Change docstrings so they render correctly with sphinx.

Sphinx doesn't like ampersands.

docathon

.gitignore

@@ -15,11 +15,13 @@
 # PyClaw-specific files to ignore
 _output
 _plots
+_plots*
 petclaw.log
 pyclaw.log
 .noseids
 _build
 build
+*.dSYM
 
 # symlink to examples directory
 src/pyclaw/examples

examples/advection_1d/advection_1d.py

@@ -8,7 +8,7 @@
 Solve the linear advection equation:
 
 .. math:: 
-    q_t + u q_x & = 0.
+    q_t + u q_x = 0.
 
 Here q is the density of some conserved quantity and u is the velocity.
 

examples/advection_2d/advection_2d.py

@@ -6,8 +6,8 @@
 
 Solve the two-dimensional advection equation
 
-.. math:: 
-    q_t + u q_x + v q_y & = 0
+.. math::
+    q_t + u q_x + v q_y = 0
 
 Here q is a conserved quantity, and (u,v) is the velocity vector.
 """

examples/advection_2d_annulus/advection_annulus.py

@@ -6,8 +6,8 @@
 
 Solve the linear advection equation:
 
-.. math:: 
-    q_t + (u(x,y) q)_x + (v(x,y) q)_y & = 0
+.. math::
+    q_t + (u(x,y) q)_x + (v(x,y) q)_y = 0
 
 in an annular domain, using a mapped grid.
 

examples/advection_reaction_2d/advection_reaction.py

@@ -6,8 +6,8 @@
 Solve the 2D advection-reaction problem
 
 .. math::
-    p_t + u(x,y,t) p_x + v(x,y,t) p_y & = \epsilon q
-    q_t + u(x,y,t) q_x + v(x,y,t) q_y & = \epsilon p
+    p_t + u(x,y,t) p_x + v(x,y,t) p_y = \epsilon q \\
+    q_t + u(x,y,t) q_x + v(x,y,t) q_y = \epsilon p
 
 Note that the left hand side of this system is the non-conservative transport
 equation for p and q.  The Riemann solver assumes that velocities are specified

examples/burgers_1d/burgers_1d.py

@@ -8,7 +8,7 @@
 Solve the inviscid Burgers' equation:
 
 .. math:: 
-    q_t + \frac{1}{2} (q^2)_x & = 0.
+    q_t + \frac{1}{2} (q^2)_x = 0.
 
 This is a nonlinear PDE often used as a very simple
 model for fluid dynamics.

examples/euler_2d/quadrants.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # encoding: utf-8
-"""
+r"""
 Euler 2D Quadrants example
 ==========================
 

examples/euler_2d/shock_forward_step.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python
 # encoding: utf-8
-"""
+r"""
 Compressible Euler flow over a forward-facing step
 ==================================================
 
 Solve the Euler equations of compressible fluid dynamics in 2D:
 
 .. math::
-    \rho_t + (\rho u)_x + (\rho v)_y & = 0 \\
-    (\rho u)_t + (\rho u^2 + p)_x + (\rho uv)_y & = 0 \\
-    (\rho v)_t + (\rho uv)_x + (\rho v^2 + p)_y & = 0 \\
-    E_t + (u (E + p) )_x + (v (E + p))_y & = 0.
+    \rho_t + (\rho u)_x + (\rho v)_y = 0 \\
+    (\rho u)_t + (\rho u^2 + p)_x + (\rho uv)_y = 0 \\
+    (\rho v)_t + (\rho uv)_x + (\rho v^2 + p)_y = 0 \\
+    E_t + (u (E + p) )_x + (v (E + p))_y = 0.
 
 
 Here :math:`\rho` is the density, (u,v) is the velocity, and E is the total energy.

examples/kpp/kpp.py

@@ -6,8 +6,8 @@
 
 Solve the KPP equation:
 
-.. math:: 
-    q_t + (\sin(q))_x + (\cos(q))_y & = 0
+.. math::
+    q_t + (\sin(q))_x + (\cos(q))_y = 0
 
 first proposed by Kurganov, Petrova, and Popov.  It is challenging for schemes
 with low numerical viscosity to capture the solution accurately.

examples/shallow_2d/radial_dam_break.py

@@ -6,10 +6,10 @@
 
 Solve the 2D shallow water equations:
 
-.. :math:
-    h_t + (hu)_x + (hv)_y & = 0 \\
-    (hu)_t + (hu^2 + \frac{1}{2}gh^2)_x + (huv)_y & = 0 \\
-    (hv)_t + (huv)_x + (hv^2 + \frac{1}{2}gh^2)_y & = 0.
+.. math::
+    h_t + (hu)_x + (hv)_y = 0 \\
+    (hu)_t + (hu^2 + \frac{1}{2}gh^2)_x + (huv)_y = 0 \\
+    (hv)_t + (huv)_x + (hv^2 + \frac{1}{2}gh^2)_y = 0.
 
 The initial condition is a circular area with high depth surrounded by lower-depth water.
 The top and right boundary conditions reflect, while the bottom and left boundaries