Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
Hi, I've uploaded since the Python3 issue is solved. For upstream please note: There are some remaining Python2 files in the test suite. Please consider the patch https://salsa.debian.org/med-team/kissplice/-/blob/master/debian/patches/tests-2to3.patch There are build time errors described below which might require your attention. Kind regards Andreas. On Fri, May 29, 2020 at 04:19:35AM +0530, Nilesh Patra wrote: > Hi, > > On Fri, 29 May 2020, 01:08 Andreas Tille, wrote: > > > Hi Moritz, > > > > On Thu, May 28, 2020 at 08:48:41PM +0200, Moritz Mühlenhoff wrote: > > > > > > JFTR, this is now fixed upstream in 2.5.0 and later: > > > http://kissplice.prabi.fr/download/: > > > > > > -- > > > Kissplice Version 2.5.0 (2020-04-06) > > > > > > New features: > > >Now compatible with python3 > > > -- > > > > Thanks for the hint. Unfortunately there are remaining issues > > in build time test and autopkgtest. even of version 2.5.1 .:-( > > > > I've Fixed the autopkgtest > > For the failing build tests: this is what I observe - this try matching > strings containing a few values with kissplice result. > > For instance, this is one of the failures: > > Expected: > 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 69 found > > Actual: > 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 22 found > > There's definitely a difference between the outputs of previous kissplice > version and current kissplice version, I tried this manually as well. > > Just _maybe_, the upstream data has been changed, and the correct data > hasn't been injected; or the implementation has changed in version, > 2.5.1and this should output 22, but the tests haven't been changed > accordingly ; or maybe this is a bug with kissplice itself. > > In either case, I'm not really about this. Maybe we should ask upstream > about it. > > Thanks and regards > Nilesh -- http://fam-tille.de
Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
Hi, On Fri, 29 May 2020, 01:08 Andreas Tille, wrote: > Hi Moritz, > > On Thu, May 28, 2020 at 08:48:41PM +0200, Moritz Mühlenhoff wrote: > > > > JFTR, this is now fixed upstream in 2.5.0 and later: > > http://kissplice.prabi.fr/download/: > > > > -- > > Kissplice Version 2.5.0 (2020-04-06) > > > > New features: > >Now compatible with python3 > > -- > > Thanks for the hint. Unfortunately there are remaining issues > in build time test and autopkgtest. even of version 2.5.1 .:-( > I've Fixed the autopkgtest For the failing build tests: this is what I observe - this try matching strings containing a few values with kissplice result. For instance, this is one of the failures: Expected: 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 69 found Actual: 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 22 found There's definitely a difference between the outputs of previous kissplice version and current kissplice version, I tried this manually as well. Just _maybe_, the upstream data has been changed, and the correct data hasn't been injected; or the implementation has changed in version, 2.5.1and this should output 22, but the tests haven't been changed accordingly ; or maybe this is a bug with kissplice itself. In either case, I'm not really about this. Maybe we should ask upstream about it. Thanks and regards Nilesh
Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
Hi Moritz, On Thu, May 28, 2020 at 08:48:41PM +0200, Moritz Mühlenhoff wrote: > > JFTR, this is now fixed upstream in 2.5.0 and later: > http://kissplice.prabi.fr/download/: > > -- > Kissplice Version 2.5.0 (2020-04-06) > > New features: >Now compatible with python3 > -- Thanks for the hint. Unfortunately there are remaining issues in build time test and autopkgtest. even of version 2.5.1 .:-( Kind regards Andreas. -- http://fam-tille.de
Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
On Tue, Dec 17, 2019 at 08:41:02AM +0100, Andreas Tille wrote: > On Wed, Oct 09, 2019 at 08:06:27AM +0200, Andreas Tille wrote: > > > > > When would be the deadline for updating our debian KisSplice package > > > before removal ? > > > > There is no actual date. Debian 11 will be released in 2021 so the > > current bug is not yet release critical. You will be on the safe side > > if you get out KisSplice at the end of this year not only from a > > Debian point of view but also in general for other users who do not > > might want to run unsupported software like Python2. > > The Debian Med team is currently an Advent bug squashing party. You could > help > us closing as much as possible bugs if you would be able to release before > Christmas. ;-) JFTR, this is now fixed upstream in 2.5.0 and later: http://kissplice.prabi.fr/download/: -- Kissplice Version 2.5.0 (2020-04-06) New features: Now compatible with python3 -- Cheers, Moritz
Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
On Wed, Oct 09, 2019 at 08:06:27AM +0200, Andreas Tille wrote: > > > When would be the deadline for updating our debian KisSplice package before > > removal ? > > There is no actual date. Debian 11 will be released in 2021 so the > current bug is not yet release critical. You will be on the safe side > if you get out KisSplice at the end of this year not only from a > Debian point of view but also in general for other users who do not > might want to run unsupported software like Python2. The Debian Med team is currently an Advent bug squashing party. You could help us closing as much as possible bugs if you would be able to release before Christmas. ;-) Kind regards Andreas. -- http://fam-tille.de
Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
Dear Vincent, thanks a lot for your quick and helpful reply. On Wed, Oct 09, 2019 at 03:59:08AM +, LACROIX VINCENT wrote: > Dear Andreas, > Yes, we have a python 3 version of KisSplice working now. This should > correspond to version 2.5.0 of KisSplice, which we plan to release in the > coming months. This sounds good! > When would be the deadline for updating our debian KisSplice package before > removal ? There is no actual date. Debian 11 will be released in 2021 so the current bug is not yet release critical. You will be on the safe side if you get out KisSplice at the end of this year not only from a Debian point of view but also in general for other users who do not might want to run unsupported software like Python2. Kind regards Andreas. -- http://fam-tille.de
Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
Dear Andreas, Yes, we have a python 3 version of KisSplice working now. This should correspond to version 2.5.0 of KisSplice, which we plan to release in the coming months. When would be the deadline for updating our debian KisSplice package before removal ? Best, Vincent De : Andreas Tille Envoyé : mardi 8 octobre 2019 17:23 À : 936...@bugs.debian.org; David Parsons; LACROIX VINCENT Objet : Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye) Control: forwarded -1 David Parsons , vincent.lacr...@univ-lyon1.fr Control: tags -1 upstream Hi, as you might probably know Python2 is End Of Live[1] and Debian is actively working on removing Python2 code from the distribution. So Debian 11 will come without Python2. This means we will either be able to port all software packages to Python3 or the package will be removed. Do you think it is feasible for you to port KisSplice to Python3? May be by using 2to3 which does quite some work automatically? If you need any help please do not hesitate to ask. Kind regards Andreas. [1] https://pythonclock.org/ -- http://fam-tille.de
Bug#936798: Please port KisSplice to Python3 (Was: Bug#936798: kissplice: Python2 removal in sid/bullseye)
Control: forwarded -1 David Parsons , vincent.lacr...@univ-lyon1.fr Control: tags -1 upstream Hi, as you might probably know Python2 is End Of Live[1] and Debian is actively working on removing Python2 code from the distribution. So Debian 11 will come without Python2. This means we will either be able to port all software packages to Python3 or the package will be removed. Do you think it is feasible for you to port KisSplice to Python3? May be by using 2to3 which does quite some work automatically? If you need any help please do not hesitate to ask. Kind regards Andreas. [1] https://pythonclock.org/ -- http://fam-tille.de
