Re: python-pybedtools: fixing the failing tests
Hi Liubov,
On Tue, Jul 17, 2018 at 05:09:59PM +0300, Liubov Chuprikova wrote:
> > It does not build for me in a pbuilder chroot. I get:
> >
> > ======================================================================
> > FAIL: shuffle, i=gzip ibam=False, {'seed': 1, 'chrom': True, 'genome':
> > 'hg19'}
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
>
> Sorry, I had not checked sid (I had no space to build one more chroot and
> was unforgivably lazy to make a room for it :-P ).
I'd recommend to use pbuilder chroot for sid (and only sid).
> You are right: I got the
> same errors after installing sid. The problem is that there are two
> different versions of bedtools (2.26 in buster and 2.27 in sid).
> Pybedtools' upstream is aware about the differences [1] and going to
> update tests in the future. What can we do in this situation?
We need to support the version in sid since we upload to sid - and for
sure we need to deal with the reasons that 2.27 does not migrate to
testing.
I admit I'd be delighted if more members of the Debian Med team would
spent some time on this kind of QA work since it is very hard to keep
track of all this more or less alone (this is not addressed to newbie's
like Liubov but to those readers of this list who think they profit from
a working software ecosystem for life sciences and want to keep it in
that quality).
Regarding bedtools its also mostly a test issue. For instance looking
at the build log for i386[2] there are quite some rounding issues like:
...
coverage.t6...3,5c3,5
< chr1 200 250 3 25 + 1.3200001
< chr2 80 130 5 25 - 3.0799999
< chr2 150 200 4 25 + 5.5599999
---
> chr1 200 250 3 25 + 1.3200000
> chr2 80 130 5 25 - 3.0800000
> chr2 150 200 4 25 + 5.5600000
fail
coverage.t6b...3,5c3,5
< chr1 200 250 3 25 + 1.3200001
< chr2 80 130 5 25 - 3.0799999
< chr2 150 200 4 25 + 5.5599999
---
> chr1 200 250 3 25 + 1.3200000
> chr2 80 130 5 25 - 3.0800000
> chr2 150 200 4 25 + 5.5600000
fail
coverage.t7...ok
...
but there is also something that might need investigation:
...
intersect.t52...1,2d0
< chr1 10 12 a1 1 +
< chr2 10 12 a2 1 -
fail
intersect.t53...ok
...
We need more people checking those issues and put testing migration of
packages on their agenda since we are not always in the comfortable
situation to throw things like this on the table of an Outreachy
student. It should also be discussed whether it is really worth
supporting other architectures than amd64 - but that should be some team
decision.
But now back to Liubov's mail ...
> > I wonder if it might be
> > a good idea to implement some generic way to run the build
> > time test as autopkgtest. This could solve the issue for
> > several Python packages.
>
> I would like to think about it someday!
That would be probably very helpful
Andreas.
> [1] https://github.com/daler/pybedtools/pull/234
> <https://github.com/arq5x/bedtools2/issues/607>
[2] https://buildd.debian.org/status/fetch.php?pkg=bedtools&arch=i386&ver=2.27.1%2Bdfsg-2&stamp=1527025121&raw=0
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