[Biojava-dev] Java 1.5 (final chance to object)

[Sicotte, Hugues (NIH/NCI)]

Last call.. OK

BioJava is one of the most turbulent bioinformatics library projects.
Much more turbulent than bioPerl or bioPython.
Often code written a few years ago does not work because older API's
get deprecated or changed. This is especially tough for people who use
BioJava
on and Off. We think two sets of API's are compatible, but there 
are lots of deprecated features. We find online examples, only to find
out they no longer work.

Stability and backward compatibility are crucial to the success of BioJava.
In fact, if the code is not too complex, I often have to write it myself
rather than
relying on BioJava. I want to write code that will still be in production
5 years from now.

I say that, not because I don't appreciate the hard work of developpers,
but because I would like the volunteer developpers to appreciate that
the users of the toolkit need stability. We live in production environments
that will not support 1.5 for a long time. I am still living in a 1.3 world.
Only projects that I am starting right now can use 1.4.2_08.


I beg you, Please reconsider moving to 1.5, it's only 5% more typing to use
1.4.

Hugues Sicotte
(a user who still doesn't get to use the RegExp package in 1.4)



-----Original Message-----
From: mark.schreiber at novartis.com [mailto:mark.schreiber at novartis.com]
Sent: Thursday, October 06, 2005 9:53 PM
To: Thomas Down
Cc: biojava-l at biojava.org; wetrull at yahoo.com; BioJava Dev
Subject: [Biojava-dev] Java 1.5 (final chance to object)


OK, there seems to have been a few reasonable objections. The consensus 
seems to be we will wait until the end of the year. I think from then on 
we will change over for biojava-live.

There was a suggestion of maintaining two branches, one would be a 
maintenance of biojava1.4 and only use JDK1.4.2, the other would be 
biojava-live and use JDK1.5. I have done this in the past and have no 
desire to do it again, it's really not that much fun. I would however like 
to reserve the option of putting JDK1.5 dependent code into the classes of 
the org.biojavax package. If this happens I will adjust the ANT build 
script such that these are not compiled if JDK1.5 is not detected. This 
should be safe as the biojava packages have no dependencies on the 
biojavax packages. Bug fixes to biojava would still be in the system. 
Additionally the org.biojavax packages are undergoing a lot of development 
right now so you shouldn't be doing any production programming with them 
anyway.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910


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