Add biogeochemical interface to ocean_simulation

[vtamsitt]

This PR addresses #107 by adding a biogeochemistry kwarg to ocean_simulation, adding user input boundary_conditions as a kwarg and moves tracer to be explicitly spelled out be the user as a kwarg.

Right now the user input boundary_conditions will be merged with hardcoded boundary conditions for T and S, unless the user supplies BCs for T and S in which case they will override the hardcoded ones. As @glwagner pointed out

it would be nice if we only replace the boundary conditions we have to, ie we keep the surface fluxes of T, S even if we need to use user-supplied T or S conditions at the bottom or on immersed boundaries

but I haven't implemented that yet.