[Biopython] Planning Biopython 1.72

[Peter Cock]

The try/except pass might be a good idea for Jython, and
any other corner cases where the C code is unavailable.

For the wheels, I am thinking of skipping the automated
tests, and then verifying the wheels by hand in order to
get the release out tomorrow... but maybe with fresh
eyes I'll be able to solve the current issue on TravisCI.

Peter


On Sun, Jun 24, 2018 at 5:40 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi Peter,
>
> I see. We could put a try: except: block around importing _aligners, and
> raise an Exception if anybody tries to instantiate a PairwiseAligner if the
> C code is not available.
> I am against putting the pairwise aligner code in a separate submodule
> since, according to the Zen of Python, flat is better than nested.
>
>
> Best,
> -Michiel
>
> On Saturday, June 23, 2018, 6:47:39 PM GMT+9, Peter Cock
> <p.j.a.cock at googlemail.com> wrote:
>
>
> On Sat, Jun 23, 2018 at 2:32 AM, Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
>>> That has made be realise that the new pairwise alignment
>> code being in Bio.Align at top level means it gets imported
>> as a side effect all over the place. With hindsight, it would
>> have been better as a sub-module to avoid this overhead.
>> What are people's thoughts here?
>>
>> Hi Peter,
>> Can you show an example where this happens? I guess
>> usually people would use "from Bio import Align"; then it
>> doesn't really matter.
>>
>> Best,
>> -Michiel
>
> Using AlignIO imports Align, which now includes the new C code.
> This means if there is a problem with the C code, lots of things
> break (including SeqIO too, which imports AlignIO when needed).
>
> For an example, look at the logs for this attempt at building
> Linux and macOS wheels for Biopython 1.72,
>
> https://travis-ci.org/biopython/biopython-wheels/builds/395533386
>
> It seems to be something silly with the paths, meaning none
> of the C code is available from the installed new wheel.
>
> I was not able to solve this last night (although the Windows
> wheels are fine, which are built on AppVeyor instead).
>
>
> Peter