Re: Any volunteer to remove csh dependency of mummer [mummer is marked for autoremoval from testing]
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.
>
> 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.
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.
Best,
Steffen
[1] https://lists.debian.org/debian-med/2020/04/msg00171.html
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