Reorganise sub-module structure

[ivyleavedtoadflax]

This is a general tidy up:

• moves prodigy functions to deep_reference_parser.prodigy module
• moves io functions to the deep_reference_parser.io module
• linting with black

There are no substantive changes to the codebase, so if they tests pass, this should be good to go.

[codecov-io]

Codecov Report

Merging #19 into master will increase coverage by 3.24%.
The diff coverage is 92.77%.

@@            Coverage Diff             @@
##           master      #19      +/-   ##
==========================================
+ Coverage   81.31%   84.56%   +3.24%     
==========================================
  Files          14       16       +2     
  Lines        1247     1192      -55     
==========================================
- Hits         1014     1008       -6     
+ Misses        233      184      -49

Impacted Files	Coverage Δ
deep_reference_parser/reference_utils.py	100% <ø> (+35.94%)	⬆️
deep_reference_parser/deep_reference_parser.py	87.87% <100%> (-0.05%)	⬇️
deep_reference_parser/prodigy/labels_to_prodigy.py	100% <100%> (ø)
deep_reference_parser/prodigy/prodigy_to_tsv.py	97.47% <100%> (ø)	⬆️
deep_reference_parser/prodigy/misc.py	68.75% <68.75%> (ø)
deep_reference_parser/io/io.py	96.87% <97.82%> (+2.43%)	⬆️

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[nsorros]

On a separate note from this PR, make test should depend on virtualenv/.installed