io: Split io.py into smaller files under new io/

[victorlin]

Description of proposed changes

This change helps modularize the functions within io.py and io_support/. With the wildcard imports in io/__init__.py, existing imports do not have to be modified.

Related issue(s)

N/A

Testing

Test files updated to reflect the new way of organizing things. Note that there is no test_metadata.py or test_print.py but the contents already have full coverage based on the Codecov report.

[codecov]

Codecov Report

Merging #949 (b31b9bc) into master (5916362) will increase coverage by 0.02%.
The diff coverage is 63.77%.

@@            Coverage Diff             @@
##           master     #949      +/-   ##
==========================================
+ Coverage   59.34%   59.36%   +0.02%     
==========================================
  Files          42       47       +5     
  Lines        6011     6014       +3     
  Branches     1539     1539              
==========================================
+ Hits         3567     3570       +3     
  Misses       2185     2185              
  Partials      259      259              

Impacted Files	Coverage Δ
augur/io/vcf.py	42.50% <42.50%> (ø)
augur/io/__init__.py	100.00% <100.00%> (ø)
augur/io/file.py	100.00% <100.00%> (ø)
augur/io/metadata.py	100.00% <100.00%> (ø)
augur/io/print.py	100.00% <100.00%> (ø)
augur/io/sequences.py	100.00% <100.00%> (ø)
augur/io/shell_command_runner.py	91.89% <100.00%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5916362...b31b9bc. Read the comment docs.

[tsibley]

Looks great to me! Definitely appreciate this direction and removal of the augur.io_support package in favor of modules under augur.io.