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

[Hannes Brandstätter-Müller]

Code duplication is removed. The new package sequencing contains the
current code (The explicit support for the new illumina format was
dropped again, since it's just the other, already existing encoding -
should we readd that or simply document it properly?)

The only thing we still need to make sure is that the file formatting
in the new module is consistent with the rest of biojava3 ({} are on
their own line, other minor stuff)

On Thu, Mar 15, 2012 at 07:09, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Hannes and Michael,
>
> no stress about the release, just make sure that the two of you are in
> agreement with whatever is in SVN. Did the code duplication get
> resolved? If we have to delay until Monday or even a bit later, that's
> no problem at all.
>
> Michael, can you ssh into portal-open-bio.org ? if yes, you just need
> to set up ssh-key auth, which should be straightforward. something
> like that: http://www.debian-administration.org/articles/530
>
> Andreas
>
> On Wed, Mar 14, 2012 at 10:44 PM, Michael Heuer <heuermh at gmail.com> wrote:
>> Hello Hannes,
>>
>> I will be working from home tomorrow since ssh is blocked at work*, if
>> anything else needs to be done before the code freeze.
>>
>> Andreas, do you have a time in mind for the deadline?  And do I need
>> my code signing key for the release process?  If so, I will have to go
>> dig up my private key which is stored who knows where for safe
>> keeping.
>>
>>   michael
>>
>> * - and because of the basketball tournament
>>
>>
>> On Thu, Mar 15, 2012 at 12:31 AM, Hannes Brandstätter-Müller
>> <biojava at hannes.oib.com> wrote:
>>> Well, it's the 15th now for me, so I'll just delete the
>>> genome.parsers.fastq and consider it frozen from my side.
>>>
>>> Hannes
>>>
>>> On Wed, Mar 14, 2012 at 21:23, Michael Heuer <heuermh at gmail.com> wrote:
>>>> Hannes Brandstätter-Müller wrote:
>>>>> Andreas Prlic <andreas at sdsc.edu> wrote:
>>>>>
>>>>>> I would tend to split as well. Are you and Hannes in agreement in how
>>>>>> to proceed with this or is there anything we should discuss?  Let me
>>>>>> know if I can help somehow in resolving this.
>>>>>
>>>>> I am in agreement, however I'd like to know if the existing parsers
>>>>> ins the genome.parsers package should be moved to the new location as
>>>>> well or if they should stay.
>>>>
>>>> If you feel that the functionality in sequencing.io.fastq package in
>>>> biojava3-sequencing compares favorably to what is currently in
>>>> genome.parsers.fastq, then I believe we should be fine removing
>>>> genome.parsers.fastq and releasing sequencing.io.fastq in
>>>> biojava3-sequencing for version 3.0.3.
>>>>
>>>> Converting and writing from DNASequence+QualityFeature to FASTQ format
>>>> is not currently supported in sequencing.io.fastq, but adding such (as
>>>> static methods to FastqTools, with additional methods in FastqVariant)
>>>> should not cause binary compatibility issues and could safely be
>>>> released in a 3.0.4 or later release.
>>>>
>>>>
>>>>> I'd prefer to keep anything that parses genomics-related file data
>>>>> somehow together - ideally even genomics and proteomics in their
>>>>> respective subgroups, but I guess since some of the stuff is already
>>>>> present and we should watch compatibility, that train has already left
>>>>> the station.
>>>>>
>>>>> Since I'm new to this as a dev, I'll let you decide where in the
>>>>> package structure we should put the parsers/tools.
>>>>
>>>> Where to put stuff is always difficult to decide, and had I been more
>>>> clever with my svn-foo this might have gone smoother.
>>>>
>>>>   michael
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------