Re: python-cyvcf2 test failures (Was: python-pybedtools: fixing the failing tests)
On 7/28/18 12:19 AM, Andreas Tille wrote:
> Hi Steffen,
>
> On Fri, Jul 27, 2018 at 07:41:21PM +0200, Steffen Möller wrote:
...
>>>> I came to the
>>>> conclusion that we should then not substitute that subdirectory with our
>>>> repository's htslib 1.8.
>>> If there is no better clue that could be a short term workaround but
>>> please make sure you talk to upstream (may be both sides htslib and
>>> cyvcf2).
>> Hm. Mixed feelings here. I am not exactly sure about what you mean but
>> this is an upstream issue in my mind. Let me summarise the situation in
>> the README.source and then observe/remind at later releases.
> I do not think that anybody of us is observing "random" README.source
> files regularly. I'd consider a bug of severity minor the more
> realistic approach that somebody might stumble upon the issue and will
> try to fix it.
Yes. Good point. The same problem we have with all those packages that
we tolerate in salsa that never made it to our project servers. While adding
all those RRIDs I was tempted a few times to complete a packaging effort
and after a while found out why the packaging came to that halt. Grrr.
The README.source is the right place, but how about putting a comment
into the changelog file whenever README.source changes? I like that. If
there are positive vibes towards that extra verbosity then let us try this
for a while and then propose this for our Debian policy.
I have it (still locally) now in the changelog, in copyright (where I
commented out the
Files-Excluded: htslib) and in README.source.
>
>>>> On a sidenote, because of incompatibilities with existing packages we
>>>> have htslib in experimental (the latest version of htslib is now 1.9).
>>> We should make some effort to upgrade this soon - there is no point
>>> for waiting until I worked down a different stock of todo items.
>> It is a bit annoying but that there are these version incompatibilities.
>> We cannot just go and substitute the 1.7 version.
> As far as I know it was just python-pysam which was not updated to 1.8.
Ah, ok. Seems like I forgot.
> I have not yet checked recently whether this is the case. This is
> another cry for more contribution. We **really** need more people doing
> regular maintenance and check what package needs an upgrade.
I am not exactly sure what kind of work that is which we need. When
packages are well maintained, like cyvcf2 now, it needs someone to
detect issues and communicate them. The detection is automated. The
communication takes time.
For non-maintained software that does not find a new maintainer the only
answer I have a request for removal. With the advent of
Docker/Singularity together with snapshot.d.o this is not too bad.
What we need is some kind of reward structure. This does not need to be
money, the one or other newspaper article about a young mother's cancer
being cured after identifying the right T cell receptors with the help
of Debian's packages would be enough for me. But that is me. Part of why
I am so much after completing workflows is that this shifts our
distribution from a package-level to a purpose-level. And if we do not
find more hands for those purposes then, well, maybe we should package
less and help using those packages more.
> Do you know any specific package which does not work with version 1.9?
No, not yet. We are at the very front of everything here. That 1.9
release is just 9 days old or so.
...
> Kind regards from DebConf 18
Enjoy!
Steffen
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