Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Paul Gevers
Hi Pirate,

On 13-01-17 08:46, Pirate Praveen wrote:
> Similar to piuparts auto rejects, I think we should add auto reject when
> autopkgtest of a reverse dependency or build dependency fails (which was
> not failing earlier) or cause FTBFS to reverse dependencies. This will
> help us prevent library updates without proper transitions breaking
> other packages. One recent example is update on python-html5lib which
> broke python-bleach even though build was failing [1].
> 
> [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=844943

I'm working on that¹ and hope we can enable it soon after Stretch release.

Paul
¹ https://lists.debian.org/debian-release/2016/12/msg00310.html



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Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Pirate Praveen
On വെള്ളി 13 ജനുവരി 2017 01:33 വൈകു, Paul Gevers wrote:
> I'm working on that¹ and hope we can enable it soon after Stretch release.

Thanks! I think it will help us in a great way in handling library
transitions.




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ITP: python-bx -- library to manage genomic data and its aligment

2017-01-13 Thread Steffen Möller
Package: wnpp
Severity: wishlist
Owner: Steffen Moeller 

* Package name: python-bx
  Version : 0.7.2
* URL : https://github.com/bxlab/bx-python
* License : MIT
  Programming Lang: Python
  Description : library to manage genomic data and its aligment

python-bx is a requirement for getting the Galaxy workflow suite closer
to our distribution.

The packaging is maintained by the Debian Med team and hosted on
https://anonscm.debian.org/cgit/debian-med/python-bx.git/



Re: Converting to dgit

2017-01-13 Thread Ghislain Vaillant
On Thu, 2017-01-12 at 21:46 +0100, Raphael Hertzog wrote:
> Hi,
> 
> On Fri, 06 Jan 2017, Ghislain Vaillant wrote:
> > > I don't use it often enough to remember all the details either.  I don't 
> > > recall the last time I had to do more than copy/paste a command from the 
> > > man 
> > > page (OK, git-dpm tag I can remember).
> > 
> > Besides, git-dpm usually tells you what command to run next, like:
> > 
> > git-dpm import-new-upstream -> git-dpm rebase-patched -> git-dpm 
> > update-patches
> > 
> > It did not take me much time to adapt to the git-dpm workflow as a
> > result. I should say that I have been a happy git-dpm user so far.
> 
> And I have been a very unhappy user with python-django. If by mistake, you
> use "gbp import-orig" instead of "git-dpm import-new-upstream" then you're
> completely screwed because git-dpm relies on metadata it manually stores
> in debian/.git-dpm, it does not rely on git's history to figure out the
> appropriate data. Same if you change any patch outside with a third party
> tool...

Well, remember that `git-dpm import-new-upstream` only records the new
upstream commit in the .git-dpm metadata and delays the actual import
of the new upstream data until you have a properly rebased patch queue.

This is to be contrasted with `gbp` where you may import the new
upstream and leave the packaging repository in an inconsistent state
(as far as the patch queue is concerned) until someone runs `gbp pq` or
`quilt` to refresh.

Then, no wonder that mixing `gbp import-orig` with git-dpm does not
work. I admire your courage for trying to fixup the git-dpm metadata
manually nonetheless. Same problem if you try to mix `git-dpm cherry-
pick` with `gbp pq import` -> `git cherry-pick` -> `gbp pq export`.

> So I have opened the manual page many times to read about the format of
> that file and tried to fix up the inconsistent meta-data.
> 
> Also it's really painful to use with multiple branches as you can't really
> merge branches together:
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=801667

This is indeed a limitation. Based on the design of the tool, git-dpm
works on a rather flat git history. Considering the workflow you
described for django, git-dpm is unlikely to ever become suitable.

> It produces a very verbose git history as soon as you have a significant
> number of patches, even if most of them do not change at all across a
> minor upstream release.

Is that such a bad thing though, I wonder? Given that the price for it
is a guaranteed consistent patch queue.

> Also it's effectively orphaned, nobody is taking care of bugs.
> 
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=801666
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=801548
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=795694

So was pristine-tar for a long time and people kept using it
nonetheless.

I also commented in #801666, so I am aware of your issues with git-dpm. 
I agree that integration with existing gbp configuration would be a
plus and help support arbitrary repository layouts, such as those
recommended in DEP-14.

I don't necessarily disagree with you, as I keep using both gbp and
git-dpm in a complementary way. I just wanted to contrast the perceived
hate towards git-dpm in this thread with some positive feedback.

Cheers,
Ghis



Bug#851255: ITP: python-rediscluster -- Python interface to a cluster of Redis key-value stores

2017-01-13 Thread Nicolas Dandrimont
Package: wnpp
Severity: wishlist
Owner: Nicolas Dandrimont 

* Package name: python-rediscluster
  Version : 0.5.3
  Upstream Author : Salimane Adjao Moustapha 
* URL : https://github.com/salimane/rediscluster-py
* License : MIT
  Programming Lang: Python
  Description : Python interface to a cluster of Redis key-value stores

 Redis is a key-value database in a similar vein to memcache but the dataset
 is non-volatile. Redis additionally provides native support for atomically
 manipulating and querying data structures such as lists and sets.
 .
 rediscluster is a Python library adapting the upstream Redis bindings to enable
 sharding among different Redis instances in a transparent, fast, and fault
 tolerant way.

This package will be maintained under the umbrella of the Debian Python Modules
Team. It is a dependency of python-limits, which in turn is a dependency of
Flask-Limiter which I intend to package.



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Scott Kitterman
On Friday, January 13, 2017 09:03:51 AM Paul Gevers wrote:
> Hi Pirate,
> 
> On 13-01-17 08:46, Pirate Praveen wrote:
> > Similar to piuparts auto rejects, I think we should add auto reject when
> > autopkgtest of a reverse dependency or build dependency fails (which was
> > not failing earlier) or cause FTBFS to reverse dependencies. This will
> > help us prevent library updates without proper transitions breaking
> > other packages. One recent example is update on python-html5lib which
> > broke python-bleach even though build was failing [1].
> > 
> > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=844943
> 
> I'm working on that¹ and hope we can enable it soon after Stretch release.
> 
> Paul
> ¹ https://lists.debian.org/debian-release/2016/12/msg00310.html

For clarity, you're discussing this being a testing migration blocker, not a 
package accept auto-reject, right?

Scott K


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Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Ondrej Novy
Hi,

2017-01-13 8:46 GMT+01:00 Pirate Praveen :

> Similar to piuparts auto rejects, I think we should add auto reject when
> autopkgtest of a reverse dependency or build dependency fails (which was
> not failing earlier) or cause FTBFS to reverse dependencies.
>

just be carefull, because there are some packages which FTBFS in debci
(example:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/swift.html
)
and it's bug in debci. Build works fine in buildd and in my local sbuild.

Maybe we should fix this first?

-- 
Best regards
 Ondřej Nový

Email: n...@ondrej.org
PGP: 3D98 3C52 EB85 980C 46A5  6090 3573 1255 9D1E 064B


how to mount /(dev|run)/shm properly? (was Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS)

2017-01-13 Thread Holger Levsen
On Fri, Jan 13, 2017 at 02:38:28PM +0100, Ondrej Novy wrote:
> just be carefull, because there are some packages which FTBFS in debci
> (example:
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/swift.html
> )
> and it's bug in debci. Build works fine in buildd and in my local sbuild.
 
while this is not related to debci, it brings up an interesting
question:

how should /dev/shm be mounted? and how /run/shm?

i'm interesting in this question for Debian stable with 3.16 and 4.6-4-9
kernels and ubuntu 16.04 running 4.4 kernels…


-- 
cheers,
Holger


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Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Paul Gevers
Hi Scott,

On 13-01-17 14:30, Scott Kitterman wrote:
> On Friday, January 13, 2017 09:03:51 AM Paul Gevers wrote:
>> On 13-01-17 08:46, Pirate Praveen wrote:
>>> Similar to piuparts auto rejects, I think we should add auto reject when
>>> autopkgtest of a reverse dependency or build dependency fails (which was
>>> not failing earlier) or cause FTBFS to reverse dependencies. This will
>>> help us prevent library updates without proper transitions breaking
>>> other packages. One recent example is update on python-html5lib which
>>> broke python-bleach even though build was failing [1].
>>>
>>> [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=844943
>>
>> I'm working on that¹ and hope we can enable it soon after Stretch release.
>>
>> Paul
>> ¹ https://lists.debian.org/debian-release/2016/12/msg00310.html
> 
> For clarity, you're discussing this being a testing migration blocker, not a 
> package accept auto-reject, right?

I am not sure if you are addressing me or Pirate, but indeed I am
working on an implementation similar to what Ubuntu does (see the link
above about the details) which will be used as unstable to testing
migration blocker. debci is the worker, but all the policy logic will be
with britney where it belongs. And of course I try to have a full
release cycle to tune it.

Paul



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Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Ole Streicher
Paul Gevers  writes:
> I am not sure if you are addressing me or Pirate, but indeed I am
> working on an implementation similar to what Ubuntu does (see the link
> above about the details) which will be used as unstable to testing
> migration blocker. debci is the worker, but all the policy logic will be
> with britney where it belongs. And of course I try to have a full
> release cycle to tune it.

Will there be a way to override this for the maintainer? Otherwise I
would see the danger that a buggy reverse dependency CI test can prevent
an important update, for example if the reverse dependency uses a long
deprecated function that is now removed.

Best regards

Ole



Bug#851272: ITP: python-limits -- Rate limiting utilities for Python

2017-01-13 Thread Nicolas Dandrimont
Package: wnpp
Severity: wishlist
Owner: Nicolas Dandrimont 

* Package name: python-limits
  Version : 1.2.1
  Upstream Author : Ali-Akber Saifee 
* URL : https://limits.readthedocs.org
* License : MIT
  Programming Lang: Python
  Description : Rate limiting utilities for Python

 limits is a Python module providing utilities to implement rate limiting using
 various strategies, such as fixed or moving windows, and various storage
 backends, such as in in-memory storage, Redis or memcached.

limits is the back-end and base implementation of the rate-limiting algorithms 
provided by Flask-Limiter. The module will be maintained inside the Debian 
Python Modules Team



Re: how to mount /(dev|run)/shm properly? (was Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS)

2017-01-13 Thread Simon McVittie
On Fri, 13 Jan 2017 at 14:14:09 +, Holger Levsen wrote:
> how should /dev/shm be mounted? and how /run/shm?

I believe the "API" is that /dev/shm is either a tmpfs with
/tmp-like permissions (01777), or a symlink to such a tmpfs.
My understanding is that /run/shm is considered to be an
implementation detail, rather than something that software should
hard-code anywhere.

Reference: glibc sysdeps/unix/sysv/linux/shm-directory.c (the original
user of /dev/shm).

systemd mounts a tmpfs on /dev/shm (it's hard-coded in as one of
the "API filesystems"), and Debian's systemd packaging puts a symlink
at /run/shm in case anything is relying on it
(/usr/lib/tmpfiles.d/debian.conf).

If I'm reading the initscripts code correctly, sysvinit does the reverse
by default, for some reason (/run/shm is the mount point and /dev/shm the
symlink). I think the motivation might have been to be able to use the
same tmpfs for /run and /run/shm, but that's a bad idea if you want to
prevent unprivileged users from performing a DoS attack on privileged system
components by filling up /run (which is why systemd gives each user their
own tmpfs at /run/user/$uid by default).

The default schroot configuration mounts a tmpfs on /dev/shm and does not
do anything special about /run/shm.

Generalizing from those, I think it's reasonable to say that in a
bare-metal system, init is responsible for arranging for /dev/shm to be
as required, and in a container or chroot, the container manager is
responsible.

S



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Ghislain Vaillant
On Fri, 2017-01-13 at 15:57 +0100, Ole Streicher wrote:
> Paul Gevers  writes:
> > I am not sure if you are addressing me or Pirate, but indeed I am
> > working on an implementation similar to what Ubuntu does (see the link
> > above about the details) which will be used as unstable to testing
> > migration blocker. debci is the worker, but all the policy logic will be
> > with britney where it belongs. And of course I try to have a full
> > release cycle to tune it.
> 
> Will there be a way to override this for the maintainer? Otherwise I
> would see the danger that a buggy reverse dependency CI test can prevent
> an important update, for example if the reverse dependency uses a long
> deprecated function that is now removed.
> 
> Best regards
> 
> Ole

I second Ole's concerns here. Strict autorejection would be assuming
that all autopkgtest testsuites are solid, which has not always been
the case in my experience.

Ghis



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Antonio Terceiro
On Fri, Jan 13, 2017 at 03:57:09PM +0100, Ole Streicher wrote:
> Paul Gevers  writes:
> > I am not sure if you are addressing me or Pirate, but indeed I am
> > working on an implementation similar to what Ubuntu does (see the link
> > above about the details) which will be used as unstable to testing
> > migration blocker. debci is the worker, but all the policy logic will be
> > with britney where it belongs. And of course I try to have a full
> > release cycle to tune it.
> 
> Will there be a way to override this for the maintainer? Otherwise I
> would see the danger that a buggy reverse dependency CI test can prevent
> an important update, for example if the reverse dependency uses a long
> deprecated function that is now removed.

You can either fix the reverse dependency, or get it removed.


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Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Antonio Terceiro
On Fri, Jan 13, 2017 at 02:38:28PM +0100, Ondrej Novy wrote:
> Hi,
> 
> 2017-01-13 8:46 GMT+01:00 Pirate Praveen :
> 
> > Similar to piuparts auto rejects, I think we should add auto reject when
> > autopkgtest of a reverse dependency or build dependency fails (which was
> > not failing earlier) or cause FTBFS to reverse dependencies.
> >
> 
> just be carefull, because there are some packages which FTBFS in debci
> (example:
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/swift.html
> )
> and it's bug in debci. Build works fine in buildd and in my local sbuild.

I think you are a little confused. That links to reproducible builds,
which has nothing to do with debci.


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Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Ole Streicher
Antonio Terceiro  writes:
> On Fri, Jan 13, 2017 at 03:57:09PM +0100, Ole Streicher wrote:
>> Paul Gevers  writes:
>> > I am not sure if you are addressing me or Pirate, but indeed I am
>> > working on an implementation similar to what Ubuntu does (see the link
>> > above about the details) which will be used as unstable to testing
>> > migration blocker. debci is the worker, but all the policy logic will be
>> > with britney where it belongs. And of course I try to have a full
>> > release cycle to tune it.
>> 
>> Will there be a way to override this for the maintainer? Otherwise I
>> would see the danger that a buggy reverse dependency CI test can prevent
>> an important update, for example if the reverse dependency uses a long
>> deprecated function that is now removed.
>
> You can either fix the reverse dependency, or get it removed.

Sorry, I don't understand this. How can I get a reverse dependency
removed (from unstable)? And why should I get responsible for poorly
maintained reverse dependencies?

Also, at least up to now, CI test failures are not necessarily
critical. It depends on the evaluation of the maintainer which severity
the problem that popped up has: often CI tests are quite picky to serve
as an early indicator for problems.

For example, a new package could write a deprecation warning which
brings the CI test of a reverse dependency to fail. The failure is in no
way critical (since the package works). But I would also not like to
ignore stderr -- I *want* to have these kinds of warnings so that I can
react before the real change happens, but I also see no reason to hurry
up here (usually, I contact upstream and wait until they have a
solution).

If you now make the first package dependent on the reverse dependency,
it will not migrate because of the CI failure, but I would also (as
maintainer of the reverse dependency) not accept to ignore stderr.

Problems like these will create additional work for all parties and are
likely to make people angry. IMO it would be much better if you would
either auto-create bug reports (which may be re-assigned), or to have an
"ignore" button somewhere.

The idea of getting informed that a certain upload causes problems in
other packages is however great.

BTW, there were some discussions at debconf about getting an E-mail on
CI test status changes; this would also be a nice thing.

Best regards

Ole






Bug#851290: ITP: flask-limiter -- Rate-limiting for Flask routes

2017-01-13 Thread Nicolas Dandrimont
Package: wnpp
Severity: wishlist
Owner: Nicolas Dandrimont 

* Package name: flask-limiter
  Version : 0.9.3
  Upstream Author : Ali-Akber Saifee
* URL : http://flask-limiter.readthedocs.org/ | 
https://github.com/alisaifee/flask-limiter
* License : MIT
  Programming Lang: Python
  Description : Rate-limiting for Flask routes

 Flask is a micro web framework for Python based on Werkzeug, Jinja 2 and good
 intentions.
 .
 Flask-Limiter provides rate limiting features to flask routes. It has support
 for a configurable backend for storage with current implementations for
 in-memory, redis and memcache.

This package will be maintained under the umbrella of the Debian Python Modules 
Team



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Ondrej Novy
Hi,

2017-01-13 17:47 GMT+01:00 Antonio Terceiro :

> I think you are a little confused. That links to reproducible builds,
> which has nothing to do with debci.
>

yep, sorry for confusion. I assumed that FTBS migration check will use data
from reproducible builds OR will use same system for running builds
(Jenkins?).

-- 
Best regards
 Ondřej Nový

Email: n...@ondrej.org
PGP: 3D98 3C52 EB85 980C 46A5  6090 3573 1255 9D1E 064B


Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Ian Jackson
Ole Streicher writes ("Re: Auto reject if autopkgtest of reverse dependencies 
fail or cause FTBFS"):
> Sorry, I don't understand this. How can I get a reverse dependency
> removed (from unstable)?

You wouldn't.  You would need to get it removed from testing.

> And why should I get responsible for poorly
> maintained reverse dependencies?

This is more of a sticking point.  I don't know what proportion of CI
failures are going to be due to poorly maintained reverse
dependencies.

But the real answer to this is that "Debian testing should be kept
releaseable" and that means that if your rdepends are busted such that
your changes cause lossage, something has to give.

> The idea of getting informed that a certain upload causes problems in
> other packages is however great.

Maybe an intermediate position would be to respond to a CI failure by:
 * Increasing the migration delay for the affecting package
 * Notifying the affected package maintainers

> BTW, there were some discussions at debconf about getting an E-mail on
> CI test status changes; this would also be a nice thing.

Yes.

Ian.

-- 
Ian JacksonThese opinions are my own.

If I emailed you from an address @fyvzl.net or @evade.org.uk, that is
a private address which bypasses my fierce spamfilter.



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Scott Kitterman
On Friday, January 13, 2017 05:46:41 PM Ole Streicher wrote:
> Antonio Terceiro  writes:
> > On Fri, Jan 13, 2017 at 03:57:09PM +0100, Ole Streicher wrote:
> >> Paul Gevers  writes:
> >> > I am not sure if you are addressing me or Pirate, but indeed I am
> >> > working on an implementation similar to what Ubuntu does (see the link
> >> > above about the details) which will be used as unstable to testing
> >> > migration blocker. debci is the worker, but all the policy logic will
> >> > be
> >> > with britney where it belongs. And of course I try to have a full
> >> > release cycle to tune it.
> >> 
> >> Will there be a way to override this for the maintainer? Otherwise I
> >> would see the danger that a buggy reverse dependency CI test can prevent
> >> an important update, for example if the reverse dependency uses a long
> >> deprecated function that is now removed.
> > 
> > You can either fix the reverse dependency, or get it removed.
> 
> Sorry, I don't understand this. How can I get a reverse dependency
> removed (from unstable)? And why should I get responsible for poorly
> maintained reverse dependencies?
> 
> Also, at least up to now, CI test failures are not necessarily
> critical. It depends on the evaluation of the maintainer which severity
> the problem that popped up has: often CI tests are quite picky to serve
> as an early indicator for problems.
> 
> For example, a new package could write a deprecation warning which
> brings the CI test of a reverse dependency to fail. The failure is in no
> way critical (since the package works). But I would also not like to
> ignore stderr -- I *want* to have these kinds of warnings so that I can
> react before the real change happens, but I also see no reason to hurry
> up here (usually, I contact upstream and wait until they have a
> solution).
> 
> If you now make the first package dependent on the reverse dependency,
> it will not migrate because of the CI failure, but I would also (as
> maintainer of the reverse dependency) not accept to ignore stderr.
> 
> Problems like these will create additional work for all parties and are
> likely to make people angry. IMO it would be much better if you would
> either auto-create bug reports (which may be re-assigned), or to have an
> "ignore" button somewhere.
> 
> The idea of getting informed that a certain upload causes problems in
> other packages is however great.
> 
> BTW, there were some discussions at debconf about getting an E-mail on
> CI test status changes; this would also be a nice thing.

Probably the simplest way to avoid problems with systems like this is to 
remove any autopkg tests your packages are shipping.

Scott K

P.S. Perverse incentives FTW.



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Simon McVittie
On Fri, 13 Jan 2017 at 18:22:53 +, Ian Jackson wrote:
> Maybe an intermediate position would be to respond to a CI failure by:
>  * Increasing the migration delay for the affecting package
>  * Notifying the affected package maintainers

I think this makes sense: it gives the maintainer and other interested
developers some time to assess whether the failure is a showstopper
(=> upload a fix/revert/workaround, or at worst file a RC bug) or not.

Or, conversely, blocking migrations but letting the relevant maintainers
remove that block might work.

On Fri, 13 Jan 2017 at 13:54:26 -0500, Scott Kitterman wrote:
> Probably the simplest way to avoid problems with systems like this is to 
> remove any autopkg tests your packages are shipping.
[...]
> P.S. Perverse incentives FTW.

This is my concern too. If you maintain a useful package with tests that
are unstable but do not imply a release-critical issue, running those
tests and recording-but-ignoring the failures seems considerably better
for Debian than either disabling the tests or removing the software
(more information is better than less information, and if the package
is useful despite the test failure then it's better to have it than not).

Possible autopkgtest extension: "Restrictions: unreliable"?

S



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Ole Streicher
Simon McVittie  writes:
> On Fri, 13 Jan 2017 at 18:22:53 +, Ian Jackson wrote:
>> Maybe an intermediate position would be to respond to a CI failure by:
>>  * Increasing the migration delay for the affecting package
>>  * Notifying the affected package maintainers
>
> I think this makes sense: it gives the maintainer and other interested
> developers some time to assess whether the failure is a showstopper
> (=> upload a fix/revert/workaround, or at worst file a RC bug) or not.
>
> Or, conversely, blocking migrations but letting the relevant maintainers
> remove that block might work.

What is the reason not to use automated bug reports here? This would
allow to use all the tools the bug system has: severities, reassigning
closing etc.

> Possible autopkgtest extension: "Restrictions: unreliable"?

This is not specific enough. Often you have some tests that are
unreliable, and others that are important. Since one usually takes the
upstream test suite (which may be huge), one has to look manually first
to decide about the further processing.

Best regards

Ole



Bug#851306: ITP: freebayes -- Bayesian haplotype-based polymorphism discovery and genotyping

2017-01-13 Thread Andreas Tille
Package: wnpp
Severity: wishlist
Owner: Andreas Tille 

* Package name: freebayes
  Version : 1.0.2
  Upstream Author : Erik Garrison
* URL : https://github.com/ekg/freebayes
* License : MIT
  Programming Lang: C++
  Description : Bayesian haplotype-based polymorphism discovery and 
genotyping
 FreeBayes is a Bayesian genetic variant detector designed to find
 small polymorphisms, specifically SNPs (single-nucleotide
 polymorphisms), indels (insertions and deletions), MNPs
 (multi-nucleotide polymorphisms), and complex events (composite
 insertion and substitution events) smaller than the length of a
 short-read sequencing alignment.


Remark: This package is maintained by the Debian Med team at
   https://anonscm.debian.org/git/debian-med/freebayes.git



Re: Bug#851306: ITP: freebayes -- Bayesian haplotype-based polymorphism discovery and genotyping

2017-01-13 Thread Scott Kitterman
On Friday, January 13, 2017 10:00:13 PM Andreas Tille wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Andreas Tille 
> 
> * Package name: freebayes
>   Version : 1.0.2
>   Upstream Author : Erik Garrison
> * URL : https://github.com/ekg/freebayes
> * License : MIT
>   Programming Lang: C++
>   Description : Bayesian haplotype-based polymorphism discovery and
> genotyping FreeBayes is a Bayesian genetic variant detector designed to
> find small polymorphisms, specifically SNPs (single-nucleotide
>  polymorphisms), indels (insertions and deletions), MNPs
>  (multi-nucleotide polymorphisms), and complex events (composite
>  insertion and substitution events) smaller than the length of a
>  short-read sequencing alignment.
> 
> 
> Remark: This package is maintained by the Debian Med team at
>https://anonscm.debian.org/git/debian-med/freebayes.git

"freebayes" seems like a very generic name for something specific to such a 
narrow field.  Maybe freebayes-genetic-variance or some such instead.

Scott K



Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Paul Gevers
Hi Ole,

On 01/13/17 21:05, Ole Streicher wrote:
> Simon McVittie  writes:
>> On Fri, 13 Jan 2017 at 18:22:53 +, Ian Jackson wrote:
>>> Maybe an intermediate position would be to respond to a CI failure by:
>>>  * Increasing the migration delay for the affecting package

I like this and will suggest it to the release team. Especially for the
start up time.

>>>  * Notifying the affected package maintainers
>>
>> I think this makes sense: it gives the maintainer and other interested
>> developers some time to assess whether the failure is a showstopper
>> (=> upload a fix/revert/workaround, or at worst file a RC bug) or not.
>>
>> Or, conversely, blocking migrations but letting the relevant maintainers
>> remove that block might work.

One can always file bug reports against the release.debian.org pseudo
package to ask for britney to ignore the autopkgtest result. One other
thing that I can envision (but maybe to early to agree on or set in
stone) is that we lower the NMU criteria for fixing (or temporarily
disabling) autopkgtest in ones reverse dependencies. In the end,
personally I don't think this is up to the "relevant maintainers" but up
to the release team. And I assume that badly maintained autopkgtest will
just be a good reason to kick a package out of testing.

On the item of notifications, I would expect that as soon as we have
this mechanism in place we would implement the notification on all the
actively maintained notification places, such as tracker.debian.org and
udd. This isn't much different than other migration criteria or
auto-removals in that respect.

> What is the reason not to use automated bug reports here? This would
> allow to use all the tools the bug system has: severities, reassigning
> closing etc.

The largest reason is that it didn't cross my mind yet and nobody else
except you has raised the idea so far. One cravat that I see though is
which system should hold the logic. The current idea is that it is
britney that determines which combinations need to be tested and thus
can use the result straight away for the migration decision. As Martin
Pitt described in the thread I referenced in my first reply, Ubuntu
already experimented with this and they came to the conclusion that it
didn't really work if two entities have to try and keep the logic in sync.

>> Possible autopkgtest extension: "Restrictions: unreliable"?
> 
> This is not specific enough. Often you have some tests that are
> unreliable, and others that are important. Since one usually takes the
> upstream test suite (which may be huge), one has to look manually first
> to decide about the further processing.

Than maybe change the wording: not-blocking, for-info, too-sensitive,
ignore or  If you know your test suite needs investigation, you can
have it not automatically block. But depending on the outcome of the
investigation, you can still file (RC) bugs.

Why I am so motivated on doing this is because I really believe this is
going to improve the quality of the release and the release process. I
really hope that more packages will be creating autopkgtests, as one now
has an incentive: it helps guaranteeing that you package will not
suddenly be kicked out of the release due to a change in your
dependencies. Personally, one of my autopkgtest has triggered a change
in MySQL (upstream even) to not suddenly drop some command line option,
but implement a deprecation period. Software was relying on the behavior
and in this case there wasn't a grace period. I am not sure that without
this "stick" it would have happened (and definitely not in time for the
specific Ubuntu release).

Paul



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Re: Auto reject if autopkgtest of reverse dependencies fail or cause FTBFS

2017-01-13 Thread Colin Watson
On Fri, Jan 13, 2017 at 07:35:10PM +, Simon McVittie wrote:
> On Fri, 13 Jan 2017 at 18:22:53 +, Ian Jackson wrote:
> > Maybe an intermediate position would be to respond to a CI failure by:
> >  * Increasing the migration delay for the affecting package
> >  * Notifying the affected package maintainers
> 
> I think this makes sense: it gives the maintainer and other interested
> developers some time to assess whether the failure is a showstopper
> (=> upload a fix/revert/workaround, or at worst file a RC bug) or not.
> 
> Or, conversely, blocking migrations but letting the relevant maintainers
> remove that block might work.

Agreed (if any of this is practical in britney).

> On Fri, 13 Jan 2017 at 13:54:26 -0500, Scott Kitterman wrote:
> > Probably the simplest way to avoid problems with systems like this is to 
> > remove any autopkg tests your packages are shipping.
> [...]
> > P.S. Perverse incentives FTW.
> 
> This is my concern too. If you maintain a useful package with tests that
> are unstable but do not imply a release-critical issue, running those
> tests and recording-but-ignoring the failures seems considerably better
> for Debian than either disabling the tests or removing the software
> (more information is better than less information, and if the package
> is useful despite the test failure then it's better to have it than not).
> 
> Possible autopkgtest extension: "Restrictions: unreliable"?

May as well just use "Restrictions: allow-stderr" and "... || true".
That's easier to do on a more fine-grained level, too.

-- 
Colin Watson   [cjwat...@debian.org]



Bug#851333: ITP: git-annex-el -- Emacs integration for git-annex

2017-01-13 Thread Sean Whitton
Package: wnpp
Severity: wishlist
Owner: Sean Whitton 

* Package name: git-annex-el
  Version : 1.0+git20160215.e61ef24
  Upstream Author : John Wiegley 
* URL : https://github.com/jwiegley/git-annex-el/
* License : GPL-2+
  Programming Lang: Emacs Lisp
  Description : Emacs integration for git-annex

I intend to maintain this as part of the pkg-emacsen team.

-- 
Sean Whitton


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Bug#851334: ITP: magit-annex -- git-annex subcommands for magit

2017-01-13 Thread Sean Whitton
Package: wnpp
Severity: wishlist
Owner: Sean Whitton 

* Package name: magit-annex
  Version : 1.3.0
  Upstream Author : Kyle Meyer , Rémi Vanicat 

* URL : https://github.com/magit/magit-annex
* License : GPL-3+
  Programming Lang: Emacs Lisp
  Description : git-annex subcommands for magit

I intend to maintain this as part of the pkg-emacsen team.

-- 
Sean Whitton


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Re: "not authorised" doing various desktoppy things

2017-01-13 Thread Martín Ferrari
On 03/01/17 17:05, Ian Jackson wrote:
> Recently, my nm-applet can no longer control my network-manager
> daemon.  I get a message saying[1]:

Did you ever get to the root of this?

I am having the same kind of problem (no way to control networking,
removable media, power settings) and a similar set-up (sysvinit,
lightdm, cinnamon). I have been experiencing these kind of problems for
months, but usually they would go away after an apt-get upgrade. Not
now, and I am afraid that we will ship stretch with this problem.


-- 
Martín Ferrari (Tincho)



ITP: python-bd2k -- general utility library for bd2k python package

2017-01-13 Thread Steffen Möller
Package: wnpp
Severity: wishlist
Owner: Steffen Moeller 

* Package name: python-bd2k
* URL : https://github.com/BD2KGenomics/bd2k-python-lib
* License : Apache
  Programming Lang: Python
  Description : general utility library for bd2k python package

The package is a 2nd degree dependency of the Toil workload distributor
expected in Debian any time soon. It is about to be group-maintained at
anonscm.debian.org/cgit/debian-med/python-bd2k