taskSavannah Administration - Tasks: task #5371, Submission of TaxonDNA

 
 

task #5371: Submission of TaxonDNA

Submitter:  Gaurav Vaidya <ggvaidya>
Submitted:  Fri 31 Mar 2006 04:01:26 PM UTC
   
 
Should Start On:  Fri 31 Mar 2006 04:00:00 PM UTC Should be Finished on:  Mon 10 Apr 2006 04:00:00 PM UTC
Category:  Project Approval Priority:  * 5 - Normal
Status:  Cancelled Privacy:  Public
Assigned to:  tizzef Open/Closed:  Closed
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Mon 22 May 2006 08:11:45 AM UTC, comment #8: 

Thanks, see you at savannah :).

Cheers

Patrick Camus <tizzef>
Thu 18 May 2006 02:51:29 PM UTC, comment #7: 

No problem! Thanks for all the help and comments!

cheers,
Gaurav

Gaurav Vaidya <ggvaidya>
Thu 18 May 2006 08:32:44 AM UTC, comment #6: 

Hi Gaurav,

Thanks for your reply.

>>> "So, as I mentioned in my last e-mail, I probably won't be able to focus on getting it working in GCJ/Classpath until the end of the month or so. I'm not sure if that'll be enough for GNU :)."


I think you are right, :) we can't wait such delay.

Hmm, do you mind to resubit your project to Savannah when you've done the job and when you went OK with all the dependencies (Classpath and GCJ compatible) ?

Cheers.

Patrick Camus <tizzef>
Tue 16 May 2006 07:25:22 AM UTC, comment #5: 

Hi Patrick,

You can get the source for TaxonDNA 0.9.2 from the Sourceforge downloads page http://prdownloads.sourceforge.net/taxondna/TaxonDNA-0.9.2-src.zip?download. I've made some changes since then, but I've only got them on my local CVS until SF gets its act together. 0.9.2 was released just last week, so it should be recent enough. Let me know if you want the cutting-edge source, and I'll upload it to this task.

I'm not very sure how well TaxonDNA 0.9.2 compiles/runs on GCJ/Classpath. A few versions ago, it was compiling and running, but without any of the features working. Since there haven't been any major changes since then, I think it should still be the same. We're going through a bug fix/final feature stage right now, and we urgently need it to be feature complete by the end of the month, so I'm focusing pretty much entirely on new features right now. So, as I mentioned in my last e-mail, I probably won't be able to focus on getting it working in GCJ/Classpath until the end of the month or so. I'm not sure if that'll be enough for GNU :).

cheers,
Gaurav

Gaurav Vaidya <ggvaidya>
Mon 15 May 2006 02:22:58 PM UTC, comment #4: 

Hi Gaurav,

Sorry for the long delay.

Hope you pass succesfully your exams. :)

Could you send me an updated tarball because the source tree doesn't reflect your update (http://cvs.sourceforge.net/viewcvs.py/taxondna/TaxonDNA).

If you do not have time to update your sources, please let me know.

Cheers.

Patrick Camus <tizzef>
Thu 27 Apr 2006 11:23:08 AM UTC, comment #3: 

Hi Patrick,

I've got TaxonDNA running in GCJ/Classpath, but it's got all manner of strange and mysterious bugs, and I've got exams coming up. Would it be better to leave this hanging for a week or two, or for me to resubmit once I've got it working GCJ/Classpath?

cheers,
Gaurav

Gaurav Vaidya <ggvaidya>
Thu 13 Apr 2006 10:54:40 AM UTC, comment #2: 

Hi Patrick,

1. gpl.txt is renamed to COPYING in CVS.
2. Copyright/license notices on UndoTask/UndoStack have been fixed.

I'll let you know once I've tested it on gcj/classpath.

cheers,
Gaurav

Gaurav Vaidya <ggvaidya>
Thu 13 Apr 2006 08:47:51 AM UTC, comment #1: 

Hi,

I'm evaluating the project you submitted for approval in Savannah.

You are using the 'Jinks' software for compiling your java code, but 'Jinks' is released under the 'IBM Public License v1.0', which is GNU GPL non compliant.

You must determine whether your project can run on a Free Software Java suite (see http://www.gnu.org/software/java/ for more information).

We recommend you to test your project using GCJ and GNU Classpath, and ensure that your Java code runs on this Free Software Java suite.

GCJ is the GNU Compiler for Java, part of the GCC (GNU Compiler Collection).  The Classpath project aims to develop a free and portable implementation of the Java API (the classes in the 'java' package).

More information is available at http://gcc.gnu.org/ and http://www.gnu.org/software/classpath/.

Please let's us know if code run on completly free operating system.

Please, update your copyright and lincense notice in the taxondna/TaxonDNA/UI/UndoTask.java and taxondna/TaxonDNA/UI/UndoStack.java files.

Last thing, rename the gpl.txt into COPYING or LICENSE.

Cheers.

Patrick Camus <tizzef>
Fri 31 Mar 2006 04:01:26 PM UTC, original submission:  

A new project has been registered at Savannah
The project account will remain inactive until a site admin approve or discard the registration.


######### REGISTRATION ADMINISTRATION #########

While this item will be useful to track the registration process, approving or discarding the registration must be done using the specific "Group Administration" page, accessible only to site administrators, effectively logged as site administrators (superuser):

  <https://savannah.nongnu.org/admin/groupedit.php?group_id=8442>


######### REGISTRATION DETAILS #########

Full Name:
----------
  TaxonDNA

System Group Name:
-----------------
  taxondna

Type:
-----
  non-GNU software & documentation

License:
--------
  GNU General Public License V2 or later

Description:
------------
  TaxonDNA evolved as an undergraduate student project of mine (which I am still maintaining for my lab at NUS: http://evolution.science.nus.edu.sg/).

I aim to create a simple biological sequence editor, allowing bioinformaticians to open, edit, and export to many of the dozens of file formats commonly used in bioinformatics. Additionally, I want to make it extremely easy for programmers to write modules which can process the sequences in some way. Thus, programmers who need to write a program to perform some sort of data analysis on biological sequence data can just write the algorithm, relying to TaxonDNA to provide them with a user interface, file import/export functionality, functions for dealing with sequence data, and so on.

TaxonDNA is currently at version 0.9.1 (although some urgent bugfixes will be coming out shortly, bumping us to 0.9.1.1). It is being used in several projects in my lab, and is thus going through a "beta" phase preparatory to full 1.0 release (probably in June/July). While the interface needs polishing, it is very usable and easy to work with. Some of the code needs rewriting, but I am 80-90% ready for 1.0.

TaxonDNA was written in Java, using the AWT. With two modifications not yet in CVS, it can be compiled on Jikes using the Kaffe classes. However, some parts of the code still need work to work around bugs Kaffe, and I still haven't completely finished testing the code on Kaffe. However, complete Jikes compatibility will be a goal for version 1.0, and complete Kaffe compatibility for 2.0.

TaxonDNA is released under the GPL. The code can be viewed online on our SourceForge archive, at http://cvs.sourceforge.net/viewcvs.py/taxondna/.

Other Software Required:
------------------------
  We use BrowserLauncher http://cvs.sourceforge.net/viewcvs.py/taxondna/TaxonDNA/Others/BrowserLauncher.java?view=markup, which "may be redistributed or modified in any form without restrictions as long as the portion of this comment from this paragraph [the license] through the end of the comment is not removed" according to its license, which I take to be a BSD-compatible license.

The current version of the program can (with two modifications) compile on Jikes; however, while it works fine on GNU/Linux/JDK, it doesn't seem to work completely in Kaffe. These bugs will be rectified by version 2.0 of the software.

Other Comments:
---------------
  As you can see, all of our code is currently hosted on SourceForge. I was pushed into looking for other hosting solutions due to very erratic CVS access in the last few weeks, although I'm already very impressed by the simplicity of the Savannah interface. Although I might continue to use sf.net for the final distribution, I'd much prefer using Savannah for bug/task/cvs and the website. The community also seems "tighter" here, allowing for more collaboration (I hope!).


Gaurav Vaidya <ggvaidya>

 

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Follow 11 latest changes.

Date Changed by Updated Field Previous Value => Replaced by
2006-05-22 tizzef StatusWait reply Cancelled
    Percent Complete90% 100%
    Open/ClosedOpen Closed
2006-05-18 tizzef Percent Complete80% 90%
2006-05-15 tizzef StatusNeed Info Wait reply
    Percent Complete20% 80%
2006-04-13 tizzef StatusWait reply Need Info
2006-04-13 tizzef StatusIn Progress Wait reply
    Percent Complete0% 20%
2006-04-05 tizzef StatusNone In Progress
2006-04-03 tizzef Assigned toNone tizzef

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