Merge pull request #248 from opesci/docs-cleanup

(Incomplete) documentation cleanup

Author: Michael Lange

docs/devito.rst

@@ -25,6 +25,14 @@ devito.compiler module
     :undoc-members:
     :show-inheritance:
 
+devito.dimension module
+--------------------------
+
+.. automodule:: devito.dimension
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 devito.finite_difference module
 -------------------------------
 
@@ -33,94 +41,98 @@ devito.finite_difference module
     :undoc-members:
     :show-inheritance:
 
-devito.function_manager module
-------------------------------
+devito.interfaces module
+------------------------
 
-.. automodule:: devito.function_manager
+.. automodule:: devito.interfaces
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.interfaces module
+devito.logger module
 ------------------------
 
-.. automodule:: devito.interfaces
+.. automodule:: devito.logger
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.operator module
-----------------------
+devito.memmap_manager module
+------------------------
 
-.. automodule:: devito.operator
+.. automodule:: devito.memmap_manager
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.propagator module
+devito.memory module
 ------------------------
 
-.. automodule:: devito.propagator
+.. automodule:: devito.memory
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.stencilkernel module
----------------------------
+devito.nodes module
+------------------------
 
-.. automodule:: devito.stencilkernel
+.. automodule:: devito.nodes
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.dimension module
------------------------
+       devito.operator module
+----------------------
 
-.. automodule:: devito.dimension
+.. automodule:: devito.operator
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.iteration module
------------------------
+devito.parameters module
+------------------------
 
-.. automodule:: devito.iteration
+.. automodule:: devito.parameters
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.expression module
+devito.pointdata module
 ------------------------
 
-.. automodule:: devito.expression
+.. automodule:: devito.pointdata
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.tools module
--------------------
+devito.profiler module
+------------------------
 
-.. automodule:: devito.tools
+.. automodule:: devito.profiler
     :members:
     :undoc-members:
     :show-inheritance:
 
-devito.logger module
---------------------
+devito.stencil module
+------------------------
 
-.. automodule:: devito.logger
+.. automodule:: devito.stencil
     :members:
     :undoc-members:
     :show-inheritance:
-    
 
-devito.at_controller module
+devito.tools module
 -------------------
 
-.. automodule:: devito.at_controller
+.. automodule:: devito.tools
     :members:
     :undoc-members:
     :show-inheritance:
 
+devito.visitor module
+-------------------
 
-
+.. automodule:: devito.visitor
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/heat.rst

@@ -42,17 +42,18 @@ We plug the stencil in an Operator, as shown, and define the values of the
 thermal conductivity :obj:`a`, the spacing between cells :obj:`h` and the
 temporal spacing :obj:`s`.::
 
-   op = Operator(
-           stencils = Eq(u.forward, stencil),
-           substitutions = {a: tc, h: dx, s: dt},
-           nt = timesteps,
-           shape = (nx, ny),
-           spc_border = 1,
-           time_border = 1)
+   op = Operator(Eq(u.forward, stencil),
+                 subs={h: spacing, s: dt, a: tc})
 
 
-To execute the generated Operator, we simply call :samp:`op.apply()`. The
-results will then be found in :obj:`u.data[1, :]`.
+To execute the generated Operator, we simply call :samp:`op.apply(u=u,
+t=timesteps)`. The results will then be found in :obj:`u.data[1, :]`.
 
-For a complete example of this code, check file `test_diffusion.py` in the
-`tests` folder.
+For a complete example of this code, please see
+`examples/diffusion/example_diffusion.py`. A more comprehensive set of
+CFD tutorials based on the excellent `12 steps to Navier-Stokes`__
+tutorial is currently under construction and will be published here soon.
+
+.. _cfdtutorial: http://lorenabarba.com/blog/cfd-python-12-steps-to-navier-stokes/
+
+__ cfdtutorial_