Conflicts resolved

Author: jeffriley

.gitignore

@@ -35,5 +35,10 @@ COMPAS
 *.synctex.gz
 *.synctex.gz(busy)
 
+# docs html
+*_build
+
+*.vscode
+
 Makefile-reinhold
 .gitignore

docs/online-docs/README.md

@@ -1 +1,99 @@
-# COMPAS-docs
+COMPAS online documentation
+===========================
+
+The COMPAS online documentation is available at this URL:
+
+    https://compas.science/docs
+
+which redirects to the underlying readthedocs page at:
+
+    https://compas.readthedocs.io/en/latest/index.html
+
+
+The source files for the online documentation are in the 'docs' directory at:
+
+    https://github.com/TeamCOMPAS/COMPAS
+
+
+The online documentation is provided via readthedocs.  To learn more about readthedocs, visit:
+
+    https://readthedocs.org/
+
+
+readthedocs uses the Sphinx document generator.  To learn more about Sphinx, visit:
+
+https://www.sphinx-doc.org/en/master/index.html
+
+
+The file 'requirements.txt', in the 'docs' directory, lists the software/python modules required
+to build the documentation.  If you plan to build the documentation locally (either so you can 
+test your changes before you push them to the repository, or just to view the documentation locally
+rather than online), you will need to install these requirements.
+
+The requirements.txt file informs readthedocs what dependencies need to be installed in order for
+readthedocs to build the online documentation. Some modules are commented ('#') in requirements.txt
+because readthedocs either doesn't require them, or installs them by default - you will need to install
+the commented modules to build the documentation locally.
+
+Python is required, so install that if it is not already installed.  Then install 'sphinx', and the
+modules listed in requirements.txt (including the ones commented).
+
+
+Updating the documentation
+--------------------------
+
+The documentation source file are ReST (Restructured text) files - similar to markdown.  With readthedocs,
+eash .rst file is compiled into a .html file, so viewable with a web browser. The documentation source
+files (the .rst files) are in 'docs/online-docs' (only the 'requirements.txt' file is required by
+readthedocs to be in the 'docs' directory - if that file is not in the 'docs' directory, or top-level
+directory of the repo, readthedocs will not build the online documentation).
+
+The 'online-docs' directory contains files and sub-directories that are structured to match the structured
+of the online documentation. Find the .rst file you want to modify, and make the changes in your favourite
+text editor. If you need to add new .rst files, follow the existing structure, and make sure you link the
+files into an index (toctree) somewhere.
+
+
+Building the documentation locally
+----------------------------------
+
+Once you have Sphinx and the dependencies (from 'requirements.txt') installed, navigate to the 'docs/online-docs'
+directory in you local COMPAS repo, and type:
+
+    make clean
+    make html
+
+If everything has been installed correctly this will first remove the existing .html files for the documentation
+(make clean), and then recreate them (make html).  During the build process you may see some warnings that some
+documents (.rst files) are not included in any toctree - that's ok, not all our pages are accessible via a table
+of contents (toctree).
+
+If the build completes successfully, there will be .html files in the 'docs/online-docs/\_build/html' directory.
+To view the newly build documentation, open 'docs/online-docs/\_build/html/index.html' with your web browser
+(e.g. type 'file://path-to-compas/docs/online-docs/\_build/html/index.html' into your web browser address bar, 
+where 'path-to-compas' is the path to your local COMPAS repo).
+
+Aside: the '\_build' directory is not required on the remote repo (and will only bloat the repo), so you should
+add it to your .gitignore.
+
+
+Pushing the changes online
+--------------------------
+
+Once you are satisfied with your changes, push the updated source files to the COMPAS repo as you would any source
+changes.  If things work properly, that's all you need to do: readthedocs has webhooks that will notice the change
+and automatically rebuild the online documentation.  The process (noticing the change, rebuilding the documentation,
+then deploying the updated web pages) could take up to 15 minutes or so. If something goes wrong and the changes are
+not noticed by readthedocs, or you just don't want to wait 15 minutes for your changes to appear on the web, you can
+log into the readthedocs project and initiate a rebuild manually.
+
+The COMPAS readthedocs project name is 'compas', and the project page is:
+
+    https://readthedocs.org/projects/compas/
+
+You need to login to the readthedocs project to do anything other than look at the dashboard. Once you are logged in 
+you can rebuild the project. To manually start the rebuild, make sure you are on the 'Overview' page (select the
+'Overview' button if you are not) and select the 'Build' button. The build may sometimes fail with an "environment"
+error - the solution is to wait a few minutes and try again (readthedocs has some concurrency and timing limits).
+Logon details can be found on the COMPAS slack workspace (devel\_compas\_documentation channel).
+

docs/online-docs/notebooks/COMPAS_Output_reduced.h5

@@ -1,25 +1,26 @@
 Tutorial: simple COMPAS run
 ===========================
 
+This tutorial assumes that you have already built the COMPAS executable as described in :doc:`../../Getting started/building-COMPAS`.
+
 For this example you will need the python script ``pythonSubmitDemo.py``, which specifies all the program options (physics assumptions, 
 output types) and runs COMPAS in the terminal. Although the primary functionality of COMPAS is to evolve a whole population of binary 
 stars rapidly, for now, let's focus on evolving a single stellar system and examining the detailed output.
 
-To start, change to the ``examples/methods_paper_plots/detailed_evolution/`` directory::
+If you haven't yet defined the ``COMPAS_ROOT_DIR`` environment variable, do that now::
 
-  cd $COMPAS_ROOT_DIR/examples/methods_paper_plots/detailed_evolution/
+    export COMPAS_ROOT_DIR=path-to-compas
 
-where you will find the script ``pythonSubmitDemo.py`` for this demo.
+where `path-to-compas` should be replaced with the path to the parent directory of the COMPAS `src` directory. Depending upon your system,
+for the ``export`` command to take effect, it may be necessary to either restart your session or execute the following command::
 
-If you haven't yet defined the ``COMPAS_ROOT_DIR`` environment variable, do that now::
+    source ~/.bashrc
 
-    export COMPAS_ROOT_DIR=~/path-to-compas/COMPAS
+To start, change to the ``examples/methods_paper_plots/detailed_evolution/`` directory::
 
-where `path-to-compas` should be replaced with the path to the parent directory of the directory in which the COMPAS executable resides.
-Depending upon your system, for the ``export`` command to take effect, it may be necessary to either restart your session or execute the
-following command::
+  cd $COMPAS_ROOT_DIR/examples/methods_paper_plots/detailed_evolution/
 
-    source ~/.bashrc
+where you will find the script ``pythonSubmitDemo.py`` for this demo.
 
 
 .. toctree::

docs/online-docs/pages/User guide/Tutorial/example-compas-run.rst

@@ -149,6 +149,10 @@ def printEvolutionaryHistory(Data):
                 MTstring='CE: both MS'
             elif Data['MT_History'][i]==7:
                 MTstring='CE: MS with CO'
+            elif Data['MT_History'][i]==8:
+                MTstring='CE merger, rad env'
+            elif Data['MT_History'][i]==9:
+                MTstring='CE merger, >RLOF'
             else:
                 MTstring='Unknown MT'