update formatting for getting_started.rst

docs/getting_started.rst

@@ -3,21 +3,26 @@ Getting Started
 
 This page details how to get started with ``lpath``.
 
-Users may install this program via [PyPI](https://pypi.org/project/lpath-md/) (recommended) or 
-from [GitHub Source](https://github.com/chonglab-pitt/lpath). By default, LPATH is installed with the bare minimum to 
+Users may install this program via `PyPI`_ (recommended) or
+from `GitHub Source`_. By default, LPATH is installed with the bare minimum to
 run analysis on classic MD simulations. Users who intend to analyze WESTPA simulations should install WESTPA 
 in the same environment.
 
-1. Install from [PyPI](https://pypi.org/project/lpath-md/):
-    ```python -m  pip install lpath-md```
-2. Install from [GitHub Source](https://github.com/chonglab-pitt/lpath):
-    1. Clone the git repository:  ```git clone https://github.com:chonglab-pitt/lpath```
+1. Install from `PyPI`_:
+
+    python -m  pip install lpath-md
+
+2. Install from `GitHub Source`_ :
+    1. Clone the git repository:  ``git clone https://github.com:chonglab-pitt/lpath``
     2. Move into the folder: ```cd lpath```
-    3. Install the program in editable mode: ```python -m pip install -e .```
+    3. Install the program in editable mode: ``python -m pip install -e .``
 3. There are a variety of optional dependencies you may install. These work with either installation options listed above.
-    1. Install with `WESTPA`: ```python -m pip install lpath-md[westpa]```
-    2. Install with terminal user interface (TUI): ```python -m pip install lpath-md[tui]```
+    1. Install with ``WESTPA``: ``python -m pip install lpath-md[westpa]``
+    2. Install with terminal user interface (TUI): ``python -m pip install lpath-md[tui]``
     3. Developers can install with [dev] (all dependencies) or [test] (minimal dependencies to run tests): ```python -m pip install lpath-md[dev]```
-    4. Options may be combined: ```python -m pip install lpath-md[westpa,tui]```
+    4. Options may be combined: ``python -m pip install lpath-md[westpa,tui]``
+4. Run all or parts of the program. See `Usage`_ for more information.
 
+.. _PyPI: https://pypi.org/project/lpath-md/
+.. _GitHub Source: https://github.com/chonglab-pitt/lpath
 .. _Usage: https://lpath.readthedocs.io/en/latest/usage.html