Return occupied booleans in retrieve

[btjanaka]

Description

Previously, we relied on sentinel values to indicate whether a given cell was occupied. Since it is entirely possible that users want to use these sentinel values in their fields, we now return a separate occupied array that indicates which cells are occupied.

Considerations:

• Chose not to support additional return types like tuple and pandas for now, as such flexibility is less essential in retrieve, and this feature can be added fairly easily later on
• We still set the sentinel values depending on the field type since it may be confusing to see arbitrary values for a given field without seeing the occupied array.
• the threshold field is now included in outputs from retrieve()

TODO

• Implement new retrieve and retrieve_single methods
• Fix tests
• Fix usage in tutorials

Questions

Status

• I have read the guidelines in
  CONTRIBUTING.md
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• I have tested my code by running pytest
• I have linted my code with pylint
• I have added a one-line description of my change to the changelog in
  HISTORY.md
• This PR is ready to go