Randall J. LeVeque

I don't know too much about it, but I think maybe just GDAL. The [documentation](https://github.com/mapbox/rasterio) says dependencies are "GDAL, GEOS, and PROJ4 libraries".

@mandli: This wave_tolerance logic is based on how speed_tolerance is handled, but I don't understand how this is supposed to be used exactly. I would have thought that `speed_tolerance[m]` is...

Two tests are failing, `tests/acoustics_2d_radial` and `tests/acoustics_2d_adjoint`. The former ran fine on my laptop and the latter did not, but I updated the `regression_data` in commit e1ff225, and now it...

I tried running it on a linux machine and I got the same results as @mandli, and digging into the `tests/acoustics_2d_radial` results, the level 3 grids it makes are slightly...

It's a small unit test problem and looking at `fort.amr` after setting `verbosity` and `verbosity_regrid` to 3, I see that the number of cells flagged already differs at time 0,...

Actually it's worse than this, even `checkpt_style > 0` options aren't documented.

I see there are other things that could also be cleaned up, e.g. amdq and apdq are declared in step2 and passed to flux2 but are only needed in flux2...

@mjberger asked "is there ever a reason to have the level parameter (level of refinement of a grid) in the bc2amr routines? While I'm sorting through millions of arguments, it...

On further reflection we decided to leave the calling sequences alone.

See also https://github.com/clawpack/geoclaw/issues/297.