Added conditional statement to real z calculation

Added if statement to the end of the loop in run.py to control whether or not to bother calculating the real z coordinate for the drifters. In the case of surface-only drifters, I suspect that no one cares what the real z depth is as the drifters bob up and down on the surface.
Added ability to control xlim/ylim in pcolor hist

Now xlim and ylim values can be input to the pcolor histogram for ease of plotting various magnifications.
small change to plotting
Eliminated sending indices into tracmass

Stopped the unnecessary practice of sending ia, ja, ka into tracmass since they can be inferred from xstart, ystart, zstart. This meant deleted several pieces of code in run.py. Also changed tools.convert_indices() to not expect i, j when converting indices.

By chance, also noticed that zsave in run.py was a little out of date and updated it so that it uses map_coordinates, similar to what happens at the end of each loop to call tracmass.
Added options to test1 initializaton in init.py

Options added to init.py are to make it easier to run tests smoothly, particularly sensitivity tests right now.
minor adjustment to zsave in run.py
little changes
Added some timing functionality

Times for some of the possibly time-consuming parts of the run script have been saved at key points in order to figure out where the most time is being spent.
User manual

Working on the ipython user manual. Updating to actual markdown.
New version of the user manual

The iPython user manual is set up pretty well currently. It works with the tracpy code and runs a simple example that can be easily expanded and played around with.
Updated README.md file with accurate instructions
Added __init__, small doc fix to plotting, tools

Added an __init__.py file with some information about tracpy and tracmass.
Added manual.pdf and updated README.md
Added .gitignore and working on README
playing with README markdown
playing with README markdown more
Miscellaneous mostly minor changes

Mostly did some changes to being able to take in the aggregated netCDF model output appropriately in inout.py functions. Also added in a line to several functions in there as a workaround to an issue with netCDF thredds files input/output. Updated the manual notebook and pdf and eliminated some extraneous lines.
New plotting routines and updated manual

'hexbin' and 'hist2d' are new options for the hist plotting function. The 'hexbin' option is the new default because it looks better than the others. Also, the manual was updated accordingly to use the hexbin plotting option.
deleted some hexbin comments
fixed savefile quirk that worked on rainier but not on hafen