io: Pass encoding and newline keyword arguments to open_file

[huddlej]

Context
Since version 1.3.0, xopen supports passing encoding and newline arguments through to the lower level open function calls for each compression method. When we added the io module to augur, we had to accept that we could not pass these arguments to the new open_file function because they wouldn't be accepted by xopen.

Description
We should require xopen version >=1.3.0 in our dependencies here and in the Bioconda recipe and update our internal calls to open_file to use encoding and newline arguments. We should also explicitly define these as keyword arguments for open_file to better document their availability.

Alternately, we could still consider implementing our own compression layer that will allow us to have more control over compression parameters like XZ compression, etc.