Bug#963593: Package ready

[Michael Hanke]

The package is done, and in local production use for a few days now. It
is hosted on github at https://github.com/mih/debian-annexremote.git
until DPMT approves my request to join the team.

Lintian 2.80 reports no issues with it.

-- 
Michael Hanke
GPG: 4096R/C073D2287FFB9E9B
http://psychoinformatics.de

Bug#963593: ITP: annexremote -- abstraction for git-annex special remote implementations

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke 

* Package name: annexremote
  Version : 1.4.3
  Upstream Author : Silvio Ankermann 
* URL : https://github.com/Lykos153/AnnexRemote
* License : GPL3
  Programming Lang: Python
  Description : abstraction for git-annex special remote implementations


This package is needed for packaging the 0.13 release of the datalad package.
Moreover, it is also used for other special remote implementations, such
as

- https://github.com/Lykos153/git-annex-remote-googledrive
- https://github.com/CONP-PCNO/git-annex-remote-globus

It is a simple package with no dependencies other than Python. I am not
aware of an alternative.

I am using it regularly. I plan to produce a package that is compliant
with the Debian Python Modules Team and have it be team maintained on
salsa.

Bug#889130: O: cctools

[Michael Hanke]

Package: wnpp
Severity: normal

Haven't used this package in a long time and the version in Debian is
two major releases behind upstream. Upstream does not use a standard
build system (but a custom configure script) that can make updates rather
time consuming.

The package has an overall low user count (popcon 43), and could be a
candidate for removal from the archive if nobody is interested in
maintaining it.

Bug#887598: ITP: jasp -- Offers standard analysis procedures in both their classical and Bayesian form

[Michael Hanke]

Hi,

just FYI there is/was a PR on JASP's GitHub with a semi complete packaging.
It had quite a few TODOs, but they should be detailed in the PR. Maybe that
is a useful starting point.

Cheers,

Michael



On Jan 21, 2018 21:35, "Andreas Tille"  wrote:

> Hi Joris,
>
> thanks for this ITP.  Please consider maintaining the package in Debian
> Science team.
>
> Kind regards
>
>   Andreas.
>
> On Thu, Jan 18, 2018 at 11:02:34AM +0100, jo...@jorisgoosen.nl wrote:
> > Package: wnpp
> > Severity: wishlist
> > Owner: Joris Goosen 
> > X-Debbugs-Cc: debian-de...@lists.debian.org
> >
> > * Package name: jasp
> >   Version : 0.8.5
> >   Upstream Author : JASP-team 
> > * URL : http://www.jasp-stats.org/
> > * License : GPL
> >   Programming Lang: C++, R
> >   Description : Offers standard analysis procedures in both their
> > classical and Bayesian form
> >
> >  JASP is a cross platform statistical software program with a
> > state-of-the-art
> >  graphical user interface. It offers standard analysis procedures in both
> >  their classical and Bayesian form.
> >  .
> >  It was designed with the user in mind: APA-formatted tables can be
> >  copy-pasted in your word processor, output can be extensively annotated,
> >  adjustment of input options dynamically changes the output, and
> selecting
> >  old output revives the associated input choices for inspection and
> > adjustment.
> >  .
> >  JASP is also statistically inclusive,
> >  as it offers both frequentist and Bayesian analysis methods.
> >  Indeed, the primary motivation for JASP is to make it easier for
> > statistical
> >  practitioners to conduct Bayesian analyses.
> >  .
> >  For more information and tutorials see: https://jasp-stats.org/
> >
> > 
> > This package is useful as it allows scientist, especially in the social
> > sciences, a friendly interface to state-of-the-art statistics techniques
> > and is under active development.
> > I plan to maintain as part of my work as one of the upstream-developers
> and
> > aim to make it fully debian compatible from the get-go.
> >
> > As far as i've understood the information on the debian-wiki we will
> need a
> > sponsor to be able to upload to the debian repositories.
>
> --
> http://fam-tille.de
>
>

Bug#886951: O: arno-iptables-firewall -- single- and multi-homed firewall script with DSL/ADSL support

[Michael Hanke]

Package: wnpp
Severity: normal

I intend to orphan the arno-iptables-firewall package. Popcon is at 468.
Upstream is very pleasant and releases are infrequent. However, I still
lack the resources to take proper care of this package.

The package description is:
 Unlike other lean iptables frontends in Debian, arno-iptables-firewall
 will setup and load a secure, restrictive firewall by just asking a few
 question. This includes configuring internal networks for internet access
 via NAT and potential network services (e.g. http or ssh).
 .
 However, it is in no way restricted to this simple setup. Some catch words
 of additional features, that can be enabled in the well documented
 configuration file are: DSL/ADSL, Port forwarding, DMZ's,
 portscan detection, MAC address filtering.

Bug#861327: ITP: fsleyes -- feature-rich viewer for volumetric images

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke <m...@debian.org>

* Package name: fsleyes
  Version : 0.10.1
  Upstream Author : Paul McCarthy <pauld.mccar...@gmail.com>
* URL : https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
* License : Apache-2
  Programming Lang: Python
  Description : feature-rich viewer for volumetric images

This is the successor of 'fslview' (currently in Debian, but stuck with
Qt4, and needs to be removed). This new viewer is a full replacement,
written in pure Python, using wx.

It requires a number of dependencies to become available in Debian
first. Namely, Python packages: fslpy, props (to be renamed to fsleyes-props),
and indexed_gzip. The latter is presently in NEW. The rest will follow
suit.

Bug#860084: ITP: libxdf -- static C++ library for loading XDF (multi-channel stream format) files

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke <m...@debian.org>

* Package name: libxdf
  Version : 0.93
  Upstream Author : Yida Lin (?)
* URL : https://github.com/Yida-Lin/libxdf
* License : GPL3
  Programming Lang: C++
  Description : static C++ library for loading XDF (multi-channel stream 
format) files


Libxdf is a cross-platform C++ library for loading multimodal,
multi-rate signals stored in XDF files. Libxdf is a core component of
bio-signal viewing application SigViewer. It can also be integrated into
other C++ applications.

The last release is just a few days old.

This is a new dependency of the sigviewer package that needs an update
to version 0.6 (#860083)

This package will be maintained by the NeuroDebian team.

At the moment upstream does not support building a shared library.

Bug#835493: ITP: indexed-gzip -- fast random access of gzip files in Python

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke <m...@debian.org>

* Package name: indexed-gzip
  Version : 0.1
  Upstream Author : Paul D McCarthy
* URL : https://github.com/pauldmccarthy/indexed_gzip
* License : BSDish https://opensource.org/licenses/zlib-license.php
  Programming Lang: Python
  Description : fast random access of gzip files in Python

[from the README]

The indexed_gzip project is a Python extension which aims to provide a
drop-in replacement for the built-in Python gzip.GzipFile class, the
IndexedGzipFile.

The standard gzip.GzipFile class exposes a random access-like interface
(via its seek and read methods), but every time you seek to a new point
in the uncompressed data stream, the GzipFile instance has to start
decompressing from the beginning of the file, until it reaches the
requested location.

An IndexedGzipFile instance gets around this performance limitation by
building an index, which contains seek points, mappings between
corresponding locations in the compressed and uncompressed data streams.
Each seek point is accompanied by a chunk (32KB) of uncompressed data
which is used to initialise the decompression algorithm, allowing us to
start reading from any seek point. If the index is built with a seek
point spacing of 1MB, we only have to decompress (on average) 512KB of
data to read from any location in the file.

Performance comparison:
https://github.com/pauldmccarthy/indexed_gzip#performance

This needs to be packaged as a dependency of a replacement of the
`fslview` (https://packages.debian.org/sid/fslview) package, which will
not make it into the next release due to its dependencies on obsolete
code (Qt4, ...).

This will be maintained by the NeuroDebian team.

Bug#798040: ITP: dcmstack -- DICOM to Nifti conversion

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke <m...@debian.org>

* Package name: dcmstack
  Version : 0.6.2
  Upstream Author : Brendan Moloney <molo...@ohsu.edu>
* URL : https://github.com/moloney/dcmstack
* License : MIT
  Programming Lang: Python
  Description : DICOM to Nifti conversion

 DICOM to Nifti conversion with the added ability to extract and summarize
 meta data from the source DICOMs. The meta data can be injected into a
 Nifti header extension or written out as a JSON formatted text file.
 .
 This package provides the Python package, command line tools (dcmstack,
 and nitool), as well as the documentation in HTML format.


This package is necessary for creating datsasets that are fully
compliant with and utilize all features of the BRAIN IMAGING DATA
STRUCTURE standard:

http://bids.neuroimaging.io

This is a new community norm for open-data in neuroimaging research.

This package will be maintained by the NeuroDebian team.

Bug#792279: ITP: nilearn -- fast and easy statistical learning on neuroimaging data

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke m...@debian.org

* Package name: nilearn
  Version : 0.1.3
  Upstream Author : Gael Varoquaux gael.varoqu...@normalesup.org
* URL : https://github.com/nilearn/nilearn
* License : BSD
  Programming Lang: Python
  Description : fast and easy statistical learning on neuroimaging data

 This Python module leverages the scikit-learn toolbox for multivariate
 statistics with applications such as predictive modelling, classification,
 decoding, or connectivity analysis.

As such, it extends the reach of sklearn (python-sklearn) into the
neuroimaging domain.

The package will be maintained by the NeuroDebian team.


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Bug#668596: irods packages update

[Michael Hanke]

Hi,

it seems that INCF has already created some IRODS packages:

https://github.com/INCF/ids-tools/wiki/Installing-the-IDS-Command-Line-Utilities

Right now (and according to INCF) things are being reorganized, so I
can't access the packages via the mentioned repo -- but it might be
worth keeping this in mind...

Michael

-- 
Michael Hanke
http://mih.voxindeserto.de


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Bug#686651: RFP: bulbs -- Python persistence framework for graph databases

[Michael Hanke]

Package: wnpp
Severity: wishlist

* Package name: bulbs
  Version : 0.2.2
  Upstream Author : James Thornton ja...@jamesthornton.com
* URL : http://bulbflow.com/
* License : BSD
  Programming Lang: Python
  Description : Python persistence framework for graph databases

From the website:

Bulbs is an open-source Python persistence framework for graph
databases.  It’s like an ORM for graphs, but instead of SQL, you use the
graph-traveral language Gremlin to query the database.

Bulbs supports pluggable backends, and you can use it to connect to
either Neo4j Server or Rexster.  Neo4j Server is Neo4j‘s official
server. Rexster is TinkerPop‘s server, and it supports any
Blueprints-enabled database, including Neo4j, OrientDB, Dex, and
OpenRDF.


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Bug#628183: ITP: freesurfer -- analysis and visualization of functional brain imaging data

[Michael Hanke]

On Tue, May 15, 2012 at 09:50:54PM +1000, Aníbal Monsalve Salazar wrote:
 Is there a Debian package of freesurfer already?
 
 May I help to upload it ot the Debian archive?

Mark Hymers (mhy) took the lead on this effort. I haven't heard back
from him regarding the status recently. Last time he mentioned that he
has some prototype package.

Michael


-- 
Michael Hanke
http://mih.voxindeserto.de



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Bug#471927: [Scratch] Scratch 1.4 source code released under GPL v2

[Michael Hanke]

On Wed, Apr 04, 2012 at 12:08:17PM +0200, Miriam Ruiz wrote:
 2012/4/4 Benj. Mako Hill m...@debian.org:
  I also think that the current text describing the trademark license
  make it clear that re-packaging is fine while using the marks (it
  says as much) so I don't forsee that this will be a problem getting
  things into Debian.
 
 Yup, I agree with your POV here. I don't expect big problems from
 ftpmasters, I hope we're right :)

A more fundamental issue could be a potential show stopper. Take a look
at the etoys package -- technically similar, FOSS license, but still in
non-free. Below a full quote from the source package's README.nonfree:

Why is EToys in non-free?
=

EToys was rejected from inclusion in the Debian main archive, because 
the
ftpmasters don't consider the sources as source. ;) Since we 
unsuccessfully
tried to convince them that EToys belongs into main already and the 
time until
Lenny will be frozen is short, I decided to upload it to non-free, for 
the
benefit of the users (so they can simply use apt-get to install etoys, 
provided 
they have non-free in their sources), even though we believe it 
satisfies all 
the requirements of the DFSG [1] and policy [2].  For Lenny+1 we plan 
to 
convince the ftpmasters to accept it in main.


Let me explain the source situation:
 
EToys comes as an image, a snapshot of all objects, which 
is loaded into a squeakvm, modified in memory, and snapshotted to
an image file again. This image cannot easily be rebuilt from pure 
source
code, but the snapshots do contain all the source code. The image is
the preferred form of modification for the EToys developer community,
this is how they work [3].
 
The Etoys image is derived from a Squeak image which is derived from a
Smalltalk image back to 1976, when the actual bootstrapping happened. 
This
is in contrast to how some Lisps work, they do a lengthy bootstrap from
source and then do a memory snapshot so they can skip the initialization
at startup time. To modify that snapshot, one changes the code and 
rebuilds 
the snapshot. But in Smalltalk, to modify the snapshot all the source 
code
tools patch live object memory directly. So we think this kind of 
source
form is enough to satisfy the DFSG.
 
Squeak source code in text form can be seen, shared and modified from 
within 
the squeakvm. That's what everybody does with Squeak source code. The 
changes 
are then either available as change sets or as Monticello packages 
(a 
version control system for Smalltalk code, see [4]), and can be 
distributed 
separatly or used to create derived versions of the modified blobs. But 
while
this works for small changes, this isn't practical to rebuild a 
complete image.
 

 [1] http://www.debian.org/social_contract#guidelines
 [2] file:///usr/share/doc/debian-policy/policy.html
 [3] 
http://lists.squeakfoundation.org/pipermail/squeak-dev/2008-May/128753.html
 [4] http://www.wiresong.ca/Monticello/


Holger Levsen, 2008-06-13

-- 
Michael Hanke
http://mih.voxindeserto.de



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Bug#664022: ITP: lazyarray -- Python module providing a NumPy-compatible lazily-evaluated array

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke m...@debian.org

* Package name: lazyarray
  Version : 0.1
  Upstream Author : Andrew P. Davison
* URL : http://bitbucket.org/apdavison/lazyarray/
* License : 3-clause-BSD
  Programming Lang: Python
  Description : Python module providing a NumPy-compatible lazily-evaluated 
array

 The 'larray' class is a NumPy-compatible numerical array where operations on
 the array (potentially including array construction) are not performed
 immediately, but are delayed until evaluation is specifically requested.
 Evaluation of only parts of the array is also possible. Consequently,
 use of an 'larray' can potentially save considerable computation time
 and memory in cases where arrays are used conditionally, or only parts of an
 array are used (for example in distributed computation, in which each MPI node
 operates on a subset of the elements of the array).


This is basically a single file package with a number of tests (98%
coverage). This package will be needed for a new release of python-pynn.
Debian has 0.7.0 right now, latest upstream is 0.7.2

http://packages.debian.org/sid/python-pynn



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Bug#633677: Bug#613337: libvia transition

[Michael Hanke]

Hi,

On Sun, Mar 04, 2012 at 11:17:56PM +0100, Julien Cristau wrote:
 On Thu, Feb  9, 2012 at 09:38:51 +0100, Michael Hanke wrote:
  I will upload a new SO version of LIBVIA shortly. Right now only ODIN
  and LIPSIA use this library. The LIBVIA dependency of ODIN will be
  dropped by the next upload (few more days).
 
 how many is few? :)

Thanks for moving this upwards on my TODO list. Of course things turned
out to be more complicated. New upstream version had some issues,
upstream needs more time, now libpng transition needs to be dealt with
for ODIN. If am lucky I can do all this sometime today. If not, I will
need few more days (TM) ;-)

Cheers,

Michael

-- 
Michael Hanke
http://mih.voxindeserto.de



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Bug#633677: Bug#613337: libvia transition

[Michael Hanke]

On Mon, Mar 05, 2012 at 09:49:16AM +0100, Michael Hanke wrote:
 Thanks for moving this upwards on my TODO list. Of course things turned
 out to be more complicated. New upstream version had some issues,
 upstream needs more time, now libpng transition needs to be dealt with
 for ODIN. If am lucky I can do all this sometime today. If not, I will
 need few more days (TM) ;-)

I prepared an upload that only deals with the via-transition for now.
However, it doesn't build in unstable due to:

The following packages have unmet dependencies:
  libvtk5.8: Depends: libnetcdf6 which is a virtual package.

libnetcdf6 is a transitional package and VTK could use a rebuild. VTK
Git shows a new package upload is coming, but it hasn't arrived yet.
Changelog:

vtk (5.8.0-7) unstable; urgency=low

  * Prepare vtk for move to multi-arch (png,tiff,z,jpeg). Closes: #661676
  * Bump to Std-Vers: 3.9.3, no changes needed.

 -- Mathieu Malaterre mathieu.malate...@gmail.com  Sun, 04 Mar 2012 21:54:19 
+0100


I guess this will resolve itself in a few days -- which I'll use to look
into the png-transition for ODIN.

Michael

-- 
Michael Hanke
http://mih.voxindeserto.de



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Bug#659641: ITP: python-quantities -- Support for physical quantities with units, based on numpy

[Michael Hanke]

Hi,

I'm attaching my packaging draft (as requested in your other email). See
my inline comments below:

On Wed, Feb 15, 2012 at 08:57:46AM +, Andrea Palazzi wrote:
 the package is already done, it was pretty easy with py2dsc; what i want to 
 do now is:
 - check the created package
 - create a git repository
 
 - add a copyright file: there's no copyright in the original .tar.gz,
 the only copyright claim that I've found is at 
 http://pypi.python.org/pypi/quantities; I've asked upstream to add an
 explicit copyright file, but had no answer up to today. BTW, can I
 write the copyright file only based on the page on python.org

Yes you can, there is also one in the attached tarball. Upstream should
add an explicit statement nevertheless.

 I would also appreciate some help on creating the git repository, I'm
 reading http://wiki.debian.org/Alioth/Git but some things aren't
 completely clear to me - e.g. will this be a collab maint project ?
 the project is debian-science ? Or what ?

collab-maint should be fine. I'd advise you to use git-buildpackage to
handle source import, etc.. If you like, I can also upload the repo that
I already have with my packaging draft and you clone it and add yourself
as package maintainer.

 I think that by the end of this week I could upload a first and
 reasonabily good version of the package to alioth.

That sounds perfect! If you need a sponsor for the upload I'd be
available for that -- just let me know.

Michael

-- 
Michael Hanke
http://mih.voxindeserto.de


quantitites_packaging.tar.gz
Description: Binary data

Bug#659641: ITP: python-quantities -- Support for physical quantities with units, based on numpy

[Michael Hanke]

Hi,

On Sun, Feb 12, 2012 at 07:49:04PM +0100, Andrea Palazzi wrote:
 Package: wnpp
 Severity: wishlist
 Owner: Andrea Palazzi palazziand...@yahoo.it
   Version : 0.10.1
   Upstream Author : Darren Dale dsdal...@gmail.com
 * URL : http://pypi.python.org/pypi/quantities
 * License : BSD
   Programming Lang: Python
   Description : Support for physical quantities with units, based on numpy

I have a packaging draft for this one, which I'm happy to contribute --
in case you haven't done it yourself yet (it is fairly straightforward).
The reaon I haven't pushed this package yet is that the unittests do
not pass and upstream didn't work on this code for a while. I filed
some bug reports, but nothing happened yet.

In any case, this package is needed as a dependency for a core pyton
library for electrophysiology data handling. Therefore I appreciate that
you are taking care of quantities.

Do you have an anticipated timeframe for an initial upload? Are you
aiming at team-maintenance within Debian Science?


Thanks,

Michael


-- 
Michael Hanke
http://mih.voxindeserto.de



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Bug#659691: ITP: neo -- IO library for electrophysiological data formats in Python

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke m...@debian.org

* Package name: neo
  Version : 0.2
  Upstream Author : Samuel Garcia, Pierre Yger, Luc Estabanez, Andrew Davison, 
Yury V. Zaytsev
* URL : http://neuralensemble.org/trac/neo
* License : BSD
  Programming Lang: Python
  Description : IO library for electrophysiological data formats in Python
 NEO stands for Neural Ensemble Objects and is a project to provide common
 class names and concepts for dealing with electro-physiological (in vivo
 and/or simulated) data with the aim of getting OpenElectrophy, NeuroTools,
 G-node and maybe other projects with similar goals more close together.
 .
 In particular Neo provides:
 .
  * a set a classes with precise definitions
  * an IO module that offer a simple API that fit many formats
  * documentation.
  * a set of examples like a format convertor



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Bug#633677: libvia transition

[Michael Hanke]

Dear Release Team,

I will upload a new SO version of LIBVIA shortly. Right now only ODIN
and LIPSIA use this library. The LIBVIA dependency of ODIN will be
dropped by the next upload (few more days). LIPSIA is currently totally
broken (#613337) and will be replaced with a new major version (probably
within the next 2-3 weeks). Before this can happen I need to upload a
new library package (ISIS; ITP #633677) that serves as the IO layer of
the new LIPSIA version, and a couple of upcoming packages. ISIS will
depend on the new VIA version.

As this transistion is a tiny one and all affected packages are
maintained by the NeuroDebian team I think that it would neither cause
trouble, nor do we need assistance.

Please let me know if I overlooked something and we should not do this
at this point.


Michael


-- 
Michael Hanke
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Bug#659282: ITP: eeglab -- electrophysiological data analysis

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke m...@debian.org

* Package name: eeglab
  Version : 11.0.0.0
  Upstream Author : Scott Makeig, Arnaud Delorme and others
* URL : http://sccn.ucsd.edu/eeglab
* License : GPL-2+
  Programming Lang: Matlab (Octave)
  Description : electrophysiological data analysis

 This is sofwware for processing continuous or event-related EEG or other
 physiological data. It is designed for use by both novice and expert
 users. In normal use, the EEGLAB graphic interface calls graphic functions
 via pop-up function windows. The EEGLAB history mechanism can save the
 resulting calls to disk for later incorporation into scripts.
 .
 This package provides EEGLAB to be used with Matlab. Note that this package
 depends on Matlab -- a commercial software that needs to be obtained and
 installed separately.


Notes
-

At this point this package basically only works with Matlab (hence
aiming at contrib). However, there is hope to enable an interesting
subset of non-GUI functionality to work with Octave. Upstream provides
a substantial unittest suite to help such an effort.

Until this can be achieved, this package, at least, strengthens Debian's
utility for electrophysiological data analysis, as eeglab is one of the
most popular tools in this field.

A number of source-less extensions from 3rd parties have been stripped
for DFSG-compliance.

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Bug#605739: Update

[Michael Hanke]

A preliminary packaging of EEGLAB11 has been done.

At this point this package basically only works with Matlab (hence
aiming at contrib). However, there is hope to enable an interesting
subset of non-GUI functionality to work with Octave. Upstream provides
a substantial unittest suite to help such an effort.

Until this can be achieved, this package, at least, strengthens Debian's
utility for electrophysiological data analysis, as eeglab is one of the
most popular tools in this field.

A number of source-less extensions from 3rd parties have been stripped
for DFSG-compliance.

The preliminary package can be fetched from http://neuro.debian.net in a
few hours.

Michael

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Bug#654748: O: qlandkartegt -- GPS mapping (GeoTiff and vector) and GPSr management

[Michael Hanke]

Package: wnpp
Severity: normal

I intend to orphan the qlandkartegt package. I do no longer use it
enough and do not have the time to give it the attention it deserves.
Open bugs are few (3), upstream is great and responsive. The packaging
is fairly modern (3.0, quilt), currently carries no upstream patches.
VCS is Git on collab-maint. Popcon is  500. The package requires an
update to the latest upstream release and some attention to the bugs.

I will also orphan the related 'garmindev' package in a second step.

If a non-DD wants to take care of this (fairly easy) package, I'm willing
to sponsor uploads.

The package description is:
 This package provides a versatile tool for GPS maps in GeoTiff format as
 well as Garmin's img vector map format. QLandkarteGT is the successor of
 QLandkarte. Among various improvements (e.g. 2D/3D map rendering and
 reduced resource demands) the major difference is its
 device-independent architecture, which is not limited to Garmin devices
 anymore. Therefore, the package also does not include device drivers.
 Drivers for a number of Garmin devices are available from the
 qlandkartegt-garmin package.
 .
 Additionally, QLandkarteGT serves as a frontend to the GDAL tools, to
 make georeferencing of scanned maps feasible for users. In contrast to
 similar tools (e.g. QGis) its straightforward interface is especially
 suited for non-scientific users.



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Bug#654749: O: garmindev -- QLandkarteGT plugins to access Garmin devices

[Michael Hanke]

Package: wnpp
Severity: normal

I intend to orphan the garmindev package. This package is a companion to
qlandkartegt That I also orphaned. Both should be adopted together.

As for qlandkartegt, I'm willing to sponsor uploads of a new non-DD
maintainer.

The package description is:
 A collection of plugins for QLandkarteGT to talk to various Garmin GPS devices,
 including GPSMap60CSx, GPSMap76, eTrexH, eTrexLegend and similar GPSr.



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Bug#654750: O: kbibtex -- BibTeX editor for KDE

[Michael Hanke]

Package: wnpp
Severity: normal

I intend to orphan the kbibtex package. I do not have enough time to
take care of this package properly. It is in pretty good shape (3.0,
quilt, 1 open bug, minimal patches), popcon 1800. The packaging is in
Git (pkg-exppsy on git.debian.org).

The primary task right now would be to investigate some spurious FTBFS
and get this latest upstream release to migrate into testing.

I'm willing to sponsor any non-DD taking over this package.


The package description is:
 An application to manage bibliography databases in the BibTeX format. KBibTeX
 can be used as a standalone program, but can also be embedded into other KDE
 applications (e.g. as bibliography editor into Kile).
 .
 KBibTeX can query online ressources (e.g. Google scholar) via customizable
 search URLs. It is also able to import complete datasets from NCBI Pubmed.
 It also supports tagging references with keywords and manages references to
 local files.
 .
 BibTeX files can be exported into HTML, XML, PDF, PS and RTF format using a
 number of citation styles.



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Bug#654750: O: kbibtex -- BibTeX editor for KDE

[Michael Hanke]

On Thu, Jan 05, 2012 at 04:48:30PM +0100, Bastien ROUCARIES wrote:
 On Thu, Jan 5, 2012 at 3:42 PM, Michael Hanke m...@debian.org wrote:
  Package: wnpp
  Severity: normal
 
  I intend to orphan the kbibtex package. I do not have enough time to
  take care of this package properly. It is in pretty good shape (3.0,
  quilt, 1 open bug, minimal patches), popcon 1800. The packaging is in
  Git (pkg-exppsy on git.debian.org).
 
 I can take care of it. Need mentoring

I'd say go for it. Please consider Andreas' suggestion to group-maintain
it under the debian-science umbrella. It would still need at least one
to be in charge. Group-maintenance might also facilitate the sponsoring
of new uploads.

Thanks for stepping up!

Michael

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Bug#641345: Preliminary package is available

[Michael Hanke]

Grab it from here:

  http://neuro.debian.net/debian/pool/main/p/pysurfer/


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Bug#641345: ITP: pysurfer -- visualize Freesurfer's data in Python

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: NeuroDebian team t...@neuro.debian.net


* Package name: pysurfer
  Version : 0.1+git
  Upstream Author : Michael Waskom, Alexandre Gramfort, Scott Burns, Satrajit 
Gosh
* URL : http://pysurfer.github.com/
* License : BSD-3
  Programming Lang: Python
  Description : visualize Freesurfer's data in Python
 This is a Python package for visualization and interaction with cortical
 surface representations of neuroimaging data from Freesurfer. It
 extends Mayavi’s powerful visualization engine with a high-level interface for
 working with MRI and MEG data.
 .
 PySurfer offers both a command-line interface designed to broadly replicate
 Freesurfer’s Tksurfer program as well as a Python library for writing scripts
 to efficiently explore complex datasets.



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Bug#633677: ITP: isis -- I/O framework for neuroimaging data

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: NeuroDebian Team t...@neuro.debian.net

* Package name: isis
  Version : 0.3.3
  Upstream Author : Lydia Hellrung (hellr...@cbs.mpg.de) et al.
* URL : http://isis-group.github.com/isis/
* License : GPL-2+
  Programming Lang: C++
  Description : I/O framework for neuroimaging data
 This framework aids access of and conversion between various established
 neuro-imaging data formats, like  Nifti, Analyze, DICOM and VISTA. ISIS
 is extensible with plugins to add support for additional data formats.

This IO framework is the base of the lipsia package and may also become
adopted by odin (both in Debian main). The completion of this packaging
effort is a prerequisite for updating the lipsia package to the latest
upstream release.



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Bug#471927: Packaging attempt

[Michael Hanke]

Hi,

last year I made an attempt to package it. It looks like licensing is a
non-issue as long as it is redistributable (which it is). The key point
is that ftp-masters consider the whole culture of squeak VMs as non-free
anyway.  Maybe they are are not aware of the point that the VM image is the
preferred form of modification. Take a look at the etoys package for the
story.

I git cloned their SVN and started stripping, unnecessary binary stuff
and evaluating whether it would work with Debian's squeak-vm. It looks
like it does.

Anyway, I got distracted repeatedly and never produced a respectable
packaging. Once I have that I'll publish the git repo. However, this
should not stop others from oding everything much quicker and better
than I could ;-)

Some open questions/tasks:

* Does it really need pulseaudio? Or: how can it be made easily
  configurable to use any of the supported audio backends?
* Ask for the sources of the binary plugins that are contained in SVN
  and shipped with scratch.
* Camera plugin got removed -- is there a replacement? Is it necessary?


Michael

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Bug#592390: Octave compatibility

[Michael Hanke]

The preliminary package has been updated to the latest upstream code recently.
Meanwhile upstream also worked on better Octave compatibility. The
status of this effort is documented here:

  http://en.wikibooks.org/wiki/SPM/Octave

There are a number of issue left to work on (both in SPM and Octave).
Volunteers are very welcome to pick one and fix it!

Michael

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Bug#618774: ITP: cctools -- cooperative computing tools

[Michael Hanke]

On Fri, Mar 25, 2011 at 11:30:06AM +0900, Charles Plessy wrote:
 Le Fri, Mar 18, 2011 at 08:36:32AM -0400, Michael Hanke a écrit :
  Package: wnpp
  Severity: wishlist
  Owner: Michael Hanke m...@debian.org
  
  * Package name: cctools
Version : 3.3.0
Upstream Author : Douglas Thain
  * URL : http://nd.edu/~ccl/software/
  * License : GPL-2
Programming Lang: C, Python
Description : cooperative computing tools
 
 Dear Michael and Luke,
 
 I just realised that both of you are preparing a package under the same name.
 Perhaps you need to discuss this before the first of you uploads.
 
 http://git.debian.org/?p=collab-maint/cctools.git
 http://git.debian.org/?p=pkg-exppsy/cctools.git

Thanks for spotting that Charles!

Luke:

I see that your package is already in Debian under the name 'chipw'. The
cctools that I'm packaging have been around under this name for some 7-8
years. What do you think about keeping the name 'chipw' for your source
package?

Regarding the binary package names I don't have a strong opinion. Maybe
we can both use more verbose names to disambiguate the software better.


What do you think?

Michael


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Bug#618774: ITP: cctools -- cooperative computing tools

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke m...@debian.org

* Package name: cctools
  Version : 3.3.0
  Upstream Author : Douglas Thain
* URL : http://nd.edu/~ccl/software/
* License : GPL-2
  Programming Lang: C, Python
  Description : cooperative computing tools
 This is a collection of software that help users to share resources in a
 complex, heterogeneous, and unreliable computing environment. This includes:
 .
  Chirp - A personal filesystem and I/O protocol that allows unprivileged users
  to share space securely, efficiently, and conveniently. When combined
  with Parrot, Chirp allows users to create custom wide-area distributed
  filesystems.
  Parrot - A transparent user-level virtual filesystem that allows any ordinary
  program to be attached to a remote storage device such as an FTP
  server or a Chirp server.
  Makeflow - A workflow system for parallel and distributed computing that uses
  a language very similar to Make.
  Work Queue - A system and API for building master-worker style programs that
  scale up to thousands of processors.
  All Pairs - A computational abstraction for running very large Cartesian
  products.
  Wavefront - A computational asbtraction for running very large dynamic
  programming problems.
  The Fault Tolerant Shell - A high-level programming language that allows
  users to combine the ease of shell scripting, the power of distributed
  programming, and the precision of compiled languages. Basically,
  parallel programming and exception handling for scripts.



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Bug#602842: Progress report

[Michael Hanke]

The libclassad package has been accepted into Debian. A condor package
draft is made and being tested right now. Discussions with upstream
regarding the merge of debian-related patches is ongoing -- stay
tuned...

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Bug#611640: Preliminary packaging

[Michael Hanke]

Preliminary packaging is done:

  https://github.com/hanke/OpenSesame
  [debian branch]

binary packages will appear at shortly

  http://neuro.debian.net/pkgs/opensesame.html

If testers are happy an official upload will follow.

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Bug#608922: ITP: matlab -- integrate local Matlab installations into the Debian system

[Michael Hanke]

On Tue, Jan 04, 2011 at 05:43:04PM +0100, Cyril Brulebois wrote:
   This package does NOT provide Matlab (TM).
 
 It really shouldn't be called “matlab” then.

The likelihood of Debian having a package that actually provides matlab
seems to be rather low. If it ever happens this package would be
obsolete and could be removed.

I assume you want to point to the problem of some people having matlab
packages that actually contain the binaries, right? How does Debian deal
with this issue? Could we have a 'skype' package?

What name do you suggest? Maybe 'matlab-package'?

Michael


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Bug#608922: ITP: matlab -- integrate local Matlab installations into the Debian system

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke m...@debian.org

* Package name: matlab
  Version : 0.0.13
  Upstream Author : Michael Hanke m...@debian.org
* URL : http://neuro.debian.net/pkgs/matlab.html
* License : GPL
  Programming Lang: POSIX shell
  Description : integrate local Matlab installations into the Debian system

 This package does NOT provide Matlab (TM). It merely helps sysadmins
 integrate local installations in the Debian system to handle this proprietary
 software in a more coherent way. Moreover, this package can be used as a
 runtime dependency for packages that install Matlab code and, for example,
 need to compile MEX extensions.
 .
 One or more Matlab installations can be registered with Debian's alternatives
 system, and a helper utility to build MEX extensions is provided. All
 configuration is conveniently done via debconf.

Moreover:

 Analogous to Octave a Makefile snippet is provided that configures the
 locations for architecture independent M-files, binary MEX-extensions, and
 there corresponding sources. This package can be used as a build-dependency
 by other packages shipping Matlab toolboxes.


Rational:

 There is already at least one package in Debian that installs MATLAB
 MEX extensions (http://packages.debian.org/sid/dynare-matlab, #608919).
 This package is inspired by the handling of MEX building implemented in
 this package, but aims at generalizing it and providing a helper for
 other packages.  The NeuroDebian project currently deals with a number
 of packages that _could_ ship MATLAB code. Moreover, we are working on
 making it easier for users and developers of formerly Matlab-only
 software to transition to Octave.  For this purpose it would be very
 useful to have both Octave and Matlab extensions available on a system,
 so that users can switch back and forth between them until full
 compatibility is reached (only going back to Matlab as long as still
 necessary) -- see http://neuro.debian.net/proj_matlab.html


From README.source:

 Although this whole package is pointless without Matlab (a large non-free
 something) the source package has been placed into 'main' for the following
 reason:

 It builds a 'matlab-dev' package that other source packages can build depend
 on to figure out where to install MEX sources and M-files (analogous to the
 way Octave packages provide this information via a Makefile snippet). This
 -dev package has nothing to do with Matlab and should go into 'main', as
 otherwise no source package that build-depends on it could go into 'main'.
 That would be suboptimal for otherwise DFSG-compliant package that simply
 also _can_ build MEX extensions (e.g. see the dynare-matlab package in the
 archive).

 The actual Matlab adaptor package is placed into 'contrib'.



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Bug#608922: ITP: matlab -- integrate local Matlab installations into the Debian system

[Michael Hanke]

On Tue, Jan 04, 2011 at 05:57:44PM +0100, Stefano Zacchiroli wrote:
 On Tue, Jan 04, 2011 at 11:49:55AM -0500, Michael Hanke wrote:
  What name do you suggest? Maybe 'matlab-package'?
 
 'matlab-integration' would be nice, but in the specific context of
 matlab might be misleading (cfr. 'octave-integration'). As a second
 choice, how about 'matlab-support'?

'matlab-support' it shall be.

Thanks for the feedback.

Michael

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Bug#519898: Status of gsoap

[Michael Hanke]

Hi,

I saw your interest in adopting gsoap. What is the status? You requested
sponsoring for a fresh upload, but that doesn't seem to have happened.
The last trace I could find was

  http://lists.debian.org/debian-mentors/2010/02/msg00397.html

I ran into a couple of issues with the current version in Debian (that
hasn't been updated for squeeze at all). If you are still interested I
can sponsor your work on gsoap -- although I'm afraid that it will be
too late for squeeze.


What do you think?

Michael

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Bug#605492: Update

[Michael Hanke]

On Tue, Nov 30, 2010 at 11:27:00AM -0500, Michael Hanke wrote:
 This software is distributed as a Matlab toolbox. However, the NIMH
 distributes a “port” of fieldtrip to Octave (at
 http://kurage.nimh.nih.gov/meglab/Meg/Software). It needs to be figured
 out who did that, whether this port can be incorporated into the
 official version, and to what degree it is complete.

According to some feedback on the fieldtrip mailing list it should work
quite well with Octave 3.2 already. However, there is no regular
testing/migration effort regarding Octave-compatibility of the
fieldtrip authors themselves.

The main obstacle for packaging right now is the lack of a build-system
to build MEX extensions for Octave and Matlab. The maintainer will
discuss this issue with the authors over the next couple of days.

Michael

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Bug#605492: ITP: fieldtrip -- toolbox for MEG and EEG analysis

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: fieldtrip
  Version : 0.20101101
  Upstream Author : Donders Institute for Brain, Cognition and Behaviour
* URL : http://fieldtrip.fcdonders.nl
* License : GPL-2+
  Programming Lang: Matlab/Octave
  Description : toolbox for MEG and EEG analysis
 The software includes algorithms for simple and advanced analysis of MEG and
 EEG data, such as time-frequency analysis, source reconstruction using dipoles,
 distributed sources and beamformers and non-parametric statistical testing. It
 supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of
 the most popular EEG systems, and new formats can be added easily. FieldTrip
 contains high-level functions that you can use to construct your own analysis
 protocols in Matlab. Furthermore, it easily allows developers to incorporate
 low-level algorithms for new EEG/MEG analysis methods.


This software is distributed as a Matlab toolbox. However, the NIMH
distributes a “port” of fieldtrip to Octave (at
http://kurage.nimh.nih.gov/meglab/Meg/Software). It needs to be figured
out who did that, whether this port can be incorporated into the
official version, and to what degree it is complete.

Packaging fieldtrip is required to complete the packaging of SPM8
(#592390).



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Bug#409849: Patches submitted upstream

[Michael Hanke]

All patches of the Debian packaging have been submitted upstream. Due to
the large size (and sometimes potentially disruptive nature) it might
take a while to get them reviewed, and hopefully included in the
upstream source tree.

However, if this is done, we are almost ready to submit AFNI for
inclusion into Debian -- just 3.5 years later!

Love it,

Michael

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Bug#592390: Preview package is available

[Michael Hanke]

Hi,

an initial packaging is available from

  http://neuro.debian.net/pkgs/matlab-spm8.html

This one only works with matlab -- the octave port is slowly moving
forward, but doesn't yet enable any significant functionality that would
be worth putting into an octave-spm8 package.

The good news is that upstream, reviewed the Debian packaging is
provides a lot of useful advise that will eventually lead to a solid
Debian package.

A major TODO item remains the packaging of the fieldtrip toolbox. I
found a port to Octave (of unknown level of completeness). ITP probably
follows soon.

Michael

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Bug#603336: ITP: classads -- library for Condor's classads expression language

[Michael Hanke]

Hey Gürkan,

On Wed, Nov 17, 2010 at 10:46:59AM +0100, Gürkan Sengün wrote:
 Hello Michael
 
 I am very glad you are packaging (or adapting the Ubuntu) Condor
 package for Debian. Thank you, if there's anything I can help with,
 tell me.

Thanks for thanks! ;-)

I'm right now wading through the code stripping binary blobs, setting up
build scripts for Java pieces, etc. My goal is to revive the old Debian
packaging (which had much more interesting features than the Ubuntu
one). If you want to join the effort, I'd be glad. Are you, by any
chance running condor in your department?

Cheers,

Michael

PS: Gerne auch in Deutsch, wenn Dir das besser gefällt.


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Bug#603336: ITP: classads -- library for Condor's classads expression language

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: classads
  Version : 1.0.9
  Upstream Author : Condor Team condor-ad...@cs.wisc.edu
* URL : http://www.cs.wisc.edu/condor/classad
* License : Apache
  Programming Lang: C++,
  Description : library for Condor's classads expression language

 A classad (classified ad) is a mapping from attribute names to expressions. In
 the simplest cases, the expressions are simple constants (integer, floating
 point, or string), thus a form of property list. Attribute expressions
 can also be more complicated. There is a protocol for evaluating an attribute
 expression of a classad vis a vis another ad. Two classads match if each ad has
 attribute requirements that evaluate to true in the context of the other ad.
 Classad  matching is used by the Condor central manager to determine the
 compatibility of jobs and workstations where they may be run.


This package is necessary for packaging Condor itself (#602842). Ubuntu
has a classads package that served as starting point of this effort.
Here is the current list of changes on top of that:

  * Shorten and slightly improve package descriptions.
  * Raise debhelper compat to 7 (already build-depended on 7).
  * Add another binary package 'classads' to install the command line
utilities. Keeping them in the runtime library package would have made it
impossible to co-install a future libclassad1 package, due to file
conflicts.
  * Move to an unversioned -dev package. There is no intention to maintain
multiple library versions in parallel.
  * No longer install unneeded .la files (squeeze release goal).
  * No longer install duplicate license files as docs.
  * Add VCS information to debian/control.
  * Move to a DEP-5 compliant debian/copyright.
  * Improve clean target in debian/rules to remove all temporary files.

The packaging is available at:

  http://git.debian.org/?p=pkg-exppsy/classads.git

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Bug#602842: ITP: condor -- workload management system

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: condor
  Version : 7.4.4
  Upstream Author : Condor Team, Computer Sciences Department, University of 
Wisconsin-Madison
  URL : http://www.cs.wisc.edu/condor
* License : Apache License, Version 2
  Programming Lang: C++, Java
  Description : workload management system

Description
---

 [from webpage]

 Condor is a specialized workload management system for
 compute-intensive jobs. Like other full-featured batch systems, Condor
 provides a job queueing mechanism, scheduling policy, priority scheme,
 resource monitoring, and resource management. Users submit their serial
 or parallel jobs to Condor, Condor places them into a queue, chooses
 when and where to run the jobs based upon a policy, carefully monitors
 their progress, and ultimately informs the user upon completion.

 While providing functionality similar to that of a more traditional
 batch queueing system, Condor's novel architecture allows it to succeed
 in areas where traditional scheduling systems fail. Condor can be used
 to manage a cluster of dedicated compute nodes (such as a Beowulf
 cluster). In addition, unique mechanisms enable Condor to effectively
 harness wasted CPU power from otherwise idle desktop workstations. For
 instance, Condor can be configured to only use desktop machines where
 the keyboard and mouse are idle. Should Condor detect that a machine is
 no longer available (such as a key press detected), in many
 circumstances Condor is able to transparently produce a checkpoint and
 migrate a job to a different machine which would otherwise be idle.
 Condor does not require a shared file system across machines - if no
 shared file system is available, Condor can transfer the job's data
 files on behalf of the user, or Condor may be able to transparently
 redirect all the job's I/O requests back to the submit machine. As a
 result, Condor can be used to seamlessly combine all of an
 organization's computational power into one resource.

Plan


At the batch queueing systems BoF at DebConf10 this software has been
discussed as a potential addition to Debian. I plan to start tracking
the 'stable' series -- maybe adding a dedicated package for the
'development' series sometime in the future (if there is enough
manpower).  Upstream already has some Debian packages, but uses external
software that is downloaded and built from source instead of exclusively
relying on Debian packages. I want to start from upstream packaging and
improve integration into the Debian system.

If you are interested in co-maintaining this package, please drop me a
note.



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Bug#602842: Package in ubuntu

[Michael Hanke]

Found a condor and classads package in Ubuntu. Condor packages are
outdated (7.2 instead of current stable series 7.4). classads package is
current. Dropped a note to the Ubuntu maintainer, asking for info about
packaging effort and potential collaboration to keep Debian and Ubuntu
packages in sync.

Michael

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Bug#409849: Segfault with lesstif -- works with openmotif

[Michael Hanke]

AFNI segfaults when built against lesstif2. The steps to replicate are:

1. Start AFNI with any dataset.
2. Add atlas as overlay.
3. Open image viewer (any slice orientation, e.g. axial)
4. Right-click on any voxel and select where am i
5. Left-click on two other voxels
6. Segfault.

GDB show that lesstif gets into a long loop doing the following over an
over:

#21788 0xb7858eb4 in XmTextSetString () from /usr/lib/libXm.so.2
#21789 0xb78591bf in ?? () from /usr/lib/libXm.so.2
#21790 0xb7595e52 in ?? () from /usr/lib/libXt.so.6
#21791 0xb7596b64 in XtSetValues () from /usr/lib/libXt.so.6
#21792 0xb78584d8 in _XmTextUpdateLineTable () from /usr/lib/libXm.so.2
#21793 0xb786c909 in ?? () from /usr/lib/libXm.so.2
#21794 0xb786bed8 in _XmStringSourceSetValue () from /usr/lib/libXm.so.2

There is an open lesstif bug that might be related:

  http://bugs.debian.org/379011

The relevant action seems to be triggered from

#21828 0xb7ba20b2 in MCW_textwin_alter () from /usr/lib/afni/lib/libmrix.so
#21829 0x08071ddc in AFNI_set_viewpoint ()

A test build of AFNI against current openmotif doesn't show this bug.

Upstream doesn't use lesstif, because of various problems. This is the
first issue that could verified and documented.

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Bug#600275: ITP: nibabel -- Python bindings to various neuroimaging data formats

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: NeuroDebian team t...@neuro.debian.net

* Package name: nibabel
  Version : 1.0.0
  Upstream Author : NiBabel developers nipy-de...@neuroimaging.scipy.org
* URL : http://nipy.sourceforge.net/nibabel
* License : Expat
  Programming Lang: Python
  Description : Python bindings to various neuroimaging data formats

 This package provides read and write access to some common medical and
 neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
 NIfTI1, MINC, as well as PAR/REC. The various image format classes give full
 or selective access to header (meta) information and access to the image data
 is made available via NumPy arrays.  NiBabel is the successor of PyNIfTI.
 .
 This package also provides a commandline tool for conversion of PAR/REC to
 NIfTI images.


This package will eventually replace the python-nifti package in Debian.



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Bug#599880: ITP: mriconvert -- medical image file conversion utility that converts DICOM files to other formats

[Michael Hanke]

Hi Steve
On Mon, Oct 11, 2010 at 11:32:17PM -0500, Steve M. Robbins wrote:
 Package: wnpp
 Severity: wishlist
 Owner: Steve M. Robbins s...@debian.org
 
 * Package name: mriconvert

Thanks for packaging this tool. I have extended Andreas Tille's entry in
the med-imaging task and also added it to
science-neuroscience-cognitive.


Michael

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Bug#409849: AFNI packaging now cmake-based and with afni-dev

[Michael Hanke]

The AFNI package has now been updated to source package format 3.0
(quilt) and uses a debhelper-dh based rules files. As of last week all
patches, including the new CMake-based build system, have been submitted
to upstream for review and potential inclusion.


Meanwhile, up-to-date packages are still avialable from http://neuro.debian.net

Michael

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Bug#567142: O: libqwt

[Michael Hanke]

On Tue, Aug 31, 2010 at 06:42:18PM -0400, Michael Hanke wrote:
 Not sure if I ever got an answer to this one -- let me contact upstream
 and clarify that finally.

Ok, upstream is looking into this issue. If it turns out that there
won't be a short-term solution, I'd volunteer to adopt the package till
fslview has been ported to qwt5 and qwt4 can be removed from the
archive. Since the qwt4 package seems to be in good standing I assume
there is no urgent need for action, correct?


Michael

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Bug#567142: O: libqwt

[Michael Hanke]

On Wed, Sep 01, 2010 at 12:12:04AM +0200, Moritz Muehlenhoff wrote:
 What are their plans of a port? This would allow us to remove qwt4.

Not sure if I ever got an answer to this one -- let me contact upstream
and clarify that finally.

Michael


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Bug#592390: ITP: spm8 -- analysis of brain imaging data sequences

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: NeuroDebian team t...@neuro.debian.net

* Package name: spm8
  Version : 8.4010
  Upstream Author : Wellcome Trust Centre for Neuroimaging s...@jiscmail.ac.uk
* URL : http://www.fil.ion.ucl.ac.uk/spm/software/spm8/
* License : GPL-2+
  Programming Lang: Matlab/Octave
  Description : analysis of brain imaging data sequences

 Statistical Parametric Mapping (SPM) refers to the construction and
 assessment of spatially extended statistical processes used to test
 hypotheses about functional brain imaging data. These ideas have been
 instantiated in software that is called SPM. It is designed for the
 analysis of fMRI, PET, SPECT, EEG and MEG.


This software is written to be used with Matlab and probably to most
widely used piece of software in neuroimaging research. The authors
state that

  Scilab and Octave are free clones of MATLAB, but SPM does not
  currently run on either. Porting SPM to these environments should be
  feasible but would require an important investment.

It looks like a port is indeed feasible: MEX extensions already build
fine with Octave, there are no dependencies to Mathworks toolboxes. For
few API incompatibilities workarounds have already been identified. We
plan to enable all non-GUI functionality that can be utilized within the
NiPyPE framework (http://packages.debian.org/sid/python-nipype), which
will also allow us to appropriately test the package.

If you have some experience with Octave and/or SPM you're welcome to
join this packaging effort. A git repository will appear on Alioth shortly.



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Bug#409849: AFNI missing templates

[Michael Hanke]

Hi,

On Tue, Jul 13, 2010 at 01:48:56PM -0400, Pam Pallett wrote:
 br...@neurodebian:~$ which @auto_tlrc
 /usr/lib/afni/bin/@auto_tlrc
 br...@neurodebian:~$ @auto_tlrc -base /usr/lib/afni/bin/TT_avg152T1+tlrc
 -input fWIPHiResSENSEs003a001.nii.gz
 Parsing ...
 Error: Template dset /usr/lib/afni/bin/TT_avg152T1+tlrc not found.
 
 Hope this bug report is useful.  And if it is not a true bug, but rather
 user error, please let me know.  Otherwise, it seems that the templates are
 missing from the package.

Thanks for your report. The AFNI package is far from being in the state
it should be -- work is under way!

Regarding your issue: Do you have the afni-atlases package installed?


Michael

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Bug#587047: ITP: gifticlib -- IO library for the GIFTI cortical surface data format

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: gifticlib
  Version : 1.0.8
  Upstream Author : Richard Reynolds reyno...@mail.nih.gov
* URL : http://www.nitrc.org/projects/gifti/
* License : Public domain
  Programming Lang: C
  Description : IO library for the GIFTI cortical surface data format

GIFTI is an XML-based file format for cortical surface data. This reference
IO implementation is developed by the Neuroimaging Informatics Technology
Initiative (NIfTI).



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Bug#579284: Preliminary package

[Michael Hanke]

A preliminary package is available from:

  http://neuro.debian.net/pkgs/voxbo.html

Michael


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Bug#584920: ITP: invesalius -- 3D medical imaging reconstruction toolkit

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: invesalius
  Version : 3.0.0
  Upstream Author : Thiago Franco de Moraes and many more
* URL : http://svn.softwarepublico.gov.br/trac/invesalius
* License : GPL
  Programming Lang: Python
  Description : 3D medical imaging reconstruction toolkit

3D medical imaging reconstruction based on a sequence of 2D DICOM files
acquired with CT or MRI equipments, providing several visualization
tools. More information is available on the webpage.

The package will probably be team-maintained by Debian Med and/or the
upstream authors themselves. A packaging effort is already on-going
since a while. I'm finally filing this ITP to properly document this and
add proper tags which open bugs block this effort.


Michael



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Bug#584436: ITP: drmaa -- Python interface to DRMAA-compliant distributed resource management systems

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: drmaa
  Version : 0.4beta3
  Upstream Author : Enrico Sirola enrico.sir...@gmail.com
* URL : http://code.google.com/p/drmaa-python
* License : BSD
  Programming Lang: Python
  Description : Python interface to DRMAA-compliant distributed resource 
management systems

 This is a Python implementation of the Distributed Resource Management (DRM)
 Application API (DRMAA). It provides all high-level functionality necessary
 to consign a job to a DRM system (e.g. Sun Gridengine), including common
 operations on jobs, such as termination or suspension.



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Bug#580662: ITP: pyoptical -- python interface to the CRS 'OptiCAL' photometer

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: pyoptical
  Version : 0.2
  Upstream Author : Valentin Haenel valentin.hae...@mail.tu-berlin.de
* URL : http://github.com/esc/pyoptical
* License : MIT/X
  Programming Lang: Python
  Description : python interface to the CRS 'OptiCAL' photometer

 The 'OptiCAL' is a photometer that is produced by Cambridge Research
 Systems (CRS).  This device is a standard tool for gamma-calibration of
 display devices in vision research. This package provides a
 free-software replacement for the Windows-software distributed by the
 manufacturer that allows querying an OptiCAL via a serial connection.
 pyoptical can be used as a library in third-party applications or as a
 standalone command line tool.



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Bug#580499: ITP: psignifit3 -- fitting and testing hypotheses about psychometric functions

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: psignifit3
  Version : 3.0.0~beta1
  Upstream Author : Ingo Fruend, Valentin Haenel
* URL : http://psignifit.sourceforge.net/
* License : MIT
  Programming Lang: C++, Python
  Description : fitting and testing hypotheses about psychometric functions

 This package allows fitting of psychometric functions to datasets while
 maintaining full control over a large number of parameters. Psignifit performs
 the calculation of confidence intervals as well as goodness-of-fit tests.

 This is the successor of 'psignifit' a commandline-based toolbox. The new
 version is primarily a python module, but other bindings will be added
 eventually.

Please note that there is already a package for the old psignifit in the
archive. I'm discussing with upstream if the new version can possibly
provide some simple wrappers to emulate the old commandline tools, in
which case the current source package could be removed.



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Bug#579284: ITP: voxbo -- processing, statistical analysis, and display of brain imaging data

[Michael Hanke]

On Tue, May 04, 2010 at 12:43:35AM +0200, Frank Lin PIAT wrote:
 On Mon, 2010-04-26 at 15:05 -0400, Michael Hanke wrote:
  Package: wnpp
  Severity: wishlist
  Owner: Michael Hanke michael.ha...@gmail.com
  
  * Package name: voxbo
Version : 1.8.5
Upstream Author : Daniel Kimberg kimberg mail.med.upenn.edu
  * URL : http://www.voxbo.org
  * License : GPL-3
Programming Lang: C++
Description : processing, statistical analysis, and display of brain 
  imaging data
 
 This is a pretty long short-description, I suggest:
   analysis, and display of brain imaging data

Yes, will do so.

   This is a toolkit for analysis of functional neuroimaging (chiefly
   fMRI) experiments and voxel-based lesion-behavior mapping. VoxBo
   supports the modified GLM (for autocorrelated data), as well as the
   standard GLM for non-autocorrelated data. The toolkit is designed to be
   interoperable with AFNI, FSL, SPM and others.
 
 The package description could mention that it is targeted for medical
 field.

Do you have any specific phrase in mind. Voxbo is not limited to medical
usecases, but first and foremost neuroimaging/cognitive neuroscience research.

Thanks,

Michael

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Bug#579588: ITK-SNAP package available (was: Howto prevent viral dependency propagation by ITK or GDCM?)

[Michael Hanke]

On Sat, May 01, 2010 at 01:52:49AM -0500, Junqian Gordon Xu wrote:
 Just want to say hhanks for working on ITK-SNAP.

You're welcome. The package is now in NEW, but you can get it
from http://neuro.debian.net/pkgs/itksnap.html already.

Michael

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Bug#579588: ITP: itksnap -- semi-automatic segmentation of structures in 3D images

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: itksnap
  Version : 2.0.0
  Upstream Author : Paul A. Yushkevich et al.
* URL : http://www.itksnap.org
* License : GPL
  Programming Lang: C++
  Description : semi-automatic segmentation of structures in 3D images

 SNAP provides semi-automatic segmentation of structures in medical
 images (e.g.  magnetic resonance images of the brain) using active
 contour methods, as well as manual delineation and image navigation.
 Noteworthy features are:
 .
  * Linked cursor for seamless 3D navigation
  * Manual segmentation in three orthogonal planes at once
  * Support for many different 3D image formats, including NIfTI
  * Support for concurrent, linked viewing and segmentation of multiple images
  * Limited support for color images (e.g., diffusion tensor maps)
  * 3D cut-plane tool for fast post-processing of segmentation results



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Bug#579470: ITP: mrtrix -- diffusion-weighted MRI white matter tractography

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: mrtrix
  Version : 0.2.8
  Upstream Author : J-D Tournier
* URL : http://www.brain.org.au/software/mrtrix
* License : GPL-3
  Programming Lang: C++
  Description : diffusion-weighted MRI white matter tractography

 Set of tools to perform diffusion-weighted MRI white matter tractography of the
 brain in the presence of crossing fibres, using Constrained Spherical
 Deconvolution, and a probabilisitic streamlines algorithm. Magenetic resonance
 images in DICOM or ANALYZE format are supported.



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Bug#579231: ITP: mricron -- magnetic resonance image conversion, viewing and analysis

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: mricron
  Version : 0.20100422.1
  Upstream Author : Chris Rorden rorden gatech.edu
* URL : http://www.cabiatl.com/mricro/mricron/index.html
* License : BSD
  Programming Lang: Pascal
  Description : magnetic resonance image conversion, viewing and analysis

 GUI-based visualization and analysis tool for (functional) magnetic reasonance
 imaging. MRIcron can be used to create 2D or 3D renderings of statistical
 overlay maps on brain anatomy images. Moreover, it aids drawing anatomical
 regions-of-interest (ROI), or lesion mapping, as well as basic analysis
 of functional timeseries (e.g. creating plots of peristimulus signal-change).
 .
 This package also provides 'dcm2nii' that supports converting DICOM and PAR/REC
 images into the NIfTI format.



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Bug#579284: ITP: voxbo -- processing, statistical analysis, and display of brain imaging data

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: voxbo
  Version : 1.8.5
  Upstream Author : Daniel Kimberg kimberg mail.med.upenn.edu
* URL : http://www.voxbo.org
* License : GPL-3
  Programming Lang: C++
  Description : processing, statistical analysis, and display of brain 
imaging data

 This is a toolkit for analysis of functional neuroimaging (chiefly
 fMRI) experiments and voxel-based lesion-behavior mapping. VoxBo
 supports the modified GLM (for autocorrelated data), as well as the
 standard GLM for non-autocorrelated data. The toolkit is designed to be
 interoperable with AFNI, FSL, SPM and others.



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Bug#579231: Preliminary package available

[Michael Hanke]

There are some open licensing issues pending, but a (presumably) working
package is available from http://neuro.debian.net.


Michael

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Bug#567142: O: libqwt

[Michael Hanke]

Hi,

On Wed, Jan 27, 2010 at 08:54:21AM -0800, Brian Nelson wrote:
 Package: wnpp
 Severity: normal
 
 Orphaning libqwt (version 4) as I no longer have an interest in
 packaging it.  Version 5 already exists as a separate package in the
 archive.
 
 The only remaining dependency on this library is fslview.  Ideally
 fslview could be updated to use qwt5, in which case this older qwt could
 be removed from the archive.

I will check whether fslview would work with qwt5, and report here.

Thanks for the note,

Michael

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Bug#567142: O: libqwt

[Michael Hanke]

On Wed, Jan 27, 2010 at 01:03:17PM -0500, Michael Hanke wrote:
 Hi,
 
 On Wed, Jan 27, 2010 at 08:54:21AM -0800, Brian Nelson wrote:
  Package: wnpp
  Severity: normal
  
  Orphaning libqwt (version 4) as I no longer have an interest in
  packaging it.  Version 5 already exists as a separate package in the
  archive.
  
  The only remaining dependency on this library is fslview.  Ideally
  fslview could be updated to use qwt5, in which case this older qwt could
  be removed from the archive.
 
 I will check whether fslview would work with qwt5, and report here.

I tried simply rebuilding it, but it doesn't work. I started composing a
patch, but the changes are numerous, so I postponed that for now.
Instead, I dropped upstream a note, asking about a possible port to
qwt5.

Michael

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Bug#556552: Preliminary package is available

[Michael Hanke]

A preliminary packaging is done und available from

  http://neuro.debian.net/pkgs/openelectrophy.html

Michael


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Bug#556552: ITP: python-openelectrophy -- data analysis framework for intra- and extra-cellular recordings

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: python-openelectrophy
  Version : 0.0.svn145
  Upstream Author : Samuel Garcia, Nicolas Fourcaud-Trocmé
* URL : http://neuralensemble.org/trac/OpenElectrophy
* License : Cecill v2
  Programming Lang: Python
  Description : data analysis framework for intra- and extra-cellular 
recordings


This package provide a library und GUI for analyzing electrophysiological data.
(imagine the rest of a long description)


There has been some debate whether the Cecill v2 license can be
considered DFSG-compatible [0]. Wikipedia says '?' [1]. It claims to be
GPL-compatible and might allow relicensing under the GPL. If it turns out to
be incompatible, I'll try to talk with upstream about it -- otherwise
the package would target 'non-free'.

The software essentially exposes a 'pyssdh' package, hence the Debian
package might be named python-pyssdh. However, the package also serves
as the 'OpenElectrophy' GUI-application (via python-qt4) and I guess
this is what users would look for. It might be reasonable to add an
additional arch:all binary package 'openelectrophy' that merely contains
the short wrapper script distributed by upstream and a link in /usr/bin
and otherwise depend on python-pyssdh -- not sure yet whether this is
the way to go.

The main (and only) form of distribution is via SVN. It has never been
released the tarball way, hence the made up version.

I am about to add this project to the relevant task pages of the
Debian-Med and -Science pure blends.

[0] http://lists.debian.org/debian-legal/2008/12/msg00045.html
[1] http://en.wikipedia.org/wiki/CeCILL



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Bug#409849: AFNI packaging now cmake-based and with afni-dev

[Michael Hanke]

The current version of the draft package does now use ffmpeg to encode
videos, instead of mpeg_encode that I stripped from the sources due to
being upstream-dead and having patent-issues.

With this change AFNI should have full functionality (besides 3dedge3
support).

The only major task that has to be done before an initial upload to
Debian is a copyright/license screening. Given the size of the AFNI
sources this is a somewhat significant effort...


Meanwhile, up-to-date packages are avialable from http://neuro/debian/net


Michael

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Bug#409849: AFNI packaging now cmake-based and with afni-dev

[Michael Hanke]

Hi,

I just pushed the changes for a new version of the AFNI packaging to
git.debian.org. It now uses a cmake-based buildsystem. The initial patch
was contributed by Bernd Feige and I further tweaked it to shrink the
size, add options for conditional building.

The Debian packaging now takes advantage of the increased flexibility
also provides a 'afni-dev' package with headers and _static_ libraries
for plugin development. The AFNI programs, however, use dynamic linking.
This allows for a dramatic reduction of the binary distribution to less
than 10% of the upstream distribution -- altogether less than 20MB
(including the altas data)!

I am currently building binary package for http://neuro/debian/net.

Please give it a try and tell me if it causes any problems.


Thanks,

Michael


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Bug#409849: First rough draft of an afni Debian package

[Michael Hanke]

On Tue, Oct 20, 2009 at 06:01:12PM -0400, Judd Storrs wrote:
 
   The place is fine, but how did you determine the subset of headers that
  should go into it. If we can automize that, it might scale a bit better
  with the future AFNI development.
 
  However, the more serious problem is that having a -dev package also
  implies that the libs can be used elsewhere -- which is actually not
  the case. Without a proper versioning scheme and sane interface policies
  we cannot expose the shared libs (that I imagined to be internal
  convenience libs) like this. What could be done is adding static libs to
  the -dev package. However, already now it is significant pain to build
  shared libs alone -- building both is even more tricky using AFNI's
  cumbersome build system...
 
 
 It's based mostly on the LIBHEADERS list in Makefile.INCLUDE. I also
 included afni.h and all its dependencies because afni.h is needed to compile
 plugins for the afni viewer. I'm working on a plugin and I noticed I
 couldn't compile, but you're right. I'm not sure which of the headers are
 needed for full functionality of the libraries. Another approach would be to
 install all the headers that don't originate from other packages.
 
 I'm not sure I would bother with static libraries.  An alternative would be
 to get rid of afni-dev altogether and include the headers in
 /usr/lib/afni/include as part of afni-common or something. LIBHEADERS are
 distributed in the binary packages from the NIH so debian would just be
 doing what they already do. NIH doesn't include afni.h so that can probably
 be omitted.

Nah, we should do it properly. If people develop plugins (and apparently
they do) we should support that with a proper -dev package. I will take
a look at this issue.

  AFNI.afnirc and AFNI.sumarc are now simply shipped as examples in the
  afni-common package, but I guess they should become somewhat more
  functional. My own config scheme in /etc/afni/afni.sh takes care of the
  most critical settings, but the majority is left untouched. I am not
  sure about implementing a proper default system-wide config setup --
  right now this per-user thingie that comes with AFNI feels incomplete
  and suboptimal. Advice is most welcome, since I am not really a
  proficient AFNI user.
 
 
 I think the way you have done it is best. It is important to avoid burdening
 the NIH developers with problems that originate from the debian packaging. I
 would leave things the way they would be if the user had downloaded the
 binary builds from the NIH directly--i.e. no configuration--let's not
 surprise the NIH. The path setting in /etc/afni/afni.sh is good because it's
 necessary. I'd resist the urge to improve unless there are debian-specific
 advantages/reasons. Otherwise it becomes another layer of confusion when
 newcomers post to the message board. The .config/AFNI stuff--that's OK, but
 AFNI already uses .afnirc etc and I doubt anybody on the message board is
 going to know about .config. My feeling is that users would expect the
 debian package to help install afni and dependencies and help keep it
 up-to-date.

Point taken. However, .config/AFNI/* (shell script) is different from
.afnirc (afni's own format) -- but yes the Debian package's behavior
should be identical to the upstream AFNI distribution. But we might
nevertheless achieve that in a slighlty more elegant way ;-)

Michael

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Bug#409849: AFNI development history imported

[Michael Hanke]

On Mon, Oct 19, 2009 at 12:25:59PM -0400, Michael Hanke wrote:
 On Mon, Oct 19, 2009 at 11:42:29AM -0400, Michael Hanke wrote:
  I will push the AFNI packaging to git.debian.org shortly (will drop a
  note here, when it is done).
 
 Now available at
 
   http://git.debian.org/?p=pkg-exppsy/afni.git;a=summary

I'n sorry, but I redid this respository. I restarted by importing all
available AFNI release tarballs since 1998. While there is no public VCS
we now have at least some history. For the future I started tracking the
daily snapshots (AFNI_latest.tgz). Whenever there is something new it is
imported in the `upstream` branch of the new git repository -- It is
actually done in a separate repos and I will push after manual review
(to make sure nothing non-free or worse gets imported...


Michael

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Bug#409849: First rough draft of an afni Debian package

[Michael Hanke]

On Mon, Oct 19, 2009 at 03:53:29PM -0400, Judd Storrs wrote:
 Excellent work! I have two updates.
 
 The first adds an afni-dev package to include headers needed to use libmri
 etc as well as to compile AFNI plugins. I wasn't sure where these should
 go--this places them inside /usr/include/afni.

The place is fine, but how did you determine the subset of headers that
should go into it. If we can automize that, it might scale a bit better
with the future AFNI development.

However, the more serious problem is that having a -dev package also
implies that the libs can be used elsewhere -- which is actually not
the case. Without a proper versioning scheme and sane interface policies
we cannot expose the shared libs (that I imagined to be internal
convenience libs) like this. What could be done is adding static libs to
the -dev package. However, already now it is significant pain to build
shared libs alone -- building both is even more tricky using AFNI's
cumbersome build system...

I got a patch from Bernd Feige that replaces the Makefiles with a cmake
setup -- which is wonderful and will solve all of our problems at once.
However, it is pretty invasive and such is usually discouraged for
Debian packaging. Right now I am reluctant to use that for the package,
but if we want a fully functional package with no compromise, there
might be no way around it. Sadly, Bernd submitted his patch upstream
some time ago and it was not accepted 

 The second patch allows either openmotif or lesstif to be used.

I'm pretty much in favor of this change, however, it might be that we
have to revert that at some point, since openmotif is non-free and
package in main must not depend on anything else but packages in main.

Although in this case it is an optional alternative build-dependency --
so it might work -- we'll see...

 Again, wonderful work!

Thanks, but I think more should be done to the default configuration.
AFNI.afnirc and AFNI.sumarc are now simply shipped as examples in the
afni-common package, but I guess they should become somewhat more
functional. My own config scheme in /etc/afni/afni.sh takes care of the
most critical settings, but the majority is left untouched. I am not
sure about implementing a proper default system-wide config setup --
right now this per-user thingie that comes with AFNI feels incomplete
and suboptimal. Advice is most welcome, since I am not really a
proficient AFNI user.


Thanks,

Michael

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Bug#409849: First rough draft of an afni Debian package

[Michael Hanke]

A first (very rough) draft of a Debian package for AFNI is now available
at:

  http://neuro.debian.net/pkgs/afni.html

It is not yet ready for Debian and is also lacking a lot of the
necessary documentation, but it should somewhat work.

Please install 'afni' and look at 'man afni'.

*ANY* comment or bugreport is very much appreciated. Please post to this
ITP bug.

This package is still a bit large, due to a lot of code duplication in
AFNI itself. I already got a patch that would help with it and I will be
looking into it over the next couple of days.

I would very much like to get recommendations for a sane default
configuration for AFNI on Debian.

I will push the AFNI packaging to git.debian.org shortly (will drop a
note here, when it is done).

There is also the need to package the AFNI atlas data. I have a draft
package already that I will also publish shortly. Just have to make sure
that I do not run into serious licensing trouble...


Stay tuned,


Michael

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Bug#409849: First rough draft of an afni Debian package

[Michael Hanke]

On Mon, Oct 19, 2009 at 11:42:29AM -0400, Michael Hanke wrote:
 I will push the AFNI packaging to git.debian.org shortly (will drop a
 note here, when it is done).

Now available at

  http://git.debian.org/?p=pkg-exppsy/afni.git;a=summary


Michael


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Bug#409849: License still too restrictive

[Michael Hanke]

My previous outbreak of joy was a little premature. The edges3D license
is still too restrictive, since it does not allow redistribution (the
key permission for at least a non-free packaging). The upstream author
of the library is Gregoire Malandain.

  http://www-sop.inria.fr/epidaure/personnel/malandain/malandain.html

I tried to contact him, but got no response (maybe someone else has more
luck).

This license problem is _the_ showstopper for AFNI packaging. Otherwise
the package seems to work fine, but without edges3D it is not possible
to include SUMA or any skull-stripping functionality. Without this AFNI
would not provide a comprehensive fMRI toolchain anymore, and IMHO that
makes it close to useless to package it.

Otherwise, I got lots of offer for help with the packaging (including a
sanitized cmake-based buildsystem, that would replace AFNI native
Makefile-jungle). However, the license issue above has to be solved
first.

Maybe if people would express their desire for an AFNI Debian package
not just to me, but also to the AFNI authors and the edges3D author
that could convince them that there actually is a problem in need of a
solution...

Good luck to us,

Michael


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Bug#410318: Prospective package available

[Michael Hanke]

A prospective package is available at:

  http://neuro.debian.net/pkgs/odin.html

if nothing critical pops up, this will be submitted to NEW soon.


Michael

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Bug#409849: License changed

[Michael Hanke]

The good news is that a particularly questionable piece of AFNI
(libEdge3) has been relicensed from a non-distribution to non-commercial
license. This is a huge step forward and will hopefully allow AFNI to go
into non-free without stripping any functionality.

Let'see,

Michael


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Bug#532619: Candidate ready

[Michael Hanke]

A package candidate is ready:

  
http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=garmindev

VCS is here:

  http://git.debian.org/?p=collab-maint/garmindev.git;a=summary


Cheers,

Michael


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Bug#537573: Progress?

[Michael Hanke]

Hi,

are there any news regarding this ITP? Is a preliminary package
available somewhere?


Thanks for your effort,

Michael


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Bug#532619: ITP: garmindev -- qlandkartegt plugins to acces Garmin devices

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: garmindev
  Version : 0.2.0
  Upstream Author : Oliver Eichler oliver.eich...@gmx.de
* URL : http://www.qlandkarte.org
* License : GPL
  Programming Lang: C++
  Description : qlandkartegt plugins to acces Garmin devices

This packages provides the access plugins for Garmin hardware that had
previously been part of qlandkarte and are now distributed separately.
This package is needed to make qlandkarteGT (ITP #507352) a full
replacement of the older qlandkarte

  http://packages.debian.org/sid/qlandkarte

so that it can be removed from the archive.


Michael

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Bug#507352: progress here?

[Michael Hanke]

Hi Winnie,

On Tue, Jun 09, 2009 at 11:30:44PM +0200, Patrick Winnertz wrote:
 Hello,
 
 is there any progress? This would be very important as qlandkarte is 
 terminated and this is the newer tool. 
 
 Hope to hear from you soon.

Good timing -- I just ITP'ed GarminDev, which is the missing piece of
qlandkartegt to finally replace the old qlandkarte in Debian.

I have two functional packages (both GT and the device plugins). They
just need a bit more polishing, before they can go into NEW. I'd be
happy if you'd be willing/able to give it a spin (copyright checking,
description polish, things like that...).

I have both packaging efforts in Git with a link to the upstream SVN via
git-svn. Shall I put them into collab-maint on Alioth? Maybe adding you
as an uploader, HINT HINT ?



Thanks in advance,

Michael


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Bug#409849: Still working on it

[Michael Hanke]

Just a quick note that this effort has not really been stopped -- it
just takes forever.

I currently have a pretty much functional package, but the copyright
screening is yet to come (although I already removed quite a bit of the
code, due to licensing issues) -- given the amount of code, this will
again take a while

Help would be very much appreciated!


Michael

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Bug#521328: Preliminary package available

[Michael Hanke]

This package is not functional and available from here:

  http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/via-bin

It needs a little more testing and a new upstream release before it gets
uploaded to NEW.

Michael


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Bug#521412: Preliminary package available

[Michael Hanke]

This package is now functional and available from here:

  http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/lipsia

It needs a little more testing and a new upstream release before it gets
uploaded to NEW.

Michael



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Bug#521328: Preliminary package available

[Michael Hanke]

On Mon, May 18, 2009 at 06:54:53PM +0200, Michael Hanke wrote:
 This package is not functional and available from here:
  ^^^

This should be 'now'.

 
   http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/via-bin
 
 It needs a little more testing and a new upstream release before it gets
 uploaded to NEW.
 
 Michael
 
 
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Bug#528616: RFA: dares - rescue files from damaged CDs and DVDs

[Michael Hanke]

Package: wnpp
Severity: normal

Hi,

I am offering 'dares' for adoption, since I am already ignoring it for
too long. The package does:

 Dares scans a CD/DVD image or a CD/DVD for files. This also works when
 the filesystem (ISO-9660 or UDF) on the disc is damaged and cannot be mounted
 anymore.

This tool has never seen any upstream release since I packaged it for
Debian and is getting old.  Both the software itself as well as the
packaging are really simple.  There are currently two open bugs.

The popcon count is 230 -- not too low, so maybe someone wants to take
care of this package in the future. Otherwise I would orphan it in a
couple of weeks. Since it seems to be upstream dead, completely removing
it from the archive might the most viable option.

If you want to take over just take what is currently in the archive and
upload a new version. Since there was no upstream release there is also
no history, hence no VCS.


Cheers,

Michael

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Description: Digital signature

Bug#521412: ITP: lipsia -- analysis suite for MRI and fMRI data

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com


* Package name: lipsia
  Version : 1.5.0
  Upstream Author : LIPSIA developers lip...@cns.mpg.de
* URL : http://www.cbs.mpg.de/institute/software/lipsia
* License : GPL
  Programming Lang: C, C++
  Description : analysis suite for MRI and fMRI data

 Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)
 .
 This is a software package for the data processing and evaluation of
 functional magnetic resonance images. The analysis of fMRI data comprises
 various aspects including filtering, spatial transformation, statistical
 evaluation as well as segmentation and visualization. All these aspects are
 covered by LIPSIA. For the statistical evaluation, a number of well established
 and peer-reviewed algorithms were implemented in LIPSIA that allow an effcient
 and user-friendly processing of fMRI data sets. As the amount of data that must
 be handled is enormous, an important aspect in the development LIPSIA was the
 efficiency of the software implementation.
 .
 LIPSIA operates exclusively on data in the VISTA data format. However, the
 package contains converters for medical image data in iBruker, ANALYZE  and
 NIfTI format -- converting VISTA images into NIfTI files is also supported.

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Bug#521328: ITP: via -- library and tools for volumetric image analysis

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke michael.ha...@gmail.com

* Package name: via
  Version : 1.5.2
  Upstream Author : LIPSIA developers lip...@cns.mpg.de
* URL : http://www.cbs.mpg.de/institute/software/lipsia
* License : GPL
  Programming Lang: C
  Description : library and tools for volumetric image analysis

 This package provides a toolkit for functional and structural (medical)
 image data processing. It consists of a library of about 50 different
 programs ranging from simple data handling routines and viewers to
 complex image transformation algorithms.
 .
 All tools operate on data in VISTA format. The package contains several
 converters from e.g. PNG, PGM or PNM to this data format and back.

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Bug#515319: More info and interest

[Michael Hanke]

Hi,

[cross posting to debian-science and debian-python]


I want to draw you attention to an RFP that might deserve more
attention:

  http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=515319

It is concerned with a Matlab-to-Python converter. The project aims to
aid the conversion of Matlab code to Python.

While this software seems to be in a rather early stage of development
it has nevertheless the potential to become a mighty tool to facilitate
the migration of an unestimable amount of Matlab code to a free
language/computing environment and hence a global migration toward the
use of free software.

These guys published a paper about their compiler in the journal
'Frontier in Neuroinformatics' (open-access as it should be ;)

  http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/005.2009/

According to the journals access statistics it receives an impressive
amount of attention. It would really cool to have that beast in the
flagship of free software (which is Debian for those who wonder ;).


Thanks,

Michael



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Bug#507352: ITP: qlandkartegt -- GPS mapping (GeoTIFF and vector) and Garmin GPSr management

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke [EMAIL PROTECTED]

* Package name: qlandkartegt
  Version : 0.9.0
  Upstream Author : Oliver Eichler [EMAIL PROTECTED]
* URL : http://www.qlandkarte.org/
* License : GPL-2
  Programming Lang: C++
  Description : GPS mapping (GeoTiff and vector) and GPSr management


This package provides a versatile tool for GPS maps in GeoTiff format as
well as Garmin's img vector map format. QLandkarteGT is the successor of
QLandkarte. Among various improvements (e.g. 2D/3D map rendering and
reduced ressource demands) the major difference is its
device-independent architecture, which is not limited to Garmin devices
anymore. Therefore, the package also does not include device drivers.
Drivers for a number of Garmin devices are available from the
yet-to-be-determined-package-name package.

Additionally, QLandkarteGT serves as a frontend to the GDAL tools, to
make georeferencing of scanned maps feasible for users. In contrast to
similar tools (e.g. QGis) its straightforward interface is especially
suited for non-scientific users.



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Bug#497448: ITP: python-griddata -- Python function to interpolate irregularly spaced data to a grid

[Michael Hanke]

On Tue, Sep 02, 2008 at 04:31:55PM +0100, Chris Walker wrote:
 Michael Hanke [EMAIL PROTECTED] writes:
 
  * URL : http://code.google.com/p/griddata-python/
  * License : MITish
 
 That URL claims the licence is GNU General Public License v2
Yeah, but not all of it ... but read on.

   This module provides a single function, 'griddata', that fits a surface
   to nonuniformly spaced data points. It behaves basically like its 
  equivalent
   in Matlab.
 
 
 How does this relate to the algorithm mentioned in
 http://lwn.net/Articles/292979/ where it says:
 
  Jeffrey Whitaker has added support for gridding irregularly spaced
  data using the Matlab (TM) equivalent griddata function.  This is a
  long-standing feature request for matplotlib and a major
  enhancement.  matplotlib now ships with Robert Kern's delaunay
  triangularization code (BSD license), which supports the default
  griddata implementation, but there are some known corner cases where
  this routine fails.  As such, Jeff has provided a python wrapper to
  the NCAR natgrid routines, whose licensing terms are a bit murkier,
  for those who need bullet proof gridding routines.  If the NCAR
  toolkit is installed, griddata will detect it and use it.  See
  http://matplotlib.sf.net/matplotlib.mlab.html#-griddata for details.
  Thanks Robert and Jeff.
That seems to be exactly the same -- great! The griddata package would
have contained NCAR, but under this circumstances it is not really
necessary, IMHO.

Godd news -- thanks for pointing it out!


Michael

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Bug#497448: ITP: python-griddata -- Python function to interpolate irregularly spaced data to a grid

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke [EMAIL PROTECTED]


* Package name: python-griddata
  Version : 0.1.2
  Upstream Author : Jeffrey Whitaker [EMAIL PROTECTED]
* URL : http://code.google.com/p/griddata-python/
* License : MITish
  Programming Lang: Python
  Description : Python function to interpolate irregularly spaced data to a 
grid

 This module provides a single function, 'griddata', that fits a surface
 to nonuniformly spaced data points. It behaves basically like its equivalent
 in Matlab.

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Bug#495093: ITP: hcluster -- Python functions for agglomerative clustering

[Michael Hanke]

Package: wnpp
Severity: wishlist
Owner: Michael Hanke [EMAIL PROTECTED]

* Package name: hcluster
  Version : 0.1.8
  Upstream Author : Damian Eads [EMAIL PROTECTED]
* URL : http://code.google.com/p/scipy-cluster/
* License : BSD
  Programming Lang: Python
  Description : Python functions for agglomerative clustering

 The module's features include:
 .
  * computing distance matrices from observation vectors
  * generating hierarchical clusters from distance matrices
  * computing statistics on clusters
  * cutting linkages to generate flat clusters
  * visualizing clusters with dendrograms
 .
 The interface is very similar to MATLAB's Statistics Toolbox API.
 The core implementation of this library is in C for efficiency.


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Bug#421703: Update for Caret 5.6

[Michael Hanke]

I have updated the package to upstream version 5.6. Inofficial packages
are here:

http://apsy.gse.uni-magdeburg.de/debian/pool/main/c/caret/

I hope the package goes into NEW soon.

Michael


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