Bug#840589: Bug#848112: Python-skimage depends on unavailable package python-dask

[Andreas Tille]

Hi Ole,

On Fri, Dec 23, 2016 at 12:14:07PM +0100, Ole Streicher wrote:
> 
> I have a fix for both, and after a final test build, I will upload.

Thanks a lot.  BTW, I'm fine if you close / lower severity of #849177.
 
Kind regards

   Andreas. 

-- 
http://fam-tille.de

Bug#848112: Python-skimage depends on unavailable package python-dask

[Ole Streicher]

Control: tags 848112 pending

Hi all,

On 23.12.2016 10:08, Andreas Tille wrote:
> Ole, if you would please commit the patch you named in #848112 and
> upload the package to make sure it can migrate right in time and will
> enable other packages to migrate as well?
> 
> HOWEVER, we have another problem:  If I build the current state in Git
> I'm running into:
> TypeError: 'numpy.float64' object cannot be interpreted as an index

I have a fix for both, and after a final test build, I will upload.

The package still seems to be in bad shape; during the docs generation
exceptions are thrown like

ValueError: 3-dimensional arrays must be of dtype unsigned byte,
unsigned short, float32 or float64
TypeError: 'numpy.float64' object cannot be interpreted as an index

They are ignored, however, but show that some work is still needed.

Cheers

Ole

Bug#840589: Bug#848112: Python-skimage depends on unavailable package python-dask

[Andreas Tille]

Hi,

On Thu, Dec 22, 2016 at 10:04:22PM -0700, Stefan van der Walt wrote:
> OK by me, too.
> 
> On December 22, 2016 9:45:10 PM Yaroslav Halchenko 
> wrote:
> 
> >On December 22, 2016 4:52:41 PM EST, Andreas Tille  wrote:
> >>place were people who intend to help can effectively join the effort.
> >>This package is blocking invesalius from migrating to testing and
> >>chances are low that it will reach stretch.  So if the problem is to
> >>pick a team I'll move it to Debian Science on 10 hours.  I really hope
> >>that this might push things if nothing is happening otherwise.
> >
> >I don't mind - move or NMU the fix

OK, thanks for the confirmation and as promised I created:

 https://anonscm.debian.org/git/debian-science/packages/skimage.git

Please note: I removed debian/gbp.conf and used the branches as
described in Debian Science policy.  If those Uploaders who finally work
on the package prefer a different layout please document this in
debian/README.source.

I also commited a patch that's simply skiping the tests mentioned in
#840589.  I do not really like this kind of "hiding eyes from problems"
workaround and thus I would not really close bug #840589 but IMHO it is
apropriate to lower its severity and work on later on this together with
upstream (those who intend to keep on maintaining the package please
open an upstream issue - will not continue here).

Ole, if you would please commit the patch you named in #848112 and
upload the package to make sure it can migrate right in time and will
enable other packages to migrate as well?

HOWEVER, we have another problem:  If I build the current state in Git
I'm running into:


==
ERROR: skimage.filters.rank.tests.test_rank.test_all
--
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
  File 
"/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/tests/test_rank.py",
 line 16, in test_all
check_all()
  File 
"/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/_shared/testing.py",
 line 232, in inner
result = func(*args, **kwargs)
  File 
"/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/tests/test_rank.py",
 line 89, in check_all
rank.windowed_histogram(image, selem))
  File 
"/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/generic.py",
 line 986, in windowed_histogram
pixel_size=n_bins)
  File 
"/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/generic.py",
 line 90, in _apply_vector_per_pixel
pixel_size=pixel_size)
  File 
"/build/skimage-0.12.3/debian/tmp/usr/lib/python2.7/dist-packages/skimage/filters/rank/generic.py",
 line 53, in _handle_input
out = np.empty(image.shape+(pixel_size,), dtype=out_dtype)
TypeError: 'numpy.float64' object cannot be interpreted as an index

--
Ran 1383 tests in 181.697s

FAILED (SKIP=54, errors=1)


I'm opening a bug against python-numpy to revert the transition that
has happened after the transition freeze (see #848758 for details).

Kind regards

 Andreas.


-- 
http://fam-tille.de

Bug#848112: Python-skimage depends on unavailable package python-dask

[Stefan van der Walt]

OK by me, too.


On December 22, 2016 9:45:10 PM Yaroslav Halchenko  
wrote:



On December 22, 2016 4:52:41 PM EST, Andreas Tille  wrote:

Hi folks,

can we please, pretty please start acting now and move this package to
a
place were people who intend to help can effectively join the effort.
This package is blocking invesalius from migrating to testing and
chances are low that it will reach stretch.  So if the problem is to
pick a team I'll move it to Debian Science on 10 hours.  I really hope
that this might push things if nothing is happening otherwise.

Kind regards

   Andreas.


I don't mind - move or NMU the fix

Bug#848112: Python-skimage depends on unavailable package python-dask

[Yaroslav Halchenko]

On December 22, 2016 4:52:41 PM EST, Andreas Tille  wrote:
>Hi folks,
>
>can we please, pretty please start acting now and move this package to
>a
>place were people who intend to help can effectively join the effort.
>This package is blocking invesalius from migrating to testing and
>chances are low that it will reach stretch.  So if the problem is to
>pick a team I'll move it to Debian Science on 10 hours.  I really hope
>that this might push things if nothing is happening otherwise.
>
>Kind regards
>
>Andreas.

I don't mind - move or NMU the fix

Bug#848112: Python-skimage depends on unavailable package python-dask

[Andreas Tille]

Hi folks,

can we please, pretty please start acting now and move this package to a
place were people who intend to help can effectively join the effort.
This package is blocking invesalius from migrating to testing and
chances are low that it will reach stretch.  So if the problem is to
pick a team I'll move it to Debian Science on 10 hours.  I really hope
that this might push things if nothing is happening otherwise.

Kind regards

Andreas.

-- 
http://fam-tille.de

Bug#848112: Python-skimage depends on unavailable package python-dask

[Ghislain Vaillant]

On 14/12/16 19:58, Stefan van der Walt wrote:

I would have absolutely no problem moving skimage to team maintenance.
If Yarik agrees, I'd appreciate some pointers on how to move forward
with that.  What I would like is to remain in the loop w.r.t. packaging
changes.  python-dask should be packaged now, I think Diane Trout of one
of the teams has been working on that the past week.


First, you'd need to pick a team (Ole suggested Debian Science or Debian 
Python Modules) and join it via their Alioth page. You might also want 
to email the team's mailing list to speed up the joining process.


Then, you'd have to setup the team maintained git repository. That's 
usually documented in the team's packaging policy and something Ole or 
myself can help you with.


Finally, just push the current content of the packaging to the new 
remote. You can then update the Vcs-Browse and Vcs-Git fields in 
d/control to the canonical path to the team's repository, change the 
Maintainer field to the chosen team and move yourselves to the Uploaders 
field.


And that's about it I think. Ole, feel free to correct me if something 
is not accurate.


Ghis

Bug#848112: Python-skimage depends on unavailable package python-dask

[Stefan van der Walt]

I would have absolutely no problem moving skimage to team maintenance. 
If Yarik agrees, I'd appreciate some pointers on how to move forward
with that.  What I would like is to remain in the loop w.r.t. packaging
changes.  python-dask should be packaged now, I think Diane Trout of one
of the teams has been working on that the past week.

Bug#848112: Python-skimage depends on unavailable package python-dask

[Ghislain Vaillant]

On 14/12/16 09:59, Ole Streicher wrote:

Since skimage is one of the central packages, I would again ask to put
it under science|python team maintenance. Especially when under some
time pressure (upcoming freeze, combined with autoremovals of packages)
it would help a lot if the problems could be debugged within a standard
Debian developer workflow, without the need to switch to github or so.


I second Ole's suggestion.

Moving to team-maintenance would really help and is pretty painless if 
you are already using git for storing the debianized sources. You would 
still remain the main maintainer(s), but one-off fixes like this could 
be pushed and rolled-out quicker by anyone from the team.


Please consider it.

Ghis

Bug#848112: Python-skimage depends on unavailable package python-dask

[Ole Streicher]

package: python-skimage
version: 0.12.3-2
severity: serious

The Python 2 version of skimage depends on a package "python-dask" that
is not available in Debian.

There is a patch that make the dependency optional; however the
dependency was not removed afterwards. For Python 3, this seems to work.

Since skimage is one of the central packages, I would again ask to put
it under science|python team maintenance. Especially when under some
time pressure (upcoming freeze, combined with autoremovals of packages)
it would help a lot if the problems could be debugged within a standard
Debian developer workflow, without the need to switch to github or so.

Best regards

Ole