Re: netcdf uploaded (Re: Package available (was Re: Micro Manager))
Josh,
On Wed, Apr 11, 2012 at 10:53 AM, Josh Moore <josh@glencoesoftware.com> wrote:
> On Apr 10, 2012, at 12:13 PM, Mathieu Malaterre wrote:
>> On Mon, Jan 16, 2012 at 6:37 PM, Mark Longair
>> <mark-debianlists@longair.net> wrote:
>>> Hi Mathieu,
>>>
>>> Mathieu Malaterre <mathieu.malaterre@gmail.com> wrote:
>>>>
>>>> Hi Mark !
>>>>
>>>> On Sat, Jan 7, 2012 at 1:35 PM, Mark Longair
>>>> <mark-debianlists@longair.net> wrote:
>>> [..]
>>>>> NetCDF Java itself also bundles a huge number of jar files in
>>>>> the source distribution, but to build the core of NetCDF you
>>>>> actually need relatively few dependencies. I made a package
>>>>> that builds just the core of NetCDF (i.e. the makeCore ant
>>>>> target) and only relies on Debian-packaged dependencies. (The
>>>>> NetCDF core is all that bio-formats requires, I believe.) That
>>>>> repository is here:
>>>>>
>>>>> https://github.com/mhl/libnetcdf-java
>>>>
>>>> Cool. I'll import that into the debian-med svn if this is ok with you:
>>>> svn.debian.org/svn/debian-med/trunk/packages/netcdf-java
>>> [..]
>>>>> The repository with my Debian packaging of bio-formats is here:
>>>>>
>>>>> https://github.com/mhl/libbio-formats-java
>>>>
>>>> cool. If this is ok with you I'll import this into debian-med svn at:
>>>> svn.debian.org/svn/debian-med/trunk/packages/bio-formats
>>> [..]
>>>
>>> That's great in both cases - thanks for doing that.
>>
>> ref:
>> http://ftp-master.debian.org/new/netcdf-java_4.3.8-BETA-1.html
>>
>> Assuming everyting goes smoothly, I can now move on to bio-formats itself.
>
> Hi Mathieu,
>
> Looking at Mark's repo (mhl/libbio-formats-java) and the patches under http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bio-formats/trunk/debian/patches/, much of what was necessary was to remove the jars and configure the build for using /usr/share, a source drop, etc. Would it help if we modified the build so there's a global switch (e.g. ant -Ddebian=true) to allow these commits to live in the mainline? (Would the jars be allowed to remain unused, or must they be deleted to adhere to the Debian guidelines?)
I am not too keen on the whole "-Ddebian=true". Even if I only use
debian distribution, there are other distros out there. Also this puts
the burden of maintaining debian related material outside of debian
organisation. I do not believe this will be beneficial for both
communities.
Instead what I have been trying to do is simply use the documented
'build.sysclasspath' [1], ant option. Mark's solution was more
invasive even if he used json scripts to automagically fix ant build
files.
So really as long as netcdf/bioformats allow use of
build.sysclasspath=first then all is fine with me. There are still a
couple of tiny patches but that was mostly me banging my head trying
to get things moving. I believe in the end the number of patches
should be much smaller.
The only patch, I really dislike so far is the following:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bio-formats/trunk/debian/patches/ij.patch?view=markup
I guess I need to check if using newer imagej release this patch goes away.
> Where possible we'd certainly like to make Debian packaging simpler. A new stable release of Bio-Formats (4.4) is planned for the summer which it would be ideal to target, giving us a chance to merge in patches and the bulk of Mark's work (especially having seen some of how he suffered!)
Again the number of patch should really be minimalistic in the end.
> I've CC'd Melissa Linkert, the Bio-Formats lead. Roger Leigh, a (previously non-Java) Debian maintainer who's recently joined the Bio-Formats project, is already subscribed to the list.
The biggest issue is that I do not believe I will be ready for the
debian freeze (should happen before summer if I recall correctly). The
whole bio-formats packaging seems very difficult to me, this is why I
can only build a minimal number of targets right now:
"jar-autogen jar-common jar-formats jar-jai jar-loci-plugins
jar-lwf-stubs jar-mdbtools jar-metakit jar-ome-xml jar-poi-loci"
Thanks for your interest and CCing people to help out ! And thanks for
bio-formats !
-M
[1] http://ant.apache.org/manual/sysclasspath.html
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