[gentoo-science] Re: Gentoo Science project status

[gentoo-science] Re: Gentoo Science project status

[George Shapovalov]

Hi devs,

First, I want to apologise, as many of you will get two copiess of this email 
and some will even see it three, this one time. I, however, wanted to make 
sure everybody has all the relevant addresses.

Second, indeed I think we should move this discussion to the list, rather than 
sending emails with bunch of CCs. I would like to remind everybody, that 
there is a mailing list: gentoo-science@lists.gentoo.org, which is supposed 
to be used for more or less general discussions related to our project and 
especially for stuff like that. Donnie: nice reminder of the sci alias, but I 
think the list is suited better for this purpose. First, it is free for all 
to sign up, so we need not take special care of interested/involved nondevs. 
More importantly, this way the discussion will not interfer with bug reports 
(and the other way around).

Wednesday, 13. May 2009, Andrey Kislyuk Ви написали:
> - Current projects. All active developers, please reply to this
> message with a list of any major items you're working on, so we can
> put them in the status report. For instance, I'm working on the
> bioperl-1.6.0 update and a few big troublesome sci-biology packages
> including ncbi-tools++, gbench, wgs-assembler and cytoscape. I know
> Markus is working on the Octave 3 stuff. What else?
Thanks for the reports sent so far. However I would like to expand this 
request a bit - it would really be nice to get a headcount. Therefore, I 
would like to ask all devs who are still involved in Scientific Gentoo to 
respond, shortly outlining the (intended) range of "responsibilities" and 
expected activity level, - even if not very active at the moment. Please 
answer to the list, so that we can keep track of the responces in one concise 
thread. Actually, I'll branch the discussion then and will create a subthread 
for this in a moment..

After collecting the responce we can update the webpage - I could do it or 
somebody else willing could step up ;).

I'll start with myself:
> - Selecting a lead. George Shapovalov is our current lead. George, if
> you're active, we'll need your help with the status update, otherwise
> we need to select a new lead. Please reply to nominate people or with
> any thoughts (we could be anarchists like the python herd and go
> without a lead!)
Well, I am here, although I am not working on any specific package(s), mostly 
reacting to organizational issues. I was indeed rather quiet last few month, 
however we have seen a steady flow of new contributors to science overlay - I 
had to do mediate one almost montly for the last year or so. Which implies, 
that we should have a good pool of potential devs, however, as always, this 
is not guaranteed - people need to stay active, not just show activity once.

As for my lead status - either is fine with me. I try to react and organize 
when something comes up, however, I am afraid, I will not have much time in 
the coming year or two for more active actions (have to push out a couple of 
papers and change position). In this regard, you could call what was going on 
an anarchy - people going about their regular routines and taking care of 
their areas of interest and organizing when necessary, but I would rather 
call it "pragmatic handling" ;). If there are some ideas about some projects 
it would be interesting to discuss them, however, as I mentioned, it has been 
quiet lately in this regard. I'd say, the real need that we may have is 
organizing another wave of recruitment. Thus I definitly wellcome the request 
for recruitment status:
> - Recruiting and recruit status. If you're being recruited or are in
> charge of a recruit, please reply so we have a head count and let us
> know the ETA for becoming a dev if you have one. 
but again, would like to expand it slightly. As the original message will only 
reach the people on the original CC list, I'd like to ask anybody who knows a 
prospective applicant/interested user to forward this rectuitment request 
correspondingly. Please ask them to subscribe to gentoo-science mailing list 
as well. Some of the old participants might even still be on the list in 
fact :).

> We need to add a 
> staffing needs section to the project page. Do we have specific
> recruiting requests? 
On the updating the recruitment page. IIRC we were discussing (somewhat 
transient discussion I must admit) this some half a year ago (with bicataly 
and somebody else on irc?). The general feeling was that our staffing needs 
are a bit different from the general Gentoo populace, as people who make a 
good fit would be proficient in (or at least familiar with) some or other 
scientific discipline. Also, such people usually have a crapload of other 
duties on their hands and/or are somewhat shy in terms of active 
participation in geek discussions/communities. Therefore we considered the 
overlay as the most promising recruitment avenue and I think we could try to 
check if any of its regualrs are ripe enough for joining with a full dev 
status. 

Nonetheless, putting the request in the open should not hart. I would, 
however, urge whoever is going to write recruitment request to be careful 
about wording. Weer there any specific plans - who and when was going to do 
this or should I write something up? (perhaps in ~2 weeks, after headcount 
somewhat settles; nug me if I slip off the radar again - I am almost always 
there, just silent).

> We also need a tracker bug for science 
> contributors who are potential recruits. 
There is one such, still open, but did not see much activity for over a year. 
Perhaps we cpuld create a new one with less text :), although that one is not 
that long. But it should be better organized - we need a separate bugs 
branching off - one per recruitment case. In fact, we just need the recruits, 
as was discussed above, and this is the main problem I'd say. Then we can 
simply add standard recruitment bugs as dependencies. What may need to go in 
the bug itself are some org discussions - summaries of which could be 
attached to keep track of things.

Oh, the bug; its #138021:
https://bugs.gentoo.org/show_bug.cgi?id=138021


George

[gentoo-science] Re: Gentoo Science project status: headcount thread

[George Shapovalov]

Please answer here if you are not listed on the project page or if you want to 
change your details there:
http://www.gentoo.org/proj/en/science/index.xml

Please state if you are involved (or want to be) in a particular subproject.

George

Re: [gentoo-science] Re: Gentoo Science project status: headcount thread

[Andrey G. Grozin]

On Thu, 14 May 2009, George Shapovalov wrote:
> Please answer here if you are not listed on the project page or if you want to
> change your details there:
> http://www.gentoo.org/proj/en/science/index.xml
I am not listed on this page

Andrey Grozin <grozin@gentoo.org>

Re: [gentoo-science] Re: Gentoo Science project status: headcount thread

[Alexey Shvetsov]

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On Четверг 14 мая 2009 13:14:51 George Shapovalov wrote:
> Please answer here if you are not listed on the project page or if you want
> to change your details there:
> http://www.gentoo.org/proj/en/science/index.xml
>
> Please state if you are involved (or want to be) in a particular
> subproject.
>
> George
Hi 

I'm not mentioned in project page but i'm doing some things for sci-chemistry 
(GROMACS and GAMESS) and some OpenIB stuff ( eclass for openib and updates for 
openfabrics steck)
-- 
Alexey 'Alexxy' Shvetsov
Gentoo/KDE
Gentoo/MIPS
Gentoo Team Ru

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Re: [gentoo-science] Re: Gentoo Science project status: headcount thread

[Thomas Kahle]

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George Shapovalov wrote:
> Please answer here if you are not listed on the project page or if you want to 
> change your details there:
> http://www.gentoo.org/proj/en/science/index.xml
> 
> Please state if you are involved (or want to be) in a particular subproject.

Thomas Kahle / junior member / sci-mathematics





-- 
Thomas Kahle

The fundamental theorem of algebra is open source. Like any other
mathematical theorem it can be applied free of charge and everybody
has access to its proof and can convince himself how it works. Why
should software be any different?


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Re: [gentoo-science] Re: Gentoo Science project status: headcount thread

[Denis Dupeyron]

Hi George,

On Thu, May 14, 2009 at 3:14 AM, George Shapovalov <george@gentoo.org> wrote:
> Please answer here if you are not listed on the project page or if you want to
> change your details there:
> http://www.gentoo.org/proj/en/science/index.xml
>
> Please state if you are involved (or want to be) in a particular subproject.

It's probably time to add me with Electronics as role.

Denis.

Re: [gentoo-science] Re: Gentoo Science project status: headcount thread

[Björn Thorwirth]

Hi!


My name is Bjoern Thorwirth. I'm a german bioinformatic researcher. ATM
I'm working towards my Ph.D. . I'm programming a lot in Python and so i
would like to help to maintain the Biopython ebuilds. Who is the actual
maintainer? Any support needed? I could start to adapt existing ebuilds
for Biopython 1.50.

regards Bjoern 

Am Donnerstag, den 14.05.2009, 11:14 +0200 schrieb George Shapovalov:
> Please answer here if you are not listed on the project page or if you want to 
> change your details there:
> http://www.gentoo.org/proj/en/science/index.xml
> 
> Please state if you are involved (or want to be) in a particular subproject.
> 
> George
> 
> 
-- 
Bjoern Thorwirth, Zentrum für Medizinische Biotechnologie,
Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
phone +49 201 183-4026, bjoern.thorwirth@uni-due.de

Re: [gentoo-science] Re: Gentoo Science project status: headcount thread

[Andrey Kislyuk]

2009/5/15 Björn Thorwirth <bjoern.thorwirth@uni-due.de>:
> I'm working towards my Ph.D. . I'm programming a lot in Python and so i
> would like to help to maintain the Biopython ebuilds. Who is the actual
> maintainer? Any support needed? I could start to adapt existing ebuilds
> for Biopython 1.50.

Bjoern-

Awesome, I'm a bioinformatics phd student myself. Good to have you on board.

There is no maintainer currently designated for BioPython. You are
welcome to submit new ebuilds to me so I'll commit them. You can also
get direct access to the Science overlay by taking the ebuild quiz and
demonstrating your knowledge of ebuild writing. If you want it, that
path eventually leads to developer status. Let us know if you want to
start that process.

-ak

Re: [gentoo-science] Re: Gentoo Science project status: headcount thread

[David Radice]

Hi George,

On Thu, May 14, 2009 at 11:14 AM, George Shapovalov <george@gentoo.org> wrote:
> Please answer here if you are not listed on the project page or if you want to
> change your details there:
> http://www.gentoo.org/proj/en/science/index.xml
>
> Please state if you are involved (or want to be) in a particular subproject.
>
> George

my name is David Radice (AKA david_e the couple of times I have been
on IRC), I am a diploma student. I mainly work on numerical methods
for PDEs.

I wrote, with the support of bicatali, the ebuild for the FreeFem++
(and the related vim-syntax) package which I am maintaining in the
overlay.

I don't intend to be involved in any particular subproject or becoming
a real dev: I don't really have time for that, even my FreeFem++
ebuild is outdated because I had not the possibility to update my
system and so I can't test the new version with the now stable Gentoo
branch (also new releases of FreeFem++ tends to be really buggy) (I
will do it probably in the next week)...

I would just like to continue being an external contributor
maintaining only a small enough set of ebuild to be able to keep them
in a good shape.

Cheers,
David

[gentoo-science] Re: Gentoo Science project status: updating project website

[George Shapovalov]

I just realized, that while we have split into multiple subprojects to handle 
all the sci related stuff in Gentoo, our page did not follow this. There are 
only vague hints at subprojects in role fields of, like, two devs. It may be 
helpfull to branch the page a bit by  adding pages for individual projects. I 
guess corresponding leads could be tasked with that ;). However I think this 
should not be obligatory.

At the very least we should have a list of subprojects with the description of 
their "coverage area". Do we even have a 1:1 mapping between subprojects and 
herds at this point? To figure this out and get some idea of what is going on 
I started a subthread asking for headcount. I think it would be helpful if 
even people who are already listed on the page answer there. Please only 
include the structural info into those replies. Discussion of project page 
update should go under this thread.

George

Re: [gentoo-science] Re: Gentoo Science project status: updating project website

[Andrey Kislyuk]

I think we should keep it all on one page, otherwise the sub-pages
will be small and short on details. We should have small tables of
devs for each subproject though. And we really need to write some
guides for using the software in the tree, to be linked at the
resources section at the bottom. I've been meaning to write an update
for the "clustering with gentoo" guide and eventually write a little
"computational biology/bioinformatics with gentoo" guide, it would be
great to have other subprojects do this.

-ak

Re: [gentoo-science] Re: Gentoo Science project status: updating project website

[Alexey Shvetsov]

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On Четверг 14 мая 2009 23:28:27 Andrey Kislyuk wrote:
> I think we should keep it all on one page, otherwise the sub-pages
> will be small and short on details. We should have small tables of
> devs for each subproject though. And we really need to write some
> guides for using the software in the tree, to be linked at the
> resources section at the bottom. I've been meaning to write an update
> for the "clustering with gentoo" guide and eventually write a little
> "computational biology/bioinformatics with gentoo" guide, it would be
> great to have other subprojects do this.
>
> -ak
I can write something about using gromacs and games
And something about cluster + gentoo + Infiniband hardware setup
-- 
Alexey 'Alexxy' Shvetsov
Gentoo/KDE
Gentoo/MIPS
Gentoo Team Ru

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Re: [gentoo-science] Re: Gentoo Science project status: updating project website

[Denis Dupeyron]

On Thu, May 14, 2009 at 3:22 AM, George Shapovalov <george@gentoo.org> wrote:
> I just realized, that while we have split into multiple subprojects to handle
> all the sci related stuff in Gentoo, our page did not follow this. There are
> only vague hints at subprojects in role fields of, like, two devs. It may be
> helpfull to branch the page a bit by  adding pages for individual projects. I
> guess corresponding leads could be tasked with that ;). However I think this
> should not be obligatory.

FWIW here's my stuff on sci-electronics that I never moved to an
official subproject page. It needs to be updated though.

http://dev.gentoo.org/~calchan/sci-electronics/

Denis.

Re: [gentoo-science] Re: Gentoo Science project status

[François Bissey]

OK time to introduce myself to people I guess.

I am Francois Bissey (aka kiwi_fb) a French physicist living
in New Zealand. I am a contributor to the overlay and have been
toying with becoming a full fledged dev for over a year.

Anyway at the moment my main focus is the refurbishment 
of the opendx/opendx-samples ebuild. I was given the task
by bicatali just before he had to take a break. Funny almost 
5 years ago I requested the inclusion of an opendx-samples
in the tree and I am now revising it.

I also work on and off on sage which is a big problem in itself.
I could possibly look at helping Andrey with reduce as while I 
haven't ever been heavily into it, it is a tool often used in my
area of physics.

I am also interested in sci-visualisation in general, waiting for
paraview 3.6 release at the moment.

Cheers,
Francois

Re: [gentoo-science] Re: Gentoo Science project status

[Andrey G. Grozin]

On Thu, 14 May 2009, Fran?ois Bissey wrote:
> I am also interested in sci-visualisation in general, waiting for
> paraview 3.6 release at the moment.
Have you looked at VisIT (https://wci.llnl.gov/codes/visit/)? Seems nice. 
Once I tried to gentooize it, but completely failed :-(

Andrey

Re: [gentoo-science] Re: Gentoo Science project status

[François Bissey]

On Thu, 14 May 2009, Andrey G. Grozin wrote:
> On Thu, 14 May 2009, Fran?ois Bissey wrote:
> > I am also interested in sci-visualisation in general, waiting for
> > paraview 3.6 release at the moment.
>
> Have you looked at VisIT (https://wci.llnl.gov/codes/visit/)? Seems nice.
> Once I tried to gentooize it, but completely failed :-(
>
Hi Andrey,

I have heard of it on the sage mailing list. I will have a look to see
if it fits my needs and if I have a clue on its gentoo-ization.

Francois

Re: [gentoo-science] Re: Gentoo Science project status

[Olivier Fisette]

Hi,

I used to be active in the sci herd (mainly in the computational biology and 
chemistry projects), but the last year has seen very little activity from me. 
I stepped down from maintaining most of my packages recently since it has 
become obvious I no longer have the time and motivation necessary to deserve 
a developer position. I plan to retire this summer after finishing a few long 
overdue tasks.

I will still want to contribute, so maybe I can find someone to work with as a 
proxy maintainer for EMBOSS and related packages. Otherwise, I will only be 
around to fill bug reports and maybe contribute to the overlay from time to 
time.

I still love Gentoo, but I have invested myself in other personal and 
professional projects and just no longer have enough free time to want to 
dedicate much of it to Gentoo, unfortunately.

With kind regards,

Olivier

-- 
Olivier Fisette (ribosome)
Gentoo Linux Developer
Scientific applications

Re: [gentoo-science] Re: Gentoo Science project status

[Norman Warthmann]

Dear list, dear ribosome,

I am just a user of gentoo and this is my first post to this list. As  
the traffic is very low, I guess I can afford to briefly express how  
thankful I am for ribosomes work.
My perception may be skewed, but to me the work of ribosome has been  
very visible and I guess it is fair to say that ribosome contributed  
big time to the fact that gentoo became the distribution of choice for  
biologist.
He was always quick in replying, writing new ebuilds and I have very  
lively memories when he developed the ebuild for the staden package  
such that it would also run on my sparc. Thank you very much Olivier  
for your work and I hope that there will be others continuing.

cheers and all the best

Norman

----
Norman Warthmann
Max Planck Institute for Developmental Biology
Dept. Molecular Biology
http://www.warthmann.com






On May 19, 2009, at 20:34 PM, Olivier Fisette wrote:

> Hi,
>
> I used to be active in the sci herd (mainly in the computational  
> biology and
> chemistry projects), but the last year has seen very little activity  
> from me.
> I stepped down from maintaining most of my packages recently since  
> it has
> become obvious I no longer have the time and motivation necessary to  
> deserve
> a developer position. I plan to retire this summer after finishing a  
> few long
> overdue tasks.
>
> I will still want to contribute, so maybe I can find someone to work  
> with as a
> proxy maintainer for EMBOSS and related packages. Otherwise, I will  
> only be
> around to fill bug reports and maybe contribute to the overlay from  
> time to
> time.
>
> I still love Gentoo, but I have invested myself in other personal and
> professional projects and just no longer have enough free time to  
> want to
> dedicate much of it to Gentoo, unfortunately.
>
> With kind regards,
>
> Olivier
>
> -- 
> Olivier Fisette (ribosome)
> Gentoo Linux Developer
> Scientific applications
>

Re: [gentoo-science] Re: Gentoo Science project status

[Andrey Kislyuk]

Hi Norman,

As a sci-biology developer, I aim to pick up where Olivier left off,
maintain packages and look for new recruits. If you have any feature
requests or bug reports, please file bugs and contact me so I know
about them and can act as soon as I can.

Thanks,
-ak


On Tue, May 19, 2009 at 14:52, Norman Warthmann <norman@warthmann.com> wrote:
> Dear list, dear ribosome,
>
> I am just a user of gentoo and this is my first post to this list. As the
> traffic is very low, I guess I can afford to briefly express how thankful I
> am for ribosomes work.
> My perception may be skewed, but to me the work of ribosome has been very
> visible and I guess it is fair to say that ribosome contributed big time to
> the fact that gentoo became the distribution of choice for biologist.
> He was always quick in replying, writing new ebuilds and I have very lively
> memories when he developed the ebuild for the staden package such that it
> would also run on my sparc. Thank you very much Olivier for your work and I
> hope that there will be others continuing.
>
> cheers and all the best
>
> Norman
>
> ----
> Norman Warthmann
> Max Planck Institute for Developmental Biology
> Dept. Molecular Biology
> http://www.warthmann.com