[Debian-med-packaging] Fwd: Updating Hmmer2 request

[Fabian Klötzl]

Forgot to mention, that I know your pain. Almost a year ago I issued a
pull request to the upcoming Mummer4, making it up to 20% faster and use
50% less memory [1]. It has gone unmerged to the day, which is quite
frustrating. However, I have good faith that the authors will accept the
PR when they are free of their other duties, so that all users will get
the benefit of an improved version (not just Debian + downstream).

Best,
Fabian

1: https://github.com/mummer4/mummer/pull/30


On 14.04.2018 14:04, Fabian Klötzl wrote:
> Hi Joshua,
> 
> Thank you for wanting to improve Hmmer for Debian users. However, I see
> a few issues with your request. Note that this is my personal opinion
> and I do not speak for the Debian Med team.
> 
> 
> On 13.04.2018 19:47, Joshua Marshall wrote:
>> Hmmer2 upstream is listed at 2.4i
> 
> The current version of hmmer2 in Debian is 2.3.2+dfsg-5, see [1].
> Judging from the official homepage of Hmmer [2] that is indeed the
> latest release.
> 
>> I have a few cleanups and fixes […] fix a few uninitialized variables
> 
> Most of these look minor, if not even superfluous [4, 5].
> 
>> which enable pthreads by default, remove support for PVM
> 
> Could you please go into detail, why you think this change is
> necessary/an improvement?
> 
>> adding a default suffix of '2'
> 
> Debian already does that, I think [3]. And if not, renaming binaries
> between two releases of a package will break existing workflows and
> confuse a lot of users.
> 
>> So with that, I'd like to make the request to update to 2.5j.  Humor me
>> if something with this is incorrect.  I think all guidelines are being
>> met for posting.
>>
> 
> There are basically two ways to incorporate your changes into Debian. 1)
> We could declare upstream as dead (even though they are not) and use
> your repository as the "new official version". 2) We pile your changes
> on top of the last public release 2.3.2. For this we require small patch
> files each implementing one of the fixes you mentioned above. Having
> just one big commit (your words) is problematic.
> 
> My favourite solution would be 2). I am looking forward to receiving
> your patches.
> 
> Best,
> Fabian
> 
> 
> 1: https://tracker.debian.org/pkg/hmmer2
> 2: http://hmmer.org/download.html
> 3: https://salsa.debian.org/med-team/hmmer2/blob/master/debian/rules#L33
> 4:
> https://github.com/MichiganTech/hmmer/commit/4a9327d49cd25129ebef313f19db6d1034bd3d21#diff-92b08d78ee5212675b1339a03afc95ddR1451
> 5:
> https://github.com/MichiganTech/hmmer/commit/4a9327d49cd25129ebef313f19db6d1034bd3d21#diff-ee177e329d3820670951a24d5ad0b521R985
> 
> 
>