fix: Pin Biopython to <=1.80

[corneliusroemer]

1.81 is incompatible with BCBio.GFF which requires a module
that was removed in 1.81
Partially resolves #1151

Checklist

• Add a message in CHANGES.md summarizing the changes in this PR that are end user focused. Keep headers and formatting consistent with the rest of the file.
• Tests pass, even for Biopython latest - which is exactly what we need

After release, make sure Bioconda gets the pin mirrored

[codecov]

Codecov Report

Base: 68.17% // Head: 68.17% // No change to project coverage 👍

Coverage data is based on head (384f36b) compared to base (03a9188).
Patch coverage: 100.00% of modified lines in pull request are covered.

❗ Current head 384f36b differs from pull request most recent head a89cccb. Consider uploading reports for the commit a89cccb to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1152   +/-   ##
=======================================
  Coverage   68.17%   68.17%           
=======================================
  Files          63       63           
  Lines        6752     6752           
  Branches     1654     1654           
=======================================
  Hits         4603     4603           
  Misses       1841     1841           
  Partials      308      308           

Impacted Files	Coverage Δ
augur/__version__.py	100.00% <100.00%> (ø)

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[tsibley]

I think pinning and a subsequent Augur release is the way to go here in the short term. Thanks for taking care of it. Then in the near term, I think either replacing BCBio.GFF or waiting for a fix in it (if it seems imminent).

A few minor notes below, but nothing super important.

1.81 is incompatible with BCBio.GFF which requires a module that was removed in 1.81

I'd suggest updating this commit message to s/module/class/ and include that the class in question is UnknownSeq.

[corneliusroemer]

@tsibley I added the class (I think you forgot to mention it) and how the error presents to users who get Biopython 1.81.

[tsibley]

Even better! :-) One minor thing is the Markdown syntax isn't quite right:

[tsibley]

(and the new commit's message says "README" but means "CHANGES")