[Neurodebian-devel] ANTS

Wed Feb 26 14:44:59 UTC 2014

On Wed, 26 Feb 2014, Gert Wollny wrote:
> >> * is the -fpermissive really needed? Or is this a leftover from 1.9?
> >was originally added in
> >commit 1d6102bbb822b917a891faad58353e8c6911cdb1
> >Author: Yaroslav Halchenko <debian at onerussian.com>
> >Date:   Fri May 4 10:31:17 2012 -0400
> >     BF: patch from Matthias Klosse for gcc 4.7 (Closes: #667099)
> >not sure if still needed.  build would show ;)
> Okay, I will test this.

cool -- thanks in advance

> >indeed itk4 is currently available only for x86, but it might come to other
> >archs eventually.  better to get ready IMHO ;)
> Okay.  BTW, I've seen that ITK is at version 4.2 in NeuroDebian,
> afaik ANTS will need 4.4 at least. Well, since we need  ANTS and ITK
> 4.5 on wheezy I will run builds over the weekend to see how this
> goes.

ANTS 2.0.0 I was packaging should work with ITK 4.4 indeed.   I have a
build of ITK 4.4 for wheezy siting around and thought to upload it
whenever it is needed (i.e. for ANTS) after initial checking ;)
FWIW -- it succeeded to build only for wheezy, not any ubuntus

I will now try a blind backport rebuild of 4.5.0-3 -- may be we could
even have that one 

> >>* As for the data, can we just add it in the debian/ directory?
> >>Since there are binary files, this may violate Debian policy, but
> >>then again it's data. There seems to be an option to set the test
> >>data root to avoid downloading.

> >could go anywhere but I do not see benefits for under debian/ instead of some
> >directory overlayed over upstream code.  It is upstream data after all, and as
> >a data collection might even be copyrightable.

> Well, I always thought everything that is not in the original
> tarball has to be provided as patches or in some other way through
> debian/. 

well -- there is no original tarball anyways (besides may be tarball of
tagged release on github)... and 3.0 source package supporting
multiple tarballs came out for a reason ;)  Ideally we should just
automate acquisition of such needed data, and that is why I thought it
might be worth a separate source/binary package....

meanwhile -- I see that itk package in Debian carries
InsightToolkit-4.4.0/.ExternalData   so might be worth looking where
they get it from

> That's the only reason I choose this approach.

I see

> If you can give me a pointer how to add properly overlay over
> upstream code that doesn't require a patch in debian/ I'll happily
> add the data differently. It seems I figured out how I can point the
> test data download url to where ever I want it :)

cool... pointers -- man dpkg-source:

   Format: 3.0 (quilt)
       A source package in this format contains at least an original tarball (.orig.tar.ext where ext can be gz, bz2, lzma and xz) and a debian tarball (.debian.tar.ext). It can also contain additional original tarballs (.orig-component.tar.ext).  component can only contain alphanumeric  char‐
       acters and dashes ("-").

       Extracting

       The  main  original  tarball  is  extracted  first, then all additional original tarballs are extracted in subdirectories named after the component part of their filename (any pre-existing directory is replaced). The debian tarball is extracted on top of the source directory after prior
       removal of any pre-existing debian directory. Note that the debian tarball must contain a debian sub-directory but it can also contain binary files outside of that directory (see --include-binaries option).

and also you could apt-get source python-dipy

which has two tarballs... get-orig-source target of debian/rules supposed
to fetch that additional one.

but once again, here it might really be better to have a separate data package
since that data might not change that often if ever.... but it would also
depend on how much data ants would also need to build/test

> I will ask about the copyright of the data.

FWIW: data itself is not copyrighted probably, but the "collection" might be.
upon a quick grep through ITK's copyright -- do not see explicit mention.
there is a good chance it would be the same data btw -- might be worth
checking... may be then ITK package could just "install" it (if it doesn't do it already) and we could jsut use it for ANTS???

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        
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