Improve doc generation

[ndavid]

Some change to improve the documentation rendering :

First for the doc configuration :

• add docs/reference/generated to .gitignore and remove existing auto-generated file.
• add _template for autosummary directive. This template is taken from numpy and help to remove module name when documenting function. (long function name to short function name)
• add an option (yalm matter) in first page to remove sidebar
• add option to sphinx config (conf.py) for pydat theme : center navbar and rename logo text.

Add for the documentation/docstring

• debug some reSt syntax of docstring for list (missing blankline)
• Keep a short first docstring line in function for function short summary (for display in table)