Debian Bug report logs - #937144
nipype: Python2 removal in sid/bullseye

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Message #5 received at maintonly@bugs.debian.org (full text, mbox, reply):

From: Matthias Klose <doko@debian.org>

To: maintonly@bugs.debian.org

Subject: nipype: Python2 removal in sid/bullseye

Date: Fri, 30 Aug 2019 07:28:24 +0000

Package: src:nipype
Version: 1.1.8-1
Severity: normal
Tags: sid bullseye
User: debian-python@lists.debian.org
Usertags: py2removal

Python2 becomes end-of-live upstream, and Debian aims to remove
Python2 from the distribution, as discussed in
https://lists.debian.org/debian-python/2019/07/msg00080.html

Your package either build-depends, depends on Python2, or uses Python2
in the autopkg tests.  Please stop using Python2, and fix this issue
by one of the following actions.

- Convert your Package to Python3. This is the preferred option.  In
  case you are providing a Python module foo, please consider dropping
  the python-foo package, and only build a python3-foo package.  Please
  don't drop Python2 modules, which still have reverse dependencies,
  just document them.
  
  This is the preferred option.

- If the package is dead upstream, cannot be converted or maintained
  in Debian, it should be removed from the distribution.  If the
  package still has reverse dependencies, raise the severity to
  "serious" and document the reverse dependencies with the BTS affects
  command.  If the package has no reverse dependencies, confirm that
  the package can be removed, reassign this issue to ftp.debian.org,
  make sure that the bug priority is set to normal and retitle the
  issue to "RM: PKG -- removal triggered by the Python2 removal".

- If the package has still many users (popcon >= 300), or is needed to
  build another package which cannot be removed, document that by
  adding the "py2keep" user tag (not replacing the py2remove tag),
  using the debian-python@lists.debian.org user.  Also any
  dependencies on an unversioned python package (python, python-dev)
  must not be used, same with the python shebang.  These have to be
  replaced by python2/python2.7 dependencies and shebang.

  This is the least preferred option.

If the conversion or removal needs action on another package first,
please document the blocking by using the BTS affects command, like

  affects <bug number of blocking py2removal bug> + src:nipype

If there is no py2removal bug for that reverse-dependency, please file
a bug on this package (similar to this bug report).

If there are questions, please refer to the wiki page for the removal:
https://wiki.debian.org/Python/2Removal, or ask for help on IRC
#debian-python, or the debian-python@lists.debian.org mailing list.

Message #82 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Stuart Prescott <stuart@debian.org>

To: 937144@bugs.debian.org

Subject: Re: Bug#937144: syrthes: Python2 removal in sid/bullseye

Date: Sat, 01 Feb 2020 01:22:11 +1100

[Message part 1 (text/plain, inline)]

Control: tags -1 + patch

Dear maintainer,

The attached patches port the build system to Python 3. The package seems to 
build OK using them but I don't know enough about this package to test them 
further and there are no autopkgtest tests to verify that the package is OK.

regards
Stuart

-- 
Stuart Prescott    http://www.nanonanonano.net/   stuart@nanonanonano.net
Debian Developer   http://www.debian.org/         stuart@debian.org
GPG fingerprint    90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7

[0001-Update-dependencies-to-use-Python-3.patch (text/x-patch, attachment)]

[0003-Use-dh_python3-in-build.patch (text/x-patch, attachment)]

[0002-Add-patches-to-build-with-Python-3.patch (text/x-patch, attachment)]

Message #89 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Stuart Prescott <stuart@debian.org>

To: Stuart Prescott <stuart@debian.org>

Cc: 937144@bugs.debian.org

Subject: Re: Bug#937144: nipype: Python2 removal in sid/bullseye

Date: Sat, 01 Feb 2020 01:32:01 +1100

[Message part 1 (text/plain, inline)]

Dear maintainer,

That first set of patches was obviously misdirected... sorry.

The attached patches port nipype to Python 3 and stop making a Python 2 
module.

However:

* I can't successfully build the package due to the debian/patches/
deb_git_hash. If I leave that in then dpkg-source cannot apply the patches. 
The contents of the orig.tar.gz do not match what is in git for the file 
nipype/COMMIT_INFO.txt so I do not know what was intended here.

* I can't successfully build the package in parallel and I can't figure out how 
to stop parallel building with CDBS. When built with -j4 there seems to be a 
race condition in building the documentation that leads to a FTBFS. It builds 
OK for me with -j1.

regards
Stuart

-- 
Stuart Prescott    http://www.nanonanonano.net/   stuart@nanonanonano.net
Debian Developer   http://www.debian.org/         stuart@debian.org
GPG fingerprint    90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7

[0001-Update-dependencies-for-Python-3.patch (text/x-patch, attachment)]

[0002-Update-code-for-Python-3.patch (text/x-patch, attachment)]

[0003-Update-rules-for-Python-3.patch (text/x-patch, attachment)]

Message #94 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Stuart Prescott <stuart@debian.org>

Cc: Yaroslav Halchenko <debian@onerussian.com>, Michael Hanke <michael.hanke@gmail.com>, NeuroDebian Team <team@neuro.debian.net>, 937144@bugs.debian.org, 932197@bugs.debian.org, 934687@bugs.debian.org

Subject: Re: Request to join the Neurodebian group

Date: Tue, 25 Feb 2020 22:44:08 +0100

Hi,

here is some update I'm also forwarding to NeuroDebian Team list to have
some public record of the current status.

On Thu, Feb 20, 2020 at 01:36:35AM +1100, Stuart Prescott wrote:
> 
> I also looked at nipype (but its source is very odd and I can't build what is 
> in the repo; I think that was .gitattributes related but end up fixing it)

I have updated nipype in the Git repository I moved to Debian Med team[1]
The latest upstream version needs a new dependency python3-etelemetry
which I packaged and uploaded to new (see #952558)
 
I've also tried to build heudiconv in Git[2].  It builds so far but tests
accessing remote locations to download data need to be disabled.  That's
where I'm stoping for now.

Kind regards

       Andreas.

[1] https://salsa.debian.org/med-team/nipype
[2] https://salsa.debian.org/med-team/heudiconv 

-- 
http://fam-tille.de

Message #99 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Yaroslav Halchenko <yoh@debian.org>

To: Andreas Tille <tille@debian.org>

Cc: Stuart Prescott <stuart@debian.org>, Michael Hanke <michael.hanke@gmail.com>, NeuroDebian Team <team@neuro.debian.net>, 937144@bugs.debian.org, 932197@bugs.debian.org, 934687@bugs.debian.org

Subject: Re: Bug#937144: Request to join the Neurodebian group

Date: Wed, 26 Feb 2020 08:37:30 -0500

thank you Andreas!!!

re etelemetry&heudiconv:  I made it optional for previous version of the
package:

	$> quilt series
	deb-no-demand-on-etelemetry

	$> git describe
	debian/0.6.0-1


On Tue, 25 Feb 2020, Andreas Tille wrote:

> Hi,

> here is some update I'm also forwarding to NeuroDebian Team list to have
> some public record of the current status.

> On Thu, Feb 20, 2020 at 01:36:35AM +1100, Stuart Prescott wrote:

> > I also looked at nipype (but its source is very odd and I can't build what is 
> > in the repo; I think that was .gitattributes related but end up fixing it)

> I have updated nipype in the Git repository I moved to Debian Med team[1]
> The latest upstream version needs a new dependency python3-etelemetry
> which I packaged and uploaded to new (see #952558)

> I've also tried to build heudiconv in Git[2].  It builds so far but tests
> accessing remote locations to download data need to be disabled.  That's
> where I'm stoping for now.

> Kind regards

>        Andreas.

> [1] https://salsa.debian.org/med-team/nipype
> [2] https://salsa.debian.org/med-team/heudiconv 
-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        

Message #104 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Stuart Prescott <stuart@debian.org>, Michael Hanke <michael.hanke@gmail.com>, NeuroDebian Team <team@neuro.debian.net>, 937144@bugs.debian.org, 932197@bugs.debian.org, 934687@bugs.debian.org

Subject: Re: Bug#937144: Request to join the Neurodebian group

Date: Wed, 26 Feb 2020 16:15:03 +0100

On Wed, Feb 26, 2020 at 08:37:30AM -0500, Yaroslav Halchenko wrote:
> thank you Andreas!!!
> 
> re etelemetry&heudiconv:  I made it optional for previous version of the
> package:
> 
> 	$> quilt series
> 	deb-no-demand-on-etelemetry
> 
> 	$> git describe
> 	debian/0.6.0-1

Thanks for the hint.  While this could possibly speet up the upload of
nipype I for myself are fine with waiting for the new Build-Depends.
Anybody who wants to speed up things is kindly invited to add this patch
and upload.

Kind regards

     Andreas. 

 
> On Tue, 25 Feb 2020, Andreas Tille wrote:
> 
> > Hi,
> 
> > here is some update I'm also forwarding to NeuroDebian Team list to have
> > some public record of the current status.
> 
> > On Thu, Feb 20, 2020 at 01:36:35AM +1100, Stuart Prescott wrote:
> 
> > > I also looked at nipype (but its source is very odd and I can't build what is 
> > > in the repo; I think that was .gitattributes related but end up fixing it)
> 
> > I have updated nipype in the Git repository I moved to Debian Med team[1]
> > The latest upstream version needs a new dependency python3-etelemetry
> > which I packaged and uploaded to new (see #952558)
> 
> > I've also tried to build heudiconv in Git[2].  It builds so far but tests
> > accessing remote locations to download data need to be disabled.  That's
> > where I'm stoping for now.
> 
> > Kind regards
> 
> >        Andreas.
> 
> > [1] https://salsa.debian.org/med-team/nipype
> > [2] https://salsa.debian.org/med-team/heudiconv 
> -- 
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik        
> 

-- 
http://fam-tille.de

Message #109 received at 937144@bugs.debian.org (full text, mbox, reply):

From: peter green <plugwash@p10link.net>

To: 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937769-quiet@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org

Subject: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Mon, 20 Apr 2020 03:36:00 +0100

(using -quiet aliases where multiple involved packages have the same maintainer listed.

Hi

I have just been running some self-contained buildability tests on bullseye and these tests indicated that the python-linecache2 and python-traceback2 source packages have been unbuildable in testing for 170+ days. Both are fixed in unstable by removing python 2 support, but can't migrate to testing because the python-unittest2 binary package depends on the python-traceback2 binary package. The python2 removal bug for python-traceback2 lists python-funcsigs as a blocker. The python2 removal bug for python-traceback2 lists nipype and numba as blockers.

unittest2 and python-funcsigs seem to be just module packages, so dropping python2 support should be simple. numba seems to be a case of leftover recommends and test-triggers so that should be a pretty easy job to clean up too.

nipype on the other hand looks like it needs a new upstream release. It seems this was previously blocked on a package passing new, but said package has now passed new.

python-funcsigs seems to have a build-dependency on python-traceback2 but not a binary dependency, this suggests that the dependency is only used to run tests at build time.

nipype and numba are not currently in testing.

This IMO leaves three potential ways forward

Option 1: fix all four packages to be python 2 free.

Option 2: Remove python2 stuff from traceback2, python-funcsigs and numba. Break the dependencies of nipype in sid.

Option 3: Remove python2 stuff from traceback2, modify python-funcsigs so it still builds the python2 package but does not run tests with python 2.

If the maintainers of nipype are willing to upload a python 3 version soon, then option 1 is IMO the preffered way forward, but a new upstream version is not something I would be prepared to NMU.

Otherwise I am inclined towards option 2. Depending on what responses I get to this mail I may implement this option through NMUs later.

Message #114 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Scott Kitterman <debian@kitterman.com>

To: peter green <plugwash@p10link.net>,938756@bugs.debian.org,952127@bugs.debian.org,952130-quiet@bugs.debian.org,937769-quiet@bugs.debian.org,937144@bugs.debian.org,943135@bugs.debian.org

Subject: Re: [Python-modules-team] Bug#938756: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Mon, 20 Apr 2020 02:50:59 +0000

On April 20, 2020 2:36:00 AM UTC, peter green <plugwash@p10link.net> wrote:
>(using -quiet aliases where multiple involved packages have the same
>maintainer listed.
>
>Hi
>
>I have just been running some self-contained buildability tests on
>bullseye and these tests indicated that the python-linecache2 and
>python-traceback2 source packages have been unbuildable in testing for
>170+ days. Both are fixed in unstable by removing python 2 support, but
>can't migrate to testing because the python-unittest2 binary package
>depends on the python-traceback2 binary package. The python2 removal
>bug for python-traceback2 lists python-funcsigs as a blocker. The
>python2 removal bug for python-traceback2 lists nipype and numba as
>blockers.
>
>unittest2 and python-funcsigs seem to be just module packages, so
>dropping python2 support should be simple. numba seems to be a case of
>leftover recommends and test-triggers so that should be a pretty easy
>job to clean up too.
>
>nipype on the other hand looks like it needs a new upstream release. It
>seems this was previously blocked on a package passing new, but said
>package has now passed new.
>
>python-funcsigs seems to have a build-dependency on python-traceback2
>but not a binary dependency, this suggests that the dependency is only
>used to run tests at build time.
>
>nipype and numba are not currently in testing.
>
>This IMO leaves three potential ways forward
>
>Option 1: fix all four packages to be python 2 free.
>
>Option 2: Remove python2 stuff from traceback2, python-funcsigs and
>numba. Break the dependencies of nipype in sid.
>
>Option 3: Remove python2 stuff from traceback2, modify python-funcsigs
>so it still builds the python2 package but does not run tests with
>python 2.
>
>If the maintainers of nipype are willing to upload a python 3 version
>soon, then option 1 is IMO the preffered way forward, but a new
>upstream version is not something I would be prepared to NMU.
>
>Otherwise I am inclined towards option 2. Depending on what responses I
>get to this mail I may implement this option through NMUs later.

Nipype in Unstable is already all kinds of broken.  I'd ignore further breaking it your analysis.  I'd suggest move forward with option 2.

Scott K

Message #119 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Thomas Goirand <thomas@goirand.fr>

To: peter green <plugwash@p10link.net>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Mon, 20 Apr 2020 09:57:30 +0200

On 4/20/20 4:36 AM, peter green wrote:
> (using -quiet aliases where multiple involved packages have the same
> maintainer listed.
> 
> Hi
> 
> I have just been running some self-contained buildability tests on
> bullseye and these tests indicated that the python-linecache2 and
> python-traceback2 source packages have been unbuildable in testing for
> 170+ days. Both are fixed in unstable by removing python 2 support, but
> can't migrate to testing because the python-unittest2 binary package
> depends on the python-traceback2 binary package. The python2 removal bug
> for python-traceback2 lists python-funcsigs as a blocker. The python2
> removal bug for python-traceback2 lists nipype and numba as blockers.
> 
> unittest2 and python-funcsigs seem to be just module packages, so
> dropping python2 support should be simple. numba seems to be a case of
> leftover recommends and test-triggers so that should be a pretty easy
> job to clean up too.
> 
> nipype on the other hand looks like it needs a new upstream release. It
> seems this was previously blocked on a package passing new, but said
> package has now passed new.
> 
> python-funcsigs seems to have a build-dependency on python-traceback2
> but not a binary dependency, this suggests that the dependency is only
> used to run tests at build time.
> 
> nipype and numba are not currently in testing.
> 
> This IMO leaves three potential ways forward
> 
> Option 1: fix all four packages to be python 2 free.
> 
> Option 2: Remove python2 stuff from traceback2, python-funcsigs and
> numba. Break the dependencies of nipype in sid.
> 
> Option 3: Remove python2 stuff from traceback2, modify python-funcsigs
> so it still builds the python2 package but does not run tests with
> python 2.

Funcsigs is a backport of the PEP 362 function signature features from
Python 3.3's inspect module. Python 2 has never been removed from this
package. Though instead, we shall remove this source package entirely
from Debian.

Traceback2 *already* has Python 2 support removed in Sid. I uploaded
this on the 21st of march, pressured by its potential autoremoval.

> If the maintainers of nipype are willing to upload a python 3 version
> soon, then option 1 is IMO the preffered way forward, but a new upstream
> version is not something I would be prepared to NMU.

There's no other choice but to fix nipype at this point, or wait until
it gets autoremoved from Testing. IMO, it'd be fine to NMU a new
upstream release if you contact the current maintainer and/or using the
delayed queue.

> Otherwise I am inclined towards option 2. Depending on what responses I
> get to this mail I may implement this option through NMUs later.

IMO, we should get unittest2 free of Py2 support ASAP, and open an FTP
team bug to get funcsigs removed from Debian.

Cheers,

Thomas Goirand (zigo)

Message #124 received at 937144@bugs.debian.org (full text, mbox, reply):

From: peter green <plugwash@p10link.net>

To: Thomas Goirand <thomas@goirand.fr>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Mon, 20 Apr 2020 13:51:10 +0100

On 20/04/2020 08:57, Thomas Goirand wrote:
>> Option 1: fix all four packages to be python 2 free.
>>
>> Option 2: Remove python2 stuff from traceback2, python-funcsigs and
>> numba. Break the dependencies of nipype in sid.
>>
>> Option 3: Remove python2 stuff from traceback2, modify python-funcsigs
>> so it still builds the python2 package but does not run tests with
>> python 2.
> Funcsigs is a backport of the PEP 362 function signature features from
> Python 3.3's inspect module.
Thanks for the info.
> Python 2 has never been removed from this
> package. Though instead, we shall remove this source package entirely
> from Debian.
# Broken Depends:
nipype: python-nipype
pytest: pypy-pytest
python-logfury: python3-logfury
python-oslo.utils: python3-oslo.utils

# Broken Build-Depends:
beaker: python3-funcsigs
kombu: python3-funcsigs
nipype: python-funcsigs
pagure: python3-funcsigs
pytest: pypy-funcsigs
python-oslo.log: python3-funcsigs
python-oslo.utils: python3-funcsigs (>= 0.4)
ripe-atlas-cousteau: python3-funcsigs

If what you say is correct then it sounds like the python3-funcsigs revese depedencies could be dealt with fairly easily.

But that still leaves the question of what to do about the dependency of pytest on pypy-funcsigs ? should pypy modules be removed from pytest and it's reverse-dependencies in the same way that regular python2 modules were? how feasible is that? are pypy-* packages only useful with python2 pypy or are they also useful with python3 pypy?

> Traceback2 *already* has Python 2 support removed in Sid. I uploaded
> this on the 21st of march, pressured by its potential autoremoval.

Sorry it seems I got my package names mixed up when writing the list of options. I said traceback2 where I meant unittest2.

> There's no other choice but to fix nipype at this point, or wait until
> it gets autoremoved from Testing.
It already was autoremoved from testing.
>   IMO, it'd be fine to NMU a new
> upstream release if you contact the current maintainer and/or using the
> delayed queue.
A new upstream release for a package I do not use is not something I feel comfortable NMUing. I was hoping that my initial mail would prompt action on the parts of the nipype maintainers but if they don't respond then I tend towards ignoring breakage of sid-only packages that need non-trivial fixes.

> IMO, we should get unittest2 free of Py2 support ASAP, and open an FTP
> team bug to get funcsigs removed from Debian.
>
> Cheers,
>
> Thomas Goirand (zigo)

Message #129 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Scott Kitterman <debian@kitterman.com>

To: 938756@bugs.debian.org, 937769-quiet@bugs.debian.org

Cc: 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org

Subject: Re: [Python-modules-team] Bug#938756: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Mon, 20 Apr 2020 09:35:32 -0400

[Message part 1 (text/plain, inline)]

On Monday, April 20, 2020 8:51:10 AM EDT peter green wrote:
> On 20/04/2020 08:57, Thomas Goirand wrote:
> >> Option 1: fix all four packages to be python 2 free.
> >> 
> >> Option 2: Remove python2 stuff from traceback2, python-funcsigs and
> >> numba. Break the dependencies of nipype in sid.
> >> 
> >> Option 3: Remove python2 stuff from traceback2, modify python-funcsigs
> >> so it still builds the python2 package but does not run tests with
> >> python 2.
> > 
> > Funcsigs is a backport of the PEP 362 function signature features from
> > Python 3.3's inspect module.
> 
> Thanks for the info.
> 
> > Python 2 has never been removed from this
> > package. Though instead, we shall remove this source package entirely
> > from Debian.
> 
> # Broken Depends:
> nipype: python-nipype
> pytest: pypy-pytest
> python-logfury: python3-logfury
> python-oslo.utils: python3-oslo.utils
> 
> # Broken Build-Depends:
> beaker: python3-funcsigs
> kombu: python3-funcsigs
> nipype: python-funcsigs
> pagure: python3-funcsigs
> pytest: pypy-funcsigs
> python-oslo.log: python3-funcsigs
> python-oslo.utils: python3-funcsigs (>= 0.4)
> ripe-atlas-cousteau: python3-funcsigs
> 
> If what you say is correct then it sounds like the python3-funcsigs revese
> depedencies could be dealt with fairly easily.
> 
> But that still leaves the question of what to do about the dependency of
> pytest on pypy-funcsigs ? should pypy modules be removed from pytest and
> it's reverse-dependencies in the same way that regular python2 modules
> were? how feasible is that? are pypy-* packages only useful with python2
> pypy or are they also useful with python3 pypy?

The Python 2 pypy variant isn't being dropped, so if pypy-funcsigs has 
rdepends, it should probably stay.  In the interest of maintaining momentum on 
the Python 2, I think it would be better to just drop python-funcsigs and sort 
out the future of pypy-funcsigs and python3-funcsigs later.

> > Traceback2 *already* has Python 2 support removed in Sid. I uploaded
> > this on the 21st of march, pressured by its potential autoremoval.
> 
> Sorry it seems I got my package names mixed up when writing the list of
> options. I said traceback2 where I meant unittest2.
> > There's no other choice but to fix nipype at this point, or wait until
> > it gets autoremoved from Testing.
> 
> It already was autoremoved from testing.
> 
> >   IMO, it'd be fine to NMU a new
> > upstream release if you contact the current maintainer and/or using the
> > delayed queue.
> 
> A new upstream release for a package I do not use is not something I feel
> comfortable NMUing. I was hoping that my initial mail would prompt action
> on the parts of the nipype maintainers but if they don't respond then I
> tend towards ignoring breakage of sid-only packages that need non-trivial
> fixes.

The current nipype maintainer is well aware of the issue.  AIUI they are 
holding off on uploading to Unstable until they are confident the Python 3 port 
is sufficiently mature.  Since it's already out of Testing and uninstallable in 
Sid, you can ignore causing further breakage (it won't get any more 
uninstallable).

> > IMO, we should get unittest2 free of Py2 support ASAP, and open an FTP
> > team bug to get funcsigs removed from Debian.

I think the original option 2 still makes the most sense.

Scott K

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Message #134 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Thomas Goirand <zigo@debian.org>

To: peter green <plugwash@p10link.net>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org

Cc: Stefano Rivera <stefanor@debian.org>, Debian Python <debian-python@lists.debian.org>

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Tue, 21 Apr 2020 23:20:16 +0200

On 4/20/20 2:51 PM, peter green wrote:
> On 20/04/2020 08:57, Thomas Goirand wrote:
>>> Option 1: fix all four packages to be python 2 free.
>>>
>>> Option 2: Remove python2 stuff from traceback2, python-funcsigs and
>>> numba. Break the dependencies of nipype in sid.
>>>
>>> Option 3: Remove python2 stuff from traceback2, modify python-funcsigs
>>> so it still builds the python2 package but does not run tests with
>>> python 2.
>> Funcsigs is a backport of the PEP 362 function signature features from
>> Python 3.3's inspect module.
> Thanks for the info.
>> Python 2 has never been removed from this
>> package. Though instead, we shall remove this source package entirely
>> from Debian.
> # Broken Depends:
> nipype: python-nipype
> pytest: pypy-pytest
> python-logfury: python3-logfury
> python-oslo.utils: python3-oslo.utils
> 
> # Broken Build-Depends:
> beaker: python3-funcsigs
> kombu: python3-funcsigs
> nipype: python-funcsigs
> pagure: python3-funcsigs
> pytest: pypy-funcsigs
> python-oslo.log: python3-funcsigs
> python-oslo.utils: python3-funcsigs (>= 0.4)
> ripe-atlas-cousteau: python3-funcsigs

You can remove all of the python-oslo* from the list. The versions in
Experimental, which are the next version of OpenStack, are fixed. In 2
weeks of time, I'll upload all what I staged in Experimental to Sid
(maybe 150 packages?) and that's going to fix it all.

For the others, probably I should start filling bugs...

> If what you say is correct then it sounds like the python3-funcsigs
> revese depedencies could be dealt with fairly easily.
> 
> But that still leaves the question of what to do about the dependency of
> pytest on pypy-funcsigs ? should pypy modules be removed from pytest and
> it's reverse-dependencies in the same way that regular python2 modules
> were? how feasible is that? are pypy-* packages only useful with python2
> pypy or are they also useful with python3 pypy?

I really don't know about pypy. Probably the pypy-pytest should indeed
go away, as the initial plan was to switch to pypy3. Maybe tumbleweed
(Stefano Rivera) would be able to answer. I'm adding him as Cc.

>> Traceback2 *already* has Python 2 support removed in Sid. I uploaded
>> this on the 21st of march, pressured by its potential autoremoval.
> 
> Sorry it seems I got my package names mixed up when writing the list of
> options. I said traceback2 where I meant unittest2.

So, if I'm following correctly, what you seem to propose, is to remove
Python 2 from unittest2. If that's the case, then I agree with such a
plan. I just didn't dare to do it yet.

Though in fact, I already worked on that, but stopped, also because
unittest2 FTBFS when I try building it on my laptop. So I've pushed it
in its normal Git repo [1] under a py2-removal branch. If anyone has
some time available to look at it, that'd be nice (I currently don't...).

Cheers,

Thomas Goirand (zigo)

[1] https://salsa.debian.org/python-team/modules/unittest2/

Message #139 received at 937144@bugs.debian.org (full text, mbox, reply):

From: stefanor@debian.org

To: Thomas Goirand <zigo@debian.org>

Cc: peter green <plugwash@p10link.net>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org, Debian Python <debian-python@lists.debian.org>

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Tue, 21 Apr 2020 21:26:54 +0000

Hi Thomas (2020.04.21_21:20:16_+0000)
> > But that still leaves the question of what to do about the dependency of
> > pytest on pypy-funcsigs ? should pypy modules be removed from pytest and
> > it's reverse-dependencies in the same way that regular python2 modules
> > were? how feasible is that? are pypy-* packages only useful with python2
> > pypy or are they also useful with python3 pypy?

Pretty much, yes.

pypy itself (the python 2.7 pypy) will continue to exist for the
foreseeable future, to support building pypy3. But we don't need to ship
modules for it. I'd be pretty happy if we had working virtualenv, and
nothing else.

SR

-- 
Stefano Rivera
  http://tumbleweed.org.za/
  +1 415 683 3272

Message #144 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Valentin Vidić <vvidic@debian.org>

To: Thomas Goirand <zigo@debian.org>

Cc: peter green <plugwash@p10link.net>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 955116@bugs.debian.org, 943135@bugs.debian.org, Stefano Rivera <stefanor@debian.org>, Debian Python <debian-python@lists.debian.org>

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Wed, 22 Apr 2020 06:23:34 +0200

On Tue, Apr 21, 2020 at 11:20:16PM +0200, Thomas Goirand wrote:
> You can remove all of the python-oslo* from the list. The versions in
> Experimental, which are the next version of OpenStack, are fixed. In 2
> weeks of time, I'll upload all what I staged in Experimental to Sid
> (maybe 150 packages?) and that's going to fix it all.

Will the new OpenStack version also fix this issue?

#955116 python-murano-pkg-check: FTBFS with Sphinx 2.4: AttributeError:
'Sphinx' object has no attribute 'info'

-- 
Valentin

Message #149 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Ondrej Novy <novy@ondrej.org>

To: Thomas Goirand <zigo@debian.org>, 952130-quiet@bugs.debian.org

Cc: peter green <plugwash@p10link.net>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org, Stefano Rivera <stefanor@debian.org>, Debian Python <debian-python@lists.debian.org>

Subject: Re: Bug#952130: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Wed, 22 Apr 2020 11:55:55 +0200

[Message part 1 (text/plain, inline)]

Hi,

út 21. 4. 2020 v 23:24 odesílatel Thomas Goirand <zigo@debian.org> napsal:

> > But that still leaves the question of what to do about the dependency of
> > pytest on pypy-funcsigs ? should pypy modules be removed from pytest and
> > it's reverse-dependencies in the same way that regular python2 modules
> > were? how feasible is that? are pypy-* packages only useful with python2
> > pypy or are they also useful with python3 pypy?
>
> I really don't know about pypy. Probably the pypy-pytest should indeed
> go away, as the initial plan was to switch to pypy3. Maybe tumbleweed
> (Stefano Rivera) would be able to answer. I'm adding him as Cc.
>

I guess I can say something about pytest because I'm maintainer of pytest,
right? :)

I'm perfectly fine with removing pypy-pytest binary package and all other
dependencies in chain. It's painfull to maintain it.

-- 
Best regards
 Ondřej Nový

[Message part 2 (text/html, inline)]

Message #154 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Thomas Goirand <zigo@debian.org>

To: Valentin Vidić <vvidic@debian.org>

Cc: peter green <plugwash@p10link.net>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 955116@bugs.debian.org, 943135@bugs.debian.org, Stefano Rivera <stefanor@debian.org>, Debian Python <debian-python@lists.debian.org>

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Wed, 22 Apr 2020 15:57:32 +0200

On 4/22/20 6:23 AM, Valentin Vidić wrote:
> On Tue, Apr 21, 2020 at 11:20:16PM +0200, Thomas Goirand wrote:
>> You can remove all of the python-oslo* from the list. The versions in
>> Experimental, which are the next version of OpenStack, are fixed. In 2
>> weeks of time, I'll upload all what I staged in Experimental to Sid
>> (maybe 150 packages?) and that's going to fix it all.
> 
> Will the new OpenStack version also fix this issue?
> 
> #955116 python-murano-pkg-check: FTBFS with Sphinx 2.4: AttributeError:
> 'Sphinx' object has no attribute 'info'

Hopefully yes. As I understand, the issue is in oslo-sphinx, which is
deprecated. I checked, and the master branch of murano-pkg-check doesn't
use oslo-sphinx (and is therefore fixed). I'm waiting for it to be
released, hopefully this week or the next one.

Cheers,

Thomas Goirand (zigo)

Message #159 received at 937144@bugs.debian.org (full text, mbox, reply):

From: peter green <plugwash@p10link.net>

To: Thomas Goirand <zigo@debian.org>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org

Cc: Stefano Rivera <stefanor@debian.org>, Debian Python <debian-python@lists.debian.org>

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Sat, 25 Apr 2020 19:12:03 +0100

On 21/04/2020 22:20, Thomas Goirand wrote:
> So, if I'm following correctly, what you seem to propose, is to remove
> Python 2 from unittest2. If that's the case, then I agree with such a
> plan. I just didn't dare to do it yet.
Yes, whichever approach is taken to dealing with funcsigs, unittest2 will need to drop it's python2 packages.
> Though in fact, I already worked on that, but stopped, also because
> unittest2 FTBFS when I try building it on my laptop. So I've pushed it
> in its normal Git repo [1] under a py2-removal branch. If anyone has
> some time available to look at it, that'd be nice (I currently don't...).
It appears that this was fixed in a NMU, but the NMU changes were never imported into the packaging repository, once I imported the NMU changes the package built fine here.

Message #164 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Moritz Mühlenhoff <jmm@inutil.org>

To: Thomas Goirand <thomas@goirand.fr>

Cc: peter green <plugwash@p10link.net>, 937769-quiet@bugs.debian.org, 952127@bugs.debian.org, 952130-quiet@bugs.debian.org, 938756@bugs.debian.org, 937144@bugs.debian.org, 943135@bugs.debian.org

Subject: Re: Bug#937769: getting python-linecache2/python-traceback2 fixes into testing (FAO traceback2, funcsigs nipype and numba maintainers).

Date: Thu, 30 Apr 2020 20:00:15 +0200

On Mon, Apr 20, 2020 at 09:57:30AM +0200, Thomas Goirand wrote:
> On 4/20/20 4:36 AM, peter green wrote:
> 
> Funcsigs is a backport of the PEP 362 function signature features from
> Python 3.3's inspect module. Python 2 has never been removed from this
> package. Though instead, we shall remove this source package entirely
> from Debian.
> 
> Traceback2 *already* has Python 2 support removed in Sid. I uploaded
> this on the 21st of march, pressured by its potential autoremoval.
> 
> > If the maintainers of nipype are willing to upload a python 3 version
> > soon, then option 1 is IMO the preffered way forward, but a new upstream
> > version is not something I would be prepared to NMU.
> 
> There's no other choice but to fix nipype at this point, or wait until
> it gets autoremoved from Testing. IMO, it'd be fine to NMU a new
> upstream release if you contact the current maintainer and/or using the
> delayed queue.

JFTR, nipype is removed from testing since August last year, so this is totally
not a blocker :-)

Cheers,
        Moritz

Message #169 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Moritz Mühlenhoff <jmm@inutil.org>

To: Andreas Tille <tille@debian.org>

Cc: Stuart Prescott <stuart@debian.org>, Michael Hanke <michael.hanke@gmail.com>, NeuroDebian Team <team@neuro.debian.net>, 937144@bugs.debian.org, 932197@bugs.debian.org, 934687@bugs.debian.org

Subject: Re: Bug#937144: Request to join the Neurodebian group

Date: Thu, 30 Apr 2020 20:02:41 +0200

On Wed, Feb 26, 2020 at 04:15:03PM +0100, Andreas Tille wrote:
> On Wed, Feb 26, 2020 at 08:37:30AM -0500, Yaroslav Halchenko wrote:
> > thank you Andreas!!!
> > 
> > re etelemetry&heudiconv:  I made it optional for previous version of the
> > package:
> > 
> > 	$> quilt series
> > 	deb-no-demand-on-etelemetry
> > 
> > 	$> git describe
> > 	debian/0.6.0-1
> 
> Thanks for the hint.  While this could possibly speet up the upload of
> nipype I for myself are fine with waiting for the new Build-Depends.
> Anybody who wants to speed up things is kindly invited to add this patch
> and upload.

What's the status here? python-etelemetry is now in the archive and testing.

Cheers,
        Moritz

Message #174 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Yaroslav Halchenko <yoh@debian.org>

To: Moritz Mühlenhoff <jmm@inutil.org>

Cc: Andreas Tille <tille@debian.org>, Stuart Prescott <stuart@debian.org>, Michael Hanke <michael.hanke@gmail.com>, NeuroDebian Team <team@neuro.debian.net>, 937144@bugs.debian.org, 932197@bugs.debian.org, 934687@bugs.debian.org

Subject: Re: Bug#937144: Request to join the Neurodebian group

Date: Thu, 30 Apr 2020 15:23:27 -0400

On Thu, 30 Apr 2020, Moritz Mühlenhoff wrote:

> On Wed, Feb 26, 2020 at 04:15:03PM +0100, Andreas Tille wrote:
> > On Wed, Feb 26, 2020 at 08:37:30AM -0500, Yaroslav Halchenko wrote:
> > > thank you Andreas!!!

> > > re etelemetry&heudiconv:  I made it optional for previous version of the
> > > package:

> > > 	$> quilt series
> > > 	deb-no-demand-on-etelemetry

> > > 	$> git describe
> > > 	debian/0.6.0-1

> > Thanks for the hint.  While this could possibly speet up the upload of
> > nipype I for myself are fine with waiting for the new Build-Depends.
> > Anybody who wants to speed up things is kindly invited to add this patch
> > and upload.

> What's the status here? python-etelemetry is now in the archive and testing.

my problem with any version of nipype ended up stalling tests with
python3.8. See e.g. https://github.com/nipy/nipype/pull/3154 for
interactions with upstream and now a dedicated issue 
https://github.com/nipy/nipype/issues/3209

I guess what we could do is to upload currently present in debian
version with python 3.8 testing disabled and hope for the best ;)  I
will exercise (update packaging and see if builds/test otherwise ok with
3.7 etc) that now

Then we wait for python3-rdflib 5.0 being uploaded (just submitted a
wishlist bug report to have it updated), and upload fresh snapshot (or
release if by then done) of nipype.

any suggestions to the plan? ;)

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        

Message #189 received at 937144@bugs.debian.org (full text, mbox, reply):

From: Yaroslav Halchenko <yoh@debian.org>

To: Moritz Mühlenhoff <jmm@inutil.org>

Cc: Andreas Tille <tille@debian.org>, Stuart Prescott <stuart@debian.org>, Michael Hanke <michael.hanke@gmail.com>, NeuroDebian Team <team@neuro.debian.net>, 937144@bugs.debian.org, 932197@bugs.debian.org, 934687@bugs.debian.org

Subject: Re: Bug#932197: Bug#937144: Request to join the Neurodebian group

Date: Sat, 12 Dec 2020 09:12:16 -0500

On Thu, 30 Apr 2020, Moritz Mühlenhoff wrote:

> > Thanks for the hint.  While this could possibly speet up the upload of
> > nipype I for myself are fine with waiting for the new Build-Depends.
> > Anybody who wants to speed up things is kindly invited to add this patch
> > and upload.

> What's the status here? python-etelemetry is now in the archive and testing.

FWIW: I just uploaded rdflib 5.0.0 (recent nipype needs that
version if any) and pushed initial changes to nipype's packaging git for
1.6.0 . Will try to find more time over weekend to finalize packaging
update (if no other new depends etc) -- needed for heudiconv package
(currently present  nipype version incorrectly handles some DWIs, FYI
for those who care ;)).

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW:   http://www.linkedin.com/in/yarik        

Message #190 received at 932197-done@bugs.debian.org (full text, mbox, reply):

From: Yaroslav Halchenko <yoh@debian.org>

To: Andreas Tille <tille@debian.org>

Cc: 932197-done@bugs.debian.org

Subject: Re: Isn't that bug done now?

Date: Mon, 4 Jan 2021 12:30:14 -0500

Version: 1.6.0-1

On Mon, 04 Jan 2021, Andreas Tille wrote:

> Hi Yaroslav,

> shouldn't this bug be closed now?

d'oh -- right, thanks! actually was done within 1.5.0~rc1-1 set of
changes marked for experimental


-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW:   http://www.linkedin.com/in/yarik        

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