[gentoo-science] Gentoo scientific overlay

[gentoo-science] Gentoo scientific overlay

[Marcus D. Hanwell]

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Hi Guys,

I just wanted to announce that I have set up an overlay for scientific 
applications in Gentoo. This is something ribosome and I discussed quite some 
time ago, and I recently set up an SVN repository and a trac site for it.

http://gentooscience.org/

Our two herd testers and I have commit access to it right now. Any other 
science herd members are welcome to accounts (please email me off list to get 
it set up). It is in the early stages and so I am open to suggestions.

I was considering the possibility of using a repo specific keyword in ebuilds 
such as ~sci so that any herd testers and/or users can add that to their 
ACCEPT_KEYWORDS in /etc/make.conf (as well as maintaining normal keyword 
practices). The intention is to add stuff to the repo for testing before it 
is ready to go into portage. Some stuff that we just can't maintain for 
whatever reason could possibly end up in their more permanently too.

It provides a great way to train herd testers in a safer (than the main 
portage tree) repository and develop ebuilds more interactively. Once stuff 
is moved into the portage tree it should of course be deleted from the 
repository.

I would welcome any feedback you guys might have. It is pretty easy to check 
out a copy of it and keep it up to date - I put instructions on the site. Be 
warned that the ebuilds in the overlay will generally be more experimental 
and may need work. Tickets can be opened for ebuilds in the overlay, but new 
ebuilds and bugs on ebuilds in portage should still be reported in the normal 
way through bugzilla. When ebuilds are added to the overlay the bug will have 
a comment added with words to that effect.

Thanks,

Marcus

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Re: [gentoo-science] Gentoo scientific overlay

[Donnie Berkholz]

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Marcus D. Hanwell wrote:
| I was considering the possibility of using a repo specific keyword in
ebuilds
| such as ~sci so that any herd testers and/or users can add that to their
| ACCEPT_KEYWORDS in /etc/make.conf (as well as maintaining normal keyword
| practices). The intention is to add stuff to the repo for testing
before it
| is ready to go into portage. Some stuff that we just can't maintain for
| whatever reason could possibly end up in their more permanently too.

I don't really see the point of ~sci, since the rest of the ebuild will
probably need to get diffed against the regular tree anyway if there are
any changes.

How do you plan to keep this in sync with changes in the regular tree?
How is our own solution superior to getting together with gentopia or
something similar that already exists?

| It provides a great way to train herd testers in a safer (than the main
| portage tree) repository and develop ebuilds more interactively. Once
stuff
| is moved into the portage tree it should of course be deleted from the
| repository.

OK, so this overlay is only for new packages, and not for changes to
existing ones?

Thanks,
Donnie
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Re: [gentoo-science] Gentoo scientific overlay

[Marcus D. Hanwell]

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On Sunday 11 December 2005 22:27, Donnie Berkholz wrote:
> Marcus D. Hanwell wrote:
> | I was considering the possibility of using a repo specific keyword in>
> ebuilds
> | such as ~sci so that any herd testers and/or users can add that to their
> | ACCEPT_KEYWORDS in /etc/make.conf (as well as maintaining normal keyword
> | practices). The intention is to add stuff to the repo for testing
> before it
>
> | is ready to go into portage. Some stuff that we just can't maintain for
> | whatever reason could possibly end up in their more permanently too.
>
> I don't really see the point of ~sci, since the rest of the ebuild will
> probably need to get diffed against the regular tree anyway if there are
> any changes.

The ~sci would get removed, but it would be a one line difference that would 
be spotted quite easily. Ebuilds would still need the relevant archs to add 
their keywords when it went into the tree but it would give an easy way for 
people to emerge stuff from the overlay that might not have their keyword.
>
> How do you plan to keep this in sync with changes in the regular tree?
> How is our own solution superior to getting together with gentopia or
> something similar that already exists?
>
Like I said anything that gets moved into portage will be deleted from the 
overlay. I could probably write a script to check for conflicts but I didn't 
envisage this being a major problem. I don't think it is necessarily superior 
to gentopia or the php overlay - what would be the advantage of getting 
together with them?

I have talked with some of the PHP and Apache guys about their overlay.

> | It provides a great way to train herd testers in a safer (than the main
> | portage tree) repository and develop ebuilds more interactively. Once
> stuff
>
> | is moved into the portage tree it should of course be deleted from the
> | repository.
>
> OK, so this overlay is only for new packages, and not for changes to
> existing ones?
>
Originally it was intended for new ebuilds, alphas, betas (e.g. the grace 
betas) and experimental stuff. I thought it would be a good place to try 
things out, and once they were working to put into portage. Also as a good 
place to help train new developers that come to the herd and foster a greater 
range of scientific applications in Gentoo.

Thanks,

Marcus

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Re: [gentoo-science] Gentoo scientific overlay

[Donnie Berkholz]

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Marcus D. Hanwell wrote:
| On Sunday 11 December 2005 22:27, Donnie Berkholz wrote:
|>How do you plan to keep this in sync with changes in the regular tree?
|>How is our own solution superior to getting together with gentopia or
|>something similar that already exists?
|>
|
| Like I said anything that gets moved into portage will be deleted from
the
| overlay. I could probably write a script to check for conflicts but I
didn't
| envisage this being a major problem. I don't think it is necessarily
superior
| to gentopia or the php overlay - what would be the advantage of getting
| together with them?

No need to maintain duplicate infrastructures.

|>OK, so this overlay is only for new packages, and not for changes to
|>existing ones?
|>
|
| Originally it was intended for new ebuilds, alphas, betas (e.g. the grace
| betas) and experimental stuff. I thought it would be a good place to try
| things out, and once they were working to put into portage. Also as a
good
| place to help train new developers that come to the herd and foster a
greater
| range of scientific applications in Gentoo.

OK. I can definitely see training. Some people do prefer overlays for
ebuilds in progress, but I prefer -* keywords and keeping them in the
tree so all the history stays in the same place. In the same vein, I use
package.mask for beta's rather than a separate overlay.

Thanks,
Donnie
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Re: [gentoo-science] Gentoo scientific overlay

[Patrick Kursawe]

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Hi all,

On Sun, Dec 11, 2005 at 08:28:34PM +0000, Marcus D. Hanwell wrote:
[scientific overlay] 
> I would welcome any feedback you guys might have. It is pretty easy to check 
> out a copy of it and keep it up to date - I put instructions on the site. Be 
> warned that the ebuilds in the overlay will generally be more experimental 
> and may need work.

Don't want to discourage anyone, but looking at the bugzilla lists for the
sci herd I get the impression that there's still quite a lot to do about
the existing ebuilds in the tree - do you really think that more
experimental stuff is the right priority?

I am not in the position to complain since I have been rather idle in the
last months (work is eating up my time) and I don't want you to get the
impression that I am trying to tell you what to do. 

Just wondering,

Patrick     

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Re: [gentoo-science] Gentoo scientific overlay

[Lucas Chiesa]

Patrick,

The idea of the overlay is not just to add new ebuilds, but to test
new patches or ebuilds for the existing packages. I'm also very busy
lately, but the idea is to fix the existing bugs and then add new
packages, and the overlay is a great place to put all our work, it is
really easy for us to test the work of others, and, with some luck,
users will use the overlay and thus test even more the ebuilds before
being in portage, improving the quality of the stable ebuilds.

Best wishes,

Lucas Chiesa (tulku)

On 12/12/05, Patrick Kursawe <phosphan@gentoo.org> wrote:
> Hi all,
>
> On Sun, Dec 11, 2005 at 08:28:34PM +0000, Marcus D. Hanwell wrote:
> [scientific overlay]
> > I would welcome any feedback you guys might have. It is pretty easy to check
> > out a copy of it and keep it up to date - I put instructions on the site. Be
> > warned that the ebuilds in the overlay will generally be more experimental
> > and may need work.
>
> Don't want to discourage anyone, but looking at the bugzilla lists for the
> sci herd I get the impression that there's still quite a lot to do about
> the existing ebuilds in the tree - do you really think that more
> experimental stuff is the right priority?
>
> I am not in the position to complain since I have been rather idle in the
> last months (work is eating up my time) and I don't want you to get the
> impression that I am trying to tell you what to do.
>
> Just wondering,
>
> Patrick
>
>
>

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Re: [gentoo-science] Gentoo scientific overlay

[Jan Marten Simons]

Marcus D. Hanwell wrote:

>... but new ebuilds and bugs on ebuilds in portage should still be reported in the normal way through bugzilla. When ebuilds are added to the overlay the bug will have a comment added with words to that effect.
>  
>
These ebuilds could be added to the overlay:

http://bugs.gentoo.org/show_bug.cgi?id=80464
http://bugs.gentoo.org/show_bug.cgi?id=77969
http://bugs.gentoo.org/show_bug.cgi?id=116146
http://bugs.gentoo.org/show_bug.cgi?id=116142
http://bugs.gentoo.org/show_bug.cgi?id=116143
http://bugs.gentoo.org/show_bug.cgi?id=116144

Some of them will need some scrubbing, but on my box they build (and 
seem to work).

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Re: [gentoo-science] Gentoo scientific overlay

[Donnie Berkholz]

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Jan Marten Simons wrote:
| These ebuilds could be added to the overlay:
|
| http://bugs.gentoo.org/show_bug.cgi?id=80464
| http://bugs.gentoo.org/show_bug.cgi?id=77969
| http://bugs.gentoo.org/show_bug.cgi?id=116146
| http://bugs.gentoo.org/show_bug.cgi?id=116142
| http://bugs.gentoo.org/show_bug.cgi?id=116143
| http://bugs.gentoo.org/show_bug.cgi?id=116144
|
| Some of them will need some scrubbing, but on my box they build (and
| seem to work).

I plan to take those and get them into the tree soon, probably they
won't need to go in the overlay.

Thanks,
Donnie
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