update docs and include api

CONTRIBUTING.md

@@ -5,27 +5,6 @@ We focus our work on python 3.7 due to the current neural network being develope
 ## Issues
 All issues are managed within the gitlab [ repository ](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/issues), if you don't have an account on the University of Edinburgh's gitlab instance and would like to submit issues please get in touch with [Prof. Peter Swain](mailto:peter.swain@ed.ac.uk ).
 
-## Branching
-* master: very sparingly and only for changes that need to be made in both
- versions as I will be merging changes from master into the development
- branches frequently
- 
-Branching cheat-sheet:
-```git
-git branch my_branch # Create a new branch called branch_name from master
-git branch my_branch another_branch #Branch from another_branch, not master
-git checkout -b my_branch # Create my_branch and switch to it
-
-# Merge changes from master into your branch
-git pull #get any remote changes in master
-git checkout my_branch
-git merge master
-
-# Merge changes from your branch into another branch
-git checkout another_branch
-git merge my_branch #check the doc for --no-ff option, you might want to use it
-```
-
 ## Data aggregation
 
 ALIBY has been tested by a few research groups, but we welcome new data sources for the models and pipeline to be as general as possible. Please get in touch with [ us ](mailto:peter.swain@ed.ac.uk ) if you are interested in testing it on your data.

docs/source/CONTRIBUTING.md

-../CONTRIBUTING.md
\ No newline at end of file

docs/source/README.md

-../../README.md
\ No newline at end of file

docs/source/index.rst

@@ -12,3 +12,5 @@
 
 .. include:: ../../README.md
    :parser: myst_parser.sphinx_
+
+.. include:: api.rst