From koenvanderdrift at gmail.com  Sat May 28 14:37:58 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Sat, 28 May 2011 14:37:58 -0400
Subject: [Biococoa-dev] modernizing BioCocoa
Message-ID: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>

All,

I recently started looking again at Cocoa programming, and what better
way to dive back into BioCocoa to get my memory refreshed!  While
reading some current Cocoa docs from Apple, I learned that since my
absence many new features have been added to ObjC, now called ObjC2.
Probably nothing new for y'all :)

Things I'm talking about are fast enumeration, garbage collecting,
properties, cleaning up warnings because of deprecated methods, and
maybe more.

So, I was thinking as a first task for me is to go through the
framework, and implement/update the code with (some of) the above
mentioned features.  This would also mean that the lowest OS that
BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
introduced.

Are there any objections to this plan? I could for instance make a new
branch for this, maybe tagged version 2.5 or 3.0?

Thanks,

- Koen.



From craig.bateman at me.com  Sat May 28 21:05:39 2011
From: craig.bateman at me.com (Craig Bateman)
Date: Sat, 28 May 2011 18:05:39 -0700
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
Message-ID: <DEE8DF77-9AF3-4D44-BD54-B173B518A387@me.com>

I looked at doing a lot of these things when I first joined, but with the requirement that everything be able to compile by gnu objc+openstep I didn't know what's allowed or not and then life got in my way and I haven't even looked at the code I started to branch so long ago...  

Sent from my iPhone

On May 28, 2011, at 11:37 AM, Koen van der Drift <koenvanderdrift at gmail.com> wrote:

> All,
> 
> I recently started looking again at Cocoa programming, and what better
> way to dive back into BioCocoa to get my memory refreshed!  While
> reading some current Cocoa docs from Apple, I learned that since my
> absence many new features have been added to ObjC, now called ObjC2.
> Probably nothing new for y'all :)
> 
> Things I'm talking about are fast enumeration, garbage collecting,
> properties, cleaning up warnings because of deprecated methods, and
> maybe more.
> 
> So, I was thinking as a first task for me is to go through the
> framework, and implement/update the code with (some of) the above
> mentioned features.  This would also mean that the lowest OS that
> BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
> introduced.
> 
> Are there any objections to this plan? I could for instance make a new
> branch for this, maybe tagged version 2.5 or 3.0?
> 
> Thanks,
> 
> - Koen.
> 
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
> 
> 



From koenvanderdrift at gmail.com  Sat May 28 21:53:03 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Sat, 28 May 2011 21:53:03 -0400
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <DEE8DF77-9AF3-4D44-BD54-B173B518A387@me.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
	<DEE8DF77-9AF3-4D44-BD54-B173B518A387@me.com>
Message-ID: <BANLkTin5pJzCzzkZHcr-eZtuwxbOi9qGEg@mail.gmail.com>

On Sat, May 28, 2011 at 9:05 PM, Craig Bateman <craig.bateman at me.com> wrote:
> I looked at doing a lot of these things when I first joined, but with the requirement that everything be able to compile by gnu objc+openstep

Yeah, good point. I may just keep a local copy for myself with all the
updates, so I won't interfere with the other targets. I can always
commit them if needed.

- Koen.



From schristley at mac.com  Sat May 28 22:23:24 2011
From: schristley at mac.com (Scott Christley)
Date: Sat, 28 May 2011 21:23:24 -0500
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
Message-ID: <3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>

Hi Koen,

Making a svn branch is a good idea, then you can work and still commit changes as you get milestones done.  If you are not sure how to create, I can send instructions.  There is an open-source ObjC2 being actively written by the llvm/clang folks, and they have been working so that it can compile all of GNUstep, but I'm not sure it is at production level yet.

Personally I would avoid garbage collecting, there is already a solid retain-release implementation with minimal leaks, and there are numerous places where autorelease pools are used to manage large chunks of temporary objects (like parsing data files), this is more efficient memory management for that time of stuff.

Cleaning up warnings would definitely be great.  Properties... maybe, but doesn't add a whole lot.  Fast enumeration is probably nice.  There is always documentation :-)  Even better is if you have the time/inclination to add some new functionality, I have a whole slew of ideas from quick to hard.

cheers
Scott

On May 28, 2011, at 1:37 PM, Koen van der Drift wrote:

> All,
> 
> I recently started looking again at Cocoa programming, and what better
> way to dive back into BioCocoa to get my memory refreshed!  While
> reading some current Cocoa docs from Apple, I learned that since my
> absence many new features have been added to ObjC, now called ObjC2.
> Probably nothing new for y'all :)
> 
> Things I'm talking about are fast enumeration, garbage collecting,
> properties, cleaning up warnings because of deprecated methods, and
> maybe more.
> 
> So, I was thinking as a first task for me is to go through the
> framework, and implement/update the code with (some of) the above
> mentioned features.  This would also mean that the lowest OS that
> BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
> introduced.
> 
> Are there any objections to this plan? I could for instance make a new
> branch for this, maybe tagged version 2.5 or 3.0?
> 
> Thanks,
> 
> - Koen.
> 
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev




From charles.parnot at gmail.com  Sat May 28 22:47:31 2011
From: charles.parnot at gmail.com (Charles Parnot)
Date: Sat, 28 May 2011 19:47:31 -0700
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
	<3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
Message-ID: <02BCC856-D727-4868-9D52-3E2E445ED387@gmail.com>

My 2 cents: there are still many GC-only bugs in Apple's frameworks, particularly those built on top of CoreFoundation, but it does not seem BioCocoa has too many dependencies on those. The main question for GC is that given the framework status of BioCocoa, this means that GC-only or non-GC restricts its use to applications that are built in either configuration. For a framework, there are actually good reasons to support both, since it allows its use for both types of apps, memory-managed or GC-based. To support both, you can basically write everything as if it was memory-managed and then it should be good for GC as well, except maybe in a few places (and except for potential performance tuning). The framework build settings can thus be set to support both, and should be tested under both environments. So basically, keep the good habits of the memory-managed style.

Properties can be added, but that's less problematic. It's mostly an issue of consistency: if you have properties somewhere, they should be everywhere, as otherwise, it makes the APIs harder to learn and use. But it's nice to have for sure.

Fast enumaration is a no-brainer, nicer and faster code.

Building for 64 bits is something to check as well, make sure it works. And then check the box.

Dropping PPC??

charles



On May 28, 2011, at 7:23 PM, Scott Christley wrote:

> Hi Koen,
> 
> Making a svn branch is a good idea, then you can work and still commit changes as you get milestones done.  If you are not sure how to create, I can send instructions.  There is an open-source ObjC2 being actively written by the llvm/clang folks, and they have been working so that it can compile all of GNUstep, but I'm not sure it is at production level yet.
> 
> Personally I would avoid garbage collecting, there is already a solid retain-release implementation with minimal leaks, and there are numerous places where autorelease pools are used to manage large chunks of temporary objects (like parsing data files), this is more efficient memory management for that time of stuff.
> 
> Cleaning up warnings would definitely be great.  Properties... maybe, but doesn't add a whole lot.  Fast enumeration is probably nice.  There is always documentation :-)  Even better is if you have the time/inclination to add some new functionality, I have a whole slew of ideas from quick to hard.
> 
> cheers
> Scott
> 
> On May 28, 2011, at 1:37 PM, Koen van der Drift wrote:
> 
>> All,
>> 
>> I recently started looking again at Cocoa programming, and what better
>> way to dive back into BioCocoa to get my memory refreshed!  While
>> reading some current Cocoa docs from Apple, I learned that since my
>> absence many new features have been added to ObjC, now called ObjC2.
>> Probably nothing new for y'all :)
>> 
>> Things I'm talking about are fast enumeration, garbage collecting,
>> properties, cleaning up warnings because of deprecated methods, and
>> maybe more.
>> 
>> So, I was thinking as a first task for me is to go through the
>> framework, and implement/update the code with (some of) the above
>> mentioned features.  This would also mean that the lowest OS that
>> BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
>> introduced.
>> 
>> Are there any objections to this plan? I could for instance make a new
>> branch for this, maybe tagged version 2.5 or 3.0?
>> 
>> Thanks,
>> 
>> - Koen.
>> 
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
> 
> 
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev

--
Charles Parnot
charles.parnot at gmail.com
twitter: @cparnot
http://mekentosj.com





From koenvanderdrift at gmail.com  Sat May 28 23:03:31 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Sat, 28 May 2011 23:03:31 -0400
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
	<3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
Message-ID: <BANLkTi=NFcn+bSjfkJrX-VuqD4noVqJAeQ@mail.gmail.com>

Hi Scott,

Yes, please send me instructions on how to make a svn branch. I'm
still reading on all the new stuff of ObjC2 and trying to get my head
around all of it, so it may be a while before I start committing
things.  Maybe you can add some of your ideas for new functionality to
a todo list in the repository?

I'll start with fast enumerations, deprecated methods, and maybe
properties for a cleaner code.

- Koen.



On Sat, May 28, 2011 at 10:23 PM, Scott Christley <schristley at mac.com> wrote:
> Hi Koen,
>
> Making a svn branch is a good idea, then you can work and still commit changes as you get milestones done. ?If you are not sure how to create, I can send instructions. ?There is an open-source ObjC2 being actively written by the llvm/clang folks, and they have been working so that it can compile all of GNUstep, but I'm not sure it is at production level yet.
>
> Personally I would avoid garbage collecting, there is already a solid retain-release implementation with minimal leaks, and there are numerous places where autorelease pools are used to manage large chunks of temporary objects (like parsing data files), this is more efficient memory management for that time of stuff.
>
> Cleaning up warnings would definitely be great. ?Properties... maybe, but doesn't add a whole lot. ?Fast enumeration is probably nice. ?There is always documentation :-) ?Even better is if you have the time/inclination to add some new functionality, I have a whole slew of ideas from quick to hard.
>
> cheers
> Scott
>
> On May 28, 2011, at 1:37 PM, Koen van der Drift wrote:
>
>> All,
>>
>> I recently started looking again at Cocoa programming, and what better
>> way to dive back into BioCocoa to get my memory refreshed! ?While
>> reading some current Cocoa docs from Apple, I learned that since my
>> absence many new features have been added to ObjC, now called ObjC2.
>> Probably nothing new for y'all :)
>>
>> Things I'm talking about are fast enumeration, garbage collecting,
>> properties, cleaning up warnings because of deprecated methods, and
>> maybe more.
>>
>> So, I was thinking as a first task for me is to go through the
>> framework, and implement/update the code with (some of) the above
>> mentioned features. ?This would also mean that the lowest OS that
>> BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
>> introduced.
>>
>> Are there any objections to this plan? I could for instance make a new
>> branch for this, maybe tagged version 2.5 or 3.0?
>>
>> Thanks,
>>
>> - Koen.
>>
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>
>



From schristley at mac.com  Sat May 28 23:09:24 2011
From: schristley at mac.com (Scott Christley)
Date: Sat, 28 May 2011 22:09:24 -0500
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <BANLkTi=NFcn+bSjfkJrX-VuqD4noVqJAeQ@mail.gmail.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
	<3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
	<BANLkTi=NFcn+bSjfkJrX-VuqD4noVqJAeQ@mail.gmail.com>
Message-ID: <D0595B03-BEEB-43AD-BBCA-4021DCFBA8C4@mac.com>

Hi Koen,

So the instructions to make an SVN branch can essentially be taken from the SVN repository tasks in the release checklist off the wiki:

http://www.bioinformatics.org/biococoa/wiki/pmwiki.php?n=Main.ReleaseChecklist

The basic idea is go to the BioCocoa directory, issue an svn copy command for the trunk into the branches directory, then commit

svn copy trunk branches/libobjc2-work
svn commit -m "Koen's branch..."

then you can work in that branch directory just like normal.

cheers
Scott

On May 28, 2011, at 10:03 PM, Koen van der Drift wrote:

> Hi Scott,
> 
> Yes, please send me instructions on how to make a svn branch. I'm
> still reading on all the new stuff of ObjC2 and trying to get my head
> around all of it, so it may be a while before I start committing
> things.  Maybe you can add some of your ideas for new functionality to
> a todo list in the repository?
> 
> I'll start with fast enumerations, deprecated methods, and maybe
> properties for a cleaner code.
> 
> - Koen.
> 
> 
> 
> On Sat, May 28, 2011 at 10:23 PM, Scott Christley <schristley at mac.com> wrote:
>> Hi Koen,
>> 
>> Making a svn branch is a good idea, then you can work and still commit changes as you get milestones done.  If you are not sure how to create, I can send instructions.  There is an open-source ObjC2 being actively written by the llvm/clang folks, and they have been working so that it can compile all of GNUstep, but I'm not sure it is at production level yet.
>> 
>> Personally I would avoid garbage collecting, there is already a solid retain-release implementation with minimal leaks, and there are numerous places where autorelease pools are used to manage large chunks of temporary objects (like parsing data files), this is more efficient memory management for that time of stuff.
>> 
>> Cleaning up warnings would definitely be great.  Properties... maybe, but doesn't add a whole lot.  Fast enumeration is probably nice.  There is always documentation :-)  Even better is if you have the time/inclination to add some new functionality, I have a whole slew of ideas from quick to hard.
>> 
>> cheers
>> Scott
>> 
>> On May 28, 2011, at 1:37 PM, Koen van der Drift wrote:
>> 
>>> All,
>>> 
>>> I recently started looking again at Cocoa programming, and what better
>>> way to dive back into BioCocoa to get my memory refreshed!  While
>>> reading some current Cocoa docs from Apple, I learned that since my
>>> absence many new features have been added to ObjC, now called ObjC2.
>>> Probably nothing new for y'all :)
>>> 
>>> Things I'm talking about are fast enumeration, garbage collecting,
>>> properties, cleaning up warnings because of deprecated methods, and
>>> maybe more.
>>> 
>>> So, I was thinking as a first task for me is to go through the
>>> framework, and implement/update the code with (some of) the above
>>> mentioned features.  This would also mean that the lowest OS that
>>> BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
>>> introduced.
>>> 
>>> Are there any objections to this plan? I could for instance make a new
>>> branch for this, maybe tagged version 2.5 or 3.0?
>>> 
>>> Thanks,
>>> 
>>> - Koen.
>>> 
>>> _______________________________________________
>>> Biococoa-dev mailing list
>>> Biococoa-dev at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>> 
>> 




From koenvanderdrift at gmail.com  Sat May 28 23:56:30 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Sat, 28 May 2011 23:56:30 -0400
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <D0595B03-BEEB-43AD-BBCA-4021DCFBA8C4@mac.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
	<3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
	<BANLkTi=NFcn+bSjfkJrX-VuqD4noVqJAeQ@mail.gmail.com>
	<D0595B03-BEEB-43AD-BBCA-4021DCFBA8C4@mac.com>
Message-ID: <BANLkTikr62MHLkS62Oqmq6SQR6t1o40sOw@mail.gmail.com>

Thanks Scott, I just committed a first set of updates. It turns out
that a lot of the for, while, or do loops in the framework are not so
straightforward, so I may just leave them as they are. FE only seems
to be for simple enumerations. But someone please correct me if this
is not the case.

I also noticed several macros to manipulate arrays in GNUStep, e.g.
ARRAY_GET_VALUE_AT_INDEX as an alternative to CoreFoundation. Does
GNUStep support FE, and if so, can those macros be replaced by FE?

Thanks,

- Koen.

On Sat, May 28, 2011 at 11:09 PM, Scott Christley <schristley at mac.com> wrote:
> Hi Koen,
>
> So the instructions to make an SVN branch can essentially be taken from the SVN repository tasks in the release checklist off the wiki:
>
> http://www.bioinformatics.org/biococoa/wiki/pmwiki.php?n=Main.ReleaseChecklist
>
> The basic idea is go to the BioCocoa directory, issue an svn copy command for the trunk into the branches directory, then commit
>
> svn copy trunk branches/libobjc2-work
> svn commit -m "Koen's branch..."
>
> then you can work in that branch directory just like normal.
>
> cheers
> Scott
>
> On May 28, 2011, at 10:03 PM, Koen van der Drift wrote:
>
>> Hi Scott,
>>
>> Yes, please send me instructions on how to make a svn branch. I'm
>> still reading on all the new stuff of ObjC2 and trying to get my head
>> around all of it, so it may be a while before I start committing
>> things. ?Maybe you can add some of your ideas for new functionality to
>> a todo list in the repository?
>>
>> I'll start with fast enumerations, deprecated methods, and maybe
>> properties for a cleaner code.
>>
>> - Koen.
>>
>>
>>
>> On Sat, May 28, 2011 at 10:23 PM, Scott Christley <schristley at mac.com> wrote:
>>> Hi Koen,
>>>
>>> Making a svn branch is a good idea, then you can work and still commit changes as you get milestones done. ?If you are not sure how to create, I can send instructions. ?There is an open-source ObjC2 being actively written by the llvm/clang folks, and they have been working so that it can compile all of GNUstep, but I'm not sure it is at production level yet.
>>>
>>> Personally I would avoid garbage collecting, there is already a solid retain-release implementation with minimal leaks, and there are numerous places where autorelease pools are used to manage large chunks of temporary objects (like parsing data files), this is more efficient memory management for that time of stuff.
>>>
>>> Cleaning up warnings would definitely be great. ?Properties... maybe, but doesn't add a whole lot. ?Fast enumeration is probably nice. ?There is always documentation :-) ?Even better is if you have the time/inclination to add some new functionality, I have a whole slew of ideas from quick to hard.
>>>
>>> cheers
>>> Scott
>>>
>>> On May 28, 2011, at 1:37 PM, Koen van der Drift wrote:
>>>
>>>> All,
>>>>
>>>> I recently started looking again at Cocoa programming, and what better
>>>> way to dive back into BioCocoa to get my memory refreshed! ?While
>>>> reading some current Cocoa docs from Apple, I learned that since my
>>>> absence many new features have been added to ObjC, now called ObjC2.
>>>> Probably nothing new for y'all :)
>>>>
>>>> Things I'm talking about are fast enumeration, garbage collecting,
>>>> properties, cleaning up warnings because of deprecated methods, and
>>>> maybe more.
>>>>
>>>> So, I was thinking as a first task for me is to go through the
>>>> framework, and implement/update the code with (some of) the above
>>>> mentioned features. ?This would also mean that the lowest OS that
>>>> BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
>>>> introduced.
>>>>
>>>> Are there any objections to this plan? I could for instance make a new
>>>> branch for this, maybe tagged version 2.5 or 3.0?
>>>>
>>>> Thanks,
>>>>
>>>> - Koen.
>>>>
>>>> _______________________________________________
>>>> Biococoa-dev mailing list
>>>> Biococoa-dev at bioinformatics.org
>>>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>>>
>>>
>
>



From schristley at mac.com  Sun May 29 02:16:00 2011
From: schristley at mac.com (Scott Christley)
Date: Sun, 29 May 2011 01:16:00 -0500
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <BANLkTikr62MHLkS62Oqmq6SQR6t1o40sOw@mail.gmail.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
	<3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
	<BANLkTi=NFcn+bSjfkJrX-VuqD4noVqJAeQ@mail.gmail.com>
	<D0595B03-BEEB-43AD-BBCA-4021DCFBA8C4@mac.com>
	<BANLkTikr62MHLkS62Oqmq6SQR6t1o40sOw@mail.gmail.com>
Message-ID: <E3591FA3-0301-431D-ACFF-EC4EFA2A3CA9@mac.com>

Hi Koen,

I wrote those macros a long time ago, because GNUstep does not have CoreFoundation.  I tend to forget to use them because I'm so used to just writing for loops ;-)  I think FE is part of the objc2 compiler, so no it isn't standard for GNUstep yet.  You could probably change the Cocoa version of the macros to use FE.

Scott

On May 28, 2011, at 10:56 PM, Koen van der Drift wrote:

> Thanks Scott, I just committed a first set of updates. It turns out
> that a lot of the for, while, or do loops in the framework are not so
> straightforward, so I may just leave them as they are. FE only seems
> to be for simple enumerations. But someone please correct me if this
> is not the case.
> 
> I also noticed several macros to manipulate arrays in GNUStep, e.g.
> ARRAY_GET_VALUE_AT_INDEX as an alternative to CoreFoundation. Does
> GNUStep support FE, and if so, can those macros be replaced by FE?
> 
> Thanks,
> 
> - Koen.
> 
> On Sat, May 28, 2011 at 11:09 PM, Scott Christley <schristley at mac.com> wrote:
>> Hi Koen,
>> 
>> So the instructions to make an SVN branch can essentially be taken from the SVN repository tasks in the release checklist off the wiki:
>> 
>> http://www.bioinformatics.org/biococoa/wiki/pmwiki.php?n=Main.ReleaseChecklist
>> 
>> The basic idea is go to the BioCocoa directory, issue an svn copy command for the trunk into the branches directory, then commit
>> 
>> svn copy trunk branches/libobjc2-work
>> svn commit -m "Koen's branch..."
>> 
>> then you can work in that branch directory just like normal.
>> 
>> cheers
>> Scott
>> 
>> On May 28, 2011, at 10:03 PM, Koen van der Drift wrote:
>> 
>>> Hi Scott,
>>> 
>>> Yes, please send me instructions on how to make a svn branch. I'm
>>> still reading on all the new stuff of ObjC2 and trying to get my head
>>> around all of it, so it may be a while before I start committing
>>> things.  Maybe you can add some of your ideas for new functionality to
>>> a todo list in the repository?
>>> 
>>> I'll start with fast enumerations, deprecated methods, and maybe
>>> properties for a cleaner code.
>>> 
>>> - Koen.
>>> 
>>> 
>>> 
>>> On Sat, May 28, 2011 at 10:23 PM, Scott Christley <schristley at mac.com> wrote:
>>>> Hi Koen,
>>>> 
>>>> Making a svn branch is a good idea, then you can work and still commit changes as you get milestones done.  If you are not sure how to create, I can send instructions.  There is an open-source ObjC2 being actively written by the llvm/clang folks, and they have been working so that it can compile all of GNUstep, but I'm not sure it is at production level yet.
>>>> 
>>>> Personally I would avoid garbage collecting, there is already a solid retain-release implementation with minimal leaks, and there are numerous places where autorelease pools are used to manage large chunks of temporary objects (like parsing data files), this is more efficient memory management for that time of stuff.
>>>> 
>>>> Cleaning up warnings would definitely be great.  Properties... maybe, but doesn't add a whole lot.  Fast enumeration is probably nice.  There is always documentation :-)  Even better is if you have the time/inclination to add some new functionality, I have a whole slew of ideas from quick to hard.
>>>> 
>>>> cheers
>>>> Scott
>>>> 
>>>> On May 28, 2011, at 1:37 PM, Koen van der Drift wrote:
>>>> 
>>>>> All,
>>>>> 
>>>>> I recently started looking again at Cocoa programming, and what better
>>>>> way to dive back into BioCocoa to get my memory refreshed!  While
>>>>> reading some current Cocoa docs from Apple, I learned that since my
>>>>> absence many new features have been added to ObjC, now called ObjC2.
>>>>> Probably nothing new for y'all :)
>>>>> 
>>>>> Things I'm talking about are fast enumeration, garbage collecting,
>>>>> properties, cleaning up warnings because of deprecated methods, and
>>>>> maybe more.
>>>>> 
>>>>> So, I was thinking as a first task for me is to go through the
>>>>> framework, and implement/update the code with (some of) the above
>>>>> mentioned features.  This would also mean that the lowest OS that
>>>>> BioCocoa will run on is OSX 10.5, which is when ObjectiveC2 was
>>>>> introduced.
>>>>> 
>>>>> Are there any objections to this plan? I could for instance make a new
>>>>> branch for this, maybe tagged version 2.5 or 3.0?
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> - Koen.
>>>>> 
>>>>> _______________________________________________
>>>>> Biococoa-dev mailing list
>>>>> Biococoa-dev at bioinformatics.org
>>>>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>>>> 
>>>> 
>> 
>> 




From koenvanderdrift at gmail.com  Sun May 29 07:27:09 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Sun, 29 May 2011 07:27:09 -0400
Subject: [Biococoa-dev] modernizing BioCocoa
In-Reply-To: <E3591FA3-0301-431D-ACFF-EC4EFA2A3CA9@mac.com>
References: <BANLkTinFspnVaW2hT3oWn4vc0Zu+tvRwTw@mail.gmail.com>
	<3ECEFBA6-83C4-4059-9BEF-2837A2E1F212@mac.com>
	<BANLkTi=NFcn+bSjfkJrX-VuqD4noVqJAeQ@mail.gmail.com>
	<D0595B03-BEEB-43AD-BBCA-4021DCFBA8C4@mac.com>
	<BANLkTikr62MHLkS62Oqmq6SQR6t1o40sOw@mail.gmail.com>
	<E3591FA3-0301-431D-ACFF-EC4EFA2A3CA9@mac.com>
Message-ID: <BANLkTi=ppwDxjDyWPJ1mYfu8_OLtks5TgA@mail.gmail.com>

On Sun, May 29, 2011 at 2:16 AM, Scott Christley <schristley at mac.com> wrote:
> Hi Koen,
>
> I wrote those macros a long time ago, because GNUstep does not have CoreFoundation. ?I tend to forget to use them because I'm so used to just writing for loops ;-) ?I think FE is part of the
> objc2 compiler, so no it isn't standard for GNUstep yet. ?You could probably change the Cocoa version of the macros to use FE.

Hmm, that probably means that all uses of FE in the code need to be
conditionalized until it is official in GNUStep.  I may have to revise
my changes that I committed yesterday then. Or keep it local and merge
it whenever it becomes official in GNUStep.  Or use those macros
instead of FE, but I don't know how CF compares to FE with regards to
speed and efficiency.

- Koen.



From koenvanderdrift at gmail.com  Sun May 29 13:35:34 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Sun, 29 May 2011 13:35:34 -0400
Subject: [Biococoa-dev] adding framework to project problem
Message-ID: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>

All,

This is driving me nuts. Just as a test case for the changes I am
making, I am using the Example project Peptides. As is well documented
all over the Internets, and I have done many times before, I added the
Framework to the product from it's current location, which is in the
branches->obj2->BioCocoa->build directory. And then add it in the
project to the Copy Files build phase.

I keep getting an error that dyld cannot find the image for the framework:

dyld: Library not loaded:
@executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
  Referenced from:
/Users/koenvanderdrift/Documents/Development/Projects/BioCocoa/Applications/Demos/trunk/build/Debug/Peptides.app/Contents/MacOS/Peptides
  Reason: image not found

I tried relative and absolute paths, but both give the error.

Interestingly, if I copy the framework to /Library/Frameworks/ and
link it into the project from that location, it works just fine. But I
don't want to copy the framework there everytime I make some changes.

So, what's going on, is this something new as well in Xcode 3?
(3.2.6).  Has anyone tried this recently and ran into the same
problem?

As I said above, this is driving me nuts...

- Koen.



From koenvanderdrift at gmail.com  Sun May 29 17:53:27 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Sun, 29 May 2011 17:53:27 -0400
Subject: [Biococoa-dev] adding framework to project problem
In-Reply-To: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
References: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
Message-ID: <BANLkTinxJP8w2-CJgFfvwP7Kb4ATUTzXGQ@mail.gmail.com>

There must be something wrong with the settings in the BC framework. I
build the BC framework (the current release version 2.2), and copied
it to the Desktop. Then I took another framework (core-plot), and also
copied it to the Desktop.  I then created a fresh new test project,
and added either BC or CP to it. With CP, the app just launches fine;
with BC, it crashes with the same error.  I tried compiling older
versions of BC, but couldn't even compile those, since they target
older OS X versions.

Hopefully someone has an answer, this needs to be fixed in the trunk,
so we can release a new version. I'm clueless at this moment.

- Koen.


On Sun, May 29, 2011 at 1:35 PM, Koen van der Drift
<koenvanderdrift at gmail.com> wrote:
> All,
>
> This is driving me nuts. Just as a test case for the changes I am
> making, I am using the Example project Peptides. As is well documented
> all over the Internets, and I have done many times before, I added the
> Framework to the product from it's current location, which is in the
> branches->obj2->BioCocoa->build directory. And then add it in the
> project to the Copy Files build phase.
>
> I keep getting an error that dyld cannot find the image for the framework:
>
> dyld: Library not loaded:
> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
> ?Referenced from:
> /Users/koenvanderdrift/Documents/Development/Projects/BioCocoa/Applications/Demos/trunk/build/Debug/Peptides.app/Contents/MacOS/Peptides
> ?Reason: image not found
>
> I tried relative and absolute paths, but both give the error.
>
> Interestingly, if I copy the framework to /Library/Frameworks/ and
> link it into the project from that location, it works just fine. But I
> don't want to copy the framework there everytime I make some changes.
>
> So, what's going on, is this something new as well in Xcode 3?
> (3.2.6). ?Has anyone tried this recently and ran into the same
> problem?
>
> As I said above, this is driving me nuts...
>
> - Koen.
>



From schristley at mac.com  Sun May 29 18:38:56 2011
From: schristley at mac.com (Scott Christley)
Date: Sun, 29 May 2011 17:38:56 -0500
Subject: [Biococoa-dev] adding framework to project problem
In-Reply-To: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
References: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
Message-ID: <FCEB7F65-D56E-4473-B3FD-D15DBF198421@mac.com>

Hi Koen,

Unfortunately this is something about the Xcode development environment that I never really understood.  In my development workflow, I copy the framework to /Library/Frameworks every time.

Scott

On May 29, 2011, at 12:35 PM, Koen van der Drift wrote:

> All,
> 
> This is driving me nuts. Just as a test case for the changes I am
> making, I am using the Example project Peptides. As is well documented
> all over the Internets, and I have done many times before, I added the
> Framework to the product from it's current location, which is in the
> branches->obj2->BioCocoa->build directory. And then add it in the
> project to the Copy Files build phase.
> 
> I keep getting an error that dyld cannot find the image for the framework:
> 
> dyld: Library not loaded:
> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
>  Referenced from:
> /Users/koenvanderdrift/Documents/Development/Projects/BioCocoa/Applications/Demos/trunk/build/Debug/Peptides.app/Contents/MacOS/Peptides
>  Reason: image not found
> 
> I tried relative and absolute paths, but both give the error.
> 
> Interestingly, if I copy the framework to /Library/Frameworks/ and
> link it into the project from that location, it works just fine. But I
> don't want to copy the framework there everytime I make some changes.
> 
> So, what's going on, is this something new as well in Xcode 3?
> (3.2.6).  Has anyone tried this recently and ran into the same
> problem?
> 
> As I said above, this is driving me nuts...
> 
> - Koen.
> 
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev




From schristley at mac.com  Sun May 29 18:40:49 2011
From: schristley at mac.com (Scott Christley)
Date: Sun, 29 May 2011 17:40:49 -0500
Subject: [Biococoa-dev] adding framework to project problem
In-Reply-To: <BANLkTinxJP8w2-CJgFfvwP7Kb4ATUTzXGQ@mail.gmail.com>
References: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
	<BANLkTinxJP8w2-CJgFfvwP7Kb4ATUTzXGQ@mail.gmail.com>
Message-ID: <E5526D26-ECD6-416E-A9F6-BD642DDD0F67@mac.com>

You might have to go through the setting for the two projects, it is probably something in the "linking" section or maybe deployment/install section.  Probably something is being hard-coded instead of using a relative path.

Scott

On May 29, 2011, at 4:53 PM, Koen van der Drift wrote:

> There must be something wrong with the settings in the BC framework. I
> build the BC framework (the current release version 2.2), and copied
> it to the Desktop. Then I took another framework (core-plot), and also
> copied it to the Desktop.  I then created a fresh new test project,
> and added either BC or CP to it. With CP, the app just launches fine;
> with BC, it crashes with the same error.  I tried compiling older
> versions of BC, but couldn't even compile those, since they target
> older OS X versions.
> 
> Hopefully someone has an answer, this needs to be fixed in the trunk,
> so we can release a new version. I'm clueless at this moment.
> 
> - Koen.
> 
> 
> On Sun, May 29, 2011 at 1:35 PM, Koen van der Drift
> <koenvanderdrift at gmail.com> wrote:
>> All,
>> 
>> This is driving me nuts. Just as a test case for the changes I am
>> making, I am using the Example project Peptides. As is well documented
>> all over the Internets, and I have done many times before, I added the
>> Framework to the product from it's current location, which is in the
>> branches->obj2->BioCocoa->build directory. And then add it in the
>> project to the Copy Files build phase.
>> 
>> I keep getting an error that dyld cannot find the image for the framework:
>> 
>> dyld: Library not loaded:
>> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
>>  Referenced from:
>> /Users/koenvanderdrift/Documents/Development/Projects/BioCocoa/Applications/Demos/trunk/build/Debug/Peptides.app/Contents/MacOS/Peptides
>>  Reason: image not found
>> 
>> I tried relative and absolute paths, but both give the error.
>> 
>> Interestingly, if I copy the framework to /Library/Frameworks/ and
>> link it into the project from that location, it works just fine. But I
>> don't want to copy the framework there everytime I make some changes.
>> 
>> So, what's going on, is this something new as well in Xcode 3?
>> (3.2.6).  Has anyone tried this recently and ran into the same
>> problem?
>> 
>> As I said above, this is driving me nuts...
>> 
>> - Koen.
>> 
> 
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev




From koenvanderdrift at gmail.com  Mon May 30 06:27:08 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Mon, 30 May 2011 06:27:08 -0400
Subject: [Biococoa-dev] adding framework to project problem
In-Reply-To: <E5526D26-ECD6-416E-A9F6-BD642DDD0F67@mac.com>
References: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
	<BANLkTinxJP8w2-CJgFfvwP7Kb4ATUTzXGQ@mail.gmail.com>
	<E5526D26-ECD6-416E-A9F6-BD642DDD0F67@mac.com>
Message-ID: <BANLkTimVsuaDYHCQQaDTDx3xDTMVovJOxw@mail.gmail.com>

Yeah, I went through all the settings (and there are many!) already
several times, but no avail. Very weird.

- Koen.

On Sun, May 29, 2011 at 6:40 PM, Scott Christley <schristley at mac.com> wrote:
> You might have to go through the setting for the two projects, it is probably something in the "linking" section or maybe deployment/install section. ?Probably something is being hard-coded instead of using a relative path.
>
> Scott
>
> On May 29, 2011, at 4:53 PM, Koen van der Drift wrote:
>
>> There must be something wrong with the settings in the BC framework. I
>> build the BC framework (the current release version 2.2), and copied
>> it to the Desktop. Then I took another framework (core-plot), and also
>> copied it to the Desktop. ?I then created a fresh new test project,
>> and added either BC or CP to it. With CP, the app just launches fine;
>> with BC, it crashes with the same error. ?I tried compiling older
>> versions of BC, but couldn't even compile those, since they target
>> older OS X versions.
>>
>> Hopefully someone has an answer, this needs to be fixed in the trunk,
>> so we can release a new version. I'm clueless at this moment.
>>
>> - Koen.
>>
>>
>> On Sun, May 29, 2011 at 1:35 PM, Koen van der Drift
>> <koenvanderdrift at gmail.com> wrote:
>>> All,
>>>
>>> This is driving me nuts. Just as a test case for the changes I am
>>> making, I am using the Example project Peptides. As is well documented
>>> all over the Internets, and I have done many times before, I added the
>>> Framework to the product from it's current location, which is in the
>>> branches->obj2->BioCocoa->build directory. And then add it in the
>>> project to the Copy Files build phase.
>>>
>>> I keep getting an error that dyld cannot find the image for the framework:
>>>
>>> dyld: Library not loaded:
>>> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
>>> ?Referenced from:
>>> /Users/koenvanderdrift/Documents/Development/Projects/BioCocoa/Applications/Demos/trunk/build/Debug/Peptides.app/Contents/MacOS/Peptides
>>> ?Reason: image not found
>>>
>>> I tried relative and absolute paths, but both give the error.
>>>
>>> Interestingly, if I copy the framework to /Library/Frameworks/ and
>>> link it into the project from that location, it works just fine. But I
>>> don't want to copy the framework there everytime I make some changes.
>>>
>>> So, what's going on, is this something new as well in Xcode 3?
>>> (3.2.6). ?Has anyone tried this recently and ran into the same
>>> problem?
>>>
>>> As I said above, this is driving me nuts...
>>>
>>> - Koen.
>>>
>>
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>
>



From koenvanderdrift at gmail.com  Mon May 30 11:40:06 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Mon, 30 May 2011 11:40:06 -0400
Subject: [Biococoa-dev] adding framework to project problem
In-Reply-To: <BANLkTimVsuaDYHCQQaDTDx3xDTMVovJOxw@mail.gmail.com>
References: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
	<BANLkTinxJP8w2-CJgFfvwP7Kb4ATUTzXGQ@mail.gmail.com>
	<E5526D26-ECD6-416E-A9F6-BD642DDD0F67@mac.com>
	<BANLkTimVsuaDYHCQQaDTDx3xDTMVovJOxw@mail.gmail.com>
Message-ID: <BANLkTimEcUQ4VJXC6K7jcQ_PzZJ1P3D1VA@mail.gmail.com>

Ok, I think I fixed it. I updated the demo apps (Peptides and
Translation), and they work now with the framework code in the latest
trunk, without the need of copying the framework to the Library
folder.

When adding the framework, I used these steps (everything is done in Xcode):

1. Add the framework to the project by right-click on Frameworks ->
Add Existing Framework, and then browse to the correct location. Make
sure it ends up under the 'Linked Framework" directory in the project
2. Drag the now added framework to the target in the 'Link Binary With
Libraries" section
3. Create a new build phase for the target, by right clicking -> Add
-> New Copy Build Phase. Make sure in the inspector to select
framework from the Destinations popup menu
4. Again, drag the framework from Linked Frameworks into the Copy Files section.

Build, and run, and it should go.

Please test, and see if it works on your system as well, and maybe
with other apps.

- Koen.



On Mon, May 30, 2011 at 6:27 AM, Koen van der Drift
<koenvanderdrift at gmail.com> wrote:
> Yeah, I went through all the settings (and there are many!) already
> several times, but no avail. Very weird.
>
> - Koen.
>
> On Sun, May 29, 2011 at 6:40 PM, Scott Christley <schristley at mac.com> wrote:
>> You might have to go through the setting for the two projects, it is probably something in the "linking" section or maybe deployment/install section. ?Probably something is being hard-coded instead of using a relative path.
>>
>> Scott
>>
>> On May 29, 2011, at 4:53 PM, Koen van der Drift wrote:
>>
>>> There must be something wrong with the settings in the BC framework. I
>>> build the BC framework (the current release version 2.2), and copied
>>> it to the Desktop. Then I took another framework (core-plot), and also
>>> copied it to the Desktop. ?I then created a fresh new test project,
>>> and added either BC or CP to it. With CP, the app just launches fine;
>>> with BC, it crashes with the same error. ?I tried compiling older
>>> versions of BC, but couldn't even compile those, since they target
>>> older OS X versions.
>>>
>>> Hopefully someone has an answer, this needs to be fixed in the trunk,
>>> so we can release a new version. I'm clueless at this moment.
>>>
>>> - Koen.
>>>
>>>
>>> On Sun, May 29, 2011 at 1:35 PM, Koen van der Drift
>>> <koenvanderdrift at gmail.com> wrote:
>>>> All,
>>>>
>>>> This is driving me nuts. Just as a test case for the changes I am
>>>> making, I am using the Example project Peptides. As is well documented
>>>> all over the Internets, and I have done many times before, I added the
>>>> Framework to the product from it's current location, which is in the
>>>> branches->obj2->BioCocoa->build directory. And then add it in the
>>>> project to the Copy Files build phase.
>>>>
>>>> I keep getting an error that dyld cannot find the image for the framework:
>>>>
>>>> dyld: Library not loaded:
>>>> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
>>>> ?Referenced from:
>>>> /Users/koenvanderdrift/Documents/Development/Projects/BioCocoa/Applications/Demos/trunk/build/Debug/Peptides.app/Contents/MacOS/Peptides
>>>> ?Reason: image not found
>>>>
>>>> I tried relative and absolute paths, but both give the error.
>>>>
>>>> Interestingly, if I copy the framework to /Library/Frameworks/ and
>>>> link it into the project from that location, it works just fine. But I
>>>> don't want to copy the framework there everytime I make some changes.
>>>>
>>>> So, what's going on, is this something new as well in Xcode 3?
>>>> (3.2.6). ?Has anyone tried this recently and ran into the same
>>>> problem?
>>>>
>>>> As I said above, this is driving me nuts...
>>>>
>>>> - Koen.
>>>>
>>>
>>> _______________________________________________
>>> Biococoa-dev mailing list
>>> Biococoa-dev at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>>
>>
>



From koenvanderdrift at gmail.com  Mon May 30 11:58:40 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Mon, 30 May 2011 11:58:40 -0400
Subject: [Biococoa-dev] BioCocoa and CoreData
In-Reply-To: <5cba6b9f0906080626q5383d8f9ifba00baef07d543d@mail.gmail.com>
References: <5cba6b9f0906080626q5383d8f9ifba00baef07d543d@mail.gmail.com>
Message-ID: <BANLkTi=G=yRATnVxdNJ_uoftbmma4QYFkg@mail.gmail.com>

Bumping this subject from a few years ago, maybe someone can answer to this?

Thanks,

- Koen.



On Mon, Jun 8, 2009 at 9:26 AM, Koen van der Drift
<koenvanderdrift at gmail.com> wrote:
> Hi,
>
>[...] I thought to write a small demo app like a simple sequence editor for
> BioCocoa that uses CoreData, just as an exercise. The excellent
> tutorial at MacResearch.org also deals with molecules, so that was
> promising. But when I thought more about it, I came to the conclusion
> that an editor is actually not a good example to use with CoreData
> (please correct me if I'm wrong). It get's more interesting when the
> app deals with more than one sequence at a time, eg when aligning
> them, or when dealing with digests from a main sequence. On top of
> that, if I use BCSequence as an attribute for my Sequence entity, I
> still need to go to all the BioCocoa classes for I/O, use all the
> accessors, etc.
>
> So, just out of curiosity, I was wondering if anyone has used CoreData
> in combination with BioCocoa? Should/can BioCocoa be adapted to be
> more CoreData friendly?



From schristley at mac.com  Mon May 30 12:11:20 2011
From: schristley at mac.com (Scott Christley)
Date: Mon, 30 May 2011 11:11:20 -0500
Subject: [Biococoa-dev] adding framework to project problem
In-Reply-To: <BANLkTimEcUQ4VJXC6K7jcQ_PzZJ1P3D1VA@mail.gmail.com>
References: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
	<BANLkTinxJP8w2-CJgFfvwP7Kb4ATUTzXGQ@mail.gmail.com>
	<E5526D26-ECD6-416E-A9F6-BD642DDD0F67@mac.com>
	<BANLkTimVsuaDYHCQQaDTDx3xDTMVovJOxw@mail.gmail.com>
	<BANLkTimEcUQ4VJXC6K7jcQ_PzZJ1P3D1VA@mail.gmail.com>
Message-ID: <88A33399-B346-4136-ABF1-6F0C11046E15@mac.com>

Hi Koen,

I get the first two steps, unfortunately I think the 3rd step creates a local copy of the BioCocoa framework inside the application, probably not the most desirable.  I haven't had a chance to play around with this yet, but will try in another week or so and can give you feedback.

cheers
Scott

On May 30, 2011, at 10:40 AM, Koen van der Drift wrote:

> Ok, I think I fixed it. I updated the demo apps (Peptides and
> Translation), and they work now with the framework code in the latest
> trunk, without the need of copying the framework to the Library
> folder.
> 
> When adding the framework, I used these steps (everything is done in Xcode):
> 
> 1. Add the framework to the project by right-click on Frameworks ->
> Add Existing Framework, and then browse to the correct location. Make
> sure it ends up under the 'Linked Framework" directory in the project
> 2. Drag the now added framework to the target in the 'Link Binary With
> Libraries" section
> 3. Create a new build phase for the target, by right clicking -> Add
> -> New Copy Build Phase. Make sure in the inspector to select
> framework from the Destinations popup menu
> 4. Again, drag the framework from Linked Frameworks into the Copy Files section.
> 
> Build, and run, and it should go.
> 
> Please test, and see if it works on your system as well, and maybe
> with other apps.
> 
> - Koen.
> 
> 
> 
> On Mon, May 30, 2011 at 6:27 AM, Koen van der Drift
> <koenvanderdrift at gmail.com> wrote:
>> Yeah, I went through all the settings (and there are many!) already
>> several times, but no avail. Very weird.
>> 
>> - Koen.
>> 
>> On Sun, May 29, 2011 at 6:40 PM, Scott Christley <schristley at mac.com> wrote:
>>> You might have to go through the setting for the two projects, it is probably something in the "linking" section or maybe deployment/install section.  Probably something is being hard-coded instead of using a relative path.
>>> 
>>> Scott
>>> 
>>> On May 29, 2011, at 4:53 PM, Koen van der Drift wrote:
>>> 
>>>> There must be something wrong with the settings in the BC framework. I
>>>> build the BC framework (the current release version 2.2), and copied
>>>> it to the Desktop. Then I took another framework (core-plot), and also
>>>> copied it to the Desktop.  I then created a fresh new test project,
>>>> and added either BC or CP to it. With CP, the app just launches fine;
>>>> with BC, it crashes with the same error.  I tried compiling older
>>>> versions of BC, but couldn't even compile those, since they target
>>>> older OS X versions.
>>>> 
>>>> Hopefully someone has an answer, this needs to be fixed in the trunk,
>>>> so we can release a new version. I'm clueless at this moment.
>>>> 
>>>> - Koen.
>>>> 
>>>> 
>>>> On Sun, May 29, 2011 at 1:35 PM, Koen van der Drift
>>>> <koenvanderdrift at gmail.com> wrote:
>>>>> All,
>>>>> 
>>>>> This is driving me nuts. Just as a test case for the changes I am
>>>>> making, I am using the Example project Peptides. As is well documented
>>>>> all over the Internets, and I have done many times before, I added the
>>>>> Framework to the product from it's current location, which is in the
>>>>> branches->obj2->BioCocoa->build directory. And then add it in the
>>>>> project to the Copy Files build phase.
>>>>> 
>>>>> I keep getting an error that dyld cannot find the image for the framework:
>>>>> 
>>>>> dyld: Library not loaded:
>>>>> @executable_path/../Frameworks/BioCocoa.framework/Versions/A/BioCocoa
>>>>>  Referenced from:
>>>>> /Users/koenvanderdrift/Documents/Development/Projects/BioCocoa/Applications/Demos/trunk/build/Debug/Peptides.app/Contents/MacOS/Peptides
>>>>>  Reason: image not found
>>>>> 
>>>>> I tried relative and absolute paths, but both give the error.
>>>>> 
>>>>> Interestingly, if I copy the framework to /Library/Frameworks/ and
>>>>> link it into the project from that location, it works just fine. But I
>>>>> don't want to copy the framework there everytime I make some changes.
>>>>> 
>>>>> So, what's going on, is this something new as well in Xcode 3?
>>>>> (3.2.6).  Has anyone tried this recently and ran into the same
>>>>> problem?
>>>>> 
>>>>> As I said above, this is driving me nuts...
>>>>> 
>>>>> - Koen.
>>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biococoa-dev mailing list
>>>> Biococoa-dev at bioinformatics.org
>>>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>>> 
>>> 
>> 




From schristley at mac.com  Mon May 30 12:21:01 2011
From: schristley at mac.com (Scott Christley)
Date: Mon, 30 May 2011 11:21:01 -0500
Subject: [Biococoa-dev] BioCocoa and CoreData
In-Reply-To: <5cba6b9f0906080626q5383d8f9ifba00baef07d543d@mail.gmail.com>
References: <5cba6b9f0906080626q5383d8f9ifba00baef07d543d@mail.gmail.com>
Message-ID: <82D0CEAA-A537-4CA2-B2FC-01E8586311A6@mac.com>

Hello Koen,

I don't have much experience with CoreData, but my understanding is that it is simple way to build database-type functionality without requiring the heavy backend database like Mysql or Postgres.  You can manage data (objects) in either a flat file or a local sqlite file.

It isn't clear to me how to use it directly by BioCocoa, but I could imagine its use at the application level.  For example, let's say you had a simple application that manages all of your sequence experiments, so you could use CoreData to save information about sample prep, experimental protocols, etc. as well as maybe information on sequence files names, where they are stored etc.  So CoreData manages the "meta-data" while BioCocoa operates on the sequence data directly.

This actually isn't too far off from the "killer app" I've been wanting to develop, right now all the biologists I know who are doing initial forays into high-throughput sequencing, are all doing ad-hoc workflows for managing data.

cheers
Scott

On Jun 8, 2009, at 8:26 AM, Koen van der Drift wrote:

> Hi,
> 
> I haven't been doing a lot of programming in a while, but with the
> WWDC starting and all the news and twittering around it, I couldn't
> resist to open up Xcode. One thing I read a lot about recently is Core
> Data (yes, I know, I'm slow, it's been out for a few years now :-),
> and at first glance it looks like a very useful technique. So I
> thought to write a small demo app like a simple sequence editor for
> BioCocoa that uses CoreData, just as an exercise. The excellent
> tutorial at MacResearch.org also deals with molecules, so that was
> promising. But when I thought more about it, I came to the conclusion
> that an editor is actually not a good example to use with CoreData
> (please correct me if I'm wrong). It get's more interesting when the
> app deals with more than one sequence at a time, eg when aligning
> them, or when dealing with digests from a main sequence. On top of
> that, if I use BCSequence as an attribute for my Sequence entity, I
> still need to go to all the BioCocoa classes for I/O, use all the
> accessors, etc.
> 
> So, just out of curiosity, I was wondering if anyone has used CoreData
> in combination with BioCocoa? Should/can BioCocoa be adapted to be
> more CoreData friendly?
> 
> cheers,
> 
> - Koen.
> 
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev




From koenvanderdrift at gmail.com  Mon May 30 13:11:04 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Mon, 30 May 2011 13:11:04 -0400
Subject: [Biococoa-dev] adding framework to project problem
In-Reply-To: <88A33399-B346-4136-ABF1-6F0C11046E15@mac.com>
References: <BANLkTinDsxg-gx1O9KAghMTN7zT38+Jx6A@mail.gmail.com>
	<BANLkTinxJP8w2-CJgFfvwP7Kb4ATUTzXGQ@mail.gmail.com>
	<E5526D26-ECD6-416E-A9F6-BD642DDD0F67@mac.com>
	<BANLkTimVsuaDYHCQQaDTDx3xDTMVovJOxw@mail.gmail.com>
	<BANLkTimEcUQ4VJXC6K7jcQ_PzZJ1P3D1VA@mail.gmail.com>
	<88A33399-B346-4136-ABF1-6F0C11046E15@mac.com>
Message-ID: <BANLkTikT=RRcdDs6QAF8j9Zng4a8gFu7cg@mail.gmail.com>

On Mon, May 30, 2011 at 12:11 PM, Scott Christley <schristley at mac.com> wrote:
> Hi Koen,
>
> I get the first two steps, unfortunately I think the 3rd step creates a local copy of the BioCocoa framework inside the application, probably not the most desirable. ?I haven't had a chance to play around with this yet, but will try in another week or so and can give you feedback.

Yes, that is indeed the case, it will copy the framework into the app.
It's a tradeoff, you can either add the framework to the app in Xcode
with some additional MB (BC is now 1.6 MB, not that bad), or require
users to install BC into their system. For the purpose of the demos, I
think the former is the easiest.

- Koen.



From koenvanderdrift at gmail.com  Mon May 30 13:16:31 2011
From: koenvanderdrift at gmail.com (Koen van der Drift)
Date: Mon, 30 May 2011 13:16:31 -0400
Subject: [Biococoa-dev] BioCocoa and CoreData
In-Reply-To: <82D0CEAA-A537-4CA2-B2FC-01E8586311A6@mac.com>
References: <5cba6b9f0906080626q5383d8f9ifba00baef07d543d@mail.gmail.com>
	<82D0CEAA-A537-4CA2-B2FC-01E8586311A6@mac.com>
Message-ID: <BANLkTi=0KoyYYEgv24nsk2=3T3DgVvnt7w@mail.gmail.com>

Ahhh, the infamous 'killer app'  :)

Yes, using CD for meta data is indeed a good suggestion, and is
something that can be kept outside of the sequence data (which are
basically plain text files in most cases. Core Data could then maybe
be used to store relationships between sequences, group them together
based on various criteria (organism, function), etc etc.

- Koen.



On Mon, May 30, 2011 at 12:21 PM, Scott Christley <schristley at mac.com> wrote:
> Hello Koen,
>
> I don't have much experience with CoreData, but my understanding is that it is simple way to build database-type functionality without requiring the heavy backend database like Mysql or Postgres. ?You can manage data (objects) in either a flat file or a local sqlite file.
>
> It isn't clear to me how to use it directly by BioCocoa, but I could imagine its use at the application level. ?For example, let's say you had a simple application that manages all of your sequence experiments, so you could use CoreData to save information about sample prep, experimental protocols, etc. as well as maybe information on sequence files names, where they are stored etc. ?So CoreData manages the "meta-data" while BioCocoa operates on the sequence data directly.
>
> This actually isn't too far off from the "killer app" I've been wanting to develop, right now all the biologists I know who are doing initial forays into high-throughput sequencing, are all doing ad-hoc workflows for managing data.
>
> cheers
> Scott
>
> On Jun 8, 2009, at 8:26 AM, Koen van der Drift wrote:
>
>> Hi,
>>
>> I haven't been doing a lot of programming in a while, but with the
>> WWDC starting and all the news and twittering around it, I couldn't
>> resist to open up Xcode. One thing I read a lot about recently is Core
>> Data (yes, I know, I'm slow, it's been out for a few years now :-),
>> and at first glance it looks like a very useful technique. So I
>> thought to write a small demo app like a simple sequence editor for
>> BioCocoa that uses CoreData, just as an exercise. The excellent
>> tutorial at MacResearch.org also deals with molecules, so that was
>> promising. But when I thought more about it, I came to the conclusion
>> that an editor is actually not a good example to use with CoreData
>> (please correct me if I'm wrong). It get's more interesting when the
>> app deals with more than one sequence at a time, eg when aligning
>> them, or when dealing with digests from a main sequence. On top of
>> that, if I use BCSequence as an attribute for my Sequence entity, I
>> still need to go to all the BioCocoa classes for I/O, use all the
>> accessors, etc.
>>
>> So, just out of curiosity, I was wondering if anyone has used CoreData
>> in combination with BioCocoa? Should/can BioCocoa be adapted to be
>> more CoreData friendly?
>>
>> cheers,
>>
>> - Koen.
>>
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
>
>