[Biococoa-dev] More goodies!!

Charles Parnot charles.parnot at gmail.com
Mon Mar 6 12:49:02 EST 2006

I don't think we need 2 repositories. Subversion is very convenient  
for branches and tags. I think Alex's final code should be included  
"as is" in the current svn directory, as a side project of BioCocoa,  
because this is usable-right-now tested code, just like BioCocoa 1.6  
is. I would do the following structure in the repository, something  
close to the usual "recommanded" layout:

......[Checkout of the latest CVS repository]
......BioCocoa 1.6   <-- BCReader from Peter
......BioCocoa 1.7   <-- BCReader from Alex
.........EntrezController 1.0  <--- From Alex
.........KDTextView 1.0   <-- From Koen
.........KDTextView 1.1   <-- From Alex

The "Goodies" directory could be named something else, like  
"Subprojects" or whatever you like, and might alternatively be moved  
to the root (under BioCocoa), and have its own Trunk, Tags and Branches.

The "Branches" directory is empty right now, but might soon have a  
"BioCocoa 1.x" branch if we want to fix bugs / add features on the  
1.7 version, and/or have a "Goodies/KDTextView 1.x" branch for the  
same reasons. Of course, the code for these should be merged in the  
BioCocoa Trunk as soon as possible too, and we probably don't want to  
generate too much code on the 1.x versions.

Let's take advantage of super-easy management of Tags and Branches  
with Subversion... Just my 2 cents!


On Mar 6, 2006, at 4:33 AM, Peter Schols wrote:

> Hi Alex and other listers,
> This BCAppkitTest works great and it will be a great addition to  
> BioCocoa!
> Over the weekend, I have worked with the - very helpful - people at  
> Bioinformatics.org to solve my login problems (it turned out to be  
> a proxy issue that was caused by a bug on their end, they have been  
> able to fix it).
> As a result, I am totally ready to start the subversion repository  
> and do the initial import.
> The main question I have now is: how should we organise the  
> repository and the BioCocoa website? There are several scenarios:
> 1. Checkout the latest version of the BioCocoa framework from CVS  
> and use that as the initial import for SVN. Make the BCAppkitTest  
> available as a download on our website (both source and compiled  
> app) but wait to put it in the repository until it's adapted to use  
> the classes in our own framework.
> 2. Checkout the latest version of the BioCocoa framework from CVS  
> and use that as the initial import for SVN. Make a second  
> repository (I think this is possible @ bioinformatics.org) and put  
> BCAppkitTest in there.
> 3. Checkout the latest version of the BioCocoa framework from CVS,  
> add the BCAppkitTest somewhere in the hierarchy of that same  
> BioCocoa folder and check this hybrid framework in to one repository.
> I think I'd prefer solution number 1 (or 2) because
> - it seems a bit weird to have part of a framework that does not  
> use the base classes available in the rest of the framework
> - it might confuse users of the framework
> - we should aim to integrate BCAppkitTest into BioCocoa asap, this  
> won't be a huge undertaking
> Please let me know your preference and I would be glad to create  
> the Subversion repository and send instructions on using it. I'd  
> also be glad to update the website and make the BCAppkitTest  
> available.
> Peter
> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote:
>> Hi guys,
>> With EnzymeX3 now in beta testing phase it's time to share the  
>> wealth...
>> I've thrown together a very simple demo app showing the three  
>> goodies I would like to donate back to the BioCocoa project:
>> 	- BCReader, the standalone BCReader classes for sequence file IO  
>> (original version Peter Schols)
>> 	- EntrezController, a controller plus view for browsing and  
>> fetching NCBI's Entrez Database
>> 	- KDTextView+, a custom NSTextView for displaying biological  
>> sequences (original version Koen van der Drift)
>> Download and enjoy at: http://www.mekentosj.com/biococoa/ 
>> BCAppkit_Test.dmg
>> Of course all feedback and bug reports are welcome (or not  
>> depending on how you interpret this sentence ;-)
>> Also, coming back to Koen's remark. There are a few things I/we  
>> could do.
>> First, it would be nice if it had these views mentioned as  
>> available on the website and the code given a place on the svn  
>> server.
>> Second, we could perhaps post a small announcement (few lines) on  
>> cocoa-dev to notify other cocoa developers, also letting them know  
>> about BioCocoa again.
>> Finally, we could compose a little message to MacResearch  
>> describing the BioCocoa project and also the availability of this  
>> code.
>> Alternatively, I can inform them about it when we release the  
>> EnzymeX final version. I believe Tom spoke a few times with the  
>> guys behind MacResearch, so we could inform them directly.. Let me  
>> know what you guys think.
>> Cheers,
>> Alex
>> *********************************************************
>>                     ** Alexander Griekspoor **
>> *********************************************************
>>               The Netherlands Cancer Institute
>>               Department of Tumorbiology (H4)
>>          Plesmanlaan 121, 1066 CX, Amsterdam
>>                    Tel:  + 31 20 - 512 2023
>>                   Fax:  + 31 20 - 512 2029
>>                   AIM: mekentosj at mac.com
>>                  E-mail: a.griekspoor at nki.nl
>>               Web: http://www.mekentosj.com
>>               4Peaks - For Peaks, Four Peaks.
>>        2004 Winner of the Apple Design Awards
>>                Best Mac OS X Student Product
>>              http://www.mekentosj.com/4peaks
>> *********************************************************
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Help science move fast forward:

Charles Parnot
charles.parnot at gmail.com

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