Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-12-31 Thread Andreas Tille
On Tue, Dec 31, 2019 at 04:22:09PM -0500, Scott Talbert wrote:
> > > That's recorded as TODO item in d/changelog now.
> > 
> > FYI, I just worked on converting envisage to python3:
> > https://salsa.debian.org/python-team/modules/python-envisage
> > 
> > I asked Dmitry S. to upload it.
> 
> Hey all, I worked more on mayavi2 and I think is probably ready enough 
> for upload: 
> 
> - Removed wxPython as dependency - only PyQt is currently supported in 
> mayavi for Python3.  This will be pulled in automatically by traitsui, 
> pyface, etc.
> 
> - Cleaned up all lintian errors/warnings
> 
> - Worked further at getting the tests working.  They are a lot closer 
> but not completely functional.
> 
> - The package builds, installs, and runs fine as best as I can tell, 
> although I don't know how to do much with it.
> 
> Feel free to upload if you think it is ready.

Uploaded.  Thanks a lot for your work on this.

> Happy New Year,

Same to you, Andreas.
 

-- 
http://fam-tille.de



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-12-31 Thread Scott Talbert
> > > python-envisage has not yet been converted to Python3 and seems to be 
> > > required:
> > > $ mayavi2
> > > Traceback (most recent call last):
> > >   File "/usr/bin/mayavi2", line 464, in 
> > > from mayavi.plugins.app import Mayavi, setup_logger
> > >   File "/usr/lib/python3/dist-packages/mayavi/plugins/app.py", line 19, 
> > > in 
> > > from .mayavi_workbench_application import MayaviWorkbenchApplication
> > >   File 
> > > "/usr/lib/python3/dist-packages/mayavi/plugins/mayavi_workbench_application.py",
> > >  line 13, in 
> > > from envisage.ui.workbench.api import WorkbenchApplication
> > > ModuleNotFoundError: No module named 'envisage'
> > 
> > That's recorded as TODO item in d/changelog now.
> 
> FYI, I just worked on converting envisage to python3:
> https://salsa.debian.org/python-team/modules/python-envisage
> 
> I asked Dmitry S. to upload it.

Hey all, I worked more on mayavi2 and I think is probably ready enough 
for upload: 

- Removed wxPython as dependency - only PyQt is currently supported in 
mayavi for Python3.  This will be pulled in automatically by traitsui, 
pyface, etc.

- Cleaned up all lintian errors/warnings

- Worked further at getting the tests working.  They are a lot closer 
but not completely functional.

- The package builds, installs, and runs fine as best as I can tell, 
although I don't know how to do much with it.

Feel free to upload if you think it is ready.

Happy New Year,
Scott



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-12-26 Thread Scott Talbert
On Tue, Dec 24, 2019 at 10:07:02AM +0100, Andreas Tille wrote:
> > python-envisage has not yet been converted to Python3 and seems to be 
> > required:
> > $ mayavi2
> > Traceback (most recent call last):
> >   File "/usr/bin/mayavi2", line 464, in 
> > from mayavi.plugins.app import Mayavi, setup_logger
> >   File "/usr/lib/python3/dist-packages/mayavi/plugins/app.py", line 19, in 
> > 
> > from .mayavi_workbench_application import MayaviWorkbenchApplication
> >   File 
> > "/usr/lib/python3/dist-packages/mayavi/plugins/mayavi_workbench_application.py",
> >  line 13, in 
> > from envisage.ui.workbench.api import WorkbenchApplication
> > ModuleNotFoundError: No module named 'envisage'
> 
> That's recorded as TODO item in d/changelog now.

FYI, I just worked on converting envisage to python3:
https://salsa.debian.org/python-team/modules/python-envisage

I asked Dmitry S. to upload it.

Scott



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-12-24 Thread Andreas Tille
On Tue, Dec 24, 2019 at 09:49:18AM +0200, Adrian Bunk wrote:
> 
> Works for me (with test failures later), but I am using plain chroot.
> 
> Problems related to running graphical tests are not something I would 
> care too much about right now, important would be that the package 
> builds and works.
> 
> After disabling the tests and dh_numpy -> dh_numpy3 in debian/rules the 
> package builds for me.
> 
> Trying to install the resulting package fails with:
> E: Package 'python3-wxgtk3.0' has no installation candidate
> E: Package 'python3-envisage' has no installation candidate
> 
> python3-wxgtk4.0 exists (not sure whether it also works with mayavi2).

I pushed all this to Git.
 
> python-envisage has not yet been converted to Python3 and seems to be 
> required:
> $ mayavi2
> Traceback (most recent call last):
>   File "/usr/bin/mayavi2", line 464, in 
> from mayavi.plugins.app import Mayavi, setup_logger
>   File "/usr/lib/python3/dist-packages/mayavi/plugins/app.py", line 19, in 
> 
> from .mayavi_workbench_application import MayaviWorkbenchApplication
>   File 
> "/usr/lib/python3/dist-packages/mayavi/plugins/mayavi_workbench_application.py",
>  line 13, in 
> from envisage.ui.workbench.api import WorkbenchApplication
> ModuleNotFoundError: No module named 'envisage'

That's recorded as TODO item in d/changelog now.

Thanks for all your hints, Andreas.

-- 
http://fam-tille.de



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-12-23 Thread Adrian Bunk
On Tue, Dec 24, 2019 at 07:50:52AM +0100, Andreas Tille wrote:
> On Mon, Dec 23, 2019 at 11:59:03PM +0200, Adrian Bunk wrote:
> > On Fri, Aug 09, 2019 at 10:39:06AM +0200, Andreas Tille wrote:
> > > self._gen_get_methods(klass, out)
> > >   File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 919, in 
> > > _gen_get_methods
> > > if len(sig) == 1 and sig[0][1] is None:
> > > TypeError: object of type 'NoneType' has no len()
> > > E: pybuild pybuild:341: build: plugin distutils failed with: exit code=1: 
> > > /usr/bin/python3 setup.py build 
> > > dh_auto_build: pybuild --build -i python{version} -p 3.7 returned exit 
> > > code 13
> > > make: *** [debian/rules:10: build] Error 255
> > > dpkg-buildpackage: error: debian/rules build gave error exit status 2
> > > I: copying local configuration
> > > E: Failed autobuilding of package
> > >...
> > 
> > This one seems fixed by removing the vtk_63.py patch.
> > Next comes some error that goes away with python3-traits (just passed NEW).
> > That's not sufficient for building, but a bit further.
> 
> Thanks a lot for your investigation.  I also made some steps further.
> It seems xvfb is needed for the tests and I added it.  The current
> failure is:
> 
> ...
>debian/rules override_dh_auto_test
> make[1]: Entering directory '/build/mayavi2-4.7.1'
> xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" dh_auto_test
> I: pybuild base:217: cd /build/mayavi2-4.7.1/.pybuild/cpython3_3.7/build; 
> python3.7 -m unittest discover -v 
> QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/1454', 
> please create it with 0700 permissions.
> QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/1454', 
> please create it with 0700 permissions.
> dbus[368675]: D-Bus library appears to be incorrectly set up: see the manual 
> page for dbus-uuidgen to correct this issue. (Failed to open 
> "/var/lib/dbus/machine-id": No such file or directo; Failed to open 
> "/etc/machine-id": No such file or directory)
>   D-Bus not built with -rdynamic so unable to print a backtrace
> Aborted
> E: pybuild pybuild:341: test: plugin distutils failed with: exit code=134: cd 
> /build/mayavi2-4.7.1/.pybuild/cpython3_3.7/build; python3.7 -m unittest 
> discover -v 
> dh_auto_test: pybuild --test -i python{version} -p 3.7 returned exit code 13
> ...
> 
> 
> Seems some dbus / systemd issue.  Any ideas?

Works for me (with test failures later), but I am using plain chroot.

Problems related to running graphical tests are not something I would 
care too much about right now, important would be that the package 
builds and works.

After disabling the tests and dh_numpy -> dh_numpy3 in debian/rules the 
package builds for me.

Trying to install the resulting package fails with:
E: Package 'python3-wxgtk3.0' has no installation candidate
E: Package 'python3-envisage' has no installation candidate

python3-wxgtk4.0 exists (not sure whether it also works with mayavi2).

python-envisage has not yet been converted to Python3 and seems to be required:
$ mayavi2
Traceback (most recent call last):
  File "/usr/bin/mayavi2", line 464, in 
from mayavi.plugins.app import Mayavi, setup_logger
  File "/usr/lib/python3/dist-packages/mayavi/plugins/app.py", line 19, in 

from .mayavi_workbench_application import MayaviWorkbenchApplication
  File 
"/usr/lib/python3/dist-packages/mayavi/plugins/mayavi_workbench_application.py",
 line 13, in 
from envisage.ui.workbench.api import WorkbenchApplication
ModuleNotFoundError: No module named 'envisage'

> Kind regards
> 
>   Andreas.

cu
Adrian



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-12-23 Thread Andreas Tille
On Mon, Dec 23, 2019 at 11:59:03PM +0200, Adrian Bunk wrote:
> On Fri, Aug 09, 2019 at 10:39:06AM +0200, Andreas Tille wrote:
> > self._gen_get_methods(klass, out)
> >   File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 919, in 
> > _gen_get_methods
> > if len(sig) == 1 and sig[0][1] is None:
> > TypeError: object of type 'NoneType' has no len()
> > E: pybuild pybuild:341: build: plugin distutils failed with: exit code=1: 
> > /usr/bin/python3 setup.py build 
> > dh_auto_build: pybuild --build -i python{version} -p 3.7 returned exit code 
> > 13
> > make: *** [debian/rules:10: build] Error 255
> > dpkg-buildpackage: error: debian/rules build gave error exit status 2
> > I: copying local configuration
> > E: Failed autobuilding of package
> >...
> 
> This one seems fixed by removing the vtk_63.py patch.
> Next comes some error that goes away with python3-traits (just passed NEW).
> That's not sufficient for building, but a bit further.

Thanks a lot for your investigation.  I also made some steps further.
It seems xvfb is needed for the tests and I added it.  The current
failure is:

...
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/mayavi2-4.7.1'
xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" dh_auto_test
I: pybuild base:217: cd /build/mayavi2-4.7.1/.pybuild/cpython3_3.7/build; 
python3.7 -m unittest discover -v 
QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/1454', 
please create it with 0700 permissions.
QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/1454', 
please create it with 0700 permissions.
dbus[368675]: D-Bus library appears to be incorrectly set up: see the manual 
page for dbus-uuidgen to correct this issue. (Failed to open 
"/var/lib/dbus/machine-id": No such file or directo; Failed to open 
"/etc/machine-id": No such file or directory)
  D-Bus not built with -rdynamic so unable to print a backtrace
Aborted
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=134: cd 
/build/mayavi2-4.7.1/.pybuild/cpython3_3.7/build; python3.7 -m unittest 
discover -v 
dh_auto_test: pybuild --test -i python{version} -p 3.7 returned exit code 13
...


Seems some dbus / systemd issue.  Any ideas?

Kind regards

  Andreas.


-- 
http://fam-tille.de



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-12-23 Thread Adrian Bunk
On Fri, Aug 09, 2019 at 10:39:06AM +0200, Andreas Tille wrote:
>...
> On Thu, Aug 08, 2019 at 04:58:03PM -0400, Yaroslav Halchenko wrote:
>...
> but unfortunately the
> configure step fails with:
> 
> ...
>dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:217: /usr/bin/python3 setup.py build 
> running build
> --
> Building TVTK classes... Traceback (most recent call last):
>   File "setup.py", line 474, in 
>   File "/usr/lib/python3/dist-packages/numpy/distutils/core.py", line 171, in 
> setup
> return old_setup(**new_attr)
>   File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 145, in 
> setup
> return distutils.core.setup(**attrs)
>   File "/usr/lib/python3.7/distutils/core.py", line 148, in setup
> dist.run_commands()
>   File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands
> self.run_command(cmd)
>   File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
> cmd_obj.run()
>   File "setup.py", line 268, in run
>   File "setup.py", line 254, in build_tvtk_classes_zip
>   File "tvtk/setup.py", line 99, in gen_tvtk_classes_zip
> gen.generate_code()
>   File "/build/mayavi2-4.7.1/tvtk/code_gen.py", line 131, in generate_code
> self._write_wrapper_class(node, tvtk_name)
>   File "/build/mayavi2-4.7.1/tvtk/code_gen.py", line 221, in 
> _write_wrapper_class
> self.wrap_gen.generate_code(node, out)
>   File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 250, in generate_code
> self._gen_methods(node, out)
>   File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 371, in _gen_methods
> self._gen_get_methods(klass, out)
>   File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 919, in 
> _gen_get_methods
> if len(sig) == 1 and sig[0][1] is None:
> TypeError: object of type 'NoneType' has no len()
> E: pybuild pybuild:341: build: plugin distutils failed with: exit code=1: 
> /usr/bin/python3 setup.py build 
> dh_auto_build: pybuild --build -i python{version} -p 3.7 returned exit code 13
> make: *** [debian/rules:10: build] Error 255
> dpkg-buildpackage: error: debian/rules build gave error exit status 2
> I: copying local configuration
> E: Failed autobuilding of package
>...

This one seems fixed by removing the vtk_63.py patch.
Next comes some error that goes away with python3-traits (just passed NEW).
That's not sufficient for building, but a bit further.

> Kind regards
> 
>   Andreas.

cu
Adrian



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-08-14 Thread Varun Hiremath
Hi Yaroslav and Andreas,

On Fri, Aug 9, 2019 at 6:57 AM Yaroslav Halchenko 
wrote:

> > Remark: Since it seems the package is not really maintained by the
> > Uploader inside the PAPT team and entering the PAPT team might take a
> > bit longer I'd consider it a sensible step to take over the package to
> > Debian Science team to enable more people an easy access to the
> > repository.  I'm not keen on "nursing" merge requests of grown up
> > Python developers just because these are not part of PAPT team.
>
> well -- I guess that should be cleared up with the PAPT team / original
> uploaders (at least with Varun ?  any objections?)
>

I currently don't have time to work on mayav2 package, but feel free to
move it to Debain Science team repository if it helps with maintaining this
package, I don't have any objections.

Thanks,
Varun


Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-08-09 Thread Yaroslav Halchenko


On Fri, 09 Aug 2019, Andreas Tille wrote:
> > 4.5.0 still causes segfaults for me (while trying to build/test python-mne
> > package).  I could not get to upstream's download page for mayavi2 (server 
> > bogs
> > out), but conda seems to have 4.6.2 https://anaconda.org/anaconda/mayavi  
> > so I guess
> > it is out there.

> Its definitely out and the watch file reports a new version which even
> supports Python3.  I've updated the packaging Git[1] to latest packaging

THANKS for looking into it!

> standards (attention, since I know NeuroDebian prefers lower versions
> of debhelper - feel free to revert my switch to debhelper 12!) and

well, we could try to backport build (after lowering) but I am not sure
if we would love to take that monster mayavi2 under our backports wing
;)

> tried to convert the build system to Python3 but unfortunately the
> configure step fails with:

> ...

> Remark: Since it seems the package is not really maintained by the
> Uploader inside the PAPT team and entering the PAPT team might take a
> bit longer I'd consider it a sensible step to take over the package to
> Debian Science team to enable more people an easy access to the
> repository.  I'm not keen on "nursing" merge requests of grown up
> Python developers just because these are not part of PAPT team.

well -- I guess that should be cleared up with the PAPT team / original
uploaders (at least with Varun ?  any objections?)

-- 
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



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-08-09 Thread Andreas Tille
Hi Yaroslav,

On Thu, Aug 08, 2019 at 04:58:03PM -0400, Yaroslav Halchenko wrote:
> Package: mayavi2
> Version: 4.5.0-1
> Severity: normal
> 
> 4.5.0 still causes segfaults for me (while trying to build/test python-mne
> package).  I could not get to upstream's download page for mayavi2 (server 
> bogs
> out), but conda seems to have 4.6.2 https://anaconda.org/anaconda/mayavi  so 
> I guess
> it is out there.

Its definitely out and the watch file reports a new version which even
supports Python3.  I've updated the packaging Git[1] to latest packaging
standards (attention, since I know NeuroDebian prefers lower versions
of debhelper - feel free to revert my switch to debhelper 12!) and
tried to convert the build system to Python3 but unfortunately the
configure step fails with:

...
   dh_auto_build -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python3 setup.py build 
running build
--
Building TVTK classes... Traceback (most recent call last):
  File "setup.py", line 474, in 
  File "/usr/lib/python3/dist-packages/numpy/distutils/core.py", line 171, in 
setup
return old_setup(**new_attr)
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 145, in 
setup
return distutils.core.setup(**attrs)
  File "/usr/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
  File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
  File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
  File "setup.py", line 268, in run
  File "setup.py", line 254, in build_tvtk_classes_zip
  File "tvtk/setup.py", line 99, in gen_tvtk_classes_zip
gen.generate_code()
  File "/build/mayavi2-4.7.1/tvtk/code_gen.py", line 131, in generate_code
self._write_wrapper_class(node, tvtk_name)
  File "/build/mayavi2-4.7.1/tvtk/code_gen.py", line 221, in 
_write_wrapper_class
self.wrap_gen.generate_code(node, out)
  File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 250, in generate_code
self._gen_methods(node, out)
  File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 371, in _gen_methods
self._gen_get_methods(klass, out)
  File "/build/mayavi2-4.7.1/tvtk/wrapper_gen.py", line 919, in _gen_get_methods
if len(sig) == 1 and sig[0][1] is None:
TypeError: object of type 'NoneType' has no len()
E: pybuild pybuild:341: build: plugin distutils failed with: exit code=1: 
/usr/bin/python3 setup.py build 
dh_auto_build: pybuild --build -i python{version} -p 3.7 returned exit code 13
make: *** [debian/rules:10: build] Error 255
dpkg-buildpackage: error: debian/rules build gave error exit status 2
I: copying local configuration
E: Failed autobuilding of package


I'd be happy if someone would take over from here since I'll be busy
with real life for the next 10 days.

Remark: Since it seems the package is not really maintained by the
Uploader inside the PAPT team and entering the PAPT team might take a
bit longer I'd consider it a sensible step to take over the package to
Debian Science team to enable more people an easy access to the
repository.  I'm not keen on "nursing" merge requests of grown up
Python developers just because these are not part of PAPT team.

Kind regards

  Andreas.


[1] https://salsa.debian.org/python-team/applications/mayavi2

-- 
http://fam-tille.de



Bug#934264: Please update (4.6.2?) and provide/switch to python3

2019-08-08 Thread Yaroslav Halchenko
Package: mayavi2
Version: 4.5.0-1
Severity: normal

4.5.0 still causes segfaults for me (while trying to build/test python-mne
package).  I could not get to upstream's download page for mayavi2 (server bogs
out), but conda seems to have 4.6.2 https://anaconda.org/anaconda/mayavi  so I 
guess
it is out there.

Also a new version of python-mne (0.18.x) already dropped python2 support, so
we need mayavi being available in python3. ATM mayavi2 seems to provide only
python2. Given that python2 is going away you might as well just switch to
provide python3 bindings only (but ideally both if only for a bit longer to
smoothen transition)

Cheers and thanks in advance

-- System Information:
Debian Release: buster/sid
  APT prefers testing
  APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 
'unstable-debug')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.19.0-5-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8), 
LANGUAGE=en_US.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages mayavi2 depends on:
ii  libc6 2.28-8
ii  libjs-jquery  3.3.1~dfsg-1
ii  python2.7.16-1
ii  python-apptools   4.4.0-3
ii  python-configobj  5.0.6-3
ii  python-envisage   4.4.0-1
ii  python-numpy [python-numpy-abi9]  1:1.16.2-1
ii  python-pkg-resources  40.8.0-1
ii  python-traits 4.6.0-1+b2
ii  python-traitsui   4.5.1-1
ii  python-vtk6   6.3.0+dfsg2-2+b5
ii  python-wxgtk3.0   3.0.2.0+dfsg-8

mayavi2 recommends no packages.

Versions of packages mayavi2 suggests:
ii  ipython   5.8.0-1
ii  python-scipy  1.1.0-7

-- debconf-show failed