[Biopython-dev] Time for Biopython 1.65?

Peter Cock p.j.a.cock at googlemail.com
Tue Nov 18 11:25:41 UTC 2014

On Tue, Nov 18, 2014 at 1:39 AM, Travis Wrightsman <twrig002 at ucr.edu> wrote:
> I'll proof read the generated API docs for formatting and spelling but I
> can't critique any code since I'm not familiar with biopython's modules and
> how they all work yet.

That would be great, thank you - a fresh set of eyes :)

On Mon, Nov 17, 2014 at 4:20 PM, Evan Parker <eparker05 at gmail.com> wrote:
> The lazy-load-pull branch has been rebased on the current master and is
> passing tests. It was previously failing tests due to the issue with the
> MySQL connector.

Good work. It looks like a few PEP8 tweaks need to be re-fixed (spaces
after # signs for example) but that's fairly harmless.

Note that Evan's code adds new classes to Bio/SeqIO/*.py which
makes it a lot more "invasive" than simply adding a new experimental
module. The code does issue the BiopythonExperimentalWarning when
the lazy argument is used in the Bio.SeqIO top level functions - but on
the other hand the new classes do not say "Experimental" or issue
warnings if used directly. Should they?

[And should we discuss this on the pull request instead?]


P.S. I'm tempted to cherry-pick Evan's fix to Bio/GenBank/__init__.py - at
least to remove the extra underscore in self.__expected_size

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