[Open Babel] Re: Wiki documentation?

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[Open Babel] Re: Wiki documentation?

Geoffrey Hutchison

As we finish up docs for the 2.0 release and an updated website, I  
wondered about converting the website to a wiki. To prevent spam,  
you'd probably have to sign in or something.

* Do you think this is a good idea?

* If there was an Open Babel wiki, would you personally contribute to  
it. (i.e., correct mistakes, add documentation, links, etc.)

* If you've used wiki software before, is there a particular package  
you think is best.

I'm hoping to lower the bar to contributions -- and thought this was  
a fun way to do it. :-)

Thanks,
-Geoff


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Re: [Open Babel] Re: Wiki documentation?

Vincent Favre-Nicolin-2
On Lundi 14 Novembre 2005 21:00, Geoffrey Hutchison wrote:
> As we finish up docs for the 2.0 release and an updated website, I
> wondered about converting the website to a wiki. To prevent spam,
> you'd probably have to sign in or something.
>
> * Do you think this is a good idea?

   yes!

> * If there was an Open Babel wiki, would you personally contribute to
> it. (i.e., correct mistakes, add documentation, links, etc.)
>
> * If you've used wiki software before, is there a particular package
> you think is best.

   I've been using moinmoin (http://moinmoin.wikiwikiweb.de) for Fox for a few
months now, and it works quite well on the sourceforge web site. It's one of
the most popular wiki engines, and it is easy to configure, either in python
or simply using css. You can look at http://objcryst.sourceforge.net/Fox/,
which is nicer (I hope) that the original site (though there are many other
"skins" available) - anyway it's easy to change the look. In fact I'm using
the wiki as the main manual for my program now.

   There are a few security gotchas, basically because the wiki pages are
world-writable on the server - since it is the "nfsnobody" user which writes
the pages on the webserver. You have to maintain a copy of the files (this
would be true for any wiki engine). I have a daily rsync, plus a
weekly/monthly archive of the wiki. So far only once have they been wiped
(2005/08/31), so it's not too bad. Not very fast, but with the web servers
nothing is real fast - the pages are generated only when necessary and then
cached, so it's reasonably optimized !
   Also for spam, I have never add any problem so far, despite the fact that
anybody can change the wiki pages. There is an antispam module in the wiki
which checks against known patterns (links to website) and can reject the
page if necessary).

   If you want, I can set up a test wiki for OB. It's real easy
(http://moinmoin.wikiwikiweb.de/SourceForge). I'd probably put the 1.5beta3
version (which my site runs now), which is reasonably mature, and includes a
GUI editor (not very fast to load), so that you don't need to learn all the
wiki syntax.

   I'm not sure restricting edition to a few users is really necessary - I
have not had any problem so far. You *can* use a a variety of permissions,
though.

        Vincent

PS: Geoff, thanks for the answer about the F-H z-matrix the other day.
Ultimately I'll directly link to OB in Fox, but I have not got around to do
that, mostly due to the lack of time to test it on different platforms
(windows mostly, Ilinux & OSX should be easy).
--
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net


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Re: [Open Babel] Re: Wiki documentation?

Vincent Favre-Nicolin-2
> I've never been a huge fan of wiki syntax, particularly the
> NameAPageWithMixedCaps bit. I was also looking at PHPWiki, which is
> used for the gcc web site (http://gcc.gnu.org/wiki) and clearly
> allows links and pages to have spaces in their names.

   The WikiName is the standard for wiki pages names, but you can perfectly
display a different, e.g. if you have a "SmilesFormat" wiki page, you can
also link to it using [:SmilesFormat:SMILES format], and the link will appear
as "SMILES format". I belive you must do that for all wiki engines.
   Also, it should be easier using the GUI wiki editor, which removes the need
to learn all the wiki syntax.

> One downside is that there will be a good number of pages to import
> with the auto-generated format documentation.

   Yes, but it is mostly plain text so it's not that difficult.

> Thanks for your suggestion -- I'll check out MoinMoin too. My guess
> is that sometime this winter I'll set up a test wiki and start
> importing some of the documentation. I'd particularly like for the
> format documentation to start listing limitations (e.g., SMILES
> doesn't store coordinates, our Gaussian code writes isotopes, etc.)

   Sure, if you need help (if you choose moin on sourceforge) just ask.

        Vincent
--
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net


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Re: [Open Babel] Re: Wiki documentation?

peter murray-rust
In reply to this post by Geoffrey Hutchison
At 20:00 14/11/2005, Geoffrey Hutchison wrote:

>As we finish up docs for the 2.0 release and an updated website, I
>wondered about converting the website to a wiki. To prevent spam,
>you'd probably have to sign in or something.
>
>* Do you think this is a good idea?

It's a really good idea. For OB it is natural to have one page per
format (and some others)


>* If there was an Open Babel wiki, would you personally contribute to
>it. (i.e., correct mistakes, add documentation, links, etc.)

Yes

>* If you've used wiki software before, is there a particular package
>you think is best.
We use moin (see http://wwmm.ch.cam.ac.uk/moin)



>I'm hoping to lower the bar to contributions -- and thought this was
>a fun way to do it. :-)

I believe that there won't be very much graffiti, but institutions
can't always take the risk - who would host this?

P.

>Thanks,
>-Geoff
>
>
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Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069



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Re: [Open Babel] Re: Wiki documentation?

Geoffrey Hutchison

On Nov 18, 2005, at 6:23 PM, peter murray-rust wrote:

> I believe that there won't be very much graffiti, but institutions  
> can't always take the risk - who would host this?

The Wiki would be hosted on SourceForge.net, like the rest of the  
Open Babel pages.

I'm not worried so much about "risk" as "how often will someone need  
to check recent changes to prevent spam, vandalism, etc." Sounds like  
it might not be too bad.

Cheers,
-Geoff


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Re: [Open Babel] Re: Wiki documentation?

Vincent Favre-Nicolin
On Samedi 19 Novembre 2005 20:08, Geoffrey Hutchison wrote:
> I'm not worried so much about "risk" as "how often will someone need
> to check recent changes to prevent spam, vandalism, etc." Sounds like
> it might not be too bad.

   So far for me nor problem, spam or vandalism. I heard of problems before
(e.g. on the mayavi.sf.net wiki), but that was with a previous release of
moinmoin.
   It is also possible to restrict publication/ adding attachments to a given
list of wiki users, if needs be.
   As for checking, I have a script to rsync locally the wiki, and mail me
every day/week when any page has changed - so checking is automatic.

        Vincent
--
Vincent Favre-Nicolin

CEA/Grenoble   DRFMC/SP2M               http://www-drfmc.ceng.cea.fr/
DRFMC/SP2M/Nano-structures et Rayonnement Synchrotron
17, rue des Martyrs 38054 Grenoble Cedex 9
38054 Grenoble Cedex 9 - France

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