Hide BiopythonDeprecationWarnings when reading certain sequence files

[victorlin]

Description of proposed changes

Biopython 1.85 shows a deprecation warning when using format='fasta' with files that start with anything but '>'.

The warning as-is should not be exposed to Augur users. It is not triggered when reading files with format='fasta-pearson', so this is the easiest thing to do continue accepting such files for Biopython >=1.85.

This way, Augur users get consistent, backwards compatible behavior no matter the Biopython version they use.

Related issue(s)

Fixes #1727

Checklist

• Automated checks pass
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• Check if you need to add tests
• Check if you need to update docs
• Merge base PR Centralize sequence read operations #1730

[corneliusroemer]

Suggestion for this elegant solution with version switch is from @tsibley: #1727 (comment)

[corneliusroemer]

I don't quite understand why we don't do the BIOPYTHON_FASTA_FORMAT version switch for biopython version inside this function.

Rather than requiring users (even internal ones) to pass the fasta argument, we should just rewrite fasta -> fasta-pearson inside the function here and note this in the docstring and our changelog.

[victorlin]

Done:

augur/augur/io/sequences.py

Lines 20 to 22 in 5c53256

	# Allow comments in FASTA format using fasta-pearson in later biopython versions
	if Version(version("biopython")) >= Version("1.85") and biopython_format == "fasta":
	biopython_format = "fasta-pearson"

[corneliusroemer]

We could abstract away this change here by doing the version switch inside of read_sequence(s) helpers instead.

[victorlin]

Done:

augur/augur/io/sequences.py

Lines 20 to 22 in 5c53256

	# Allow comments in FASTA format using fasta-pearson in later biopython versions
	if Version(version("biopython")) >= Version("1.85") and biopython_format == "fasta":
	biopython_format = "fasta-pearson"

[corneliusroemer]

A unit test testing that a variety of fasta's are supported would be cool maybe, we already know that our integration tests catch it, but not unit ones.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 73.01%. Comparing base (fbb56fe) to head (5c53256).

Additional details and impacted files

@@                          Coverage Diff                           @@
##           victorlin/centralize-sequence-read    #1731      +/-   ##
======================================================================
+ Coverage                               72.94%   73.01%   +0.06%     
======================================================================
  Files                                      79       79              
  Lines                                    8316     8326      +10     
  Branches                                 1696     1698       +2     
======================================================================
+ Hits                                     6066     6079      +13     
+ Misses                                   1961     1959       -2     
+ Partials                                  289      288       -1     

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