Explicitly record EMBL/GenBank molecule type

[peterjc]

This builds on my recent commits to improve the EMBL/GenBank topology parsing (see fd7b171 and the subsequent commits which refactored to cover some corner cases, and add more tests), and will really close #363

Note this means record.annotations["topology"] and record.annotations["molecule_type"] together essentially replace the legacy handling of the composite residue type dating from early GenBank/EMBL files where this was one field.

[peterjc]

TravisCI is happy except for pypy3 which is failing in general.

[peterjc]

@kblin could you cast your eyes over this please?

[codecov-io]

Current coverage is 80.39% (diff: 78.78%)

Merging #1005 into master will increase coverage by <.01%

@@             master      #1005   diff @@
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  Files           319        319          
  Lines         48762      48792    +30   
  Methods           0          0          
  Messages          0          0          
  Branches          0          0          
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+ Hits          39199      39224    +25   
- Misses         9563       9568     +5   
  Partials          0          0          

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[kblin]

Sorry, missed that notification again. I really need a better setup where my GitHub notifications go in my mail client, as GitHub is unable to send them to the right address.

The only worry I have is that I do see quite a bunch of GenBank files that have neither "linear" nor "circular", but the way I read the check in the GenBank parser, that would trigger the ParserFailureError("Unexpected topology %r should be linear or circular" % topology) error.

[peterjc]

Sorry, I could have waited but ended up working on a bunch of related EMBL/GenBank bits at the end of last week and wanted to merge it sooner rather than later.

[Update - reworded after double checking the code:]
Regarding the error for values other than linear and circular, that does also allow blank - which would mean nothing in the annotations dictionary at all. See the line above, if topology: and the pattern in the scanner of stripping white space before calling the consumer method.

Perhaps I need to reword the exception slightly?

[kblin]

Nah, it's fine. I just looked over the code too quickly. Looking good. Belated 👍 from me :)

[peterjc]

Thanks :)