Send filter warnings to stderr

[victorlin]

Description of proposed changes

To be consistent with other warnings, for example:

• augur/augur/filter.py

  Line 913 in e4fdf59

  print(f"WARNING: A 'date' column could not be found to group-by year or month.", file=sys.stderr)

• augur/augur/filter.py

  Line 954 in e4fdf59

  print(f"WARNING: Some of the specified group-by categories couldn't be found: {', '.join(unknown_groups)}", file=sys.stderr)

• augur/augur/filter.py

  Lines 1617 to 1621 in e4fdf59

  	print(
  	"WARNING: The sequence index is out of sync with the provided sequences.",
  	"Metadata and strain output may not match sequence output.",
  	file=sys.stderr
  	)

Caught the inconsistency while implementing 9bcbccc6.

Related issue(s)

None

Testing

Updated tests accordingly.

[codecov]

Codecov Report

Merging #862 (6cf8d73) into master (bdfbe82) will increase coverage by 0.03%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##           master     #862      +/-   ##
==========================================
+ Coverage   34.27%   34.31%   +0.03%     
==========================================
  Files          41       41              
  Lines        5941     5937       -4     
  Branches     1520     1518       -2     
==========================================
+ Hits         2036     2037       +1     
+ Misses       3823     3818       -5     
  Partials       82       82              

Impacted Files	Coverage Δ
augur/filter.py	68.28% <0.00%> (ø)
augur/validate.py	40.59% <0.00%> (-0.90%)	⬇️
augur/export_v2.py	11.03% <0.00%> (+0.03%)	⬆️

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