Remove utils.myopen(), add tests for io.open_file()

[victorlin]

Description of proposed changes

Motivated by work in #854.

Related issue(s)

N/A

Testing

Added tests for io.open_file().

[codecov]

Codecov Report

Merging #926 (785b232) into master (440f7c6) will increase coverage by 24.99%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           master     #926       +/-   ##
===========================================
+ Coverage   34.59%   59.59%   +24.99%     
===========================================
  Files          42       43        +1     
  Lines        6044     6056       +12     
  Branches     1549     1550        +1     
===========================================
+ Hits         2091     3609     +1518     
+ Misses       3879     2188     -1691     
- Partials       74      259      +185     

Impacted Files	Coverage Δ
augur/utils.py	56.90% <ø> (+12.58%)	⬆️
augur/titer_model.py	19.96% <100.00%> (ø)
augur/dates.py	87.17% <0.00%> (-12.83%)	⬇️
bin/augur	80.00% <0.00%> (ø)
augur/util_support/date_disambiguator.py	96.07% <0.00%> (+1.96%)	⬆️
augur/io.py	100.00% <0.00%> (+2.43%)	⬆️
augur/import_beast.py	10.71% <0.00%> (+3.57%)	⬆️
augur/util_support/color_parser.py	100.00% <0.00%> (+3.57%)	⬆️
augur/util_support/node_data_reader.py	100.00% <0.00%> (+4.87%)	⬆️
augur/sequence_traits.py	14.92% <0.00%> (+5.97%)	⬆️
... and 24 more

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[huddlej]

Whoa...I didn't realize this function was still in use! It looks like the only usage is now in the titer_model.py module. Instead of maintaining myopen, I would replace the reference to it in titer_model.py with io.open_file and then delete the function from utils.py.

That open_file function is already tested, so we wouldn't need to add any more tests as part of this change.

[victorlin]

@huddlej thanks for providing that context, I didn't realize open_file/xopen does the same thing but probably better. I chose to keep the tests but move them to test_io.py, for completeness in testing read/write of txt/gz/xz files.