Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Hi Stefan, On Thu, Dec 05, 2019 at 10:18:01AM -0800, Stefan van der Walt wrote: > On Wed, 04 Dec 2019 09:53:03 +0100, Andreas Tille wrote: > > Hmmm, I think the Cython files are generated in the build I did. > > Sorry, I missed that! I saw at the bottom of the log: > > E AttributeError: type object 'skimage.feature.orb_cy.array' has no > attribute '__reduce_cython__' > > Which is an error that has been fixed in Cython 0.28, supposedly: > > https://github.com/cython/cython/issues/1894 > > But it looks like your compilation is using 0.29, so not sure why that > is happening: > > Get: 26 http://deb.debian.org/debian sid/main amd64 cython3 amd64 > 0.29.14-0.1+b1 [2117 kB] Yes, that's the case. > One possibility is that NumPy was compiled with an older version of > Cython: > > https://github.com/cython/cython/issues/1953#issuecomment-398128940 > > Do you know how I can check the source files for the NumPy 1.17 build > that is used here? According to https://buildd.debian.org/status/fetch.php?pkg=numpy=amd64=1%3A1.17.4-3=1574041583=0 it was Get:48 https://cdn-aws.deb.debian.org/debian unstable/main amd64 cython3 amd64 0.29.14-0.1 [1474 kB] > The other errors seem to be because no suitable image plugin is > registered. This can typically be fixed by installing matplotlib or > imageio beforehand, I added Build-Depends: python3-imageio as well - but this did not change anything. > but it looks like you *do* have matplotlib > installed. Yep. > Maybe the Cython module imports break everything so badly > that the plugins cannot even load. H, seems this is the only remaining explanation. I admit I have no idea. > > Its correct that the _Maintainer_ is set to Debian Science team. But > > the actual members of the team (in Debian terminology the _Uploaders_) > > are you and Yaroslav. > > Thanks for updating that; I never had the ability to upload to anything > other than mentors. In the Debian Science team it is perfectly sufficient to commit changes to the Git repository at salsa.debian.org and asking for sponsoring on the Debian Science mailing list. I'd love to take over sponsorship in case you might want to commit in this way. Kind regards Andreas. -- http://fam-tille.de -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Stefan van der Walt wrote: One possibility is that NumPy was compiled with an older version of Cython:[...] Do you know how I can check the source files for the NumPy 1.17 build that is used here? Source: https://sources.debian.org/src/numpy/1:1.17.4-3/ Build log: https://buildd.debian.org/status/package.php?p=numpy numpy was built with cython3 0.29.14-0.1. (Not +b1, but I _think_ "Add Python3.8 as supported version" means the ability to run cython3 itself in python3.8, not the ability to compile modules for python3.8.) -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Hi Andreas, On Wed, 04 Dec 2019 09:53:03 +0100, Andreas Tille wrote: > Hmmm, I think the Cython files are generated in the build I did. Sorry, I missed that! I saw at the bottom of the log: E AttributeError: type object 'skimage.feature.orb_cy.array' has no attribute '__reduce_cython__' Which is an error that has been fixed in Cython 0.28, supposedly: https://github.com/cython/cython/issues/1894 But it looks like your compilation is using 0.29, so not sure why that is happening: Get: 26 http://deb.debian.org/debian sid/main amd64 cython3 amd64 0.29.14-0.1+b1 [2117 kB] One possibility is that NumPy was compiled with an older version of Cython: https://github.com/cython/cython/issues/1953#issuecomment-398128940 Do you know how I can check the source files for the NumPy 1.17 build that is used here? The other errors seem to be because no suitable image plugin is registered. This can typically be fixed by installing matplotlib or imageio beforehand, but it looks like you *do* have matplotlib installed. Maybe the Cython module imports break everything so badly that the plugins cannot even load. > Its correct that the _Maintainer_ is set to Debian Science team. But > the actual members of the team (in Debian terminology the _Uploaders_) > are you and Yaroslav. Thanks for updating that; I never had the ability to upload to anything other than mentors. Best regards, Stéfan -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Hi Stefan, thanks a lot for your feedback. On Tue, Dec 03, 2019 at 12:38:24PM -0800, Stefan van der Walt wrote: > The problem here stems from an old version of Cython. My recommended > approach would be to build from the git tag instead of the source tarball > (i.e., the version without pre-generated Cython files). Hmmm, I think the Cython files are generated in the build I did. The build log says: ... dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config. Compiling /build/skimage-0.16.2/skimage/_shared/geometry.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/_shared/transform.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/_shared/interpolation.pyx because it changed. Partial import of skimage during the build process. [1/3] Cythonizing /build/skimage-0.16.2/skimage/_shared/geometry.pyx [3/3] Cythonizing /build/skimage-0.16.2/skimage/_shared/transform.pyx [2/3] Cythonizing /build/skimage-0.16.2/skimage/_shared/interpolation.pyx Compiling /build/skimage-0.16.2/skimage/draw/_draw.pyx because it changed. [1/1] Cythonizing /build/skimage-0.16.2/skimage/draw/_draw.pyx Compiling /build/skimage-0.16.2/skimage/feature/corner_cy.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/feature/censure_cy.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/feature/orb_cy.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/feature/brief_cy.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/feature/_texture.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/feature/_hessian_det_appx.pyx because it changed. Compiling /build/skimage-0.16.2/skimage/feature/_hoghistogram.pyx because it changed. [4/7] Cythonizing /build/skimage-0.16.2/skimage/feature/brief_cy.pyx [5/7] Cythonizing /build/skimage-0.16.2/skimage/feature/censure_cy.pyx [1/7] Cythonizing /build/skimage-0.16.2/skimage/feature/_hessian_det_appx.pyx [6/7] Cythonizing /build/skimage-0.16.2/skimage/feature/corner_cy.pyx [3/7] Cythonizing /build/skimage-0.16.2/skimage/feature/_texture.pyx [2/7] Cythonizing /build/skimage-0.16.2/skimage/feature/_hoghistogram.pyx [7/7] Cythonizing /build/skimage-0.16.2/skimage/feature/orb_cy.pyx ... > I don't think the Cython-related patches that were applied since would then > be necessary. The packaging does not contain any Cython-related patches as far as I can see. For the Debian packaging we usually prefer tagged releases. While I could be convinced to derive from this principle it is not really clear to me in how far your explanation matches the issue. May be its just me since I'm not so comfortable with Cython so I'd rather ask back to make sure I understand you correctly. > I will no longer be doing packaging work for scikit-image, so feel free to > remove me from the maintainer list (I thought it had already been transferred > to the science team a while ago). Its correct that the _Maintainer_ is set to Debian Science team. But the actual members of the team (in Debian terminology the _Uploaders_) are you and Yaroslav. I just pushed the following commit: $ git diff HEAD^ diff --git a/debian/changelog b/debian/changelog index 4baf3e7e..e294c4bf 100644 --- a/debian/changelog +++ b/debian/changelog @@ -4,6 +4,8 @@ skimage (0.16.2-1) UNRELEASED; urgency=medium * New upstream version * Standards-Version: 4.4.1 * More default d/rules + * Drop Stefan van der Walt from Uploaders since he confirmed not to +do packaging work any more (thanks for your previous work Stefan) -- Andreas Tille Mon, 02 Dec 2019 10:07:39 +0100 diff --git a/debian/control b/debian/control index deee0d75..bd692cc2 100644 --- a/debian/control +++ b/debian/control @@ -1,7 +1,6 @@ Source: skimage Maintainer: Debian Science Maintainers -Uploaders: Stefan van der Walt , - Yaroslav Halchenko +Uploaders: Yaroslav Halchenko Section: python Priority: optional Build-Depends: cython3 (>= 0.23), Kind regards, Andreas. -- http://fam-tille.de -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Hi Andreas and Ole, The problem here stems from an old version of Cython. My recommended approach would be to build from the git tag instead of the source tarball (i.e., the version without pre-generated Cython files). I don't think the Cython-related patches that were applied since would then be necessary. I will no longer be doing packaging work for scikit-image, so feel free to remove me from the maintainer list (I thought it had already been transferred to the science team a while ago). Best regards, Stéfan -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Hi Ole, I had a quick look what you mean and tried to make the build more standard[1]. The build issues are remaining and need some work. Kind regards, Andreas. [1] https://salsa.debian.org/science-team/skimage/commit/d787835f7293dc105b9b8cf37d59c1f9fbf46110 On Mon, Dec 02, 2019 at 01:01:07PM +0100, Ole Streicher wrote: > Hi Andreas, > > I think that is the moment where the skimage build should be simplified > to the "official" build process: Python convention is that symbols > starting with an underscore are internal only (and ofcourse subject to > quick and unannounced changes). debian/bin/process_pyx.py however > depends on them (_build.py and f.e. the _changed() function). IMO this > should be taken out completely in favor of a standard, simplified build. > No idea however how difficult this is. > > Cheers > > Ole > > > I tried my luck with #945389 since two Debian Med packages are depending > > from skimage. So at first I tried to upgrade to the latest upstream > > version to possibly forward some reasonable bug report. Unfortunately > > the build starts very early: > > > > ... > > debian/rules build > > py3versions: no X-Python3-Version in control file, using supported versions > > /usr/bin/make -j 4 -f debian/rules _build > > make[1]: Entering directory '/build/skimage-0.16.2' > > py3versions: no X-Python3-Version in control file, using supported versions > > python3.7 debian/bin/process_pyx.py 4 > > Traceback (most recent call last): > > File "debian/bin/process_pyx.py", line 13, in > > from _build import _changed, process_tempita_pyx > > ImportError: cannot import name '_changed' from '_build' > > (/build/skimage-0.16.2/debian/bin/_build.py) > > make[1]: *** [debian/rules:71: debian/build-stamp-pyx] Error 1 > > ... > > -- http://fam-tille.de -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Hi Ole, On Mon, Dec 02, 2019 at 01:01:07PM +0100, Ole Streicher wrote: > Hi Andreas, > > I think that is the moment where the skimage build should be simplified > to the "official" build process: Python convention is that symbols > starting with an underscore are internal only (and ofcourse subject to > quick and unannounced changes). debian/bin/process_pyx.py however > depends on them (_build.py and f.e. the _changed() function). IMO this > should be taken out completely in favor of a standard, simplified build. > No idea however how difficult this is. Me neither. Official Uploaders in CC to clarify the idea behind it. Stefan / Yaroslav could you comment on this? Could you please also declare your intention to work on this package in the future? If you realise that you do not manage to work on it please say so to make sure we try to find active Uploaders. Kind regards Andreas. > > > I tried my luck with #945389 since two Debian Med packages are depending > > from skimage. So at first I tried to upgrade to the latest upstream > > version to possibly forward some reasonable bug report. Unfortunately > > the build starts very early: > > > > ... > > debian/rules build > > py3versions: no X-Python3-Version in control file, using supported versions > > /usr/bin/make -j 4 -f debian/rules _build > > make[1]: Entering directory '/build/skimage-0.16.2' > > py3versions: no X-Python3-Version in control file, using supported versions > > python3.7 debian/bin/process_pyx.py 4 > > Traceback (most recent call last): > > File "debian/bin/process_pyx.py", line 13, in > > from _build import _changed, process_tempita_pyx > > ImportError: cannot import name '_changed' from '_build' > > (/build/skimage-0.16.2/debian/bin/_build.py) > > make[1]: *** [debian/rules:71: debian/build-stamp-pyx] Error 1 > > ... > > -- http://fam-tille.de -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#945389: Tried to upgrade skimage to see whether #945389 is fixed but failed
Control: tags -1 help Hi, I tried my luck with #945389 since two Debian Med packages are depending from skimage. So at first I tried to upgrade to the latest upstream version to possibly forward some reasonable bug report. Unfortunately the build starts very early: ... debian/rules build py3versions: no X-Python3-Version in control file, using supported versions /usr/bin/make -j 4 -f debian/rules _build make[1]: Entering directory '/build/skimage-0.16.2' py3versions: no X-Python3-Version in control file, using supported versions python3.7 debian/bin/process_pyx.py 4 Traceback (most recent call last): File "debian/bin/process_pyx.py", line 13, in from _build import _changed, process_tempita_pyx ImportError: cannot import name '_changed' from '_build' (/build/skimage-0.16.2/debian/bin/_build.py) make[1]: *** [debian/rules:71: debian/build-stamp-pyx] Error 1 ... Any hint what to do? Kind regards Andreas. -- http://fam-tille.de -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
