[Biopython] Biopython 1.78 plans - please help with testing

[Peter Cock]

Hello all,

If anyone has tested the current master as requested, I have not
seen any replies or new reports about the alphabet removal.

I've now updated our wheel building repository to stage wheels on
Anaconda (alongside various other scientific python packages) in
place of the expired Rackspace hosting. That means in principle
we should be OK to build Biopython 1.78 now.

There were no comments about where best to put the information
currently on https://github.com/biopython/biopython/issues/3156 -
I intend to move it to a dedicated page on the website (and update
the exceptions to point there instead).

Are there any remaining issues people feel should delay the release,
or shall I start it in a few days time?

Thanks,

Peter

On Sun, Aug 16, 2020 at 12:27 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hello all,
>
> Michiel and I would like to do the Biopython 1.78 release soon, hopefully
> in August.
>
> Right now I would encourage all of you familiar with installing from
> source to try
> the latest Biopython from github, and report any issues you find:
>
> https://github.com/biopython/biopython/issues
>
> The main change is in the removal of Bio.Alphabet, and I want our
> documentation
> ready to make this as painless a change as possible. We think the tutorial
> is ready,
> and I have now updated the code snippets on the website as well (see
> https://github.com/biopython/biopython.github.io for this).
>
> Would it help to share a preview of the tutorial on the website? Some time
> back
> we had the stable release side by side with a manually updated dev version.
>
> We have a few use cases here for sequencing input/ouput where you need to
> specify the kind of sequence (DNA, RNA or protein), which is one of the few
> reasons you might still have been using Bio.Alphabet in your code:
>
> https://github.com/biopython/biopython/issues/3156
>
> Any thoughts on where that should be put? Left as an issue; a page on the
> website;
> a blog post on www.open-bio.org; in the DEPRECATED file, other?
>
> There is one small stumbling block to the actual release: we need to update
> the temporary staging area used for pre-built wheels before uploading them
> to PyPI. The rackspace storage we and the numpy community were using has
> expired, but the consensus seems to be using anaconda.org instead:
>
> https://github.com/biopython/biopython-wheels/issues/6
>
> Thank you all,
>
> Peter
>
>
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