[gentoo-science] Scientific Gentoo reorg: the proposal

[gentoo-science] Scientific Gentoo reorg: the proposal

[George Shapovalov]

First, thanks to everybody who responded! (not that tehre were many ;)).
Interestingly, the most positive result so far seems to be two people 
expressing interest to join :), so we need at least one more mentor I'd say..

I'll start by refreshing general changes that were proposed:

1. Make Scientific Gentoo a top-level and create subprojects
 -  this did not seem to get any complaints. So, when we are done with the 
mainpart I'll try to update the page, like move it to a proper location, redo 
the blurb and provide links to subprojects. Then I'll ask corresponding teams 
to produce some descriptions for the corresponding subprojects (its the 
same .xml essentially, just change the description paraagraph). But lets 
first get done with the reorg itself..

2. Create smaller, topical herds to split 316 packages we have under sci right 
now.
 -  Looks like most people assumed a natural herding of packages by categories 
(of course sci-libs should not be a separate herd, packages under it should 
fall under whatever makes sense), so lets try to start by creating a layout 
that follows. Here are the categories, as they stand now:

aldar portage # for fn in sci-*; do echo "$fn:  $(ls -1 $fn|wc -l)"; done
sci-astronomy:  11
sci-biology:  58
sci-calculators:  26
sci-chemistry:  50
sci-electronics:  34
sci-geosciences:  8
sci-libs:  62
sci-mathematics:  34
sci-misc:  19
sci-visualization:  20

Further is based on a quick glance at ChangeLog's (since I did not get much 
responce from actual mainatiners ;), so I may have missed somebody/listed 
somebody extra. Please check and comment accordingly)

sci-astronomy: 11 
an Ok size I'd say, devs:
morfic, phosphan, zx, ribosome, aliz, corsair, mr_bones_

sci-biology:  58
rather large, may be worth splitting more, no particular suggestions yet 
though, devs:
ribosome, blubb, corsair, j4rg0n, mcummings, sediener, pbienst, apokorny, 
hansmi?, phosphan, lostlogic?

sci-calculators:  26
split off math at some point IIRC (or was that a discussion that it should be 
separate and it started like that from the inception?). size: Ok,  devs:
centic?, cryos, ribosome, spyderous?, many people who appear one or twice..

sci-chemistry:  50
may be worth splitting up as well. One suggestion is to make a category for 
sci-crystallography. I seem to have persuaded  Jan Marten Simons to at least 
try :). If he indeed is willing to take on this subject it may be well worth 
creating this category, or at least herd..
devs:
spyderous, markusle?, phosphan, marcus, hannes, ribosome?, kugelfang, 
agriffis, hansmi?


sci-electronics:  34
Ok size,  devs:
calchan, chrb?, agriffis?, phosphan, ribosome, blubb?, plasmaroo, hansmi, 
cryos?, gustavoz?


sci-geosciences:  8
good size (for maintainers :)), devs:
ribosome, spyderous, cryos, nerdboy, mholzer?

sci-mathematics:  34
Ok size. There were calls to split it into symbolic and numeric, also -proof 
was suggested (but I understand the packages for that one are not in the tree 
yet). 3-tier categories might be nice here :) (as in sci-math-symbolic, 
sci-math-numeric..).  devs:
plasmaroo, agriffis?, mattam, cryos, ribosome?, markusle, spock, phosphan

sci-misc:  19
Size is Ok, but, if we follow the idea, should probably stay under sci (herd)
devs:
cryos, hansmi?, phosphan, ribosome, kugelfang?, pbienst, blubb? 

sci-visualization:  20
Ok size, may be combined with -calculators? or -math? (herding, if it makes 
sense, category should stay), devs:
markusle, phosphan, ribosome, cryos, kugelfang, latexer?, j4rg0n?, corsair?, 
spyderous


Furthere, 
sci-cad was suggested and it looks like there may be a critical mass of > 5 
packages, but more planning is necessary on this one..

There was a suggestion for sci-phonetics or sci-linguistics. There is a dev 
(translator's team, so he will need to be mentored for the "generic 
development") who is willing to take on those, however I first need to see 
how many packages would be there. If anything it will be good to have him as 
a part of the team, even if this does not qualify for a full category (but 
still should be good for herd I guess..)

There were talks about creating sci-physics category, however I cannot find 
traces of that atm (or was it on irc?). If there really are apps for 
sci-physics it can start combined with sci-astronomy (or not, need a list of 
packages..)

Any comments on the structure? Also, while sci-xxx is a "natural" name for the 
category (considering our present layout) it is somewhat cumbersome for the 
herd. I guess sci- part may be dropped, then, should the rest stay spelled 
out or people would prefere shortcuts, like math for mathematics, etc?

George
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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[C Y]

--- George Shapovalov <george@gentoo.org> wrote:

> sci-mathematics:  34
> Ok size. There were calls to split it into symbolic and numeric, also
> -proof  was suggested (but I understand the packages for that one are
> not in the tree yet). 3-tier categories might be nice here :) (as in
> sci-math-symbolic, sci-math-numeric..).  devs:
> plasmaroo, agriffis?, mattam, cryos, ribosome?, markusle, spock,
> phosphan

As to the sci-proof suggestion, I have discussed ebuilds with the
Isabelle mailing list and they do not seem to be in favor of it. 
Apparently the work flow for that tool is such that they prefer to
maintain everything in a user level directory, as a monolithic whole. 
I don't know how other projects (HOL, etc.) feel about it.

> sci-visualization:  20
> Ok size, may be combined with -calculators? or -math? (herding, if it
> makes sense, category should stay), devs:
> markusle, phosphan, ribosome, cryos, kugelfang, latexer?, j4rg0n?,
> corsair?, spyderous

I'd say keep this category, personally.

> Furthere, 
> sci-cad was suggested and it looks like there may be a critical mass
> of > 5 packages, but more planning is necessary on this one..

I was able to kludge together a functional brl-cad ebuild, and I know
qcad has been in there for ages.  Most of the other options will need
ebuilds written.  Whoever writes the one for SALOME will need to be
good.

> There were talks about creating sci-physics category, however I
> cannot find traces of that atm (or was it on irc?). If there really
> are apps for sci-physics it can start combined with sci-astronomy (or
> not, need a list of packages..)

Physics packages (not all of which may be in gentoo at the moment)

mpb (mit photonic bands - does have ebuild)

root (in sci-libs, maybe it should stay there?)
geant4 http://geant4.web.cern.ch/geant4/ (it can be installed on Gentoo
but no ebuild yet)
(other stuff from http://lcgapp.cern.ch/project/ is probably of
interest)

http://fermitools.fnal.gov/abstracts/transport/abstract.html
http://fermitools.fnal.gov/abstracts/turtle/abstract.html

There are other tools of interest here: 
http://fermitools.fnal.gov/categories/index.html but I suspect many of
them have a wider application that just physics

Other possibilities:
http://www.freehep.org/ - probably a lot that might be included here.
http://wwwasd.web.cern.ch/wwwasd/paw/

The license is a bit wonky but there is this:
http://www.physics.cornell.edu/sss/

Doubtless there are others I am not familiar with.  Outside of the HEP
world there is less that is free, but oh well.

> Any comments on the structure? Also, while sci-xxx is a "natural"
> name for the 
> category (considering our present layout) it is somewhat cumbersome
> for the 
> herd. I guess sci- part may be dropped, then, should the rest stay
> spelled 
> out or people would prefere shortcuts, like math for mathematics,
> etc?

Personally I would rather keep the sci- prefix, just to keep all the
science related software alphabetically together, but I know that's a
silly reason.  Out of curosity, how is it cumbersome for the herd?

Cheers,
CY

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[George Shapovalov]

Hi C Y

Thanks for comments.

Looks like there are some misconceptions about herds which are understandable 
to devs (whom this reorg concerns primarily), but not that clear to users. 
Since the users are the ones more active in the dscussion, it seems :), I 
think I need to do a bit of explanation.

Basically - herds are the internal organizational stuff, they are not visible 
to users, and developers who maintain stuff deal with them all the time. It 
is a way to traffic bug reports and (internal) correspondence - for example 
most herds have emai laliases setup, that forward all the messages generated 
by bugzilla and other stuff to the relevant devs.. 

неділя, 25. червень 2006 23:23, C Y Ви написали:
> > sci-visualization:  20
> > Ok size, may be combined with -calculators? or -math? (herding, if it
> > makes sense, category should stay), devs:
> > markusle, phosphan, ribosome, cryos, kugelfang, latexer?, j4rg0n?,
> > corsair?, spyderous
>
> I'd say keep this category, personally.
Yes, that's what I said in that smal blurb in parenthesis - may be it makes 
sense to have one herd for two categories, if the packages there are 
maintained by the same people (but this has to be seen first), but we 
shouldn't touch the category. Although that message was probably cryptic to 
the people not dealing with the "internals". I hope above explanation makes 
it more clear. 

> Personally I would rather keep the sci- prefix, just to keep all the
> science related software alphabetically together, but I know that's a
> silly reason.  Out of curosity, how is it cumbersome for the herd?
Oh, they should absolutely stay, as far as categories are concerned. We had 
that discussion when we split (1-tier) sci category into 2-tier categories 
that we have now. Categories in generall will stay the same, only may be few 
of the larger ones will be split again. 

This whole discussion mostly concerns the internal organization of 
maintainance - how the devs deal with them, stuff that is largerly not seen 
from outside. So, you will still be able to browse the packages as now. 
However, as far as herd names are concerned (which users can only see in 
metadata.xml files and which some housekeeping tools may use), having this 
sci- prefix is not as advantageous. Primary "users" of herd names are devs, 
who know what they maintain, and there are not that many of us. On some 
occasions when we need to type herd name (admittedly rare) this may be 
tiresome, and not as nicely looking (maybe). So, basically, I do not feel 
that we have to absolutely keep sci- (in herd names) and we might as well try 
to compress the remainder. However I do not insist either way, - I would like 
to hear here opinions of the "primary users" of herd names - that is 
maintainers who will deal with them..

George

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[jak]

  Hi,

I am not a developer so maybe I should not make suggestions, but I would
like to mention that there is a group of scientific applications in
Python. Some of them are now in dev-python category. It seems that there
are still some unresolved issues there.

First, there are three basic array packages: dev-python/numeric
dev-python/numarray dev-python/numpy. They should be, at least optionally,
built using lapack. This was discussed in the beginning of 2005, see
#81520. I have just discovered that there is some update in the overlay.

Second, it was proposed (see #124276) to replace numeric and numarray with
numpy, which I consider premature, as there are interesting modules and
applications that do not use numpy yet. It would be advantageous, however,
 to be able to choose array type where available. For example: f2py now
depends only on numeric, but when numpy is installed it uses it rather
than numeric. Eventually I had to remove numpy and install f2py manually.
As I remember, also pytables can use either numeric or numarray but
presently depends only on the latter.

Should Scientific Python, now in python herd, be in sci? I have just
submitted MMTK library, which was written by the same person, see #137989.
This two packages probably should be maintained together. What about a
nice, pure python, chemistry drawing program bkchem – see #95178.

 Best wishes,

Jaroslaw Kalinowski

==============================================
This is a list of packages that depend on num*

find /usr/portage/ -name '*.ebuild' -exec grep -q dev-python/numeric '{}'
\; -printf '%h\n' | sort | uniq

/usr/portage/dev-python/f2py
/usr/portage/dev-python/fonttools
/usr/portage/dev-python/gnuplot-py
/usr/portage/dev-python/matplotlib
/usr/portage/dev-python/numeric
/usr/portage/dev-python/pycairo
/usr/portage/dev-python/pycdf
/usr/portage/dev-python/pyclimate
/usr/portage/dev-python/pygame
/usr/portage/dev-python/pygtk
/usr/portage/dev-python/pyqwt
/usr/portage/dev-python/python-biggles
/usr/portage/dev-python/python-gtkextra
/usr/portage/dev-python/rpy
/usr/portage/dev-python/scientificpython
/usr/portage/dev-python/ttfquery
/usr/portage/dev-python/visual
/usr/portage/games-arcade/pydance
/usr/portage/sci-biology/biopython
/usr/portage/sci-biology/ecell
/usr/portage/sci-chemistry/pymol
/usr/portage/sci-libs/plplot
/usr/portage/sci-libs/pymmlib
/usr/portage/sci-libs/scipy
/usr/portage/sci-misc/camfr
/usr/portage/sci-visualization/scigraphica

find /usr/portage/ -name '*.ebuild' -exec grep -q dev-python/numpy '{}' \;
-printf '%h\n' | sort | uniq

/usr/portage/dev-python/matplotlib
/usr/portage/dev-python/numpy
/usr/portage/sci-libs/pymmlib
/usr/portage/sci-libs/scipy

find /usr/portage/ -name '*.ebuild' -exec grep -q dev-python/numarray '{}'
\; -printf '%h\n' | sort | uniq

/usr/portage/dev-lang/gdl
/usr/portage/dev-python/cgkit
/usr/portage/dev-python/matplotlib
/usr/portage/dev-python/numarray
/usr/portage/dev-python/pyqwt
/usr/portage/dev-python/pytables
/usr/portage/dev-python/visual
/usr/portage/sci-visualization/veusz
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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Peter Bienstman]

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On Sunday 25 June 2006 20:46, George Shapovalov wrote:

> There were talks about creating sci-physics category, however I cannot find
> traces of that atm (or was it on irc?). If there really are apps for
> sci-physics it can start combined with sci-astronomy (or not, need a list
> of packages..)

sci-misc/camfr and sci-misc/mpb could go to sci-physics

Cheers,

Peter

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Denis Dupeyron]

On 6/25/06, George Shapovalov <george@gentoo.org> wrote:
> 1. Make Scientific Gentoo a top-level and create subprojects
>  -  this did not seem to get any complaints. So, when we are done with the
> mainpart I'll try to update the page, like move it to a proper location, redo
> the blurb and provide links to subprojects. Then I'll ask corresponding teams
> to produce some descriptions for the corresponding subprojects (its the
> same .xml essentially, just change the description paraagraph). But lets
> first get done with the reorg itself..

Is the plan to have one subproject for each sci-* category ?

> sci-biology:  58
> rather large, may be worth splitting more, no particular suggestions yet
[...]
> sci-chemistry:  50
> may be worth splitting up as well. One suggestion is to make a category for
[...}
> sci-mathematics:  34
> Ok size. There were calls to split it into symbolic and numeric, also -proof

I'm not sure we should go from not enough herds to too many in one
single step. I suppose the people managing the different subcategories
will be the same anyway, so I fail to see the point here. Or is there
some other problem you're trying to address that I don't see ? My
opinion is that we may want to do this, but only as a second step at a
later time, once we have some feedback on how the new organization
works.

I believe the problem is less about the number of packages, and more
about the very specific topics touched by science apps. I would be
totally unable to run a biology or crystallography app to check it
works after I wrote the ebuild (I mean besides checking it doesn't
segfault). Inside the sci-electronics category, to continue with me as
example, I have no problem trying to run any app and playing with some
examples or tutorials to verify it works. Even if it's not exactly my
area, and even if it means that I need to invest some time in trying
to understand what the app does and how. I know I will end-up
understanding, which is definitely not the case with, say, a biology
app (unless we have a package that's related to female anatomy).

This said, once the packages are properly categorized, the number of
packages only matters compared to the time they take to maintain (some
are more complicated than others) and the number of devs maintaining
them. Splitting categories into more sub-categories won't change that
ratio. So I'd suggest we split packages based on topics, not on
numbers.

> sci-electronics:  34
> Ok size,  devs:
> calchan, chrb?, agriffis?, phosphan, ribosome, blubb?, plasmaroo, hansmi,
> cryos?, gustavoz?

I confirm that you can count on me for anything that's in sci-electronics.

> sci-misc:  19
> Size is Ok, but, if we follow the idea, should probably stay under sci (herd)
> devs:
> cryos, hansmi?, phosphan, ribosome, kugelfang?, pbienst, blubb?

Agreed. But it should be clear who maintains each of them, or that
will become nobody. What I mean is that for any package in the other
categories, the name of the (sub-)herd in the metadata is usually
sufficient. For packages in this category, and in sci-libs by the way,
we could require there is at least one dev name.

> sci-cad was suggested and it looks like there may be a critical mass of > 5
> packages, but more planning is necessary on this one..
>
> There was a suggestion for sci-phonetics or sci-linguistics. There is a dev
> (translator's team, so he will need to be mentored for the "generic
> development") who is willing to take on those, however I first need to see
> how many packages would be there. If anything it will be good to have him as
> a part of the team, even if this does not qualify for a full category (but
> still should be good for herd I guess..)
>
> There were talks about creating sci-physics category, however I cannot find
> traces of that atm (or was it on irc?). If there really are apps for
> sci-physics it can start combined with sci-astronomy (or not, need a list of
> packages..)

We talked about this on irc already, but it's worth mentioning it
again on this list. Be careful that adding new packages or categories
before getting the benefits of the reorganization, like hopefully
getting more devs onboard, will just add more work for the current
devs. This may definitely scare potential recruits (not talking about
the current ones that may leave or lose interest due to too much
work).

> Any comments on the structure? Also, while sci-xxx is a "natural" name for the
> category (considering our present layout) it is somewhat cumbersome for the
> herd. I guess sci- part may be dropped, then, should the rest stay spelled
> out or people would prefere shortcuts, like math for mathematics, etc?

Good idea. It could be argued that sci-electronics could be more
properly called tech-electronics, for example. The same for the maybe
future sci-cad category. So dropping the ambiguous prefix is an
elegant solution to this.

As a conclusion, assuming the above details can be worked out /
clarified, I'm very much in favor of the proposed plan.

Denis.
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[gentoo-science] Re: [gentoo-dev] Scientific Gentoo reorg: the proposal

[Alexandre Buisse]

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On Mon, Jun 26, 2006 at 14:26:16 +0200, George Shapovalov wrote:

> sci-mathematics:  34
> Ok size. There were calls to split it into symbolic and numeric, also -proof 
> was suggested (but I understand the packages for that one are not in the tree 
> yet). 3-tier categories might be nice here :) (as in sci-math-symbolic, 
> sci-math-numeric..).  devs:
> plasmaroo, agriffis?, mattam, cryos, ribosome?, markusle, spock, phosphan

Sign me up for sci-proof (even if it is only a subset of
sci-mathematics). As far as I know, there is only coq, but I am working
on adding agda, and we'll see from there...

Regards,
/Alexandre
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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[George Shapovalov]

понеділок, 26. червень 2006 14:44, Denis Dupeyron Ви написали:
> Is the plan to have one subproject for each sci-* category ?
That is one possibility. My stance is "whatever makes sense" - projects are 
the means to organize, so I'd just follow the herd structure. However the 
projects are more visible (that web page and some blurb after all..), so 
following the categories makes a good sense as well. But not limited to.

For example there were a few initiatives proposed earlier on, such as HPC - 
high performance computing. That one did not go far however under Scientific 
Gentoo, but I think the more natural place for it would have been 
under -cluster anyways (and that one seems to be reasonably active anyways). 
There were talks about "closer involvment with academia", but nothing even 
close to a sustainable idea ever came out of it (not that much time was spent 
on that either), still, this just shows potential projects.

So, we can have Scientific Gentoo at top level consisting of active 
subprojects (Scientific Overlay could be one such that is presently active, 
for example) and maintainance subprojects - that's a rough idea that we can 
fill with particulars if enough interest arises..

> > sci-biology:  58
> > rather large, may be worth splitting more, no particular suggestions yet
> > sci-chemistry:  50
> > may be worth splitting up as well. One suggestion is to make a category
> > for
> > sci-mathematics:  34
> > Ok size. There were calls to split it into symbolic and numeric, also
> > -proof
>
> I'm not sure we should go from not enough herds to too many in one
> single step. I suppose the people managing the different subcategories
Incidentally I was thinking about this as well :), see comment #2 in bug 
#138049 that I just created.

> will be the same anyway, so I fail to see the point here. Or is there
> some other problem you're trying to address that I don't see ? My
Actually yes - one of the major goals of this reorg is to create sufficiently 
small herds, so that people are not afraid to join. For example plasmaroo 
maintains many electronics packages but he is not on sci herd, but agreed to 
join if we split electronics off. So, while now it seems herds will have 
mostly the same people listed, we may expect this to change when others, not 
in sci, start to add themselves to smaller groups..

Right now sci is kind of a "stale community", as everybody just supports 
mostly his ebuilds and roughly knows who touches what. However this structure 
is not exposed (via normal ways), and that at 300+ packages, thus creating a 
non-trivial barrier of entry. One of my primary goals is to lover this 
barrier..

> I believe the problem is less about the number of packages, and more
> about the very specific topics touched by science apps. I would be
[...]
> them. Splitting categories into more sub-categories won't change that
> ratio. So I'd suggest we split packages based on topics, not on
> numbers.
Yes, so I am not going to push for anything. I just wanted to "test waters" 
here - on whether there is a feeling that some category should be split or 
not. As such, sci-biology will likely stay - there were no comments on that 
one. However there was an interest in splitting off sci-crystallography from 
chemistry for example, creating -physics and possibly splitting math-proof 
from sci-math. It is clear that herds should be created, to represent 
developer's wishes, categorisation should be decided based on how many 
packages are there for each and on the desire of actual maintainers to 
perform such action.

> > sci-electronics:  34
>
> I confirm that you can count on me for anything that's in sci-electronics.
Thanks! So, this is a clear candidate for the herd to be created soon then :).


> > sci-misc:  19
> > Size is Ok, but, if we follow the idea, should probably stay under sci
> > (herd) devs:
> > cryos, hansmi?, phosphan, ribosome, kugelfang?, pbienst, blubb?
>
> Agreed. But it should be clear who maintains each of them, or that
> will become nobody. What I mean is that for any package in the other
It won't be worse than it is now anyways :), but the way to regulate this is 
exactly as you suggest below:

> categories, the name of the (sub-)herd in the metadata is usually
> sufficient. For packages in this category, and in sci-libs by the way,
> we could require there is at least one dev name.



> We talked about this on irc already, but it's worth mentioning it
> again on this list. Be careful that adding new packages or categories
> before getting the benefits of the reorganization, like hopefully
> getting more devs onboard, will just add more work for the current
> devs. This may definitely scare potential recruits (not talking about
> the current ones that may leave or lose interest due to too much
> work).
Well, of course, the recruitment should start early, as it takes quite some 
time. Besides, what better material to train a recruit on is there than the 
ebuilds he submitted? That was my usual mentoring practive and it seems to 
work well :). 
Please see bug #138021 (this is addressed to all devs). I listed the three 
people who expressed interest in becoming maintainers and have made 
contributions. I can mentor one, but  we need two more mentors..

>
> > Any comments on the structure? Also, while sci-xxx is a "natural" name
> > for the category (considering our present layout) it is somewhat
> > cumbersome for the herd. I guess sci- part may be dropped, then, should
> > the rest stay spelled out or people would prefere shortcuts, like math
> > for mathematics, etc?
>
> Good idea. It could be argued that sci-electronics could be more
> properly called tech-electronics, for example. The same for the maybe
> future sci-cad category. So dropping the ambiguous prefix is an
> elegant solution to this.
Um, are you talking about herd or category names here? Categories will not 
change, except for some possibly being split (they were around for far too 
long if any reason is necessary). Herd names can be almost arbitrary - they 
are not visible from outside and devs will know what they are woring on :). 
So, as far as herds are concerned, this is mostly a matter of taste..

Addressing the categories yet again: I think we could really benefit from a 
more rich hierarchy, by creating category names like say sci/math/proof or 
sci/chemistry/crystallography (and not requiring all leafs to be the same 
depth), but this is out of question, as portage would have to support that 
and this just won't happen any time soon (provided this will not be killed 
outright by screams to go to a flat "tree" of package names only and any 
categorization done in metadata - yes, that was for real last time this was 
discussed :))

George

> As a conclusion, assuming the above details can be worked out /
> clarified, I'm very much in favor of the proposed plan.
>
> Denis.

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[George Shapovalov]

I have created a tracker bug, so that we can finally start organizing activity 
and may see something done :).
https://bugs.gentoo.org/show_bug.cgi?id=138049

This is a tracker bug, to keep things in perspective. For every herd/category 
where there is interest/activity please create a new bug, if one does not yet 
exist and post proposed packages (if they are not under corresponding 
category) and check whether your involvment status is right (i.e. post me to 
or removal note). This will simplify tracking of what we will have to do 
significantly..

George
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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Donnie Berkholz]

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jak@biogeo.uw.edu.pl wrote:
> First, there are three basic array packages: dev-python/numeric
> dev-python/numarray dev-python/numpy. They should be, at least optionally,
> built using lapack. This was discussed in the beginning of 2005, see
> #81520. I have just discovered that there is some update in the overlay.
> 
> Second, it was proposed (see #124276) to replace numeric and numarray with
> numpy, which I consider premature, as there are interesting modules and
> applications that do not use numpy yet. It would be advantageous, however,
>  to be able to choose array type where available. For example: f2py now
> depends only on numeric, but when numpy is installed it uses it rather
> than numeric. Eventually I had to remove numpy and install f2py manually.
> As I remember, also pytables can use either numeric or numarray but
> presently depends only on the latter.

I imagine patches would be welcome.

> Should Scientific Python, now in python herd, be in sci? I have just
> submitted MMTK library, which was written by the same person, see #137989.
> This two packages probably should be maintained together. What about a
> nice, pure python, chemistry drawing program bkchem – see #95178.

I've just added the sci herd as a second herd in the metadata.

Thanks,
Donnie


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[gentoo-science] sci-proof

[C Y]

--- Alexandre Buisse <nattfodd@gentoo.org> wrote:

> Sign me up for sci-proof (even if it is only a subset of
> sci-mathematics). As far as I know, there is only coq, but I am
> working on adding agda, and we'll see from there...

I know of coq and otter in the "already present" category.  Candidates
for inclusion:

Isabelle (the devs don't see the need for a package - fair warning)
HOL http://hol.sourceforge.net/
Mizar (anybody know what the license is?) http://www.mizar.org
IMPS http://imps.mcmaster.ca/ (I think the license looks OK, but it 
     would probably need to be added to portage.)
nqthm http://www.computationallogic.com/software/nqthm/, maybe 
      http://www.computationallogic.com/software/pc-nqthm/ as well 
     (might be a bit dated now, but probably still worth including - 
      it's GPL)
ProofPower http://www.lemma-one.com/ProofPower/index/
PVS has a problematic license - it could be set up but I'm not sure
    if it's worthwhile.
NuPrl http://www.cs.cornell.edu/Info/Projects/NuPrl/ - this is another 
      one where I can't find the license, but it's an excellent 
      candidate for inclusion.
Larch might be of interest - http://www.sds.lcs.mit.edu/spd/larch/
MetaPRL http://metaprl.org/

Also interesting might be the Pcoq interface, although I don't know if
it is maintained any longer:  http://www-sop.inria.fr/lemme/pcoq/

I'm sure I missed a few.  Anyway, certainly enough to start :-).

Cheers,
CY

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Marcus D. Hanwell]

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On Sunday 25 June 2006 19:46, George Shapovalov wrote:
> First, thanks to everybody who responded! (not that tehre were many ;)).
> Interestingly, the most positive result so far seems to be two people
> expressing interest to join :), so we need at least one more mentor I'd
> say..

Sorry about not responding until now - really busy in real life. I am 
currently in the thesis write up and job hunting stage of my PhD with three 
months of funding left - so my Gentoo time may well be fairly limited during 
the next few months. I will do what I can as and when though.
>
> I'll start by refreshing general changes that were proposed:
>
> 1. Make Scientific Gentoo a top-level and create subprojects
>  -  this did not seem to get any complaints. So, when we are done with the
> mainpart I'll try to update the page, like move it to a proper location,
> redo the blurb and provide links to subprojects. Then I'll ask
> corresponding teams to produce some descriptions for the corresponding
> subprojects (its the same .xml essentially, just change the description
> paraagraph). But lets first get done with the reorg itself..

This sounds good to me. I think this will certainly be a positive move for the 
work done with scientific applications in Gentoo.
>
> 2. Create smaller, topical herds to split 316 packages we have under sci
> right now.
>  -  Looks like most people assumed a natural herding of packages by
> categories (of course sci-libs should not be a separate herd, packages
> under it should fall under whatever makes sense), so lets try to start by
> creating a layout that follows. Here are the categories, as they stand now:
>
> Further is based on a quick glance at ChangeLog's (since I did not get much
> responce from actual mainatiners ;), so I may have missed somebody/listed
> somebody extra. Please check and comment accordingly)

Commented in your tracker bug on my involvement - all sounds quite reasonable 
to me. Although I would hate to dilute down too much and end up with one 
developer herds as they are not very productive in general.
>
> There were talks about creating sci-physics category, however I cannot find
> traces of that atm (or was it on irc?). If there really are apps for
> sci-physics it can start combined with sci-astronomy (or not, need a list
> of packages..)

I would go either way - crystallography and structural packages are also quite 
physicsy depending upon your perspective...
>
> Any comments on the structure? Also, while sci-xxx is a "natural" name for
> the category (considering our present layout) it is somewhat cumbersome for
> the herd. I guess sci- part may be dropped, then, should the rest stay
> spelled out or people would prefere shortcuts, like math for mathematics,
> etc?

I would personally favour dropping the sci- and going for shortened names such 
as maths/math, geo. If there is a great deal of opposition I don't think it 
matters too much though.

Back to work anyway... I am usually around on IRC too if anyone wants to chat 
about this stuff. It is a manic week this week though, so may be not so much.

Thanks,

Marcus

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Re: [gentoo-science] sci-proof

[M. Edward (Ed) Borasky]

C Y wrote:
> I'm sure I missed a few.  Anyway, certainly enough to start :-).
>   
Well -- if we're going to get *that* specialized <weg>, how about adding
"maria" (which is in Debian -- it's a Petri net reachability analyzer),
the PEPA Workbench (in Java ... most likely not in Debian), PRISM
(http://www.cs.bham.ac.uk/~dxp/prism/download.php) and PDQ
(http://perfdynamics.com).

Seriously, though, PRISM is a quite useful and magnificent piece of
open-source work. Nearly all the other software in this domain
(probabilistic model checking and Markov process modeling) is either
commercial or tied up in an "academic (non-commercial)" non-free license
of some kind.
> Cheers,
> CY
>
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Re: [gentoo-science] sci-proof

[Alexandre Buisse]

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On Tue, Jun 27, 2006 at 12:57:12 +0200, M. Edward (Ed) Borasky wrote:

> 
> 
> C Y wrote:
> > I'm sure I missed a few.  Anyway, certainly enough to start :-).
> >   
> Well -- if we're going to get *that* specialized <weg>, how about adding
> "maria" (which is in Debian -- it's a Petri net reachability analyzer),
> the PEPA Workbench (in Java ... most likely not in Debian), PRISM
> (http://www.cs.bham.ac.uk/~dxp/prism/download.php) and PDQ
> (http://perfdynamics.com).
>
>
> Seriously, though, PRISM is a quite useful and magnificent piece of
> open-source work. Nearly all the other software in this domain
> (probabilistic model checking and Markov process modeling) is either
> commercial or tied up in an "academic (non-commercial)" non-free license
> of some kind.

Well, model checking is outside the (admittedly very narrow) scope of
software I'm interested/skilled in, which deals mostly with proof
assistant. If enough interest is shown, I could try to add them, but
after we are done with the proof assistants (another possibility would
of course be for you to become a dev yourself and maintain them :)).

Regards,
/Alexandre

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Flammie Pirinen]

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2006-06-25, George Shapovalov sanoi, jotta:

> There was a suggestion for sci-phonetics or sci-linguistics. There is
> a dev (translator's team, so he will need to be mentored for the
> "generic development") who is willing to take on those,

That would be me. Hi, all! I’d assume that the mentoring and becoming a
developer process for me will not be much different than anyone else.

> however I
> first need to see how many packages would be there. If anything it
> will be good to have him as a part of the team, even if this does not
> qualify for a full category (but still should be good for herd I
> guess..)

At current I’m only familiar with a few phonetics software, that could
be added. Also, many of the phonetics libraries are already in tree, in
app-accessibility (e.g. festival and all related stuff).

From other linguistics software I've been thinking e.g. natural
language grammar system Malaga
<http://home.arcor.de/bjoern-beutel/malaga/>, and perhaps related
grammar dictionaries. If the grammar dictionaries are added as separate
packages, they will at least increase the number of packages in
nicely :-)

-- 
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and FlameEyes’ bot <http://dev.gentoo.org/~flammie>.

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Re: [gentoo-science] sci-proof

[M. Edward (Ed) Borasky]

Alexandre Buisse wrote:
> Well, model checking is outside the (admittedly very narrow) scope of
> software I'm interested/skilled in, which deals mostly with proof
> assistant. If enough interest is shown, I could try to add them, but
> after we are done with the proof assistants (another possibility would
> of course be for you to become a dev yourself and maintain them :)).
>   
Maybe when I retire from my day job :).

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Alexandre Buisse]

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On Tue, Jun 27, 2006 at 16:16:58 +0200, Flammie Pirinen wrote:

> 2006-06-25, George Shapovalov sanoi, jotta:
> 
> > There was a suggestion for sci-phonetics or sci-linguistics. There is
> > a dev (translator's team, so he will need to be mentored for the
> > "generic development") who is willing to take on those,
> 
> That would be me. Hi, all! I’d assume that the mentoring and becoming a
> developer process for me will not be much different than anyone else.

If you don't me having only a remote interest and no real experience in
the field of linguistic software (well, I did some formal language and
grammar stuff, but nothing related to natural language), I could mentor
you.

Regards,
/Alexandre
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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Flammie Pirinen]

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2006-06-27, Alexandre Buisse sanoi, jotta:

> On Tue, Jun 27, 2006 at 16:16:58 +0200, Flammie Pirinen wrote:
> > I’d assume that the mentoring and
> > becoming a developer process for me will not be much different than
> > anyone else.
> 
> If you don't me having only a remote interest and no real experience
> in the field of linguistic software (well, I did some formal language
> and grammar stuff, but nothing related to natural language), I could
> mentor you.

Ah, I think georges has also suggested to mentor me? Either ways is
fine with me of course. I don’t know everything that mentoring process
for ebuild developers contains, but I don’t think it requires mentor to
have thorough understanding of mentee’s software as such? As long as
you are able to see that my ebuilds do not destroy everyone’s
computers, it should be fine, shouldn’t it?-)

-- 
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and FlameEyes’ bot <http://dev.gentoo.org/~flammie>.

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[George Shapovalov]

вівторок, 27. червень 2006 23:12, Flammie Pirinen Ви написали:
> Ah, I think georges has also suggested to mentor me? Either ways is
Well, strictly speaking I said "we" will mentor you ;). (btw, its george - 
georges is just my nick on irc, I had to change to it since I lost the 
original george some time ago..).

Seriously speaking, please see bug #138021
https://bugs.gentoo.org/show_bug.cgi?id=138021
and leave comments who takes whom, so that we stay organized.  Since I don't 
have any particular preferences I can simply take "the last person" :), or 
just somebody, if we don't have three mentors all at once..
But looks like we already got one (nattfodd ;)), may be spyderous or cryos 
will take je_fro (since he claims to have dealt with them)?

George

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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Donnie Berkholz]

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George Shapovalov wrote:
> But looks like we already got one (nattfodd ;)), may be spyderous or cryos 
> will take je_fro (since he claims to have dealt with them)?

I suppose I could take je_fro or jamasi, they're both working on stuff
somewhere near my areas of interest (biochemistry and crystallography).

But I can't do both! Somebody needs to pick one of them. =) It may be
that time zones overlap better with George and Jan, and me and Jeffrey.
Knowing what times the recruits are available on IRC could help.

Thanks,
Donnie


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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Jan Marten Simons]

Am Mittwoch, 28. Juni 2006 00:38 schrieb Donnie Berkholz:
> [...] It may be
> that time zones overlap better with George and Jan, and me and Jeffrey.
> Knowing what times the recruits are available on IRC could help.

For me that'd be (in Berlin-Timezone) ~14:00 to 17:00 from work and later in 
the evening and sporadic visits on weekends from home.
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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Donnie Berkholz]

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Jan Marten Simons wrote:
> Am Mittwoch, 28. Juni 2006 00:38 schrieb Donnie Berkholz:
>> [...] It may be
>> that time zones overlap better with George and Jan, and me and Jeffrey.
>> Knowing what times the recruits are available on IRC could help.
> 
> For me that'd be (in Berlin-Timezone) ~14:00 to 17:00 from work and later in 
> the evening and sporadic visits on weekends from home.

Can you translate that to UTC, e.g. with judicious use of `date -u -d
'14:00 BDT'` or whatever your timezone is?

Thanks,
Donnie


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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Jan Marten Simons]

Am Mittwoch, 28. Juni 2006 17:24 schrieb Donnie Berkholz:
> > For me that'd be (in Berlin-Timezone) ~14:00 to 17:00 from work and later
> > in the evening and sporadic visits on weekends from home.
>
> Can you translate that to UTC, e.g. with judicious use of `date -u -d
> '14:00 BDT'` or whatever your timezone is?
>
date -u -d '14:00 CEST'
Do Jun 29 12:00:00 UTC 2006
date -u -d '17:00 CEST'
Do Jun 29 15:00:00 UTC 2006

HTH,
Jan
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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[Donnie Berkholz]

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Jan Marten Simons wrote:
> Am Mittwoch, 28. Juni 2006 17:24 schrieb Donnie Berkholz:
>>> For me that'd be (in Berlin-Timezone) ~14:00 to 17:00 from work and later
>>> in the evening and sporadic visits on weekends from home.
>> Can you translate that to UTC, e.g. with judicious use of `date -u -d
>> '14:00 BDT'` or whatever your timezone is?
>>
> date -u -d '14:00 CEST'
> Do Jun 29 12:00:00 UTC 2006
> date -u -d '17:00 CEST'
> Do Jun 29 15:00:00 UTC 2006

Eek, that definitely doesn't work for me. That's 5-8 a.m. local time.

Thanks,
Donnie


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Re: [gentoo-science] Scientific Gentoo reorg: the proposal

[George Shapovalov]

четвер, 29. червень 2006 17:49, Donnie Berkholz Ви написали:
> Jan Marten Simons wrote:
> > Am Mittwoch, 28. Juni 2006 17:24 schrieb Donnie Berkholz:
> >>> For me that'd be (in Berlin-Timezone) ~14:00 to 17:00 from work and
> >>> later in the evening and sporadic visits on weekends from home.
Yes, this should be fine with me, - I am in the same timezone. As I just 
mentioned on that bug #138021 (where we were supposed to keep this 
discussion ;)) nattfodd can take flammie, it makes sense for you to take 
je_fro and then I can take jamasi.

Alexandre, Donnie: please open the bugs with recruiters, as usual when you are 
ready. No real push to start ASAP considering the season and the reorg stuff, 
lets just not forget about this..

George

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