[Biojava-dev] sorry about biojava-live/trunk repository mess; was Re: biojava-legacy 1.8.2 release plan

[Michael Heuer]

All,

In addition to committing changes to biojava-legacy/trunk for the
1.8.2 release, I have now merged the updated fastq code from
biojava-legacy/trunk to biojava-live/trunk for the upcoming 3.0.3
release.  In the process I have made a mess of the revision history
for biojava-live/trunk, since I was not doing a good job coordinating
with Hannes' changes.

(see rev 9567 in particular)
http://code.open-bio.org/biojava-live/trunk/biojava3-genome/?root=biojava&view=log
http://code.open-bio.org/biojava-live/trunk/biojava3-sequencing/?root=biojava&view=log

At present there are two copies of the fastq package, one in
org.biojava3.sequencing.io.fastq in a re-added biojava3-sequencing
module, and one in org.biojava3.genome.parsers.fastq in
biojava3-genome.  Before the 3.0.3 we need to resolve this.

I'm more of a splitter than a lumper when it comes to maven modules;
the pros of keeping biojava3-sequencing as a separate module

 - self-contained package, only dependent on biojava3-core
 - same API and module structure as biojava-legacy (although different package)
 - biojava3-sequencing adds a new third party compile scope dependency
(on Google Guava, version 11.0.1)
 - would be the home for Phred, ABI, and similar code if/when migrated
from biojava-legacy

and the cons

 - narrow scope feature-wise for a module
 - FASTQ parsing is not all that different from FASTA parsing
conceptually, although no code is shared

Please let me know what you think.

Sorry about creating this mess.  Since I have re-added a directory
that had been removed in an earlier commit, you may receive a
complaint from subversion about biojava3-sequencing on update.

   michael


On Thu, Mar 8, 2012 at 11:31 PM, Michael Heuer <heuermh at gmail.com> wrote:
> ok, scratch my previous plan.  I have committed the new fastq code to
> biojava-legacy for the 1.8.2 release and started this legacy cookbook
> page
>
> http://biojava.org/wiki/BioJava:Cookbook:SeqIO:FASTQ
>
> Please let me know what you think.  I have performance benchmark
> numbers if anyone needs convincing that this API is an improvement
> over the current one.
>
>   michael
>
>
> On Thu, Mar 8, 2012 at 1:33 PM, Michael Heuer <heuermh at gmail.com> wrote:
>> Andreas Prlic wrote:
>>
>>> thanks for volunteering for making a biojava-1.x release! Let's do
>>> this in sync together with the 3.x series. What about doing the
>>> releases next Friday, March 16th?
>>
>> Sure, that works for me.
>>
>>
>>>> I assume the documentation on cutting a release at
>>>> http://biojava.org/wiki/BioJava:Make_release
>>>> is still relevant?
>>>
>>> In fact this is not up-to-date any more.
>>>
>>> The code is now Mavenized and the key-task for the person making the
>>> release is to set up ssh-keys to the portal-obf server prior to making
>>> this release. After that you can make a release as simply as that:
>>>
>>> mvn release:clean release:prepare release:perform
>>
>> Much better.
>>
>>   michael