2]).html(item[1]));
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- setTimeout(function() {
- displayNextItem();
- }, 5);
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.ajax({url: requestUrl,
- dataType: "text",
- complete: function(jqxhr, textstatus) {
- var data = jqxhr.responseText;
- if (data !== '' && data !== undefined) {
- var summary = Search.makeSearchSummary(data, searchterms, hlterms);
- if (summary) {
- listItem.append(summary);
- }
- }
- Search.output.append(listItem);
- setTimeout(function() {
- displayNextItem();
- }, 5);
- }});
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- setTimeout(function() {
- displayNextItem();
- }, 5);
- }
- }
- // search finished, update title and status message
- else {
- Search.stopPulse();
- Search.title.text(_('Search Results'));
- if (!resultCount)
- Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
- else
- Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
- Search.status.fadeIn(500);
- }
- }
- displayNextItem();
+ _displayNextItem(results, results.length, highlightTerms, searchTerms);
},
/**
* search for object names
*/
- performObjectSearch : function(object, otherterms) {
- var filenames = this._index.filenames;
- var docnames = this._index.docnames;
- var objects = this._index.objects;
- var objnames = this._index.objnames;
- var titles = this._index.titles;
-
- var i;
- var results = [];
-
- for (var prefix in objects) {
- for (var iMatch = 0; iMatch != objects[prefix].length; ++iMatch) {
- var match = objects[prefix][iMatch];
- var name = match[4];
- var fullname = (prefix ? prefix + '.' : '') + name;
- var fullnameLower = fullname.toLowerCase()
- if (fullnameLower.indexOf(object) > -1) {
- var score = 0;
- var parts = fullnameLower.split('.');
- // check for different match types: exact matches of full name or
- // "last name" (i.e. last dotted part)
- if (fullnameLower == object || parts[parts.length - 1] == object) {
- score += Scorer.objNameMatch;
- // matches in last name
- } else if (parts[parts.length - 1].indexOf(object) > -1) {
- score += Scorer.objPartialMatch;
- }
- var objname = objnames[match[1]][2];
- var title = titles[match[0]];
- // If more than one term searched for, we require other words to be
- // found in the name/title/description
- if (otherterms.length > 0) {
- var haystack = (prefix + ' ' + name + ' ' +
- objname + ' ' + title).toLowerCase();
- var allfound = true;
- for (i = 0; i < otherterms.length; i++) {
- if (haystack.indexOf(otherterms[i]) == -1) {
- allfound = false;
- break;
- }
- }
- if (!allfound) {
- continue;
- }
- }
- var descr = objname + _(', in ') + title;
-
- var anchor = match[3];
- if (anchor === '')
- anchor = fullname;
- else if (anchor == '-')
- anchor = objnames[match[1]][1] + '-' + fullname;
- // add custom score for some objects according to scorer
- if (Scorer.objPrio.hasOwnProperty(match[2])) {
- score += Scorer.objPrio[match[2]];
- } else {
- score += Scorer.objPrioDefault;
- }
- results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
- }
+ performObjectSearch: (object, objectTerms) => {
+ const filenames = Search._index.filenames;
+ const docNames = Search._index.docnames;
+ const objects = Search._index.objects;
+ const objNames = Search._index.objnames;
+ const titles = Search._index.titles;
+
+ const results = [];
+
+ const objectSearchCallback = (prefix, match) => {
+ const name = match[4]
+ const fullname = (prefix ? prefix + "." : "") + name;
+ const fullnameLower = fullname.toLowerCase();
+ if (fullnameLower.indexOf(object) < 0) return;
+
+ let score = 0;
+ const parts = fullnameLower.split(".");
+
+ // check for different match types: exact matches of full name or
+ // "last name" (i.e. last dotted part)
+ if (fullnameLower === object || parts.slice(-1)[0] === object)
+ score += Scorer.objNameMatch;
+ else if (parts.slice(-1)[0].indexOf(object) > -1)
+ score += Scorer.objPartialMatch; // matches in last name
+
+ const objName = objNames[match[1]][2];
+ const title = titles[match[0]];
+
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ const otherTerms = new Set(objectTerms);
+ otherTerms.delete(object);
+ if (otherTerms.size > 0) {
+ const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
+ if (
+ [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
+ )
+ return;
}
- }
+ let anchor = match[3];
+ if (anchor === "") anchor = fullname;
+ else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
+
+ const descr = objName + _(", in ") + title;
+
+ // add custom score for some objects according to scorer
+ if (Scorer.objPrio.hasOwnProperty(match[2]))
+ score += Scorer.objPrio[match[2]];
+ else score += Scorer.objPrioDefault;
+
+ results.push([
+ docNames[match[0]],
+ fullname,
+ "#" + anchor,
+ descr,
+ score,
+ filenames[match[0]],
+ ]);
+ };
+ Object.keys(objects).forEach((prefix) =>
+ objects[prefix].forEach((array) =>
+ objectSearchCallback(prefix, array)
+ )
+ );
return results;
},
- /**
- * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions
- */
- escapeRegExp : function(string) {
- return string.replace(/[.*+\-?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
- },
-
/**
* search for full-text terms in the index
*/
- performTermsSearch : function(searchterms, excluded, terms, titleterms) {
- var docnames = this._index.docnames;
- var filenames = this._index.filenames;
- var titles = this._index.titles;
+ performTermsSearch: (searchTerms, excludedTerms) => {
+ // prepare search
+ const terms = Search._index.terms;
+ const titleTerms = Search._index.titleterms;
+ const docNames = Search._index.docnames;
+ const filenames = Search._index.filenames;
+ const titles = Search._index.titles;
- var i, j, file;
- var fileMap = {};
- var scoreMap = {};
- var results = [];
+ const scoreMap = new Map();
+ const fileMap = new Map();
// perform the search on the required terms
- for (i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- var files = [];
- var _o = [
- {files: terms[word], score: Scorer.term},
- {files: titleterms[word], score: Scorer.title}
+ searchTerms.forEach((word) => {
+ const files = [];
+ const arr = [
+ { files: terms[word], score: Scorer.term },
+ { files: titleTerms[word], score: Scorer.title },
];
// add support for partial matches
if (word.length > 2) {
- var word_regex = this.escapeRegExp(word);
- for (var w in terms) {
- if (w.match(word_regex) && !terms[word]) {
- _o.push({files: terms[w], score: Scorer.partialTerm})
- }
- }
- for (var w in titleterms) {
- if (w.match(word_regex) && !titleterms[word]) {
- _o.push({files: titleterms[w], score: Scorer.partialTitle})
- }
- }
+ const escapedWord = _escapeRegExp(word);
+ Object.keys(terms).forEach((term) => {
+ if (term.match(escapedWord) && !terms[word])
+ arr.push({ files: terms[term], score: Scorer.partialTerm });
+ });
+ Object.keys(titleTerms).forEach((term) => {
+ if (term.match(escapedWord) && !titleTerms[word])
+ arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
+ });
}
// no match but word was a required one
- if ($u.every(_o, function(o){return o.files === undefined;})) {
- break;
- }
+ if (arr.every((record) => record.files === undefined)) return;
+
// found search word in contents
- $u.each(_o, function(o) {
- var _files = o.files;
- if (_files === undefined)
- return
-
- if (_files.length === undefined)
- _files = [_files];
- files = files.concat(_files);
-
- // set score for the word in each file to Scorer.term
- for (j = 0; j < _files.length; j++) {
- file = _files[j];
- if (!(file in scoreMap))
- scoreMap[file] = {};
- scoreMap[file][word] = o.score;
- }
+ arr.forEach((record) => {
+ if (record.files === undefined) return;
+
+ let recordFiles = record.files;
+ if (recordFiles.length === undefined) recordFiles = [recordFiles];
+ files.push(...recordFiles);
+
+ // set score for the word in each file
+ recordFiles.forEach((file) => {
+ if (!scoreMap.has(file)) scoreMap.set(file, {});
+ scoreMap.get(file)[word] = record.score;
+ });
});
// create the mapping
- for (j = 0; j < files.length; j++) {
- file = files[j];
- if (file in fileMap && fileMap[file].indexOf(word) === -1)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
+ files.forEach((file) => {
+ if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
+ fileMap.get(file).push(word);
+ else fileMap.set(file, [word]);
+ });
+ });
// now check if the files don't contain excluded terms
- for (file in fileMap) {
- var valid = true;
-
+ const results = [];
+ for (const [file, wordList] of fileMap) {
// check if all requirements are matched
- var filteredTermCount = // as search terms with length < 3 are discarded: ignore
- searchterms.filter(function(term){return term.length > 2}).length
+
+ // as search terms with length < 3 are discarded
+ const filteredTermCount = [...searchTerms].filter(
+ (term) => term.length > 2
+ ).length;
if (
- fileMap[file].length != searchterms.length &&
- fileMap[file].length != filteredTermCount
- ) continue;
+ wordList.length !== searchTerms.size &&
+ wordList.length !== filteredTermCount
+ )
+ continue;
// ensure that none of the excluded terms is in the search result
- for (i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- titleterms[excluded[i]] == file ||
- $u.contains(terms[excluded[i]] || [], file) ||
- $u.contains(titleterms[excluded[i]] || [], file)) {
- valid = false;
- break;
- }
- }
+ if (
+ [...excludedTerms].some(
+ (term) =>
+ terms[term] === file ||
+ titleTerms[term] === file ||
+ (terms[term] || []).includes(file) ||
+ (titleTerms[term] || []).includes(file)
+ )
+ )
+ break;
- // if we have still a valid result we can add it to the result list
- if (valid) {
- // select one (max) score for the file.
- // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
- var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
- results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
- }
+ // select one (max) score for the file.
+ const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
+ // add result to the result list
+ results.push([
+ docNames[file],
+ titles[file],
+ "",
+ null,
+ score,
+ filenames[file],
+ ]);
}
return results;
},
@@ -496,34 +499,33 @@ var Search = {
/**
* helper function to return a node containing the
* search summary for a given text. keywords is a list
- * of stemmed words, hlwords is the list of normal, unstemmed
+ * of stemmed words, highlightWords is the list of normal, unstemmed
* words. the first one is used to find the occurrence, the
* latter for highlighting it.
*/
- makeSearchSummary : function(htmlText, keywords, hlwords) {
- var text = Search.htmlToText(htmlText);
- if (text == "") {
- return null;
- }
- var textLower = text.toLowerCase();
- var start = 0;
- $.each(keywords, function() {
- var i = textLower.indexOf(this.toLowerCase());
- if (i > -1)
- start = i;
- });
- start = Math.max(start - 120, 0);
- var excerpt = ((start > 0) ? '...' : '') +
- $.trim(text.substr(start, 240)) +
- ((start + 240 - text.length) ? '...' : '');
- var rv = $('<p class="context"></p>').text(excerpt);
- $.each(hlwords, function() {
- rv = rv.highlightText(this, 'highlighted');
- });
- return rv;
- }
+ makeSearchSummary: (htmlText, keywords, highlightWords) => {
+ const text = Search.htmlToText(htmlText).toLowerCase();
+ if (text === "") return null;
+
+ const actualStartPosition = [...keywords]
+ .map((k) => text.indexOf(k.toLowerCase()))
+ .filter((i) => i > -1)
+ .slice(-1)[0];
+ const startWithContext = Math.max(actualStartPosition - 120, 0);
+
+ const top = startWithContext === 0 ? "" : "...";
+ const tail = startWithContext + 240 < text.length ? "..." : "";
+
+ let summary = document.createElement("div");
+ summary.classList.add("context");
+ summary.innerText = top + text.substr(startWithContext, 240).trim() + tail;
+
+ highlightWords.forEach((highlightWord) =>
+ _highlightText(summary, highlightWord, "highlighted")
+ );
+
+ return summary;
+ },
};
-$(document).ready(function() {
- Search.init();
-});
+_ready(Search.init);
diff --git a/docs/build/html/binary_c_parameters.html b/docs/build/html/binary_c_parameters.html
index 7fe4e66bf12b21bac90056eb57e1d4f984eae110..829930da2f7e84d394ed6fb8bd07a7aece1506c1 100644
--- a/docs/build/html/binary_c_parameters.html
+++ b/docs/build/html/binary_c_parameters.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -108,14 +109,14 @@
}
</style>
<section id="binary-c-parameters">
-<h1>Binary_c parameters<a class="headerlink" href="#binary-c-parameters" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Binary_c parameters<a class="headerlink" href="#binary-c-parameters" title="Permalink to this heading">ïƒ</a></h1>
<p>The following chapter contains all the parameters that the current version of binary_c can handle, along with their descriptions and other properties.</p>
<dl class="simple">
-<dt>This information was obtained by the following binary_c build:</dt><dd><p><strong>binary_c git branch</strong>: HEAD <strong>binary_c git revision</strong>: 5853:20220225:db09898b6 <strong>Built on</strong>: Feb 25 2022 19:21:31</p>
+<dt>This information was obtained by the following binary_c build:</dt><dd><p><strong>binary_c git branch</strong>: branch_david <strong>binary_c git revision</strong>: 6072:20220603:69cdd3f72 <strong>Built on</strong>: Jun 3 2022 14:44:39</p>
</dd>
</dl>
<section id="section-stars">
-<h2>Section: stars<a class="headerlink" href="#section-stars" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: stars<a class="headerlink" href="#section-stars" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: metallicity</div>
<div class="line"><strong>Description</strong>: This sets the metallicity of the stars, i.e. the amount (by mass) of matter which is not hydrogen or helium. If you are using the BSE algorithm, this must be 1e-4 <= metallicity <= 0.03. See also nucsyn_metallicity and effective_metallicity.</div>
@@ -689,6 +690,13 @@
<div class="line"><strong>Extra</strong>: Ignore</div>
</div>
<div class="line-block">
+<div class="line"><strong>Parameter</strong>: PPISN_massloss_multiplier</div>
+<div class="line"><strong>Description</strong>: (Pulsational) Pair-Instability Supernova CO massloss multiplier: Value by which the (P)PISN massloss is multiplied. Currently only works with the new prescription. THe additional mass loss is not affected multiplied by this.</div>
+<div class="line"><strong>Parameter input type</strong>: Float</div>
+<div class="line"><strong>Default value</strong>: 1</div>
+<div class="line"><strong>Extra</strong>: Ignore</div>
+</div>
+<div class="line-block">
<div class="line"><strong>Parameter</strong>: use_LWN_fallback</div>
<div class="line"><strong>Description</strong>: Flag whether to use the Nazehdin-Lovegrove-Woosley hydrogen envelope ejection at failed supernova.</div>
<div class="line"><strong>Parameter input type</strong>: Integer</div>
@@ -1498,7 +1506,7 @@
</div>
</section>
<section id="section-binary">
-<h2>Section: binary<a class="headerlink" href="#section-binary" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: binary<a class="headerlink" href="#section-binary" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: separation</div>
<div class="line"><strong>Description</strong>: Set the orbital separation (actually the semi-major axis) of the binary (internal index 0, stellar indices 0 and 1) in solar radii. Note that if the orbital period is given, it is used to calculate the separation. So if you want to set the separation instead, either do not set the orbital period or set the orbital period to zero (0.0).</div>
@@ -2660,7 +2668,7 @@
</div>
</section>
<section id="section-nucsyn">
-<h2>Section: nucsyn<a class="headerlink" href="#section-nucsyn" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: nucsyn<a class="headerlink" href="#section-nucsyn" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: third_dup</div>
<div class="line"><strong>Description</strong>: If True, enables third dredge up. Requires NUCSYN and NUCSYN_THIRD_DREDGE_UP.</div>
@@ -2923,11 +2931,39 @@
</div>
</section>
<section id="section-output">
-<h2>Section: output<a class="headerlink" href="#section-output" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: output<a class="headerlink" href="#section-output" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: david_logging_function</div>
<div class="line"><strong>Description</strong>: Function to choose which kind of information gets logged Requires DAVID. Choices are: 0= None, >0 for custom logging functions</div>
<div class="line"><strong>Parameter input type</strong>: Integer</div>
+<div class="line"><strong>Default value</strong>: -1</div>
+<div class="line"><strong>Extra</strong>: Ignore</div>
+</div>
+<div class="line-block">
+<div class="line"><strong>Parameter</strong>: david_tzo_logging</div>
+<div class="line"><strong>Description</strong>: Flag to enable logging for TZO project</div>
+<div class="line"><strong>Parameter input type</strong>: Integer</div>
+<div class="line"><strong>Default value</strong>: 0</div>
+<div class="line"><strong>Extra</strong>: Ignore</div>
+</div>
+<div class="line-block">
+<div class="line"><strong>Parameter</strong>: david_ppisn_logging</div>
+<div class="line"><strong>Description</strong>: Flag to enable logging for PPISN project</div>
+<div class="line"><strong>Parameter input type</strong>: Integer</div>
+<div class="line"><strong>Default value</strong>: 0</div>
+<div class="line"><strong>Extra</strong>: Ignore</div>
+</div>
+<div class="line-block">
+<div class="line"><strong>Parameter</strong>: david_rlof_episode_logging</div>
+<div class="line"><strong>Description</strong>: Flag to enable the RLOF episode logging</div>
+<div class="line"><strong>Parameter input type</strong>: Integer</div>
+<div class="line"><strong>Default value</strong>: 0</div>
+<div class="line"><strong>Extra</strong>: Ignore</div>
+</div>
+<div class="line-block">
+<div class="line"><strong>Parameter</strong>: david_rlof_ensemble_logging</div>
+<div class="line"><strong>Description</strong>: Flag to enable the RLOF ensemble logging</div>
+<div class="line"><strong>Parameter input type</strong>: Integer</div>
<div class="line"><strong>Default value</strong>: 0</div>
<div class="line"><strong>Extra</strong>: Ignore</div>
</div>
@@ -3217,7 +3253,7 @@
</div>
</section>
<section id="section-input">
-<h2>Section: input<a class="headerlink" href="#section-input" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: input<a class="headerlink" href="#section-input" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: MINT_dir</div>
<div class="line"><strong>Description</strong>: Location of MINT algorithm data.</div>
@@ -3334,7 +3370,7 @@
</div>
</section>
<section id="section-i-o">
-<h2>Section: i/o<a class="headerlink" href="#section-i-o" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: i/o<a class="headerlink" href="#section-i-o" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: go</div>
<div class="line"><strong>Description</strong>: batchmode control command</div>
@@ -3397,7 +3433,7 @@
</div>
</section>
<section id="section-algorithms">
-<h2>Section: algorithms<a class="headerlink" href="#section-algorithms" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: algorithms<a class="headerlink" href="#section-algorithms" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: repeat</div>
<div class="line"><strong>Description</strong>: If > 1, repeats the system as many times as required. Handy if you’re using Monte-Carlo kicks and want to sample the parameter space well. Also, if you are running speed tests this is good to give a statistically more reasonable result. (See e.g. ‘tbse pgo’).</div>
@@ -3412,7 +3448,7 @@
</div>
</section>
<section id="section-misc">
-<h2>Section: misc<a class="headerlink" href="#section-misc" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Section: misc<a class="headerlink" href="#section-misc" title="Permalink to this heading">ïƒ</a></h2>
<div class="line-block">
<div class="line"><strong>Parameter</strong>: random_seed</div>
<div class="line"><strong>Description</strong>: Random number seed, usually a (possibly negative) integer. Useful for exactly reproducing the evolution of a system which involves a kick (which is a Monte-Carlo, i.e. pseudorandom, process).</div>
@@ -3506,9 +3542,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 10354b9c3e96c9288e376e93aeb3a20ea2fe08ea..f3a60592442ccee51632442779f1534255562d51 100644
--- a/docs/build/html/custom_logging_functions.html
+++ b/docs/build/html/custom_logging_functions.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.custom_logging_functions">
-<span id="custom-logging-functions-module"></span><h1>custom_logging_functions module<a class="headerlink" href="#module-binarycpython.utils.custom_logging_functions" title="Permalink to this headline">ïƒ</a></h1>
+<span id="custom-logging-functions-module"></span><h1>custom_logging_functions module<a class="headerlink" href="#module-binarycpython.utils.custom_logging_functions" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing functions for the custom logging functionality.
The functions here make it possible for the user to define binaryc output logs on runtime</p>
<dl class="py function">
@@ -329,9 +330,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 82e477f4efd2cd944cfe20976c31a217e7aec08f..fca7c720edad6d7f065fa00b253a4932a2d18bfa 100644
--- a/docs/build/html/dicts.html
+++ b/docs/build/html/dicts.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.dicts">
-<span id="dicts-module"></span><h1>dicts module<a class="headerlink" href="#module-binarycpython.utils.dicts" title="Permalink to this headline">ïƒ</a></h1>
+<span id="dicts-module"></span><h1>dicts module<a class="headerlink" href="#module-binarycpython.utils.dicts" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing functions that binary_c-python uses to modify dictionaries.</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.dicts.AutoVivificationDict">
@@ -525,9 +526,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 cf2b64e2378e90ad1fdf1bf7c4074d2308b21a7c..204462b0c3a864e91e52f68f0f25602ac5de010d 100644
--- a/docs/build/html/ensemble.html
+++ b/docs/build/html/ensemble.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,13 +125,13 @@
}
</style>
<section id="module-binarycpython.utils.ensemble">
-<span id="ensemble-module"></span><h1>ensemble module<a class="headerlink" href="#module-binarycpython.utils.ensemble" title="Permalink to this headline">ïƒ</a></h1>
+<span id="ensemble-module"></span><h1>ensemble module<a class="headerlink" href="#module-binarycpython.utils.ensemble" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing functions to interact with binary_c’s
population ensemble using the binarycpython package</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.ensemble.BinarycDecoder">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.ensemble.</span></span><span class="sig-name descname"><span class="pre">BinarycDecoder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">object_hook</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_float</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_int</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_constant</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">object_pairs_hook</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/ensemble.html#BinarycDecoder"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.ensemble.BinarycDecoder" title="Permalink to this definition">ïƒ</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">json.decoder.JSONDecoder</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">JSONDecoder</span></code></p>
<p>Custom decoder to transform the numbers that are strings to actual floats</p>
<dl class="py method">
<dt class="sig sig-object py" id="binarycpython.utils.ensemble.BinarycDecoder.decode">
@@ -143,7 +144,7 @@ population ensemble using the binarycpython package</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.ensemble.BinarycEncoder">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.ensemble.</span></span><span class="sig-name descname"><span class="pre">BinarycEncoder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skipkeys</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensure_ascii</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_circular</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_nan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sort_keys</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separators</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/ensemble.html#BinarycEncoder"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.ensemble.BinarycEncoder" title="Permalink to this definition">ïƒ</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">json.encoder.JSONEncoder</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">JSONEncoder</span></code></p>
<p>Encoding class function to attempt to convert things to strings.</p>
<dl class="py method">
<dt class="sig sig-object py" id="binarycpython.utils.ensemble.BinarycEncoder.default">
@@ -275,9 +276,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 652d029227e4faa505fac33435cfe124ca24642b..7a9ce64832467183d4331029aeeda46fa0aa5c84 100644
--- a/docs/build/html/example_notebooks.html
+++ b/docs/build/html/example_notebooks.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -112,7 +113,7 @@
}
</style>
<section id="example-notebooks">
-<h1>Example notebooks<a class="headerlink" href="#example-notebooks" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example notebooks<a class="headerlink" href="#example-notebooks" title="Permalink to this heading">ïƒ</a></h1>
<p>We have a set of notebooks that explain and show the usage of the binarycpython features. The notebooks are also stored in the examples/ directory in the <a class="reference external" href="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python/-/tree/master/examples">repository</a></p>
<p>The order of the notebooks below is more or less the recommended order to read. The last couple of notebooks are example usecases</p>
<div class="toctree-wrapper compound">
@@ -214,9 +215,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 651e155932df8549e1082af985216a01752989e2..8f303bd92fe4f7c99c942da6067ef1bc51a2aa0f 100644
--- a/docs/build/html/examples/notebook_BHBH.html
+++ b/docs/build/html/examples/notebook_BHBH.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -300,7 +301,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -361,14 +362,13 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Example-use-case:-Binary-black-hole-systems">
-<h1>Example use case: Binary black hole systems<a class="headerlink" href="#Example-use-case:-Binary-black-hole-systems" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example use case: Binary black hole systems<a class="headerlink" href="#Example-use-case:-Binary-black-hole-systems" title="Permalink to this heading">ïƒ</a></h1>
<p>TODO: introduce the notebook</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">temp_dir</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.run_system_wrapper</span> <span class="kn">import</span> <span class="n">run_system</span>
<span class="n">TMP_DIR</span> <span class="o">=</span> <span class="n">temp_dir</span><span class="p">(</span><span class="s2">"notebooks"</span><span class="p">,</span> <span class="s2">"notebook_BHBH"</span><span class="p">)</span>
@@ -379,8 +379,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">log_filename</span> <span class="o">=</span> <span class="s2">"log_file"</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">log_filename</span> <span class="o">=</span> <span class="s2">"log_file"</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="n">M_1</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span>
<span class="n">BH_prescription</span><span class="o">=</span><span class="s1">'BH_BELCZYNSKI'</span><span class="p">,</span>
<span class="n">log_filename</span><span class="o">=</span><span class="n">log_filename</span><span class="p">,</span>
@@ -417,8 +416,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="n">M_1</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="n">M_1</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span>
<span class="n">M_2</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
<span class="n">orbital_period</span><span class="o">=</span><span class="mi">2000</span><span class="p">,</span> <span class="c1"># days</span>
<span class="n">BH_prescription</span><span class="o">=</span><span class="s1">'BH_BELCZYNSKI'</span><span class="p">,</span>
@@ -635,9 +633,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-
-<span></span><span class="c1"># BHBH detector : returns BHBH system data, or None if not found</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><br/><span></span><span class="c1"># BHBH detector : returns BHBH system data, or None if not found</span>
<span class="k">def</span> <span class="nf">BHBH</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="n">vb</span> <span class="o">=</span> <span class="kc">False</span> <span class="c1"># set to True for debugging</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
@@ -687,8 +683,7 @@ BHBH system is unbound
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="k">def</span> <span class="nf">search_for_BHBH</span><span class="p">(</span><span class="n">maxcount</span><span class="p">,</span><span class="o">**</span><span class="n">opts</span><span class="p">):</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">search_for_BHBH</span><span class="p">(</span><span class="n">maxcount</span><span class="p">,</span><span class="o">**</span><span class="n">opts</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="n">opts</span><span class="p">)</span>
<span class="n">found</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">count</span> <span class="o">=</span> <span class="mi">0</span>
@@ -724,8 +719,7 @@ BHBH system is unbound
<span class="n">wind_mass_loss</span><span class="o">=</span><span class="s1">'WIND_ALGORITHM_BINARY_C_2020'</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">search_for_BHBH</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
@@ -1040,8 +1034,7 @@ System 100 has separation -154.61
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
<span class="n">M_1</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span>
<span class="n">M_2</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
<span class="n">orbital_period</span><span class="o">=</span><span class="mi">2000</span><span class="p">,</span> <span class="c1"># days</span>
@@ -1266,8 +1259,7 @@ Found bound BHBH system
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
<span class="n">M_1</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span>
<span class="n">M_2</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
<span class="n">metallicity</span><span class="o">=</span><span class="mf">0.001</span><span class="p">,</span>
@@ -1339,8 +1331,7 @@ closer, more grvitationally-bound systems).</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
<span class="n">M_1</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span>
<span class="n">M_2</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
<span class="n">metallicity</span><span class="o">=</span><span class="mf">0.0001</span><span class="p">,</span>
@@ -1370,8 +1361,7 @@ System 1 has separation -3069.7
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
<span class="n">M_1</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span>
<span class="n">M_2</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
<span class="n">metallicity</span><span class="o">=</span><span class="mf">0.001</span><span class="p">,</span>
@@ -1386,8 +1376,7 @@ System 1 has separation -3069.7
<span class="n">d</span> <span class="o">=</span> <span class="n">search_for_BHBH</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
<span class="k">if</span> <span class="n">d</span> <span class="o">!=</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">d</span><span class="p">[</span><span class="s1">'separation'</span><span class="p">]</span> <span class="o"><</span> <span class="mf">10.0</span><span class="p">:</span>
<span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
@@ -5548,8 +5537,7 @@ system 2 / 100
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -5574,9 +5562,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 61c302a406906459157280bd679079d8d4ad0000..b73f4b633b2bbcfb55ca32db31aac077c975999a 100644
--- a/docs/build/html/examples/notebook_HRD.html
+++ b/docs/build/html/examples/notebook_HRD.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -307,7 +308,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -368,14 +369,13 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Example-use-case:-Hertzsprung-Russell-diagrams">
-<h1>Example use case: Hertzsprung-Russell diagrams<a class="headerlink" href="#Example-use-case:-Hertzsprung-Russell-diagrams" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example use case: Hertzsprung-Russell diagrams<a class="headerlink" href="#Example-use-case:-Hertzsprung-Russell-diagrams" title="Permalink to this heading">ïƒ</a></h1>
<p>In this notebook we compute Hertzsprung-Russell diagrams (HRDs) of single and binary stars.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">math</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
@@ -383,20 +383,18 @@ div.rendered_html tbody tr:hover {
<span class="kn">from</span> <span class="nn">binarycpython.utils.grid</span> <span class="kn">import</span> <span class="n">Population</span>
<span class="n">TMP_DIR</span> <span class="o">=</span> <span class="n">temp_dir</span><span class="p">(</span><span class="s2">"notebooks"</span><span class="p">,</span> <span class="s2">"notebook_HRD"</span><span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<section id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this heading">ïƒ</a></h2>
<p>First we set up a new population object. Our stars evolve to <span class="math notranslate nohighlight">\(13.7\mathrm{Gyr}\)</span>, the age of the Universe, and we assume the metallicity <span class="math notranslate nohighlight">\(Z=0.02\)</span>. These are rough approximations: a real population was born some finite time ago, so cannot possibly evolve to <span class="math notranslate nohighlight">\(13.7\mathrm{Gyr}\)</span>, and stars are not really born with a metallicity of <span class="math notranslate nohighlight">\(0.02\)</span>. These approximations only affect very low mass stars, so we assume all our stars have mass <span class="math notranslate nohighlight">\(M\geq 1 \mathrm{M}_\odot\)</span>, and metallicity
does not change evolution too much except in massive stars through the dependence of their winds on metallicity, so we limit our study to <span class="math notranslate nohighlight">\(M\leq 10 \mathrm{M}_\odot\)</span>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create population object</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create population object</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="c1"># Setting values can be done via .set(<parameter_name>=<value>)</span>
@@ -410,20 +408,18 @@ does not change evolution too much except in massive stars through the dependenc
<span class="n">tmp_dir</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">,</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">1</span>
<span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
</section>
<section id="Stellar-Grid">
-<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this heading">ïƒ</a></h2>
<p>We now construct a grid of stars, varying the mass from <span class="math notranslate nohighlight">\(1\)</span> to <span class="math notranslate nohighlight">\(10\mathrm{M}_\odot\)</span> in nine steps (so the masses are integers).</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
<span class="c1"># Set resolution and mass range that we simulate</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="mi">10</span><span class="p">}</span>
<span class="n">massrange</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
@@ -472,15 +468,14 @@ Added grid variable: {
</div>
</section>
<section id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this heading">ïƒ</a></h2>
<p>We now construct the HRD output.</p>
<p>We choose stars prior to and including the thermally-pulsing asymptotic giant branch (TPAGB) phase that have <span class="math notranslate nohighlight">\(>0.1\mathrm{M}_\odot\)</span> of material in their outer hydrogen envelope (remember the core of an evolved star is made of helium or carbon/oxygen/neon). This prevents us showing the post-AGB phase which is a bit messy and we avoid the white-dwarf cooling track.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">custom_logging_statement</span> <span class="o">=</span> <span class="s2">"""</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">custom_logging_statement</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">Foreach_star(star)</span>
<span class="s2">{</span>
<span class="s2"> if(star->stellar_type <= TPAGB &&</span>
@@ -505,8 +500,7 @@ Added grid variable: {
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">C_logging_code</span><span class="o">=</span><span class="n">custom_logging_statement</span>
<span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
@@ -542,8 +536,7 @@ Foreach_star(star)
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">datalinedict</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">datalinedict</span>
<span class="kn">import</span> <span class="nn">re</span>
<span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
@@ -591,7 +584,7 @@ adding: parse_function=<function parse_function at 0x14bf2250fdc0> to grid
</div>
</section>
<section id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">population.evolve()</span></code></p>
<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at the [grid options docs] (<a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html</a>) for more details.</p>
@@ -599,8 +592,7 @@ adding: parse_function=<function parse_function at 0x14bf2250fdc0> to grid
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># set number of threads</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># set number of threads</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="c1"># verbose output at level 1 is sufficient</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
@@ -741,8 +733,7 @@ dict_keys([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0])
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -758,8 +749,7 @@ dict_keys([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0])
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># make an HRD using Seaborn and Pandas</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># make an HRD using Seaborn and Pandas</span>
<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="n">pd</span><span class="o">.</span><span class="n">set_option</span><span class="p">(</span><span class="s2">"display.max_rows"</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="s2">"display.max_columns"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
@@ -799,8 +789,7 @@ dict_keys([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0])
<span class="n">p</span><span class="o">.</span><span class="n">invert_xaxis</span><span class="p">()</span>
<span class="n">p</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">"$\log_</span><span class="si">{10}</span><span class="s2"> (T_\mathrm</span><span class="si">{eff}</span><span class="s2"> / \mathrm</span><span class="si">{K}</span><span class="s2">)$"</span><span class="p">)</span>
<span class="n">p</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">"$\log_</span><span class="si">{10}</span><span class="s2"> (L/$L$_{☉})$"</span><span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nboutput docutils container">
@@ -839,14 +828,13 @@ Text(0, 0.5, '$\\log_{10} (L/$L$_{☉})$')
<p>We now have an HRD. It took longer to make the plot than to run the stars with <em>binary_c</em>!</p>
</section>
<section id="Binary-stars">
-<h2>Binary stars<a class="headerlink" href="#Binary-stars" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Binary stars<a class="headerlink" href="#Binary-stars" title="Permalink to this heading">ïƒ</a></h2>
<p>Now we put a secondary star of mass <span class="math notranslate nohighlight">\(0.5\mathrm{M}_\odot\)</span> at a distance of <span class="math notranslate nohighlight">\(10\mathrm{R}_\odot\)</span> to see how this changes things. Then we rerun the population. At such short separations, we expect mass transfer to begin on or shortly after the main sequence.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">M_2</span> <span class="o">=</span> <span class="mf">0.5</span><span class="p">,</span> <span class="c1"># Msun</span>
<span class="n">separation</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="c1"># Rsun</span>
<span class="n">multiplicity</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="c1"># binaries</span>
@@ -980,9 +968,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-
-<span></span><span class="n">hrd</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'HRD'</span><span class="p">]</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><br/><span></span><span class="n">hrd</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'HRD'</span><span class="p">]</span>
<span class="k">for</span> <span class="n">nstar</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">hrd</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"star "</span><span class="p">,</span><span class="n">nstar</span><span class="p">)</span>
@@ -1055,8 +1041,7 @@ Text(0, 0.5, '$\\log_{10} (L/$L$_{☉})$')
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">M_2</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># Msun</span>
<span class="n">separation</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span> <span class="c1"># Rsun</span>
<span class="n">multiplicity</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="c1"># binaries</span>
@@ -1192,8 +1177,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">hrd</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'HRD'</span><span class="p">]</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">hrd</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'HRD'</span><span class="p">]</span>
<span class="k">for</span> <span class="n">nstar</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">hrd</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"star "</span><span class="p">,</span><span class="n">nstar</span><span class="p">)</span>
@@ -1266,8 +1250,7 @@ Text(0, 0.5, '$\\log_{10} (L/$L$_{☉})$')
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">hrd</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'HRD'</span><span class="p">]</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">hrd</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'HRD'</span><span class="p">]</span>
<span class="k">for</span> <span class="n">nstar</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">hrd</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"star "</span><span class="p">,</span><span class="n">nstar</span><span class="p">)</span>
@@ -1339,8 +1322,7 @@ very start.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -1366,9 +1348,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 38d274dc306c7537ced1f335ecf0677b4f048cbc..d1338c7a1d723436131d3a3a36742d8e6acc0264 100644
--- a/docs/build/html/examples/notebook_api_functionality.html
+++ b/docs/build/html/examples/notebook_api_functionality.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -307,7 +308,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -368,7 +369,7 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Tutorial:-Using-the-API-functionality-of-binary_c-python">
-<h1>Tutorial: Using the API functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Using-the-API-functionality-of-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Tutorial: Using the API functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Using-the-API-functionality-of-binary_c-python" title="Permalink to this heading">ïƒ</a></h1>
<p>This notebook shows how to use the API functions that interface with binary_c. It usually is better to use wrapper functions that internally use these API functions, because most of the output here is very raw</p>
<p>Binarycpython uses the Python-C extension framework to interface Python with C. The sourcecode for this is contained in <code class="docutils literal notranslate"><span class="pre">src/binary_c_python.c</span></code>, and the functions are available via <code class="docutils literal notranslate"><span class="pre">from</span> <span class="pre">binarycpython</span> <span class="pre">import</span> <span class="pre">_binary_c_bindings</span></code>.</p>
<p>The following functions are available through the API: (run cell below)</p>
@@ -376,8 +377,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
<span class="n">help</span><span class="p">(</span><span class="n">_binary_c_bindings</span><span class="p">)</span>
</pre></div>
</div>
@@ -500,15 +500,14 @@ FILE
</li>
</ul>
<section id="Example-usage:">
-<h2>Example usage:<a class="headerlink" href="#Example-usage:" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Example usage:<a class="headerlink" href="#Example-usage:" title="Permalink to this heading">ïƒ</a></h2>
<section id="Setting-up,-using-and-freeing-store">
-<h3>Setting up, using and freeing store<a class="headerlink" href="#Setting-up,-using-and-freeing-store" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Setting up, using and freeing store<a class="headerlink" href="#Setting-up,-using-and-freeing-store" title="Permalink to this heading">ïƒ</a></h3>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># allocating store memory</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># allocating store memory</span>
<span class="n">store_memaddr</span> <span class="o">=</span> <span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_store_memaddr</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="n">store_memaddr</span><span class="p">)</span>
@@ -544,14 +543,13 @@ SINGLE_STAR_LIFETIME 10 28.4838
</div>
</section>
<section id="Getting-information-from-binary_c">
-<h3>Getting information from binary_c<a class="headerlink" href="#Getting-information-from-binary_c" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Getting information from binary_c<a class="headerlink" href="#Getting-information-from-binary_c" title="Permalink to this heading">ïƒ</a></h3>
<p>We can get information for a parameter via return_help(parameter_name): This will return an unparsed output</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_help</span><span class="p">(</span><span class="s1">'M_1'</span><span class="p">))</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_help</span><span class="p">(</span><span class="s1">'M_1'</span><span class="p">))</span>
</pre></div>
</div>
</div>
@@ -576,8 +574,7 @@ Default : 0
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_help_all</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()[:</span><span class="mi">10</span><span class="p">]))</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_help_all</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()[:</span><span class="mi">10</span><span class="p">]))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"(abridged)"</span><span class="p">)</span>
</pre></div>
</div>
@@ -605,8 +602,7 @@ M_4 : The initial mass of star four (in solar units, internally this is star ind
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_arglines</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()[:</span><span class="mi">4</span><span class="p">]))</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">_binary_c_bindings</span><span class="o">.</span><span class="n">return_arglines</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()[:</span><span class="mi">4</span><span class="p">]))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"(abridged)"</span><span class="p">)</span>
</pre></div>
</div>
@@ -628,8 +624,7 @@ M_1 = 0
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Here we set up the argument string that is passed to the bindings</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Here we set up the argument string that is passed to the bindings</span>
<span class="n">argstring</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">binary_c M_1 </span><span class="si">{M_1}</span><span class="s2"> orbital_period </span><span class="si">{orbital_period}</span><span class="s2"> eccentricity </span><span class="si">{eccentricity}</span><span class="s2"> metallicity </span><span class="si">{metallicity}</span><span class="s2"> max_evolution_time </span><span class="si">{max_evolution_time}</span><span class="s2"></span>
<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
@@ -660,8 +655,7 @@ MINIMUM PERIOD 0.00632092
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Here we set up the argument string that is passed to the bindings</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Here we set up the argument string that is passed to the bindings</span>
<span class="n">argstring</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">binary_c M_1 </span><span class="si">{M_1}</span><span class="s2"> orbital_period </span><span class="si">{orbital_period}</span><span class="s2"> eccentricity </span><span class="si">{eccentricity}</span><span class="s2"> metallicity </span><span class="si">{metallicity}</span><span class="s2"> max_evolution_time </span><span class="si">{max_evolution_time}</span><span class="s2"></span>
<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
@@ -692,8 +686,7 @@ MAXIMUM MASS RATIO 0.0141
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -720,9 +713,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 d60de9b8c365bc96b8e9049dbdf39764a0ef43ca..f706a0f6a0b47bd2ea60e6c9ba9ee55742ad6ac5 100644
--- a/docs/build/html/examples/notebook_common_envelope_evolution.html
+++ b/docs/build/html/examples/notebook_common_envelope_evolution.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -306,7 +307,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -367,15 +368,14 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Example-use-case:-Common-envelope-evolution">
-<h1>Example use case: Common-envelope evolution<a class="headerlink" href="#Example-use-case:-Common-envelope-evolution" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example use case: Common-envelope evolution<a class="headerlink" href="#Example-use-case:-Common-envelope-evolution" title="Permalink to this heading">ïƒ</a></h1>
<p>In this notebook we look at how common-envelope evolution (CEE) alters binary-star orbits. We construct a population of low- and intermediate-mass binaries and compare their orbital periods before and after CEE. Not all stars evolve into this phase, so we have to run a whole population to find those that do. We then have to construct the pre- and post-CEE distributions and plot them.</p>
<p>First, we import a few required Python modules.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">math</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">temp_dir</span>
@@ -385,14 +385,13 @@ div.rendered_html tbody tr:hover {
</div>
</div>
<section id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this heading">ïƒ</a></h2>
<p>We set up a new population object. Our stars evolve to <span class="math notranslate nohighlight">\(13.7\text{ }\mathrm{Gyr}\)</span>, the age of the Universe, and we assume the metallicity <span class="math notranslate nohighlight">\(Z=0.02\)</span>. We also set the common-envelope ejection efficiency <span class="math notranslate nohighlight">\(\alpha_\mathrm{CE}=1\)</span> and the envelope structure parameter <span class="math notranslate nohighlight">\(\lambda=0.5\)</span>. More complex options are available in <em>binary_c</em>, such as <span class="math notranslate nohighlight">\(\lambda\)</span> based on stellar mass, but this is just a demonstration example so let’s keep things simple.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create population object</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create population object</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="c1"># grid options</span>
@@ -423,14 +422,13 @@ adding: lambda_ce=0.5 to BSE_options
</div>
</section>
<section id="Stellar-Grid">
-<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Stellar Grid<a class="headerlink" href="#Stellar-Grid" title="Permalink to this heading">ïƒ</a></h2>
<p>We now construct a grid of stars, varying the mass from <span class="math notranslate nohighlight">\(1\)</span> to <span class="math notranslate nohighlight">\(6\text{ }\mathrm{M}_\odot\)</span>. We avoid massive stars for now, and focus on the (more common) low- and intermediate-mass stars. We also limit the period range to <span class="math notranslate nohighlight">\(10^4\text{ }\mathrm{d}\)</span> because systems with longer orbital periods will probably not undergo Roche-lobe overflow and hence common-envelope evolution is impossible.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
<span class="c1"># Set resolution and mass range that we simulate</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="mi">10</span><span class="p">,</span> <span class="s2">"q"</span> <span class="p">:</span> <span class="mi">10</span><span class="p">,</span> <span class="s2">"per"</span><span class="p">:</span> <span class="mi">10</span><span class="p">}</span>
<span class="n">massrange</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">6</span><span class="p">]</span>
@@ -550,14 +548,13 @@ Added grid variable: {
</div>
</section>
<section id="Logging-and-handling-the-output">
-<h2>Logging and handling the output<a class="headerlink" href="#Logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Logging and handling the output<a class="headerlink" href="#Logging-and-handling-the-output" title="Permalink to this heading">ïƒ</a></h2>
<p>We now construct the pre- and post-common envelope evolution data for the first common envelope that forms in each binary. We look at the comenv_count variable, we can see that when it increases from 0 to 1 we have found our object. If this happens, we stop evolution of the system to save CPU time.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">custom_logging_statement</span> <span class="o">=</span> <span class="s2">"""</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">custom_logging_statement</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">/*</span>
<span class="s2"> * Detect when the comenv_count increased</span>
@@ -589,8 +586,7 @@ Added grid variable: {
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">C_logging_code</span><span class="o">=</span><span class="n">custom_logging_statement</span>
<span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
@@ -633,8 +629,7 @@ if(stardata->model.comenv_count == 1 &&
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">bin_data</span><span class="p">,</span><span class="n">datalinedict</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">bin_data</span><span class="p">,</span><span class="n">datalinedict</span>
<span class="kn">import</span> <span class="nn">re</span>
<span class="c1"># log-period distribution bin width (dex)</span>
@@ -691,14 +686,13 @@ adding: parse_function=<function parse_function at 0x149c95c56c10> to grid
</div>
</section>
<section id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>Now we actually run the population. This may take a little while. You can set num_cores higher if you have a powerful machine.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># set number of threads</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># set number of threads</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="c1"># set number of threads (i.e. number of CPU cores we use)</span>
<span class="n">num_cores</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
@@ -1005,8 +999,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -1022,8 +1015,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># make a plot of the distributions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># make a plot of the distributions</span>
<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">copy</span>
@@ -1069,8 +1061,7 @@ There were no errors found in this run.
<span class="n">p</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">"$\log_</span><span class="si">{10}</span><span class="s2"> (P_\mathrm</span><span class="si">{orb}</span><span class="s2"> / \mathrm</span><span class="si">{day}</span><span class="s2">)$"</span><span class="p">)</span>
<span class="n">p</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">"Number of stars"</span><span class="p">)</span>
<span class="c1">#p.set(xlim=(-5,5)) # might be necessary?</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nboutput docutils container">
@@ -1131,9 +1122,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 96daa798c058048e5b5e0c9f2ce8669e7c2493f5..19bed65d7fc22e6637de5caeda3ec48f7cff5e42 100644
--- a/docs/build/html/examples/notebook_custom_logging.html
+++ b/docs/build/html/examples/notebook_custom_logging.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -312,7 +313,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -373,14 +374,13 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Tutorial:-Using-custom-logging-routines-with-binary_c-python">
-<h1>Tutorial: Using custom logging routines with binary_c-python<a class="headerlink" href="#Tutorial:-Using-custom-logging-routines-with-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Tutorial: Using custom logging routines with binary_c-python<a class="headerlink" href="#Tutorial:-Using-custom-logging-routines-with-binary_c-python" title="Permalink to this heading">ïƒ</a></h1>
<p>In this notebook you’ll learn how to use the custom logging functionality</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</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">autogen_C_logging_code</span><span class="p">,</span>
<span class="n">binary_c_log_code</span><span class="p">,</span>
@@ -403,14 +403,13 @@ div.rendered_html tbody tr:hover {
<p>The custom logging functionality can be used when running systems via <code class="docutils literal notranslate"><span class="pre">run_system()</span></code>, via <code class="docutils literal notranslate"><span class="pre">Population.evolve()</span></code> and <code class="docutils literal notranslate"><span class="pre">Population.evolve_single()</span></code>, and directly via the API</p>
<p>Within the logging statement we can access information from the stardata object, as well as use logical statements to determine when to log information. What we cannot do, however, is access functions that are not <em>publicly available</em>. For very elaborate printing routines it is still advised to actually hardcode the print statement into binary_c itself.</p>
<section id="Usage">
-<h2>Usage<a class="headerlink" href="#Usage" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Usage<a class="headerlink" href="#Usage" title="Permalink to this heading">ïƒ</a></h2>
<p>There are two methods to create the C-code that will be compiled: - Automatically generate the print statement and use the wrapper to generate the full function string, by using <code class="docutils literal notranslate"><span class="pre">autogen_C_logging_code</span></code> - Create your custom print statement and use the wrapper to generate the full function string, by writing out the print statement. Here the logging statement obviously has to be valid C code</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># generate logging lines. Here you can choose whatever you want to have logged, and with what header</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># generate logging lines. Here you can choose whatever you want to have logged, and with what header</span>
<span class="c1"># this generates working print statements</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="n">autogen_C_logging_code</span><span class="p">(</span>
<span class="p">{</span>
@@ -433,8 +432,7 @@ Printf("MY_STELLAR_DATA %g %g\n",((double)stardata->model.time),((dou
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># You can also decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals.</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># You can also decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals.</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="s1">'Printf("MY_STELLAR_DATA time=</span><span class="si">%g</span><span class="s1"> mass=</span><span class="si">%g</span><span class="se">\\</span><span class="s1">n", stardata->model.time, stardata->star[0].mass)'</span>
<span class="nb">print</span><span class="p">(</span><span class="n">logging_line</span><span class="p">)</span>
</pre></div>
@@ -452,8 +450,7 @@ Printf("MY_STELLAR_DATA time=%g mass=%g\n", stardata->model.time, sta
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Generate the entire 'script' by wrapping the logging line</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Generate the entire 'script' by wrapping the logging line</span>
<span class="n">custom_logging_code</span> <span class="o">=</span> <span class="n">binary_c_log_code</span><span class="p">(</span><span class="n">logging_line</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">custom_logging_code</span><span class="p">)</span>
</pre></div>
@@ -489,8 +486,7 @@ void binary_c_API_function custom_output_function(struct stardata_t * stardata)
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># logging statement</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># logging statement</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="s1">'Printf("MY_STELLAR_DATA time=</span><span class="si">%g</span><span class="s1"> mass=</span><span class="si">%g</span><span class="se">\\</span><span class="s1">n", stardata->model.time, stardata->star[0].mass)'</span>
<span class="c1"># Entire script</span>
@@ -516,14 +512,13 @@ MY_STELLAR_DATA time=2e-06 mass=2
</pre></div></div>
</div>
<section id="Using-custom-logging-with-the-population-object">
-<h3>Using custom logging with the population object<a class="headerlink" href="#Using-custom-logging-with-the-population-object" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Using custom logging with the population object<a class="headerlink" href="#Using-custom-logging-with-the-population-object" title="Permalink to this heading">ïƒ</a></h3>
<p>Custom logging can be used for a whole population by setting the print statement (so not the entire logging script) in <code class="docutils literal notranslate"><span class="pre">C_logging_code</span></code></p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Set up population</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Set up population</span>
<span class="n">pop</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="c1"># Set some BSE parameters</span>
@@ -575,14 +570,13 @@ EXAMPLE_POST_MS 1.045084306856e+02 4.99191 4.99192 9.57443 7.81395 2
</div>
</section>
<section id="Using-custom-logging-when-running-directly-from-the-API">
-<h3>Using custom logging when running directly from the API<a class="headerlink" href="#Using-custom-logging-when-running-directly-from-the-API" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Using custom logging when running directly from the API<a class="headerlink" href="#Using-custom-logging-when-running-directly-from-the-API" title="Permalink to this heading">ïƒ</a></h3>
<p>When running a system directly with the API we need to manually load the custom logging into memory (via <code class="docutils literal notranslate"><span class="pre">create_and_load_logging_function</span></code>) and pass the memory address to the binary_c binding via <code class="docutils literal notranslate"><span class="pre">_binary_c_bindings.run_system(argstring,</span> <span class="pre">custom_logging_func_memaddr=custom_logging_memaddr)</span></code></p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># generate logging lines</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># generate logging lines</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="n">autogen_C_logging_code</span><span class="p">(</span>
<span class="p">{</span>
<span class="s2">"MY_STELLAR_DATA"</span><span class="p">:</span> <span class="p">[</span><span class="s2">"model.time"</span><span class="p">,</span> <span class="s2">"star[0].mass"</span><span class="p">],</span>
@@ -637,17 +631,16 @@ MY_STELLAR_DATA 2e-06 15
</section>
</section>
<section id="Examples-of-logging-strings">
-<h2>Examples of logging strings<a class="headerlink" href="#Examples-of-logging-strings" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Examples of logging strings<a class="headerlink" href="#Examples-of-logging-strings" title="Permalink to this heading">ïƒ</a></h2>
<p>Below are some examples of logging strings</p>
<section id="Compact-object">
-<h3>Compact object<a class="headerlink" href="#Compact-object" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Compact object<a class="headerlink" href="#Compact-object" title="Permalink to this heading">ïƒ</a></h3>
<p>This logging will print the timestep when the star becomes a compact object. After it does, we change the maximum time to be the current time, effectively terminating the evolution</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">example_logging_string_CO</span> <span class="o">=</span> <span class="s2">"""</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">example_logging_string_CO</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">if(stardata->star[0].stellar_type>=NS)</span>
<span class="s2">{</span>
<span class="s2"> if (stardata->model.time < stardata->model.max_evolution_time)</span>
@@ -693,14 +686,13 @@ EXAMPLE_LOG_CO 2.848380621869e+01 1.33469 9.1865 1.72498e-05 724.338
</div>
</section>
<section id="Logging-mass-evolution-and-the-supernova">
-<h3>Logging mass evolution and the supernova<a class="headerlink" href="#Logging-mass-evolution-and-the-supernova" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Logging mass evolution and the supernova<a class="headerlink" href="#Logging-mass-evolution-and-the-supernova" title="Permalink to this heading">ïƒ</a></h3>
<p>This logging code prints the mass evolution and the moment the star goes supernova</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">example_logging_string_CO</span> <span class="o">=</span> <span class="s2">"""</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">example_logging_string_CO</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">Printf("EXAMPLE_MASSLOSS </span><span class="si">%30.12e</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%g</span><span class="se">\\</span><span class="s2">n",</span>
<span class="s2"> //</span>
<span class="s2"> stardata->model.time, // 1</span>
@@ -766,8 +758,7 @@ EXAMPLE_SN 1.050651207308e+01 1.59452 9.34213 20 12 13 5 1 6.55458 4
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -794,9 +785,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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_ensembles.html b/docs/build/html/examples/notebook_ensembles.html
index 76a2cae54861edbd6c37ff7c95fdd29f21453e2e..78b0174eaf171e833a36f223bba32e34564a5e2a 100644
--- a/docs/build/html/examples/notebook_ensembles.html
+++ b/docs/build/html/examples/notebook_ensembles.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -283,7 +284,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -347,8 +348,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -369,9 +369,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 b9f9214ad53de9dad361181a6f9930a368e99ab9..a2c13b252a8cc7840309018b17558e094783ec80 100644
--- a/docs/build/html/examples/notebook_extra_features.html
+++ b/docs/build/html/examples/notebook_extra_features.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -306,7 +307,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -367,15 +368,14 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Tutorial:-Extra-features-and-functionality-of-binary_c-python">
-<h1>Tutorial: Extra features and functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Extra-features-and-functionality-of-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Tutorial: Extra features and functionality of binary_c-python<a class="headerlink" href="#Tutorial:-Extra-features-and-functionality-of-binary_c-python" title="Permalink to this heading">ïƒ</a></h1>
<p>In this notebook we’ll go over some of the extra features and functionality that was not covered in the other notebooks.</p>
<p>Within the module <code class="docutils literal notranslate"><span class="pre">binarycpython.utils.functions</span></code> there are many functions that can be useful when using binarycpython. We can see which functions are in there, again by using the <code class="docutils literal notranslate"><span class="pre">help()</span></code></p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">Population</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">Population</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">get_help</span><span class="p">,</span>
<span class="n">get_help_all</span><span class="p">,</span>
@@ -387,7 +387,7 @@ div.rendered_html tbody tr:hover {
</div>
</div>
<section id="getting-extra-information-about-binary_c-parameters">
-<h2>getting extra information about binary_c parameters<a class="headerlink" href="#getting-extra-information-about-binary_c-parameters" title="Permalink to this headline">ïƒ</a></h2>
+<h2>getting extra information about binary_c parameters<a class="headerlink" href="#getting-extra-information-about-binary_c-parameters" title="Permalink to this heading">ïƒ</a></h2>
<p>There are several functions that can be used to get information about the parameters in binary_c:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">get_help(parameter)</span></code>: Function to get information about the specific input parameter. Prints the output on default but returns a dictionary containing the information.</p></li>
@@ -399,8 +399,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">get_help</span><span class="p">(</span><span class="s1">'M_1'</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">get_help</span><span class="p">(</span><span class="s1">'M_1'</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -435,8 +434,7 @@ default:
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># get_help_all()</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># get_help_all()</span>
</pre></div>
</div>
</div>
@@ -444,8 +442,7 @@ default:
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># get_help_super()</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># get_help_super()</span>
</pre></div>
</div>
</div>
@@ -453,21 +450,19 @@ default:
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># get_defaults()</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># get_defaults()</span>
</pre></div>
</div>
</div>
</section>
<section id="Build-information-of-binary_c">
-<h2>Build information of binary_c<a class="headerlink" href="#Build-information-of-binary_c" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Build information of binary_c<a class="headerlink" href="#Build-information-of-binary_c" title="Permalink to this heading">ïƒ</a></h2>
<p>It can be useful to fetch the information with which the current version of binary_c has been configured with. We can do that through the Population object, by calling the instance method <code class="docutils literal notranslate"><span class="pre">return_binary_c_version_info</span></code>. This function will parse the version info of binary_c and return a dictionary with all the settings.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">version_info</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span><span class="o">.</span><span class="n">return_binary_c_version_info</span><span class="p">(</span><span class="n">parsed</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">version_info</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span><span class="o">.</span><span class="n">return_binary_c_version_info</span><span class="p">(</span><span class="n">parsed</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">version_info</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
</pre></div>
</div>
@@ -482,20 +477,19 @@ dict_keys(['networks', 'isotopes', 'argpairs', 'ense
</div>
</section>
<section id="Example-parse-function">
-<h2>Example parse function<a class="headerlink" href="#Example-parse-function" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Example parse function<a class="headerlink" href="#Example-parse-function" title="Permalink to this heading">ïƒ</a></h2>
<p>TODO: In the functions module there is an example parse function that can be used in conjunction with run_system.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
</section>
<section id="Dictionary-modification">
-<h2>Dictionary modification<a class="headerlink" href="#Dictionary-modification" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Dictionary modification<a class="headerlink" href="#Dictionary-modification" title="Permalink to this heading">ïƒ</a></h2>
<ul class="simple">
<li><p>merge_dicts</p></li>
<li><p>update_dicts</p></li>
@@ -524,9 +518,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 642efceba99d1c4e9f96d988007c7377332a02c8..2131fceaafad8dd343b9f32c5e05627da296a5b5 100644
--- a/docs/build/html/examples/notebook_individual_systems.html
+++ b/docs/build/html/examples/notebook_individual_systems.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -305,7 +306,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -366,11 +367,11 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Tutorial:-Running-individual-systems-with-binary_c-python">
-<h1>Tutorial: Running individual systems with binary_c-python<a class="headerlink" href="#Tutorial:-Running-individual-systems-with-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Tutorial: Running individual systems with binary_c-python<a class="headerlink" href="#Tutorial:-Running-individual-systems-with-binary_c-python" title="Permalink to this heading">ïƒ</a></h1>
<p>This notebook will show you how to run single systems and analyze their results.</p>
<p>It can be useful to have some functions to quickly run a single system to, for example, inspect what evolutionary steps a specific system goes through, to plot the mass loss evolution of a single system, etc.</p>
<section id="Single-system-with-run_system_wrapper">
-<h2>Single system with run_system_wrapper<a class="headerlink" href="#Single-system-with-run_system_wrapper" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Single system with run_system_wrapper<a class="headerlink" href="#Single-system-with-run_system_wrapper" title="Permalink to this heading">ïƒ</a></h2>
<p>The simplest method to run a single system is to use the run_system wrapper. This function deals with setting up the argument string, makes sure all the required parameters are included and handles setting and cleaning up the custom logging functionality (see notebook_custom_logging).</p>
<p>As arguments to this function we can add any of the parameters that binary_c itself actually knows, as well as:</p>
<ul class="simple">
@@ -382,8 +383,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">temp_dir</span>
<span class="n">TMP_DIR</span> <span class="o">=</span> <span class="n">temp_dir</span><span class="p">(</span><span class="s2">"notebooks"</span><span class="p">,</span> <span class="s2">"notebook_individual_systems"</span><span class="p">)</span>
</pre></div>
@@ -393,8 +393,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.run_system_wrapper</span> <span class="kn">import</span> <span class="n">run_system</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.run_system_wrapper</span> <span class="kn">import</span> <span class="n">run_system</span>
<span class="c1"># help(run_system) # Uncomment to see the docstring</span>
</pre></div>
</div>
@@ -403,8 +402,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="n">M_1</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="n">M_1</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>
</pre></div>
</div>
@@ -423,8 +421,7 @@ SINGLE_STAR_LIFETIME 1 12461.1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">log_filename</span> <span class="o">=</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">TMP_DIR</span><span class="p">,</span> <span class="s1">'test_logfile.txt'</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">log_filename</span> <span class="o">=</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">TMP_DIR</span><span class="p">,</span> <span class="s1">'test_logfile.txt'</span><span class="p">)</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">run_system</span><span class="p">(</span><span class="n">M_1</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">log_filename</span><span class="o">=</span><span class="n">log_filename</span><span class="p">,</span> <span class="n">api_log_filename_prefix</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">log_filename</span><span class="p">,</span> <span class="s1">'r'</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="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
@@ -455,8 +452,7 @@ SINGLE_STAR_LIFETIME 1 12461.1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.custom_logging_functions</span> <span class="kn">import</span> <span class="n">binary_c_log_code</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.custom_logging_functions</span> <span class="kn">import</span> <span class="n">binary_c_log_code</span>
<span class="c1"># Create the print statement</span>
<span class="n">custom_logging_print_statement</span> <span class="o">=</span> <span class="s2">"""</span>
@@ -494,8 +490,7 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 1 1 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="n">output</span><span class="p">):</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="n">output</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Example function to parse the output of binary_c</span>
<span class="sd"> """</span>
@@ -536,8 +531,7 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 1 1 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="c1"># Load data into dataframe</span>
<span class="n">example_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>
@@ -573,14 +567,13 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 1 1 1
</div>
</section>
<section id="Single-system-via-population-object">
-<h2>Single system via population object<a class="headerlink" href="#Single-system-via-population-object" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Single system via population object<a class="headerlink" href="#Single-system-via-population-object" title="Permalink to this heading">ïƒ</a></h2>
<p>When setting up your population object (see notebook_population), and configuring all the parameters, it is possible to run a single system using that same configuration. It will use the parse_function if set, and running a single system is a good method to test if everything works accordingly.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.grid</span> <span class="kn">import</span> <span class="n">Population</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.grid</span> <span class="kn">import</span> <span class="n">Population</span>
<span class="c1"># help(Population) # Uncomment to see the docstring</span>
</pre></div>
</div>
@@ -590,8 +583,7 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 1 1 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create the population object</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create the population object</span>
<span class="n">example_pop</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="c1"># Set some parameters</span>
@@ -626,8 +618,7 @@ SINGLE_STAR_LIFETIME 10 28.4838
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">custom_logging_print_statement</span> <span class="o">=</span> <span class="s2">"""</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">custom_logging_print_statement</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">Printf("EXAMPLE_MASSLOSS </span><span class="si">%30.12e</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%d</span><span class="se">\\</span><span class="s2">n",</span>
<span class="s2"> //</span>
<span class="s2"> stardata->model.time, // 1</span>
@@ -679,8 +670,7 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 10 10 10 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">json</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -729,8 +719,7 @@ EXAMPLE_MASSLOSS 2.000000000000e-06 10 10 10 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">parse_function</span><span class="o">=</span><span class="n">object_parse_function</span><span class="p">,</span>
<span class="n">output_dir</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">,</span>
<span class="n">api_log_filename_prefix</span><span class="o">=</span><span class="n">TMP_DIR</span>
@@ -763,7 +752,7 @@ dict_keys(['time', 'mass', 'initial_mass', 'stellar_
</div>
</section>
<section id="Single-system-via-API-functionality">
-<h2>Single system via API functionality<a class="headerlink" href="#Single-system-via-API-functionality" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Single system via API functionality<a class="headerlink" href="#Single-system-via-API-functionality" title="Permalink to this heading">ïƒ</a></h2>
<p>It is possible to construct your own functionality to run a single system by directly calling the API function to run a system. Under the hood all the other functions and wrappers actually use this API.</p>
<p>There are fewer failsafes for this method, so this make sure the input is correct and binary_c knows all the arguments you pass in.</p>
<p>for more details on this API function see <code class="docutils literal notranslate"><span class="pre">notebook_api_functions</span></code></p>
@@ -772,8 +761,7 @@ dict_keys(['time', 'mass', 'initial_mass', 'stellar_
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># For a binary system we need to pass in these arguments</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># For a binary system we need to pass in these arguments</span>
<span class="n">M_1</span> <span class="o">=</span> <span class="mf">15.0</span> <span class="c1"># Msun</span>
<span class="n">M_2</span> <span class="o">=</span> <span class="mf">14.0</span> <span class="c1"># Msun</span>
<span class="n">separation</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># 0 = ignored, use period</span>
@@ -836,9 +824,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 e2425a1a0b7550d9d5294cf307d04f2b12185f88..e52372bd1a4f4dcf75268c8d5e275e82593ea993 100644
--- a/docs/build/html/examples/notebook_luminosity_function_binaries.html
+++ b/docs/build/html/examples/notebook_luminosity_function_binaries.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -306,7 +307,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -367,7 +368,7 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Example-use-case:-Zero-age-stellar-luminosity-function-in-binaries">
-<h1>Example use case: Zero-age stellar luminosity function in binaries<a class="headerlink" href="#Example-use-case:-Zero-age-stellar-luminosity-function-in-binaries" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example use case: Zero-age stellar luminosity function in binaries<a class="headerlink" href="#Example-use-case:-Zero-age-stellar-luminosity-function-in-binaries" title="Permalink to this heading">ïƒ</a></h1>
<p>In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of binary stars using binary_c.</p>
<p>Before you go through this notebook, you should look at notebook_luminosity_function.ipynb which is for the - conceptually more simple - single stars.</p>
<p>We start by loading in some standard Python modules and the binary_c module.</p>
@@ -375,8 +376,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">math</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.grid</span> <span class="kn">import</span> <span class="n">Population</span>
@@ -385,15 +385,14 @@ div.rendered_html tbody tr:hover {
</div>
</div>
<section id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this heading">ïƒ</a></h2>
<p>To set up and configure the population object we need to make a new instance of the <code class="docutils literal notranslate"><span class="pre">Population</span></code> object and configure it with the <code class="docutils literal notranslate"><span class="pre">.set()</span></code> function.</p>
<p>In our case, we only need to set the maximum evolution time to something short, because we care only about zero-age main sequence stars which have, by definition, age zero.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create population object</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create population object</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="c1"># If you want verbosity, set this before other things</span>
@@ -424,7 +423,7 @@ verbosity is 1
</div>
</section>
<section id="Adding-grid-variables">
-<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this heading">ïƒ</a></h2>
<p>The main purpose of the Population object is to handle the population synthesis side of running a set of stars. The main method to do this with binarycpython, as is the case with Perl binarygrid, is to use grid variables. These are loops over a predefined range of values, where a probability will be assigned to the systems based on the chosen probability distributions.</p>
<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (other notebooks cover these examples). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
<p>To add a grid variable to the population object we use <code class="docutils literal notranslate"><span class="pre">population.add_grid_variable</span></code></p>
@@ -432,8 +431,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># help(population.add_grid_variable)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># help(population.add_grid_variable)</span>
</pre></div>
</div>
</div>
@@ -442,8 +440,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
<span class="c1"># help(binarycpython.utils.distribution_functions)</span>
</pre></div>
</div>
@@ -459,8 +456,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Set resolution and mass range that we simulate</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Set resolution and mass range that we simulate</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="mi">40</span><span class="p">}</span> <span class="c1"># start with resolution = 10, and increase later if you want "more accurate" data</span>
<span class="n">massrange</span> <span class="o">=</span> <span class="p">(</span><span class="mf">0.07</span><span class="p">,</span> <span class="mf">100.0</span><span class="p">)</span> <span class="c1"># we work with stars of mass 0.07 to 100 Msun</span>
<span class="n">total_probability</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="c1"># theoretical integral of the mass probability density function over all masses</span>
@@ -475,8 +471,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Set up the binary grid in "cubic" M1 - M2=q*M1 - log10 period space</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Set up the binary grid in "cubic" M1 - M2=q*M1 - log10 period space</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
@@ -533,7 +528,7 @@ verbosity is 1
</div>
</section>
<section id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this heading">ïƒ</a></h2>
<p>By default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c) or we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality. For our current purposes, it
works perfectly well.</p>
<p>After configuring what will be printed, we need to make a function to parse the output. This can be done by setting the parse_function parameter in the population object (see also notebook <code class="docutils literal notranslate"><span class="pre">notebook_individual_systems.ipynb</span></code>).</p>
@@ -542,8 +537,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create custom logging statement</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create custom logging statement</span>
<span class="c1">#</span>
<span class="c1"># we check that the model number is zero, i.e. we're on the first timestep (stars are born on the ZAMS)</span>
<span class="c1"># we make sure that the stellar type is <= MAIN_SEQUENCE, i.e. the star is a main-sequence star</span>
@@ -605,8 +599,7 @@ works perfectly well.</p>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">C_logging_code</span><span class="o">=</span><span class="n">custom_logging_statement</span>
<span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<p>The parse function must now catch lines that start with “ZERO_AGE_MAIN_SEQUENCE_STAR†and process the associated data.</p>
@@ -614,8 +607,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># import the bin_data function so we can construct finite-resolution probability distributions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># import the bin_data function so we can construct finite-resolution probability distributions</span>
<span class="c1"># import the datalinedict to make a dictionary from each line of data from binary_c</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">bin_data</span><span class="p">,</span><span class="n">datalinedict</span>
<span class="kn">import</span> <span class="nn">re</span>
@@ -661,7 +653,7 @@ works perfectly well.</p>
</div>
</section>
<section id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">population.evolve()</span></code></p>
<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
@@ -669,8 +661,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># set number of threads</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># set number of threads</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="c1"># verbose output is not required</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
@@ -1084,8 +1075,7 @@ Done population run!
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -1101,8 +1091,7 @@ Done population run!
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># make a plot of the luminosity distribution using Seaborn and Pandas</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># make a plot of the luminosity distribution using Seaborn and Pandas</span>
<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">pad_output_distribution</span>
@@ -1171,8 +1160,7 @@ Done population run!
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -1198,9 +1186,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 9ea09290eb2d4e22bd7e6637bb2b3e1ecb82e7c9..7bcc07b38b52e76d3c0570570ccfa76d5f97949c 100644
--- a/docs/build/html/examples/notebook_luminosity_function_single.html
+++ b/docs/build/html/examples/notebook_luminosity_function_single.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -308,7 +309,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -369,15 +370,14 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Example-use-case:-Zero-age-stellar-luminosity-function">
-<h1>Example use case: Zero-age stellar luminosity function<a class="headerlink" href="#Example-use-case:-Zero-age-stellar-luminosity-function" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example use case: Zero-age stellar luminosity function<a class="headerlink" href="#Example-use-case:-Zero-age-stellar-luminosity-function" title="Permalink to this heading">ïƒ</a></h1>
<p>In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of single stars using binary_c.</p>
<p>We start by loading in some standard Python modules and the binary_c module.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">math</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
@@ -391,15 +391,14 @@ div.rendered_html tbody tr:hover {
</div>
</div>
<section id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this heading">ïƒ</a></h2>
<p>To set up and configure the population object we need to make a new instance of the <code class="docutils literal notranslate"><span class="pre">Population</span></code> object and configure it with the <code class="docutils literal notranslate"><span class="pre">.set()</span></code> function.</p>
<p>In our case, we only need to set the maximum evolution time to something short, because we care only about zero-age main sequence stars which have, by definition, age zero.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create population object</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create population object</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="c1"># If you want verbosity, set this before other things</span>
@@ -432,7 +431,7 @@ verbosity is 1
</div>
</section>
<section id="Adding-grid-variables">
-<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this heading">ïƒ</a></h2>
<p>The main purpose of the Population object is to handle the population synthesis side of running a set of stars. The main method to do this with binarycpython, as is the case with Perl binarygrid, is to use grid variables. These are loops over a predefined range of values, where a probability will be assigned to the systems based on the chosen probability distributions.</p>
<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (other notebooks cover these examples). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
<p>To add a grid variable to the population object we use <code class="docutils literal notranslate"><span class="pre">population.add_grid_variable</span></code></p>
@@ -440,8 +439,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># help(population.add_grid_variable)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># help(population.add_grid_variable)</span>
</pre></div>
</div>
</div>
@@ -450,8 +448,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
<span class="c1"># help(binarycpython.utils.distribution_functions)</span>
</pre></div>
</div>
@@ -467,8 +464,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Set resolution and mass range that we simulate</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Set resolution and mass range that we simulate</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="mi">40</span><span class="p">}</span> <span class="c1"># start with resolution = 10, and increase later if you want "more accurate" data</span>
<span class="n">massrange</span> <span class="o">=</span> <span class="p">(</span><span class="mf">0.07</span><span class="p">,</span> <span class="mf">100.0</span><span class="p">)</span> <span class="c1"># we work with stars of mass 0.07 to 100 Msun</span>
<span class="n">total_probability</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="c1"># theoretical integral of the mass probability density function over all masses</span>
@@ -483,8 +479,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Mass</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Mass</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">tmp_dir</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">,</span>
@@ -521,7 +516,7 @@ verbosity is 1
</div>
</section>
<section id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this heading">ïƒ</a></h2>
<p>By default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c) or we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality. For our current purposes, it
works perfectly well.</p>
<p>After configuring what will be printed, we need to make a function to parse the output. This can be done by setting the parse_function parameter in the population object (see also notebook <code class="docutils literal notranslate"><span class="pre">notebook_individual_systems.ipynb</span></code>).</p>
@@ -530,8 +525,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create custom logging statement</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create custom logging statement</span>
<span class="c1">#</span>
<span class="c1"># we check that the model number is zero, i.e. we're on the first timestep (stars are born on the ZAMS)</span>
<span class="c1"># we make sure that the stellar type is <= MAIN_SEQUENCE, i.e. the star is a main-sequence star</span>
@@ -558,8 +552,7 @@ works perfectly well.</p>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">C_logging_code</span><span class="o">=</span><span class="n">custom_logging_statement</span>
<span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<p>The parse function must now catch lines that start with “ZERO_AGE_MAIN_SEQUENCE_STAR†and process the associated data.</p>
@@ -567,8 +560,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># import the bin_data function so we can construct finite-resolution probability distributions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># import the bin_data function so we can construct finite-resolution probability distributions</span>
<span class="c1"># import the datalinedict to make a dictionary from each line of data from binary_c</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">bin_data</span><span class="p">,</span><span class="n">datalinedict</span>
@@ -609,7 +601,7 @@ works perfectly well.</p>
</div>
</section>
<section id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">population.evolve()</span></code></p>
<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
@@ -617,8 +609,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># set number of threads</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># set number of threads</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="c1"># verbose output is not required</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
@@ -639,8 +630,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -648,8 +638,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># make a plot of the luminosity distribution using Seaborn and Pandas</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># make a plot of the luminosity distribution using Seaborn and Pandas</span>
<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">pad_output_distribution</span>
@@ -682,14 +671,13 @@ works perfectly well.</p>
<p>Does this look like a reasonable stellar luminosity function to you? The implication is that the most likely stellar luminosity is 105.8 L☉! Clearly, this is not very realistic… let’s see what went wrong.</p>
</section>
<section id="ZAMS-Luminosity-distribution-with-the-initial-mass-function">
-<h2>ZAMS Luminosity distribution with the initial mass function<a class="headerlink" href="#ZAMS-Luminosity-distribution-with-the-initial-mass-function" title="Permalink to this headline">ïƒ</a></h2>
+<h2>ZAMS Luminosity distribution with the initial mass function<a class="headerlink" href="#ZAMS-Luminosity-distribution-with-the-initial-mass-function" title="Permalink to this heading">ïƒ</a></h2>
<p>In the previous example, all the stars in our grid had an equal weighting. This is very unlikely to be true in reality: indeed, we know that low mass stars are far more likely than high mass stars. So we now include an initial mass function as a three-part power law based on Kroupa (2001). Kroupa’s distribution is a three-part power law: we have a function that does this for us (it’s very common to use power laws in astrophysics).</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Update the probability distribution to use the three-part power law IMF</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Update the probability distribution to use the three-part power law IMF</span>
<span class="n">population</span><span class="o">.</span><span class="n">update_grid_variable</span><span class="p">(</span>
<span class="n">name</span><span class="o">=</span><span class="s2">"M_1"</span><span class="p">,</span>
<span class="n">probdist</span><span class="o">=</span><span class="s2">"three_part_powerlaw(M_1, 0.1, 0.5, 1.0, 150, -1.3, -2.3, -2.3)"</span><span class="p">,</span>
@@ -701,8 +689,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Clean and re-evolve the population</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Clean and re-evolve the population</span>
<span class="n">population</span><span class="o">.</span><span class="n">clean</span><span class="p">()</span>
<span class="n">analytics</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">evolve</span><span class="p">()</span>
@@ -715,8 +702,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># plot luminosity distribution</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># plot luminosity distribution</span>
<span class="n">ldist</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'luminosity distribution'</span><span class="p">]</span>
<span class="c1"># pad the distribution with zeros where data is missing</span>
@@ -739,15 +725,14 @@ works perfectly well.</p>
<p>We could simply increase the resolution to compensate, but this is very CPU intensive and a complete waste of time and resources. Instead, let’s try sampling the masses of the stars in a smarter way.</p>
</section>
<section id="A-better-sampled-grid">
-<h2>A better-sampled grid<a class="headerlink" href="#A-better-sampled-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>A better-sampled grid<a class="headerlink" href="#A-better-sampled-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>The IMF has many more low-mass stars than high-mass stars. So, instead of sampling M1 linearly, we can sample it in log space.</p>
<p>To do this we first rename the mass grid variable so that it is clear we are working in (natural) logarithmic phase space.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Rename the old variable (M_1) because we want it to be called lnM_1 now</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Rename the old variable (M_1) because we want it to be called lnM_1 now</span>
<span class="n">population</span><span class="o">.</span><span class="n">rename_grid_variable</span><span class="p">(</span><span class="s2">"M_1"</span><span class="p">,</span><span class="s2">"lnM_1"</span><span class="p">)</span>
</pre></div>
</div>
@@ -757,8 +742,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># update the sampling, note that the IMF is dprob/dM1, and the phase</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># update the sampling, note that the IMF is dprob/dM1, and the phase</span>
<span class="c1"># space is now sampled in lnM1, so we multiply by M_1 to</span>
<span class="c1"># because M * dprob/dM = dprob/dlnM</span>
<span class="n">population</span><span class="o">.</span><span class="n">update_grid_variable</span><span class="p">(</span>
@@ -777,8 +761,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Clean and re-evolve the population</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Clean and re-evolve the population</span>
<span class="n">population</span><span class="o">.</span><span class="n">clean</span><span class="p">()</span>
<span class="n">analytics</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">evolve</span><span class="p">()</span>
@@ -792,8 +775,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># plot luminosity distribution</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># plot luminosity distribution</span>
<span class="n">ldist</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'luminosity distribution'</span><span class="p">]</span>
<span class="c1"># pad the distribution with zeros where data is missing</span>
@@ -828,8 +810,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -855,9 +836,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 be30de97687b76f54d79ecde0ae259bdde6a004f..362517d9436b880b32415c2e777c220eb253f4d7 100644
--- a/docs/build/html/examples/notebook_massive_remnants.html
+++ b/docs/build/html/examples/notebook_massive_remnants.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -308,7 +309,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -369,15 +370,14 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Example-use-case:-Massive-star-luminosity">
-<h1>Example use case: Massive star luminosity<a class="headerlink" href="#Example-use-case:-Massive-star-luminosity" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example use case: Massive star luminosity<a class="headerlink" href="#Example-use-case:-Massive-star-luminosity" title="Permalink to this heading">ïƒ</a></h1>
<p>In this notebook we compute the luminosity function of the zero-age main-sequence by running a population of single stars using binary_c.</p>
<p>We start by loading in some standard Python modules and the binary_c module.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">math</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
@@ -391,15 +391,14 @@ div.rendered_html tbody tr:hover {
</div>
</div>
<section id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this heading">ïƒ</a></h2>
<p>To set up and configure the population object we need to make a new instance of the <code class="docutils literal notranslate"><span class="pre">Population</span></code> object and configure it with the <code class="docutils literal notranslate"><span class="pre">.set()</span></code> function.</p>
<p>In our case, we only need to set the maximum evolution time to something short, because we care only about zero-age main sequence stars which have, by definition, age zero.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create population object</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create population object</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="c1"># If you want verbosity, set this before other things</span>
@@ -432,7 +431,7 @@ verbosity is 1
</div>
</section>
<section id="Adding-grid-variables">
-<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this heading">ïƒ</a></h2>
<p>The main purpose of the Population object is to handle the population synthesis side of running a set of stars. The main method to do this with binarycpython, as is the case with Perl binarygrid, is to use grid variables. These are loops over a predefined range of values, where a probability will be assigned to the systems based on the chosen probability distributions.</p>
<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (other notebooks cover these examples). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
<p>To add a grid variable to the population object we use <code class="docutils literal notranslate"><span class="pre">population.add_grid_variable</span></code></p>
@@ -440,8 +439,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># help(population.add_grid_variable)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># help(population.add_grid_variable)</span>
</pre></div>
</div>
</div>
@@ -450,8 +448,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">binarycpython.utils.distribution_functions</span>
<span class="c1"># help(binarycpython.utils.distribution_functions)</span>
</pre></div>
</div>
@@ -467,8 +464,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Set resolution and mass range that we simulate</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Set resolution and mass range that we simulate</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="mi">40</span><span class="p">}</span> <span class="c1"># start with resolution = 10, and increase later if you want "more accurate" data</span>
<span class="n">massrange</span> <span class="o">=</span> <span class="p">(</span><span class="mf">0.07</span><span class="p">,</span> <span class="mf">100.0</span><span class="p">)</span> <span class="c1"># we work with stars of mass 0.07 to 100 Msun</span>
<span class="n">total_probability</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="c1"># theoretical integral of the mass probability density function over all masses</span>
@@ -483,8 +479,7 @@ verbosity is 1
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Mass</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Mass</span>
<span class="n">population</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">tmp_dir</span><span class="o">=</span><span class="n">TMP_DIR</span><span class="p">,</span>
@@ -504,7 +499,7 @@ verbosity is 1
</div>
</section>
<section id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this heading">ïƒ</a></h2>
<p>By default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c) or we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality. For our current purposes, it
works perfectly well.</p>
<p>After configuring what will be printed, we need to make a function to parse the output. This can be done by setting the parse_function parameter in the population object (see also notebook <code class="docutils literal notranslate"><span class="pre">notebook_individual_systems.ipynb</span></code>).</p>
@@ -513,8 +508,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create custom logging statement</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create custom logging statement</span>
<span class="c1">#</span>
<span class="c1"># we check that the model number is zero, i.e. we're on the first timestep (stars are born on the ZAMS)</span>
<span class="c1"># we make sure that the stellar type is <= MAIN_SEQUENCE, i.e. the star is a main-sequence star</span>
@@ -541,8 +535,7 @@ works perfectly well.</p>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="n">C_logging_code</span><span class="o">=</span><span class="n">custom_logging_statement</span>
<span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<p>The parse function must now catch lines that start with “ZERO_AGE_MAIN_SEQUENCE_STAR†and process the associated data.</p>
@@ -550,8 +543,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># import the bin_data function so we can construct finite-resolution probability distributions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># import the bin_data function so we can construct finite-resolution probability distributions</span>
<span class="c1"># import the datalinedict to make a dictionary from each line of data from binary_c</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">bin_data</span><span class="p">,</span><span class="n">datalinedict</span>
@@ -592,7 +584,7 @@ works perfectly well.</p>
</div>
</section>
<section id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">population.evolve()</span></code></p>
<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
@@ -600,8 +592,7 @@ works perfectly well.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># set number of threads</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># set number of threads</span>
<span class="n">population</span><span class="o">.</span><span class="n">set</span><span class="p">(</span>
<span class="c1"># verbose output is not required</span>
<span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
@@ -647,8 +638,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -664,8 +654,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># make a plot of the luminosity distribution using Seaborn and Pandas</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># make a plot of the luminosity distribution using Seaborn and Pandas</span>
<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">pad_output_distribution</span>
@@ -714,14 +703,13 @@ There were no errors found in this run.
<p>Does this look like a reasonable stellar luminosity function to you? The implication is that the most likely stellar luminosity is 105.8 L☉! Clearly, this is not very realistic… let’s see what went wrong.</p>
</section>
<section id="ZAMS-Luminosity-distribution-with-the-initial-mass-function">
-<h2>ZAMS Luminosity distribution with the initial mass function<a class="headerlink" href="#ZAMS-Luminosity-distribution-with-the-initial-mass-function" title="Permalink to this headline">ïƒ</a></h2>
+<h2>ZAMS Luminosity distribution with the initial mass function<a class="headerlink" href="#ZAMS-Luminosity-distribution-with-the-initial-mass-function" title="Permalink to this heading">ïƒ</a></h2>
<p>In the previous example, all the stars in our grid had an equal weighting. This is very unlikely to be true in reality: indeed, we know that low mass stars are far more likely than high mass stars. So we now include an initial mass function as a three-part power law based on Kroupa (2001). Kroupa’s distribution is a three-part power law: we have a function that does this for us (it’s very common to use power laws in astrophysics).</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Update the probability distribution to use the three-part power law IMF</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Update the probability distribution to use the three-part power law IMF</span>
<span class="n">population</span><span class="o">.</span><span class="n">update_grid_variable</span><span class="p">(</span>
<span class="n">name</span><span class="o">=</span><span class="s2">"M_1"</span><span class="p">,</span>
<span class="n">probdist</span><span class="o">=</span><span class="s2">"three_part_powerlaw(M_1, 0.1, 0.5, 1.0, 150, -1.3, -2.3, -2.3)"</span><span class="p">,</span>
@@ -733,8 +721,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Clean and re-evolve the population</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Clean and re-evolve the population</span>
<span class="n">population</span><span class="o">.</span><span class="n">clean</span><span class="p">()</span>
<span class="n">analytics</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">evolve</span><span class="p">()</span>
@@ -772,8 +759,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[14]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># plot luminosity distribution</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># plot luminosity distribution</span>
<span class="n">ldist</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'luminosity distribution'</span><span class="p">]</span>
<span class="c1"># pad the distribution with zeros where data is missing</span>
@@ -812,15 +798,14 @@ There were no errors found in this run.
<p>We could simply increase the resolution to compensate, but this is very CPU intensive and a complete waste of time and resources. Instead, let’s try sampling the masses of the stars in a smarter way.</p>
</section>
<section id="A-better-sampled-grid">
-<h2>A better-sampled grid<a class="headerlink" href="#A-better-sampled-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>A better-sampled grid<a class="headerlink" href="#A-better-sampled-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>The IMF has many more low-mass stars than high-mass stars. So, instead of sampling M1 linearly, we can sample it in log space.</p>
<p>To do this we first rename the mass grid variable so that it is clear we are working in (natural) logarithmic phase space.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[15]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Rename the old variable (M_1) because we want it to be called lnM_1 now</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Rename the old variable (M_1) because we want it to be called lnM_1 now</span>
<span class="n">population</span><span class="o">.</span><span class="n">rename_grid_variable</span><span class="p">(</span><span class="s2">"M_1"</span><span class="p">,</span><span class="s2">"lnM_1"</span><span class="p">)</span>
</pre></div>
</div>
@@ -830,8 +815,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[16]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># update the sampling, note that the IMF is dprob/dM1, and the phase</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># update the sampling, note that the IMF is dprob/dM1, and the phase</span>
<span class="c1"># space is now sampled in lnM1, so we multiply by M_1 to</span>
<span class="c1"># because M * dprob/dM = dprob/dlnM</span>
<span class="n">population</span><span class="o">.</span><span class="n">update_grid_variable</span><span class="p">(</span>
@@ -850,8 +834,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[17]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Clean and re-evolve the population</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Clean and re-evolve the population</span>
<span class="n">population</span><span class="o">.</span><span class="n">clean</span><span class="p">()</span>
<span class="n">analytics</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">evolve</span><span class="p">()</span>
@@ -890,8 +873,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[18]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># plot luminosity distribution</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># plot luminosity distribution</span>
<span class="n">ldist</span> <span class="o">=</span> <span class="n">population</span><span class="o">.</span><span class="n">grid_results</span><span class="p">[</span><span class="s1">'luminosity distribution'</span><span class="p">]</span>
<span class="c1"># pad the distribution with zeros where data is missing</span>
@@ -933,8 +915,7 @@ There were no errors found in this run.
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -960,9 +941,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 edb81b7a631f2091f161abf11123bb28a4ddcb3f..e80d93be64f9e7b30ed1f429334f63c625fb4673 100644
--- a/docs/build/html/examples/notebook_population.html
+++ b/docs/build/html/examples/notebook_population.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -312,7 +313,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -373,7 +374,7 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Tutorial:-Running-populations-with-binary_c-python">
-<h1>Tutorial: Running populations with binary_c-python<a class="headerlink" href="#Tutorial:-Running-populations-with-binary_c-python" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Tutorial: Running populations with binary_c-python<a class="headerlink" href="#Tutorial:-Running-populations-with-binary_c-python" title="Permalink to this heading">ïƒ</a></h1>
<p>This notebook will show you how to evolve a population of stars</p>
<p>Much of the code in the binarycpython package is written to evolve a population of stars through the Population object, rather than running a single system. Let’s go through the functionality of this object step by step and set up some example populations.</p>
<p>At the bottom of this notebook there are some complete example scripts</p>
@@ -381,8 +382,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.custom_logging_functions</span> <span class="kn">import</span> <span class="n">temp_dir</span>
<span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">Population</span>
@@ -394,7 +394,7 @@ div.rendered_html tbody tr:hover {
</div>
</div>
<section id="Setting-up-the-Population-object">
-<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting up the Population object<a class="headerlink" href="#Setting-up-the-Population-object" title="Permalink to this heading">ïƒ</a></h2>
<p>To set up and configure the population object we need to make an object instance of the <code class="docutils literal notranslate"><span class="pre">Population</span></code> object, and add configuration via the <code class="docutils literal notranslate"><span class="pre">.set()</span></code> function.</p>
<p>There are three categories of options that the Population object can set: - BSE options: these options will be used for the binary_c calls, and are recognized by comparing the arguments to a known list of available arguments of binary_c. To see which options are available, see section <code class="docutils literal notranslate"><span class="pre">`binary_c</span> <span class="pre">parameters</span></code> in the documentation <<a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/binary_c_parameters.html">https://ri0005.pages.surrey.ac.uk/binary_c-python/binary_c_parameters.html</a>>`__. You can access these through <code class="docutils literal notranslate"><span class="pre">population.bse_options['<bse</span> <span class="pre">option</span> <span class="pre">name>']</span></code> after you
have set them.</p>
@@ -406,8 +406,7 @@ have set them.</p>
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create population object</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create population object</span>
<span class="n">example_pop</span> <span class="o">=</span> <span class="n">Population</span><span class="p">()</span>
<span class="c1"># If you want verbosity, set this before other things</span>
@@ -470,8 +469,7 @@ example_pop.dat
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">example_pop</span><span class="o">.</span><span class="n">export_all_info</span><span class="p">()</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">example_pop</span><span class="o">.</span><span class="n">export_all_info</span><span class="p">()</span>
</pre></div>
</div>
</div>
@@ -498,7 +496,7 @@ ok ret
</div>
</section>
<section id="Adding-grid-variables">
-<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Adding grid variables<a class="headerlink" href="#Adding-grid-variables" title="Permalink to this heading">ïƒ</a></h2>
<p>The main purpose of the Population object is to handle the population synthesis side of running a set of stars. The main method to do this with binarycpython, as is the case with Perl binarygrid, is to use grid variables. These are loops over a predefined range of values, where a probability will be assigned to the systems based on the chosen probability distributions.</p>
<p>Usually we use either 1 mass grid variable, or a trio of mass, mass ratio and period (See below for full examples of all of these). We can, however, also add grid sampling for e.g. eccentricity, metallicity or other parameters.</p>
<p>In some cases it could be easier to set up a for loop that sets that parameter and calls the evolve function several times, e.g. when you want to vary a prescription (usually a discrete, unweighted parameter)</p>
@@ -508,8 +506,7 @@ ok ret
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">help</span><span class="p">(</span><span class="n">example_pop</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">help</span><span class="p">(</span><span class="n">example_pop</span><span class="o">.</span><span class="n">add_grid_variable</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -628,8 +625,7 @@ add_grid_variable(name: str, parameter_name: str, longname: str, valuerange: Uni
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># import binarycpython.utils.distribution_functions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># import binarycpython.utils.distribution_functions</span>
<span class="c1"># help(binarycpython.utils.distribution_functions)</span>
</pre></div>
</div>
@@ -639,8 +635,7 @@ add_grid_variable(name: str, parameter_name: str, longname: str, valuerange: Uni
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Add grid variables</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Add grid variables</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"M_1"</span><span class="p">:</span> <span class="mi">20</span><span class="p">}</span>
<span class="c1"># Mass</span>
@@ -683,13 +678,12 @@ add_grid_variable(name: str, parameter_name: str, longname: str, valuerange: Uni
<span class="c1"># parameter_name="orbital_period",</span>
<span class="c1"># dphasevol="dlog10per",</span>
<span class="c1"># )</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
</section>
<section id="Setting-logging-and-handling-the-output">
-<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Setting logging and handling the output<a class="headerlink" href="#Setting-logging-and-handling-the-output" title="Permalink to this heading">ïƒ</a></h2>
<p>On default, binary_c will not output anything (except for ‘SINGLE STAR LIFETIME’). It is up to us to determine what will be printed. We can either do that by hardcoding the print statements into <code class="docutils literal notranslate"><span class="pre">binary_c</span></code> (see documentation binary_c). Or, we can use the custom logging functionality of binarycpython (see notebook <code class="docutils literal notranslate"><span class="pre">notebook_custom_logging.ipynb</span></code>), which is faster to set up and requires no recompilation of binary_c, but is somewhat more limited in its functionality.</p>
<p>After configuring what will be printed, we need to make a function to parse the output. This can be done by setting the parse_function parameter in the population object (see also notebook <code class="docutils literal notranslate"><span class="pre">notebook_individual_systems.ipynb</span></code>).</p>
<p>In the code below we will set up both the custom logging, and a parse function to handle that output</p>
@@ -697,8 +691,7 @@ add_grid_variable(name: str, parameter_name: str, longname: str, valuerange: Uni
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># Create custom logging statement: in this case we will log when the star turns into a compact object, and then terminate the evolution.</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create custom logging statement: in this case we will log when the star turns into a compact object, and then terminate the evolution.</span>
<span class="n">custom_logging_code</span> <span class="o">=</span> <span class="s2">"""</span>
<span class="s2">if(stardata->star[0].stellar_type >= 13)</span>
<span class="s2">{</span>
@@ -754,8 +747,7 @@ if(stardata->star[0].stellar_type >= 13)
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Example parse function</span>
<span class="sd"> """</span>
@@ -811,7 +803,7 @@ adding: parse_function=<function parse_function at 0x7f2b6ca163a0> to grid
</div>
</section>
<section id="Evolving-the-grid">
-<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Evolving the grid<a class="headerlink" href="#Evolving-the-grid" title="Permalink to this heading">ïƒ</a></h2>
<p>Now that we configured all the main parts of the population object, we can actually run the population! Doing this is straightforward: <code class="docutils literal notranslate"><span class="pre">example_pop.evolve()</span></code></p>
<p>This will start up the processing of all the systems. We can control how many cores are used by settings <code class="docutils literal notranslate"><span class="pre">num_cores</span></code>. By setting the <code class="docutils literal notranslate"><span class="pre">verbosity</span></code> of the population object to a higher value we can get a lot of verbose information about the run, but for now we will set it to 0.</p>
<p>There are many grid_options that can lead to different behaviour of the evolution of the grid. Please do have a look at those: <a class="reference external" href="https://ri0005.pages.surrey.ac.uk/binary_c-python/grid_options_descriptions.html">grid options docs</a>, and try</p>
@@ -819,8 +811,7 @@ adding: parse_function=<function parse_function at 0x7f2b6ca163a0> to grid
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># change verbosity</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># change verbosity</span>
<span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">verbosity</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="c1">## Executing a population</span>
@@ -877,8 +868,7 @@ Added analytics to metadata
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">analytics</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -892,14 +882,13 @@ Added analytics to metadata
</div>
</section>
<section id="Noteworthy-functionality">
-<h2>Noteworthy functionality<a class="headerlink" href="#Noteworthy-functionality" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Noteworthy functionality<a class="headerlink" href="#Noteworthy-functionality" title="Permalink to this heading">ïƒ</a></h2>
<p>Some extra features that are available from via the population object are: - write_binary_c_calls_to_file: Function to write the calls that would be passed to binary_c to a file</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">help</span><span class="p">(</span><span class="n">example_pop</span><span class="o">.</span><span class="n">write_binary_c_calls_to_file</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">help</span><span class="p">(</span><span class="n">example_pop</span><span class="o">.</span><span class="n">write_binary_c_calls_to_file</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -935,8 +924,7 @@ write_binary_c_calls_to_file(output_dir: Optional[str] = None, output_filename:
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">verbosity</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">example_pop</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">verbosity</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">calls_filename</span> <span class="o">=</span> <span class="n">example_pop</span><span class="o">.</span><span class="n">write_binary_c_calls_to_file</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="n">calls_filename</span><span class="p">)</span>
@@ -969,16 +957,15 @@ binary_c M_1 4.430329401616038 eccentricity 0.02 max_evolution_time 15000 orbita
</div>
</section>
<section id="Full-examples-of-population-scripts">
-<h2>Full examples of population scripts<a class="headerlink" href="#Full-examples-of-population-scripts" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Full examples of population scripts<a class="headerlink" href="#Full-examples-of-population-scripts" title="Permalink to this heading">ïƒ</a></h2>
<section id="Single-star-population">
-<h3>Single star population<a class="headerlink" href="#Single-star-population" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Single star population<a class="headerlink" href="#Single-star-population" title="Permalink to this heading">ïƒ</a></h3>
<p>Below is a full setup for a population of single stars</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Example parsing function</span>
<span class="sd"> """</span>
@@ -1166,14 +1153,13 @@ time mass zams_mass probability radius stellar_type
</div>
</section>
<section id="Binary-star-population">
-<h3>Binary star population<a class="headerlink" href="#Binary-star-population" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Binary star population<a class="headerlink" href="#Binary-star-population" title="Permalink to this heading">ïƒ</a></h3>
<p>We can also set up a population that samples binary systems, by adding extra grid variables. Below is an example of a full script that runs a binary population and registers when a double compact object is formed. The logging is rather compact and should be expanded to be more useful. Also note that we run very little systems in the following example, as its just intended to show how the code works.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[14]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">parse_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Example parsing function</span>
<span class="sd"> """</span>
@@ -1418,9 +1404,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 756a185e7bec06ad1a67f4df1bbbc1fc7ca9fee1..8c10e67ab4a11dc61b0343340cdf7aa1d7501965 100644
--- a/docs/build/html/examples/notebook_solar_system.html
+++ b/docs/build/html/examples/notebook_solar_system.html
@@ -14,10 +14,11 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -300,7 +301,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -361,15 +362,14 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Example-use-case:-Solar-system-using-the-API-functionality">
-<h1>Example use case: Solar system using the API functionality<a class="headerlink" href="#Example-use-case:-Solar-system-using-the-API-functionality" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Example use case: Solar system using the API functionality<a class="headerlink" href="#Example-use-case:-Solar-system-using-the-API-functionality" title="Permalink to this heading">ïƒ</a></h1>
<p>We use the API interface to construct a model of the Solar system.</p>
<p>First we must construct the argument string that we pass to binary_c</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">os</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">temp_dir</span>
<span class="kn">from</span> <span class="nn">binarycpython</span> <span class="kn">import</span> <span class="n">_binary_c_bindings</span>
@@ -414,8 +414,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">re</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">re</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">math</span>
<span class="c1">#pd.set_option("display.max_rows", None, "display.max_columns", None)</span>
@@ -460,8 +459,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">dataframes</span> <span class="o">=</span> <span class="p">{}</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">dataframes</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">planet</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
<span class="n">dataframes</span><span class="p">[</span><span class="n">planet</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">planet</span><span class="p">],</span>
<span class="n">dtype</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> <span class="c1"># required! argh!</span>
@@ -485,9 +483,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-
-<span></span><span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><br/><span></span><span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="c1"># set up seaborn for use in the notebook</span>
@@ -542,9 +538,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-
-<span></span><span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><br/><span></span><span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="c1"># set up seaborn for use in the notebook</span>
@@ -614,9 +608,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 bd995749539161b7270d7de86c753db7d9a615e2..5cc325ecf10eb05a95afb325cc6bf64deeba798d 100644
--- a/docs/build/html/examples/old/basic_example.html
+++ b/docs/build/html/examples/old/basic_example.html
@@ -14,10 +14,11 @@
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
+ <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
@@ -283,7 +284,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -344,14 +345,13 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Basic-example">
-<h1>Basic example<a class="headerlink" href="#Basic-example" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Basic example<a class="headerlink" href="#Basic-example" title="Permalink to this heading">ïƒ</a></h1>
<p>Running a single system</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">binarycpython</span>
@@ -365,8 +365,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="c1"># You can decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals.</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># You can decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals.</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="s1">'Printf("MY_STELLAR_DATA time=</span><span class="si">%g</span><span class="s1"> radius=</span><span class="si">%g</span><span class="se">\\</span><span class="s1">n",stardata->model.time,stardata->star[0].radius)'</span>
<span class="c1"># Generate entire shared lib code around logging lines</span>
@@ -405,8 +404,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -430,8 +428,7 @@ div.rendered_html tbody tr:hover {
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -453,9 +450,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 55957aa9869a49fd7be45626c2fe8f9912c3c1ed..e4f7632ee64494917c0b9d470ad3b77dfbd554db 100644
--- a/docs/build/html/examples/old/workshop_example_notebook.html
+++ b/docs/build/html/examples/old/workshop_example_notebook.html
@@ -14,10 +14,11 @@
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
+ <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
- <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
+ <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<script src="../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
@@ -283,7 +284,7 @@ div.nboutput.container div.output_area > div[class^='highlight']{
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt a.copybtn {
+.prompt .copybtn {
display: none;
}
@@ -344,29 +345,27 @@ div.rendered_html tbody tr:hover {
}
</style>
<section id="Binary_c-and-python-example-notebook">
-<h1>Binary_c and python example notebook<a class="headerlink" href="#Binary_c-and-python-example-notebook" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Binary_c and python example notebook<a class="headerlink" href="#Binary_c-and-python-example-notebook" title="Permalink to this heading">ïƒ</a></h1>
<p>The following notebook servers as an example of how the binary_c python wrapper works and how it could be used.</p>
<p>By: David Hendriks 30 nov 2019</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[16]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">binarycpython</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">binarycpython</span>
<span class="kn">import</span> <span class="nn">binary_c_python_api</span>
</pre></div>
</div>
</div>
<section id="Core-api-wrapper-functions:">
-<h2>Core api wrapper functions:<a class="headerlink" href="#Core-api-wrapper-functions:" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Core api wrapper functions:<a class="headerlink" href="#Core-api-wrapper-functions:" title="Permalink to this heading">ïƒ</a></h2>
<section id="run_binary()">
-<h3>run_binary()<a class="headerlink" href="#run_binary()" title="Permalink to this headline">ïƒ</a></h3>
+<h3>run_binary()<a class="headerlink" href="#run_binary()" title="Permalink to this heading">ïƒ</a></h3>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[17]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="n">m1</span> <span class="o">=</span> <span class="mf">15.0</span> <span class="c1"># Msun</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">m1</span> <span class="o">=</span> <span class="mf">15.0</span> <span class="c1"># Msun</span>
<span class="n">m2</span> <span class="o">=</span> <span class="mf">14.0</span> <span class="c1"># Msun</span>
<span class="n">separation</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># 0 = ignored, use period</span>
<span class="n">orbital_period</span> <span class="o">=</span> <span class="mf">4530.0</span> <span class="c1"># days</span>
@@ -415,13 +414,12 @@ example_header_2 2e-07 15 14 1 1 3540.3 0
</div>
</section>
<section id="run_binary_with_log">
-<h3>run_binary_with_log<a class="headerlink" href="#run_binary_with_log" title="Permalink to this headline">ïƒ</a></h3>
+<h3>run_binary_with_log<a class="headerlink" href="#run_binary_with_log" title="Permalink to this heading">ïƒ</a></h3>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[18]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">tempfile</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">tempfile</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="n">m1</span> <span class="o">=</span> <span class="mf">15.0</span> <span class="c1"># Msun</span>
@@ -490,13 +488,12 @@ Probability : 1
</div>
</section>
<section id="run-binary-with-custom-logging-line">
-<h3>run binary with custom logging line<a class="headerlink" href="#run-binary-with-custom-logging-line" title="Permalink to this headline">ïƒ</a></h3>
+<h3>run binary with custom logging line<a class="headerlink" href="#run-binary-with-custom-logging-line" title="Permalink to this heading">ïƒ</a></h3>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[19]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils</span> <span class="kn">import</span> <span class="n">custom_logging_functions</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython.utils</span> <span class="kn">import</span> <span class="n">custom_logging_functions</span>
<span class="c1"># generate logging lines. Here you can choose whatever you want to have logged, and with what header</span>
<span class="c1"># this generates working print statements</span>
<span class="n">logging_line</span> <span class="o">=</span> <span class="n">custom_logging_functions</span><span class="o">.</span><span class="n">autogen_C_logging_code</span><span class="p">(</span>
@@ -567,10 +564,10 @@ MY_STELLAR_DATA time=4e-07 mass=15
</section>
</section>
<section id="Using-utils-functions">
-<h2>Using utils functions<a class="headerlink" href="#Using-utils-functions" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Using utils functions<a class="headerlink" href="#Using-utils-functions" title="Permalink to this heading">ïƒ</a></h2>
<p>In the utils.functions there are some functions that make it easier to interact with the core api functions.</p>
<section id="run_system()">
-<h3>run_system()<a class="headerlink" href="#run_system()" title="Permalink to this headline">ïƒ</a></h3>
+<h3>run_system()<a class="headerlink" href="#run_system()" title="Permalink to this heading">ïƒ</a></h3>
<p>This function serves as an example on the function run_system and parse_output. There is more functionality with this method and several tasks are done behind the scene.</p>
<p>Requires pandas, numpy to run.</p>
<p>run_system: mostly just makes passing arguments to the function easier. It also loads all the necessary defaults in the background parse_output: Takes the raw output of binary_c and selects those lines that start with the given header. Note, if you dont use the custom_logging functionality binary_c should be configured to have output that starts with that given header</p>
@@ -579,8 +576,7 @@ MY_STELLAR_DATA time=4e-07 mass=15
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[20]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">run_system</span><span class="p">,</span> <span class="n">parse_output</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.functions</span> <span class="kn">import</span> <span class="n">run_system</span><span class="p">,</span> <span class="n">parse_output</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -609,8 +605,7 @@ MY_STELLAR_DATA time=4e-07 mass=15
<span class="n">df2</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">result_example_header_2</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>
<span class="n">df2</span><span class="o">.</span><span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s1">'time'</span><span class="p">,</span> <span class="s1">'mass_1'</span><span class="p">,</span> <span class="s1">'mass_2'</span><span class="p">,</span> <span class="s1">'st1'</span><span class="p">,</span> <span class="s1">'st2'</span><span class="p">,</span> <span class="s1">'sep'</span><span class="p">,</span> <span class="s1">'ecc'</span><span class="p">]</span>
<span class="nb">print</span><span class="p">(</span><span class="n">df2</span><span class="p">)</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
@@ -663,14 +658,13 @@ example_header_2 2e-07 10 20 1 1 2.81762e+08 0
</div>
</section>
<section id="run_system()-and-custom-logging">
-<h3>run_system() and custom logging<a class="headerlink" href="#run_system()-and-custom-logging" title="Permalink to this headline">ïƒ</a></h3>
+<h3>run_system() and custom logging<a class="headerlink" href="#run_system()-and-custom-logging" title="Permalink to this heading">ïƒ</a></h3>
<p>Function that will use a automatically generated piece of logging code. Compile it, load it into memory and run a binary system. See run_system on how several things are done in the background here.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[21]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">binarycpython.utils.custom_logging_functions</span> <span class="kn">import</span> <span class="p">(</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></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">autogen_C_logging_code</span><span class="p">,</span>
<span class="n">binary_c_log_code</span><span class="p">,</span>
<span class="p">)</span>
@@ -736,14 +730,13 @@ example_header_2 2e-07 10 20 1 1 2.81762e+08 0
</section>
</section>
<section id="Other-example">
-<h2>Other example<a class="headerlink" href="#Other-example" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Other example<a class="headerlink" href="#Other-example" title="Permalink to this heading">ïƒ</a></h2>
<p>Checking how much mass stars lose on the main sequence.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="k">def</span> <span class="nf">run_and_calc_mass</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">run_and_calc_mass</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"> Function to run a given system and look at the mass lost in the main sequence of the star</span>
<span class="sd"> """</span>
@@ -780,16 +773,14 @@ example_header_2 2e-07 10 20 1 1 2.81762e+08 0
<span class="c1"># Return the mass fraction (wrt initial mass)</span>
<span class="k">return</span> <span class="n">fraction</span>
-
-</pre></div>
+<br/></pre></div>
</div>
</div>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">time</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">time</span>
<span class="n">metallicity_002</span> <span class="o">=</span> <span class="mf">0.02</span>
<span class="n">metallicity_001</span> <span class="o">=</span> <span class="mf">0.01</span>
@@ -838,8 +829,7 @@ Took 14.214274644851685s
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[22]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">nrows</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">ncols</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">12</span><span class="p">,</span><span class="mi">8</span><span class="p">))</span>
@@ -868,8 +858,7 @@ Took 14.214274644851685s
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[ ]:
</pre></div>
</div>
-<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
-<span></span>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
@@ -892,9 +881,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 793a0acc5e8774aa2131a343c17bf32fa7d981f2..a0f437cbb4d64db68a2f75b665c4b6570b96cc27 100644
--- a/docs/build/html/functions.html
+++ b/docs/build/html/functions.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.functions">
-<span id="functions-module"></span><h1>functions module<a class="headerlink" href="#module-binarycpython.utils.functions" title="Permalink to this headline">ïƒ</a></h1>
+<span id="functions-module"></span><h1>functions module<a class="headerlink" href="#module-binarycpython.utils.functions" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing most of the utility functions for the binarycpython package</p>
<p>Functions here are mostly functions used in other classes/functions, or
useful functions for the user</p>
@@ -732,9 +733,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 600fdd60acc2ee97d11b50daad980937e3721b80..4cc0a541e17c7a54880169355b66677ab008c1b8 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -13,6 +13,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -1087,9 +1088,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 0a83dfaa82f6d85a004ae7d2acc25117698e93e4..3b7d545b88c528df328b3be670a5cd04ae3b865c 100644
--- a/docs/build/html/grid.html
+++ b/docs/build/html/grid.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.grid">
-<span id="population-class-module"></span><h1>Population class module<a class="headerlink" href="#module-binarycpython.utils.grid" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-module"></span><h1>Population class module<a class="headerlink" href="#module-binarycpython.utils.grid" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the Population grid class object.</p>
<p>Here all the functionality of a Population object is defined.</p>
<p>TODO: the save_snapshots and save_snapshot, are they actually distinct?</p>
@@ -146,10 +147,11 @@
</ul>
</dd>
</dl>
+<p>TODO: Some of the methods that we have defined in the (mixin) class are designed to be used as a portal to information (return_binary_c_version_info for example.) THe current design is that they are all instance methods, but that is not always necessary. We can decorate them with @staticmethod, or @classmethod to make it easier to use them (<a class="reference external" href="https://realpython.com/instance-class-and-static-methods-demystified/">https://realpython.com/instance-class-and-static-methods-demystified/</a>)</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.grid.Population">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.grid.</span></span><span class="sig-name descname"><span class="pre">Population</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/binarycpython/utils/grid.html#Population"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.grid.Population" title="Permalink to this definition">ïƒ</a></dt>
-<dd><p>Bases: <a class="reference internal" href="population_extensions/analytics.html#binarycpython.utils.population_extensions.analytics.analytics" title="binarycpython.utils.population_extensions.analytics.analytics"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.analytics.analytics</span></code></a>, <a class="reference internal" href="population_extensions/cache.html#binarycpython.utils.population_extensions.cache.cache" title="binarycpython.utils.population_extensions.cache.cache"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.cache.cache</span></code></a>, <a class="reference internal" href="population_extensions/dataIO.html#binarycpython.utils.population_extensions.dataIO.dataIO" title="binarycpython.utils.population_extensions.dataIO.dataIO"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.dataIO.dataIO</span></code></a>, <a class="reference internal" href="population_extensions/distribution_functions.html#binarycpython.utils.population_extensions.distribution_functions.distribution_functions" title="binarycpython.utils.population_extensions.distribution_functions.distribution_functions"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.distribution_functions.distribution_functions</span></code></a>, <a class="reference internal" href="population_extensions/grid_logging.html#binarycpython.utils.population_extensions.grid_logging.grid_logging" title="binarycpython.utils.population_extensions.grid_logging.grid_logging"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.grid_logging.grid_logging</span></code></a>, <a class="reference internal" href="population_extensions/grid_options_defaults.html#binarycpython.utils.population_extensions.grid_options_defaults.grid_options_defaults" title="binarycpython.utils.population_extensions.grid_options_defaults.grid_options_defaults"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.grid_options_defaults.grid_options_defaults</span></code></a>, <a class="reference internal" href="population_extensions/gridcode.html#binarycpython.utils.population_extensions.gridcode.gridcode" title="binarycpython.utils.population_extensions.gridcode.gridcode"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.gridcode.gridcode</span></code></a>, <a class="reference internal" href="population_extensions/HPC.html#binarycpython.utils.population_extensions.HPC.HPC" title="binarycpython.utils.population_extensions.HPC.HPC"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.HPC.HPC</span></code></a>, <a class="reference internal" href="population_extensions/metadata.html#binarycpython.utils.population_extensions.metadata.metadata" title="binarycpython.utils.population_extensions.metadata.metadata"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.metadata.metadata</span></code></a>, <a class="reference internal" href="population_extensions/Moe_di_Stefano_2017.html#binarycpython.utils.population_extensions.Moe_di_Stefano_2017.Moe_di_Stefano_2017" title="binarycpython.utils.population_extensions.Moe_di_Stefano_2017.Moe_di_Stefano_2017"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.Moe_di_Stefano_2017.Moe_di_Stefano_2017</span></code></a>, <a class="reference internal" href="population_extensions/spacing_functions.html#binarycpython.utils.population_extensions.spacing_functions.spacing_functions" title="binarycpython.utils.population_extensions.spacing_functions.spacing_functions"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.spacing_functions.spacing_functions</span></code></a>, <a class="reference internal" href="population_extensions/version_info.html#binarycpython.utils.population_extensions.version_info.version_info" title="binarycpython.utils.population_extensions.version_info.version_info"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.version_info.version_info</span></code></a></p>
+<dd><p>Bases: <a class="reference internal" href="population_extensions/analytics.html#binarycpython.utils.population_extensions.analytics.analytics" title="binarycpython.utils.population_extensions.analytics.analytics"><code class="xref py py-class docutils literal notranslate"><span class="pre">analytics</span></code></a>, <a class="reference internal" href="population_extensions/cache.html#binarycpython.utils.population_extensions.cache.cache" title="binarycpython.utils.population_extensions.cache.cache"><code class="xref py py-class docutils literal notranslate"><span class="pre">cache</span></code></a>, <a class="reference internal" href="population_extensions/dataIO.html#binarycpython.utils.population_extensions.dataIO.dataIO" title="binarycpython.utils.population_extensions.dataIO.dataIO"><code class="xref py py-class docutils literal notranslate"><span class="pre">dataIO</span></code></a>, <a class="reference internal" href="population_extensions/distribution_functions.html#binarycpython.utils.population_extensions.distribution_functions.distribution_functions" title="binarycpython.utils.population_extensions.distribution_functions.distribution_functions"><code class="xref py py-class docutils literal notranslate"><span class="pre">distribution_functions</span></code></a>, <a class="reference internal" href="population_extensions/grid_logging.html#binarycpython.utils.population_extensions.grid_logging.grid_logging" title="binarycpython.utils.population_extensions.grid_logging.grid_logging"><code class="xref py py-class docutils literal notranslate"><span class="pre">grid_logging</span></code></a>, <a class="reference internal" href="population_extensions/grid_options_defaults.html#binarycpython.utils.population_extensions.grid_options_defaults.grid_options_defaults" title="binarycpython.utils.population_extensions.grid_options_defaults.grid_options_defaults"><code class="xref py py-class docutils literal notranslate"><span class="pre">grid_options_defaults</span></code></a>, <a class="reference internal" href="population_extensions/gridcode.html#binarycpython.utils.population_extensions.gridcode.gridcode" title="binarycpython.utils.population_extensions.gridcode.gridcode"><code class="xref py py-class docutils literal notranslate"><span class="pre">gridcode</span></code></a>, <a class="reference internal" href="population_extensions/HPC.html#binarycpython.utils.population_extensions.HPC.HPC" title="binarycpython.utils.population_extensions.HPC.HPC"><code class="xref py py-class docutils literal notranslate"><span class="pre">HPC</span></code></a>, <a class="reference internal" href="population_extensions/metadata.html#binarycpython.utils.population_extensions.metadata.metadata" title="binarycpython.utils.population_extensions.metadata.metadata"><code class="xref py py-class docutils literal notranslate"><span class="pre">metadata</span></code></a>, <a class="reference internal" href="population_extensions/Moe_di_Stefano_2017.html#binarycpython.utils.population_extensions.Moe_di_Stefano_2017.Moe_di_Stefano_2017" title="binarycpython.utils.population_extensions.Moe_di_Stefano_2017.Moe_di_Stefano_2017"><code class="xref py py-class docutils literal notranslate"><span class="pre">Moe_di_Stefano_2017</span></code></a>, <a class="reference internal" href="population_extensions/spacing_functions.html#binarycpython.utils.population_extensions.spacing_functions.spacing_functions" title="binarycpython.utils.population_extensions.spacing_functions.spacing_functions"><code class="xref py py-class docutils literal notranslate"><span class="pre">spacing_functions</span></code></a>, <a class="reference internal" href="population_extensions/version_info.html#binarycpython.utils.population_extensions.version_info.version_info" title="binarycpython.utils.population_extensions.version_info.version_info"><code class="xref py py-class docutils literal notranslate"><span class="pre">version_info</span></code></a></p>
<p>Population Object. Contains all the necessary functions to set up, run and process a
population of systems</p>
<dl class="py method">
@@ -376,9 +378,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 3278ba4b77e928855ef2ddcbc7e366dd9c904130..58e959378e26e8cb1bceb4ac4cb6f13b2b4cc05e 100644
--- a/docs/build/html/grid_options_descriptions.html
+++ b/docs/build/html/grid_options_descriptions.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -102,11 +103,11 @@
}
</style>
<section id="population-grid-code-options">
-<h1>Population grid code options<a class="headerlink" href="#population-grid-code-options" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Population grid code options<a class="headerlink" href="#population-grid-code-options" title="Permalink to this heading">ïƒ</a></h1>
<p>The following chapter contains all grid code options, along with their descriptions
There are 29 options that are not described yet.</p>
<section id="public-options">
-<h2>Public options<a class="headerlink" href="#public-options" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Public options<a class="headerlink" href="#public-options" title="Permalink to this heading">ïƒ</a></h2>
<p>The following options are meant to be changed by the user.</p>
<div class="line-block">
<div class="line"><strong>C_auto_logging</strong>: Dictionary containing parameters to be logged by binary_c. The structure of this dictionary is as follows: the key is used as the headline which the user can then catch. The value at that key is a list of binary_c system parameters (like star[0].mass)</div>
@@ -443,7 +444,7 @@ There are 29 options that are not described yet.</p>
</div>
</section>
<section id="moe-di-stefano-sampler-options">
-<h2>Moe & di Stefano sampler options<a class="headerlink" href="#moe-di-stefano-sampler-options" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Moe & di Stefano sampler options<a class="headerlink" href="#moe-di-stefano-sampler-options" title="Permalink to this heading">ïƒ</a></h2>
<p>The following options are meant to be changed by the user.</p>
<div class="line-block">
<div class="line"><strong>JSON</strong>: No description available yet</div>
@@ -530,7 +531,7 @@ q extrapolation (below 0.15) method
</div>
</section>
<section id="private-options">
-<h2>Private options<a class="headerlink" href="#private-options" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Private options<a class="headerlink" href="#private-options" title="Permalink to this heading">ïƒ</a></h2>
<p>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.</p>
<div class="line-block">
<div class="line"><strong>_Moe2017_JSON_data</strong>: Location to store the loaded Moe&diStefano2017 dataset</div>
@@ -646,9 +647,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 27543889c65f60671713587a013dccd45848a228..390650c73e4d28383190696fa5937953f5561fdb 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -97,37 +98,32 @@
}
</style>
<section id="welcome-to-binary-c-python-s-documentation">
-<h1>Welcome to binary_c-python’s documentation!<a class="headerlink" href="#welcome-to-binary-c-python-s-documentation" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Welcome to binary_c-python’s documentation!<a class="headerlink" href="#welcome-to-binary-c-python-s-documentation" title="Permalink to this heading">ïƒ</a></h1>
</section>
<section id="python-module-for-binary-c">
-<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this heading">ïƒ</a></h1>
<p>Docstring coverage:</p>
<a class="reference external image-reference" href="./badges/docstring_coverage.svg"><img alt="docstring coverage" src="_images/docstring_coverage.svg" /></a>
<p>Test coverage:</p>
<a class="reference external image-reference" href="./badges/test_coverage.svg"><img alt="test coverage" src="_images/test_coverage.svg" /></a>
+<p>Powered by:</p>
+<a class="reference external image-reference" href="http://www.astropy.org/"><img alt="" src="http://www.astropy.org/" /></a>
<p>Binary population synthesis code that interfaces with binary_c. Based on a original work by Jeff Andrews. Updated and extended for Python3 by David Hendriks, Robert Izzard.</p>
<p>The current release is version <a class="reference external" href="VERSION">version</a>, make sure to use that version number when installing!</p>
-<section id="requirements">
-<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">ïƒ</a></h2>
+<section id="installation">
+<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this heading">ïƒ</a></h2>
+<p>To install binary_c-python we need to make sure we meet the requirements of installation, and</p>
+<section id="python-requirements">
+<h3>Python requirements<a class="headerlink" href="#python-requirements" title="Permalink to this heading">ïƒ</a></h3>
<p>To run this code you need to at least have installations of:</p>
<ul class="simple">
-<li><p>Python 3.6 or higher</p></li>
-<li><p>binary_c version 2.1.7 or higher</p></li>
-</ul>
-<p>And the following python packages (which will get installed automatically when installing with pip):</p>
-<ul class="simple">
-<li><p>numpy</p></li>
-<li><p>pytest</p></li>
-<li><p>h5py</p></li>
-<li><p>pathos</p></li>
-<li><p>pandas</p></li>
-<li><p>astropy</p></li>
-<li><p>matplotlib</p></li>
-<li><p>py_rinterpolate</p></li>
+<li><p>Python 3.7 or higher (3.6 is EOL, and we are using 3.9 for development)</p></li>
+<li><p>binary_c version 2.2.0 or higher</p></li>
</ul>
+<p>The packages that are required for this code to run are listed in the requirements.txt, which automatically gets read out by setup.py</p>
</section>
<section id="environment-variables">
-<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this heading">ïƒ</a></h3>
<p>Before compilation you need to have certain environment variables:</p>
<p>Required:</p>
<ul class="simple">
@@ -138,55 +134,77 @@
</ul>
</section>
<section id="build-instructions">
-<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this heading">ïƒ</a></h3>
<p>First, make sure you have built binary_c (See <code class="docutils literal notranslate"><span class="pre">$BINARY_C/doc/binary_c2.pdf</span></code> section: installation for all the installation instructions for <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>)) and that it functions correctly.</p>
+</section>
<section id="installation-via-pip">
-<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this heading">ïƒ</a></h3>
<p>To install this package via pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">binarycpython</span>
</pre></div>
</div>
-<p>This will install the latest stable installation that is available on pip.</p>
+<p>This will install the latest stable installation that is available on Pip. The version on the master branch should be the same version as the latest stable version on Pip</p>
</section>
<section id="installation-from-source">
-<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">ïƒ</a></h3>
-<p>We can also install the package from source, which is useful for development versions and when you want to modify the code. It is recommended that you install this into a virtual environment. From within the root directory, run</p>
+<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this heading">ïƒ</a></h3>
+<p>We can also install the package from source, which is useful for development versions and when you want to modify the code. It is recommended that you install this into a virtual environment. From within the <code class="docutils literal notranslate"><span class="pre">commands/</span></code> directory, run</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">install</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
-<p>This will install the package, along with all the dependencies.</p>
+<p>This will install the package, along with all the dependencies, into the current active (virtual) python environment.</p>
<p>If this is not the first time you install the package, but rather rebuild it because you made changes in either binary_c or binarycpython, you can run</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">install_without_dependencies</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
<p>to reinstall just binarycpython.</p>
<section id="after-installation">
-<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this headline">ïƒ</a></h4>
+<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this heading">ïƒ</a></h4>
<p>After installing the code via source it is useful to run the test suite before doing any programming with it. The test suite is stored in <code class="docutils literal notranslate"><span class="pre">binarycpython/tests</span></code> and running <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">main.py</span></code> in there will run all the tests.</p>
</section>
</section>
</section>
+<section id="usage">
+<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this heading">ïƒ</a></h2>
<section id="examples">
-<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Examples<a class="headerlink" href="#examples" title="Permalink to this heading">ïƒ</a></h3>
<p>See the examples/ directory for example scripts and notebooks. The documentation contains example pages as well.</p>
</section>
<section id="usage-notes">
-<h2>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this heading">ïƒ</a></h3>
<p>Make sure that with every change/recompilation you make in <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>, you also rebuild this package. Whenever you change the sourcecode of this package, you need to reinstall it into your virtualenvironment as well</p>
</section>
<section id="documentation">
-<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Documentation<a class="headerlink" href="#documentation" title="Permalink to this heading">ïƒ</a></h3>
<p>Look in the docs/ directory. Within the build/html/ there is the html version of the documentation. The</p>
</section>
+</section>
<section id="development">
-<h2>Development:<a class="headerlink" href="#development" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Development:<a class="headerlink" href="#development" title="Permalink to this heading">ïƒ</a></h2>
<p>If you want to contribute to the code, then it is recommended that you install the packages in <code class="docutils literal notranslate"><span class="pre">development_requirements.txt</span></code>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">r</span> <span class="n">development_requirements</span><span class="o">.</span><span class="n">txt</span>
</pre></div>
</div>
+<p>Please do not hesitate to contact us to discuss any developments.</p>
+<section id="building-documentation">
+<h3>Building documentation<a class="headerlink" href="#building-documentation" title="Permalink to this heading">ïƒ</a></h3>
+<p>To build the documentation manually, run</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">generate_docs</span><span class="o">.</span><span class="n">sh</span>
+</pre></div>
+</div>
+<p>from within the <code class="docutils literal notranslate"><span class="pre">commands/</span></code> directory</p>
+</section>
+<section id="running-unit-tests">
+<h3>Running unit tests<a class="headerlink" href="#running-unit-tests" title="Permalink to this heading">ïƒ</a></h3>
+<p>To generate the unit test and docstring coverage report, run</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">generate_reports</span><span class="o">.</span><span class="n">sh</span>
+</pre></div>
+</div>
+<p>from within the <code class="docutils literal notranslate"><span class="pre">commands/</span></code> directory</p>
+</section>
</section>
<section id="faq-issues">
-<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this headline">ïƒ</a></h2>
+<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this heading">ïƒ</a></h2>
+<p>Here we provide a non-exhaustive list of some issues we encountered and solutions for these:</p>
<p>Building issues with binary_c itself:</p>
<ul class="simple">
<li><p>see the documentation of binary_c (in doc/).</p></li>
@@ -208,12 +226,8 @@
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="readme_link.html">Python module for binary_c</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="readme_link.html#requirements">Requirements</a></li>
-<li class="toctree-l2"><a class="reference internal" href="readme_link.html#environment-variables">Environment variables</a></li>
-<li class="toctree-l2"><a class="reference internal" href="readme_link.html#build-instructions">Build instructions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="readme_link.html#examples">Examples</a></li>
-<li class="toctree-l2"><a class="reference internal" href="readme_link.html#usage-notes">Usage notes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="readme_link.html#documentation">Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="readme_link.html#installation">Installation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="readme_link.html#usage">Usage</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#development">Development:</a></li>
<li class="toctree-l2"><a class="reference internal" href="readme_link.html#faq-issues">FAQ/Issues:</a></li>
</ul>
@@ -283,7 +297,7 @@
</section>
</section>
<section id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this heading">ïƒ</a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
@@ -309,9 +323,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 42d63fe44121086349ccbf884c543f6d9494c3e1..e549cd6e99c14e8e3e203589f68bd698953b5c4b 100644
--- a/docs/build/html/modules.html
+++ b/docs/build/html/modules.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -123,7 +124,7 @@
}
</style>
<section id="binarycpython-code">
-<h1>Binarycpython code<a class="headerlink" href="#binarycpython-code" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Binarycpython code<a class="headerlink" href="#binarycpython-code" title="Permalink to this heading">ïƒ</a></h1>
<p>This chapter contains the (auto)documentation for all the functions and modules in the source code of binarycpython</p>
<div class="toctree-wrapper compound">
<ul>
@@ -173,9 +174,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index 78075ad6aaeb850cb4fc53841a12889ef640b72f..0e2adadbe69a117ae80b5890f11c2d83f5cb4c1f 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/plot_functions.html b/docs/build/html/plot_functions.html
index 5829713b79c3e197abcfdaf8e119cb55071f0eb5..8df452016271492d9d540629f0de201b26877fb5 100644
--- a/docs/build/html/plot_functions.html
+++ b/docs/build/html/plot_functions.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.plot_functions">
-<span id="plot-functions-module"></span><h1>plot_functions module<a class="headerlink" href="#module-binarycpython.utils.plot_functions" title="Permalink to this headline">ïƒ</a></h1>
+<span id="plot-functions-module"></span><h1>plot_functions module<a class="headerlink" href="#module-binarycpython.utils.plot_functions" title="Permalink to this heading">ïƒ</a></h1>
<p>Module that contains functionality to plot some properties of (binary) systems.</p>
<p>Different routines are defined here to plot orbits, masses, angular momenta etc.</p>
<dl class="simple">
@@ -377,9 +378,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 f3ba0ac7e7fd47d4ed579fe52937834f8ad5893f..5bc9d2ee7b7863c4d54ee31ffcaf97bff0c2b582 100644
--- a/docs/build/html/population_extensions/HPC.html
+++ b/docs/build/html/population_extensions/HPC.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.HPC">
-<span id="population-class-extension-hpc-module"></span><h1>Population class extension: HPC module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.HPC" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-hpc-module"></span><h1>Population class extension: HPC module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.HPC" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the functions to HPC functionality</p>
<p>These functions form a single API through which you can access HPC resources.</p>
<p>Generally, you should call an HPC function rather than the Slurm or Condor interface
@@ -135,7 +136,7 @@ Condor API.</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.population_extensions.HPC.HPC">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">binarycpython.utils.population_extensions.HPC.</span></span><span class="sig-name descname"><span class="pre">HPC</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/binarycpython/utils/population_extensions/HPC.html#HPC"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.population_extensions.HPC.HPC" title="Permalink to this definition">ïƒ</a></dt>
-<dd><p>Bases: <a class="reference internal" href="condor.html#binarycpython.utils.population_extensions.condor.condor" title="binarycpython.utils.population_extensions.condor.condor"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.condor.condor</span></code></a>, <a class="reference internal" href="slurm.html#binarycpython.utils.population_extensions.slurm.slurm" title="binarycpython.utils.population_extensions.slurm.slurm"><code class="xref py py-class docutils literal notranslate"><span class="pre">binarycpython.utils.population_extensions.slurm.slurm</span></code></a></p>
+<dd><p>Bases: <a class="reference internal" href="condor.html#binarycpython.utils.population_extensions.condor.condor" title="binarycpython.utils.population_extensions.condor.condor"><code class="xref py py-class docutils literal notranslate"><span class="pre">condor</span></code></a>, <a class="reference internal" href="slurm.html#binarycpython.utils.population_extensions.slurm.slurm" title="binarycpython.utils.population_extensions.slurm.slurm"><code class="xref py py-class docutils literal notranslate"><span class="pre">slurm</span></code></a></p>
<p>Extension to the population grid object that contains functionality to handle handle the Moe & distefano distributions</p>
<dl class="py method">
<dt class="sig sig-object py" id="binarycpython.utils.population_extensions.HPC.HPC.HPC_can_join">
@@ -374,9 +375,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 d37b691675271486c9ab4af769baad4c79d928c5..149ef3e366d0a5906cbb40dd5355c2fd7906d00c 100644
--- a/docs/build/html/population_extensions/Moe_di_Stefano_2017.html
+++ b/docs/build/html/population_extensions/Moe_di_Stefano_2017.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.Moe_di_Stefano_2017">
-<span id="population-class-extension-moe-di-stefano-2017-module"></span><h1>Population class extension: Moe_di_Stefano_2017 module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.Moe_di_Stefano_2017" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-moe-di-stefano-2017-module"></span><h1>Population class extension: Moe_di_Stefano_2017 module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.Moe_di_Stefano_2017" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the functions to handle the Moe&Distrefano data</p>
<p>This class object is an extension to the population grid object</p>
<dl class="py class">
@@ -192,9 +193,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 f7664a72398b861a09cc59f80cbc55557fd5a1a4..1a0fa6f4dd4c36098e6de298e41a11c74587001f 100644
--- a/docs/build/html/population_extensions/analytics.html
+++ b/docs/build/html/population_extensions/analytics.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.analytics">
-<span id="population-class-extension-analytics-module"></span><h1>Population class extension: analytics module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.analytics" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-analytics-module"></span><h1>Population class extension: analytics module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.analytics" title="Permalink to this heading">ïƒ</a></h1>
<p>The class extension for the population object that contains analytics functionality</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.population_extensions.analytics.analytics">
@@ -181,9 +182,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 65b41b49e116d7c00b401b1a3e11a0a72b3c6b15..6f3b0bf612925a484aef64d0bbd03b9ddcc380e5 100644
--- a/docs/build/html/population_extensions/cache.html
+++ b/docs/build/html/population_extensions/cache.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.cache">
-<span id="population-class-extension-cache-module"></span><h1>Population class extension: cache module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.cache" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-cache-module"></span><h1>Population class extension: cache module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.cache" title="Permalink to this heading">ïƒ</a></h1>
<p>File containing the class extension for the population object that contains cache functionality</p>
<p>Module containing (e.g. LRU) cache functionality for binary_c-python.</p>
<p>We use cachetools when possible because this allows us to set up the
@@ -138,7 +139,7 @@ Please see the LRU_* options in there.</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.population_extensions.cache.cache.NullCache">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NullCache</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/binarycpython/utils/population_extensions/cache.html#cache.NullCache"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#binarycpython.utils.population_extensions.cache.cache.NullCache" title="Permalink to this definition">ïƒ</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">cachetools.Cache</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Cache</span></code></p>
<p>A cachetools cache object that does as little as possible and never matches.</p>
<dl class="py method">
<dt class="sig sig-object py" id="binarycpython.utils.population_extensions.cache.cache.NullCache.__delitem__">
@@ -215,9 +216,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 9082669422b04084fc80abd93664e5b833bb8c33..73872ab0441b9aafe0ee085f969b222dc843b5d1 100644
--- a/docs/build/html/population_extensions/condor.html
+++ b/docs/build/html/population_extensions/condor.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.condor">
-<span id="population-class-extension-condor-module"></span><h1>Population class extension: condor module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.condor" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-condor-module"></span><h1>Population class extension: condor module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.condor" title="Permalink to this heading">ïƒ</a></h1>
<p>The class extension for the population object that contains the Condor functionality</p>
<p>TODO: there are many uses of $<variable name> in this file but this is not perl and we should replace them by actual format placeholders</p>
<dl class="py class">
@@ -234,9 +235,9 @@ TODO: Comment this function better</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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 412aa2aff23d37883d422d06af10bafcce34ea92..5e625963f1b5e0bea513836a88fed07a19260f32 100644
--- a/docs/build/html/population_extensions/dataIO.html
+++ b/docs/build/html/population_extensions/dataIO.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.dataIO">
-<span id="population-class-extension-dataio-module"></span><h1>Population class extension: dataIO module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.dataIO" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-dataio-module"></span><h1>Population class extension: dataIO module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.dataIO" title="Permalink to this heading">ïƒ</a></h1>
<p>File containing the class extension for the population object that contains data input-output (IO) functions</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.population_extensions.dataIO.dataIO">
@@ -393,9 +394,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 f1d6fcc1661691c1cc4010f02159af9896182ab8..2a08d81af855e23066d0c422e159ffcf5ebafe14 100644
--- a/docs/build/html/population_extensions/distribution_functions.html
+++ b/docs/build/html/population_extensions/distribution_functions.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.distribution_functions">
-<span id="population-class-extension-distribution-functions-module"></span><h1>Population class extension: distribution_functions module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.distribution_functions" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-distribution-functions-module"></span><h1>Population class extension: distribution_functions module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.distribution_functions" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the predefined distribution functions</p>
<p>The user can use any of these distribution functions to
generate probability distributions for sampling populations</p>
@@ -340,7 +341,7 @@ TODO: fix description to be correct for python</p>
<dd class="field-even"><p>returns 0</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>returns the value of 1/(max_bound-min_bound) If val is provided, it will check whether min_bound < val <= max_bound. if not</p>
+<dd class="field-odd"><p>returns the value of 1/(max_bound-min_bound). If val is provided, it will check whether min_bound < val <= max_bound. if not</p>
</dd>
</dl>
</dd></dl>
@@ -833,9 +834,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 87fc47987167c93a6aad78c4c6d8a9ca1dd26aac..368d37c4aa9718eaf86779c135a51112831bd85e 100644
--- a/docs/build/html/population_extensions/grid_logging.html
+++ b/docs/build/html/population_extensions/grid_logging.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.grid_logging">
-<span id="population-class-extension-grid-logging-module"></span><h1>Population class extension: grid_logging module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.grid_logging" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-grid-logging-module"></span><h1>Population class extension: grid_logging module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.grid_logging" title="Permalink to this heading">ïƒ</a></h1>
<p>The class extension for the population object that contains logging functionality</p>
<dl class="py class">
<dt class="sig sig-object py" id="binarycpython.utils.population_extensions.grid_logging.grid_logging">
@@ -179,9 +180,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 70b90c9d1707fdf5b1eaaaa1aa61db872b09c80b..0ce8ebc5702386569d94d6c4b95def2e5796f6c7 100644
--- a/docs/build/html/population_extensions/grid_options_defaults.html
+++ b/docs/build/html/population_extensions/grid_options_defaults.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.grid_options_defaults">
-<span id="population-class-extension-grid-options-defaults-module"></span><h1>Population class extension: grid_options_defaults module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.grid_options_defaults" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-grid-options-defaults-module"></span><h1>Population class extension: grid_options_defaults module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.grid_options_defaults" title="Permalink to this heading">ïƒ</a></h1>
<dl class="simple">
<dt>Module that contains the default options for the population grid code along with the description for these options, in the form of dictionaries:</dt><dd><ul class="simple">
<li><p>grid_options_defaults_dict: dictionary containing the default values for all the options</p></li>
@@ -242,9 +243,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 848265f276f8854215d512827b8523a9762f22e9..843b9174016170853811864d6e6cbb98dc8bf681 100644
--- a/docs/build/html/population_extensions/gridcode.html
+++ b/docs/build/html/population_extensions/gridcode.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.gridcode">
-<span id="population-class-extension-gridcode-module"></span><h1>Population class extension: gridcode module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.gridcode" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-gridcode-module"></span><h1>Population class extension: gridcode module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.gridcode" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the gridcode generation functions for the binarycpython package.</p>
<p>This class object is an extension to the population grid object</p>
<dl class="py class">
@@ -298,9 +299,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 ce11c6cd323946ba914f12431727b804532b5291..1ca5312d646be1a26ea25f0f355ac538ef93490a 100644
--- a/docs/build/html/population_extensions/metadata.html
+++ b/docs/build/html/population_extensions/metadata.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.metadata">
-<span id="population-class-extension-metadata-module"></span><h1>Population class extension: metadata module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.metadata" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-metadata-module"></span><h1>Population class extension: metadata module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.metadata" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the metadata functions for the binarycpython package.</p>
<p>This class object is an extension to the population grid object</p>
<dl class="py class">
@@ -167,9 +168,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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/slurm.html b/docs/build/html/population_extensions/slurm.html
index 2fca66f7e302aa947828111e8f9e9b65a6fe73a8..65a436b2de13b620b3600f2ec6d5c86eb9f0d1c2 100644
--- a/docs/build/html/population_extensions/slurm.html
+++ b/docs/build/html/population_extensions/slurm.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.slurm">
-<span id="population-class-extension-slurm-module"></span><h1>Population class extension: slurm module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.slurm" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-slurm-module"></span><h1>Population class extension: slurm module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.slurm" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the Slurm functions for the binarycpython package.</p>
<p>This class object is an extension to the population grid object</p>
<dl class="py class">
@@ -235,9 +236,9 @@ TODO: Comment this function better</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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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/spacing_functions.html b/docs/build/html/population_extensions/spacing_functions.html
index 186fcce7c7608a8eab060d5dad67181c0ff04bb8..7f33a16dcd628b63716fc5fefa787c408016f74e 100644
--- a/docs/build/html/population_extensions/spacing_functions.html
+++ b/docs/build/html/population_extensions/spacing_functions.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.spacing_functions">
-<span id="population-class-extension-spacing-functions-module"></span><h1>Population class extension: spacing_functions module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.spacing_functions" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-spacing-functions-module"></span><h1>Population class extension: spacing_functions module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.spacing_functions" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the spacing functions for the binarycpython package. Very under-populated at the moment, but more are likely to come soon</p>
<p>This class object is an extension to the population grid object</p>
<dl class="simple">
@@ -322,9 +323,9 @@ not that the integral is 1.0</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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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/version_info.html b/docs/build/html/population_extensions/version_info.html
index a9bc813c43d9d392377264d0b1ec349dc31cf68e..82fab3d95017e93cf6f4c0b8c2db02c56265e970 100644
--- a/docs/build/html/population_extensions/version_info.html
+++ b/docs/build/html/population_extensions/version_info.html
@@ -14,6 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="../_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.population_extensions.version_info">
-<span id="population-class-extension-version-info-module"></span><h1>Population class extension: version_info module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.version_info" title="Permalink to this headline">ïƒ</a></h1>
+<span id="population-class-extension-version-info-module"></span><h1>Population class extension: version_info module<a class="headerlink" href="#module-binarycpython.utils.population_extensions.version_info" title="Permalink to this heading">ïƒ</a></h1>
<p>File containing the class object containing the functions to handle binary_c version info.</p>
<p>This class will be used to extend the population object</p>
<p>NOTE: could these functions not just be normal functions rather than class methods? I see hardly any use of the self</p>
@@ -199,9 +200,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index f194b6c66bfb777f6e879e616723ea259bd506b3..bcd57d756e66a972c9b7bb652367fa35ed87cb91 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -13,6 +13,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -222,9 +223,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/readme_link.html b/docs/build/html/readme_link.html
index 435d699be24747f7b298310f92f8d72743d5f3a0..7465f5537bbb0df98721bf39acb75d0ffeec4730 100644
--- a/docs/build/html/readme_link.html
+++ b/docs/build/html/readme_link.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -41,9 +42,10 @@
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Python module for binary_c</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#environment-variables">Environment variables</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions">Build instructions</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#installation">Installation</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#python-requirements">Python requirements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#environment-variables">Environment variables</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#build-instructions">Build instructions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#installation-via-pip">Installation via PIP:</a></li>
<li class="toctree-l3"><a class="reference internal" href="#installation-from-source">Installation from source:</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#after-installation">After installation</a></li>
@@ -51,10 +53,17 @@
</li>
</ul>
</li>
-<li class="toctree-l2"><a class="reference internal" href="#examples">Examples</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#usage-notes">Usage notes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#documentation">Documentation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#development">Development:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#usage">Usage</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#usage-notes">Usage notes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#documentation">Documentation</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#development">Development:</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#building-documentation">Building documentation</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#running-unit-tests">Running unit tests</a></li>
+</ul>
+</li>
<li class="toctree-l2"><a class="reference internal" href="#faq-issues">FAQ/Issues:</a></li>
</ul>
</li>
@@ -115,34 +124,29 @@
}
</style>
<section id="python-module-for-binary-c">
-<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this headline">ïƒ</a></h1>
+<h1>Python module for binary_c<a class="headerlink" href="#python-module-for-binary-c" title="Permalink to this heading">ïƒ</a></h1>
<p>Docstring coverage:</p>
<a class="reference external image-reference" href="./badges/docstring_coverage.svg"><img alt="docstring coverage" src="_images/docstring_coverage.svg" /></a>
<p>Test coverage:</p>
<a class="reference external image-reference" href="./badges/test_coverage.svg"><img alt="test coverage" src="_images/test_coverage.svg" /></a>
+<p>Powered by:</p>
+<a class="reference external image-reference" href="http://www.astropy.org/"><img alt="" src="http://www.astropy.org/" /></a>
<p>Binary population synthesis code that interfaces with binary_c. Based on a original work by Jeff Andrews. Updated and extended for Python3 by David Hendriks, Robert Izzard.</p>
<p>The current release is version <a class="reference external" href="VERSION">version</a>, make sure to use that version number when installing!</p>
-<section id="requirements">
-<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">ïƒ</a></h2>
+<section id="installation">
+<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this heading">ïƒ</a></h2>
+<p>To install binary_c-python we need to make sure we meet the requirements of installation, and</p>
+<section id="python-requirements">
+<h3>Python requirements<a class="headerlink" href="#python-requirements" title="Permalink to this heading">ïƒ</a></h3>
<p>To run this code you need to at least have installations of:</p>
<ul class="simple">
-<li><p>Python 3.6 or higher</p></li>
-<li><p>binary_c version 2.1.7 or higher</p></li>
-</ul>
-<p>And the following python packages (which will get installed automatically when installing with pip):</p>
-<ul class="simple">
-<li><p>numpy</p></li>
-<li><p>pytest</p></li>
-<li><p>h5py</p></li>
-<li><p>pathos</p></li>
-<li><p>pandas</p></li>
-<li><p>astropy</p></li>
-<li><p>matplotlib</p></li>
-<li><p>py_rinterpolate</p></li>
+<li><p>Python 3.7 or higher (3.6 is EOL, and we are using 3.9 for development)</p></li>
+<li><p>binary_c version 2.2.0 or higher</p></li>
</ul>
+<p>The packages that are required for this code to run are listed in the requirements.txt, which automatically gets read out by setup.py</p>
</section>
<section id="environment-variables">
-<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Environment variables<a class="headerlink" href="#environment-variables" title="Permalink to this heading">ïƒ</a></h3>
<p>Before compilation you need to have certain environment variables:</p>
<p>Required:</p>
<ul class="simple">
@@ -153,55 +157,77 @@
</ul>
</section>
<section id="build-instructions">
-<h2>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Build instructions<a class="headerlink" href="#build-instructions" title="Permalink to this heading">ïƒ</a></h3>
<p>First, make sure you have built binary_c (See <code class="docutils literal notranslate"><span class="pre">$BINARY_C/doc/binary_c2.pdf</span></code> section: installation for all the installation instructions for <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>)) and that it functions correctly.</p>
+</section>
<section id="installation-via-pip">
-<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this headline">ïƒ</a></h3>
+<h3>Installation via PIP:<a class="headerlink" href="#installation-via-pip" title="Permalink to this heading">ïƒ</a></h3>
<p>To install this package via pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">binarycpython</span>
</pre></div>
</div>
-<p>This will install the latest stable installation that is available on pip.</p>
+<p>This will install the latest stable installation that is available on Pip. The version on the master branch should be the same version as the latest stable version on Pip</p>
</section>
<section id="installation-from-source">
-<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">ïƒ</a></h3>
-<p>We can also install the package from source, which is useful for development versions and when you want to modify the code. It is recommended that you install this into a virtual environment. From within the root directory, run</p>
+<h3>Installation from source:<a class="headerlink" href="#installation-from-source" title="Permalink to this heading">ïƒ</a></h3>
+<p>We can also install the package from source, which is useful for development versions and when you want to modify the code. It is recommended that you install this into a virtual environment. From within the <code class="docutils literal notranslate"><span class="pre">commands/</span></code> directory, run</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">install</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
-<p>This will install the package, along with all the dependencies.</p>
+<p>This will install the package, along with all the dependencies, into the current active (virtual) python environment.</p>
<p>If this is not the first time you install the package, but rather rebuild it because you made changes in either binary_c or binarycpython, you can run</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">install_without_dependencies</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
<p>to reinstall just binarycpython.</p>
<section id="after-installation">
-<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this headline">ïƒ</a></h4>
+<h4>After installation<a class="headerlink" href="#after-installation" title="Permalink to this heading">ïƒ</a></h4>
<p>After installing the code via source it is useful to run the test suite before doing any programming with it. The test suite is stored in <code class="docutils literal notranslate"><span class="pre">binarycpython/tests</span></code> and running <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">main.py</span></code> in there will run all the tests.</p>
</section>
</section>
</section>
+<section id="usage">
+<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this heading">ïƒ</a></h2>
<section id="examples">
-<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Examples<a class="headerlink" href="#examples" title="Permalink to this heading">ïƒ</a></h3>
<p>See the examples/ directory for example scripts and notebooks. The documentation contains example pages as well.</p>
</section>
<section id="usage-notes">
-<h2>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Usage notes<a class="headerlink" href="#usage-notes" title="Permalink to this heading">ïƒ</a></h3>
<p>Make sure that with every change/recompilation you make in <code class="docutils literal notranslate"><span class="pre">binary_c</span></code>, you also rebuild this package. Whenever you change the sourcecode of this package, you need to reinstall it into your virtualenvironment as well</p>
</section>
<section id="documentation">
-<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">ïƒ</a></h2>
+<h3>Documentation<a class="headerlink" href="#documentation" title="Permalink to this heading">ïƒ</a></h3>
<p>Look in the docs/ directory. Within the build/html/ there is the html version of the documentation. The</p>
</section>
+</section>
<section id="development">
-<h2>Development:<a class="headerlink" href="#development" title="Permalink to this headline">ïƒ</a></h2>
+<h2>Development:<a class="headerlink" href="#development" title="Permalink to this heading">ïƒ</a></h2>
<p>If you want to contribute to the code, then it is recommended that you install the packages in <code class="docutils literal notranslate"><span class="pre">development_requirements.txt</span></code>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">r</span> <span class="n">development_requirements</span><span class="o">.</span><span class="n">txt</span>
</pre></div>
</div>
+<p>Please do not hesitate to contact us to discuss any developments.</p>
+<section id="building-documentation">
+<h3>Building documentation<a class="headerlink" href="#building-documentation" title="Permalink to this heading">ïƒ</a></h3>
+<p>To build the documentation manually, run</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">generate_docs</span><span class="o">.</span><span class="n">sh</span>
+</pre></div>
+</div>
+<p>from within the <code class="docutils literal notranslate"><span class="pre">commands/</span></code> directory</p>
+</section>
+<section id="running-unit-tests">
+<h3>Running unit tests<a class="headerlink" href="#running-unit-tests" title="Permalink to this heading">ïƒ</a></h3>
+<p>To generate the unit test and docstring coverage report, run</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">generate_reports</span><span class="o">.</span><span class="n">sh</span>
+</pre></div>
+</div>
+<p>from within the <code class="docutils literal notranslate"><span class="pre">commands/</span></code> directory</p>
+</section>
</section>
<section id="faq-issues">
-<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this headline">ïƒ</a></h2>
+<h2>FAQ/Issues:<a class="headerlink" href="#faq-issues" title="Permalink to this heading">ïƒ</a></h2>
+<p>Here we provide a non-exhaustive list of some issues we encountered and solutions for these:</p>
<p>Building issues with binary_c itself:</p>
<ul class="simple">
<li><p>see the documentation of binary_c (in doc/).</p></li>
@@ -241,9 +267,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/run_system_wrapper.html b/docs/build/html/run_system_wrapper.html
index 3aacb64f0002adf5113f55d612fcc3ef60e73708..191f406e2285630a1d672c60aff379e755808531 100644
--- a/docs/build/html/run_system_wrapper.html
+++ b/docs/build/html/run_system_wrapper.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
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</style>
<section id="module-binarycpython.utils.run_system_wrapper">
-<span id="run-system-wrapper-module"></span><h1>run_system_wrapper module<a class="headerlink" href="#module-binarycpython.utils.run_system_wrapper" title="Permalink to this headline">ïƒ</a></h1>
+<span id="run-system-wrapper-module"></span><h1>run_system_wrapper module<a class="headerlink" href="#module-binarycpython.utils.run_system_wrapper" title="Permalink to this heading">ïƒ</a></h1>
<p>Module containing the utility function run_system,
which handles a lot of things by analysing the passed kwargs</p>
<dl class="py function">
@@ -193,9 +194,9 @@ and returns what the parse_function returns</p>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
<br><br>
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+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index e478c8d056289da31b72c59ec70cd766b495bf59..72c37cfa075c0e83476eae9ffa6ef9396c0d3057 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
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<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -100,9 +101,9 @@
provided by <a href="https://readthedocs.org">Read the Docs</a>.
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+Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
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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","<no title>","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 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"directli": 9, "string": 9, "compact": 9, "mass": [9, 14, 15], "supernova": 9, "extra": 11, "featur": 11, "about": 11, "build": [11, 23, 40], "pars": 11, "dictionari": 11, "modif": 11, "individu": 12, "singl": [12, 16], "run_system_wrapp": [12, 41], "via": [12, 23, 40], "zero": [13, 14], "ag": [13, 14], "luminos": [13, 14, 15], "ad": [13, 14, 15, 16], "variabl": [13, 14, 15, 16, 23, 40], "zam": [14, 15], "distribut": [14, 15], "initi": [14, 15], "A": [14, 15], "better": [14, 15], "sampl": [14, 15], "massiv": 15, "noteworthi": 16, "full": 16, "script": 16, "solar": 17, "basic": 18, "core": 19, "wrapper": 19, "run_binari": 19, "run_binary_with_log": 19, "line": 19, "util": 19, "run_system": 19, "other": 19, "class": [21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39], "code": [22, 24], "option": 22, "public": 22, "moe": 22, "di": 22, "stefano": 22, "sampler": 22, "privat": 22, "welcom": 23, "s": 23, "document": [23, 40], "instal": [23, 40], "requir": [23, 40], "environ": [23, 40], "instruct": [23, 40], "pip": [23, 40], "sourc": [23, 40], "after": [23, 40], "note": [23, 40], "develop": [23, 40], "unit": [23, 40], "test": [23, 40], "faq": [23, 40], "issu": [23, 40], "indic": 23, "tabl": 23, "binarycpython": 24, "plot_funct": 25, "extens": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39], "hpc": 26, "moe_di_stefano_2017": 27, "analyt": 28, "cach": 29, "condor": 30, "dataio": 31, "distribution_funct": 32, "grid_log": 33, "grid_options_default": 34, "gridcod": 35, "metadata": 36, "slurm": 37, "spacing_funct": 38, "version_info": 39, "stellar_typ": 42, "useful_func": 43}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "nbsphinx": 4, "sphinx": 56}})
\ No newline at end of file
diff --git a/docs/build/html/stellar_types.html b/docs/build/html/stellar_types.html
index f626d45b7b19f082151d41c1f0d7c0205893962e..21aeae4863b66f56666a8a5c6f7842d0d41cfcf2 100644
--- a/docs/build/html/stellar_types.html
+++ b/docs/build/html/stellar_types.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.stellar_types">
-<span id="stellar-types-module"></span><h1>stellar_types module<a class="headerlink" href="#module-binarycpython.utils.stellar_types" title="Permalink to this headline">ïƒ</a></h1>
+<span id="stellar-types-module"></span><h1>stellar_types module<a class="headerlink" href="#module-binarycpython.utils.stellar_types" title="Permalink to this heading">ïƒ</a></h1>
<dl class="simple">
<dt>Module containing two stellar type dicts:</dt><dd><ul class="simple">
<li><p>STELLAR_TYPE_DICT: dictionary with long names</p></li>
@@ -153,9 +154,9 @@
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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 e7a32829052d148ab7262d387561ab96238d337e..945c0369631bb78b7def9b9f1eadd828ca0502d6 100644
--- a/docs/build/html/useful_funcs.html
+++ b/docs/build/html/useful_funcs.html
@@ -14,6 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
+ <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="_static/js/theme.js"></script>
@@ -124,7 +125,7 @@
}
</style>
<section id="module-binarycpython.utils.useful_funcs">
-<span id="useful-funcs-module"></span><h1>useful_funcs module<a class="headerlink" href="#module-binarycpython.utils.useful_funcs" title="Permalink to this headline">ïƒ</a></h1>
+<span id="useful-funcs-module"></span><h1>useful_funcs module<a class="headerlink" href="#module-binarycpython.utils.useful_funcs" title="Permalink to this heading">ïƒ</a></h1>
<p>Collection of useful functions.</p>
<p>Part of this is copied/inspired by Rob’s binary_stars module</p>
<dl class="simple">
@@ -350,9 +351,9 @@ 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 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" 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 439fc328aaa186d66a18b7531ff35ee0515fa692..457fbbe14a6f5de344f3f818f001f1638ff2a08b 100644
--- a/docs/source/_templates/footer.html
+++ b/docs/source/_templates/footer.html
@@ -2,8 +2,8 @@
{%- block extrafooter %}
<br><br>
-Generated on binarycpython git branch: development_0.9.3/2.2.1 git revision 15fbbaba24e219ad1d2633582e4a420dc4e08955 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 a790e18a79348c20b62cbfa1af89c3f8cb1b167b 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 HEAD: git revision: "5853:20220225:db09898b6" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/HEAD">git url</a>.
+Using binary_c with bit branch branch_david: git revision: "6072:20220603:69cdd3f72" url: <a href="https://gitlab.surrey.ac.uk/ri0005/binary_c/-/tree/branch_david">git url</a>.
{% endblock %}
\ No newline at end of file
diff --git a/docs/source/binary_c_parameters.rst b/docs/source/binary_c_parameters.rst
index 81bd07a9350f8d9aa75d828d9f5a0e2fe4e27520..1019b88d5098494448bf034ed2666e40cbd40cfa 100644
--- a/docs/source/binary_c_parameters.rst
+++ b/docs/source/binary_c_parameters.rst
@@ -4,7 +4,7 @@ The following chapter contains all the parameters that the current version of bi
This information was obtained by the following binary_c build:
- **binary_c git branch**: HEAD **binary_c git revision**: 5853:20220225:db09898b6 **Built on**: Feb 25 2022 19:21:31
+ **binary_c git branch**: branch_david **binary_c git revision**: 6072:20220603:69cdd3f72 **Built on**: Jun 3 2022 14:44:39
Section: stars
@@ -492,6 +492,12 @@ Section: stars
| **Default value**: 0
| **Extra**: Ignore
+| **Parameter**: PPISN_massloss_multiplier
+| **Description**: (Pulsational) Pair-Instability Supernova CO massloss multiplier: Value by which the (P)PISN massloss is multiplied. Currently only works with the new prescription. THe additional mass loss is not affected multiplied by this.
+| **Parameter input type**: Float
+| **Default value**: 1
+| **Extra**: Ignore
+
| **Parameter**: use_LWN_fallback
| **Description**: Flag whether to use the Nazehdin-Lovegrove-Woosley hydrogen envelope ejection at failed supernova.
| **Parameter input type**: Integer
@@ -2378,6 +2384,30 @@ Section: output
| **Parameter**: david_logging_function
| **Description**: Function to choose which kind of information gets logged Requires DAVID. Choices are: 0= None, >0 for custom logging functions
| **Parameter input type**: Integer
+| **Default value**: -1
+| **Extra**: Ignore
+
+| **Parameter**: david_tzo_logging
+| **Description**: Flag to enable logging for TZO project
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
+| **Parameter**: david_ppisn_logging
+| **Description**: Flag to enable logging for PPISN project
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
+| **Parameter**: david_rlof_episode_logging
+| **Description**: Flag to enable the RLOF episode logging
+| **Parameter input type**: Integer
+| **Default value**: 0
+| **Extra**: Ignore
+
+| **Parameter**: david_rlof_ensemble_logging
+| **Description**: Flag to enable the RLOF ensemble logging
+| **Parameter input type**: Integer
| **Default value**: 0
| **Extra**: Ignore