fix some docs and the io.read solver detection (#127)

Author: zingale

docs/source/mesh_basics.rst

@@ -22,10 +22,10 @@ We import the basic mesh functionality as:
 
 .. code-block:: python
 
-   import mesh.patch as patch
-   import mesh.fv as fv
-   import mesh.boundary as bnd
-   import mesh.array_indexer as ai
+   import pyro.mesh.patch as patch
+   import pyro.mesh.fv as fv
+   import pyro.mesh.boundary as bnd
+   import pyro.mesh.array_indexer as ai
 
 There are several main objects in the patch class that we interact with:
 

docs/source/output.rst

@@ -48,7 +48,7 @@ the ghost cells).
 .. code-block:: python
 
    import matplotlib.pyplot as plt
-   import util_pyro.io as io
+   import pyro.util.io_pyro as io
    sim = io.read("sedov_unsplit_0000.h5")
    dens = sim.cc_data.get_var("density")
    plt.plot(dens.g.x, dens[:,dens.g.ny//2])

docs/source/running.rst

@@ -1,9 +1,10 @@
 Running
 =======
 
-Pyro can be run in two ways: either from the commandline, using the ``pyro_sim.py``
-script 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: 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.
 
 Commandline
 ------------
@@ -18,7 +19,7 @@ For example, to run the Sedov problem with the compressible solver we would do:
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible sedov inputs.sedov
+   pyro_sim.py compressible sedov inputs.sedov
 
 This knows to look for ``inputs.sedov`` in ``compressible/problems/``
 (alternately, you can specify the full path for the inputs file).
@@ -27,15 +28,15 @@ To run the smooth Gaussian advection problem with the advection solver, we would
 
 .. prompt:: bash
 
-   ./pyro_sim.py advection smooth inputs.smooth
+   pyro_sim.py advection smooth inputs.smooth
 
 Any runtime parameter can also be specified on the command line, after
 the inputs file. For example, to disable runtime visualization for the
 above run, we could do:
 
 .. prompt:: bash
 
-   ./pyro_sim.py advection smooth inputs.smooth vis.dovis=0
+   pyro_sim.py advection smooth inputs.smooth vis.dovis=0
 
 
 .. note::
@@ -63,11 +64,11 @@ Kelvin-Helmholtz problem ``kh``, we would do the following:
 
 .. code-block:: python
 
-    from pyro import Pyro
-    pyro = Pyro("compressible")
-    pyro.initialize_problem(problem_name="kh",
-                            inputs_file="inputs.kh")
-    pyro.run_sim()
+    from pyro.pyro_sim import Pyro
+    p = Pyro("compressible")
+    p.initialize_problem(problem_name="kh",
+                         inputs_file="inputs.kh")
+    p.run_sim()
 
 Instead of using an inputs file to define the problem parameters, we can define a
 dictionary of parameters and pass them into the :func:`initialize_problem
@@ -79,9 +80,9 @@ visualization for the previous example, we would do:
 .. code-block:: python
 
     parameters = {"vis.dovis":0}
-    pyro.initialize_problem(problem_name="kh",
-                            inputs_file="inputs.kh",
-                            inputs_dict=parameters)
+    p.initialize_problem(problem_name="kh",
+                         inputs_file="inputs.kh",
+                         inputs_dict=parameters)
 
 It's possible to evolve the simulation forward timestep by timestep manually using
 the :func:`single_step <pyro.pyro_sim.Pyro.single_step>` function (rather than allowing
@@ -90,7 +91,7 @@ simulation forward by a single step, we'd run
 
 .. code-block:: python
 
-    pyro.single_step()
+    p.single_step()
 
 This will fill the boundary conditions, compute the timestep ``dt``, evolve a
 single timestep and do output/visualization (if required).

pyro/util/io_pyro.py

@@ -62,7 +62,7 @@ def read(filename):
                 bc_solver = "compressible"
             else:
                 bc_solver = solver_name
-            bcmod = importlib.import_module("{}.{}".format(bc_solver, "BC"))
+            bcmod = importlib.import_module(f"pyro.{bc_solver}.BC")
             for name in custom_bcs:
                 bnd.define_bc(name, bcmod.user, is_solid=custom_bcs[name])
 
@@ -107,7 +107,7 @@ def read(filename):
             my_particles = None
 
         if solver_name is not None:
-            solver = importlib.import_module(solver_name)
+            solver = importlib.import_module(f"pyro.{solver_name}")
 
             sim = solver.Simulation(solver_name, problem_name, None)
             sim.n = n