Status of paleomix (Was: Please list your contributions to COVID-19 sprint as intput for my DebConf20 talk)

[Andreas Tille]

Hi Steffen and Antoni,

On Wed, Jul 29, 2020 at 11:10:40PM +0200, Steffen Möller wrote:
> Hi Antoni,
> 
> had a look at [0] and liked it. @Andreas [who has worked on the package
> prior to your commits], ping me if you want me to proceed.

I pinged again
https://github.com/MikkelSchubert/paleomix/issues/15
I admit I feel a bit blocked by the fact that upstream is promising
a new Python3 only version and is not happy about our Python2 to
Python3 conversion code of the old version.  Feel free to decide -
I'm not using this program and can not decide what might be the best
in the interest of our users.

> What I am
> tempted to comment on:
> 
>  - the python3-setuptools I would have left at the top since this is
> something "meta" that does not describe what the package is
> implementing, but ... hey ... I may be wrong here, alphabetical as you
> have it is just as fine

I admit I put usually python3-setuptools on top but I would not question
any other good reason to move it somewhere else.  IMHO it would be the
best idea if dh-python would simply depend from python3-setuptools and
we could leave it out generally since its needed in nearly all Python
packages anyway.

>  - I was impressed by the sed to get the paths right for testing. The
> difficulty is with the increased complexity of the packaging. In
> pre-Covid-19 times I typically sent pull requests upstream whenever
> possible to avoid shifts in complexity to impede with the maintenance of
> the Debian packages. With you all around, though, and to get it all into
> the distribution as quickly and well-tested as possible, I am just as happy.

I confirm that I'm happy as well! :-)
 
> So - thank you tons! Approved from my side.

In short: I'm fine if someone decides its ready to upload and we
can migrate to official Paleomix with Python3 later.

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: Please list your contributions to COVID-19 sprint as intput for my DebConf20 talk

[Pierre Gruet]

Hi Andreas,

Congratulations for getting this opportunity to talk about our work!

Personally, I have worked on
* Sumaclust (and its close relatives Sumatra and Sumalibs);
* Dependencies of Snpeff, which is part of the Covid-19 task.

Bye,
Pierre

Le 28/07/2020 à 08:43, Andreas Tille a écrit :
> Hi,
> 
> my talk proposal for DebConf20[1] was accepted recently.  I would like
> to thank all contributers (who "stayed home and contributed" ;-) ) in
> this talk.  To make sure I will not miss anybody please be so kind and
> send me an e-mail with a list of your contributions - I'm afraid I would
> forget something if I try to assemble it all.
> 
> Feel free to add your contribution here to this thread on the mailing
> list - I see no reason to hide it in some private mail (which is fine
> anyway if you prefer this).
> 
> Thanks again to all those who contributed and who keep on contributing
> 
>Andreas.
> 
> [1] 
> https://debconf20.debconf.org/talks/21-stay-home-and-contribute-to-debian-med/
> 

Re: Status of paleomix (Was: Please list your contributions to COVID-19 sprint as intput for my DebConf20 talk)

[Steffen Möller]

Hi Andreas and Antoni,

On 30.07.20 10:07, Andreas Tille wrote:
> Hi Steffen and Antoni,
>
> On Wed, Jul 29, 2020 at 11:10:40PM +0200, Steffen Möller wrote:
>> Hi Antoni,
>>
>> had a look at [0] and liked it. @Andreas [who has worked on the package
>> prior to your commits], ping me if you want me to proceed.
> I pinged again
> https://github.com/MikkelSchubert/paleomix/issues/15
> I admit I feel a bit blocked by the fact that upstream is promising
> a new Python3 only version and is not happy about our Python2 to
> Python3 conversion code of the old version.  Feel free to decide -
> I'm not using this program and can not decide what might be the best
> in the interest of our users.

That was a good pointer. So, let's leave it for a few days and see what
upstream says.

If there is no further action then we should upload what we have and
update as soon as there is something to update. I'll send some emoji to
support your ping.

Best,

Steffen

[RFS] minc-tools

[Nilesh Patra]

Hi,
I've fixed gcc-10 FTBFS for minc-tools as reported here in RC bug #957542.
It now builds with passing tests.
I've pushed my changes to the team-repo[1]
Please:

gbp clone --pristine-tar https://salsa.debian.org/med-team/minc-tools

OR

Grant DM access: PGP key fingerprint:
3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1

Thanks and regards
Nilesh

Re: [RFS] minc-tools

[Steffen Möller]

allowed

On 30.07.20 16:37, Nilesh Patra wrote:
> Hi,
> I've fixed gcc-10 FTBFS for minc-tools as reported here in RC bug
> |#957542.|
> It now builds with passing tests.
> I've pushed my changes to the team-repo[1]
> Please:
>
> gbp clone --pristine-tar https://salsa.debian.org/med-team/minc-tools
> 
>
> OR
>
> Grant DM access: PGP key fingerprint:
> 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
>
> Thanks and regards
> Nilesh

Re: Status of paleomix (Was: Please list your contributions to COVID-19 sprint as intput for my DebConf20 talk)

[Antoni Villalonga]

On Thu, Jul 30, 2020 at 10:07:37AM +0200, Andreas Tille wrote:
> On Wed, Jul 29, 2020 at 11:10:40PM +0200, Steffen Möller wrote:
> >  - the python3-setuptools I would have left at the top since this is
> > something "meta" that does not describe what the package is
> > implementing, but ... hey ... I may be wrong here, alphabetical as you
> > have it is just as fine

I love the spanish expression "Donde fueres, haz lo que vieres". It's similar
to "When in Rome, do as the Romans".

I have no reason to keep an alphabetic order, so I'll move setuptools deps to
the top as you usually do in all med-team packages (and probably other
packagers do as well).

Do you think I should try to get last upstream code before debian release?
There are some more upstream commits since june 16th.

Regards,

-- 
Antoni Villalonga
https://friki.cat/

Videoconference Friday 2020-07-31 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020))

[Andreas Tille]

Hi,

I hope these weekly announcements are not boring for readers of
debian-devel list.  I can confirm that we made quite some progress in
Debian Med COVID-19 tasks and received a lot of support from newcomers
but there are lots of remaining tasks - so newcomers are always welcome.
   
For those who would like to join our next videomeeting it will happen at
   
 
https://www.timeanddate.com/worldclock/fixedtime.html?msg=Debian+CoViD-19+Biohackathon+Video+Conference&iso=20200731T20&p1=37&ah=1

The meeting is on the Debian Social channel

 https://jitsi.debian.social/DebianMedCovid19

These weekly video meetings were started in the Debian Med
Biohackathon[1].  The topic is what contributors have done in the past
week and to coordinate the work for next week.
To repeat myself: Newcomers are always welcome.

Have fun
   
   Andreas.

[1] https://lists.debian.org/debian-devel-announce/2020/03/msg00010.html

-- 
http://fam-tille.de