First proposal for advanced mode, see #111
Corrected some prints and removed exit 0
Merge branch 'advanced_mode' of https://github.com/jhmatthews/python into dev
Implemented a first attempt at an advanced mode accessed with -d flag
added option to turn on and off dvds diagnostics
Fixed a simple emrge conflict (space)
removed deps for test
removed more files generated by configure
Merge pull request #121 from jhmatthews/delete_gsl_dependencies

Delete locally generated gsl files
Revised contents of py_progs
Included setup_py_dir again
Commenting and moving around code
Merge branch 'advanced_mode' of https://github.com/jhmatthews/python into advanced_mode
Included diag.o in makefile py_wind_objects
Adopted astropy file formats for spectrum and py_wind, and updated py_read_output.py
Merge pull request #123 from jhmatthews/astropy_formats

Adopted astropy file formats for spectrum and py_wind, and updated py_read_output.py
edited loops in lucy mazzali to not go off end of arrays
multiple changes- DEBUG statements replaced with Debug in get_atomicdata, added function to modes which controls whether to print out a summary of the atomic data to file, replaced a few other instances of #if DEBUG.
edited get_atomicdata to use separate variable to modes structure as does not include python.h
Included geo.fill in all calculations of tau_sobolev.

Also made all calculations of the sobolev optical depth explicitly use
the sobolev() function. This involved changing get_ion_density to use
a general three-vector x rather than the photon pointer, declaring
a wind pointer in p_escape, and changing the second argument of
sobolev to be a three-vector x rather than a PhotPtr. The philosophy
being that you shouldn't a PhotPtr to calculate a tau, just
a position and a line pointer - the example being that we have to calculate
p_escape in cells.