Re: New version of muscle with changed options compared to previous versions [muscle_5.1-1_source.changes ACCEPTED into unstable]
Hi,
On 2022-01-17 20:43, Andreas Tille wrote:
> Am Mon, Jan 17, 2022 at 05:45:49PM +0200 schrieb Andrius Merkys:
>> I consider myself a muscle user, albeit mostly for teaching. Integration
>> with biopython is quite important aspect to me as well.
>>
>> Although stability is a desired quality, algorithm improvement is
>> probably more important. However, I did not compare the new muscle with
>> its predecessors thus I cannot say which change outweighs which.
>
> See the change in debian/tests/run-unit-test in this commit[1] which
> requires renaming very basic command line options - I assume *all*
> command line options have changed somehow.
Thanks for a pointer. The change in the CLI does not seem to be that
involving to me. What is also important, IMO, is how the new muscle
reacts to old command line options. If it dies with a meaningful
message, this will let its users know about the changed interface. The
change would be way less acceptable otherwise.
The addition to debian/NEWS reads very nice. It convinces me the added
benefits of new muscle outweighs the price of adapting to its CLI changes.
>> I do not think that maintaining two parallel muscle packages is really
>> worth the work. Having muscle 5.1 and biopython supporting only muscle 3
>> will cause confusion. As for failing tests of other packages, it is
>> probably best to gently prod their upstreams to implement support for
>> new muscle.
>
> I confirm this is my plan but I wanted to hear opinions like yours.
Great!
> [1] https://salsa.debian.org/med-team/muscle/-/commit/73cb0469278f0d074a866518d7edcd3850f23221
Best,
Andrius
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