[Debian-med-packaging] Bug#842815: Help needed for HDF5 1.10 transition of libsis-jhdf5-java

[Bernd Rinn]

Hello Andreas,

There are some good news: For porting JHDF5 to HDF 1.10, I got help from
Gerd Heber. I have been fixing some looes ends in the last couple of
days and now the porting is now. I still want to do some improvements to
the library (not dependent on the underlying HDF5 version) and need to
work on the Windows build, but there is nothing that would keep you from
updating the port in Debian unstable. The build procedure for Linux
won't change anymore.

The current version of JHDF5 building on top of HDF5 1.10.3-pre1, you
will find in (branch master):

https://sissource.ethz.ch/sispub/jhdf5

I plan to do in about 2 weeks time a JHDF5 pre-release to get feedback
from users outside my organization. The release should then be based on
HDF5 1.10.3 once that version has been released by the HDF group. If you
have anyone who could test the pre-release version or your port, please
feel free to forward this email to him or her.

All the best,
Bernd

On 08/04/2018 08:06 AM, Andreas Tille wrote:
> Hello Bernd,
> 
> On Mon, May 28, 2018 at 09:18:28AM +0200, Bernd Rinn wrote:
>> Hello Andreas,
>>
>> On 05/27/2018 07:12 AM, Andreas Tille wrote:
>>> Hello Bernd,
>>>
>>> sorry for nagging again but we now have another Dependency from
>>> sis-jhdf5 which makes a fix for this issue even more interesting.  As I
>>> said before I would also try a patch if you might hesitate to issue a
>>> completely new release.
>>
>> It is embarrassing to admit that I still haven't found the time to port
>> JHDF5 to HDF5 1.10.
>>
>> If you can come up with a patch to bridge to time that would be greatly
>> appreciated!
> 
> Since I personally do not even know what HDF5 is I can not help myself
> and as far as Gilles Filippini stated[1] chances are pretty low that we
> from Debian will be able to come up with a patch.  What do you think
> about the remark
> 
>    Have you considered using libhdf5-java[2] or libjhdf5-java instead?
> 
> Well, several projects are using libsis-hdf5-java but it might be to
> join forces with one single Java library which keeps up with current
> development.  I have no idea in how far libsis-hdf5-java is different
> for the other libs but could you somehow imagine to unify the interface
> and join forces?
> 
> Kind regards
> 
>       Andreas.
> 
> [1] https://lists.debian.org/debian-science/2018/05/msg00112.html
> [2] https://support.hdfgroup.org/HDF5/
> [3] 
> 
>>> On Wed, Sep 06, 2017 at 12:50:56PM +0200, Andreas Tille wrote:
>>>> Hello Bernd,
>>>>
>>>> On Wed, 23 Nov 2016 06:54:21 +0100, you wrote
>>>>> the migration of JHDF5 to HDF5 1.10 is ongoing and mostly depend on me
>>>>> having a block of time I can spend on it. Your analysis of the work that
>>>>> needs to be done is right from what I can see. The plan is to switch to
>>>>> using the JNI library from the HDF group wherever possible (it may still
>>>>> be necessary to have a small JNI library though as some calls appear to
>>>>> be missing).
>>>>>
>>>>> I will keep you updated.
>>>>
>>>> Is there any news, may be only a patch for the existing version we
>>>> could try to fix the Debian package?
>>>>
>>>> Kind regards
>>>>
>>>>        Andreas.
>>>>
>>>> -- 
>>>> http://fam-tille.de
>>>>
>>>> _______________________________________________
>>>> Debian-med-packaging mailing list
>>>> Debian-med-packaging at lists.alioth.debian.org
>>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>>>>
>>>
>>
>> -- 
>> Dr. Bernd Rinn
>> Head Scientific IT Services
>> ETH Zurich IT Services
>> SIB Swiss Institute of Bioinformatics
>> Weinbergstr. 11 (WEC D 19), 8092 Zürich, Switzerland, +41 44 632 0608
>> Mattenstr. 26 (BSB 1.01), 4058 Basel, Switzerland, +41 61 387 3130
>>
> 
> 
> 

-- 
Dr. Bernd Rinn
Head Scientific IT Services
ETH Zurich IT Services
SIB Swiss Institute of Bioinformatics
Weinbergstr. 11 (WEC D 19), 8092 Zürich, Switzerland, +41 44 632 0608
Mattenstr. 26 (BSB 1.01), 4058 Basel, Switzerland, +41 61 387 3130

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