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Improvements to the JSON interface

Gregory Ashton requested to merge jsonify-part-the-second into master

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

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