clean:
- -rm html-stamp source-stamp
+ -rm html-stamp source-stamp upload-website-stamp
$(MAKE) -C artwork clean
source: source-stamp
source-stamp: build/db.db
- PYTHONPATH=. python neurodebian/dde.py \
+ PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
--cfg neurodebian.cfg \
--db build/db.db \
--outdir build/src \
build/db.db:
mkdir -p build
- PYTHONPATH=. python neurodebian/dde.py \
+ PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
--cfg neurodebian.cfg \
--db build/db.db \
updatedb
rsync -rvzlhp --delete \
--exclude=debian --exclude=debian-local --exclude=_files \
--chmod=Dg+s,g+rw $(WWW_DIR) $(WWW_UPLOAD_URI)
+ : # Touch stamp here so we get it updated on every upload
+ touch $@-stamp
+
+# call upload iff .git/index was modified, i.e. new changes got pulled in
+upload-website-stamp: .git/index
+ $(MAKE) upload-website
.PHONY: removedb removecache updatedb upload-website clean distclean pics html
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# all cuurently supported dists
allnddists="nd+debian-lenny nd+debian-squeeze nd+debian-wheezy nd+debian-sid \
- nd+ubuntu-natty nd+ubuntu-maverick nd+ubuntu-lucid nd+ubuntu-karmic nd+ubuntu-hardy"
+ nd+ubuntu-hardy nd+ubuntu-karmic nd+ubuntu-lucid nd+ubuntu-maverick nd+ubuntu-natty nd+ubuntu-oneiric"
alldists="$allnddists debian-lenny debian-squeeze debian-wheezy debian-sid"
# default is debian
mirror="http://ubuntu.media.mit.edu/ubuntu"
fi
-if [ ! -d $aptcache ]; then mkdir $aptcache; fi
+if [ ! -d $aptcache ]; then mkdir -p $aptcache; fi
+neurodebian (0.26) unstable; urgency=low
+
+ [ Michael Hanke & Yaroslav Halchenko]
+ * website:
+ - lots of changes: blog, artwork, survey, testimonials, etc.
+ * nd_* tools:
+ - added support for Ubuntu 11.04 -- Oneiric
+ - new tool nd_build_testrdepends to test either upcoming version of a
+ package would break any reverse build-depends
+ - new tool nd_adddistall to generate cow chroots for all distributions
+ - nd_build now returns non-0 code upon any failure to build
+ * VM:
+ - tuned for releasing 6.0.4 -- addressed issue with dkms build of
+ guest additions
+ - NeuroDebian "Welcome Wizard" pulls scipy instead of only numpy for
+ "Scientific Python"
+ * Boosted policy to 3.9.2 -- no changes
+
+ -- Yaroslav Halchenko <debian@onerussian.com> Mon, 17 Oct 2011 00:10:27 -0400
+
neurodebian (0.25) unstable; urgency=low
* Various improvements to the webportal.
Maintainer: NeuroDebian Team <team@neuro.debian.net>
Uploaders: Michael Hanke <mih@debian.org>, Yaroslav Halchenko <debian@onerussian.com>
Build-Depends: debhelper (>= 7.0.50~), xcftools, help2man, inkscape, imagemagick, python-html5lib
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
Homepage: http://neuro.debian.net
Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/neurodebian.git
Vcs-Git: git://git.debian.org/git/pkg-exppsy/neurodebian.git
Package: neurodebian-dev
Architecture: all
-Depends: ${misc:Depends}, devscripts, cowbuilder, python, neurodebian-keyring
-Recommends: virtualbox-ose, virtualbox-ose-fuse, zerofree, moreutils
-Suggests:
+Depends: ${misc:Depends}, devscripts, cowbuilder, neurodebian-keyring
+Recommends: python, zerofree, moreutils, time, ubuntu-keyring
+Suggests: virtualbox-ose, virtualbox-ose-fuse
Description: NeuroDebian development tools
neuro.debian.net sphinx website sources and development tools used by
NeuroDebian to provide backports for a range of Debian/Ubuntu
+++ /dev/null
-Source: elastix
-Tasks: debian-med/imaging
-Homepage: http://elastix.isi.uu.nl/index.php
-Author: Stefan Klein, Marius Staring
-Language: C++
-License: BSD-3
-WNPP: 607030
-Version: 4.4
-Pkg-Description: toolbox for rigid and nonrigid registration of images
- elastix is open source software, based on the well-known Insight
- Segmentation and Registration Toolkit (ITK). The software consists of
- a collection of algorithms that are commonly used to solve (medical)
- image registration problems. The modular design of elastix allows the
- user to quickly configure, test, and compare different registration
- methods for a specific application. A command-line interface enables
- automated processing of large numbers of data sets, by means of
- scripting.
-Published-Title: elastix: a toolbox for intensity based medical image registration
-Published-Authors: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim
-Published-In: IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205
-Published-Year: 2010
-Registration: http://elastix.isi.uu.nl/download.php
--- /dev/null
+Source: isis
+Tasks: debian-med/imaging
+Homepage: http://isis-group.github.com/isis/
+Author: Lydia Hellrung (hellrung@cbs.mpg.de) et al.
+Language: C++
+License: GPL-2+
+Version: 0.3.3
+Responsible: NeuroDebian Team <team@neuro.debian.net>
+Pkg-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.
+Why: IO layer for Lipsia and maybe soon Odin.
--- /dev/null
+Source: neo
+Tasks: debian-science/electrophysiology
+Homepage: http://neuralensemble.org/trac/neo
+License: BSD
+Author: Samuel Garcia, Pierre Yger, Luc Estabanez, Andrew Davison, Yury V. Zaytsev
+Language: Python
+Version: 0.1
+Vcs-SVN: https://neuralensemble.org/svn/neo/
+Pkg-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
+Remark: Upstream says not worth packaging before v0.2 is released.
--- /dev/null
+Source: pandas
+Tasks: debian-science/statistics
+Homepage: http://pandas.sourceforge.net
+Author: Wes McKinney <wesmckinn@gmail.com>
+Language: Python, Cython
+License: BSD-3
+Version: 0.4.0
+Pkg-Description: data structures for "relational" or "labeled" data
+ pandas is a Python package providing fast, flexible, and expressive
+ data structures designed to make working with "relational" or
+ "labeled" data both easy and intuitive. It aims to be the fundamental
+ high-level building block for doing practical, real world data
+ analysis in Python. pandas is well suited for many different kinds of
+ data:
+ .
+ - Tabular data with heterogeneously-typed columns, as in an SQL
+ table or Excel spreadsheet
+ - Ordered and unordered (not necessarily fixed-frequency) time
+ series data.
+ - Arbitrary matrix data (homogeneously typed or heterogeneous) with
+ row and column labels
+ - Any other form of observational / statistical data sets. The data
+ actually need not be labeled at all to be placed into a pandas
+ data structure
+Pkg-URL: http://neuro.debian.net/pkgs/cctools.html
+WNPP: 641464
--- /dev/null
+Source: psychlops
+Tasks: debian-science/psychophysics
+Homepage: http://psychlops.sourceforge.jp
+Language: C++
+License: GPL
+Version: 1.5.0
+Pkg-Description:
+ Psychlops is a free C++ library to offer the easy way to develop a
+ demonstration of various types of visual stimulus used in the Vision
+ science.
+ .
+ Binary builds are available only for OS X and Windows. Sources
+ available from sf's SVN:
+ http://sourceforge.jp/projects/psychlops/svn/view/cpp/
--- /dev/null
+Source: pymeg
+Tasks: debian-science/electrophysiology,
+ debian-med/imaging
+Homepage: https://github.com/badbytes/pymeg/wiki
+Author: Dan Collins <quaninux@gmail.com>
+Language: Python
+License: GPL-3
+Version: unknown
+Pkg-Description: suite for analysis of magnetoencephalography (MEG) data
+ PyMEG is a project in Python to do various neuroimaging processing
+ with magnetoencephalography (MEG) data. The purpose of this project,
+ is to create a suite of functions to do MEG analysis in Python.
+Remark: Needs DFSG-ification.
+ According to the author is not yet ready for the use by
+ mortals -- wasn't released yet.
--- /dev/null
+Source: pysurfer
+Tasks: debian-science/neuroscience-cognitive, debian-med/imaging
+Homepage: http://pysurfer.github.com/
+Author: Michael Waskom, Alexandre Gramfort, Scott Burns, Satrajit Gosh
+Language: Python
+License: BSD-3
+Version: 0.1+git....
+WNPP: 641345
+Pkg-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.
+Responsible: NeuroDebian Team <team@neuro.debian.net>
+++ /dev/null
-Source: pyxnat
-Tasks: debian-science/neuroscience-cognitive,
- debian-med/imaging-dev
-Homepage: http://packages.python.org/pyxnat
-Author: Yannick Schwartz <yannick.schwartz@cea.fr>
-Language: Python
-License: BSD
-Version: 0.6.2
-WNPP: 609820
-Pkg-Description: interface to access neuroimaging data on XNAT servers
- XNAT is an extensible database for neuroimaging data. pyxnat is a
- Python library that relies on the REST API provided by the XNAT
- platform since its 1.4 version. The main objective of pyxnat is to
- ease communications with an XNAT server to plug-in external tools or
- python scripts to process the data. pyxnet features:
- .
- - resources browsing capabilities
- - read and write access to resources
- - complex searches
- - disk-caching of requested files and resources
-Responsible: NeuroDebian Team <team@neuro.debian.net>
--- /dev/null
+Source: stabilitycalc
+Tasks: debian-med/imaging
+Homepage: https://github.com/bbfrederick/stabilitycalc
+License: BSD
+Author: Blaise Frederick
+Language: Python
+Version: 0.1
+Pkg-URL: http://neuro.debian.net/pkgs/stabilitycalc.html
+Responsible: NeuroDebian Team <team@neuro.debian.net>
+Vcs-Git: https://github.com/bbfrederick/stabilitycalc.git
+Pkg-Description: evaluate fMRI scanner stability
+ Command-line tools to calculate numerous fMRI scanner stability metrics, based
+ on the FBIRN quality assurance test protocol. Any 4D volumetric timeseries
+ image in NIfTI format is supported input. Output is a rich HTML report.
r-cran-glmnet python-rpy2 python-nibabel-snapshot
python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab-support
svgtune rorden-mri-tutorial caret-data python-joblib python-sphinx fail2ban
+ python-pandas neurodebian
# Information about prospective packages to be imported from taskfiles
prospective =
mni-icbm152-nlin-2009 = mni-icbm152-nlin-2009a mni-icbm152-nlin-2009b mni-icbm152-nlin-2009c
fsl = fsl fsl-doc fsl-atlases fsl-possum-data fsl-first-data fsl-feeds fsl-mni152-templates
fslview = fslview fslview-doc
-python-mvpa = python-mvpa python-mvpa-snapshot
+python-mvpa = python-mvpa python-mvpa-snapshot python-mvpa2
libgiftiio-dev = libgiftiio-dev gifti-bin
openmeeg-tools = openmeeg-tools libopenmeeg-dev python-openmeeg libopenmeeg1
libbiosig-dev = libbiosig-dev python-biosig octave-biosig biosig-tools libbiosig0
libfreenect-dev = libfreenect0.0 libfreenect-dev libfreenect-demos python-freenect freenect
psychtoolbox-3 = octave-psychtoolbox-3 matlab-psychtoolbox-3 psychtoolbox-3-doc
openmeeg = libopenmeeg-dev libopenmeeg1 openmeeg-tools python-openmeeg
+pandas = python-pandas
+pysurfer = python-surfer
+pyxnat = python-pyxnat
+openwalnut = openwalnut-qt4
+neurodebian = neurodebian-dev neurodebian-desktop neurodebian-keyring neurodebian-popularity-contest neurodebian-guest-additions
[mirrors]
de = http://apsy.gse.uni-magdeburg.de/debian
[mirror names]
de = Germany (University of Magdeburg)
gr = Greece (Aristotle University of Thessaloniki)
-us-ca = USA-CA (Paul Ivanov)
+us-ca = USA-CA (Paul Ivanov, California)
us-nh = USA-NH (Dartmouth College)
us-tn = USA-TN (Vanderbilt)
http://neuro.debian.net/debian/dists/lucid/Release
http://neuro.debian.net/debian/dists/maverick/Release
http://neuro.debian.net/debian/dists/natty/Release
+ http://neuro.debian.net/debian/dists/oneiric/Release
http://neuro.debian.net/debian/dists/etch/Release
http://neuro.debian.net/debian/dists/lenny/Release
http://neuro.debian.net/debian/dists/squeeze/Release
# EOL: October 2012
natty = Ubuntu 11.04 "Natty Narwhal" (natty)
# EOL: April 2013
-oneiric = Upcoming Ubuntu 11.10 "Oneiric Ocelot" (oneiric)
+oneiric = Ubuntu 11.10 "Oneiric Ocelot" (oneiric)
[release backport ids]
# the purpose of these ids is to have version suffixes for backported packages
odin = 153
python-mvpa = 162
python-nipype = 325
+python-surfer = 517
+python-pyxnat = 453
slicer = 50
spm8 = 24
voxbo = 73
if q.has_key('popcon'):
db[p]['main']['debian_popcon'] = q['popcon']
# if we have debian, need to get ubuntu
- q = dde_get(query_url + "/packages/prio-ubuntu-natty/%s" % p)
+ q = dde_get(query_url + "/packages/prio-ubuntu-oneiric/%s" % p)
if q and q.has_key('popcon'):
db[p]['main']['ubuntu_popcon'] = q['popcon']
else:
div.body p.caption {
text-align: inherit;
+ font-size: 95%;
+ font-style: italic;
}
div.body td {
--- /dev/null
+:date: 2011-09-26 15:00:00
+:tags: neuroscience, software, spotlight
+
+In the spotlight ...
+====================
+
+We are about to start a new series of blog posts introducing software packages
+for psychological and neuroscience research. In this series, guest authors can
+present (their) software and highlight interesting features that make it stand
+out from similar solution. This series also is an opportunity to give an
+overview on what software solution exist to solve a particular problem. If you
+are interested in writing about something that you use, wrote, or recommend:
+:ref:`contact us <support>`.
+
--- /dev/null
+:date: 2011-09-26 16:00:00
+:tags: neuroscience, software, spotlight, guest post, opensesame, sebastiaan mathot
+:author: Sebastiaan Mathôt
+:author_email: s.mathot@vu.nl
+
+In the spotlight: OpenSesame
+============================
+
+I suspect that many of you will not be familiar with me or my software, so
+let's start with a brief introduction. My name is Sebastiaan Mathôt. I'm the
+lead developer of OpenSesame_, a graphical tool for creating psychological and
+neuroscientific experiments.
+
+About OpenSesame
+----------------
+
+The reason that I started working on OpenSesame, aside from the inherent
+pleasure that a geek like myself derives from developing software, was my
+dissatisfaction with the tools that were available. Not that there's a shortage
+of experiment building software, not at all. And for people with reasonable
+programming skills there are many viable options: MatLab/ Octave in combination
+with the `Psychophysics Toolbox`_, Python in combination with VisionEgg_ or
+PsychoPy_, to name but a few (most of these are, incidentally, available through
+NeuroDebian). But for people with relatively modest programming skills, such as
+most students doing a Bachelor's or Master's project, there aren't that many
+options. In my experience, people will generally end up using a proprietary
+program, such as E-Prime, Inquisit, or what have you. These offer a reasonably
+intuitive graphical interface, but at a price. First, these packages are
+expensive and, due to licensing restrictions, people are frequently unable to
+install them on their personal computers. Second, they are limited in their
+functionality and in their interoperability with other software.
+
+.. figure:: pics/blog/opensesame_stimulus.png
+
+ One of the unique features of OpenSesame is the ability to draw your
+ stimuli. You can combine this what-you-see-is-what-you-get approach with
+ scripting, to easily create flexible stimulus displays.
+
+Therefore, I wanted to develop a graphical environment for building
+experiments, centered around the Python programming language. The idea was to
+give users the type of comprehensive graphical interface that they have come to
+expect from proprietary packages, but for free, and without taking away any of
+the power that Python has to offer. And, almost a year, 12 public releases, and
+more than 10,000 downloads later, the result is OpenSesame!
+
+Back-end independence
+---------------------
+
+In this post I want to highlight one of OpenSesame's features: back-end
+independence. This may sound a bit technical and boring, but it's not. Well...
+maybe a little boring. In fact, it should be a little boring, because it's a
+feature that you're not supposed too notice, unless you need it.
+
+So what do I mean by "back-end independence"? Experiments are all about
+presenting stimuli. Most often visual stimuli on a computer display, sometimes
+sounds, tactile stimuli, etc. From the perspective of a programmer, there are
+many ways to present such stimuli. Put differently, there are many programming
+libraries that you can use.
+
+For example, if you want to write a program that controls a computer display,
+you can use a Python library called PyGame_. PyGame has been designed with
+video-games in mind, but, experiments being conceptually so similar (although
+not typically as entertaining), it is also well suited for creating
+experiments. For this reason, I initially designed OpenSesame around PyGame.
+
+This seemed like a good idea at the time, but there was a huge drawback. If
+people wanted to use OpenSesame, they were forced to use PyGame as well. It was
+a package deal, so if PyGame didn't support a particular feature, neither did
+OpenSesame. That wasn't very nice. And it also wasn't necessary, because there
+was nothing in OpenSesame that inherently required PyGame. It was just an
+arbitrary design choice that I had made at the outset.
+
+So I decided to decouple the "back-end" (i.e., all the functions that had been
+handled by PyGame up to that point) from the rest of OpenSesame. This means
+that the user can now choose which back-end he or she wants to use for
+controlling the display etc. Importantly, OpenSesame continues to function in
+the same way, regardless of which back-end is selected. For users who don't
+care or know what a back-end is, let alone which back-end they prefer, PyGame
+still serves as a default.
+
+.. figure:: pics/blog/opensesame_backend.png
+
+ You can easily select your favorite back-end using the graphical interface.
+ The same experiment can be run, (usually) completely unmodified, using any
+ of the three available back-ends.
+
+So what's the upshot of all this? Right now, the most direct benefit is that
+you can use OpenGL and PsychoPy in your OpenSesame experiments. PsychoPy in
+particular provides lots of functions (drawing Gabor patches etc.) that are
+very convenient when creating experiments. Previously, users couldn't use
+these, because PsychoPy doesn't play nice with PyGame (even though it actually
+uses, or can use, PyGame under the hood). Now they can, so that's a definite
+plus. And in the future I may add more back-ends, depending on popular demand.
+For example, VisionEgg is another library for creating experiments. VisionEgg
+is quite popular and could probably be used as a back-end as well.
+
+This means that users of OpenSesame now have both a comprehensive graphical
+interface and powerful programming libraries at their disposal. They can
+choose. Most of the experiment can usually be created using the GUI, which is
+especially appealing for the less tech-savvy among us. But, for more
+complicated parts, Python scripting can be used and, consequently, users have
+access to a wide range of libraries.
+
+I think that OpenSesame's back-end independence is a nice example (one of many,
+I hasten to add) of how free software can work together. If it hadn't been
+possible to use PsychoPy and OpenGL in OpenSesame, I would have probably ended
+up duplicating lots of functionality. That would have been very time consuming.
+Time that I have now spent on refining other parts of OpenSesame, unique parts
+and not simply duplicates of existing functionality.
+
+And ultimately, I believe that this type of interoperability is why free
+software will continue to grow.
+
+.. _PyGame: http://pygame.org
+.. _PsychoPy: http://psychopy.org/
+.. _VisionEgg: http://www.visionegg.org/
+.. _Psychophysics Toolbox: http://psychtoolbox.org
+.. _OpenSesame: http://www.cogsci.nl/opensesame
+
+
Coffee Art
**********
+2011-09-01 18.48.53
+-------------------
+
+.. figure:: /pics/coffeeart/2011-09-01_18.48.53.jpg
+
+2011-08-25 00:00:00
+-------------------
+
+.. figure:: /pics/coffeeart/2011-08-2X.jpg
+
+2011-03-23 13:44:26
+-------------------
+.. figure:: /pics/coffeeart/2011-03-23_13.44.26.jpg
2010-10-22 09:58:31
-------------------
Publications
============
+Hanke, M. (2011). `More than batteries included: NeuroDebian
+<_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
+*Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
+Paris, France.
+
+Halchenko, Y. O. (2011). `Ï€'s in Debian or Scientific Debian: NumPy, SciPy and beyond
+<_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
+*Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
+Paris, France.
+
Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
*Frontiers in Neuroinformatics, 5:8*.
**June 26-30, 2011** `HBM 2011 <http://www.humanbrainmapping.org/HBM2011>`_, Québec City, Canada
Debian/NeuroDebian booth `#108 <http://www.humanbrainmapping.org/files/2011MeetingFiles/Exhibit_Floor_Plan-5_10_2011.PDF>`__
**July 21-23, 2011** `PsychoPy Workshop and Codesprint <https://scanlab.psych.yale.edu/public/psychopy>`_, New Haven, CT, USA
+
**August 25-30, 2011** `EuroSciPy 2011/ Python in NeuroScience <http://www.euroscipy.org/conference/euroscipy2011>`_, Paris, France
2011/08/27, 16:30 -- 17:00, Scientific track
-.. Generated on Tue Feb 1 12:05:45 EST 2011
+.. Generated on Sun Oct 2 14:27:59 EDT 2011
.. Do not edit directly
Quotes from NIH R01 grant proposal letters of recommendation
+.. quote::
+ :author: Prof. Alfonso Caramazza
+ :affiliation: Director, Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
+ :date: 2011-06-27
+ :tags: lofs
+ :group: Research institutions
+
+ NeuroDebian is an effective solution to support a heterogeneous working environment. [...] NeuroDebian is useful also for education purpose.
+
+
.. quote::
:author: Prof. Thomas J. Grabowski, Jr.
:affiliation: Director, Integrated Brain Imaging Center, University of Washington, Seattle, Washington, USA
NeuroDebian project made our library available to an unprecedented number of users [...] as a system administrator, I rely on NeuroDebian for setting up and keeping up-to-date the software installed on the numerous clients and servers used by more than 150 scientists
+.. quote::
+ :author: Prof. Todd F. Heatherton
+ :affiliation: Lincoln Feline Professor, Psychology and Brain Sciences Department
+ :date: 2011-06-22
+ :tags: lofs, dartmouth, vm
+ :group: Participating institutions
+
+ We have found the NeuroDebian VM so easy to us and so simple to maintain that we're currently in the process of converting some of our workstations to full NeuroDebian installations
+
+
+.. quote::
+ :author: Prof. Peter U. Tse
+ :affiliation: Associate Professor, Psychology and Brain Sciences Department
+ :date: 2007-12-31
+ :tags: lofs, dartmouth, team
+ :group: Participating institutions
+
+ [...] vibrant NeuroDebian team [...] has been a great asset to the Psychology and Brain sciences department at Dartmouth. On multiple occasions they have provided support and advice beyond the scope of the NeuroDebian effort, showing their knowledge of methodological developments in the neuroscience field and making us aware of recent technological advances we could benefit from in our research.
+
+
+.. quote::
+ :author: Prof. Stefan Pollmann
+ :affiliation:
+ :date: 2010-09-02
+ :tags: lofs, money
+ :group: Participating institutions
+
+ My lab is using NeuroDebian for almost five years now [...] The minimal maintenance cost allow us to operate our research and computing infrastructure [...] even without a dedicated system administrator. Consequently, these resources could be invested into scientific personnel instead.
+
+
+.. quote::
+ :author: Prof. Brian Avants
+ :affiliation: Research Assistant Professor of Radiology, University of Pennsylvania, Philadelphia, USA
+ :date: 2010-09-16
+ :tags: lofs, practices, standartization, mentorship, dissemination, impact
+ :group: Research software projects
+
+ The NeuroDebian team taught me a great deal about how to systematize software development for reliable dissemination [...] This speaks very highly of the deep skillset and commitment to user support represented in the NeuroDebian project, which will have high impact on the field and help standardize both the analysis and the interpretation of neuroimaging data.
+
+
.. quote::
:author: Dr. Matthew Brett
:affiliation: Specialist researcher, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
[...] your team are ideally placed to make this system work. I have worked with Yaroslav Halchenko and Michael Hanke. [...] Their record on working together as a team, and individually, is easy to find, and speaks for itself. Their demonstrated combination of seemingly inexhaustible energy, openness and skill has been of enormous benefit to our own project and community.
+.. quote::
+ :author: Prof. Gene Cooperman
+ :affiliation: College of Computer and Information Science, Northeastern University, Boston, USA
+ :date: 2011-06-21
+ :tags: lofs
+ :group: Research software projects
+
+ [...] we have benefited from the NeuroDebian team through their mentoring and direct efforts to improve the DMTCP software for wider distribution.
+
+
+.. quote::
+ :author: Sebastian Eichelbaum
+ :affiliation: OpenWalnut project, Image and Signal Processing Group, Institute of Computer Science, University of Leipzig, Germany
+ :date: 2011-06-30
+ :tags: lofs, mentoring
+ :group: Research software projects
+
+ We are currently preparing our first software-release in NeuroDebian and found it to be easy and straight-forward with a great support.
+
+
.. quote::
:author: Prof. Bruce Fischl
:affiliation: Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA
Having FreeSurfer integrated into the Debian operating system by the NeuroDebian team would have enormous benefits for us, and for the thousands of users of FreeSurfer across the world.
+.. quote::
+ :author: Stephan Gerhard
+ :affiliation: Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
+ :date: 2011-06-21
+ :tags: lofs, support, Debian, open science
+ :group: Research software projects
+
+ The Debian project provides the scientific community with a truly universal operating system. The breadth and quality of its community-driven development and technical support is superior to many other available commercial alternatives. It provides a sound basis for the open science movement.
+
+
.. quote::
:author: Dr. Satrajit Ghosh
:affiliation: Research scientist, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- :date: 2010-09-06
+ :date: 2011-06-13
:tags: lofs, software distribution
:group: Research software projects
[...] distributing the software via NeuroDebian generates valuable feedback which is indispensable for the development of free software. When working with the NeuroDebian team in the past, I have found their members to be very cooperative, target-oriented and responsive.
+.. quote::
+ :author: Mario Kleiner
+ :affiliation: Dipl. Inf., Psychtoolbox lead developer, Department for Cognitive and Computational Psychophysics, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
+ :date: 2011-06-21
+ :tags: lofs, vm, contributions, practices
+ :group: Research software projects
+
+ We find the approach taken by NeuroDebian and the progress it made so far very pleasant and promising. [...] The NeuroDebian team helped us to improve the quality of our software and of some of our processes by review, constructive suggestions and even software patches. The availability of the NeuroDebian Virtual Machine was instrumental for fast porting of the Psychtoolbox to a 64 bit Linux environment.
+
+
.. quote::
:author: Dr. Gabriele Lohmann
:affiliation: Lipsia lead developer, Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
The dinifti tool was one of the first to appear in Debian and ever since it's inclusion in the distribution, I have received invaluable feedback from the Debian community
+.. quote::
+ :author: Sebastiaan Mathôt
+ :affiliation: OpenSesame lead developer, Vrije Universiteit, Amsterdam, The Netherlands
+ :date: 2011-07-29
+ :tags: lofs, software distribution, mentorship, Debian
+ :group: Research software projects
+
+ The NeuroDebian team has helped me to make my software (OpenSesame) available to the wider public in a much more professional fashion than I would have been able to do for myself.
+
+
.. quote::
:author: Dr. Eilif Muller
:affiliation: Post-doctoral researcher, Brain Mind Institute, EPFL, Lausanne, Switzerland
Having such a group of experts [NeuroDebian developers] that search for open-source software solutions, refine them and then make them trivially easy for users to install and try out is of absolutely invaluable benefit to the research community and to the funding bodies that would, otherwise, be paying much larger sums in commercial software licensing fees.
+.. quote::
+ :author: Dr. Fernando Perez
+ :affiliation: IPython developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
+ :date: 2010-09-08
+ :tags: lofs, contributions, team
+ :group: Research software projects
+
+ Their [NeuroDebian developers] commitment to strongly tested, validated and documented tools for computational-based research in neuroscience is exemplary, and we owe them a great debt of gratitude for the contributions they have already made [...]
+
+
.. quote::
:author: Dr. Ariel Rokem
:affiliation: NiTime developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
NeuroDebian is playing a key role in the creation of an ``eco-system'' of open-source solutions for neuroscience [...] The standards and practices disseminated by the NeuroDebian project allowed me to start using this tool [PsychoPy] efficiently and rapidly and to contribute back to the project within a few months.
+.. quote::
+ :author: Prof. Per B. Sederberg
+ :affiliation: Department of Psychology, Ohio State University, Columbus, Ohio, USA
+ :date: 2010-09-16
+ :tags: lofs, impact, quality
+ :group: Research software projects
+
+ [...] NeuroDebian will undoubtedly have a large impact on the quality of neuroscience research, both directly and indirectly, by making almost every known software package related to neuroscience work available in a stable and secure environment and broadening the standard set of techniques researchers can employ.
+
+
.. quote::
:author: Prof. Stephen M. Smith
:affiliation: Associate Director, Centre for Functional Magnetic, Resonance Imaging of the Brain University of Oxford, Oxford, UK
Since 2007 we completely rely on the NeuroDebian project to provide users of the Debian/Ubuntu platform with FSL software packages and corresponding technical support. [...] we have received a continuous stream of bug fixes and improvements that have been developed by members of the Debian community. [...] we were able to benefit from work of people that would not otherwise contribute to the development of FSL – without any additional investment of my lab, but solely due to FSL’s presence in the Debian archive.
+.. quote::
+ :author: Dr. Gaël Varoquaux
+ :affiliation: Parietal project, INRIA, Neurospin research center, Gif sur Yvette, France
+ :date: 2010-09-01
+ :tags: lofs, reproducibility, dissemination
+ :group: Research software projects
+
+ The availability of a common platform [NeuroDebian] for many different neuroimaging software solutions makes it much easier to compare solutions and pick the tool of choice for a given research problem.
+
+
+.. quote::
+ :author: Patrik Andersson
+ :affiliation: Image Sciences Institute, University Medical Center Utrecht, the Netherlands
+ :date: 2011-06-15
+ :tags: lofs, vm
+ :group: Individual laboratories and researchers
+
+ I have been using NeuroDebian for my work on multivariate classification of fMRI data [...] It is of great value, because I have access to both Windows and Debian OS on my laptop, where I do all my analysis.
+
+
+.. quote::
+ :author: Prof. Hiroyuki Akama
+ :affiliation: Associate Professor, Graduate School of Decision Science and Technology, Tokyo Institute of Technology, Tokyo, Japan begin{lofquote} I am a heavy user of NeuroDebian-Virtual Machine on Windows 64-bit platform. end{lofquote}
+ :date: 2011-06-15
+ :tags: lofs, vm
+ :group: Individual laboratories and researchers
+
+ I am a heavy user of NeuroDebian-Virtual Machine on Windows 64-bit platform.
+
+
.. quote::
:author: Paolo Avesani
:affiliation: Neuroinformatics Laboratory, Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
Both the software and online support forums provided by NeuroDebian have been invaluable for my machine-learning studies of fMRI data.
+.. quote::
+ :author: Prof. Jodene Goldenring Fine
+ :affiliation: Department of Counseling, Education Psychology, and Special Education, Michigan State University, USA
+ :date: 2011-06-18
+ :tags: lofs, vm, quality, support, speed
+ :group: Individual laboratories and researchers
+
+ [...] I couldn't believe my great luck when after just an hour or so I had a complete [NeuroDebian] system running and my research was back on track. [...] Your service and support are critical to keeping researchers effectively working on their research, rather than on maintenance issues that negatively affect our productivity. [...] I was working on versions of AFNI and FSL that were several generations behind [...] Now I will always be up-to-date. [...] Because I am now running a virtual machine, I can keep my data files [with me].
+
+
.. quote::
:author: Scott Gorlin
:affiliation: Ph.D. student, Department of Brain and Cognitive Science Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
[NeuroDebian is] an extremely time saving solution
+.. quote::
+ :author: Jonas Kubilius
+ :affiliation: Ph.D. student, Laboratories of Biological and Experimental Psychology, K. U. Leuven, Belgium
+ :date: 2011-06-18
+ :tags: lofs, reproducibility, vm, impact, sharing, open science
+ :group: Individual laboratories and researchers
+
+ [...] NeuroDebian allows both researchers and the public to easily replicate the entire experimental procedure, a feature rendered difficult or often impossible by proprietary software packages that most scientists rely on nowadays. I have been increasingly using NeuroDebian in a Virtual Machine because Linux operating systems are not supported by the university. [...] Moreover, powered by NeuroDebian’s openness, I see a reason to publish the full code of our experimental and analysis scripts. [NeuroDebian] makes the goal of open science finally viable.
+
+
.. quote::
:author: Kaunitz Lisandro Nicolas
:affiliation: Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
.. quote::
- :author: Prof. Stefan Pollmann
- :affiliation: Lehrstuhl für Allgemeine Psychologie, Otto-von-Guericke Universität, Magdeburg, Germany
- :date: 2010-09-02
- :tags: lofs, money
+ :author: Dr. Felipe Picon
+ :affiliation: Child and Adolescent Psychiatrist, Department of Psychiatry of Federal University of Rio Grande do Su, Porto Alegre, RS, Brazil
+ :date: 2011-06-14
+ :tags: lofs, ease
:group: Individual laboratories and researchers
- My lab is using NeuroDebian for almost five years now [...] The minimal maintenance cost allow us to operate our research and computing infrastructure [...] even without a dedicated system administrator. Consequently, these resources could be invested into scientific personnel instead.
+ We have been relying on NeuroDebian [...] for our work on Adult ADHD neuroimaging and find it to be very useful.
.. quote::
- :author: Dr. Daqiang Sun
- :affiliation: Post-doctoral researcher, Department of Psychology, University of California, Los Angeles, USA
- :date: 2010-09-15
- :tags: lofs, speed
+ :author: Dr. Bhavani Shankara Bagepally
+ :affiliation: Department of Psychiatry, National Institute of Mental Health And Neurosciences (NIMHANS), Bangalore, India
+ :date: 2011-06-15
+ :tags: lofs, ease
:group: Individual laboratories and researchers
- It [NeuroDebian] is and will continue to be invaluable in our multiple NIH-funded research projects. NeuroDebian nicely takes care of the burden of software deployment and management on my computers and allows me to concentrate on the imaging analysis itself [...]
+ Neuroscience software [...] easily available at a single point with hastle free installation and easy updating.
.. quote::
- :author: Dr. Gaël Varoquaux
- :affiliation: Parietal project, INRIA, Neurospin research center, Gif sur Yvette, France
- :date: 2010-09-01
- :tags: lofs, reproducibility, dissemination
+ :author: Dr. Daqiang Sun
+ :affiliation: Post-doctoral researcher, Department of Psychology, University of California, Los Angeles, USA
+ :date: 2010-09-15
+ :tags: lofs, speed
:group: Individual laboratories and researchers
- The availability of a common platform [NeuroDebian] for many different neuroimaging software solutions makes it much easier to compare solutions and pick the tool of choice for a given research problem.
+ It [NeuroDebian] is and will continue to be invaluable in our multiple NIH-funded research projects. NeuroDebian nicely takes care of the burden of software deployment and management on my computers and allows me to concentrate on the imaging analysis itself [...]
.. quote::
Our research would be considerably more difficult without necessary software solutions transparently provided and supported by the NeuroDebian project.
-.. quote::
- :author: Patrik Andersson
- :affiliation: Image Sciences Institute, University Medical Center Utrecht, the Netherlands
- :date: 2011-06-15
- :tags: lofs, vm
- :group: Individual laboratories and researchers
-
- I have been using NeuroDebian for my work on multivariate classification of fMRI data [...] It is of great value, because I have access to both Windows and Debian OS on my laptop, where I do all my analysis.
-
-.. quote::
- :author: Dr. Felipe Picon
- :affiliation: Child and Adolescent Psychiatrist, Department of Psychiatry of Federal University of Rio Grande do Su, Porto Alegre, RS, Brazil
- :date: 2011-06-15
- :tags: lofs, ease
- :group: Individual laboratories and researchers
-
- We have been relying on NeuroDebian [...] for our work on Adult ADHD neuroimaging and find it to be very useful.
-
-.. quote::
- :author: Dr. Bhavani Shankara Bagepally
- :affiliation: Department of Psychiatry, National Institute of Mental Health And Neruosciences (NIMHANS), Bangalore, India
- :tags: lofs, ease
- :group: Individual laboratories and researchers
-
- Neuroscience software [...] easily available at a single point with hastle free installation and easy updating.
.. quote::
:author: Dr. C. J. Werner
:affiliation: Clinical and Cognitive Neuroscience, Dept. of Neurology, University Hospital RWTH Aachen, Germany
:date: 2011-06-15
- :tags: lofs, vm, teaching
+ :tags: lofs, vm, teaching, dissemination
:group: Individual laboratories and researchers
[NeuroDebian] makes my lectures on neuroimaging much more convenient and ``hands-on'' by deploying virtual machines on student's laptops [...] a quick, elegant and cost-free solution, enabling students to work on real fMRI data in no time.
-.. quote::
- :author: Dr. Peter U. Tse
- :affiliation: Associate Professor, Psychology and Brain Sciences Department, Dartmouth College, Hanover, USA
- :date: 2011-06-16
- :tags: lofs, team
- :group: Individual laboratories and researchers
-
- [...] vibrant NeuroDebian team [...] has been a great asset [...] showing their knowledge of methodological developments in the neuroscience field and making us aware of recent technological advances we could benefit from in our research.
:source: NITRC NeuroDebian reviews
[...] Best part for me is that I can run it in a VM without having to worry about replacing my native OS.
+
+.. quote::
+ :author: Robert Buccigrossi
+ :date: 2011-09-22
+ :tags: nitrc, ease
+ :group: Individual laboratories and researchers
+ :source: NITRC forum: http://www.nitrc.org/forum/message.php?msg_id=5013
+
+ Dr. Halchenko's statement "Discover http://neuro.debian.net and be happy" may sound a bit like a sales pitch, but it is rather good advice. We have been experimenting with the rapid instantiation of computational environments containing neuroimaging tools from NITRC, and the NeuroDebian repository makes installing and updating the tools through apt-related package managers rather trivial.
#constant unlikely to occur in a docname and legal as a filename
MAGIC_SEPARATOR = '---###---'
+def parse_date(datestring):
+ try:
+ parser = parse_date.parser
+ except AttributeError:
+ import dateutil.parser
+ parser = dateutil.parser.parser()
+ parse_date.parser = parser
+ return parser.parse(datestring)
+
def setup(app):
"""
see: http://sphinx.pocoo.org/ext/appapi.html
if not isinstance(app, Sphinx): return
app.add_config_value('feed_base_url', '', 'html')
app.add_config_value('feed_description', '', 'html')
+ app.add_config_value('feed_filename', 'rss.xml', 'html')
app.add_config_value('feed_title', '', 'html')
app.add_config_value('feed_subtitle', '', 'html')
app.add_config_value('feed_author_name', '', 'html')
{'all': {'filename': 'rss.xml', 'categories': None}},
'html')
app.connect('html-page-context', create_feed_item)
- app.connect('html-page-context', inject_feed_url)
app.connect('build-finished', emit_feed)
app.connect('builder-inited', create_feed_container)
app.connect('env-purge-doc', remove_dead_feed_item)
def create_feed_container(app):
"""
- create lazy filesystem stash for keeping RSS entry fragments, since we don't
- want to store the entire site in the environment (in fact, even if we did,
- it wasn't persisting for some reason.)
+ create lazy filesystem stash for keeping RSS entry fragments, since we
+ don't want to store the entire site in the environment (in fact, even if
+ we did, it wasn't persisting for some reason.)
"""
global feed_entries
rss_fragment_path = os.path.realpath(os.path.join(app.outdir, '..', 'rss_entry_fragments'))
feed_entries = FSDict(work_dir=rss_fragment_path)
- app.builder.env.feed_url = app.config.feed_base_url + '/' + 'feed_container'
+ app.builder.env.feed_url = app.config.feed_base_url + '/' + \
+ app.config.feed_filename
def inject_feed_url(app, pagename, templatename, ctx, doctree):
#We like to provide our templates with a way to link to the rss output file
ctx['rss_link'] = app.builder.env.feed_url #app.config.feed_base_url + '/' + app.config.feed_filename
+
def create_feed_item(app, pagename, templatename, ctx, doctree):
"""
Here we have access to nice HTML fragments to use in, say, an RSS feed.
We serialize them to disk so that we get them preserved across builds.
+
+ We also inject useful metadata into the context here.
"""
global feed_entries
- import dateutil.parser
from absolutify_urls import absolutify
- date_parser = dateutil.parser.parser()
metadata = app.builder.env.metadata.get(pagename, {})
if 'date' not in metadata:
return #don't index dateless articles
try:
- pub_date = date_parser.parse(metadata['date'])
+ pub_date = parse_date(metadata['date'])
+ app.builder.env.metadata.get(pagename, {})
except ValueError, exc:
#probably a nonsensical date
app.builder.warn('date parse error: ' + str(exc) + ' in ' + pagename)
return
-
- # title, link, description, author_email=None,
+
+ # RSS item attributes, w/defaults:
+ # title, link, description, author_email=None,
# author_name=None, author_link=None, pubdate=None, comments=None,
# unique_id=None, enclosure=None, categories=(), item_copyright=None,
# ttl=None,
else:
item['author_email'] = app.config.feed_author_email
feed_entries[nice_name(pagename, pub_date)] = item
+
+ #Now, useful variables to keep in context
+ ctx['rss_link'] = app.builder.env.feed_url
+ ctx['pub_date'] = pub_date
def remove_dead_feed_item(app, env, docname):
"""
global feed_entries
import os.path
+ title = app.config.feed_title
+ if not title:
+ title = app.config.project
+
feed_dict = {
- 'title': app.config.feed_title,
+ 'title': title,
'subtitle': app.config.feed_subtitle,
'link': app.config.feed_base_url,
'feed_url': app.config.feed_base_url,
connectionists
cvnet
visionlist
+ face-research-list@lists.stir.ac.uk
# Defaults #
############
-bp_distribution=${BACKPORT_DISTRIBUTION:-lenny-backports}
-bp_version_suffix=${BACKPORT_VERSION_SUFFIX:-bpo50}
+bp_distribution=${BACKPORT_DISTRIBUTION:-squeeze-backports}
+bp_version_prefix=${BACKPORT_VERSION_PREFIX:-~}
+bp_version_suffix=${BACKPORT_VERSION_SUFFIX:-bpo60}
bp_maintainer_name=${DEBFULLNAME:-unamed}
bp_maintainer_email=${DEBEMAIL:-unknown}
bp_update_maintainer=1
ideally indicating the backport target distribution. The resulting package
version will follow this schema:
- <originalversion>~<suffix>+<digit>
+ <originalversion><prefix><suffix>+<digit>
- e.g.: 1.2.3-4~bpo50+1
+ e.g.: 1.2.3-4~bpo60+1 with default <prefix>=~
+
+-p <string>, --version-prefix <string>
+ Version prefix that will be prepended to the backport version. By default it
+ is ~ but want to be changed (e.g. to +) for forward-porting to next releases.
--verbose
Enable additional status messages.
bp_distribution="lenny-backports"
Backport target distribution (see --backport-distribution)
-bp_version_suffix="bpo50"
+bp_version_prefix="~"
+ Version suffix (see --version-prefix)
+
+bp_version_suffix="bpo60"
Version suffix (see --version-suffix)
bp_maintainer_name="Unknown fellow"
# Note that we use `"$@"' to let each command-line parameter expand to a
# separate word. The quotes around `$@' are essential!
# We need CLOPTS as the `eval set --' would nuke the return value of getopt.
-CLOPTS=`getopt -o h,d:,s: --long help,verbose-help,version,target-distribution:,version-suffix:,maint-name:,maint-email:,no-color,no-backport-patches,verbose,mod-control:,no-maintainer-update, -n 'backport-dsc' -- "$@"`
+CLOPTS=`getopt -o h,d:,s:,p: --long help,verbose-help,version,target-distribution:,version-suffix:,version-prefix:,maint-name:,maint-email:,no-color,no-backport-patches,verbose,mod-control:,no-maintainer-update, -n 'backport-dsc' -- "$@"`
if [ $? != 0 ] ; then
echo "Terminating..." >&2
case "$1" in
-d|--target-distribution) shift; bp_distribution=$1; shift;;
-s|--version-suffix) shift; bp_version_suffix=$1; shift;;
+ -p|--version-prefix) shift; bp_version_prefix=$1; shift;;
--maint-name) shift; bp_maintainer_name=$1; shift;;
--maint-email) shift; bp_maintainer_email=$1; shift;;
--no-maintainer-update) bp_update_maintainer=0; shift;;
wdir=$(mktemp -d -t backport-dsc.XXXXXX)
sdir=$wdir/${src_name}-${src_version}
-bp_version="~${bp_version_suffix}+"
+bp_version="${bp_version_prefix}${bp_version_suffix}+"
# setup environment for dpkg
# common options
opts="--distribution $dist --debootstrap debootstrap --aptcache $aptcache"
+if echo $family | grep -q ubuntu; then
+ # Use ubuntu's keyring since otherwise debootstrap would fail
+ opts+=" --debootstrapopts --keyring=/usr/share/keyrings/ubuntu-archive-keyring.gpg"
+fi
+
mkdir -p ${cowbuilderroot}/cow
for a in i386 amd64; do
cowbuilder --create --basepath ${cow} $opts \
--components "$components" \
--mirror "$mirror" \
- --debootstrapopts --arch --debootstrapopts $a \
+ --debootstrapopts --arch=$a \
--othermirror "deb http://neuro.debian.net/debian $dist main contrib non-free"
- # deploy our key manually since archive with package is not yet
- # available at this point
- cp --preserve=mode {,${cow}}/etc/apt/trusted.gpg.d/neurodebian-archive-keyring.gpg
+ # deploy our key manually since archive with package is not yet
+ # available at this point
+ mkdir -p ${cow}/etc/apt/trusted.gpg.d
+ cp --preserve=mode {,${cow}}/etc/apt/trusted.gpg.d/neurodebian-archive-keyring.gpg
+ # Old ubuntus might not have capability to ready from that key yet,
+ # so we would need to manually add it
+ if [ $dist = 'karmic' ] || [ $dist = 'hardy' ]; then
+ chroot ${cow} bash -c "apt-get install -y --force-yes gnupg \
+ && /usr/bin/apt-key add /etc/apt/trusted.gpg.d/neurodebian-archive-keyring.gpg \
+ && /usr/bin/apt-get update"
+ fi
else
cowbuilder --create --basepath ${cow} $opts \
--components "$components" \
--mirror "$mirror" \
- --debootstrapopts --arch --debootstrapopts $a
+ --debootstrapopts --arch=$a
fi
done
--- /dev/null
+#!/bin/bash
+# Little helper to bootstrap all ND chroots as specified in
+# /etc/neurodebian/cmdsettings.sh unless a list provided in command line
+
+. /etc/neurodebian/cmdsettings.sh
+
+[ -z "$@" ] && dists="$alldists" || dists="$@"
+
+echo "Initiating creation of chroots for $dists"
+
+set -eu
+
+CMD=
+MSGS="SUMMARY:\n"
+for dist in $dists; do
+ if [ -e "$cowbuilderroot/cow/$dist-amd64.cow" ]; then
+ status=exists
+ else
+ $CMD sudo nd_adddist ${dist%%-*} ${dist#*-} && status=ok || status=failed
+ fi
+ MSGS+=" $(printf '%-30s\\t%s' $dist $status)\n"
+done
+echo -en $MSGS
+
shift; shift; shift; shift
fi
+# failed will be set to 1 if any build fails
+failed=
for a in $arch; do
# default
options="$opts"
--buildresult . \
--logfile "${buildfile}" \
$options \
- "$@" && status='OK' || status='FAILED'
-
+ "$@" && status='OK' || { status='FAILED'; failed=1; }
timeinfo=$(tail -n 1 "${tsfile}")
# Update the summary of builds
touch summary.build # Assure existence
echo -e "${buildfile}\t$status\t$timeinfo" >> summary.build # Add current one
rm -f "${tsfile}"
done
+# Exit with failure status if any built failed
+[ -z $failed ] || exit 1
drelease=${d##*-}
bpdsc=$(nd_backport $drelease $dscfile | tail -n1 | sed -e 's/^.* //g')
- nd_build $dfamily $drelease $bpdsc "$@"
+ nd_build $dfamily $drelease $bpdsc "$@" || :
done
--- /dev/null
+#!/bin/bash
+
+# no undefined
+set -u
+# no failures
+set -e
+
+CMD=
+#echo
+
+family=$1
+dist=$2
+arch=$3 # limit to 1 for now
+
+dscfile=$4
+dscfilef=$(readlink -f $dscfile)
+dscfilef_base=${dscfilef%%.dsc}
+
+pkg=${dscfile%_*}
+
+#? TODO -- should be a parameter as well?
+
+testdir=${dscfilef_base}_$arch.testrdepends.$family-$dist
+bindir=$testdir/bin
+debdir=$testdir/debs
+srcdir=$testdir/srcs
+oldbuildsdir=$srcdir/old
+newbuildsdir=$srcdir/new
+
+echo "I: Building the new package for $pkg"
+
+mkdir -p $debdir $srcdir $bindir
+$CMD nd_build $family $dist $arch $dscfile --buildresult=$debdir
+
+cd $debdir
+dpkg-scanpackages . >| Packages
+cd - > /dev/null
+
+echo "I: Fetching all bdepends for $pkg in $family $dist under $arch"
+# need first to provide the necessary scripts out there
+cp -p $(dirname $0)/nd_fetch_bdepends $bindir
+$CMD nd_execute $family $dist $arch --bindmounts $testdir $bindir/nd_fetch_bdepends $pkg $srcdir
+
+echo "I: preparing the hook"
+cat << EOF >| $bindir/D00add_custom_repo
+echo 'deb file://$debdir ./' >| /etc/apt/sources.list.d/custom.list
+apt-get update
+EOF
+chmod a+x $bindir/D00add_custom_repo
+
+echo "I: Going throught the packages and testing the builds"
+cd $srcdir
+summary_file=${testdir}.summary
+echo -e "\nTesting builds against $dscfile" >> $summary_file
+for dsc in *.dsc; do
+ echo " I: Building $dsc with native versions"
+ src=${dsc%%_*}
+ dscbase=${dsc%%.dsc}
+ nd_build $family $dist $arch $dsc --buildresult=$oldbuildsdir \
+ && old=ok || old=FAILED
+ mv ${dscbase}_$arch.build $oldbuildsdir
+ echo " I: Building $dsc with new versions"
+ nd_build $family $dist $arch $dsc --buildresult=$newbuildsdir \
+ --hookdir=$bindir --bindmount=$testdir \
+ && new=ok || new="FAILED $newbuildsdir/${dscbase}_$arch.build"
+ mv ${dscbase}_$arch.build $newbuildsdir
+ printf '%-40s\t%5s\t%5s\n' $dsc "$old" "$new" >> $summary_file
+done
--- /dev/null
+#!/bin/bash
+
+if [ -z "$1" ]; then
+cat << EOT
+Script to log into a particular COW and execute some command.
+
+Synopsis
+--------
+
+ nd_execute <family> <codename> <arch> [cowbuilderopts] command
+
+EOT
+exit 1
+fi
+
+family=$1
+dist=$2
+arch=$3
+bmdir=
+#$4
+
+set -e
+
+if [ -z "$family" ]; then
+ echo "You need to provide a distribution family ('debian', 'ubuntu'); prefix with 'nd+' to enable the NeuroDebian repository."
+ exit 1
+fi
+
+if [ -z "$dist" ]; then
+ echo "You need to provide a distribution codename (e.g. 'lenny', 'squeeze')."
+ exit 1
+fi
+
+if [ -z "$arch" ]; then
+ echo "You need to provide an architecture (e.g. 'i386', 'amd64')."
+ exit 1
+fi
+
+. /etc/neurodebian/cmdsettings.sh
+
+shift; shift; shift; # get rid of those from future use of $@
+
+# common options
+opts="--distribution $dist --aptcache $aptcache --buildplace $buildplace"
+
+
+#if [ -n "bmdir" ]; then
+# options="$opts --bindmounts $bmdir"
+#else
+ options="$opts"
+#fi
+
+cowbuilder --execute \
+ --basepath ${cowbuilderroot}/cow/${family}-${dist}-${arch}.cow \
+ $options \
+ "$@"
--- /dev/null
+#!/bin/bash
+
+pkg=$1
+tdir=$2
+
+# provide deb-src by uncommenting
+sed -i -e 's,^#deb-src,deb-src,g' /etc/apt/sources.list
+
+mkdir -p $tdir
+cd $tdir
+apt-get update
+apt-get install -y devscripts dctrl-tools
+build-rdeps $pkg >| build-rdeps.output
+
+# Fetch all the sources
+grep -v -e '^[-A-Z]' -e '^ *$' build-rdeps.output \
+ | tee build-rdeps.list \
+ | while read pkg; do
+ apt-get source --download-only $pkg
+done
--- /dev/null
+#!/bin/bash
+
+if [ -z "$1" ]; then
+cat << EOT
+Script to re-build entire archive from one release for another.
+
+Often usecase -- rebuilding for a new Ubuntu brew every 6 months.
+
+Synopsis
+--------
+
+ nd_rebuildarchive old_release new_release
+
+e.g.
+
+ nd_rebuildarchive natty oneiric
+
+EOT
+exit 1
+fi
+
+set -eu
+
+old_dist=$1
+dist=$2
+
+# some NeuroDebian variables hardcoded in for now
+repo_server=neuro.debian.net
+repo_user=neurodebian
+repo_toppath=www
+repo_urlpath=debian
+repo_distspath=$repo_toppath/$repo_urlpath/dists
+
+family=nd+ubuntu
+
+list_file="$old_dist-$dist.list"
+summary_file="$old_dist-$dist.summary"
+
+[ -e "$list_file" ] || \
+ ssh -l $repo_user $repo_server cat $repo_distspath/$old_dist/*/source/Sources.gz \
+ | zgrep -e '^\(Package\|Directory\| [a-z0-9]\{32\} [0-9]* \S*.dsc$\)' \
+ | sed -e 's,.* \([^ ][^ ]*\)$,\1,g' | tr '\n' ' '| sed -e 's,\.dsc,.dsc\n,g' \
+ > "$list_file"
+
+CMD=
+#echo
+dist_id=$(nd_querycfg "release backport ids" "$dist")
+cat $list_file \
+| while read name topdir dscfile; do
+ echo "I: Forwardporting for $dist_id $dscfile"
+
+ [ -e $dscfile ] \
+ || dget -d http://$repo_server/$repo_urlpath/$topdir/$dscfile || {
+ echo -e "E: $dscfile\t\tFAILED to fetch" >> $summary_file
+ continue
+ }
+
+
+ bpdscfile=$(/home/neurodebian/neurodebian/tools/backport-dsc \
+ --target-distribution "$dist" \
+ --no-maintainer-update \
+ --version-prefix "+" \
+ --version-suffix "$dist_id" \
+ "$dscfile" | tail -n1 | sed -e 's/^.* //g')
+
+ echo " I: Building backported dscfile: $bpdscfile"
+
+ $CMD sudo nd_build $family $dist $bpdscfile && {
+ echo -e "I: $bpdscfile\t\tOk" >> $summary_file
+ } || {
+ echo -e "E: $bpdscfile\t\tFAILED to build" >> $summary_file
+ }
+done
\ No newline at end of file