update source documentation

Author: kathyxchen

docs/source/conf.py

@@ -37,7 +37,8 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
-    'sphinx.ext.intersphinx']
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.autosectionlabel',]
 
 intersphinx_mapping = {
     'python': ('https://docs.python.org/', None),

docs/source/index.rst

@@ -16,8 +16,8 @@ The Github repository is located `here <https://github.com/FunctionLab/selene>`_
 
    overview/overview
    overview/installation
-   overview/tutorials
    overview/cli
+   overview/tutorials
    overview/faq
 
 .. toctree::

docs/source/overview/cli.rst

@@ -2,7 +2,7 @@
 Selene CLI operations and outputs
 =================================
 
-Selene provides a command-line interface (CLI) that takes in a user-specified configuration file containing the operations the user wants to run and the parameters required for these operations. It is automatically installed using a setuptools entrypoint so it can be called with the bash function ``selene_sdk`` from anywhere in the bash. It can also be called with ``python -m selene_sdk``. See :ref:`Operations` for more detail.
+Selene provides a command-line interface (CLI) that takes in a user-specified configuration file containing the operations the user wants to run and the parameters required for these operations. It is automatically installed using a setuptools entrypoint so it can be called with ``python -m selene_sdk``. 
 
 The sections that follow describe in detail how the various components that make up the configuration file are specified. For operation-specific sections (e.g. training, evaluation), we also explain what the expected outputs are.
 

docs/source/overview/installation.rst

@@ -58,4 +58,4 @@ Additional dependency for running the CLI (versions 0.4.8 and below)
 --------------------------------------------------------------------
 
 Please install ``docopt`` before running the command-line script ``selene_cli.py`` provided in the repository. 
-In newer versions of Selene, the CLI can be run by calling ``selene_sdk`` or ``python -m selene_sdk`` from anywhere in bash (assuming you have installed the library, through conda/pip/local install - ``python setup.py install``).
+In newer versions of Selene, the CLI can be run by calling ``python -m selene_sdk`` from anywhere in bash (assuming you have installed the library, through conda/pip/local install - ``python setup.py install``).