Hi Andreas, Hi Steffen, Steffen Möller, on 2020-07-24 12:32:58 +0200: > Hi Andreas, hi Étienne, > > On 24.07.20 09:43, Andreas Tille wrote: > > Hi Étienne, > > > > On Thu, Jul 23, 2020 at 11:08:01PM +0200, Étienne Mollier wrote: > >> I ran a git push --all, this seems to be good now. > > I merged this into master, removed csh also from docs (should have been > > done even formerly due to the .csh extensions which are removed from the > > scripts and uploaded. Thanks Andreas for having taken the time to review, do changes deemed necessary and upload. :) > > Dealing with mummer brings back the question of an upgrade to 4.0~beta2. > > This was discussed here before[1]. Steffen suggests a separate package. > > What about others? > > > > I've checked mummer 4.0~beta2 and it seems upstream switched to sh > > there - so our move was in some way in agreement with upstream. > I think we see the v3 mummer used quite a bit today while newer workflows > likely will depend on v4. Not expecting the api to remain the same, nor the > biological implications, we should treat the tools like we treat our > libraries, > seeing the analogy when tools are embedded in workflows to sharing code that > is dynamically linked. > > The workflows embedding Mummer we do not expect to synchronize > their transition/migration - if they synchronize at all. I expect > history to repeat with what > we experienced with hmmer when it migrated from 2 to 3. I believe I'm not in the best position to comment on an update from mummer3 -> 4 but, I reminded about #956751 (something about a Gnuplot option that became obsolete in Gnuplot v5). If the package mummer is updated to 4.0~beta2, then this is solved upstream. If a mummer3 is kept alongside a mummer4, maybe this will need a patch earlier. Just something I had in mind, nothing release critical... > Disclaimer: If I got this right then v4 no longer has the contributor of > v3 from > my neighbouring university, so I am a bit sentimental about it, too. Well we all have some history behind us. :) Kind Regards, -- Étienne Mollier <etienne.mollier@mailoo.org> Old rsa/3072: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d New rsa/4096: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity.
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