Improvements to the JSON interface

Some small improvements to the JSON interface

1. Convert all open calls to with open to avoid read/write errors
2. Add a json object encoder/decoder to handle conversions of conmplex, arrays, and dataframes
3. Clean up the read_in_result method
4. Store pandas dict in list orientation
5. Minor fixes to documentation
6. Set of tests to check the encoding/decoding doesn't miss any data