Deprecate Bio.Index

[peterjc]

This pull request addresses issue #...

• I hereby agree to dual licence this and any previous contributions under both
  the Biopython License Agreement AND the BSD 3-Clause License.

• I have read the CONTRIBUTING.rst file, have run flake8 locally, and
  understand that AppVeyor and TravisCI will be used to confirm the Biopython unit
  tests and style checks pass with these changes.

• I have added my name to the alphabetical contributors listings in the files
  NEWS.rst and CONTRIB.rst as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

[codecov]

Codecov Report

Merging #2205 into master will increase coverage by 1.37%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2205      +/-   ##
==========================================
+ Coverage   83.31%   84.68%   +1.37%     
==========================================
  Files         316      317       +1     
  Lines       51217    51451     +234     
==========================================
+ Hits        42671    43573     +902     
+ Misses       8546     7878     -668

Impacted Files	Coverage Δ
Bio/Index.py	34.14% <100%> (+2.5%)	⬆️
Bio/SearchIO/_model/query.py	91.5% <0%> (-0.93%)	⬇️
Bio/PDB/mmtf/DefaultParser.py	100% <0%> (ø)
Bio/SearchIO/HHsuiteIO/hhsuite2_text.py	97.03% <0%> (+0.02%)	⬆️
Bio/Align/__init__.py	87.43% <0%> (+0.03%)	⬆️
Bio/GenBank/Scanner.py	82.8% <0%> (+0.04%)	⬆️
Bio/SeqIO/InsdcIO.py	93.08% <0%> (+0.04%)	⬆️
Bio/AlignIO/MafIO.py	92.92% <0%> (+0.04%)	⬆️
Bio/Phylo/Consensus.py	83.1% <0%> (+0.05%)	⬆️
Bio/GenBank/__init__.py	93.76% <0%> (+0.06%)	⬆️
... and 38 more

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[peterjc]

No replies on the mailing list yet either:
https://mailman.open-bio.org/pipermail/biopython/2019-August/016655.html