--db build/db.db \
--outdir build/src \
--pkgaddenum pkgs \
+ --extracts /home/www/neuro.debian.net/www/debian/extracts \
commandisirrelevant
rm -f html-stamp
touch $@
--- /dev/null
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+neurodebian (0.22) unstable; urgency=low
+
+ [ Yaroslav Halchenko ]
+ * blends-inject :
+ * [6833800] 0.0.6: skip files based on regexp and "emptiness"
+ * [69030fb] 0.0.7: NF/BF -- obtain source name from control,
+ skip hash-commented control entries
+ * [bed4bfa] added future/blends skeleton file (skel) and a set of
+ new blends files
+ * tools/*
+ * [66e4c32] fixed passing of optional cmdline args in nd_ tools:
+ must use "$@" instead of plain $*
+ * [fd2c503] tools/nd_build: generate/update summary.build file with
+ OK/FAILED per .build
+ * [0872417] Slight clarifications in the description of
+ -popularity-contest package
+
+ [ Michael Hanke ]
+ * [56d8e62] Enable TODO items in sphinx.
+ * [b98b0b7] Move mailing list links into common list.
+ * [56fde2f] Draft for a project list and two proposals.
+ * [a12bc58] Link new projects list into the FAQ
+ * [82b92d5] Renamed matlab -> matlab-support
+ * [69f6512] Put icon links to extracts from DSCs (README, changelog,
+ copyright)
+
+ -- Yaroslav Halchenko <debian@onerussian.com> Mon, 10 Jan 2011 11:06:54 -0500
+
+neurodebian (0.21) unstable; urgency=low
+
+ * Fixing bashism in popcon post-scripts -- no "+=" operator
+
+ -- Yaroslav Halchenko <debian@onerussian.com> Tue, 07 Dec 2010 08:48:53 -0500
+
+neurodebian (0.20) unstable; urgency=low
+
+ * New package neurodebian-popularity-contest, which all backported
+ packages will depend on.
+
+ -- Yaroslav Halchenko <debian@onerussian.com> Mon, 06 Dec 2010 14:27:56 -0500
+
neurodebian (0.19) unstable; urgency=low
* Initial release.
Recommends: virtualbox-ose, virtualbox-ose-fuse, zerofree
Suggests:
Description: NeuroDebian development tools
- Pacifier
+ neuro.debian.net sphinx website sources and development tools used by
+ NeuroDebian to provide backports for a range of Debian/Ubuntu
+ releases.
Package: neurodebian-desktop
Architecture: all
-Depends: ${misc:Depends}, ssh-askpass-gnome | ssh-askpass, desktop-base, gnome-icon-theme
+Depends: ${misc:Depends}, ssh-askpass-gnome | ssh-askpass, desktop-base, gnome-icon-theme,
+ neurodebian-popularity-contest
Suggests:
Description: neuroscience research environment
- Pacifier
+ This package contains NeuroDebian artwork (icons, background image)
+ and a NeuroDebian menu featuring most popular neuroscience tools
+ automatically installed upon initial invocation.
Package: neurodebian-keyring
The NeuroDebian project digitally signs its Release files. This package
contains the archive keys used for that.
+Package: neurodebian-popularity-contest
+Architecture: all
+Depends: ${misc:Depends}, popularity-contest
+Description: Helper for NeuroDebian popularity contest submissions
+ This package is a complement to the generic popularity-contest
+ package to enable anonymous submission of usage statistics to
+ NeuroDebian in addition to the popcon submissions to the underlying
+ distribution (e.g. Debian or Ubuntu) popcon server.
+ .
+ Your participation in popcon is important for following reasons:
+ - Popular packages receive more attention from developers, bugs are
+ fixed faster and updates are provided quicker.
+ - Assure that we do not drop support for a previous release of Debian
+ or Ubuntu while are active users.
+ - User statistics could be used by upstream research software
+ developers to acquire funding for continued development.
+ .
+ It has an effect only if you have decided to participate in the
+ Popularity Contest of your distribution, i.e. Debian or Ubuntu.
+ You can always enable or disable your participation in popcon by
+ running 'dpkg-reconfigure popularity-contest' as root.
Package: neurodebian-guest-additions
Architecture: all
--- /dev/null
+#!/bin/bash -e
+
+popcon_conf=/etc/popularity-contest.conf
+if [ "$1" = "configure" -o "$1" = "abort-upgrade" ]; then
+ # Adjust popularity-contest.conf
+ if [ -e "$popcon_conf" ]; then
+ # Fix dashism missing += operator
+ if grep -q 'SUBMITURLS+="' "$popcon_conf"; then
+ echo "Adjusting addition of new entries in $popcon_conf for dash."
+ sed -i -e 's,SUBMITURLS+=",SUBMITURLS="$SUBMITURLS,g' "$popcon_conf"
+ fi
+ if ! grep -q 'SUBMITURLS.*neuro.debian.net' "$popcon_conf"; then
+ echo "Adding NeuroDebian url for Popularity Contest submissions."
+ echo -e 'SUBMITURLS="$SUBMITURLS http://neuro.debian.net/cgi-bin/popcon-submit.cgi"' >> "$popcon_conf"
+ fi
+ fi
+fi
+
+#DEBHELPER#
--- /dev/null
+#!/bin/sh -e
+
+#DEBHELPER#
+
+# If requested to be purged -- remove our entry
+popcon_conf=/etc/popularity-contest.conf
+if [ "$1" = "purge" ]; then
+ # Adjust popularity-contest.conf
+ if [ -e "$popcon_conf" ]; then
+ echo "Removing NeuroDebian url for Popularity Contest submissions."
+ # First remove any explicit mentioning and then empty additions
+ sed -i -e 's,http://neuro.debian.net/cgi-bin/popcon-submit.cgi,,g' \
+ -e '/SUBMITURLS+=" *"/d' \
+ -e '/SUBMITURLS="$SUBMITURLS *"/d' \
+ "$popcon_conf"
+ fi
+fi
--- /dev/null
+Source: BCI2000
+Tasks: debian-science/bci
+Homepage: http://bci2000.org
+Author: Gerwin Schalk and Company
+Language: C++
+License: non-free (non-redistributable, non-commercial)
+Version: 2.1
+Pkg-Description: platform for brain-computer interface systems
+ BCI2000 supports a variety of data acquisition systems, brain
+ signals, and study/feedback paradigms. During operation, BCI2000
+ stores data in a common format (BCI2000 native or GDF), along with
+ all relevant event markers and information about system
+ configuration. BCI2000 also includes several tools for data
+ import/conversion (e.g., a routine to load BCI2000 data files
+ directly into Matlab) and export facilities into ASCII.
+ .
+ BCI2000 also facilitates interactions with other software. For
+ example, Matlab scripts can be executed in real-time from within
+ BCI2000, or BCI2000 filters can be compiled to execute as stand-alone
+ programs. Furthermore, a simple network-based interface allows for
+ interactions with external programs written in any programming
+ language. For example, a robotic arm application that is external to
+ BCI2000 may be controlled in real time based on brain signals
+ processed by BCI2000, or BCI2000 may use and store along with brain
+ signals behavioral-based inputs such as eye-tracker coordinates.
+Remark: Besides non-commercial restriction, it is required that
+ "ACADEMIC USER must be an investigator / lab director (and not a
+ post-doc or student)". Re-distribution (to third-party) is also
+ forbidden.
+Registration: http://www.bci2000.org/MTA
--- /dev/null
+Source: BCPy2000
+Tasks: debian-science/bci
+Homepage: http://bci2000.org/downloads/BCPy2000/BCPy2000.html
+Author: Jeremy Hill, Thomas Schreiner, Christian Puzicha and Jason Farquhar
+Language: Python, C++
+License: LGPL-3+ and GPL-3+ and non-free (BCI2000)
+Version: 20100708
+Pkg-Description: platform for brain-computer interface systems
+ BCPy2000 provides a platform for rapid, flexible development of
+ experimental brain-computer interface systems. It is based on, and
+ hosted by, the BCI2000 project. From the developer's point of view,
+ the implementation is carried out in Python, taking advantage of
+ various high-level packages: VisionEgg for stimulus presentation,
+ NumPy and SciPy for signal processing and classification, and IPython
+ for interactive debugging.
+ .
+ Being a BCI2000 system, it is modular, consisting of an Application
+ module (the stimulus presentation part), a Signal Processing module
+ (the machine-learning part), and a Signal Source module (the toy data
+ generation part). You can choose to use Python to implement one, two,
+ or all three of these modules, and use other pre-existing BCI2000
+ modules for the remainder of the system (for example, for the Signal
+ Source, you can choose from BCI2000's comprehensive range of EEG
+ acquisition modules). The modules communicate over TCP/IP, so they
+ can run on different machines (and possibly different operating
+ systems) if necessary.
--- /dev/null
+Source: bluespike
+Tasks: debian-science/electrophysiology
+Homepage: https://github.com/globalvariable/BlueSpike
+Author: Mehmet Kocaturk <kocaturk@gmail.com>
+Language: C
+License: GPL-2+
+Version: 0.3
+WNPP: 611211
+Pkg-Description: Data Acquisition and Neural Spike Processing Software
+ BlueSpike is an electrophysiology tool to perform real-time data
+ acquisition, visualization and sorting of neuronal spikes. It
+ continuously acquires data every 1 ms and realizes digital signal
+ processing on retrieved data. Contains four components:
+ .
+ - KernelSpike: a kernel module.
+ - SpikeViewever
+ - SpikeSorter
+ - Channel Reviewer
+Published-Title: Real-time experimental interface for electrophysiology experiments
+Published-Authors: Mehmet Kocaturk <kocaturk@gmail.com> et al.
+Published-In: SfN2010, Poster 818.22/OOO43
+Published-Year: 2010
Source: chronus
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Homepage: http://www.chronux.org/
License: GPL-2+
Author: Gerald Dalley, Catherine Loader
--- /dev/null
+Source: condor
+Tasks: debian-science/distributedcomputing
+Homepage: http://www.cs.wisc.edu/condor
+Responsible: NeuroDebian Team <team@neuro.debian.net>
+Language: C++, Perl
+Author: Condor Team <condor-admin@cs.wisc.edu>
+License: Apache-2.0
+WNPP: 233482
+Published-Title: Condor - A Hunter of Idle Workstations
+Published-Authors: Michael Litzkow, Miron Livny, and Matt Mutka
+Published-In: Proceedings of the 8th International Conference of Distributed Computing Systems, pp. 104-111
+Published-Year: 1988
+Registration: http://www.cs.wisc.edu/condor/downloads-v2/
+Pkg-Description: workload management system
+ 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. It chooses when and where to run the jobs
+ based upon a policy, carefully monitors their progress, and ultimately
+ informs the user upon completion.
+ .
+ Unlike more traditional batch queueing system, Condor can also effectively
+ harness wasted CPU power from otherwise idle desktop workstations. 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.
--- /dev/null
+Source: eeglab
+Tasks: debian-science/neuroscience-cognitive,
+ debian-med/imaging
+Homepage: http://sccn.ucsd.edu/eeglab
+Responsible: NeuroDebian Team <team@neuro.debian.net>
+Language: C, Matlab/Octave
+Version: 9
+Author: Arnaud Delorme <arno@ucsd.edu>, Scott Makeig <smakeig@ucsd.edu>
+License: GPL-2+
+WNPP: 605739
+Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics
+Published-Authors: Delorme A and Makeig S
+Published-In: Journal of Neuroscience Methods 134:9-21
+Published-Year: 2004
+Pkg-Description: toolbox for processing and visualization of electrophysiological data
+ EEGLAB is an interactive Matlab toolbox for processing continuous and
+ event-related EEG, MEG and other electrophysiological data
+ incorporating independent component analysis (ICA), time/frequency
+ analysis, artifact rejection, event-related statistics, and several
+ useful modes of visualization of the averaged and single-trial data.
+Registration: http://sccn.ucsd.edu/eeglab/install.html
--- /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: Emokit
+Tasks: debian-science/bci,
+ debian-med/imaging-dev
+Homepage: https://github.com/daeken/Emokit
+Author: Cody Brocious <cody.brocious@gmail.com>
+Language: Python, C
+License: BSD-3
+Version: Unknown
+Vcs-Browser: https://github.com/daeken/Emokit
+Vcs-Git: git://github.com/daeken/Emokit.git
+Pkg-Description: Emotiv EPOC headset Python interface
+ Emotive is an interface to a budget Emotiv EPOC EEG headset.
--- /dev/null
+Source: hart
+Tasks: debian-science/dataacquisition
+Homepage: http://hart.sourceforge.net/
+Author: HART Developers
+Language: C
+License: GPL
+Version: 0.4
+Pkg-Description: toolbox to generate DAQ Scicos-blocks for hardware
+ The HART (Hardware Access in Real-Time) Toolbox can be used to
+ generate Scicos-blocks for hardware that have a C/C++ interface. The
+ blocks can be used under Linux for soft and hard real time tasks
+ (RTAI). Blocks are provided for DAQ (COMEDI)
--- /dev/null
+Source: iNVT
+Tasks: debian-science/neuroscience-modeling
+Homepage: http://ilab.usc.edu/toolkit/
+Author: iLab at USC
+Language: C++ + Perl, Tcl, Matlab
+License: GPL-2+
+Version: 0.0.0.14308 (SVN revision)
+Pkg-Description: iLab Neuromorphic Vision C++ Toolkit
+ The iLab Neuromorphic Vision C++ Toolkit (iNVT, pronounced
+ ``invent'') is a comprehensive set of C++ classes for the development
+ of neuromorphic models of vision. Neuromorphic models are
+ computational neuroscience algorithms whose architecture and function
+ is closely inspired from biological brains. The iLab Neuromorphic
+ Vision C++ Toolkit comprises not only base classes for images,
+ neurons, and brain areas, but also fully-developed models such as our
+ model of bottom-up visual attention and of Bayesian surprise.
+ .
+ Features at a glance:
+ * Low-level neural network simulation classes.
+ * High-level neuromorphic classes.
+ * Neuromorphic models of visual attention.
+ * Hardware interfacing
+ * Parallel processing classes for the simulation of complex models.
+ * Neuromorphic modeling environment.
+Registration: http://ilab.usc.edu/cgi-bin/yabb/YaBB.pl?board=;action=register
--- /dev/null
+Source: klustakwik
+Tasks: debian-science/electrophysiology
+Homepage: http://klustakwik.sourceforge.net
+Published-Title: Accuracy of Tetrode Spike Separation as Determined by Simultaneous Intracellular and Extracellular Measurements
+Published-Authors: Kenneth D. Harris, Darrell A. Henze, Jozsef Csicsvari, Hajime Hirase, and György Buzsáki
+Published-In: Journal of Neurophysiology, 84, 401-414
+Published-Year: 2000
+Pkg-Description: spike sorting tool
+ A program for unsupervised classification of multidimensional
+ continuous data. It arose from a specific need - automatic sorting of neuronal
+ action potential waveforms.
--- /dev/null
+Tasks: debian-science/neuroscience-modeling
+Suggests: nest
+License: non-FOSS
+Responsible: Yury V. Zaytsev <yury@shurup.com>
+Published-Authors: Gewaltig M-O and Diesmann M
+Published-Title: NEST (Neural Simulation Tool)
+Published-In: Scholarpedia 2(4):1430
+Published-Year: 2007
+Vcs-Browser: http://git.zaytsev.net/?p=nest-packaging.git;a=summary
+Vcs-Git: git://git.zaytsev.net/nest-packaging.git
+Pkg-URL: http://git.zaytsev.net/?p=nest-packaging.git;a=summary
+Pkg-Description: A simulator for networks of spiking neurons
+ NEST is a simulation system for large networks of biologically realistic
+ point-neurons and neurons with a small number of electrical compartments.
+Remark: Mentioned packaging is not providing NEST itself but rather only packaging materials so you could build package yourself.
+Homepage: http://www.nest-initiative.org/index.php/Software:About_NEST
+Registration: http://www.nest-initiative.org/download/Software:Download.php
+
Source: neurodata
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Homepage: http://sourceforge.net/projects/neurodata/
Language: C++, Octave/Matlab, Perl
Source: nspike
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Homepage: http://nspike.sourceforge.net
Language: C++
Version: 1.9.3
--- /dev/null
+Source: opensesame
+Tasks: debian-science/psychophysics
+Homepage: http://www.cogsci.nl/software/opensesame
+Author: Sebastiaan Mathôt <s.mathot@psy.vu.nl>
+License: GPL-3
+Pkg-Description: graphical experiment builder for the social sciences
+ OpenSesame is a graphical experiment builder. OpenSesame provides an
+ easy to use, point-and-click interface for creating psychological
+ experiments. In addition to a powerful sketchpad for creating visual
+ stimuli, OpenSesame features a sampler and synthesizer for sound
+ playback. For more complex tasks, OpenSesame supports Python
+ scripting using the built-in editor with syntax highlighting.
+Pkg-URL: http://files.cogsci.nl/software/opensesame/
+Published-Title: OpenSesame (Version 0.22) [Computer software and manual]
+Published-Authors: Mathôt, S., & Theeuwes, J.
+Published-In: http://www.cogsci.nl/software/opensesame
+Published-Year: Retrieved December 18, 2010
+Responsible: Sebastiaan Mathôt <s.mathot@psy.vu.nl>
+WNPP: 611640
--- /dev/null
+Source: openvibe
+Tasks: debian-science/bci,
+ debian-med/physics
+Homepage: http://openvibe.inria.fr
+License: LGPL
+WNPP: 580247
+Pkg-Description: platform for the design, test and use of BCI
+ OpenViBE enables to design, test and use Brain-Computer Interfaces (BCI).
+ OpenViBE is a software for real-time neurosciences (that is, for
+ real-time processing of brain signals). It can be used to acquire, filter,
+ process, classify and visualize brain signals in real time.
+Author: OpenViBE Team
+Language: C++
--- /dev/null
+Source: PyBCI
+Tasks: debian-science/bci
+Homepage: http://pybci.sourceforge.net/
+Author: Benedikt Zoefel
+Language: Python, C++
+License: MIT
+Version: 0.4
+Vcs-Browser: http://pybci.git.sourceforge.net/git/gitweb-index.cgi
+Vcs-Git: git://pybci.git.sourceforge.net/gitroot/pybci/pybci
+Pkg-Description: Brain Computer Interface module for Brain Vision Recorder
+ This module gives you the possibility to create a Brain Computer
+ Interface (BCI), and herewith to get EEG data online and evaluate the
+ data while you are receiving it. The module is made for all users of
+ the Brain Vision Recorder because of the therein implemented function
+ of Remote Data Access. It is not possible to use it with another EEG
+ Recorder Software, but this will be a project in the future.
+ .
+ Using the PyBCI module, you are able to get a numpy data array in up
+ to every few ten milliseconds and therewith evaluate the data almost
+ in realtime with other powerful Python packages, for example using
+ PyMVPA.
+Remark: No activity since Sep 2009
--- /dev/null
+Source: pyff
+Tasks: debian-science/bci
+Homepage: http://bbci.de/pyff/
+License: GPL-2+
+Author: Bastian Venthur <venthur at cs tu-berlin de>
+Language: Python
+Version: 2010.7
+Vcs-Browser: https://github.com/venthur/pyff
+Vcs-Git: git://github.com/venthur/pyff.git
+Published-Title: Pyff --- A Pythonic Framework for Feedback Applications and Stimulus Presentation in Neuroscience
+Published-Authors: Bastian Venthur, Simon Scholler, John Williamson, Sven Dähne, Matthias S Treder, Maria T Kramarek, Klaus-Robert Müller and Benjamin Blankertz
+Published-In: Frontiers in Neuroscience
+Published-Year: 2010
+Published-DOI: 10.3389/fnins.2010.00179
+Pkg-Description: Brain Computer Interface (BCI) framework
+ Pyff is a Pythonic Feedback Framework which provides a platform
+ independent framework to develop BCI feedback applications in
+ Python. It was designed to make the development of feedback
+ applications as easy as possible. Pyff framework moves feedback
+ implementations to a general purpose, and easy to learn language like
+ Python. Python provides many so called bindings to other libraries,
+ which allow it to develop high quality multimedia feedback
+ applications, with little effort.
+ .
+ The framework communicates with the rest of the BCI system via a
+ standardized communication protocol using UDP and XML and is
+ therefore suitable to be used with any BCI system that may be adapted
+ to send its control signal via UDP in the specified format.
--- /dev/null
+Source: pyxid
+Tasks: debian-science/psychophysics
+Homepage: https://github.com/cedrus-opensource/pyxid
+Author: Grant Limberg <glimberg@cedrus.com>
+Language: Python
+License: BSD-3
+Version: 1.0~b6
+WNPP: 607213
+Pkg-Description: interfacing with Cedrus XID and StimTracker devices
+ pyxid is a Python library for interfacing with Cedrus XID (eXperiment
+ Interface Device) and StimTracker devices. XID devices are used in
+ software such as SuperLab, Presentation, and ePrime for receiving
+ input as part of stimulus/response testing experiments.
+ .
+ pyxid handles all of the low level device handling for XID devices in
+ python projects.
--- /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>
Source: qrtailab
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Homepage: http://qrtailab.sourceforge.net/
Author: Holger Nahrstaedt
License: LGPL-2
Source: relacs
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Homepage: http://www.relacs.net
License: GPL-2+
Author: Jan Benda <benda@bio.lmu.de>
--- /dev/null
+Source: rtxi
+Tasks: debian-science/electrophysiology
+Homepage: http://www.rtxi.org
+License: GPL-2+
+Author: Jonathan Bettencourt <jbetten@med.cornell.edu>
+Language: C++
+Version: 1.1.2
+Pkg-Description: real-time data acquisition and control applications in biological research
+ The Real-Time eXperiment Interface (RTXI) is a collaborative
+ open-source software development project aimed at producing a
+ real-time Linux based software system for hard real-time data
+ acquisition and control applications in biological research.
+ .
+ Core functionality of RTXI gets extended via plugins, such as
+ - Data Recorder
+ - Virtual Dendrite
+ - Spike-triggered Average
+ - Phase Response Curve
+ - Signal processing
--- /dev/null
+Source:
+Tasks: debian-science/bci,
+ debian-science/neuroscience-modeling
+ debian-med/imaging
+Homepage:
+Author:
+Language:
+License:
+Version:
+Vcs-Browser:
+Vcs-Git:
+Pkg-Description:
+
+Pkg-URL:
+Published-Title:
+Published-Authors:
+Published-In:
+Published-Year:
+Published-DOI:
+Responsible:
+Registration:
+Remark:
+Why:
Source: spike
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Language: C++, Octave/Matlab
License: BSD-3 and Academic Free License
Source: stimfit
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Homepage: http://code.google.com/p/stimfit/
Version: 0.10.0
Author: Christoph Schmidt-Hieber <c.schmidt-hieber@wibr.ucl.ac.uk>
Source: trellis-neuro
-Tasks: debian-science/neuroscience-electrophysiology
+Tasks: debian-science/electrophysiology
Homepage: http://sourceforge.net/projects/trellis-neuro/
License: GPL-3+ and LGPL-3+
Author: Ripple, LLC
--- /dev/null
+Source: tscope
+Tasks: debian-science/psychophysics
+Homepage: http://users.ugent.be/~masteven/tscope
+Author: Michael Stevens <Michael.Stevens@UGent.be>
+Language: C
+License: GPL
+Version: 1.0.176
+Pkg-Description: C/C++ experiment programming library for cognitive scientists
+ Tscope is a C/C++ experiment programming library for cognitive
+ scientists. It provides functions for graphics,
+ sound, timing, randomization and response registration.
+Published-Title: Tscope: A C library for programming cognitive experiments on the MS Windows platform
+Published-Authors: Stevens, M., Lammertyn, J., Verbruggen, F., & Vandierendonk, A.
+Published-In: Behavior Research Methods, 38, 280-286.
+Published-Year: 2006
+Remark: Primarily targeting Windows platform, provides some functionality on Linux
--- /dev/null
+Source: visionegg
+Tasks: debian-science/psychophysics,
+ debian-med/psychology
+Homepage: http://www.visionegg.org
+License: LGPL
+WNPP: 365856
+Pkg-Description: Python library for 2D/3D visual stimulus generation
+ The Vision Egg is a programming library that uses standard, inexpensive
+ computer graphics cards to produce visual stimuli for vision research
+ experiments.
+Published-Title: Vision Egg: An Open-Source Library for Realtime Visual Stimulus Generation
+Published-Authors: Andrew Straw
+Published-In: Frontiers in Neuroinformatics
+Published-Year: 2008
+Published-URL: http://frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/004.2008/
+Published-DOI: 10.3389/neuro.11.004.2008
# Packages listed in the following taskfiles will be featured on the website
# _if_ they are also present in the repository
select taskfiles =
- svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-electrophysiology
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/bci
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/electrophysiology
svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-cognitive
svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-datasets
svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-modeling
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/psychophysics
svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging
svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging-dev
+ svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/psychology
# Additional selection filter (similar to 'select taskfiles'), only listing
# package names
select names = libnifti2 odin mitools afni-atlases python-pyssdh python-networkx
r-cran-glmnet python-rpy2 python-nibabel-snapshot
- python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab
+ python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab-support
svgtune
# Information about prospective packages to be imported from taskfiles
prospective =
- svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-electrophysiology
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/bci
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/electrophysiology
svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-cognitive
svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-datasets
svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-modeling
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/psychophysics
svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging
svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging-dev
openmeeg-tools = openmeeg-tools libopenmeeg-dev python-openmeeg libopenmeeg1
libbiosig-dev = libbiosig-dev python-biosig octave-biosig biosig-tools libbiosig0
libgdf-dev = libgdf-dev libgdf0 libgdf0-dbg libgdf-dev gdf-tools octave-gdf matlab-gdf
-spm8 = matlab-spm8 spm8-common spm8-data spm8-doc
+spm8 = matlab-spm8 spm8-data spm8-doc
+libfreenect-dev = libfreenect0.0 libfreenect-dev libfreenect-demos python-freenect freenect
+psychtoolbox-3 = octave-psychtoolbox-3 matlab-psychtoolbox-3 psychtoolbox-3-doc
[mirrors]
de = http://apsy.gse.uni-magdeburg.de/debian
import codecs
import subprocess
import time
+import re
# templating
from jinja2 import Environment, PackageLoader
for stanza in deb822.Packages.iter_paragraphs(fh):
if stanza.has_key('Depends'):
pkg = stanza['Depends']
+ elif stanza.has_key('Recommends'):
+ pkg = stanza['Recommends']
elif stanza.has_key('Suggests'):
pkg = stanza['Suggests']
else:
if st.has_key('Depends'):
pkg = st['Depends']
+ elif st.has_key('Recommends'):
+ pkg = st['Recommends']
elif st.has_key('Suggests'):
pkg = st['Suggests']
else:
return db
+def assure_unicode(s):
+ """Assure that argument is unicode
+
+ Necessary if strings are not carrying out Pythonish 'u' prefix to
+ signal UTF8 strings, but are in fact UTF8
+ """
+ if type(s) is unicode:
+ return s
+ elif type(s) is str:
+ # attempt regular unicode call and if fails -- just decode it
+ # into utf8
+ try:
+ return unicode(s)
+ except UnicodeDecodeError, e:
+ return s.decode('utf8')
+ else:
+ return assure_unicode(str(s))
+
def convert_longdescr(ld):
ld = ld.replace('% ', '%% ')
ld = ld.replace('#NEWLINEMARKER# ', '\n\n')
# cleanup any leftover (e.g. trailing markers)
ld = ld.replace('#NEWLINEMARKER#', '')
+ # safe-guard ReST active symbols
+ ld = re.sub(r'([\'`*])', r'\\\1', ld)
return ld
-def generate_pkgpage(pkg, cfg, db, template, addenum_dir):
+def generate_pkgpage(pkg, cfg, db, template, addenum_dir, extracts_dir):
+ print pkg
# local binding for ease of use
pkgdb = db[pkg]
# do nothing if there is not at least the very basic stuff
underline = '*' * (len(title) + 2)
title = '%s\n %s\n%s' % (underline, title, underline)
+ ex_dir = None
+ if 'sv' in pkgdb['main']:
+ ex_dir = os.path.join(extracts_dir, pkgdb['main']['sv'].split()[0])
+ if not os.path.exists(ex_dir):
+ ex_dir = None
page = template.render(
pkg=pkg,
title=title,
- long_description=convert_longdescr(pkgdb['main']['long_description']),
+ long_description=convert_longdescr(
+ assure_unicode(pkgdb['main']['long_description'])),
cfg=cfg,
db=pkgdb,
- fulldb=db)
+ fulldb=db,
+ extracts_dir=ex_dir,
+ op=os.path)
# the following can be replaced by something like
# {% include "sidebar.html" ignore missing %}
# in the template whenever jinja 2.2 becomes available
sl.close()
-def write_pkgpages(jinja_env, cfg, db, outdir, addenum_dir):
+def write_pkgpages(jinja_env, cfg, db, outdir, addenum_dir, extracts_dir):
create_dir(outdir)
create_dir(os.path.join(outdir, 'pkgs'))
# and now each individual package page
pkg_template = jinja_env.get_template('pkg.rst')
for p in db.keys():
- page = generate_pkgpage(p, cfg, db, pkg_template, addenum_dir)
+ page = generate_pkgpage(p, cfg, db, pkg_template, addenum_dir, extracts_dir)
# when no page is available skip this package
if page is None:
continue
op.add_option("--pkgaddenum", action="store", dest="addenum_dir",
type="string", default=None, help="None")
+ op.add_option("--extracts", action="store", dest="extracts_dir",
+ type="string", default=None, help="None")
+
def main():
op = OptionParser(version="%prog 0.0.2")
jinja_env = Environment(loader=PackageLoader('neurodebian', 'templates'))
# generate package pages and TOC and write them to files
- write_pkgpages(jinja_env, cfg, db, opts.outdir, opts.addenum_dir)
+ write_pkgpages(jinja_env, cfg, db, opts.outdir, opts.addenum_dir, opts.extracts_dir)
write_sourceslist(jinja_env, cfg, opts.outdir)
<p><a href="{{ db.main.homepage }}">
<img border="0" src="../_static/go-home.png" title="Go to {{ pkg }} homepage" /></a>
+ {%- if extracts_dir -%}
+ {%- if op.exists(op.join(extracts_dir, 'copyright')) -%}
+ <a href="../debian/extracts/{{ db.main.sv.split()[0] }}/copyright">
+ <img border="0" src="../_static/legal.png" title="Copyright information for this package" /></a>
+ {%- endif -%}
+ {%- if op.exists(op.join(extracts_dir, 'changelog')) -%}
+ <a href="../debian/extracts/{{ db.main.sv.split()[0] }}/changelog">
+ <img border="0" src="../_static/debian-changelog.png" title="Debian changelog of this software" /></a>
+ {%- endif -%}
+ {%- if op.exists(op.join(extracts_dir, 'README.Debian')) -%}
+ <a href="../debian/extracts/{{ db.main.sv.split()[0] }}/README.Debian">
+ <img border="0" src="../_static/info.png" title="Information on Debian-specific aspects of this software" /></a>
+ {%- endif -%}
+ {%- endif -%}
{%- if cfg.has_option("nitrc ids", pkg) -%}
<a href="http://www.nitrc.org/project?group_id={{ cfg.get("nitrc ids", pkg) }}">
<img border="0" src="../_static/nitrc_listed.png" title="See the entry on nitrc.org" /></a>
`register <{{ db.main.registration }}>`_. Available user statistics might be
helpful to acquire funding for this project and therefore foster continued
development in the future.
+
{% endif -%}
{% if db.blends and db.blends.remark %}
.. note::
{{ db.blends.remark | indent(width=2, indentfirst=true) }}
+
{% endif -%}
{% if db.nitrc or db.main.debian_popcon or db.main.ubuntu_popcon or
:ref:`front page <repository_howto>`.
{% endif %}
{{ dist[0] }} [{{ distpkg.component}}]:
- `{{distpkg.version}} <../../debian/{{ distpkg.poolurl }}>`_ [{{ ', '.join(distpkg.architecture) }}]
+ `{{distpkg.version}} <../../debian/{{ distpkg.poolurl }}>`__ [{{ ', '.join(distpkg.architecture) }}]
{% if loop.last %}
.. seealso::
+{% if "neuro.debian.net" in distpkg.maintainer %}
+ - Maintainer: {{ distpkg.maintainer }}
+ - Bug reports: neurodebian-users_
+{% else %}
- Original Maintainer: {{ distpkg.maintainer }}
(if there is any chance that some problem is specific to the package
- distributed through the NeuroDebian repository, please contact
- team@neuro.debian.net instead of the original
+ distributed through the NeuroDebian repository, please email
+ neurodebian-users_ instead of the original
maintainer)
{% endif %}
+{% endif %}
{% else %}
*There are no packages in the NeuroDebian repository.*
{% endfor %}
{% if loop.first %}
{% endif %}
{{ dist[0] }} [{{ distpkg.component}}]:
- `{{distpkg.version}} <http://packages.debian.org/search?suite={{ distpkg.release}}&keywords={{ pkg }}>`_ [{{ ', '.join(distpkg.architecture) }}]
+ `{{distpkg.version}} <http://packages.debian.org/search?suite={{ distpkg.release}}&keywords={{ pkg }}>`__ [{{ ', '.join(distpkg.architecture) }}]
{% if loop.last %}
.. seealso::
{% if loop.first %}
{% endif %}
{{ dist[0] }} [{{ distpkg.component }}]:
- `{{distpkg.version}} <http://packages.ubuntu.com/search?suite={{ distpkg.release }}&keywords={{ pkg }}>`_ [{{ ', '.join(distpkg.architecture) }}]
+ `{{distpkg.version}} <http://packages.ubuntu.com/search?suite={{ distpkg.release }}&keywords={{ pkg }}>`__ [{{ ', '.join(distpkg.architecture) }}]
{% if loop.last %}
.. seealso::
{% else %}
*There are no official Ubuntu packages available.*
{% endfor %}
+
+.. include:: ../link_names.txt
{% for dist, mirrors in repos|dictsort %}
-* {{ dist }}: {% for mirror, list in mirrors|sort %}[`{{ mirror }} <_static/{{ list }}>`_] {% endfor %}
+* {{ dist }}: {% for mirror, list in mirrors|sort %}[`{{ mirror }} <_static/{{ list }}>`__] {% endfor %}
{% endfor %}
--- /dev/null
+all: electrophysiology_post.html
+%.html: %.rst
+ rst2html $< $@
--- /dev/null
+Dear Electrophysiology Neuroscientists,
+=======================================
+
+As you might know, during November 13-17, the NeuroDebian team ran its
+first Debian booth at the annual meeting of the `Society for
+Neuroscience`_ (SfN2010_) in San Diego, USA. Our generic report `is
+available from NeuroDebian website <http://neuro.debian.net/booth_sfn2010.html>`_.
+
+In this post we want to summarize our findings on the status of Free
+and Open Source Software (FOSS) in the domain of
+neuro-electrophysiology.
+
+- Majority of electrophysiology researchers are locked into software
+ platforms provided by the vendors of the used hardware
+- There exist a number of FOSS platforms for all (?) stages necessary
+ for setting up the research workflow but their adoption in hindered
+ by difficulty to setup and maintain. That in turn results in the
+ absence of a set of commonly accepted and used ultimate FOSS
+ solutions in the field
+- Majority of FOSS and some of the commercial data acquisition
+ solutions use Linux-based systems, relying on an additional stack
+ for real-time kernel support (e.g. RTAI_) and often the Comedi_
+ library for interfacing with the (most often proprietary) hardware
+- Some commercial companies are interested in sharing their products
+ as FOSS (e.g. Ripple LLC: Trellis-Neuro) and getting them ready for
+ inclusion into Debian
+- Many labs develop their solutions and are willing to share but
+- Nearly all researchers using Linux, already use Debian_ (or
+ Debian-derived such as Ubuntu_) Linux distribution as the platform
+ but primarily rely on manual deployment (download, build, install or
+ compose a custom Live media such as DVD or USB) of the 3rd-party and
+ their own products
+
+Existing Electrophysiology FOSS
+-------------------------------
+
+We have initiated a `Debian Science Electrophysiology task page
+<http://blends.alioth.debian.org/science/tasks/electrophysiology>`_
+to collect all relevant FOSS for the field and signal their status in
+respect to inclusion in Debian distribution or presence of not (yet)
+official Debian packages. The list is constantly growing (and
+changing), so if you spot some relevant FOSS absent, please `let us
+know <team@neuro.debian.net>`_.
+
+Here is a brief summary listing per application sub-domain:
+
+XXX may be listing is just not needed and duplicate of what could be
+found on the tasks page, although there it is not very
+structured... so may be it is better to come up with a verbal
+description
+
+Data acquisition
+~~~~~~~~~~~~~~~~
+
+`Debian Science Data Acquisition task page
+<http://blends.alioth.debian.org/science/tasks/dataacquisition>`_
+provides similar summary for software such as RTAI_, Xenomai_, Comedi_
+which enables data acquisition.
+
+- Nspike -- electrophysiological and behavioral data collection
+
+TODO:
+- provide verbal summary on existing solutions
+- mention RT-Preempt kernel images being available
+- point to 'cooked' solutions on how to build using RTAI-patches
+- existing pre-built RTAI kernel packages:
+
+ http://www.linuxcnc.org/lucid/
+ carries for hardy and lucid
+ pointed there from http://hart.sourceforge.net/
+
+Online Frameworks
+~~~~~~~~~~~~~~~~~
+
+- Relacs -- framework for closed-loop neurophysiological experiments
+- RTXI -- real-time data acquisition and control applications in biological research
+- Trellis-Neuro -- interface to neurophysiology data acquisition and stimulation instruments
+
+TODO:
+ - pointers to the SfN posters for RTXI, Mehmet's setups
+
+
+Offline data analysis
+~~~~~~~~~~~~~~~~~~~~~
+
+- Chronus -- Matlab toolbox for analysis of neural signals
+- KlustaKwik -- spike sorting tool
+- Neurodata -- Octave/Matlab suite to analyze data acquired from electrophysiology experiments
+- Openelectrophy -- data analysis framework for intra- and extra-cellular recordings
+- Sigviewer -- GUI viewer for biosignals such as EEG, EMG, and ECG
+- Spike -- information-theoretic spike train analysis techniques
+- Stimfit -- viewing and analyzing of electrophysiological data
+
+
+
+.. _chap_debian_booth_sfn2010: http://neuro.debian.net/booth_sfn2010.html
+.. _blends_neuroscience_electrophysiology: http://blends.alioth.debian.org/science/tasks/electrophysiology
+
+.. _annual meeting: http://www.sfn.org/am2010/
+.. _SfN2010: http://www.sfn.org/am2010/
+.. _Society for Neuroscience: http://www.sfn.org/
+.. _RTAI: https://www.rtai.org
+.. _Xenomai: http://www.xenomai.org
+.. _Comedi: http://www.comedi.org
+.. _Debian: http://www.debian.org
+.. _Ubuntu: http://www.ubuntu.com
This specification describes DebTest -- a framework with conventions and tools
that allow Debian to distribute test batteries developed by upstream or Debian
-developers. DebTest will enable an extensive testing of a deployed Debian
-system or a particular software of interest in a uniform fashion.
+developers. DebTest aims to enable developers and users to perform extensive
+testing of a deployed Debian system or a particular software of interest in a
+uniform fashion.
== Rationale ==
Ideally software packaged for Debian comes with an exhaustive test suite that
-can be used to determine whether this software works as expected on the Debian
-platform. However, especially for complex software, these test suites are often
-resource hungry (CPU time, memory, diskspace, network bandwidth) and cannot be
-ran at package build time by buildds. Consequently, test suites are typically
-utilized manually only by the respective packager on a particular machine, before
-uploading a new version to the archive.
-
-However, Debian is an integrated system and packaged software typically
-relies on functionality provided by other Debian packages (e.g. shared
-libraries) instead of shipping duplicates with different versions in every
-package -- for many good reasons. Unfortunately, there is also a downside to
-this: Debian packages often use versions of 3rd-party tools different from
-those tested by upstream, and moreover, the actual versions of dependencies
-might change frequently between subsequent uploads of a dependent package. Currently
+can be used to determine whether this particular software works as expected on
+the Debian platform. However, especially for complex software, these test
+suites are often resource hungry (CPU time, memory, disk space, network
+bandwidth) and cannot be ran at package build time by buildds. Consequently,
+test suites are typically utilized manually and only by the respective packager
+on a particular machine, before uploading a new version to the archive.
+
+However, Debian is an integrated system and packaged software typically relies
+on functionality provided by other Debian packages (e.g. shared libraries)
+instead of shipping duplicates with different versions in every package -- for
+many good reasons. Unfortunately, there is also a downside to this: Debian
+packages often use versions of 3rd-party tools that are different from those
+tested by upstream, and moreover, the actual versions of dependencies might
+change frequently between subsequent uploads of a dependent package. Currently
a change in a dependency that introduces an incompatibility cannot be detected
-reliably even if upstream provides a test suite that would have caught
-the breakage. Therefore integration testing heavily relies on users to detect
-incorrect functioning and file bug reports. Although there are archive-wide
-QA efforts (e.g. constantly rebuilding all packages) these tests can only
-detect API/ABI breakage or functionality tested during build-time checks --
-they are not exhaustive for the aforementioned reasons.
+reliably even if upstream provides a test suite that would have caught the
+breakage. Therefore integration testing heavily relies on users to detect
+incorrect functioning and file bug reports. Although there are archive-wide QA
+efforts (e.g. constantly rebuilding all packages) these tests can only detect
+API/ABI breakage or functionality tested during build-time checks -- they are
+not exhaustive for the aforementioned reasons.
This is a proposal to, first of all, package upstream test suites in a way that
they can be used to run expensive archive-wide QA tests. However, this is also
-a proposal to establish means to test interactions between software from multiple
-Debian packages to provide more thorough continued integration and regression testing
-for the Debian systems.
+a proposal to establish means to test interactions between software from
+multiple Debian packages to provide more thorough continued integration and
+regression testing for the Debian systems.
== Use Cases ==
This includes the test suite of the authors of his favorite software, but
also all distribution test suites provided by Debian developers (see above).
- * Sylvestre is a Debian developer of a core computational library
- new version (or a custom build) of which promises performance
+ * Sylvestre maintains a core computational library in Debian.
+ A new version (or other modification) of this library promises performance
advantages. Using DebTest he could not only verify the absence of
regressions but also to obtain direct performance comparison
against the previous version across a range of applications.
{% block sidebarsearch %}
{{ super() }}
+<p>
+<form method="POST" action="https://openhatch.org/+do/project.views.wanna_help_do">
+ <input type="hidden" name="from_offsite" value="True" />
+ <input type="hidden" value="7781" name="project"/>
+ <input type="submit" value="I want to help" rel="tipsy-south" id="openhatch-wannahelp-button" original-title="Click to add yourself to the list of people who want to contribute. People of all levels are welcome!"/>
+</form>
+</p>
+<style>
+ @import url('https://openhatch.org/static/css/tipsy.css');
+</style>
+<style type="text/css">
+#openhatch-wannahelp-button:hover, #openhatch-wannahelp-button:focus {
+ background-image:url('https://openhatch.org/static/images/wannahelp-button-bg-hover.png');
+ color:#222; text-decoration:none; }
+#openhatch-wannahelp-button { width: 90%; height: 3em; margin-bottom: 1em; background: #C8E29D
+ url('https://openhatch.org/static/images/wannahelp-button-bg.png') repeat-x
+ scroll center top; border:3px solid #fff; cursor:pointer; cursor: hand;
+ font-family: Helvetica, sans-serif; font-size:13pt; font-weight:normal;
+ text-align:center; text-shadow:0 1px 0 #fff; white-space:normal; }
+#openhatch-wannahelp-button { -moz-border-radius: 8px; color: #444; float:left;
+ padding:10px 20px; display:block; padding:0px 8px; }
+#openhatch-wannahelp-button:focus { outline-color:-moz-use-text-color;
+ outline-style:none; outline-width:medium; }
+</style>
+<!-- Disabling openhatche's copy of jquery, even though loosing cool tipsy functionality for now
+<script type="text/javascript" src="https://openhatch.org/static/packed/selections_for_widget.js?1271800811"></script>
+-->
<p><a href="https://www.ohloh.net/stack_entries/new?project_id=neurodebian&ref=sample"><img
src="{{ pathto('_static/ohloh_iuseit.png', 1) }}" border="0" alt="Click to get yourself listed as a NeuroDebian user" /></a></p>
<p><a href="http://www.nitrc.org/projects/neurodebian"><img
.. _tri-fold flyers: http://neuro.debian.net/_files/brochure_debian-neurodebian.pdf
.. _sources are available: http://git.debian.org/?p=pkg-exppsy/neurodebian.git;a=tree;hb=HEAD;f=artwork/brochure
.. _Debian wiki: http://wiki.debian.org/Cloud
-.. _new Debian Science Blend task: http://blends.alioth.debian.org/science/tasks/neuroscience-electrophysiology
+.. _new Debian Science Blend task: http://blends.alioth.debian.org/science/tasks/electrophysiology
.. _download the poster: http://neuro.debian.net/_files/NeuroDebian_SfN2010.png
.. _other donations to the Debian project: http://www.debian.org/donations
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
#extensions = []
sys.path.append(os.path.abspath('.'))
-extensions = ['sphinxext.quote']
+extensions = ['sphinxext.quote',
+ 'sphinx.ext.todo']
+
+# show todo items
+todo_include_todos = True
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
.. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
+I want to help. How do I get involved?
+--------------------------------------
+
+ We always need people to help with maintaining existing package. If you need
+ some additional software packaged and you want to try it on your own, we would
+ be happy to mentor you. We also have a :ref:`list of ongoing and planned
+ projects <projects>`, each listing a number of tasks that need to be done.
+
+ If you found something you are interested in, please email the
+ neurodebian-devel_ mailing list and let us know about it. Thanks!
+
+
When does a package migrate from NeuroDebian into Debian proper?
----------------------------------------------------------------
--------------------------------------------------------------------------
No. The term :term:`non-free` refers to an archive section. NeuroDebian uses
- exactly the same :ref:`archive sections as Debian proper
- <http://www.debian.org/doc/debian-policy/ch-archive.html>`. The *non-free*
+ exactly the same `archive sections as Debian proper
+ <http://www.debian.org/doc/debian-policy/ch-archive.html>`_. The *non-free*
section contains packages that have certain restrictions regarding **your
freedom** to employ them for a particular purpose. In contrast, for packages
in the *main* section your are completely free to do whatever and in whatever
archive, as well as backported or simply rebuilt packages also available
elsewhere. Please see the :ref:`faq` for more information about the goals of
this project, and :ref:`read what people say about it <testimonials>`.
-If you appreciate this service, please |spread|.
+Take a look at the :ref:`list of our current and planned projects <projects>` if
+you want to get involved. If you appreciate this service, please |spread|.
.. note::
<a href="datasets.html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
<a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
<a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
+ <a href="projects.html"><img border="0" src="_static/workarea.png" title="Current and planned projects: Get involved!" /></a>
</p>
.. _Ubuntu: http://www.ubuntu.com
express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
for all their work.
-.. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software
-
.. _support:
Contacts
* neurodebian-devel_: Technical mailing list for discussions on
NeuroDebian development
-.. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
-.. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
-.. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream
-
Acknowledgements
================
vm
coffeeart
photoalbum
+ projects
testimonials
.. probably should be purged altogether
.. toctree::
:hidden:
+ booth_sfn2010
datasets
livecd
- vm_welcome
quotes-nihr01
quotes-nitrc
-
+ sources_lists
+ vm_welcome
.. include:: link_names.txt
.. include:: substitutions.txt
.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy
.. _`Debian Med`: http://debian-med.alioth.debian.org
.. _`Debian Science`: http://wiki.debian.org/DebianScience
+.. _Comedi: http://www.comedi.org
+.. _RTAI: https://www.rtai.org
+.. |RTAI| replace:: :abbr:`RTAI (Real Time Application Interface)`
.. Functional imaging labs
.. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk
.. _`wikipedia reflection`: http://en.wikipedia.org/wiki/Reflection_(mathematics)
.. _`wikipedia direction cosine`: http://en.wikipedia.org/wiki/Direction_cosine
+.. Some common terms as links outside and abbreviations
+.. _FOSS: http://en.wikipedia.org/wiki/Free_and_Open_Source_Software
+.. |FOSS| replace:: :abbr:`FOSS (Free and Open Source Software)`
+
.. Homepages
.. _yoh: http://www.onerussian.com
.. _mih: http://mih.voxindeserto.de
.. Debian specifics
.. _ITP: http://www.debian.org/devel/wnpp
.. _ITPs: http://www.debian.org/devel/wnpp
+.. |ITP| replace:: :abbr:`ITP (Intent to Package)`
+.. |RFP| replace:: :abbr:`RFP (Request for packaging)`
+.. |DBTS| replace:: :abbr:`DBTS (Debian Bug Tracking System)`
+
+.. mailing lists
+.. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
+.. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
+.. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream
+
+.. task pages
+.. _neuroscience-electrophysiology: http://blends.alioth.debian.org/science/tasks/neuroscience-electrophysiology
+.. _task_bci: http://blends.alioth.debian.org/science/tasks/bci
+.. _task_dataacquisition: http://blends.alioth.debian.org/science/tasks/dataacquisition
+.. _task_psychophysics: http://blends.alioth.debian.org/science/tasks/psychophysics>
+
+.. more to sort out
+.. _NeuralEnsemble: http://www.neuralensemble.org
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_afni:
+
+**************
+Packaging AFNI
+**************
+
+:ref:`AFNI <pkg_afni>` is an environment for processing and displaying
+functional MRI data. It provides a complete analysis toolchain, including 3D
+cortical surface models, and mapping of volumetric data (SUMA).
+
+Packaging AFNI for Debian is part of our general efforts to provide
+comprehensive neuro-imaging research support.
+
+Status
+------
+
+A fully functional package is available from the NeuroDebian repository.
+Current work focuses on continuously tracking upstream development and making
+the package fit for Debian proper.
+
+To ease development a `Git repository`_ has been created that contains the
+history of AFNI development since 1998. Because upstream doesn't expose a
+version control system the repository is populated with daily snapshots of the
+sources.
+
+A new CMake-based build-system has been developed for AFNI.
+
+.. _Git repository: http://git.debian.org/?p=pkg-exppsy/afni.git
+
+.. todo:: AFNI packaging
+
+ * Refurbish the afni-data package to meet Debian standards.
+ * Push remaining patches upstream. A first wave has been submitted, but not
+ yet adopted. It remains uncertain if the CMake buildsystem gets accepted.
+ * Perform a final license check. Lots of 3rd-party code has already been
+ removed from the package to allow for legal redistribution (e.g. edges3D
+ library).
+ * Develop a test suite for AFNI. We received a suitable dataset to implement
+ a test running a full retinotopic mapping analysis.
+
+References
+----------
+
+* `Debian ITP bug report <http://bugs.debian.org/409849>`_ with information on
+ the packaging progress.
+* `Git repository`_ with the full source code and the Debian packaging.
+* `List of patches <http://git.debian.org/?p=pkg-exppsy/afni.git;a=tree;f=debian/patches;hb=HEAD>`_
+ applied to the Debian package (i.e. the difference to the upstream AFNI
+ source code).
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_debtest:
+
+*************************
+Thorough testing: DebTest
+*************************
+
+Ideally software comes with an exhaustive test suite that can be used to
+determine whether this particular software works as expected on the Debian
+platform. However, especially for complex software, these test suites are often
+resource hungry (CPU time, memory, disk space, network bandwidth) and cannot be
+ran at package build time by Debian's buildds. Consequently, test suites are
+typically utilized manually and only by the respective packager on a particular
+machine, before uploading a new version to the archive.
+
+However, Debian is an integrated system and packaged software typically relies
+on functionality provided by other Debian packages (e.g. shared libraries)
+instead of shipping duplicates with different versions in every package -- for
+many good reasons. Unfortunately, there is also a downside to this: Debian
+packages often use versions of 3rd-party tools that are different from those
+tested by upstream, and moreover, the actual versions of dependencies might
+change frequently between subsequent uploads of a dependent package. Currently
+a change in a dependency that introduces an incompatibility cannot be detected
+reliably even if upstream provides a test suite that would have caught the
+breakage. Therefore integration testing heavily relies on users to detect
+incorrect functioning and file bug reports. Although there are archive-wide QA
+efforts (e.g. constantly rebuilding all packages) these tests can only detect
+API/ABI breakage or functionality tested during build-time checks -- they are
+not exhaustive for the aforementioned reasons.
+
+This is a proposal to, first of all, package upstream test suites in a way that
+they can be used to run expensive archive-wide QA tests. However, this is also
+a proposal to establish means to test interactions between software from
+multiple Debian packages to provide more thorough continued integration and
+regression testing for the Debian systems.
+
+
+To address these open issues we are working on *DebTest* -- a framework with
+conventions and tools that allow Debian to distribute test batteries developed
+by upstream or Debian developers. It aims at complementing existing QA efforts
+by going beyond single-package, build-time tests and cover interactions between
+software from multiple Debian packages to provide more thorough continued
+integration and regression testing for the Debian systems DebTest aims to
+enable developers and users to perform extensive testing of a deployed Debian
+system or a particular software of interest in a uniform fashion.
+
+
+Status
+------
+
+The project is still in an early conceptual stage. We are currently working on
+a SPEC_ draft that will be submitted to the Debian community for further
+discussion of the desired properties of a more comprehensive testing framework.
+Furthermore, we started looking for existing (free) software solutions that
+might be used to implement such a framework.
+
+We have already started packaging :ref:`versatile datasets <full_dataset_list>`
+that can be used to develop test suites.
+
+
+.. todo:: DebTest
+
+ * Finish the SPEC_.
+ * Initiate discussion.
+ * Identify and package relevant neuroscience datasets that can be used to
+ develop multi-software regression/pipeline tests.
+
+.. _SPEC: http://git.debian.org/?p=pkg-exppsy/neurodebian.git;a=blob_plain;f=sandbox/proposal_regressiontestframwork.moin
+
+
+References
+----------
+
+* :ref:`full_dataset_list`
+* `DebTest discussions on debian-devel <http://lists.debian.org/debian-devel/2011/01/msg00704.html>`_
+
+.. include:: link_names.txt
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_electrophysiology:
+
+*****************
+Electrophysiology
+*****************
+
+The majority of the electrophysiology research community in neuroscience is
+`locked-in` the proprietary software solutions which accompanying data
+acquisition hardware. That impairs their ability to adopt novel data analysis
+methodologies and experimental setups. There already exist a variety of
+primarily Linux-based FOSS_ solutions in this domain. But software
+development and dissemination is often impaired by the absence of the efforts
+centralization and existing problems with the support of the core components
+by the used operating systems. Nevertheless, Debian_ and its derivatives
+already dominate as the operating systems of choice by such projects.
+
+We are planing to help addressing existing issues in the core necessary
+components provided by Debian_ to help upstream authors with streamlining
+their development. Furthermore we are planing to package some popular
+deployment-ready |FOSS| solutions and make them an integral part of Debian_.
+
+Status
+------
+
+We have collected information on interesting and alive projects in this domain
+within neuroscience-electrophysiology_ task page. To gather information on
+the needs of the researchers interested in this field we have researched
+researchers demands while helding a :ref:`Debian booth at SfN10 conference
+<chap_debian_booth_sfn2010>`. To further elaborate the work plan, we have
+initiated discussions with upstream authors (private correspondence and on
+neurodebian-devel_, neurodebian-upstream_ mailing lists).
+
+.. todo:: Electrophysiology coverage
+
+ * Help to ensure adequate status in Debian of the necessary core components,
+ e.g. Comedi, RTAI (see DBTS: 606122, 608091, 609633):
+ * Consider packaging prebuilt kernels with RTAI patches/support to make
+ available from NeuroDebian repository
+
+.. _606122: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606122
+.. _608091: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=608091
+.. _609633: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=609633
+
+..
+ .. _: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=
+
+
+References
+----------
+
+* RTAI_
+* Comedi_
+* `Debian-Science Electrophysiology task page <http://blends.alioth.debian.org/science/tasks/electrophysiology>`_.
+* `Debian-Science Data acquisition task page <http://blends.alioth.debian.org/science/tasks/dataacquisition>`_.
+* `Debian-Science Brain-Computer Interface task page <http://blends.alioth.debian.org/science/tasks/bci>`_.
+* NeuralEnsemble_
+
+
+.. include:: link_names.txt
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_freesurfer:
+
+********************
+Packaging FreeSurfer
+********************
+
+Status
+------
+
+We are in contact with Freesurfer developers and are awaiting the resolution of
+legal issues that currently prevent legal redistribution of FreeSurfer.
+
+This project will continue as soon as the Freesurfer source code is available
+under |FOSS| license terms.
+
+..
+ .. todo::
+
+
+..
+ References
+ ----------
+
+ <references>
+
+.. include:: link_names.txt
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_matlab:
+
+*********************************
+Integrating Matlab-based software
+*********************************
+
+There is a vast amount of Matlab-based software for neuro-imaging and
+psychological research. For various reasons, such software has not been
+considered for integration into Debian in the past. However, recent advances of
+the Octave_ project allow running a significant number of Matlab tools without
+the proprietary environment.
+
+To ease the transition to a completely open-source research environment, we are
+following a two-fold approach. On one hand we start packaging all relevant
+Octave-compatible software for Debian. On the other hand we work on a proper
+integration of (still) Matlab-only software.
+
+The latter shall be achieved by providing a support Debian package that can
+represent local Matlab installations to the Debian package management system.
+Moreover, this package provides helper tools that ease building MEX extensions
+from source during package installation with a local Matlab and therefor allow
+for inclusion of such packages into Debian 'contrib' suite (given an appropriate
+licence).
+
+The goal is to provide researchers with fully functional Matlab software, that
+can be used with Matlab on Debian systems, while benefiting from all advantages
+of Debian integration. However, at the same time researchers should have the
+possibility to seamlessly switch to Octave_ whenever possible or necessary (e.g.
+a laptop being out of reach of a university's license server), and eventually
+completely migrate to Octave when full compatibility for a particular software
+is achieved.
+
+This effort includes talking to upstream projects about the possibility to run
+with Octave, as well as developing patches to achieve such compatibility.
+
+.. _Octave: http://www.gnu.org/software/octave
+
+Status
+------
+
+A :ref:`Matlab-support package <pkg_matlab-support>` draft is ready, available
+from NeuroDebian, and has been uploaded to `Debian NEW queue
+<http://ftp-master.debian.org/new.html>`_ .
+
+Packaging of individual Matlab-based software has started. This includes
+:ref:`SPM <pkg_matlab-spm8>` and :ref:`Fieldtrip <pkg_fieldtrip>` (see
+references_ for more packages). Expanding the coverage is planned.
+
+.. todo:: Integrating Matlab-based software
+
+ * Finish packaging of fieldtrip which is necessary to complete the packaging
+ of SPM.
+ * Adapt the packaging of `dynare <http://packages.debian.org/sid/dynare-matlab>`_
+ in Debian to use the new support package. Once this is done and reviewed by
+ its maintainers the support package can be submitted for inclusion into
+ Debian proper.
+ * Create :ref:`matlab-psychtoolbox-3 <pkg_matlab-psychtoolbox-3>` to
+ complement :ref:`octave-psychtoolbox-3 <pkg_octave-psychtoolbox-3>`.
+ * Create :ref:`matlab-biosig <pkg_matlab-biosig>` to
+ complement :ref:`octave-biosig <pkg_octave-biosig>`.
+ * Package `EEGLAB <http://bugs.debian.org/605739>`_.
+ * Upload :ref:`libgdf <pkg_libgdf-dev>` (including :ref:`matlab-gdf
+ <pkg_matlab-gdf>`) to Debian proper as soon as :ref:`matlab-support
+ <pkg_matlab-support>` is accepted
+
+References
+----------
+
+* `SPM packaging progress <http://bugs.debian.org/592390>`_ report.
+* `Fieldtrip packaging progress <http://bugs.debian.org/605492>`_ report.
+* `EEGLab packaging progress <http://bugs.debian.org/605739>`_ report.
+* `PsychToolbox packaging progress <http://bugs.debian.org/606557>`_ report.
+
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_neuralmodeling:
+
+***************
+Neural Modeling
+***************
+
+We aim to cover tools for scientists interested in modeling of real neural
+systems at different levels (from single neuron to complex networks).
+
+
+Status
+------
+
+This effort initiated with packaging of :ref:`Brian <pkg_python-brian>`
+already available from NeuroDebian repository.
+
+.. todo:: Neural modeling software coverage
+
+ * Complete packaging of :ref:`PyNN <pkg_python-pynn>`
+ * Complete packaging of :ref:`PCSIM <pkg_python-pcsim>`
+ * Complete packaging of :ref:`NEURON <pkg_neuron>`
+
+
+References
+----------
+
+* `Debian-Science Modeling of neural systems task page <http://blends.alioth.debian.org/science/tasks/neuroscience-modeling>`_.
+* NeuralEnsemble_
+
+
+.. include:: link_names.txt
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_psychophysics:
+
+************
+Psychopysics
+************
+
+Our goal is to equip Debian systems with FOSS solutions to carry out any
+experiment relating physical stimuli and their psychological effects.
+
+Status
+------
+
+We have already made some popular tools, such as :ref:`PyEPL
+<pkg_python-pyepl>` and :ref:`Psychopy <pkg_psychopy>`, a part of the official
+Debian_ distribution and working on extending support of other tools and
+libraries used in psychopysics research to interface with the stimuli delivery
+and responses collection hardware.
+
+.. todo:: Tailor Debian for psychopysics research
+
+ * Complete packaging of :ref:`Psychtoolbox-3 <pkg_octave-psychtoolbox-3>`
+ * Provide convenience package and guidelines for assuring robust
+ performance of the provided stimuli presentation software (e.g. setting
+ permissions for enabling RT scheduling, memory locking etc)
+
+
+References
+----------
+
+* `Debian-Science Psychophysics task page <http://blends.alioth.debian.org/science/tasks/psychophysics>`_.
+
+.. include:: link_names.txt
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_snapshots:
+
+***********************************
+NeuroDebian repository snapshotting
+***********************************
+
+The official Debian snapshotting service (http://snapshot.debian.org) allows
+obtaining any version of any software that was ever present in Debian, and
+provides a complete state of the Debian archive with all software versions
+corresponding to a specific date. We are going to adopt this service to
+provide this functionality for the NeuroDebian repository itself, thus
+covering backports of our packages for all supported Debian and Ubuntu
+releases, as well as staging packages that have not been accepted into Debian,
+but may already be used by researchers. Used in conjunction with the official
+Debian snapshotting repository, it would allow for the reconstruction of
+entire research environments or simply for installation of a particular
+previous version of a product of interest.
+
+
+.. _`Debian snapshotting service`: http://snapshot.debian.org/
+
+
+Status
+------
+
+We have adapted http://snapshot.debian.org implementation to snapshot
+NeuroDebian repository and snapshotting service was deployed on 2010-10-12.
+
+.. todo:: NeuroDebian snapshotting service
+
+ * Provide web-frontend to access existing snapshots within NeuroDebian
+ website.
+
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _project_<name>:
+
+**************
+<title>
+**************
+
+<description>
+
+Status
+------
+
+<status report>
+
+.. todo:: <title>
+
+
+References
+----------
+
+<references>
+
+.. include:: link_names.txt
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _projects:
+
+********************
+NeuroDebian Projects
+********************
+
+We share a lot of common interests with other teams in Debian. So we are
+actively collaborating with `Debian Med`_ and `Debian Science`_ projects to
+improve Debian_ infrastructure and software coverage to fulfil our goals.
+
+This page provides an overview of current and planned NeuroDebian_ projects. Each description
+lists a couple of tasks remaining to reach the goal of a
+particular project. If you want to contribute, take a look at them and email the
+neurodebian-devel_ mailing list with your intention to help.
+
+
+Expanding coverage
+------------------
+
+* :ref:`project_matlab`
+* Neuroimaging
+
+ - :ref:`project_afni`
+ - :ref:`Packaging SPM8 <project_matlab>`
+ - :ref:`project_freesurfer`
+
+* :ref:`project_psychophysics`
+* :ref:`project_electrophysiology`
+* :ref:`Neural modeling <project_neuralmodeling>`
+
+Please refer to the `complete list of perspective packages
+<http://qa.debian.org/wnpp.php?login=team%40neuro.debian.net>`_ which we are
+working on (|ITP|\s) or just placed on the radars of Debian project (|RFP|\s).
+
+
+Infrastructure
+--------------
+
+* :ref:`project_debtest`
+* :ref:`project_snapshots`
+* :ref:`coffeeart`
+
+
+Cross-platform availability
+---------------------------
+
+* :ref:`chap_vm`
+* Live CD (`preliminary version <http://neuro.debian.net/debian/live/>`_)
+* Cloud computing
+
+
+Expertise transfer
+------------------
+
+* `Best practices for deploying scientific software <https://github.com/neurodebian/SciDeployGuide>`_
+* Advise (e.g. on legal, deployment aspects) and contribute upstream projects
+* Whenever necessary mentor and sponsor uploads of relevant projects into Debian_
+
+
+Promotion
+---------
+
+* `Publications <http://neuro.debian.net/index.html#publications>`_ and
+ promotional materials
+
+ - `Debian / NeuroDebian tri-fold
+ <http://neuro.debian.net/_files/brochure_debian-neurodebian.pdf>`_
+
+* Conferences presence. To promote NeuroDebian_ project we consider
+ (conditioned on funding and agreements with organizers) presenting
+ NeuroDebian_ at
+
+ - `HBM 2011 <http://www.humanbrainmapping.org/HBM2011>`_
+ - `Invite us <mailto:team@neuro.debian.net>`_
+
+* `Inviting contributions and new members to join the NeuroDebian project
+ <https://openhatch.org/+projects/NeuroDebian>`_
+
+
+..
+ Planned projects
+ ----------------
+
+..
+ Finished projects
+ -----------------
+
+ .. toctree::
+ :maxdepth: 1
+
+ vm
+
+.. toctree::
+ :hidden:
+ :maxdepth: 1
+
+ proj_afni
+ proj_debtest
+ proj_electrophys
+ proj_psychophysics
+ proj_freesurfer
+ proj_matlab
+ proj_neuralmodeling
+ proj_snapshots
+ proj_template
+ livecd
+ coffeeart
+
+
+.. include:: link_names.txt
-.. Generated on Fri Oct 22 13:05:28 EDT 2010
+.. Generated on Tue Feb 1 12:05:45 EST 2011
.. Do not edit directly
+Quotes from NIH R01 grant proposal letters of recommendation
+============================================================
+
+.. note::
+ Only the quotes which were approved for redistribution by the original
+ authors are included.
+
+
+
.. quote::
:author: Prof. Thomas J. Grabowski, Jr.
:affiliation: Director, Integrated Brain Imaging Center, University of Washington, Seattle, Washington, USA
.. Selected quotes from NITRC portal
+Quotes from NITRC project page
+==============================
+
.. quote::
:author: Anonymous
:date: 2010-05-05
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _todo:
+
+************
+The Big TODO
+************
+
+This is a comprehensive list of all ToDo items documented on the NeuroDebian
+website.
+
+.. todolist::
Downloads
---------
-* NeuroDebian 6.0.0 image (32bit) [coming soon; leave a comment below if you
- need it urgently]
+* `NeuroDebian 6.0.1 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.1_i386.zip>`_ [~560MB]
*This image should work on virtually all systems that are supported by*
VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
is not compatible with a host machine.*
-* `NeuroDebian 6.0.0 image (64bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.0_amd64.zip>`_ [~570MB]
+* `NeuroDebian 6.0.1 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.1_amd64.zip>`_ [~570MB]
*This image only works on 64bit host machines with active hardware
virtualization support. The should include all recent Apple hardware and most
64bit Windows systems.*
+.. note::
+
+ You can verify that you have downloaded archives correctly using
+ `md5sums -c MD5SUMS
+ <http://neuro.debian.net/debian/vm/MD5SUMS>`_ . You can also verify
+ the authenticity of the `MD5SUMS
+ <http://neuro.debian.net/debian/vm/MD5SUMS>`_ itself using `gpg
+ --verify MD5SUMS.gpg
+ <http://neuro.debian.net/debian/vm/MD5SUMS.gpg>`_ signed with
+ NeuroDebian archive key.
+
* `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
Solaris)
all=~/deb/gits/pkg-exppsy/neurodebian/future/blends/*
~/deb/gits/*/debian/blends
~/deb/gits/pkg-exppsy/*/debian/blends
+ # Python regular expression on which files to skip
+ # Default is listed below
+ #skip=.*[~#]$
Format of debian/blends
__author__ = 'Yaroslav Halchenko'
__prog__ = os.path.basename(sys.argv[0])
-__version__ = '0.0.5'
+__version__ = '0.0.7'
__copyright__ = 'Copyright (c) 2010 Yaroslav Halchenko'
__license__ = 'GPL'
for k_ in PKG_FIELDS: # prune older depends
pkg.pop(k_, None)
pkg['Pkg-Name'] = pkg[k] = bname.lower()
- pkg['Pkg-Source'] = sname.lower()
+ if sname is not None:
+ sname = sname.lower()
+ pkg['Pkg-Source'] = sname
pkgs.append(pkg)
pkg.tasks = dict( (t.strip(), deb822.Deb822Dict()) for t in tasks )
pkg.format = format_
if format_clean:
format_ = format_[:-6]
elif kl == 'tasks':
- tasks = v.split(',')
+ tasks = [x.strip() for x in v.split(',')]
newtasks = pkg is not None # either we need to provide tune-ups
# for current package
elif kl in PKG_FIELDS: # new package
- if source is None:
+ if source is None and not format_ in ['extended']:
source = v
pkg = new_pkg(pkg, v, source, tasks)
newtasks = False
('Pkg-Description',
lambda: debianm.get_description(pkg['Pkg-Name'])),
('Responsible', debianm.get_responsible),
- ('Homepage', lambda: debianm.source.get('Homepage', None))):
+ ('Homepage', lambda: debianm.source.get('Homepage', None)),
+ ('Pkg-source', lambda: debianm.source.get('Source', None)),
+ ):
if pkg.get(k, None):
continue
v = m()
entries = open(taskfile).readlines()
known = False
# We need to search by name and by source
- # We need to search for every possible type of dependecy
- regexp = re.compile('^ *(%s) *: *(%s) *$' %
- ('|'.join(PKG_FIELDS),
- '|'.join((pkg.name, pkg.source))),
- re.I)
+ # We need to search for every possible type of dependency
+ regexp_str = '^ *(%s) *: *(%s) *$' \
+ % ('|'.join(PKG_FIELDS),
+ '|'.join((pkg.name, pkg.source)).replace('+', '\+'))
+ verbose(4, "Searching for presence in %s using regexp: '%s'"
+ % (taskfile, regexp_str))
+ regexp = re.compile(regexp_str, re.I)
for istart, e in enumerate(entries):
if regexp.search(e):
verbose(4, "Found %s in position %i: %s" %
if v.get('Source', None):
self._source = v
else:
- self._binaries[v['Package']] = v
+ # Since it might be hash-commented out
+ if 'Package' in v:
+ self._binaries[v['Package']] = v
def get_license(self, package=None, first_only=True):
"""Return a license(s). Parsed out from debian/copyright if it is
print "Subject: %s\n\n%s" % (subject, body)
+def is_template(p):
+ """Helper to return true if pkg definition looks like a template
+ and should not be processed
+ """
+ # We might want to skip some which define a skeleton
+ # (no source/homepage/etc although fields are there)
+ for f in ['vcs-browser', 'pkg-url', 'pkg-description',
+ 'published-Title', 'pkg-name', 'homepage',
+ 'author']:
+ if f in p and p[f] != "":
+ return False
+ return True
+
+
def main():
p = OptionParser(
options.wnpp_mode = 'ITP'
# Load configuration
- config = ConfigParser()
+ config = ConfigParser(defaults={'skip': '.*[~#]$'})
config.read(options.config_file)
if options.all_mode:
if not len(infiles):
infiles = [join(options.topdir or './', 'debian/blends')] # default one
+ skip_re = re.compile(config.get('paths', 'skip', None))
+
for blends_file in infiles:
verbose(1, "Processing %s" % blends_file)
if not exists(blends_file):
error("Cannot find a file %s. Either provide a file or specify top "
"debian directory with -d." % blends_file, 1)
-
+ if skip_re.match(blends_file):
+ verbose(2, "W: Skipped since matches paths.skip regexp")
+ continue
pkgs = parse_debian_blends(blends_file)
if options.topdir is None:
if dirname(blends_file).endswith('/debian'):
topdir = options.topdir
expand_pkgs(pkgs, topdir=topdir)
+
+ pkgs = [p for p in pkgs if not is_template(p)]
+ if not len(pkgs):
+ verbose(2, "W: Skipping since seems to contain templates only")
+ continue
if options.wnpp_mode is not None:
print_wnpp(pkgs, config, options.wnpp_mode)
else:
exit 1
fi
+upstream_name=${dscfile%%_*}
+
+# To overcome bash desire to claim empty array unbound under 'set -u'
+# above, lets just specify empty rule for sed when nothing to be done
+mod_control=""
+if [ "$upstream_name" != "neurodebian" ]; then
+ # Avoid injection into neurodebian package itself
+ mod_control='s/\(^Depends:\) */\1 neurodebian-popularity-contest, /g'
+fi
+
# assemble an appropriate backport-dsc call
backport-dsc \
--maint-name "NeuroDebian Maintainers" \
--maint-email "team@neuro.debian.net" \
--target-distribution "$release" \
--version-suffix "$(nd_querycfg "release backport ids" "$release")" \
+ --mod-control "$mod_control" \
"$dscfile"
-
-# not adding the auto-dep for now
-# --mod-control 's/^Depends:.*$/&, neurodebian-trailer/' \
options="$opts --debbuildopts -B"
fi
echo "Building for $family $dist $a ..."
+ buildfile="${dscfile%.dsc}_${a}.build"
cowbuilder --build $dscfile \
--basepath ${cowbuilderroot}/cow/${family}-${dist}-${a}.cow \
--buildresult . \
- --logfile ${dscfile%.dsc}_${a}.build \
+ --logfile "${buildfile}" \
$options \
- $*
+ "$@" && status='OK' || status='FAILED'
+ # Update the summary of builds
+ touch summary.build # Assure existence
+ sed -i -e '/${buildfile}/d' summary.build # Prune previous entry
+ echo -e "${buildfile}\t$status" >> summary.build # Add current one
done
shift;
nd_updatedist debian sid amd64
-nd_build debian sid amd64 $dscfile $*
+nd_build debian sid amd64 $dscfile "$@"
cowbuilder --login \
--basepath ${cowbuilderroot}/cow/${family}-${dist}-${arch}.cow \
$options \
- $*
+ "$@"
# values set here. However, setting the values still prevents the questions
# from being shown, even if values come from dhcp.
d-i netcfg/get_hostname string neurodebian
+d-i netcfg/invalid_hostname string neurodebian
# d-i netcfg/get_domain string unassigned-domain
# Disable that annoying WEP key dialog.
# d-i netcfg/wireless_wep string
# The wacky dhcp hostname that some ISPs use as a password of sorts.
-#d-i netcfg/dhcp_hostname string radish
+# d-i netcfg/dhcp_hostname string neurodebian
# If non-free firmware is needed for the network or other hardware, you can
# configure the installer to always try to load it, without prompting. Or
# The user account will be added to some standard initial groups. To
# override that, use this.
-d-i passwd/user-default-groups string audio cdrom video plugdev dip sudo
+d-i passwd/user-default-groups string audio cdrom floppy video plugdev dip sudo
### Apt setup
# You can choose to install non-free and contrib software.
# hostname: neurodebian
# domain: ''
+# Needs to be assured since it got reset to debian
+hostname neurodebian
+sed -i -e 's/^127\.0\.1\.1.*/127.0.1.1\tneurodebian/g' /etc/hosts
+
# all file in one partition
# root: not there
-e "s/^deb-src/#deb-src/" /etc/apt/sources.list
etckeeper commit "Initial VM setup done"
+
+# Create a link to automatically mounted Shared folder
+# Created by the Welcome Wizard
+#sudo -u brain ln -s /mnt/host /home/brain/
# TODO: arguments later on to become cmdline args
#iso=debian-squeeze-di-beta1-amd64-businesscard.iso
-iso=debian-testing-i386-businesscard.iso
+iso=debian-testing-${ARCH:=amd64}-businesscard.iso
di_cd=$(readlink -f $PWD/../../../neurodebian-images/$iso)
di_host=hydra # where to look for di preseed
vendor="NeuroDebian"
vm_version="6.0.1"
vm_ostype=Debian
+vendor_url="http://neuro.debian.net"
+product_url="${vendor_url}/vm.html"
# Generic definitions
eula="This virtual appliance contains Free and Open Source Software (FOSS) released under licenses compliant with the Debian Free Software Guidelines (DFSG, see http://www.debian.org/social_contract), such as, GPL, BSD, MIT, etc. Such software is free to be used or customized for any purpose.
vm_arch_name=" (64bit)"
fi
-vm_disk="$build_dir/nd-${vm_version}_${vm_arch}.vdi"
-vm_name="${vendor} VirtualMachine${vm_arch_name}"
-vm_ovf="${dist_dir}/${vendor}_${vm_version}_${vm_arch}.ovf"
+vm_fprefix="${vendor}_${vm_version}_${vm_arch}" # common prefix for files
+#vm_disk="$build_dir/nd-${vm_version}_${vm_arch}.vdi"
+vm_disk="$build_dir/${vm_fprefix}.vdi"
+vm_name="${vendor} ${vm_version} ${vm_arch_name}"
+vm_ovf="${dist_dir}/${vm_fprefix}.ovf"
product_name="${vendor} VirtualMachine (${vm_arch})"
_info() {
clean_buildvm # clean things up
+#exit
# Check that no previous VM was left (can happen if previous failures
# were "valid")
if VBoxManage list vms | grep -q "^\"${vm_name}\".*"; then
_info Create HardDisk for the VM
VBoxManage createhd --filename $vm_disk \
- --size 20000 --format VDI
+ --size 20480 --format VDI
# documented but not implemented:
# --comment "Drive for NeuroDebian VM installer"
VBoxManage export "${vm_name}" -o "$vm_ovf" \
--vsys 0 \
- --product "${vendor} VirtualMachine (${vm_arch})" \
- --producturl "http://neuro.debian.net/vm.html" \
+ --product "${product_name}" \
+ --producturl "${product_url}" \
--vendor "${vendor}" \
--vendorurl "http://neuro.debian.net" \
--version "$vm_version" \
projects / neurodebian.git / commitdiff
