I want to contribute

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I want to contribute

sph k2
Hi!

My name is Henrik. I have almost two years of experience of object-oriented programming and feel comfortable with Java, C#/C++, Python, MATLAB, GTK and Java Swing. Next month I will start my education to Master of Engeneering at the Royal Institute of Technology in Sweden.

I just subscribed to this mailing list and I hope to contribute to Debian Science! Please contact me about how I can join this project.

Yours sincerely
Henrik
[hidden email]


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Re: I want to contribute

Egon Willighagen-2
Hi Henrik,

2010/7/12 sph k2 <[hidden email]>:
> My name is Henrik. I have almost two years of experience of object-oriented
> programming and feel comfortable with Java, C#/C++, Python, MATLAB, GTK and
> Java Swing. Next month I will start my education to Master of Engeneering at
> the Royal Institute of Technology in Sweden.

Is that in Stockholm?

> I just subscribed to this mailing list and I hope to contribute to Debian
> Science! Please contact me about how I can join this project.

Like with most Open Source projects, you join by contributing.
Therefore, the first question should really be, how can you
contribute. I can recommend finding something you actually work
with... for example, a tool packaged for Debian you already use, or
could use.

Example Java science software in Debian includes the Chemistry
Development Kit (libcdk-java) which needs a package update, but I am
sure you would make many Debian users happy if you would package Jmol
(http://jmol.org/) for Debian. (I am/was lead developer for both, and
reside in Uppsala).

A second common approach is to look at bug reports for packages within
the Debian Science project, and work on patches to solve those bugs.

Can you elaborate on what you would like to do? That makes it a lot
easier for people on this list to suggest possible tasks...

Regards,

Egon

--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


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Re: I want to contribute

Andreas Tille-5
On Wed, Jul 14, 2010 at 11:53:10AM +0200, Egon Willighagen wrote:
> I am
> sure you would make many Debian users happy if you would package Jmol
> (http://jmol.org/) for Debian. (I am/was lead developer for both, and
> reside in Uppsala).

I can confirm that Jmol would be quite interesting.  Here is some information
about the packaging status of Jmol:

   http://debian-med.alioth.debian.org/tasks/bio#jmol

However, I would strongly recommend contacting the issuer of the ITP
and suggest moving SVN from pkg-escience to debian-science SVN.
 
> A second common approach is to look at bug reports for packages within
> the Debian Science project, and work on patches to solve those bugs.

Here you can easily pick a bug which concerns a package in your
personal field of interest:

   http://blends.alioth.debian.org/science/bugs/
 
Kind regards

    Andreas.

--
http://fam-tille.de


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packaging jmol, was Re: I want to contribute

Steffen Möller
Hello,

On 07/14/2010 02:44 PM, Andreas Tille wrote:

> On Wed, Jul 14, 2010 at 11:53:10AM +0200, Egon Willighagen wrote:
>  
>> I am
>> sure you would make many Debian users happy if you would package Jmol
>> (http://jmol.org/) for Debian. (I am/was lead developer for both, and
>> reside in Uppsala).
>>    
> I can confirm that Jmol would be quite interesting.  Here is some information
> about the packaging status of Jmol:
>  
yes, jmol is indeed overdue. As it happens I know that Eric from the CC
line is also interested in packaging jmol. Eric, how far have you got?
The vicinity of upstream-Egon to "sph k2" who drafted the original
request, would somehow suggests to spare you the effort, Eric, and
rather proceed directly to Jalview.
>    http://debian-med.alioth.debian.org/tasks/bio#jmol
>
> However, I would strongly recommend contacting the issuer of the ITP
> and suggest moving SVN from pkg-escience to debian-science SVN.
>  
:) any move is fine with me. This 2006 effort of mine at
http://svn.debian.org/wsvn/pkg-escience/jmol/trunk/debian/?rev=0&sc=0
was sufficiently frustrating.


Many greetings

Steffen


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Re: packaging jmol, was Re: I want to contribute

Eric Talevich
On Wed, Jul 14, 2010 at 10:18 AM, Steffen Möller <[hidden email]> wrote:
Hello,

On 07/14/2010 02:44 PM, Andreas Tille wrote:
> On Wed, Jul 14, 2010 at 11:53:10AM +0200, Egon Willighagen wrote:
>
>> I am
>> sure you would make many Debian users happy if you would package Jmol
>> (http://jmol.org/) for Debian. (I am/was lead developer for both, and
>> reside in Uppsala).
>>
> I can confirm that Jmol would be quite interesting.  Here is some information
> about the packaging status of Jmol:
>
yes, jmol is indeed overdue. As it happens I know that Eric from the CC
line is also interested in packaging jmol. Eric, how far have you got?
The vicinity of upstream-Egon to "sph k2" who drafted the original
request, would somehow suggests to spare you the effort, Eric, and
rather proceed directly to Jalview.

I haven't gotten anywhere with Jmol yet, so if Egon would like to package it, please go right ahead. :)
 
-Eric
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Re: packaging jmol, was Re: I want to contribute

Alex John-2
Hello,

I'm Alex and I'd like to help package jmol if anyone is willing to introduce me to the procedure (first time with packaging). 

Cheers
Alex

On Jul 14, 2010, at 10:23 PM, Eric Talevich <[hidden email]> wrote:

On Wed, Jul 14, 2010 at 10:18 AM, Steffen Möller <[hidden email]> wrote:
Hello,

On 07/14/2010 02:44 PM, Andreas Tille wrote:
> On Wed, Jul 14, 2010 at 11:53:10AM +0200, Egon Willighagen wrote:
>
>> I am
>> sure you would make many Debian users happy if you would package Jmol
>> (http://jmol.org/) for Debian. (I am/was lead developer for both, and
>> reside in Uppsala).
>>
> I can confirm that Jmol would be quite interesting.  Here is some information
> about the packaging status of Jmol:
>
yes, jmol is indeed overdue. As it happens I know that Eric from the CC
line is also interested in packaging jmol. Eric, how far have you got?
The vicinity of upstream-Egon to "sph k2" who drafted the original
request, would somehow suggests to spare you the effort, Eric, and
rather proceed directly to Jalview.

I haven't gotten anywhere with Jmol yet, so if Egon would like to package it, please go right ahead. :)
 
-Eric
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Re: packaging jmol, was Re: I want to contribute

Egon Willighagen-2
Hi Alex,

On Wed, Jul 14, 2010 at 5:04 PM, Alex John <[hidden email]> wrote:
> I'm Alex and I'd like to help package jmol if anyone is willing to introduce
> me to the procedure (first time with packaging).

If you google for "debian packaging tutorial", you will find plenty of
material. E.g.:

http://www.debian-administration.org/articles/336
http://www.debian-administration.org/article/Rolling_your_own_Debian_packages_part_2

And, of course the Maintainers Guide is the primary source of information:

http://www.debian.org/doc/maint-guide/

Once you have crafted your debian/ folder with all files, and it is
Lintian error free, it is time to ask for a 'sponsor'... make sure to
discuss you efforts as soon as possible, and preferably share the
files of your debian/ folder publically, such as the debian-science
SVN...:

http://svn.debian.org/

Browse any section for examples:

http://svn.debian.org/viewsvn/debian-science/

Because Jmol is written in Java, you should also have a look at some
debian/ folders for other Java software:

http://svn.debian.org/wsvn/pkg-java

and check the Debian Java wiki:

http://wiki.debian.org/Java

I'll be available for Jmol building questions, but do not have time to
make a package for it...

Egon

--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


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Re: packaging jmol, was Re: I want to contribute

Andreas Tille-5
In reply to this post by Alex John-2
On Wed, Jul 14, 2010 at 11:04:15PM +0800, Alex John wrote:
> I'm Alex and I'd like to help package jmol if anyone is willing to introduce me to the procedure (first time with packaging).

In case you want to contribute you should probably create an account on
alioth.debian.org and apply for becoming a member of Debian Science
project to be able to commit to the SVN.

Feel free to ask further questions in case something remains unclear

    Andreas.

--
http://fam-tille.de


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Re: packaging jmol, was Re: I want to contribute

Michael Banck
Hi,

On Wed, Jul 14, 2010 at 10:14:05PM +0200, Andreas Tille wrote:
> On Wed, Jul 14, 2010 at 11:04:15PM +0800, Alex John wrote:
> > I'm Alex and I'd like to help package jmol if anyone is willing to introduce me to the procedure (first time with packaging).
>
> In case you want to contribute you should probably create an account on
> alioth.debian.org and apply for becoming a member of Debian Science
> project to be able to commit to the SVN.
>
> Feel free to ask further questions in case something remains unclear

We wouldn't mind having it in the debichem repository, either.  I'd be
willing to co-maintain it.


cheers,

Michael


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Re: packaging jmol, was Re: I want to contribute

Steffen Möller
On 07/16/2010 11:31 AM, Michael Banck wrote:

> Hi,
>
> On Wed, Jul 14, 2010 at 10:14:05PM +0200, Andreas Tille wrote:
>  
>> On Wed, Jul 14, 2010 at 11:04:15PM +0800, Alex John wrote:
>>    
>>> I'm Alex and I'd like to help package jmol if anyone is willing to introduce me to the procedure (first time with packaging).
>>>      
>> In case you want to contribute you should probably create an account on
>> alioth.debian.org and apply for becoming a member of Debian Science
>> project to be able to commit to the SVN.
>>
>> Feel free to ask further questions in case something remains unclear
>>    
> We wouldn't mind having it in the debichem repository, either.  I'd be
> willing to co-maintain it.
>  
This sounds all ultimately lovely. Please check out if a checkout of my
previous attempt in the pkg-escience repository is helpful - I have no
recollection about that effort, but at least as a start for Alex is
should be somewhat interesting to look at.

I once gave it status "yellow" which is a rather good sign, the comment
I left for a missing of a compatibility check with the free Java
compilers and machine are now mute.
http://svn.debian.org/wsvn/pkg-escience/jmol/trunk/

Good luck!

Steffen


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Re: packaging jmol, was Re: I want to contribute

Andreas Tille-2
In reply to this post by Michael Banck
On Fri, Jul 16, 2010 at 11:31:57AM +0200, Michael Banck wrote:
> We wouldn't mind having it in the debichem repository, either.  I'd be
> willing to co-maintain it.

Using DebiChem SVN and do it in group maintenance in the DebiChem team
would most probably the best choice.  Please keep me informed once you  
have moved the SVN because I need to update the Debian Med tasks file
which is listing Jmol as prospective package.

Kind regards

       Andreas.

--
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RE: I want to contribute

sph k2
In reply to this post by Egon Willighagen-2
> Is that in Stockholm?

Yes it is!

> Can you elaborate on what you would like to do? That makes it a lot
> easier for people on this list to suggest possible tasks...

I would like to contribute as a developer/programmer by writing code for a Debian Science project and I am willing to program in Java, C#/C++ or Python. I could do anything from building a GUI to writing a class for a specific problem. I am hoping joining a Debian Science project as a developer will improve my programming skills.

Are there any tasks for me?
Is there a project I can join as a developer?

Yours sincerely
Henrik
[hidden email]



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Re: I want to contribute

Egon Willighagen-2
2010/7/17 Henrik null <[hidden email]>:
> Are there any tasks for me?
> Is there a project I can join as a developer?

One thing I could personally use help with:

libcdk-java has a new upstream release, but which could be upgraded to
compile against jgrapht 0.8 ...

But otherwise, it is probably best to start with an existing bug
report... and start making patches.

Egon

--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


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Re: packaging jmol, was Re: I want to contribute

Michael Banck
In reply to this post by Egon Willighagen-2
Hi,

On Wed, Jul 14, 2010 at 06:54:12PM +0200, Egon Willighagen wrote:

> Because Jmol is written in Java, you should also have a look at some
> debian/ folders for other Java software:
>
> http://svn.debian.org/wsvn/pkg-java
>
> and check the Debian Java wiki:
>
> http://wiki.debian.org/Java
>
> I'll be available for Jmol building questions, but do not have time to
> make a package for it...

I just took a look at Jmol, and noticed the ant build fails as
selfSignedCertificate/* is not packaged in jmol-11.8.25-full.tar.gz.  Is
there another source tarball, are those two files to be checked out from
subversion and applied locally, can/must this be disabled, or is there
something else I am missing?


Thanks,

Michael


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