Re: python-cyvcf2 test failures (Was: python-pybedtools: fixing the failing tests)
Hello again,
python-cyvcf2 was this accepted into unstable. That was quick.
@Liubov, you are most cordially invited to join the packaging of
whatever package you like. Just add yourself as an uploader and send a
ping for the upload. You did a very nice job on pybedtools [need to
investigate where this is stuck now] and cyvcf2, can't praise you enough
for that.
On the path to bcbio is also python-pysam that has a new version out.
That would then be the opportunity to test its compatibilty with htslib
1.9. Not this week.
Best,
Steffen
On 7/20/18 2:57 PM, Liubov Chuprikova wrote:
> Ouch, sorry! I first planned to write also a bit about python-cyvcf2
> that is why I included it in the Subjest. Then I decided to devote to
> it a separate letter, but forgot to remove it from the Subject.
>
> Since this has happened, I am to mention cyvcf2 here.
>
> On Sun, 8 Jul 2018 at 01:23 Steffen Möller <steffen_moeller@gmx.de
> <mailto:steffen_moeller@gmx.de>> wrote:
>
> - cyvcf2 is in a new version 0.9.0 now, but, well, tests fail.
>
>
> There was a new upstream version recently in which one of the tests
> (issue44) was supposed to be fixed, but hadn't yet [1]. I tried to dig
> into this and its other test failures, but they seem to be quite
> tricky for me. So I think, Steffen's claim for someone's help with
> cyvcf2 and its dependency htslib still remains on the table:
>
>
> It comes
> with its own version of htslib, which may well contribute to the
> situation since I had nothing better to do than to substitute it with
> the one the distribution ships. Is anybody close to upstream on this
> list to have a look?
>
>
> With regards,
> Liubov
>
> [1] https://github.com/brentp/cyvcf2/issues/89#issuecomment-406354822
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