Reorg core, docstrings, and tests

[karllark]

Reorganizing the core to make it possible to run for a single population instead of only an image. This should allow for simpler runs including fitting on clusters and easier tests.

Updating docstrings and tests as I (re)learn the code in detail as well.

[codecov-commenter]

Codecov Report

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  Coverage          ?   21.42%           
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  Files             ?        7           
  Lines             ?      308           
  Branches          ?        0           
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  Hits              ?       66           
  Misses            ?      242           
  Partials          ?        0           

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[karllark]

Here is an overview of what got changed by this pull request:

Complexity increasing per file
==============================
- megabeast/tests/test_read_input.py  4
- megabeast/tools/plot_parameter_maps.py  3
- megabeast/tools/plot_input_data.py  35
- megabeast/read_input.py  5
- megabeast/tools/make_naive_maps.py  14
- megabeast/megabeast_fit.py  6

Clones added
============
- megabeast/tools/plot_input_data.py  3

See the complete overview on Codacy

[karllark]

Merging to get the current work in. Things are not really working, but need to work on docs before getting back to fixing the code.