[Biopython-dev] CI for Windows

[Peter Cock]

I forgot to email this good news at the end of last week, but this
is now live on the official repository:

https://ci.appveyor.com/project/biopython/biopython/history

I did tweet about it though:

https://twitter.com/Biopython/status/878261573344649217

Note I did have to turn off testing of some Bio.Cluster doctests
in the Tutorial to get this to pass - that needs looking at but
doctests are notoriously fragile with differences in Python
version or OS:

https://github.com/biopython/biopython/issues/1288#issuecomment-310677878

There is still room for improvement, e.g. test coverage reporting:

https://github.com/biopython/biopython/issues/1297

Peter

On Thu, May 25, 2017 at 6:04 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hello all,
>
> By copying the NumPy AppVeyor setup, I was able to get a useful
> Windows test run on my first attempt for Biopython (running via my
> personal fork, not the official GitHub repository):
>
> https://github.com/numpy/numpy/blob/master/appveyor.yml
>
> https://github.com/peterjc/biopython/blob/appveyor/.appveyor.yml
>
> https://ci.appveyor.com/project/peterjc/biopython/build/0.0.1
>
> Interestingly even though initially run with a minimal set of
> dependencies this has shown up some errors under Python 3 - despite
> not being reported as a failure (which I've since solved by calling
> run_tests.py directly), logged here:
>
> https://github.com/biopython/biopython/issues/1257
>
> I went a little further and enabled the BioSQL tests and several other
> Python dependencies:
>
> https://ci.appveyor.com/project/peterjc/biopython/build/0.0.5
>
> This still has a lot of scope for improvement.
>
> Right now the tests seem not to be using the compiled bits of
> Biopython (e.g. test_KDTree.py, likely a path issue, or down to using
> pip over setup.py directly for the install).
>
> It might make sense to share the same Tox setup we use for the Linux
> TravisCI checks covering a range of Python versions and optional
> dependencies.
>
> Also, there is the possibility of using AppVeyor to build the Windows
> installers and wheels for each release...
>
> Peter
>
>
>
> On Sat, Nov 19, 2016 at 11:02 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> Hi Shyam,
>>
>> I'm definitely interested!
>>
>> Ben Fulton (CC'd) had a look at this a while back,
>> I'm not sure how close he got but we don't yet have
>> anything included in the main Biopython repository
>> on GitHub yet:
>>
>> https://github.com/benfulton/biopython/tree/appveyor
>>
>> On a related point, I hope to replace the only regular
>> Windows Buildbot machine which is a very elderly
>> 32 bit Windows XP machine with a Windows 7
>> machine later this year:
>>
>> http://testing.open-bio.org/biopython/tgrid
>>
>> Peter
>>
>> On Sat, Nov 19, 2016 at 9:24 PM, Shyam Saladi <saladi at caltech.edu> wrote:
>>> Hi all --
>>>
>>> Is there any interest in setting up continuous integration testing for
>>> Windows? I recently did this for another, perhaps toy, software package
>>> using AppVeyor and would be willing to try my hand with biopython.
>>>
>>> Thanks,
>>> Shyam
>>>