[Biococoa-dev] More goodies!!

Peter Schols peter.schols at bio.kuleuven.be
Mon Mar 6 14:04:30 EST 2006 

Hi Charles,

If I get you right, you would prefer option 3, so you'd move the  
"AlexCode" to a separate folder in the trunk?
I'm a bit confused... sorry

Peter



On 06 Mar 2006, at 18:49, Charles Parnot wrote:

> 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:
>
> BioCoao
> ...Trunk
> ......
> ......[Checkout of the latest CVS repository]
> ......
> ...Tags
> ......BioCocoa 1.6   <-- BCReader from Peter
> ......BioCocoa 1.7   <-- BCReader from Alex
> ......Goodies
> .........EntrezController 1.0  <--- From Alex
> .........KDTextView 1.0   <-- From Koen
> .........KDTextView 1.1   <-- From Alex
> ...Branches
> ......Goodies
>
>
> 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!
>
> charles
>
>
> 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
>>>
>>> *********************************************************
>>>
>>> _______________________________________________
>>> Biococoa-dev mailing list
>>> Biococoa-dev at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>>>
>>
>>
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>
> --
> Xgrid-at-Stanford
> Help science move fast forward:
> http://cmgm.stanford.edu/~cparnot/xgrid-stanford
>
> Charles Parnot
> charles.parnot at gmail.com
>
>
>
>
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