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