Some docs tweaks (#222)

Author: zingale

docs/source/design.rst

@@ -47,7 +47,7 @@ two sub-directories for problems and tests, appearing as:
 * *solver-name*
 
   * ``problems/`` : the problem setups and inputs file that work for this solver.
-     In some cases, this might be a symlink to a similar solver that we inherit from.
+    In some cases, this might be a symlink to a similar solver that we inherit from.
 
   * ``tests/``. reference output (HDF5 files) used for the regression testing.
 

docs/source/running.rst

@@ -1,10 +1,11 @@
 Running
 =======
 
-Pyro can be run in two ways: either from the commandline, using the
-``pyro_sim.py`` script (this will be installed into your search path)
-and passing in the solver, problem and inputs as arguments, or by
-using the :func:`Pyro <pyro.pyro_sim.Pyro>` class.
+Pyro can be run in two ways:
+
+* from the commandline, using the ``pyro_sim.py`` script (this will be installed into your search path)
+
+* by using the :func:`Pyro <pyro.pyro_sim.Pyro>` class directly in ipython or Jupyter
 
 Commandline
 ------------
@@ -79,7 +80,7 @@ visualization for the previous example, we would do:
 
 .. code-block:: python
 
-    parameters = {"vis.dovis":0}
+    parameters = {"vis.dovis": 0}
     p.initialize_problem(problem_name="kh",
                          inputs_file="inputs.kh",
                          inputs_dict=parameters)
@@ -132,11 +133,13 @@ as:
    ...
    cfl = rp.get_param("hydro.cfl")
 
-When pyro is run, the file ``inputs.auto`` is output containing the
-full list of runtime parameters, their value for the simulation, and
-the comment that was associated with them from the ``_defaults``
-files. This is a useful way to see what parameters are in play for a
-given simulation.
+.. tip::
+
+   When pyro is run, the file ``inputs.auto`` is output containing the
+   full list of runtime parameters, their value for the simulation, and
+   the comment that was associated with them from the ``_defaults``
+   files. This is a useful way to see what parameters are in play for a
+   given simulation.
 
 All solvers use the following parameters: