[submodule "3rd/jquery.livetwitter"]
path = 3rd/jquery.livetwitter
url = git://github.com/elektronaut/jquery.livetwitter.git
+[submodule "3rd/bigmess"]
+ path = 3rd/bigmess
+ url = git://github.com/neurodebian/bigmess.git
+[submodule "3rd/nvd3"]
+ path = 3rd/nvd3
+ url = git://github.com/novus/nvd3.git
--- /dev/null
+Subproject commit 65601e6ca109f3a4eb7c07be0930db0fc1cd26f2
-Subproject commit 04254280bb3fee6e8d8f8ac638a6acf488151453
+Subproject commit 875f6d393511778395515d17319d15f899cd23af
--- /dev/null
+Subproject commit ba44aa30533688953a1f8bfc6fd32dc903c446e6
-#WWW_UPLOAD_URI = neuro.debian.net:/home/www/neuro.debian.net/www
-WWW_UPLOAD_URI = ../www
+#WWW_UPLOAD_URI = neurodebian@neurodebian.ovgu.de:/home/neurodebian/www
+WWW_UPLOAD_URI = ../../www
WWW_DIR = build/html/
WWW_UPLOAD_URI_STATIC=$(WWW_UPLOAD_URI)/_static
+BIGMESS_OPTS = -c neurodebian.cfg
+BIGMESS_CMD = PYTHONPATH=.:3rd/bigmess:$(PYTHONPATH) 3rd/bigmess/bin/bigmess
+BIGMESS = $(BIGMESS_CMD) $(BIGMESS_OPTS)
+
# Lentghy one due to updatedb
all: updatedb upload-website mirmon
# Quick one -- just rebuilds html if new changes and adjusts the status of the mirrors
refresh: upload-website-stamp mirmon
+website-build-depends:
+ : # Python modules
+ sudo apt-get install python-sphinx python-argparse python-xdg python-debian python-html5lib
+ : # JavaScripts
+ sudo apt-get install libjs-jquery-easing libjs-jquery-mousewheel libjs-jquery-fancybox
+
pics:
$(MAKE) -C artwork
html: pics source
rsync -rvlhpt sphinx/ build/src
- cd artwork; cp button_w200.png logo_tuned/fmri_w200.png ../build/src/_static; cd ..
+ cd artwork; cp button_w200.png logo_tuned/fmri_w200.png *-logo_h50.png ../build/src/_static; cd ..
cp 3rd/jquery.livetwitter/jquery.livetwitter.min.js build/src/_static
cp neurodebian.cfg build/src/_static
cd build/src && $(MAKE) html BUILDDIR=$(CURDIR)/build 2>&1
+ ln -fs /usr/share/javascript build/html/
mv $(WWW_DIR)/_static/robots.txt $(WWW_DIR)/
cp -r build/src/lists $(WWW_DIR)/
cp -r sphinx/survey/2011/figures/* $(WWW_DIR)/_images/
source: source-stamp
-source-stamp: build/db.db
- PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
- --cfg neurodebian.cfg \
- --db build/db.db \
- --outdir build/src \
- --pkgaddenum pkgs \
- --extracts /home/www/neuro.debian.net/www/debian/extracts \
- commandisirrelevant
- rm -f html-stamp
+source-stamp:
+ mkdir -p build/src/pkgs/
+ mkdir -p build/src/lists/
+ mkdir -p build/src/_static/
+ mkdir -p build/src/pkglists/
+ $(BIGMESS) mkpkgs -d build/src/pkgs/
+ $(BIGMESS) mkaptcfgs -d build/src/lists/
+ $(BIGMESS) mkmirrorsstat -d build/src
+ $(BIGMESS) mkrepocfg > build/src/sources_lists
+ $(BIGMESS) mkpkgtocs -d build/src/pkglists > build/src/pkgs.rst
+ cp 3rd/nvd3/*.min.js build/src/_static/
+ cp 3rd/nvd3/lib/d3*.min.js build/src/_static/
+ cp 3rd/nvd3/src/nv*.css build/src/_static/
touch $@
+cachefiles:
+ $(BIGMESS) cachefiles -f
-removecache:
- -rm -rf build/cache
-
-removedb:
- -rm -f build/db.db
-
-
-updatedb: removedb removecache build/db.db
-
-
-build/db.db:
- mkdir -p build
- PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
- --cfg neurodebian.cfg \
- --db build/db.db \
- updatedb
- -rm -f source-stamp
-
+updatedb: cachefiles
+ $(BIGMESS) updatedb
+ -rm source-stamp
upload-website: html
rsync -rvzlhp --delete \
cat $(WWW_UPLOAD_URI_STATIC)/{index-header,mirrors-status,index-trailer}.ihtml \
>| $(WWW_UPLOAD_URI)/mirrors-status.html
-.PHONY: removedb removecache updatedb upload-website clean distclean pics html mirmon
+.PHONY: removedb removecache cachefiles updatedb upload-website clean distclean pics html mirmon
qrcode_sticker.pdf
qrcode_sticker.png
derivatives.png
+ccn-logo_h50.png
+uni-md-logo_h50.png
+dartmouth-logo.png
+dartmouth-logo_h50.png
all:: pics
SVGIS=$(shell /bin/ls *.svgtune | sed -e 's/.svgtune/_tuned/g')
+ICONSIZED=ccn-logo_h50.png uni-md-logo_h50.png dartmouth-logo_h50.png
-pics: $(SVGIS)
+pics: $(SVGIS) $(ICONSIZED)
clean::
for p in *.svg; do rm -f $${p%*.svg}.{pdf,eps,png}; done
rm -rf *_tuned
+ rm -f $(ICONSIZED)
ignore-%:
@grep -q "^$*$$" .gitignore || { \
@echo "Rendering $@"
@inkscape -z -f "$<" -e "$@" -w 200
+# icon sized versions
+%_h50.png: %.png ignore-%_h50.png
+ @echo "Generating downscaled $@"
+ @convert -geometry x50 "$<" "$@"
# Some enforced conversions to overcome problems with transparency issues
# in PDFs
requiring the most recent versions of software.
%\item[Testing] \emph{Constantly changing future release candidate}\\
-\item[``Always-ready-to-release'']\hfill\emph{Testing} (now \emph{wheezy})\\
+\item[``Always-ready-to-release'']\hfill\emph{Testing} (now \emph{jessie})\\
% What to become a next \emph{Stable} release candidate.\\
Software versions known to be secure and of good quality.
% Software migrated from \emph{Unstable} which is known to be of good
of software.
%\item[Stable] \emph{Official release}\\
-\item[Official release]\hfill\emph{Stable} (now \emph{squeeze})\\
+\item[Official release]\hfill\emph{Stable} (now 7.2, \emph{wheezy})\\
% Software verified to be well tested and secure,
% Very stable (hence the name) and secure
% but might be lacking the most recent versions.\\% of the software.\\
\emph{Testing} is assured to be robust. %, on average bi-yearly.
Complementary updates keep the
system secure. \\
- \emph{Stable} is the best choice where stability and security are of
+ \emph{Stable} is the best choice where reliability and security are of
primary importance.
\end{description}
\ndsubsection{It has names}
The code names of Debian releases are names of characters from the Toy
-Story animation, e.g. sid, squeeze, lenny. \emph{Unstable}
+Story animation, \emph{e.g.} sid, jessie, wheezy. \emph{Unstable}
flavor always called \emph{sid}, while a new name chosen for every
upcoming release and assigned to \emph{Testing} to become a code name
of the release when it becomes \emph{Stable}.\\ At the moment
-\emph{squeeze} is \emph{Testing}, and \emph{lenny} is \emph{Stable}.
-As soon as \emph{squeeze} gets released, \emph{Testing} will be given
-a new name -- \emph{wheezy}.
+\emph{jessie} is \emph{Testing}, and \emph{wheezy} is \emph{Stable}.
+As soon as \emph{jessie} gets released, \emph{Testing} will be given
+a new name.% -- \emph{jessie}.
\end{comment}
\ndsubsection{Three Debian components}
\item[Live CD/DVD] \url{http://www.debian.org/CD/live/}
\item[Run in a Virtual Machine] \url{http://neuro.debian.net/vm.html}
\item[Development version] \url{http://www.debian.org/devel/debian-installer}
+\item[Use in a cloud] \url{https://wiki.debian.org/Cloud}
\end{description}
% \ndsubsection{Get \emph{Testing/Unstable} Debian}
\ndsubsection{How to install software}
GUI (Synaptic): \textit{Select and click ``Apply''}\\
-\includegraphics[width=\columnwidth]{shots/synaptic-fslview}
+\begin{center}
+\vspace{-1.2em}
+\includegraphics[width=0.95\columnwidth]{shots/synaptic-fslview}
+\vspace{-0.7em}
+\end{center}
Command line: \texttt{apt-get install <packagename>}
\ndsubsection{How to get support}
+\hspace{1em}\url{http://www.debian.org/support}
+
\begin{description}[nolistsep,leftmargin=1pc,style=nextline]
-\item[Overview]
-\url{http://www.debian.org/support}
+%\item[Overview]
%\item[GUI]
% Use \emph{Synaptic Package Manager}
\vspace{-0.1em}
\end{flushright}
\textit{Distributed computing:} Condor, DMTCP, IPython, \ldots \\
-\textit{Electrophysiology:} BioSig, EEGLAB, Sigviewer, \ldots\\
+\textit{Electrophysiology:} BioSig, Neo, Sigviewer, \ldots\\
\textit{Machine Learning:} MDP, PyMVPA, sklearn, \ldots\\
-\textit{Neural Modeling:} Brian, CNrun, PyNN, XPPAUT, \ldots\\
-\textit{Imaging:} AFNI, FSL, Mricron, NiPy, SPM, \ldots\\
-\textit{Psychophysics:} PsychoPy, Psychtoolbox, PyEPL, \ldots\\
+\textit{Neural Modeling:} Brian, CNrun, PyNN, XPPAUT \ldots\\
+\textit{Imaging:} AFNI, CMTK, FSL, Mricron, NiPy \ldots\\
+\textit{Psychophysics:} PsychoPy, Psychtoolbox-3, PyEPL \ldots\\
\vspace{-0.8em}
% TODO: Environments... -- list avail cloud env using NeuroDebian
\ndsubsection{Work-in-progress}
\begin{description}[nolistsep,leftmargin=1pc,style=nextline]
\item[Increased coverage]
-\textit{Electrophysiology:} Fieldtrip, Spyke Viewer, \ldots \\
-\textit{Neural Modeling:} NEURON, (NEST), LFPy, \\
+\textit{Electrophysiology:} Fieldtrip \\
+\textit{Neural Modeling:} NEURON, (NEST), LFPy \\
\textit{Imaging:} DTI-TK, Freesurfer, XNAT, \ldots
% \epigraph{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.}{Prof. Bruce Fischl}{Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA}
\item[Improved quality assurance]
- Extended integration and regression testing
+ Extended integration and regression testing\\
+ \url{http://testkraut.readthedocs.org}
\item[Available snapshotting service]
% Entire NeuroDebian repository for any given past moment
All versions of packages readily available
\item[Data as the 1st-class citizen]
- \url{http://neuro.debian.net/datasets.html}
+ \url{http://neuro.debian.net/datasets.html}\\
+ \url{http://github.com/neurodebian/datagit}
% yoh: see TODO above -- we can say that it is available already
%\item[Universal availability]
% % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em]
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+ id="path6689"
+ style="fill:black"
+ inkscape:export-filename="/home/alrferreira/Desktop/debian-gnu-banner.png"
+ inkscape:export-xdpi="64.494591"
+ inkscape:export-ydpi="64.494591" />
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+ inkscape:connector-curvature="0"
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+ style="fill:black"
+ inkscape:export-filename="/home/alrferreira/Desktop/debian-gnu-banner.png"
+ inkscape:export-xdpi="64.494591"
+ inkscape:export-ydpi="64.494591" />
+ <path
+ inkscape:connector-curvature="0"
+ class="st0"
+ d="M 496.9823,85.280203 480.75933,99.205621 464.53319,85.280203 480.75933,71.354772 496.9823,85.280203 z"
+ id="path6693"
+ style="fill:#d70751;fill-opacity:1"
+ inkscape:export-filename="/home/alrferreira/Desktop/debian-gnu-banner.png"
+ inkscape:export-xdpi="64.494591"
+ inkscape:export-ydpi="64.494591" />
+ </g>
+ </g>
+ <path
+ sodipodi:type="star"
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+ sodipodi:type="arc"
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+</svg>
--- /dev/null
+@inproceedings{GBC+2010,
+ title={Nipype: opensource platform for unified and replicable interaction with existing neuroimaging tools},
+ author={Ghosh, S and Burns, C and Clark, D and Gorgolewski, K and Halchenko, Y and Madison, C and Tungaraza, R and Millman, KJ},
+ booktitle={16th Annual Meeting of the Organization for Human Brain Mapping},
+ pages={106},
+ year={2010}
+}
+
+@article{NDR+2011,
+ title={Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis},
+ author={Nemoto, Kiyotaka and Dan, Ippeita and Rorden, Christopher and Ohnishi, Takashi and Tsuzuki, Daisuke and Okamoto, Masako and Yamashita, Fumio and Asada, Takashi},
+ journal={BMC medical imaging},
+ volume={11},
+ number={1},
+ pages={3},
+ year={2011},
+ publisher={BioMed Central Ltd}
+}
+
+@article{YIO+2012,
+ title={Simulation Platform: A cloud-based online simulation environment},
+ author={Yamazaki, Tadashi and Ikeno, Hidetoshi and Okumura, Yoshihiro and Satoh, Shunji and Kamiyama, Yoshimi and Hirata, Yutaka and Inagaki, Keiichiro and Ishihara, Akito and Kannon, Takayuki and Usui, Shiro},
+ journal={Neural networks},
+ volume={24},
+ number={7},
+ pages={693--698},
+ year={2011},
+ publisher={Elsevier}
+}
+
+@article{GDL+2011,
+ title={The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes},
+ author={Gerhard, Stephan and Daducci, Alessandro and Lemkaddem, Alia and Meuli, Reto and Thiran, Jean-Philippe and Hagmann, Patric},
+ journal={Frontiers in neuroinformatics},
+ volume={5},
+ year={2011},
+ publisher={Frontiers Media SA}
+}
+
+@article{Agu2012,
+ title={FIASCO, VoxBo, and MEDx: Behind the code},
+ author={Aguirre, Geoffrey K},
+ journal={NeuroImage},
+ volume={62},
+ number={2},
+ pages={765--767},
+ year={2012},
+ publisher={Elsevier}
+}
+
+@article{MST2012,
+ author={Mathôt, S. and Schreij, D. and Theeuwes, J.},
+ year={2012},
+ title={OpenSesame: An open-source, graphical experiment builder for the social sciences},
+ journal={Behavior Research Methods},
+ volume={44},
+ pages={314--324},
+ doi={10.3758/s13428-011-0168-7}
+}
+
+@inproceedings{SLZ+2011,
+ title={A cloud-based data-sharing and analysis cyberinfrastructure for neuroinformatics},
+ author={Stoner, R and Larson, S and Zaslavsky, I and Hill, S and Ellisman, M and Courchesne, E},
+ booktitle={Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics. doi: 10.3389/conf. fninf},
+ volume={34},
+ year={2011}
+}
+
+@article{SMT+2011,
+ title={Integrative visualization of temporally varying medical image patterns},
+ author={Soh, Jung and Mei Xiao, Thao Do and Meruvia-Pastor, Oscar and Sensen, Christoph W},
+ journal={Journal of integrative bioinformatics},
+ volume={8},
+ number={2},
+ pages={161},
+ year={2011}
+}
+
+@inproceedings{MDT+2012,
+ title={Mouse neuroimaging phenotyping in the cloud},
+ author={Minervini, Massimo and Damiano, Mario and Tucci, Valter and Bifone, Angelo and Gozzi, Alessandro and Tsaftaris, Sotirios A},
+ booktitle={Image Processing Theory, Tools and Applications (IPTA), 2012 3rd International Conference on},
+ pages={55--60},
+ year={2012},
+ organization={IEEE}
+}
+
+@inproceedings{GDS+2012,
+ title={A hierachical configuration system for a massively parallel neural hardware platform},
+ author={Galluppi, Francesco and Davies, Sergio and Rast, Alexander and Sharp, Thomas and Plana, Luis A and Furber, Steve},
+ booktitle={Proceedings of the 9th conference on Computing Frontiers},
+ pages={183--192},
+ year={2012},
+ organization={ACM}
+}
+
+@article{CCT+2012,
+ title={Meta-analytic clustering of the insular cortex Characterizing the meta-analytic connectivity of the insula when involved in active tasks},
+ author={Cauda, Franco and Costa, Tommaso and Torta, Diana ME and Sacco, Katiuscia and D'Agata, Federico and Duca, Sergio and Geminiani, Giuliano and Fox, Peter T and Vercelli, Alessandro},
+ journal={Neuroimage},
+ year={2012},
+ publisher={Elsevier}
+}
+
+@article{GEF+2012,
+ title={Oral contraceptive use changes brain activity and mood in women with previous negative affect on the pill—A double-blinded, placebo-controlled randomized trial of a levonorgestrel-containing combined oral contraceptive},
+ author={Gingnell, Malin and Engman, Jonas and Frick, Andreas and Moby, Lena and Wikstr{\"o}m, Johan and Fredrikson, Mats and Sundstr{\"o}m-Poromaa, Inger},
+ journal={Psychoneuroendocrinology},
+ year={2012},
+ publisher={Elsevier}
+}
+
+@article{GMB+2012,
+ title={Menstrual cycle effects on amygdala reactivity to emotional stimulation in premenstrual dysphoric disorder},
+ author={Gingnell, Malin and Morell, Arvid and Bannbers, Elin and Wikstr{\"o}m, Johan and Poromaa, Inger Sundstr{\"o}m},
+ journal={Hormones and behavior},
+ year={2012},
+ publisher={Elsevier}
+}
+
+@article{Mil2012,
+title = "Open Neuroscience Solutions for the Connectome-wide Association Era",
+journal = "Neuron",
+volume = "73",
+number = "2",
+pages = "214--218",
+year = "2012",
+doi = "10.1016/j.neuron.2011.11.004",
+url = "http://www.sciencedirect.com/science/article/pii/S0896627311010038",
+author = "Michael Peter Milham"
+}
+
+@article{Vis2012,
+ author={ViÅŸan, Ana-Maria},
+ title={Temporal meta-programming: treating time as a spatial dimension},
+ year={2012},
+ journal={Computer Science Dissertations},
+ volume={27},
+ url={http://hdl.handle.net/2047/d20002935}
+}
buildplace="${cowbuilderroot}/build"
# all currently supported dists
-allnddists="nd+debian-squeeze nd+debian-wheezy nd+debian-sid \
- nd+ubuntu-hardy nd+ubuntu-karmic nd+ubuntu-lucid nd+ubuntu-maverick nd+ubuntu-natty nd+ubuntu-oneiric nd+ubuntu-precise nd+ubuntu-quantal"
-alldists="$allnddists debian-squeeze debian-wheezy debian-sid"
+allnddists="nd+debian-squeeze nd+debian-wheezy nd+debian-jessie nd+debian-sid \
+ nd+ubuntu-lucid nd+ubuntu-precise nd+ubuntu-quantal nd+ubuntu-raring nd+ubuntu-saucy"
+alldists="$allnddists debian-squeeze debian-wheezy debian-jessie debian-sid"
# default is debian
aptcache="${cowbuilderroot}/debian_aptcache"
--- /dev/null
+* make ARCHS argument for cmdsettings.sh to be used by the tools so we could build on sparcs etc
+* add ipython-notebook/qtconsole (and probably ipython1x over ipython01x for >= wheezy) to welcomewizard
-neurodebian (0.29) unstable; urgency=low
+neurodebian (0.32) UNRELEASED; urgency=low
+
+ * nd_* tools:
+ - cmdsettings.sh: drop building for EOLed hardy, add raring
+
+ --
+
+neurodebian (0.31) neurodebian; urgency=low
+
+ * debian/copyright:
+ - adjusted for dep5 v1.0. compliance
+ * website:
+ - updated URL of the Magdeburg mirror
+ - more testimonials, derivatives information
+ * VM (6.999.b4.20121231):
+ - small fixes (cleanup etc)
+ * nd_* tools:
+ - backport-dsc: assure adding log entries to freshly created changelog
+ entry
+ - removed karmic, maverick and natty from build targets -- their support
+ ended
+
+ -- Yaroslav Halchenko <debian@onerussian.com> Tue, 12 Mar 2013 20:41:56 -0400
+
+neurodebian (0.30) neurodebian; urgency=low
+
+ * Preparing a new VM image (6.999.b4.20121206) - based on upcoming wheezy
+ release's beta4
+ - uses XFCE4 instead of Gnome(3) -- Depends on gdm | lightdm now,
+ uses urxvt as the default xterm
+ - nd-vmsetupwizard: extended list of topic choices
+ - vm/tools (with contributions from Tiziano Zito)
+ - does not require external webserver (uses Python's standard)
+ - basic cmdline options handling to avoid hard-coded values
+ - preseed.cfg is now templated
+ * website:
+ - new mirror ([de-m])
+ * nd_* tools:
+ - nd_build_testrdepends:
+ - signs the repository
+ - should work now with non-sid distributions
+ - nd_querycfg:
+ - generalized to query any config file
+
+ -- Yaroslav Halchenko <debian@onerussian.com> Wed, 19 Dec 2012 10:45:02 -0500
+
+neurodebian (0.29) neurodebian; urgency=low
[ Yaroslav Halchenko & Michael Hanke ]
* website:
-- Yaroslav Halchenko <debian@onerussian.com> Mon, 01 Oct 2012 12:26:37 -0400
-neurodebian (0.28) unstable; urgency=low
+neurodebian (0.28) neurodebian; urgency=low
[ Michael Hanke & Yaroslav Halchenko]
* website:
-- Yaroslav Halchenko <debian@onerussian.com> Thu, 19 Jul 2012 23:46:00 -0400
-neurodebian (0.27) unstable; urgency=low
+neurodebian (0.27) neurodebian; urgency=low
* nd_* tools:
- backport-dsc: escape "~" to prevent expansion into $HOME
-- Yaroslav Halchenko <debian@onerussian.com> Mon, 07 Nov 2011 17:59:54 -0500
-neurodebian (0.26) unstable; urgency=low
+neurodebian (0.26) neurodebian; urgency=low
[ Michael Hanke & Yaroslav Halchenko]
* website:
-- Yaroslav Halchenko <debian@onerussian.com> Mon, 17 Oct 2011 00:10:27 -0400
-neurodebian (0.25) unstable; urgency=low
+neurodebian (0.25) neurodebian; urgency=low
* Various improvements to the webportal.
* Support for Ubuntu natty
-- Michael Hanke <mih@debian.org> Fri, 29 Apr 2011 09:19:15 -0400
-neurodebian (0.24) unstable; urgency=low
+neurodebian (0.24) neurodebian; urgency=low
* Tuning up VM setup
* [ed8864b] lightweighting of VM image (removing -dev packages)
-- Yaroslav Halchenko <debian@onerussian.com> Tue, 08 Feb 2011 12:41:28 -0500
-neurodebian (0.23) unstable; urgency=low
+neurodebian (0.23) neurodebian; urgency=low
[ Michael Hanke ]
* [de48f60] Condor to Blends
-- Yaroslav Halchenko <debian@onerussian.com> Mon, 07 Feb 2011 14:44:30 -0500
-neurodebian (0.22) unstable; urgency=low
+neurodebian (0.22) neurodebian; urgency=low
[ Yaroslav Halchenko ]
* blends-inject :
-- Yaroslav Halchenko <debian@onerussian.com> Mon, 10 Jan 2011 11:06:54 -0500
-neurodebian (0.21) unstable; urgency=low
+neurodebian (0.21) neurodebian; 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
+neurodebian (0.20) neurodebian; 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
+neurodebian (0.19) neurodebian; urgency=low
* Initial release.
Package: neurodebian-guest-additions
Architecture: all
Pre-Depends: virtualbox-ose-guest-utils, virtualbox-ose-guest-x11, virtualbox-ose-guest-dkms
-Depends: ${misc:Depends}, sudo, neurodebian-desktop, gdm | gdm3, update-manager-gnome, update-notifier
-Recommends: chromium-browser
+Depends: ${misc:Depends},
+ sudo,
+ neurodebian-desktop,
+ gdm | lightdm,
+ zenity,
+Recommends: chromium-browser,
+ update-manager-gnome, update-notifier,
Description: NeuroDebian guest additions (DO NOT INSTALL OUTSIDE VIRTUALBOX)
This package configures a Debian installation as a guest operating system
in a VirtualBox-based virtual machine for NeuroDebian.
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-Name: NeuroDebian
-Maintainer: NeuroDebian team <team@neuro.debian.net>
-Source: http://neuro.debian.net
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: NeuroDebian
+Upstream-Contact: NeuroDebian team <team@neuro.debian.net>
+Source-Location: http://git.debian.org/?p=pkg-exppsy/neurodebian.git
Files: *
-Copyright: 2009-2010 NeuroDebian Team
+Copyright: 2009-2013 NeuroDebian Team
License: GPL-3+
On Debian systems the full text of the GNU General Public License can be found
in the `/usr/share/common-licenses/GPL-3' file.
Files: artwork/openlogo*.svg
-Copyright 1999, Software in the Public Interest
+Copyright: 1999 Software in the Public Interest
License: MIT
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
xdg/directories/* usr/share/desktop-directories
xdg/desktop/neurodebian-* usr/share/applications
tools/nd-autoinstall usr/bin
+xdg/Xresources/neurodebian etc/X11/Xresources
#!/bin/bash -e
-gdm_conf=/etc/gdm/gdm.conf
-if [ "$1" = "configure" -o "$1" = "abort-upgrade" ]; then
- if [ -z "$(grep 'AutomaticLogin=brain' $gdm_conf)" ]; then
- echo "Enabling autologin of user 'brain'."
+# GNOME2
+_set_gdm_auto_login() {
+ gdm_conf="$1"
+ gnome_ver="$2"
+ if [ ! -e $gdm_conf ]; then
+ echo "I: No config file $gdm_conf GNOME $gnome_ver found"
+ elif [ -z "$(grep 'AutomaticLogin=brain' $gdm_conf)" ]; then
+ echo "I: Enabling autologin of user 'brain' for GNOME $gnome_ver."
sed -i -e 's/^\[daemon\]$/\[daemon\]\nAutomaticLoginEnable=true\nAutomaticLogin=brain\n/' $gdm_conf
+ # update gconf defaults tree
+ update-gconf-defaults
fi
+}
+
+# XFCE4
+_set_lightdm_auto_login() {
+ lightdm_conf="$1"
+ if [ ! -e $lightdm_conf ]; then
+ echo "I: No config file $lightdm_conf found"
+ elif [ ! -z "$(grep '^# *autologin-user=' $lightdm_conf)" ]; then
+ echo "I: Enabling autologin of user 'brain' for lightdm."
+ sed -i -e 's/^# *autologin-user=.*$/autologin-user=brain/' $lightdm_conf
+ fi
+
+}
+
+gdm_conf=/etc/gdm/gdm.conf
+if [ "$1" = "configure" -o "$1" = "abort-upgrade" ]; then
+
+ [ -e /etc/gdm/gdm.conf ] && _set_gdm_auto_login /etc/gdm/gdm.conf 2 || :
+ [ -e /etc/gdm3/daemon.conf ] && _set_gdm_auto_login /etc/gdm3/daemon.conf 3 || :
- # update gconf defaults tree
- update-gconf-defaults
+ [ -e /etc/lightdm/lightdm.conf ] && _set_lightdm_auto_login /etc/lightdm/lightdm.conf || :
fi
#DEBHELPER#
-[dde]
-pkgquery_url = http://dde.debian.net/dde/q/udd
-
-[packages]
-# 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/distributedcomputing
- 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-sklearn 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 python-skimage neurodebian numdiff nuitka pytables
- guacamole freeipmi remake
-
-# Information about prospective packages to be imported from taskfiles
-prospective =
- svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/distributedcomputing
- 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
-
-[blend package aliases]
-# alias a package name from a blend taskfile to an arbitray number of additional
-# package names -- if the original name should appear in the package list it has
-# to be added as an alias as well
-cctools = coop-computing-tools
-mni-icbm152-nlin-2009 = mni-icbm152-nlin-2009a mni-icbm152-nlin-2009b mni-icbm152-nlin-2009c
-eeglab = matlab-eeglab11 eeglab11-sampledata
-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-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
-libgdf-dev = libgdf-dev libgdf0 libgdf0-dbg libgdf-dev gdf-tools octave-gdf matlab-gdf
-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
-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
-pytables = python-tables
-isis = isis-utils libisis-core-dev python-isis libisis-ioplugins-common libisis-ioplugins-dicom libisis-qt4-dev
-guacamole = guacamole guacd libguac-dev libguac3 libguac-client-rdp guacamole-tomcat libguac-client-vnc0
-neo = python-neo
-openvibe = openvibe-bin openvibe-data openvibe-dev openvibe-libs openvibe-plugins
-
[mirrors]
au = http://mirror.aarnet.edu.au/pub/neurodebian
de-m = http://neurodebian.g-node.org
-de-md = http://apsy.gse.uni-magdeburg.de/debian
+de-md = http://neurodebian.ovgu.de/debian
de-v = http://nd.zetatech.org
gr = http://neurobot.bio.auth.gr/neurodebian
jp = http://neuroimaging.sakura.ne.jp/neurodebian
-ua = http://www.neuro.webdisk.com.ua
+# yoh: Disabled -- N/A for a while and maintainer didn't respond
+# ua = http://www.neuro.webdisk.com.ua
us-ca = http://neurodeb.pirsquared.org
us-nh = http://neuro.debian.net/debian
us-tn = http://masi.vuse.vanderbilt.edu/neurodebian
us-nh = USA-NH (Dartmouth College)
us-tn = USA-TN (Vanderbilt)
-[neurodebian]
+[mirrors monitor]
+# stamp file
+stampfile = .timestamp
+# Email to announce problems to
+#email = yoh@onerussian.com
+# seconds to wait for a response from the server before considering
+# server non-responsive
+#timeout = 30 ; seconds
+# how many hours to allow for a mirror to be stale before emailing
+warn-threshold = 24 ; hours
+# how frequently to email in hours
+#email-period = 24 ; hours
+
+
+[release files]
# Release files of all repositories to be contained in the website
-# Package info files for all these releases will be downloaded. A long list
-# of releases makes a website update a lot slower
-releases =
- http://neuro.debian.net/debian/dists/data/Release
- http://neuro.debian.net/debian/dists/hardy/Release
- http://neuro.debian.net/debian/dists/karmic/Release
- 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/precise/Release
- http://neuro.debian.net/debian/dists/quantal/Release
- http://neuro.debian.net/debian/dists/squeeze/Release
- http://neuro.debian.net/debian/dists/wheezy/Release
- http://neuro.debian.net/debian/dists/sid/Release
-
-[release codenames]
-# each item here will result in the respective release being advertised
+# Package info files for all these releases will be downloaded.
+# Each item here will result in the respective release being advertised
# on the website, i.e. sources.list being available and config form contains
# a corresponding item -- please prune an entry when a release is no longer
# supported
-# the 'data' entry should not be changed, as this exact setting also serves as
-# a test condition in the DDE code
+data = http://neuro.debian.net/debian/dists/data/Release
+#EOL hardy = http://neuro.debian.net/debian/dists/hardy/Release
+#EOL karmic = http://neuro.debian.net/debian/dists/karmic/Release
+# EOL: April 2013 (Desktop) April 2015 (Server)
+lucid = http://neuro.debian.net/debian/dists/lucid/Release
+#EOL maverick = http://neuro.debian.net/debian/dists/maverick/Release
+#EOL natty = http://neuro.debian.net/debian/dists/natty/Release
+#EOL oneiric = http://neuro.debian.net/debian/dists/oneiric/Release
+# EOL: April 2017 (LTS)
+precise = http://neuro.debian.net/debian/dists/precise/Release
+# EOL: Apr 2014
+quantal = http://neuro.debian.net/debian/dists/quantal/Release
+# EOL: Jan 2014
+raring = http://neuro.debian.net/debian/dists/raring/Release
+# EOL: July 2014
+saucy = http://neuro.debian.net/debian/dists/saucy/Release
+# EOL: May 2014
+squeeze = http://neuro.debian.net/debian/dists/squeeze/Release
+wheezy = http://neuro.debian.net/debian/dists/wheezy/Release
+jessie = http://neuro.debian.net/debian/dists/jessie/Release
+sid = http://neuro.debian.net/debian/dists/sid/Release
+
+[release bases]
+debian = http://amd64-geomirror.debian.net/debian
+ubuntu = http://de.archive.ubuntu.com/ubuntu
+
+[task files]
+datasets = http://anonscm.debian.org/gitweb/?p=pkg-exppsy/neurodebian-blend.git;a=blob_plain;f=tasks/datasets
+distributedcomputing = http://anonscm.debian.org/gitweb/?p=pkg-exppsy/neurodebian-blend.git;a=blob_plain;f=tasks/distributedcomputing
+education = http://anonscm.debian.org/gitweb/?p=pkg-exppsy/neurodebian-blend.git;a=blob_plain;f=tasks/education
+electrophysiology = http://anonscm.debian.org/gitweb/?p=pkg-exppsy/neurodebian-blend.git;a=blob_plain;f=tasks/electrophysiology
+mri = http://anonscm.debian.org/gitweb/?p=pkg-exppsy/neurodebian-blend.git;a=blob_plain;f=tasks/mri
+neuralmodeling = http://anonscm.debian.org/gitweb/?p=pkg-exppsy/neurodebian-blend.git;a=blob_plain;f=tasks/neuralmodeling
+psychophysics = http://anonscm.debian.org/gitweb/?p=pkg-exppsy/neurodebian-blend.git;a=blob_plain;f=tasks/psychophysics
+
+[release names]
+# Map code names to release names and description
data = Datasets (data)
-#etch = Debian GNU/Linux 4.0 (etch)
+etch = Debian GNU/Linux 4.0 (etch)
lenny = Debian GNU/Linux 5.0 (lenny)
squeeze = Debian GNU/Linux 6.0 (squeeze)
-wheezy = Debian testing (wheezy)
+wheezy = Debian GNU/Linux 7.0 (wheezy)
+jessie = Debian testing (jessie)
sid = Debian unstable (sid)
-# EOL: May 12 2011 (Desktop) April 2013 (Server)
hardy = Ubuntu 08.04 LTS "Hardy Heron" (hardy)
-# EOL: Oct 23 2010
-#jaunty = Ubuntu 09.04 "Jaunty Jackalope" (jaunty)
-# EOL: April 2011
+jaunty = Ubuntu 09.04 "Jaunty Jackalope" (jaunty)
karmic = Ubuntu 09.10 "Karmic Koala" (karmic)
-# EOL: April 2013 (Desktop) April 2015 (Server)
lucid = Ubuntu 10.04 LTS "Lucid Lynx" (lucid)
-# EOL: April 2012
maverick = Ubuntu 10.10 "Maverick Meerkat" (maverick)
-# EOL: October 2012
natty = Ubuntu 11.04 "Natty Narwhal" (natty)
-# EOL: April 2013
oneiric = Ubuntu 11.10 "Oneiric Ocelot" (oneiric)
-# EOL: April 2017 (LTS)
precise = Ubuntu 12.04 LTS "Precise Pangolin" (precise)
-# EOL: April 2014
quantal = Ubuntu 12.10 "Quantal Quetzal" (quantal)
+raring = Ubuntu 13.04 "Raring Ringtail" (raring)
+saucy = Ubuntu 13.10 "Saucy Salamander" (saucy)
+
+[metadata]
+# base url: <url>/<src_pkg-name>/<file>
+source extracts baseurl = http://neuro.debian.net/debian/extracts
+# files to query
+source extracts filenames = upstream README.Debian copyright
+
+[build]
+# various configuration options for tweaking the build process
+# each option can also be prefixed with a build environment ID, such as
+# 'debian' or 'ubuntu' to further customize behavior. For example, using
+# different backport maintainer for Debian and Ubuntu backports would look
+# like this:
+#debian backport maintainer = some guy
+#ubuntu backport maintainer = some other guy
+
+# list of environments to build for: each item in this space-separated list
+# is a tuple of a build family ID and a release name joined by a dash, e.g.
+# debian-sid
+environments = nd+debian-sid nd+debian-jessie nd+debian-wheezy nd+debian-squeeze
+ nd+ubuntu-raring nd+ubuntu-quantal nd+ubuntu-precise nd+ubuntu-lucid
+# what command to use for package building: pbuilder or cowbuilder
+builder = pbuilder
+
+# directory configurations: It is possible to use environment variable and '~'
+# for these items
+# directory for storing build chroots
+chroot basedir = ~/chroots
+# base directory for builds are performed
+build basedir = ~/build
+# directory for placing built package in
+result directory = ~/built_deb
+debian result directory = ~/built_deb/debian
+nd+debian result directory = ~/built_deb/neurodebian
+nd+ubuntu result directory = ~/built_deb/neurodebian
+# directory for condor batch build log files
+condor logdir = ~/condorlog
+# directory for caching downloaded packages. If this is empty, not caching is
+# done (useful if something like apt-cacher is in place).
+aptcache =
+
+# what architectures to build for
+architectures = amd64 i386
+
+# architecture to be used for building arch 'all' packages
+archall architecture = amd64
+
+# additional options for dpkg-buildpackage
+# do not use this for -sa, -B and friends: the 'build_pkg' command has a
+# --source-include option for this
+#debbuild options =
+
+# main mirror for chroots
+nd+debian mirror = http://medusa:3142/http.debian.net/debian
+nd+ubuntu mirror = http://medusa:3142/archive.ubuntu.com/ubuntu
+
+# additional mirror(s) for the chroot (thay take precedence over the main mirror
+# the release codename is automatically filled in where '%%(release)s' is given
+nd+debian othermirror = deb http://medusa:3142/neurodebian.ovgu.de/debian %%(release)s main contrib non-free
+nd+ubuntu othermirror = deb http://medusa:3142/neurodebian.ovgu.de/debian %%(release)s main contrib non-free
+
+# additional keyring to be used by debbootstrap and APT
+nd+ubuntu bootstrap keyring = /usr/share/keyrings/ubuntu-archive-keyring.gpg
+nd+debian keyring = ~/tools/neurodebian/keys/neurodebian-archive-keyring.gpg
+nd+ubuntu keyring = ~/tools/neurodebian/keys/neurodebian-archive-keyring.gpg
+
+# Repository components to enable in a build chroot
+#components=
+debian components = main
+nd+debian components = main contrib non-free
+nd+ubuntu components = main universe multiverse
+
+# force including sources in any build (for one arch in a batch)
+nd+debian source include = yes
+nd+ubuntu source include = yes
+
+# Maintainer setting for backported packages
+backport maintainer = NeuroDebian Team <team@neuro.debian.net>
+
+# sed expression for modifying the control file of backported packages
+backport modify control = s/\(^Depends:\) */\1 neurodebian-popularity-contest, /g
+
+# space-separate list of source package name for which to NOT apply the control
+# modification expression
+backport modify control blacklist =
[release backport ids]
-# the purpose of these ids is to have version suffixes for backported packages
-# that allow proper sorting (upgradability) across distribution releases
-# For Debian we'll use ndXX (where XX is the version of the Debian release,
-# e.g. 50; analog to backports.org) and for Ubuntu we'll use ndXX.XX.
+# IDs for individual releases that are used as version suffixes when
+# backporting packages. The ensure a proper upgrade path, these IDs should
+# be increasing (alpha-numeric sorting) for releases following each other.
data = nd
etch = nd40
lenny = nd50
squeeze = nd60
wheezy = nd70
+jessie = nd80
sid = nd
hardy = nd08.04
intrepid = nd08.10
oneiric = nd11.10
precise = nd12.04
quantal = nd12.10
-
-[nitrc ids]
-afni = 23
-ants = 130
-camino = 253
-caret = 34
-cmtk = 212
-connectomeviewer = 355
-dicomnifti = 218
-fsl = 25
-fslview = 25
-gifti-bin = 75
-imagej = 256
-itksnap = 110
-jist = 228
-libminc-dev = 129
-libgiftiio-dev = 75
-libnifti2 = 26
-libnifti-dev = 26
-matlab-spm8 = 24
-minc-tools = 129
-mipav = 70
-mitools = 153
-mricron = 152
-mrtrix = 128
-nifti-bin = 26
-odin = 153
-python-mvpa = 162
-python-nipype = 325
-python-surfer = 517
-python-pyxnat = 453
-slicer = 50
-spm8 = 24
-voxbo = 73
-openmeeg = 514
-
+raring = nd13.04
+saucy = nd13.10
+++ /dev/null
-#!/usr/bin/env python
-"""Tell me who you are!
-"""
-
-import pysvn
-import json
-import numpy as np
-
-from ConfigParser import SafeConfigParser
-from optparse import OptionParser, OptionGroup, OptionConflictError
-
-# Lets first assure no guarding (but annoying) warnings
-import warnings
-warnings.simplefilter('ignore', FutureWarning)
-warnings.filterwarnings('ignore',
- 'Module debian_bundle was already imported.*', UserWarning)
-
-from debian import deb822
-import apt # initializes the "_system" ;)
-from apt_pkg import version_compare
-
-import sys
-import os
-import copy
-import shutil
-import urllib2
-import urllib
-import codecs
-import subprocess
-import time
-import re
-
-# templating
-from jinja2 import Environment, PackageLoader
-
-from pprint import PrettyPrinter
-
-
-class AptListsCache(object):
- def __init__(self, cachedir='build/cache',
- ro_cachedirs=None,
- init_db=None):
- self.cachedir = cachedir
-
- if not ro_cachedirs is None:
- self.ro_cachedirs = ro_cachedirs
- else:
- self.ro_cachedirs = []
-
- # create cachedir
- create_dir(self.cachedir)
-
- def get(self, url, update=False):
- """Looks in the cache if the file is there and takes the cached one.
- Otherwise it is downloaded first.
-
- Knows how to deal with http:// and svn:// URLs.
-
- :Return:
- file handler
- """
- # look whether it is compressed
- cext = url.split('.')[-1]
- if cext in ['gz', 'bz2']:
- target_url = url[:-1 * len(cext) -1]
- else:
- # assume not compressed
- target_url = url
- cext = None
-
- # turn url into a filename -- mimik what APT does for
- # /var/lib/apt/lists/
- tfilename = '_'.join(target_url.split('/')[2:])
-
- # if we need to download anyway do not search
- if update:
- cfilename = os.path.join(self.cachedir, tfilename)
- else:
- # look for the uncompressed file anywhere in the cache
- cfilename = None
- for cp in [self.cachedir] + self.ro_cachedirs:
- if os.path.exists(os.path.join(cp, tfilename)):
- cfilename = os.path.join(cp, tfilename)
-
- # nothing found?
- if cfilename is None:
- # add cache item
- cfilename = os.path.join(self.cachedir, tfilename)
- update = True
-
- # if updated needed -- download
- if update:
- #print 'Caching file from %s' % url
-
- if url.startswith('svn://'):
- # export from SVN
- pysvn.Client().export(url, cfilename)
- if url.startswith('http://'):
- # download
- tempfile, ignored = urllib.urlretrieve(url)
-
- # decompress
- decompressor = None
- if cext == 'gz':
- decompressor = 'gzip'
- elif cext == 'bz2':
- decompressor = 'bzip2'
- elif cext == None:
- decompressor = None
- else:
- raise ValueError, \
- "Don't know how to decompress %s files" \
- % cext
-
- if not decompressor is None:
- if subprocess.call([decompressor, '-d', '-q', '-f',
- tempfile]) == 1:
- raise RuntimeError, \
- "Something went wrong while decompressing '%s'" \
- % tempfile
-
- # move decompressed file into cache
- shutil.move(os.path.splitext(tempfile)[0], cfilename)
-
- # XXX do we need that if explicit filename is provided?
- urllib.urlcleanup()
-
- # open cached file
- fh = codecs.open(cfilename, 'r', 'utf-8')
-
- return fh
-
-
-def add_pkgfromtaskfile(db, urls):
- cache = AptListsCache()
- pkgs = []
-
- for task in urls:
- fh = cache.get(task)
-
- # loop over all stanzas
- 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:
- continue
-
- # account for multiple packages per line
- if pkg.count(','):
- pkgs += [p.strip() for p in pkg.split(',')]
- else:
- pkgs.append(pkg.strip())
-
- for p in pkgs:
- if not db.has_key(p):
- db[p] = get_emptydbentry()
-
- return db
-
-def get_emptydbentry():
- return {'main': {}}
-
-def import_blendstask(cfg, db, url):
- cache = AptListsCache()
- fh = cache.get(url)
- task_name = None
-
- # figure out blend's task page URL, since they differ from blend to blend
- urlsec = url.split('/')
- blendname = urlsec[-3]
- if blendname == 'debian-med':
- taskpage_url = 'http://debian-med.alioth.debian.org/tasks/'
- elif blendname == 'debian-science':
- taskpage_url = 'http://blends.alioth.debian.org/science/tasks/'
- else:
- raise ValueError('Unknown blend "%s"' % blendname)
- taskpage_url += urlsec[-1]
-
- for st in deb822.Packages.iter_paragraphs(fh):
- if st.has_key('Task'):
- task_name = st['Task']
- task = (blendname, task_name, taskpage_url)
-
- 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:
-# print 'Warning: Cannot determine name of prospective package ' \
-# '... ignoring. Dump follows:'
-# print st
- continue
-
- # take care of pkg lists
- for p in pkg.split(', '):
- if not db.has_key(p):
- print 'Ignoring blend package "%s"' % p
- continue
-
- info = {}
-
- # blends info
- info['tasks'] = [task]
- if st.has_key('License'):
- info['license'] = st['License']
- if st.has_key('Responsible'):
- info['responsible'] = st['Responsible']
-
- # pkg description
- if st.has_key('Pkg-Description'):
- descr = st['Pkg-Description'].split('\n')
- info['description'] = descr[0].strip()
- info['long_description'] = \
- u'\n'.join(descr[1:])
-
- # charge the basic property set
- db[p]['main']['description'] = info['description']
- db[p]['main']['long_description'] = info['long_description']
- if st.has_key('WNPP'):
- db[p]['main']['debian_itp'] = st['WNPP']
- if st.has_key('Pkg-URL'):
- db[p]['main']['other_pkg'] = st['Pkg-URL']
- if st.has_key('Homepage'):
- db[p]['main']['homepage'] = st['Homepage']
-
- # Publications
- if st.has_key('Published-Title'):
- title = st['Published-Title']
- if title[-1] == '.':
- # trip trailing dot -- added later
- pub = {'title': title[:-1]}
- else:
- pub = {'title': title}
- if st.has_key('Published-Authors'):
- pub['authors'] = st['Published-Authors']
- if st.has_key('Published-Year'):
- pub['year'] = st['Published-Year']
- if st.has_key('Published-In'):
- pub['in'] = st['Published-In']
- if st.has_key('Published-URL'):
- pub['url'] = st['Published-URL']
- if st.has_key('Published-DOI'):
- pub['doi'] = st['Published-DOI']
- # need at least one URL
- if not pub.has_key('url'):
- pub['url'] = "http://dx.doi.org/%s" % st['Published-DOI']
-
- db[p]['main']['publication'] = pub
-
- # Registration
- if st.has_key('Registration'):
- db[p]['main']['registration'] = st['Registration']
-
- # Remarks
- if st.has_key('Remark'):
- # prepend a single space to make it look like a long description
- info['remark'] = convert_longdescr(' ' + st['Remark'])
-
- # only store if there isn't something already
- if not db[p].has_key('blends'):
- db[p]['blends'] = info
- else:
- # just add this tasks name and id
- db[p]['blends']['tasks'].append(task)
-
- # handle pkg name aliases
- if p in cfg.options('blend package aliases'):
- src_entry = db[p].copy()
- # remove original entry
- del db[p]
- # copy the entry into all aliases
- for alias in cfg.get('blend package aliases', p).split():
- print "Aliasing %s to %s" % (p, alias)
- db[alias] = copy.deepcopy(src_entry)
-
- return db
-
-
-def get_releaseinfo(rurl):
- cache = AptListsCache()
- # root URL of the repository
- baseurl = '/'.join(rurl.split('/')[:-1])
- # get the release file from the cache
- release_file = cache.get(rurl)
-
- # create parser instance
- rp = deb822.Release(release_file)
-
- # architectures on this dist
- archs = rp['Architectures'].split()
- components = rp['Components'].split()
- # compile a new codename that also considers the repository label
- # to distinguish between official and unofficial repos.
- label = rp['Label']
- origin = rp['Origin']
- codename = rp['Codename']
- labelcode = '_'.join([rp['Label'], rp['Codename']])
-
- # cleanup
- release_file.close()
-
- return {'baseurl': baseurl, 'archs': archs, 'components': components,
- 'codename': codename, 'label': label, 'labelcode': labelcode,
- 'origin': origin}
-
-
-def build_pkgsurl(baseurl, component, arch):
- return '/'.join([baseurl, component, 'binary-' + arch, 'Packages.bz2'])
-
-
-def import_release(cfg, db, rurl):
- cache = AptListsCache()
-
- ri = get_releaseinfo(rurl)
-
- # compile the list of Packages files to parse and parse them
- for c in ri['components']:
- for a in ri['archs']:
- # compile packages URL
- pkgsurl = build_pkgsurl(ri['baseurl'], c, a)
-
- # retrieve from cache
- packages_file = cache.get(pkgsurl)
-
- # parse
- for stanza in deb822.Packages.iter_paragraphs(packages_file):
- db = _store_pkg(cfg, db, stanza, ri['origin'], ri['codename'], c, ri['baseurl'])
-
- # cleanup
- packages_file.close()
-
- return db
-
-def _store_pkg(cfg, db, st, origin, codename, component, baseurl):
- """
- :Parameter:
- st: Package section
- """
- pkg = st['Package']
-
- # only care for known packages
- if not db.has_key(pkg):
-# print 'Ignoring NeuroDebian package "%s"' % pkg
- return db
-
- distkey = (trans_codename(codename, cfg), 'neurodebian-' + codename)
-
- if db[pkg].has_key(distkey):
- info = db[pkg][distkey]
- else:
- info = {'architecture': []}
-
- # fill in data
- if not st['Architecture'] in info['architecture']:
- info['architecture'].append(st['Architecture'])
- info['maintainer'] = st['Maintainer']
- if st.has_key('Homepage'):
- info['homepage'] = st['Homepage']
- info['version'] = st['Version']
-
- # origin
- info['distribution'] = origin
- info['release'] = codename
- info['component'] = component
-
- # pool url
- info['poolurl'] = '/'.join([os.path.dirname(st['Filename'])])
-
- # pkg description
- descr = st['Description'].replace('%', '%%').split('\n')
- info['description'] = descr[0].strip()
- info['long_description'] = u'\n'.join(descr[1:])
-
- db[pkg][distkey] = info
-
- # charge the basic property set
- db[pkg]['main']['description'] = info['description']
- db[pkg]['main']['long_description'] = info['long_description']
- if st.has_key('Source'):
- db[pkg]['main']['sv'] = "%s %s" % (st['Source'], st['Version'])
- else:
- db[pkg]['main']['sv'] = "%s %s" % (st['Package'], st['Version'])
- if st.has_key('Homepage'):
- db[pkg]['main']['homepage'] = st['Homepage']
- if st.has_key('Recommends'):
- db[pkg]['main']['recommends'] = st['Recommends']
-
- return db
-
-
-def trans_codename(codename, cfg):
- """Translate a known codename into a release description.
-
- Unknown codenames will simply be returned as is.
- """
- # if we know something, tell
- if codename in cfg.options('release codenames'):
- return cfg.get('release codenames', codename)
- else:
- return codename
-
-
-def create_dir(path):
- if os.path.exists(path):
- return
-
- ps = path.split(os.path.sep)
-
- for i in range(1,len(ps) + 1):
- p = os.path.sep.join(ps[:i])
-
- if not os.path.exists(p):
- os.mkdir(p)
-
-
-def dde_get(url, fail=False):
- # enforce delay to be friendly to DDE
- time.sleep(3)
- try:
- data = json.load(urllib2.urlopen(url+"?t=json"))['r']
- print "SUCCESS:", url
- return data
- except urllib2.HTTPError, e:
- print "NOINFO:", url, type(e)
- return False
- except urllib2.URLError, e:
- print "URLERROR:", url, type(e)
- if fail:
- print "Permanant failure"
- return False
- print "Try again after 30 seconds..."
- time.sleep(30)
- return dde_get(url, fail=True)
- except (StopIteration):
- print "NOINFO:", url
- return False
- except Exception, e:
- print "UDD-DOWN?:", url, type(e)
- return False
-
-
-def nitrc_get(spec, fail=False):
- nitrc_url = 'http://www.nitrc.org/export/site/projects.json.php'
- try:
- # change into this from python 2.6 on
- #data = json.loads(urllib2.urlopen(nitrc_url + '?spec=%s' % spec).read())
- data = json.load(urllib2.urlopen(nitrc_url + '?spec=%s' % spec))
- print "NITRC-SUCCESS:", spec
- except urllib2.HTTPError, e:
- print "NITRC-NOINFO:", spec, type(e)
- return False
- except urllib2.URLError, e:
- print "NITRC-URLERROR:", spec, type(e)
- if fail:
- print "Permanant failure"
- return False
- print "Try again after 30 seconds..."
- time.sleep(30)
- return nitrc_get(spec, fail=True)
- return data
-
-
-def parse_nitrc(data):
- if data is False:
- return None
- # simplify -- there is only one project in the data
- project = data['projects'][0]
- nitrc_filtered = {'downloads': 0,
- 'id': project['id']}
- for pkg in project['packages']:
- for release in pkg['releases']:
- for file in release['files']:
- nitrc_filtered['downloads'] += file['download_count']
- return nitrc_filtered
-
-
-def import_nitrc(cfg, db):
- for p in db.keys():
- if not cfg.has_option("nitrc ids", p):
- continue
- nitrc_spec = cfg.get("nitrc ids", p)
- nitrc_data = nitrc_get(nitrc_spec)
- nitrc_excerpt = parse_nitrc(nitrc_data)
- if not nitrc_excerpt is None:
- db[p]['nitrc'] = nitrc_excerpt
- return db
-
-
-def import_dde(cfg, db):
- query_url = cfg.get('dde', 'pkgquery_url')
- for p in db.keys():
- # get freshest
- q = dde_get(query_url + "/packages/all/%s" % p)
- if q:
- # copy all stuff, while preserving non-overlapping information
- for k, v in q.iteritems():
- db[p]['main'][k] = v
- # get latest popcon info for debian and ubuntu
- # cannot use origin field itself, since it is none for few packages
- # i.e. python-nifti
- origin = q['drc'].split()[0]
- if origin == 'ubuntu':
- if q.has_key('popcon'):
- db[p]['main']['ubuntu_popcon'] = q['popcon']
- # if we have ubuntu, need to get debian
- q = dde_get(query_url + "/packages/prio-debian-sid/%s" % p)
- if q and q.has_key('popcon'):
- db[p]['main']['debian_popcon'] = q['popcon']
- elif origin == 'debian':
- 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-precise/%s" % p)
- if q and q.has_key('popcon'):
- db[p]['main']['ubuntu_popcon'] = q['popcon']
- else:
- print("Ignoring unkown origin '%s' for package '%s'." \
- % (origin, p))
-
- # now get info for package from all releases in UDD
- q = dde_get(query_url + "/dist/p:%s" % p)
- if not q:
- continue
- # hold all info about this package per distribution release
- info = {}
- for cp in q:
- distkey = (trans_codename(cp['release'], cfg),
- "%s-%s" % (cp['distribution'], cp['release']))
- if not info.has_key(distkey):
- info[distkey] = cp
- # turn into a list to append others later
- info[distkey]['architecture'] = [info[distkey]['architecture']]
- # accumulate data for multiple over archs
- else:
- comp = version_compare(cp['version'],
- info[distkey]['version'])
- # found another arch for the same version
- if comp == 0:
- info[distkey]['architecture'].append(cp['architecture'])
- # found newer version, dump the old ones
- elif comp > 0:
- info[distkey] = cp
- # turn into a list to append others later
- info[distkey]['architecture'] = [info[distkey]['architecture']]
- # simply ignore older versions
- else:
- pass
-
- # finally assign the new package data
- for k, v in info.iteritems():
- db[p][k] = v
-
- 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):
- """
-
- yoh: I think all this long description conversion will keep giving
- us problems since per se there is no strict regulations,
- especially in blends files
- """
- descr = u''
- ld = ld.replace('% ', '%% ')
- ld = ld.replace(r'\t', ' ') # just in case assuming tab 4
- ld = ld.split('\n')
- re_leadblanks = re.compile("^ *")
- re_itemized = re.compile("^[o*-+] +")
- re_itemized_gr = re.compile("^( *)([-o*+] +)?(.*?)$")
- re_description_gr = re.compile("^( *[^-]+ - )(.*?)$")
-
- def unwrap_lines(lines):
- out = []
- indent_levels = [-1]
- for l in lines:
- match = re_itemized_gr.search(l).groups()
- if ((len(match[0]) in indent_levels and match[1] is None)
- or (len(match[0]) > max(indent_levels)+4)) \
- and match[2].strip() != '.':
- # append to previous
- if not out[-1].endswith(" "):
- out[-1] += " "
- out[-1] += match[2]
- else:
- out.append(l)
-
- indent_levels = [len(match[0])]
- if match[1] is not None:
- indent_levels += [len(match[0]) + len(match[1])]
- if match[2].strip() == '.':
- # reset though if '.'
- indent_levels = [-1]
- return out
-
- def dedent_withlevel(lines):
- """Dedent `lines` given in a list provide dedented lines and how much was dedented
- """
- nleading = min([re_leadblanks.search(l).span()[1]
- for l in lines])
- return [l[nleading:] for l in lines], nleading
-
- def block_lines(ld, level=0):
- # so we got list of lines
- # dedent all of them first
- ld, level = dedent_withlevel(ld)
-
- # lets collect them in blocks/paragraphs
- # 1. into paragraphs split by '.'
- blocks, block = [], None
-
- # next block can begin if
- # 1. . line
- # 2. it was an itemized list and all items begin with
- # the same symbol or get further indented accordingly
- # so let's first check if it is an itemized list
- itemized_match = re_itemized.search(ld[0])
- if itemized_match:
- allow_indents = " "*itemized_match.span()[1]
- else:
- allow_indents = None
- for l in ld:
- if block is None or l.strip() == '.' \
- or (len(l) and ( len(block) and (
- (l.startswith(' ') and not block[-1].startswith(' '))
- or
- (not l.startswith(' ') and block[-1].startswith(' '))))):
- block = []
- blocks.append(block)
- if l.strip() != '.':
- block.append(l)
- if len(blocks) == 1:
- return blocks[0]
- else:
- return [block_lines(b, level+1) for b in blocks if len(b)]
-
- def blocks_to_rst(bls, level=0):
- # check if this block is an itemized beast
- #itemized_match = re_itemized_gr.search(bls[0][0])
- #if itemized_match:
- # res += ' 'allow_indents = " "*itemized_match.span()[1]
- out = ''
- for b in bls:
- if isinstance(b, list):
- if len(b) == 1:
- out += " "*level + b[0] + '\n\n'
- else:
- out += blocks_to_rst(b, level+1)
- else:
- e = " "*level + b + '\n'
- if not re_itemized.search(b):
- pass
- #e += '\n'
- elif len(e) and e[0] == ' ':
- # strip 1 leading blank
- e = e[1:]
- out += e
- out += '\n'
- return out
-
- ld = unwrap_lines(ld)
- bls = block_lines(ld)
- return blocks_to_rst(bls)
-
-
-def underline_text(text, symbol):
- underline = symbol * len(text)
- return '%s\n%s\n' % (text, underline)
-
-
-def generate_pkgpage(pkg, cfg, db, template, addenum_dir, extracts_dir):
- # local binding for ease of use
- pkgdb = db[pkg]
- # do nothing if there is not at least the very basic stuff
- if not pkgdb['main'].has_key('description'):
- return
- title = '**%s** -- %s' % (pkg, pkgdb['main']['description'])
- title = underline_text(title, '*')
-
- 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
- long_description = 'Description missing'
- if 'long_description' in pkgdb['main']:
- long_description=convert_longdescr(
- assure_unicode(pkgdb['main']['long_description']))
- page = template.render(
- pkg=pkg,
- title=title,
- long_description=long_description,
- cfg=cfg,
- db=pkgdb,
- 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
- addenum = os.path.join(os.path.abspath(addenum_dir), '%s.rst' % pkg)
- if os.path.exists(addenum):
- page += '\n\n.. include:: %s\n' % addenum
- return page
-
-
-def store_db(db, filename):
- pp = PrettyPrinter(indent=2)
- f = codecs.open(filename, 'w', 'utf-8')
- f.write(pp.pformat(db))
- f.close()
-
-
-def read_db(filename):
- f = codecs.open(filename, 'r', 'utf-8')
- db = eval(f.read())
- return db
-
-def write_sourceslist(jinja_env, cfg, outdir):
- create_dir(outdir)
- create_dir(os.path.join(outdir, 'lists'))
-
- repos = {}
- for release in cfg.options('release codenames'):
- if release == 'data':
- # no seperate list for the data archive
- continue
- transrel = trans_codename(release, cfg)
- repos[transrel] = []
- for mirror in cfg.options('mirrors'):
- listname = '%s.%s' % (release, mirror)
- repos[transrel].append((mirror, listname))
- lf = open(os.path.join(outdir, 'lists', listname), 'w')
- for rel in ('data', release):
- aptcfg = '%s %s main contrib non-free\n' % (cfg.get('mirrors', mirror),
- rel)
- lf.write('deb %s' % aptcfg)
- lf.write('#deb-src %s' % aptcfg)
- lf.close()
-
- id2codename = dict([(cfg.get('release backport ids', r), r)
- for r in cfg.options('release codenames')])
- id2relname = dict([(cfg.get('release backport ids', r), trans_codename(r, cfg))
- for r in cfg.options('release codenames')])
- mirror2name = dict([(m, cfg.get('mirror names', m))
- for m in cfg.options('mirrors')])
- mirror2url = dict([(m, cfg.get('mirrors', m))
- for m in cfg.options('mirrors')])
- srclist_template = jinja_env.get_template('sources_lists.rst')
- sl = open(os.path.join(outdir, 'sources_lists'), 'w')
- sl.write(srclist_template.render(id2codename=id2codename,
- id2relname=id2relname,
- mirror2name=mirror2name,
- mirror2url=mirror2url))
- sl.close()
-
-
-def write_mirmonlists(cfg, outdir):
- """Write list of mirrors in the format suitable for mirmon
-
- It will reuse the same 'lists' directory
- """
- print "I: Composing mirmon lists"
- outdir = os.path.join(outdir, 'lists')
- create_dir(outdir)
-
- for sec, sep in (('mirrors', ' '),
- ('mirror names', ' - ')):
- entries = ['%s%s%s' % (mirror, sep, cfg.get(sec, mirror))
- for mirror in cfg.options('mirrors')]
- f = open(os.path.join(outdir, 'mirmon-%s.txt' % sec.replace(' ', '-')),
- 'w')
- f.write('\n'.join(entries + ['']))
- f.close()
-
-
-def sort_by_tasks(db):
- tasks = {}
- for pkg in db.keys():
- if not 'blends' in db[pkg]:
- # no blend info
- continue
- blendinfo = db[pkg]['blends']
- if not 'tasks' in blendinfo:
- # no task info in blend data
- continue
- taskinfo = blendinfo['tasks']
- for task in taskinfo:
- taskname = task[1]
- if not taskname in tasks:
- tasks[taskname] = []
- else:
- tasks[taskname].append(pkg)
- return tasks
-
-
-def sort_by_maintainer(db):
- maints = {}
- maint_ids = {}
- for pkg in db.keys():
- maint = None
- pkginfo = db[pkg]
- # start with the blends info
- if 'blends' in pkginfo and 'responsible' in pkginfo['blends']:
- maint = pkginfo['blends']['responsible']
- if not 'main' in db[pkg] and maint is None:
- # no info
- continue
- info = db[pkg]['main']
- if not 'maintainer' in info and maint is None:
- # no maintainer info
- continue
- if 'original_maintainer' in info and not info['original_maintainer'] is None:
- maint = info['original_maintainer']
- elif 'maintainer' in info and not info['maintainer'] is None:
- maint = info['maintainer']
- if maint is None:
- # no sane maintainer info
- continue
- # safeguard: <> confuses sphinx and we don't care about different emails
- maint = maint[:maint.find('<')].strip()
- # kick out non-ascii ones (should not be, but too tired to find the bug)
- try:
- codecs.ascii_decode(maint)
- except UnicodeEncodeError:
- continue
- if not maint.lower() in maints:
- maints[maint.lower()] = []
- maint_ids[maint.lower()] = [maint]
- else:
- maint_ids[maint.lower()].append(maint)
- maints[maint.lower()].append(pkg)
- # remove duplicates
- out = {}
- for m in maints:
- out[maint_ids[m][0]] = np.unique(maints[m])
- return out
-
-
-def sort_by_release(db):
- rels = {}
- for pkg in db.keys():
- pkginfo = db[pkg]
- for sec in pkginfo:
- if not isinstance(sec, tuple):
- # only releases are of interest
- continue
- relname = sec[0]
- if not relname in rels:
- rels[relname] = []
- else:
- rels[relname].append(pkg)
- # remove duplicates
- for r in rels:
- rels[r] = np.unique(rels[r])
- return rels
-
-
-def write_pkgpages(jinja_env, cfg, db, outdir, addenum_dir, extracts_dir):
- create_dir(outdir)
- create_dir(os.path.join(outdir, 'pkgs'))
- create_dir(os.path.join(outdir, 'pkglists'))
- # template for individual package listings
- toc_template = jinja_env.get_template('pkgs_toc.rst')
- # the high-level package list overview
- hltoc = codecs.open(os.path.join(outdir, 'pkgs.rst'), 'w', 'utf-8')
- hltoc.write('.. _pkglists:\n\n')
- hltoc.write(underline_text('Software packages', '='))
- defs = [(sort_by_tasks(db), 'By purpose', 'Packages for %s'),
- (sort_by_release(db), 'By release', 'Packages for %s'),
- (sort_by_maintainer(db), 'By maintainer', 'Packages by %s')]
- for def_ in defs:
- # TOC for each thingie
- pkgsdict, sectitle, title_tmpl = def_
- hltoc.write(underline_text(sectitle, '-'))
- ids = pkgsdict.keys()
- ids.sort()
- for id_ in ids:
- label = ('pkgs-%s-%s' % (sectitle, id_)).lower().replace(' ', '_').replace('/', '_')
- # filter out crap
- filtered_pkgs = [p for p in pkgsdict[id_] if p in db]
- if not len(filtered_pkgs):
- continue
- plist = toc_template.render(
- label=label,
- title=underline_text(title_tmpl % id_, '='),
- pkgs=filtered_pkgs,
- db=db)
- toc = codecs.open(os.path.join(outdir,
- 'pkglists',
- '%s.rst' % label),
- 'w', 'utf-8')
- toc.write(plist)
- toc.close()
- hltoc.write('* :ref:`%s`\n' % label)
- hltoc.write('\n\n')
-
-
- # now a complete list of all packages
- hltoc.write(underline_text('Complete list', '-'))
- toc = codecs.open(os.path.join(outdir, 'pkglists', 'pkgs-all.rst'),
- 'w', 'utf-8')
- toc.write(toc_template.render(label='full_pkg_list',
- title=underline_text('Complete package list', '='),
- pkgs=db.keys(), db=db))
- toc.close()
- hltoc.write('* :ref:`full_pkg_list`\n')
- hltoc.close()
-
- # 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, extracts_dir)
- # when no page is available skip this package
- if page is None:
- continue
- pf = codecs.open(os.path.join(outdir, 'pkgs', p + '.rst'), 'w', 'utf-8')
- pf.write(page)
- pf.close()
-
-
-def prepOptParser(op):
- # use module docstring for help output
- op.usage = "%s [OPTIONS]\n\n" % sys.argv[0] + __doc__
-
- op.add_option("--db",
- action="store", type="string", dest="db",
- default=None,
- help="Database file to read. Default: None")
-
- op.add_option("--cfg",
- action="store", type="string", dest="cfg",
- default=None,
- help="Repository config file.")
-
- op.add_option("-o", "--outdir",
- action="store", type="string", dest="outdir",
- default=None,
- help="Target directory for ReST output. Default: None")
-
- op.add_option("-r", "--release-url",
- action="append", dest="release_urls",
- help="None")
-
- 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")
- prepOptParser(op)
-
- (opts, args) = op.parse_args()
-
- if len(args) != 1:
- print('There needs to be exactly one command')
- sys.exit(1)
-
- cmd = args[0]
-
- if opts.cfg is None:
- print("'--cfg' option is mandatory.")
- sys.exit(1)
- if opts.db is None:
- print("'--db' option is mandatory.")
- sys.exit(1)
-
-
- cfg = SafeConfigParser()
- cfg.read(opts.cfg)
-
- if cmd == 'debug_ld':
- # load the db from file
- db = read_db(opts.db)
-
- for p in db.keys():
- #for p in ['dtitk', 'psychopy', 'psytoolkit', 'ginkgo-cadx', 'gridengine-master', 'cctools']:
- if not 'long_description' in db[p]['main']:
- continue
- ld = db[p]['main']['long_description']
-
- print ">>>>>>>>> ", p
- #print ld
- print "----"
- print convert_longdescr(ld)
- raise SystemExit
- # load existing db, unless renew is requested
- if cmd == 'updatedb':
- db = {}
- if cfg.has_option('packages', 'select taskfiles'):
- db = add_pkgfromtaskfile(db, cfg.get('packages',
- 'select taskfiles').split())
-
- # add additional package names from config file
- if cfg.has_option('packages', 'select names'):
- for p in cfg.get('packages', 'select names').split():
- if not db.has_key(p):
- db[p] = get_emptydbentry()
-
- # get info from task files
- if cfg.has_option('packages', 'prospective'):
- for url in cfg.get('packages', 'prospective').split():
- db = import_blendstask(cfg, db, url)
-
- # parse NeuroDebian repository
- if cfg.has_option('neurodebian', 'releases'):
- for rurl in cfg.get('neurodebian', 'releases').split():
- db = import_release(cfg, db, rurl)
-
- # collect package information from DDE
- db = import_dde(cfg, db)
- # get info from NITRC
- db = import_nitrc(cfg, db)
- # store the new DB
- store_db(db, opts.db)
- # and be done
- return
-
- # load the db from file
- db = read_db(opts.db)
-
- # fire up jinja
- 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, opts.extracts_dir)
-
- write_sourceslist(jinja_env, cfg, opts.outdir)
-
- write_mirmonlists(cfg, opts.outdir)
-
-if __name__ == "__main__":
- main()
+++ /dev/null
-
-.. _pkg_{{ pkg }}:
-
-
-{{ title }}
-
-{{ long_description }}
-
-External links:
-
-.. raw:: html
-
- <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>
- {%- endif -%}
- {% if db.blends %}{% for blend, name, url in db.blends.tasks -%}
- {%- if blend == 'debian-med' -%}
- <a href="{{ url }}#{{ pkg }}">
- <img border="0" src="../_static/debianmed.png" title="Part of Debian Med {{ name }} task" /></a>
- {%- endif -%}
- {%- if blend == 'debian-science' -%}
- <a href="{{ url }}#{{ pkg }}">
- <img border="0" src="../_static/debianscience.png" title="Part of Debian Science {{ name }} task" /></a>
- {%- endif -%}
- {%- endfor -%}
- {%- endif -%}
- </p>
-
-{% if db.main.publication %}
-Citable reference:
- *{{ db.main.publication.authors }}* ({{ db.main.publication.year }}).
- {%- if db.main.publication.url %} `{{ db.main.publication.title }} <{{ db.main.publication.url }}>`_.
- {%- else %} {{ db.main.publication.title }}.
- {%- endif %} {{ db.main.publication.in }}.
- {%- if db.main.publication.doi %} (`DOI <http://dx.doi.org/{{ db.main.publication.doi }}>`_)
- {%- endif %}
-{% endif %}
-
-{% if db.main.registration -%}
-.. note::
- The software authors ask users to
- `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
- db.main.recommends or db.main.suggests -%}
-Package Details
-===============
-
-{% if db.nitrc or db.main.debian_popcon or db.main.ubuntu_popcon %}
-Package popularity
-------------------
-{% if db.main.debian_popcon -%}
-- Debian [1]_: {{ db.main.debian_popcon.insts }} (`more info <http://qa.debian.org/popcon.php?package={{ db.main.sv.split()[0] }}>`__)
-{% endif -%}
-{% if db.main.ubuntu_popcon -%}
-- Ubuntu [1]_: {{ db.main.ubuntu_popcon.insts }} (`more info <http://popcon2.net/package/{{ db.main.sv.split()[0] }}.html#graph-1>`__)
-{% endif %}
-{% if db.nitrc and db.nitrc.downloads -%}
-- NITRC [2]_: {{ db.nitrc.downloads }}
-{% endif %}
-
-.. [1] Due to the nature of this data, the reported number can only be
- considered a conservative estimate of the lower bound of the true
- number of installations.
-
-.. [2] This is the total number of downloads from NITRC for this software,
- comprising all releases for all platforms -- typically not Debian
- packages.
-{% endif -%}
-{% endif -%}
-
-{% if db.main.recommends or db.main.suggests %}
-Related packages
-----------------
-{% if db.main.recommends %}
-{%- for pkg in db.main.recommends.split(',') %}
-{%- if pkg.split('|')[0].strip() in fulldb %}
-* :ref:`pkg_{{ pkg.strip() }}`
-{%- else %}
-* {{ pkg }}
-{% endif -%}{% endfor %}{% endif %}
-{%- if db.main.suggests %}
-{%- for pkg in db.main.suggests.split(',') %}
-{%- if pkg.split('|')[0].strip() in fulldb %}
-* :ref:`pkg_{{ pkg.strip() }}`
-{%- else %}
-* {{ pkg.strip() }}
-{% endif -%}{% endfor %}{% endif %}
-{% endif %}
-
-Binary packages
-===============
-
-NeuroDebian
------------
-
-{% for dist, distpkg in db|dictsort if dist[1].startswith('neurodebian') -%}
-{% if loop.first -%}
-The repository contains binary packages for the following distribution
-releases and system architectures. The corresponding source packages
-are available too.
-
-.. note::
-
- Do not download this package manually if you plan to use it
- regularly. Instead configure your package manager to use this
- repository by following the instructions on the :ref:`front page
- <repository_howto>`.
-{% endif %}
-{{ dist[0] }} [{{ distpkg.component}}]:
- `{{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 email
- neurodebian-users_ instead of the original
- maintainer)
-{% endif %}
-{% endif %}
-{% else %}
-*There are no packages in the NeuroDebian repository.*
-{% endfor %}
-
-
-Debian
-------
-
-{% for dist, distpkg in db|dictsort if dist[1].startswith('debian') %}
-{% if loop.first %}
-{% endif %}
-{{ dist[0] }} [{{ distpkg.component}}]:
- `{{distpkg.version}} <http://packages.debian.org/search?suite={{ distpkg.release}}&keywords={{ pkg }}>`__ [{{ ', '.join(distpkg.architecture) }}]
-
-{% if loop.last %}
-.. seealso::
-
- - Maintainer: {{ distpkg.maintainer }}
- - Bug reports: `Debian bugtracking system <http://bugs.debian.org/src:{{ distpkg.source }}>`__
-{% endif %}
-{% else %}
-*There are no official Debian packages available.*
-
-{% if db.main.debian_itp %}
-However, a Debian packaging effort has been officially announced.
-Please see the corresponding
-`intent-to-package bug report <http://bugs.debian.org/{{ db.main.debian_itp }}>`__
-for more information about its current status.
-{% endif %}
-{% endfor %}
-
-
-Ubuntu
-------
-
-{% for dist, distpkg in db|dictsort if dist[1].startswith('ubuntu') %}
-{% if loop.first %}
-{% endif %}
-{{ dist[0] }} [{{ distpkg.component }}]:
- `{{distpkg.version}} <http://packages.ubuntu.com/search?suite={{ distpkg.release }}&keywords={{ pkg }}>`__ [{{ ', '.join(distpkg.architecture) }}]
-
-{% if loop.last %}
-.. seealso::
-
- - Maintainer: {{ distpkg.maintainer }}
- - Bug reports: `Ubuntu Launchpad <https://bugs.launchpad.net/ubuntu/+source/{{ distpkg.source }}>`__
-{% endif %}
-{% else %}
-*There are no official Ubuntu packages available.*
-{% endfor %}
-
-{% if db.main.other_pkg and not "neuro.debian" in db.main.other_pkg -%}
-
-Other Debian/Ubuntu Packages
-----------------------------
-
-- {{ db.main.other_pkg }}
-
-{% endif %}
-
-
-.. include:: ../link_names.txt
+++ /dev/null
-.. _{{ label }}:
-
-{{ title }}
-
-{% for p in pkgs|sort %}
-* :ref:`{{ p }} <pkg_{{ p }}>` ({{ db[p].main.description }})
-{%- endfor %}
-
+++ /dev/null
-.. raw:: html
-
- <select id="release" name="release">
- <option value="">Select a release</option>
-{%- for id, relname in id2relname|dictsort(true, 'value') %}
- <option value="{{ id }}">{{ relname }}</option>
-{%- endfor %}
- </select>
- <select id="mirror" name="mirror">
-{%- for id, mirrorname in mirror2name|dictsort %}
-{%- if id == 'us-nh' %}
- <option selected value="{{ id }}">{{ mirrorname }}</option>
-{%- else %}
- <option value="{{ id }}">{{ mirrorname }}</option>
-{%- endif %}
-{%- endfor %}
- </select>
-
- <div class="highlight-python" id="reposetup">
- <pre id="code">
- After selecting a release the setup code will be shown here.
- </pre>
- </div>
- <script>
- <!--
-
- var rel2name = {
-{%- for id, codename in id2codename|dictsort %}
- "{{ id }}" : "{{ codename }}",
-{%- endfor %}
- };
-
- var mirrors = {
-{%- for id, url in mirror2url|dictsort %}
- "{{ id }}" : "{{ url }}",
-{%- endfor %}
- };
-
- function createrepourl(rel, mir) {
- if(rel in rel2name && mir in mirrors) {
-
- var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel2name[rel] + "."
- + mir + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
- + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
- return retrepo;
- }
-
- };
- function updateout(rel, mir) {
- $('#code').text(createrepourl(rel, mir));
- };
- $('#release').change(function() {
- var singleValues = $("#release").val();
- var mirrorVal = $("#mirror").val();
- updateout(singleValues, mirrorVal);
- });
- $('#mirror').change(function() {
- var singleValues = $("#release").val();
- var mirrorVal = $("#mirror").val();
- updateout(singleValues, mirrorVal);
- });
-
- //-->
- </script>
-
--- /dev/null
+.package-info-links {
+ float: right;
+ margin-left: 1em;
+ padding-left: 1em;
+ border-left: 1px solid #ccc;
+}
+
+.package-info-links dd {
+ margin-left: 0px;
+}
+
+.package-info-links dd {
+ margin-left: 0px;
+}
+
+.package-info-links ul {
+ margin-left: 0;
+ padding-left: 0;
+ list-style-type: none;
+}
+
+.package-info-links a {
+ display: block;
+ padding: 3px;
+}
+
+.pkg-install-link,
+.pkg-bugreport-link{
+ width: 100%;
+ text-align: center;
+ display: inline;
+}
+
+.pkg-install-link a,
+.pkg-bugreport-link a {
+ color: #444;
+ font-weight: bold;
+ padding: 0.5em;
+}
+
+.pkg-bugreport-link a {
+ background-color: #ffe7e7;
+ border-top: 1px solid #d70751;
+ border-bottom: 1px solid #d70751;
+}
+
+.pkg-install-link a {
+ background-color: #e7e7ff;
+ border-top: 1px solid #20435C;
+ border-bottom: 1px solid #20435C;
+}
+
+.pkg-install-link a:hover {
+ background-color: #20435C;
+}
+
+.pkg-bugreport-link a:hover {
+ background-color: #d70751;
+}
+
+.pkg-install-link a:hover,
+.pkg-bugreport-link a:hover {
+ text-decoration: none;
+ color: white;
+}
+
+.license-reminder {
+ color: #d70751;
+ font-weight: bold;
+}
+
+.package-availability {
+ padding-top: 2em;
+}
+
+.package-availability caption {
+ font-style: italic;
+ text-align: left;
+ margin-bottom: .5em;
+}
* Sphinx Doc Design
*/
+@import "bigmess.css";
+
body {
font-family: sans-serif;
font-size: 100%;
- background-color: #444;
+ background-color: #fff;
color: #000;
margin: 0;
padding: 0;
/* :::: LAYOUT :::: */
div.document {
- background-color: #afafaf;
+ background-color: #fff;
}
div.documentwrapper {
div.body {
background-color: white;
+ background-image: url(hotbrain_bg.jpg);
+ background-repeat:no-repeat;
+ background-position:100% 100%;
+ background-attachment:fixed;
padding: 0 20px 30px 20px;
}
list-style-image:url(neurodebian_bullet.png);
}
+iframe.twitter-timeline {
+ border-bottom: 1px dotted #aaa;
+ margin-left: 1%;
+ width: 99%;
+}
+
div.tweet {
border-bottom: 1px dotted #aaa;
margin-left: 2em;
}
div.footer {
- color: #fff;
+ color: #000;
width: 100%;
padding: 9px 0 9px 0;
text-align: center;
font-size: 75%;
}
-div.footer a {
- color: #fff;
- text-decoration: underline;
-}
-
div.related {
background-color: #2c3c3d;
- color: #fff;
+ color: #888;
width: 100%;
line-height: 30px;
font-size: 90%;
+ float: right;
}
div.related h3 {
}
div.related a {
- color: white;
+ color: #fff;
}
/* ::: TOC :::: */
text-align: left;
}
+ul.simple {
+ margin-bottom: 1em;
+}
+
ul.keywordmatches li.goodmatch a {
font-weight: bold;
}
div.body h5,
div.body h6 {
font-family: 'Trebuchet MS', sans-serif;
- background-color: #f2f2f2;
+ background-color: rgba(242, 242, 242, 0.5);
font-weight: normal;
color: #20435c;
border-bottom: 1px solid #ccc;
padding: 3px 0 3px 10px;
}
-div.body h1 { margin-top: 0; font-size: 200%; }
+div.body h1 { margin-top: 0em; font-size: 180%; padding-top: 1em;}
div.body h2 { font-size: 160%; }
div.body h3 { font-size: 140%; }
div.body h4 { font-size: 120%; }
}
div.note {
- background-color: #eaf2f9;
+ background-color: rgba(234, 242, 249, 0.6);
border: 1px solid #3d7aa5;
border-left: none;
border-right: none;
color: #060;
}
+dt {
+ font-weight: bold;
+ margin-top: 1em;
+}
+
dt:target,
.highlight {
background-color: #fbe54e;
pre {
padding: 5px;
- background-color: #efc;
+ background-color: rgba(238, 255, 204, 0.6);
color: #333;
border: 1px solid #ac9;
border-left: none;
text-align: left;
}
+.button {
+ background-color: transparent;
+ font-weight: normal;
+ color: #20435c;
+ border: 1px solid #ccc;
+ padding: 3px;
+ text-align: center;
+ cursor: pointer;
+}
+
+div.buttonbar {
+ background-color: #fff;
+ font-size: 70%;
+}
+
+div.buttonbar a:hover {
+ text-decoration: none;
+}
+
+div.buttonbar a:hover img {
+ background-color: #ffc7da;
+}
+
+div.buttonbar ul {
+ list-style: none;
+ padding: 0px;
+}
+
+div.buttonbar li {
+ display: inline;
+ margin: 5px;
+ text-align: center;
+}
+
+div.buttonbar.leftbar li {
+ float: left;
+}
+
+div.buttonbar.rightbar li {
+ float: right;
+}
+
+div#randomquote {
+}
+
+div#randomquote blockquote.epigraph {
+ padding: 0 2em 2em 2em;
+ background-color: transparent;
+ font-style: italic;
+ font-size: 80%;
+ border: 0px
+}
+
+#troubleshooting dt,
+div#frequently-asked-questions dt {
+ font-weight: bold;
+ margin-top: 1em;
+ margin-left: 1em;
+ cursor: pointer;
+ display: list-item;
+ list-style-image:url(neurodebian_bullet.png);
+}
+div#frequently-asked-questions dt:after {
+ content: "\203A\203A";
+ padding-left: .25em;
+}
+
+div#sitemap ul {
+ float: left;
+ list-style: none;
+}
+.linkmore {
+ margin-top: -2em;
+ float: right;
+ font-size: 70%;
+}
+
+.nojavascriptinstructions {
+ font-size: 70%;
+}
+
+.expandinstructions {
+ font-size: 70%;
+ display: none;
+}
+
+.linkmore:before,
+.nojavascriptinstructions:before,
+.expandinstructions:before {
+ content: "["
+}
+
+.linkmore:after,
+.nojavascriptinstructions:after,
+.expandinstructions:after {
+ content: "]"
+}
+
+
+.highlighted {
+ background-color: yellow;
+}
+
+#searchbox p {
+ display: inline;
+}
+
+.inlineimage {
+ vertical-align: baseline;
+}
+
+a img.inlineimage:hover {
+ background-color: #820430;
+}
--- /dev/null
+var colors_debian = d3.scale.linear()
+ .domain([1.43, 1.58]).range(["white", "#dd1155"])
+var colors_ubuntu = d3.scale.linear()
+ .domain([1.43, 1.58]).range(["white", "#dd4814"])
+
+keyColor = function(d, i) {
+ var version = parseFloat(d.key.substr(0, 4))
+ if (d.key.indexOf("ubuntu") > 0)
+ return colors_ubuntu(version)
+ else
+ return colors_debian(version);
+}
+
+d3.json('/_files/nd_popconstats.json', function(data) {
+ nv.addGraph(function() {
+ chart = nv.models.stackedAreaChart()
+ .x(function(d) { return d[0] })
+ .y(function(d) { return d[1] })
+ .color(keyColor)
+ .clipEdge(true);
+
+ chart.stacked.style('stacked');
+
+ chart.xAxis
+ .tickFormat(function(d) {
+ return d3.time.format('%d %b %Y')(new Date(d)) });
+
+ chart.yAxis
+ .tickFormat(d3.format(',d'));
+
+ d3.select('#popconchart')
+ .datum(data)
+ .transition().duration(500).call(chart);
+
+ nv.utils.windowResize(chart.update);
+
+ return chart;
+ });
+})
--- /dev/null
+d3.json('/_files/nd_subscriptionstats.json', function(data) {
+
+ // yoh: can't find a sane way to use ordinal scale here
+ // so let's create linear scale for indices within known releases
+
+ // collect debian and ubuntu releases we are dealing with to create
+ // proper color scales
+ // Will be Ubuntu for true
+ var releases = {false:[], true:[]}
+
+ data.forEach(function(d, i) {
+ releases[d.key.indexOf("Ubuntu") > -1].push(d.key)
+ })
+
+ var colors = {false: d3.scale.linear()
+ .domain([0, releases[false].length]).range(["white", "#dd1155"]),
+ true: d3.scale.linear()
+ .domain([0, releases[true].length]).range(["white", "#dd4814"])}
+
+ releaseKeyColor = function(d, i) {
+ var isubuntu = d.key.indexOf("Ubuntu") > -1
+ return colors[isubuntu](releases[isubuntu].indexOf(d.key)+1)
+ }
+
+ nv.addGraph(function() {
+ chart = nv.models.stackedAreaChart()
+ .x(function(d) { return d[0] })
+ .y(function(d) { return d[1] })
+ .color(releaseKeyColor)
+ .clipEdge(true);
+
+ chart.stacked.style('stacked');
+
+ chart.xAxis
+ .tickFormat(function(d) {
+ return d3.time.format('%d %b %Y')(new Date(d)) });
+
+ chart.yAxis
+ .tickFormat(d3.format(',.2f'));
+
+ d3.select('#subscriptionchart')
+ .datum(data)
+ .transition().duration(500).call(chart);
+
+ nv.utils.windowResize(chart.update);
+
+ return chart;
+ });
+})
{% block extrahead %}
<meta name="keywords" content="debian, neuroscience">
+ <script language="javascript" type="text/javascript"
+ src="/javascript/jquery-mousewheel/jquery.mousewheel.min.js"></script>
+ <script language="javascript" type="text/javascript"
+ src="/javascript/jquery-easing/jquery.easing.min.js"></script>
+ <script language="javascript" type="text/javascript"
+ src="/javascript/jquery-fancybox/jquery.fancybox.min.js"></script>
+ <link rel="stylesheet" href="/javascript/jquery-fancybox/jquery.fancybox.css"
+ type="text/css" media="screen" />
{% endblock %}
-{% block rootrellink %}
- <li><a href="http://www.debian.org" target="_blank">Debian</a> || </li>
- <li><a href="{{ pathto('index') }}">Neuroscience</a> : </li>
- <li><a href="{{ pathto('pkgs') }}">Software</a> | </li>
- <li><a href="{{ pathto('pkglists/pkgs-by_release-datasets_(data)') }}">Datasets</a> | </li>
- <li><a href="{{ pathto('vm') }}">Virtual Machine</a> | </li>
- <li><a href="{{ pathto('faq') }}">FAQ</a> | </li>
- <li><a href="{{ pathto('testimonials') }}">Testimonials</a> </li>
-{% endblock %}
+{% block header %}
+ <div class="buttonbar leftbar">
+ <ul>
+ <li><a href="http://www.debian.org" target="_blank"><img border="0" src="/_static/debian.png" title="Visit debian.org" /><br />Debian</a></li>
+ <li><a href="{{ pathto('index') }}"><img border="0" src="/_static/neurodebian.png" title="Go to the home page" /><br />Home</a></li>
+ <li><a href="{{ pathto('pkgs') }}"><img border="0" src="/_static/package.png" title="List of available software" /><br />Software</a></li>
+ <li><a href="{{ pathto('pkglists/toc_pkgs_for_release_data') }}"><img border="0" src="/_static/datasets.png" title="List of available datasets" /><br />Data</a></li>
+ <li><a href="{{ pathto('vm') }}"><img border="0" src="/_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /><br />VM</a></li>
+ <li><a href="{{ pathto('projects') }}"><img border="0" src="/_static/workarea.png" title="Current and planned projects: Get involved!" /><br />Contribute</a></li>
+ <li><a href="{{ pathto('derivatives') }}"><img border="0" src="/_static/derivatives.png" title="Projects that use NeuroDebian as a foundation" /><br />Derived</a></li>
+ <li><a href="/blog/index.html"><img border="0" src="/_static/rssfeeds.png" title="Read news, and how-to's in the NeuroDebian Insider Blog. Subscribe!" /><br />Blog</a></li>
+ <li><a href="{{ pathto('faq') }}"><img border="0" src="/_static/faq.png" title="Frequently asked questions" /><br />FAQ</a></li>
+ </ul>
+ </div>
-{% block relbaritems %}
-<li class="right"><a href="#disqus_thread">Comments</a> |</li>
+ <div class="buttonbar rightbar">
+ <ul>
+ <li><a href="http://www.ipsy.ovgu.de/psychoinformatics.html" target="_blank"><img border="0" src="/_static/uni-md-logo_h50.png" title="Psychoinformatics lab, University of Magdeburg, Germany" height="50" /></a></li>
+ <li><img border="0" src="/_static/ccn-logo_h50.png" title="Center for Cognitive Neuroscience, Dartmouth College, USA" height="50" /></li>
+ <li><a href="http://www.dartmouth.edu" target="_blank"><img border="0" src="/_static/dartmouth-logo_h50.png" title="Dartmouth College, USA" height="50" /></a></li>
+ </ul>
+ </div>
{% endblock %}
-{% block sidebar1 %}{% endblock %}
-
-{% block sidebar2 %}
-{{ sidebar() }}
-{% endblock %}
+{% block rootrellink %}{% endblock %}
+{% block relbaritems %}
+<li class="right"><a href="#disqus_thread">Comments</a> |</li>
{% 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
-src="{{ pathto('_static/nitrc_listed.png', 1) }}" border="0" alt="NITRC-listed" /></a></p>
+{% endblock %}
+<li class="right" style="position:relative;top:3px"><div class="g-plusone"></div></li>
+<li class="right" style="position:relative;top:1px"><a href="https://twitter.com/share" class="twitter-share-button" data-size="large" data-hashtags="neurodebian" data-dnt="true"></a></li?
{% endblock %}
+{% block sidebar1 %}{% endblock %}
+{% block sidebar2 %}{% endblock %}
{% block footer %}
+<div class="clearer"></div>
{{ super() }}
-<div class="footer">
+<div class="footer" style="padding-top:0px">
The source code for this portal is licensed under the
<a href="http://www.gnu.org/licenses/gpl-3.0.html"
title="Text of the GPL-3 license">GPL-3</a> and is available on
title="Browse or clone the Git repository">
git.debian.org</a>.
</div>
+<!-- G+ button logic -->
+<script type="text/javascript" src="https://apis.google.com/js/plusone.js">
+ {parsetags: 'explicit'}
+</script>
+<script type="text/javascript">gapi.plusone.go();</script>
+<!-- Twitter -->
+<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
+<!-- trigger convenience setup with javascript enabled -->
+<script type="text/javascript">
+ $('.foldup dt').click(function(e){
+ Â Â Â $(this).nextUntil('dt').toggle();
+ });
+ $('.foldup dd').hide();
+ $('.expandinstructions').show();
+ $('.nojavascriptinstructions').hide();
+</script>
+<!-- turn all [youtube] links into buttons and open them in fancy player-->
+<script type="text/javascript">
+$(document).ready(function(){
+ $('a[href^="http://www.youtube.com/watch"]').click(function() {
+ $.fancybox({
+ 'title': this.title,
+ 'href': this.href.replace(new RegExp("watch\\?v=", "i"), 'v/'),
+ 'type': 'swf',
+ 'swf': {'wmode': 'transparent', 'allowfullscreen': 'true'}
+ });
+ return false;
+ });
+ $('a[href^="http://www.youtube.com/watch"]').each(function() {
+ var content = $(this).html();
+ if (content.charAt(0) == '[' && content.charAt(content.length-1) == ']') {
+ $(this).html('<img class="inlineimage" src="/_static/video_button.png" alt="video link button" title="' + content + '" />');
+ } else {
+ return content;
+ };
+ });
+});
+</script>
{% endblock %}
<!-- HEADNOTES -->
{{ super() }}
-
<h2>Comments</h2>
<div id="disqus_thread"></div>
<script type="text/javascript">
(document.getElementsByTagName('HEAD')[0] || document.getElementsByTagName('BODY')[0]).appendChild(s);
}());
</script>
+
{% endblock %}
--- /dev/null
+{%- if pagename != "search" %}
+<li id="searchbox">
+ <form class="search" style="display:inline" action="{{ pathto('search') }}" method="get">
+ <input type="search" size="15" maxlength="1000" value="search for..." name="q" onfocus="this.value=''" />
+ <input type="submit" value="{{ _('Go') }}" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</li>
+{%- endif %}
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _chap_about:
+
+*****************
+About NeuroDebian
+*****************
+
+.. _chap_contacts:
+
+Contacts
+========
+
+`Email us directly <team@neuro.debian.net>`_ with any "private"
+communication. Otherwise please use our public mailing lists, which
+exist not only to provide user-support but also to establish
+communication channels within the NeuroDebian community
+
+.. _chap_mailinglists:
+
+* neurodebian-users_: Discussions and support of NeuroDebian users
+
+* neurodebian-upstream_: General discussions and knowledge sharing
+ among developers of neuroscience software. We also use it
+ to update you with summaries of recent relevant developments in
+ Debian project
+
+* neurodebian-devel_: Technical mailing list for discussions on
+ NeuroDebian development
+
+You are welcome also to join #neurodebian IRC room on OFTC network if
+you have quick questions or want to join a live discussion.
+
+.. _chap_team:
+
+The team
+========
+
+`Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
+<http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
+`Experimental Psychology Debian packaging project
+<http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
+leaders. However, the whole project would not be possible without the work of
+over 3,000 Debian_ developers and contributors who are as enthusiastically
+building the Debian operating system.
+A number of packages that are available from the NeuroDebian repository have
+been contributed by various individuals and other teams in Debian, such as
+`Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
+maintainers_ that help to make Debian_ the ultimate software platform for
+neuroscience.
+
+.. _maintainers: pkgs.html#by-maintainer
+.. include:: link_names.txt
-2010
-====
+Blog posts in 2010
+==================
.. toctree::
:maxdepth: 1
-2011
-====
+Blog posts in 2011
+==================
.. toctree::
:maxdepth: 1
-2012
-====
+Blog posts in 2012
+==================
.. toctree::
:maxdepth: 1
--- /dev/null
+:date: 2013-06-03 14:00:00
+:tags: debian, neuroscience, software, matlab, multiarch
+
+.. _chap_matlab_64bit_on_32bit:
+
+
+Running 64bit Matlab on 32bit host OS
+=====================================
+
+Some of you have experienced problems due the recent move of Mathworks to
+drop 32-bit Linux builds of their products (i.e. Matlab R2013a and
+co.). Please note that this is not the first time Mathworks values its own
+costs higher than the benefits of a few scientists. In 1998 PowerPC builds
+for Macs were abandoned, causing a `furious reaction
+<http://www.mathworks.com/matlabcentral/newsreader/view_thread/5910>`__
+of the community.
+
+Luckily, users of the fresh Debian stable release *wheezy* (or more recent
+variants of Debian and its derivatives) who still need a 32bit OS on
+64bit-capable hardware can take advantage of the new `multiarch
+<http://wiki.debian.org/Multiarch>`_ support. Multiarch allows for
+multiple architecturesi to co-exist on a hardware/kernel
+that is capable of supporting both (e.g. i386 and amd64).
+
+Below we describe how you can use multiarch support and in few simple steps
+that prepare your existing 32bit user-land for running 64bit Matlab.
+
+
+Procedure
+---------
+
+- [2-10 min] Install 64-bit kernel and reboot::
+
+ sudo apt-get install linux-image-amd64
+
+- [1-3 min] Enable multi-arch support for amd64 architecture::
+
+ sudo dpkg --add-architecture amd64
+ sudo apt-get update
+
+- [1-5 min] Install 64bit libraries (and compilers) needed for matlab::
+
+ sudo apt-get install libstdc++6:amd64 zlib1g:amd64 libncurses5:amd64 \
+ libxp6:amd64 libstdc++6-4.4-dev:amd64 libxt6:amd64 libxmu6:amd64 libxtst6:amd64 \
+ g++:amd64 gcc:amd64 binutils:amd64
+
+Now your 64bit matlab (which you hopefully "registered" with
+:ref:`matlab-support <binary_pkg_matlab-support>`) is ready to run.
+
+If you have any comments (typos, improvements, etc) -- feel welcome to
+leave a comment below, or `contact us`_ .
+
+.. _contact us: http://neuro.debian.net/#contacts
--- /dev/null
+Blog posts in 2013
+==================
+
+.. toctree::
+ :maxdepth: 1
+ :glob:
+
+ 2013*
+
:maxdepth: 2
:glob:
+ 2013/index
2012/index
2011/index
2010/index
Coffee Art
**********
+2013-03-08 09:37:13
+-------------------
+
+.. figure:: /pics/coffeeart/20130308_093713.jpg
+
+2013-02-22 10:01:26
+-------------------
+
+.. figure:: /pics/coffeeart/20130222_100126.jpg
+
+2013-02-21 12:54:10
+-------------------
+
+.. figure:: /pics/coffeeart/20130221_125410.jpg
+
+2012-12-03 08:35:05
+-------------------
+
+.. figure:: /pics/coffeeart/20121203_083505.jpg
+
+2012-11-08 16:03:36
+-------------------
+
+.. figure:: /pics/coffeeart/20121108_160336.jpg
+
+2012-11-01 08:58:25
+-------------------
+
+.. figure:: /pics/coffeeart/20121101_085825.jpg
+
+2012-03-01 14:00:37
+-------------------
+
+.. figure:: /pics/coffeeart/20120301_140037.jpg
+
+2012-02-06 09:21:40
+-------------------
+
+.. figure:: /pics/coffeeart/20120206_092140.jpg
+
+
2011-12-30 12:28:37
-------------------
.. figure:: /pics/coffeeart/IMG_6647.JPG
+.. raw:: html
+
+ <script type="text/javascript">
+ $(document).ready(function(){
+ $('.figure img').each(function() {
+ $(this).wrap('<a class="figurelink" href="' + $(this).attr('src') + '" rel="coffee"></a>');
+ });
+ $('a.figurelink').fancybox();
+ });
+ </script>
# General information about the project.
project = u'Debian Neuroscience Package Repository'
-copyright = u'2009-2011, NeuroDebian Team'
+copyright = u'2009-2013, NeuroDebian Team <team@neuro.debian.net>'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# The full version, including alpha/beta/rc tags.
release = ''
+# Monkey patch "English" language regular expression so we could
+# search for package names as well
+import re
+word_re = re.compile(r'[-.\w]+(?u)')
+
+import sphinx.search
+# older versions (before 1.1.3, 1.0.7 for sure) had no language
+# customizations
+if hasattr(sphinx.search, 'word_re'):
+ sphinx.search.word_re = word_re
+else:
+ from sphinx.search.en import SearchEnglish
+ SearchEnglish._word_re = word_re
+
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
language = 'en'
# given in html_static_path.
html_style = 'neurodebian.css'
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {'nosidebar': True}
+
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
html_title = project
.. replace with icons eventually
-`Live CD/USB Media`_ | `Virtual Appliances`_ | `Cloud Solutions`_
+`Hybrid Live Media`_ | `Live CD/USB Media`_ | `Virtual Appliances`_ | `Cloud Solutions`_
NeuroDebian_ is not a *Linux distribution* in a traditional sense because we
are working within Debian_ project thus not providing our custom installer
These projects are not maintained by NeuroDebian_ team. Please direct all
you support inquiries to respective authors/maintainers.
+
+Hybrid Live Media
+=================
+
+NEST Live Media
+---------------
+
++---------------------------+----------------------------------------------------------------+
+|**Author** | Yury V. Zaytsev <zaytsev@fz-juelich.de> |
++---------------------------+----------------------------------------------------------------+
+|**Homepage** | http://www.nest-initiative.org/index.php/Software:Download |
++---------------------------+----------------------------------------------------------------+
+|**Purpose** | Demonstration live media for conferences and students |
++---------------------------+----------------------------------------------------------------+
+|**Features** | - Based on Ubuntu 12.04 LTS (i386 only) |
+| | - ISO for DVDs and sticks, OVA for VirtualBox |
++---------------------------+----------------------------------------------------------------+
+|**Pre-installed Software** | NeuroDebian |
+| | PyNN, Brian |
+| | Custom: |
+| | NEST, NEURON |
++---------------------------+----------------------------------------------------------------+
+|**Download** | http://www.nest-initiative.org/download/gplreleases/ [~1.5G] |
++---------------------------+----------------------------------------------------------------+
+|**References** | https://github.com/nest/livecd-scripts |
++---------------------------+----------------------------------------------------------------+
+
Live CD/USB Media
=================
| | - Based on Ubuntu_ 11.04 |
+---------------------------+-------------------------------------------------------+
|**Pre-installed Software** | NeuroDebian |
-| | XPPAUT_ 6.11b, python-brian_ |
+| | XPPAUT_ 6.11b, python-brian_ |
| | Custom: |
| | Genesis_ 2.3, Neuron_ 7.2, XPPAUT_ 6.10 |
+---------------------------+-------------------------------------------------------+
+---------------------------+-------------------------------------------------------+
|**Purpose** | XNAT_ deployment |
+---------------------------+-------------------------------------------------------+
-|**Features** | - XNAT_ 1.5 |
+|**Features** | - XNAT_ 1.5 |
| | - 64-bit only |
| | - Based on NeuroDebian VM appliance |
+---------------------------+-------------------------------------------------------+
NeuroCloud
----------
-http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/I016856/1
+http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=EP/I016856/1
+
+NITRC Computational Environment
+-------------------------------
+
+`NITRC-CE @ Amazon Marketplace <https://aws.amazon.com/marketplace/pp/B00AW0MBLO/ref=srh_res_product_title?ie=UTF8&sr=0-2&qid=1358898165456>`_
.. * INCF Cloud App?
-.. * NITRC?
.. include:: link_names.txt
Frequently Asked Questions
**************************
-Why NeuroDebian?
-----------------
-
- In the course of our own research endeavors |we| have joined forces to
- develop `PyMVPA -- a Python framework for multivariate pattern analysis of
- neural data <http://www.pymvpa.org>`_. To conveniently deploy PyMVPA for
- anyone using Debian-derived distributions this package repository was created
- initially. Besides the PyMVPA_ project |we| collaborate with the `NiPy team
- <http://neuroimaging.scipy.org>`_ on various projects, such as NiBabel_ and
- NiPype_. Quickly NeuroDebian_ became the ultimate integrated environment for
- all these projects -- and we are constantly working on enriching this
- environment with as many additional relevant software as possible.
-
-
-Why is NeuroDebian not a Pure Blend?
-------------------------------------
-
- Because there is no need for it to become one, as the existing Debian Pure
- Blends already offer the desired functionality *within* Debian. Similar to
- Pure Blends, NeuroDebian's goal is to provide software for neuroscientists
- using the Debian operating system, and therefore the ultimate goal is to get
- all relevant software **into Debian**.
+.. raw:: html
- However, various reasons exist that prevent a particular software from
- entering Debian. Some are temporary, i.e. a package is already useable, but
- some technical bits do not meet Debian's standards (yet) or a licensing issue
- needs to be resolved first. For some software the licensing is so restrictive
- that it cannot be distributed by Debian, and hence cannot even go into its
- *non-free* branch. Unfortunately, sometimes these issues cannot be solved to
- a degree that is acceptable for Debian. For some other packages Debian itself
- is not ready yet, e.g. huge data packages with neuroscience data (:ref:`with
- sometimes over 1GB <pkg_fsl-first-data>`).
-
- NeuroDebian aims to be a platform that provides a staging area for
- neuroscience software packages on their way into Debian. All packages are
- properly registered in the relevant `Debian Pure Blends`_, e.g.
- `Debian Science Cognitive Neuroscience`_ or `Debian Med Imaging`_. Inside
- Debian these efforts already provide a suitable framework for this purpose,
- and hence there is no need to establish yet another one.
-
-.. _Debian Pure Blends: http://wiki.debian.org/DebianPureBlends
-.. _Debian Science Cognitive Neuroscience: http://blends.alioth.debian.org/science/tasks/neuroscience-cognitive
-.. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
+ <div class="expandinstructions">Click on an item to expand it</div>
+
+.. container:: foldup
+ Why NeuroDebian?
+ In the course of our own research endeavors |we| have joined forces to
+ develop `PyMVPA -- a Python framework for multivariate pattern analysis of
+ neural data <http://www.pymvpa.org>`_. To conveniently deploy PyMVPA for
+ anyone using Debian-derived distributions this package repository was created
+ initially. Besides the PyMVPA_ project |we| collaborate with the `NiPy team
+ <http://neuroimaging.scipy.org>`_ on various projects, such as NiBabel_ and
+ NiPype_. Quickly NeuroDebian_ became the ultimate integrated environment for
+ all these projects -- and we are constantly working on enriching this
+ environment with as many additional relevant software as possible.
-I want to help. How do I get involved?
---------------------------------------
- We always need people to help maintaining existing packages. 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!
+ Debian, Debian, Debian -- What about Ubuntu?
+ NeuroDebian offers backported binary packages for recent Ubuntu releases
+ whenever possible. However, since Ubuntu (like many other derivatives) uses
+ Debian as its foundation, it is more efficient to spend time maintaining
+ packages in Debian, instead of having to directly contribute to countless
+ child-distributions. After the appearance of new packages in Debian, Ubuntu
+ typically synchronizes them quickly and they become available in the *Ubuntu
+ universe* -- a repository of Debian packages rebuilt for a particular Ubuntu
+ release. We are not constantly rebuilding of all available NeuroDebian
+ packages for new Ubuntu releases. Therefore, you might find some packages
+ temporarily being available for older Ubuntu releases only -- until the point
+ when a new package version is made and gets built for all currently supported
+ releases.
+
+
+ How do I get a new neuroscience-related FOSS into (Neuro)Debian?
+ The goal of NeuroDebian is to package neuroscience software for Debian. Hence
+ getting software into NeuroDebian means trying to get it into Debian. There are
+ at least two possibilities to achieve that:
+
+ * You can approach packaging it yourself. Start by filing an ITP_ (Intent to
+ Package) bugreport and, if you are not a Debian developer, `ask us
+ <team@neuro.debian.net>`_ to mentor your upload to Debian_.
+
+ * `Contact us <team@neuro.debian.net>`_ and we'll do the work for you, but
+ then it might take a little longer, depending on our current workload and
+ interest in a particular software.
-When does a package migrate from NeuroDebian into Debian proper?
-----------------------------------------------------------------
+ I have heard that some packages are non-free. Will you charge me for them?
+ No. The term :term:`non-free` refers to an archive section. NeuroDebian uses
+ 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
+ context you like. Regardless of the actual license or archive section, all
+ packages in NeuroDebian are provided free of charge and under the licensing
+ terms of the original developers.
- In short: When it is ready. The longer answer is that there is nothing
- special to packages in NeuroDebian in comparison to packages conducted
- elsewhere. Packaging efforts are announced to Debian via ITPs_ and the
- packaging itself is available in some version control system -- typically in
- the Git repositories of the `pkg-exppsy group on Debian's Alioth server`_, or
- another VCS, or on http://mentors.debian.net.
- The only difference is that a particular package becomes available through the
- NeuroDebian repository before it has passed all checks for compliance with
- Debian's standards. But even after a package becomes part of Debian the
- NeuroDebian repository continues to provide binary packages of new versions
- for a certain set of Debian and Ubuntu releases (aka backports).
+ When does a package migrate from NeuroDebian into Debian proper?
+ In short: When it is ready. The longer answer is that there is nothing
+ special to packages in NeuroDebian in comparison to packages conducted
+ elsewhere. Packaging efforts are announced to Debian via ITPs_ and the
+ packaging itself is available in some version control system -- typically in
+ the Git repositories of the `pkg-exppsy group on Debian's Alioth server`_, or
+ another VCS, or on http://mentors.debian.net.
-.. _ITPs: http://www.debian.org/devel/wnpp
-.. _pkg-exppsy group on Debian's Alioth server: http://alioth.debian.org/projects/pkg-exppsy/
+ The only difference is that a particular package becomes available through the
+ NeuroDebian repository before it has passed all checks for compliance with
+ Debian's standards. But even after a package becomes part of Debian, the
+ NeuroDebian repository continues to provide binary packages of new versions
+ for a recent set of Debian and Ubuntu releases (aka backports).
+ .. _pkg-exppsy group on Debian's Alioth server: http://alioth.debian.org/projects/pkg-exppsy/
-Debian, Debian, Debian -- What about Ubuntu?
---------------------------------------------
- NeuroDebian offers backported binary packages for recent Ubuntu releases
- whenever possible. However, since Ubuntu (like many other derivatives) uses
- Debian as its foundation, it is more efficient to spend time maintaining
- packages in Debian, instead of having to directly contribute to countless
- child-distributions. After the appearance of new packages in Debian, Ubuntu
- typically synchronizes them quickly and they become available in the *Ubuntu
- universe* -- a repository of Debian packages rebuilt for a particular Ubuntu
- release. We are not constantly rebuilding of all available NeuroDebian
- packages for new Ubuntu releases. Therefore, you might find some packages
- temporarily being available for older Ubuntu releases only -- until the point
- when a new package version is made and gets built for all currently supported
- releases.
+ How to create a mirror of the repository?
+ The NeuroDebian repository can be mirrored with rsync. If you are interested
+ in sponsoring storage space and bandwidth for another mirror, please
+ `contact us <team@neuro.debian.net>`_.
-How to create a mirror of the repository?
------------------------------------------
+ .. _sec_pkg_authentication:
- The NeuroDebian repository can be mirrored with rsync. If you are interested
- in sponsoring storage space and bandwidth for another mirror, please
- `contact us <team@neuro.debian.net>`_.
+ What means "The following signatures couldn't be verified..."?
+ When you start using this repository, you probably get warning messages
+ like this::
+ The following signatures couldn't be verified because
+ the public key is not available.
-How do I get a new neuroscience-related FOSS into (Neuro)Debian?
-----------------------------------------------------------------
+ Or you will be asked questions like this over and over::
-The goal of NeuroDebian is to package neuroscience software for Debian. Hence
-getting software into NeuroDebian means trying to get it into Debian. There are
-at least two possibilities to achieve that:
+ WARNING: The following packages cannot be authenticated!
+ ...
+ Install these packages without verification [y/N]?
-* You can approach packaging it yourself. Start by filing an ITP_ (Intent to
- package) bugreport) and `ask us <team@neuro.debian.net>`_ to mentor your
- upload to Debian_, if you are not a Debian developer.
+ This is because your APT installation initially does not know the GPG
+ key that is used to sign the release files of this repository. It is easy to
+ make APT happy again. The simplest way is to install the ``neurodebian-keyring``
+ package that is available from the NeuroDebian repository. Alternatively:
-* `Contact us <team@neuro.debian.net>`_ -- but then it might take a little
- longer, depending on our current workload and interest in a particular
- software.
+ 1. Get the key. Either download the `repository key from here
+ <_static/neuro.debian.net.asc>`_
+ or fetch it from http://wwwkeys.pgp.net (2649A5A9).
+
+ 2. Now feed the key into APT by invoking::
+
+ apt-key add #file#
+
+ Where `#file#` has to be replaced with the location of the key file you just
+ downloaded. You need to have superuser-privileges to do this (either do it
+ as root or use sudo).
-I have heard that some packages are non-free. Will you charge me for them?
---------------------------------------------------------------------------
+ Why is NeuroDebian not a Pure Blend?
+ This is in the works, but...
- No. The term :term:`non-free` refers to an archive section. NeuroDebian uses
- 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
- context you like. Regardless of the actual license or archive section, all
- packages in NeuroDebian are provided free of charge and under the licensing
- terms of the original developers.
+ There is no need for it to become one, as the existing Debian Pure Blends
+ already offer the desired functionality *within* Debian. Similar to Pure
+ Blends, NeuroDebian's goal is to provide software for neuroscientists using
+ the Debian operating system, and therefore the ultimate goal is to get all
+ relevant software **into Debian**.
-.. _sec_pkg_authentication:
+ However, various reasons exist that prevent a particular software from
+ entering Debian. Some are temporary, i.e. a package is already useable, but
+ some technical bits do not meet Debian's standards (yet) or a licensing issue
+ needs to be resolved first. For some software the licensing is so restrictive
+ that it cannot be distributed by Debian, and hence cannot even go into its
+ *non-free* branch. Unfortunately, sometimes these issues cannot be solved to
+ a degree that is acceptable for Debian. For some other packages Debian itself
+ is not ready yet, e.g. huge data packages with neuroscience data (:ref:`with
+ sometimes over 1GB <pkg_fsl-first-data>`).
-What means "The following signatures couldn't be verified..."?
---------------------------------------------------------------
+ NeuroDebian aims to be a platform that provides a staging area for
+ neuroscience software packages on their way into Debian. All packages are
+ properly registered in the relevant `Debian Pure Blends`_, e.g.
+ `Debian Science Cognitive Neuroscience`_ or `Debian Med Imaging`_. Inside
+ Debian these efforts already provide a suitable framework for this purpose,
+ and hence there is no need to establish yet another one.
-When you start using this repository, you probably get warning messages
-like this::
+ .. _Debian Pure Blends: http://wiki.debian.org/DebianPureBlends
+ .. _Debian Science Cognitive Neuroscience: http://blends.alioth.debian.org/science/tasks/neuroscience-cognitive
+ .. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
- The following signatures couldn't be verified because
- the public key is not available.
-Or you will be asked questions like this over and over::
+ I want to help. How do I get involved?
+ We always need people to help maintaining existing packages. 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.
- WARNING: The following packages cannot be authenticated!
- ...
- Install these packages without verification [y/N]?
+ If you found something you are interested in, please email the
+ neurodebian-devel_ mailing list and let us know about it. Thanks!
-This is because your APT installation initially does not know the GPG
-key that is used to sign the release files of this repository. It is easy to
-make APT happy again. The simplest way is to install the ``neurodebian-keyring``
-package that is available from the NeuroDebian repository. Alternatively:
-1. Get the key. Either download the `repository key from here
- <_static/neuro.debian.net.asc>`_
- or fetch it from http://wwwkeys.pgp.net (2649A5A9).
+ How can I cite NeuroDebian?
+ Please cite the following paper:
-2. Now feed the key into APT by invoking::
-
- apt-key add #file#
-
- Where `#file#` has to be replaced with the location of the key file you just
- downloaded. You need to have superuser-privileges to do this (either do it
- as root or use sudo).
-
-
-How can I cite NeuroDebian?
----------------------------
-
-Please cite the following paper:
-
- Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
- next step: An integrated, community-driven computing platform for neuroscience
- <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
- *Frontiers in Neuroinformatics*, 6:22.
+ Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
+ next step: An integrated, community-driven computing platform for neuroscience
+ <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
+ *Frontiers in Neuroinformatics*, 6:22.
.. include:: link_names.txt
.. _WELCOme:
-***************************************************
- Welcome to the Ultimate Platform for Neuroscience
-***************************************************
+*********************************************
+ The Ultimate Neuroscience Software Platform
+*********************************************
-.. quotes::
- :random: 1
+NeuroDebian provides a large collection of popular neuroscience research
+software for the Debian_ operating system as well as Ubuntu_ and other
+derivatives. Popular packages include :ref:`AFNI <binary_pkg_afni>`,
+:ref:`FSL <binary_pkg_fsl-complete>`, :ref:`PyMVPA <binary_pkg_python-mvpa2>` and
+:ref:`many others <pkg_tocs>`. While we do strive to maintain a high level of
+quality, we make no guarantee that a given package works as expected, so use
+them at your own risk. If you do encounter problems or you just like to say
+thanks, simply :ref:`send us an email <chap_contacts>`.
-NeuroDebian provides a turnkey software platform for neuroscience
-that is created by integrating research tools with the Debian_ operating
-system. If you are using such software on Debian_ or its derivatives,
-such as Ubuntu_, chances are that you are already using NeuroDebian.
-
-This website provides a :ref:`supplementary repository <repository_howto>` with
-both unofficial or prospective packages which are not (yet) available from the
-main Debian_ archive, as well as backported or simply rebuilt latest versions
-of software. NeuroDebian serves as an "upstream" to some :ref:`derivative
-<chap_derivatives>` projects. Please see the :ref:`faq` for more information
-about the goals of this project, and :ref:`read what people say about it
-<testimonials>`. Take a look at the :ref:`list of our current and planned
-projects <projects>` if you want to get involved. This service is provided "as
-is". There is no guarantee that a package works as expected, so use them at
-your own risk. If you encounter problems, please `report <#contacts>`_ them.
-Please help us |spread|:
+Learn more about NeuroDebian, the goals of this project, and help us |spread|!
Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
next step: An integrated, community-driven computing platform for neuroscience
.. raw:: html
- <p>
- <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
- <a href="pkglists/pkgs-by_release-datasets_(data).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>
- <a href="derivatives.html"><img border="0" src="_static/derivatives.png" title="NeuroDebian Derivatives" /></a>
- <a href="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></a>
- </p>
-
-.. _Ubuntu: http://www.ubuntu.com
-
-.. _news:
+ <div class="linkmore"><a href="publications.html" name="publications">more publications</a></div>
+ <div class="clearer"></div>
+ <!-- for dynamic quote update via javascript -->
+ <hr />
+ <div id="randomquote" title="Feedback from the community">
-News
-====
+.. quotes::
+ :random: 1
.. raw:: html
- <script src="_static/jquery.livetwitter.min.js"></script>
- <div id="identica_widget"></div>
- <script type="text/javascript">
- $("#identica_widget").liveTwitter('neurodebian',
- {service: 'identi.ca',
- mode: 'user_timeline',
- limit: 10,
- rate: 300000});
- </script>
+ </div><!-- randomquote -->
+ <div class="linkmore"><a href="testimonials.html">more testimonials</a></div>
-For more news and information see our :ref:`blog <blog>`. Older news items are
-available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
-subscribe to the NeuroDebian news.
-
-.. _identi.ca: http://identi.ca/neurodebian
-.. _twitter: http://twitter.com/NeuroDebian
+.. _Ubuntu: http://www.ubuntu.com
.. _repository_howto:
-
-
-
-How to use this repository
-==========================
-
-To enable the NeuroDebian repository on your system, select your Debian or
-Ubuntu release and a `repository mirror`_ from the lists below. Upon selection
-a short command snippet will be displayed that can be copied and pasted into
-a terminal session. These commands will configure the system package manager
-with the NeuroDebian repository key and package source information.
-
-.. include:: sources_lists
-
-Once this is done, you have to update the package index and you are ready to
-install packages. Use your favorite package manager, e.g. synaptic, adept. In
-the terminal you can use :command:`apt-get`::
-
- sudo apt-get update
- sudo apt-get install mricron
-
-.. note::
-
- Not every package is available for all distributions/releases. For information
- about which package version is available for which release and architecture,
- please have a look at the corresponding package pages.
-
-.. raw:: html
-
- <p><img border="0" src="_files/nd_subscriptionstats.png" title="Statistics of new repository subscriptions for all supported releases. Note: subscription is only done once per machine." /></p>
-
-Popularity Contest
-------------------
-
-We encourage you to participate in the `popularity
-contest <http://popcon.debian.org>`_ (popcon), which anonymously
-collects the list of packages you installed/use on your system.
-Collecting such statistics is of particular importance for research
-software projects as a prove of an existing user-base. If upon
-installation of the system you rejected the invitation to participate
-you can always change your decision by running::
-
- sudo dpkg-reconfigure popularity-contest
-
-.. note::
-
- If you are deploying multiple systems through cloning, to not have
- all systems considered as one, it would be necessary to re-generate
- the random MY_HOSTID. Following commands ran as root should do it
- (as root) without any interactive dialog::
-
- sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
- DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
-
-In addition to popcon pages for your "core" distribution (e.g. `Debian
-<http://popcon.debian.org/>`__ or `Ubuntu
-<http://popcon.ubuntu.com/>`__) you can see/get statistics for
-submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
-know that you are already contributing back to the community.
-
.. _chap_installation:
-Ways to use NeuroDebian
-=======================
-
-Virtual machine
----------------
-
-If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
-provided as a convenient testing and evaluation environment. After a few
-simple steps to setup the virtual machine, you will be able to use NeuroDebian_
-as an integral part of your existing working environment without any sacrifice.
-The virtual machine is also a suitable environment to temporarily deploy
-neuroscience software on machines running other operating systems, e.g. for the
-purpose of teaching a neuroimaging data analysis course in a multipurpose
-computer lab.
+Get NeuroDebian
+===============
+.. include:: reposetup.rst
-Debian installation
--------------------
+.. _news:
-Having been exposed to the wonders of NeuroDebian_ you are no longer
-satisfied with your previous choice of operating system? We would
-recommend installing Debian_ to replace or complement (dual-boot) your
-existing OS. Please visit `"Getting Debian"
-<http://www.debian.org/distrib/>`_ to obtain the images for your
-hardware architecture and then simply add |repos|.
+News
+====
+.. raw:: html
-.. _chap_team:
+ <a class="twitter-timeline" href="https://twitter.com/NeuroDebian"
+ data-widget-id="360194288006606848"
+ data-link-color="#820430"
+ height="150px"
+ data-show-replies="false"
+ data-chrome="noheader nofooter transparent">Tweets by @NeuroDebian</a>
+ <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
+ <div class="nojavascriptinstructions">
+ The news widget requires javascript
+ </div>
-The team
-========
+.. _identi.ca: http://identi.ca/neurodebian
+.. _twitter: http://twitter.com/NeuroDebian
-`Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
-<http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
-`Experimental Psychology Debian packaging project
-<http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
-leaders. However, the whole project would not be possible without the work of
-over 3,000 Debian_ developers and contributors who are as enthusiastically
-building the Debian operating system.
-A number of packages that are available from the NeuroDebian repository have
-been contributed by various individuals and other teams in Debian, such as
-`Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
-maintainers_ that help to make Debian_ the ultimate software platform for
-neuroscience.
-.. _maintainers: pkgs.html#by-maintainer
+.. raw:: html
+ <hr />
+ <div id="sitemap">
+ <!-- Some anchors to orient users of old-website urls -->
+ <a name="acknowledgements"/>
+ <a name="contacts"/>
+ <a name="the-team"/>
+ <a name="debian-installation"/>
+ <a name="virtual-machine"/>
+ <a name="ways-to-use-neurodebian"> </a>
+
+* **About**
+* :ref:`The Team <chap_team>`
+* :ref:`FAQ <faq>`
+* :ref:`Blog <blog>`
+* :ref:`chap_popularity`
+* :ref:`chap_publications`
+* :ref:`chap_acknowledgements`
+* :ref:`testimonials`
+* :ref:`coffeeart`
+
+.. start a new list
+
+* **Services**
+* :ref:`Software <pkg_tocs>`
+* :ref:`Data <toc_pkgs_for_release_data>`
+* :ref:`Appliance <chap_vm>`
+* :ref:`Mirrors <chap_mirrors_stats>`
+
+.. start a new list
+
+* **Community**
+* :ref:`Contacts <chap_contacts>`
+* :ref:`Mailing lists <chap_mailinglists>`
+* `OpenHatch <https://openhatch.org/+projects/NeuroDebian>`_
+* `Identi.ca <http://identi.ca/neurodebian>`_
+* `Twitter <http://twitter.com/NeuroDebian>`_
+* `Google+ <https://plus.google.com/104292290917252528951>`_
+* `YouTube <http://www.youtube.com/neurodebian>`_
+* `GitHub <https://github.com/neurodebian>`_
+
+.. start a new list
+
+* **Related**
+* `Debian <http://www.debian.org>`_
+* `Debian Med <http://www.debian.org/devel/debian-med>`_
+* `INCF <http://software.incf.org/software/neurodebian>`_
+* `NITRC <http://www.nitrc.org/projects/neurodebian>`_
-.. _support:
-
-Contacts
-========
+.. raw:: html
-`Email us directly <team@neuro.debian.net>`_ with any "private"
-communication. Otherwise please use our public mailing lists, which
-exist not only to provide user-support but also to establish
-communication channels within the NeuroDebian community
-
-* neurodebian-users_: Discussions and support of NeuroDebian users
-
-* neurodebian-upstream_: General discussions and knowledge sharing
- among developers of neuroscience software. We also use it
- to update you with summaries of recent relevant developments in
- Debian project
-
-* neurodebian-devel_: Technical mailing list for discussions on
- NeuroDebian development
-
-You are welcome also to join #neurodebian IRC room on OFTC network if
-you have quick questions or want to join a live discussion.
-
-Acknowledgements
-================
-
-We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
-Italian espresso <coffeeart>`.
-
-.. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
-
-Thanks to the following institutions and individuals for hosting a mirror:
-
-* `Department of Psychological and Brain Sciences at Dartmouth College`_
- *[us-nh]* (primary mirror)
-* `Department of Experimental Psychology at the University of Magdeburg`_
- *[de-md]*
-* `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
-* `Paul Ivanov`_ *[us-ca]*
-* `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
- *[us-tn]*
-* `Australia's research and education network (AARNET)
- <http://www.aarnet.edu.au>`_ *[au]*
-* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
-* Iaroslav Iurchenko *[ua]*
-* `Nikolaus Valentin Haenel`_ *[de-v]*
-* `INCF G-Node at Ludwig-Maximilians-Universität München <http://www.g-node.org>`_ *[de-m]*
-
-If your are interested in mirroring the repository, please see the :ref:`faq`.
-
-.. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
-.. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
-.. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
-.. _Paul Ivanov: http://www.pirsquared.org
-.. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
-.. _Nikolaus Valentin Haenel: http://haenel.co
-
-
-Publications
-============
-
-Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously.
-<http://neuro.debian.net/_files/Hanke_FearTheWombat_Brainhack2012.pdf>`_ *Talk
-given at* `Brainhack <http://brainhack.org/2012/04/06/brainhack-2012-unconference>`_ 2012 at the
-Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany.
-[`video <http://youtu.be/8t6znEOEDVo>`_]
-
-Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian
-OR Just using Debian is not enough
-<http://neuro.debian.net/_files/Hanke_UsingDebianIsNotEnough_ESRF2012.pdf>`_.
-Talk given at the workshop "Debian for Scientific Facilities Days" at the
-European Synchrotron Radiation Facility (ESRF), Grenoble, France.
-
-Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
-next step: An integrated, community-driven computing platform for neuroscience
-<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
-6:22.
-
-Hanke, M. (2012). `The why and how of getting packaged
-<_files/Hanke_GetPackaged_CodeJam5_2012.pdf>`_.
-*Talk given at BrainScaleS CodeJam 5, Convergence in Computational Neuroscience*,
-University of Edinburgh, Edinburgh, UK.
-
-Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
-contemporary research in neuroimaging: PyMVPA and NeuroDebian
-<_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
-*Talk given at the University of Pennsylvania School of Medicine*,
-Philadelphia, PA, USA.
-
-Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
-NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
-*Talk given at the Max-Planck-Institute for Human Cognitive and Brain
-Sciences*, Leipzig, Germany.
-
-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*.
-
-Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
-platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
-*Poster presented at the annual meeting of the Organisation for Human Brain
-Mapping*, Quebec City, Canada.
-
-Hanke, M. (2011). `Integrating Condor into the Debian operating system
-<_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
-*Talk given at* `CondorWeek 2011
-<http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
-Madison, Wisconsin, USA.
-
-Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
-SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
-Neuroscience*, San Diego, USA.
-
-Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
-(2010). `Having trouble getting your Nature paper? Maybe you are not using the
-right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
-annual meeting of the Society for Neuroscience*, San Diego, USA.
-
-Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
-neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
-*Talk given at* DebConf10_, New York City, USA. [video:
-`low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
-`high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
-
-Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
-efficiency in cognitive neuroscience research with NeuroDebian
-<_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
-meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
-
-Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
-statistical learning, and open-source software to make research more
-efficient, more open, and more fun
-<_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
-`Dartmouth College`_, New Hampshire, USA.
-
-.. _DebConf10: http://debconf10.debconf.org/
-.. _Dartmouth College: http://www.dartmouth.edu/
+ </div><div class="clearer"></div>
+ <hr />
.. toctree::
blog/index
faq
+ thanks
+ popularity
+ about
pkgs
spread
vm
+ publications
coffeeart
photoalbum
projects
testimonials
testimonials-topics
+ vm_welcome
+ derivatives
+
+.. are these supposed to be visible?
+.. toctree::
+ :hidden:
+
+ machines
+ todo
+
+.. toctree::
+ :hidden:
+ :glob:
+
+ pkgs/*
+ pkglists/*
.. probably should be purged altogether
.. toctree::
:hidden:
- booth_sfn2010
- datasets
livecd
quotes-nihr01
quotes-nitrc
- sources_lists
- vm_welcome
.. include:: link_names.txt
.. include:: substitutions.txt
+
+.. raw:: html
+
+ <script type="text/javascript">
+ $(document).ready(function($) {
+ //setInterval(function(){
+ $.get('testimonials.html', function(data) {
+ var quotes = $("blockquote", data);
+ var idx = Math.floor(quotes.length * Math.random());
+ $('#randomquote').html(quotes[idx]);
+ }); // update callback
+ //}, 60000); // set interval
+ }); // doc ready
+ //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
+
+ function foldbuttontoggle(foldname) {
+ var foldid = '#' + foldname;
+ var buttonid = foldid + 'button';
+ $(buttonid).on('click', function() {
+ $('#' + foldname).slideToggle();
+ if ($(buttonid).html() == "↓↓↓") {
+ $(buttonid).html("↑↑↑");
+ }
+ else {
+ $(buttonid).html("↓↓↓");
+ }
+ });
+ $(foldid).slideUp();
+ $(buttonid).html("↓↓↓");
+ };
+
+ </script>
--- /dev/null
+Install a package
+=================
+
+Step 1
+------
+
+*[skip this steps if your are using the NeuroDebian virtual machine or if your
+machine is already configured to use this repository]*
+
+.. include:: reposetup.rst
+
+Step 2
+------
+
+To install the ``###pkgname###`` package on your system or virtual machine,
+open a terminal and execute the following command::
+
+ sudo apt-get install ###pkgname###
+
+.. raw:: html
+
+ <script type="text/javascript">
+ var split = location.search.replace('?', '').split('=')
+ if ( split[0] == 'p' ) {
+ $(document.body).html($(document.body).html().replace('###pkgname###', split[1]));
+ }
+ </script>
.. _Lin4Neuro: http://www.nemotos.net/lin4neuro
.. _fail2ban: http://www.fail2ban.org
+.. Debian releases
+.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
+.. _Debian 7.0 (wheezy): http://www.debian.org/releases/wheezy
+.. _Debian 8.0 (jessie): http://www.debian.org/releases/jessie
+
+.. Desktop environments
+.. _GNOME: http://www.gnome.org/
+.. _GNOME3: http://www.gnome.org/gnome-3/
+.. _XFCE: http://www.xfce.org/
+.. _XFCE4: http://www.xfce.org/
+
.. Functional imaging labs
.. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk
.. _FMRIB: http://www.fmrib.ox.ac.uk
.. |ITP| replace:: :abbr:`ITP (Intent to Package)`
.. |RFP| replace:: :abbr:`RFP (Request for packaging)`
.. |DBTS| replace:: :abbr:`DBTS (Debian Bug Tracking System)`
-
+.. _debian-installer: http://www.debian.org/devel/debian-installer/
.. mailing lists
.. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
.. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _chap_popularity:
+
+*********************
+Popularity Statistics
+*********************
+
+Repository subscriptions
+========================
+
+Interactive visualization of new NeuroDebian repository subscriptions. Plotted
+are each week's average number of daily subscriptions for all Debian and Ubuntu
+releases. Statistics for individual releases can be compared by clicking on the
+respective curves and labels in the legend.
+
+Note that each machine only needs to be subscribed to the repository once, and
+only subscriptions done via the website are counted.
+
+
+.. raw:: html
+
+ <link href="/_static/nv.d3.css" rel="stylesheet" type="text/css">
+ <div><svg style="height:500px" id="subscriptionchart"></svg></div>
+
+ <script src="/_static/d3.v2.min.js"></script>
+ <script src="/_static/nv.d3.min.js"></script>
+ <script src="/_static/subscriptionchart.js"></script>
+
+
+Popularity Contest
+==================
+
+We encourage you to participate in the `popularity
+contest <http://popcon.debian.org>`_ (popcon), which anonymously
+collects the list of packages you installed/use on your system.
+Collecting such statistics is of particular importance for research
+software projects as a proof of existing user-base.
+
+In addition to popcon stats for your "core" distribution (e.g. `Debian
+<http://popcon.debian.org/>`__ or `Ubuntu
+<http://popcon.ubuntu.com/>`__), an interactive plot below summarizes number
+of submissions to NeuroDebian's popcon server.
+
+.. raw:: html
+
+ <div><svg style="height:500px" id="popconchart"></svg></div>
+
+ <script src="/_static/popconchart.js"></script>
+
+You can get more information about submissions from `NeuroDebian Popularity
+Contest <http://neuro.debian.net/popcon/>`__ page.
+
+If upon installation of the system you rejected the invitation to participate
+you can always change your decision by running::
+
+ sudo dpkg-reconfigure popularity-contest
+
+.. note::
+
+ If you are deploying multiple systems through cloning, to not have
+ all systems considered as one, it would be necessary to re-generate
+ the random MY_HOSTID. Following commands ran as root should do it
+ (as root) without any interactive dialog::
+
+ sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
+ DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
+
+
+.. include:: link_names.txt
Promotion
---------
+.. raw:: html
+
+ <div class="expandinstructions">Click on an item to expand it</div>
+
* `Publications <http://neuro.debian.net/index.html#publications>`_ and
promotional materials
- - `Debian / NeuroDebian tri-fold
+ - `(Neuro)Debian tri-fold
<http://neuro.debian.net/_files/brochure_debian-neurodebian.pdf>`_
* Conferences presence of the team presenting Debian_,
**May 2-6, 2011** `Paradyn/Condor Week <http://www.cs.wisc.edu/condor/ParadynCondorWeek2011>`_, Madison, Wisconsin, USA
Hanke, M. `Talk: Integrating Condor into the Debian operating system <http://www.cs.wisc.edu/condor/ParadynCondorWeek2011/presentations/hanke-condor-debian.pdf>`__
+
**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
- Halchenko, Yaroslav O. `Talk: π's in Debian or Scientific Debian: NumPy,
- SciPy and beyond <http://www.euroscipy.org/talk/4379>`__
+ Halchenko, Yaroslav O. `Talk: π's in Debian or Scientific Debian: NumPy,
+ SciPy and beyond <http://www.euroscipy.org/talk/4379>`__
2011/08/29, 14:00 -- 14:30, Neuroimaging data processing
Halchenko, Yaroslav O. `Talk: The virtues and sins of PyMVPA <http://pythonneuro.sciencesconf.org/899>`__
2011/08/30, 10:30 -- 10:45, Workflows and pipelines for data processing
Hanke, M. `Talk: More than batteries included: NeuroDebian <http://pythonneuro.sciencesconf.org/883>`__
2011/08/30, 12:00 -- 12:15, Data management and databasing
- Hanke, M. `Talk: NiBabel: Conductor for a cacophony of neuro-imaging file formats <http://pythonneuro.sciencesconf.org/901>`__
+ Hanke, M. `Talk: NiBabel: Conductor for a cacophony of neuro-imaging file formats <http://pythonneuro.sciencesconf.org/901>`__
**September 8, 2011** `INCF Cross-Task Force Hackathon <http://atlasing.incf.org/wiki/Sept8>`_, Boston, MA, USA
**November 12-16, 2011** `SfN 2011 <http://www.sfn.org/am2011/>`_, Washington, District Columbia, USA
Booth #3207
- `Invite us <mailto:team@neuro.debian.net>`_
+* `Invite us <mailto:team@neuro.debian.net>`_ to talk about NeuroDebian.
* `Inviting contributions and new members to join the NeuroDebian project
<https://openhatch.org/+projects/NeuroDebian>`_
--- /dev/null
+
+.. _chap_publications:
+
+************
+Publications
+************
+
+This is a list of publication from the NeuroDebian team on various
+NeuroDebian-related topics:
+
+Halchenko, Y.O. and Hanke, M. (2013). `Open is not enough: benefits from Debian as an integrated, community-driven computing platform.
+<http://neuro.debian.net/_files/Halchenko_OpenIsNotEnough_UCAR2013.pdf>`_ *Talk
+given at* `SEA-2013 <http://sea.ucar.edu/event/open-not-enough-benefits-debian-integrated-community-driven-computing-platform>`_
+conference, University Corporation for Atmospheric Research (UCAR), Boulder CO, USA.
+
+Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously.
+<http://neuro.debian.net/_files/Hanke_FearTheWombat_Brainhack2012.pdf>`_ *Talk
+given at* `Brainhack <http://brainhack.org/2012/04/06/brainhack-2012-unconference>`_ 2012 at the
+Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany.
+[`video <http://youtu.be/8t6znEOEDVo>`_]
+
+Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian
+OR Just using Debian is not enough
+<http://neuro.debian.net/_files/Hanke_UsingDebianIsNotEnough_ESRF2012.pdf>`_.
+Talk given at the workshop "Debian for Scientific Facilities Days" at the
+European Synchrotron Radiation Facility (ESRF), Grenoble, France.
+
+Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
+next step: An integrated, community-driven computing platform for neuroscience
+<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
+6:22.
+
+Hanke, M. (2012). `The why and how of getting packaged
+<_files/Hanke_GetPackaged_CodeJam5_2012.pdf>`_.
+*Talk given at BrainScaleS CodeJam 5, Convergence in Computational Neuroscience*,
+University of Edinburgh, Edinburgh, UK.
+
+Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
+contemporary research in neuroimaging: PyMVPA and NeuroDebian
+<_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
+*Talk given at the University of Pennsylvania School of Medicine*,
+Philadelphia, PA, USA.
+
+Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
+NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
+*Talk given at the Max-Planck-Institute for Human Cognitive and Brain
+Sciences*, Leipzig, Germany.
+
+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*.
+
+Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
+platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
+*Poster presented at the annual meeting of the Organisation for Human Brain
+Mapping*, Quebec City, Canada.
+
+Hanke, M. (2011). `Integrating Condor into the Debian operating system
+<_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
+*Talk given at* `CondorWeek 2011
+<http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
+Madison, Wisconsin, USA.
+
+Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
+SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
+Neuroscience*, San Diego, USA.
+
+Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
+(2010). `Having trouble getting your Nature paper? Maybe you are not using the
+right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
+annual meeting of the Society for Neuroscience*, San Diego, USA.
+
+Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
+neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
+*Talk given at* DebConf10_, New York City, USA. [video:
+`low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
+`high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
+
+Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
+efficiency in cognitive neuroscience research with NeuroDebian
+<_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
+meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
+
+Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
+statistical learning, and open-source software to make research more
+efficient, more open, and more fun
+<_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
+`Dartmouth College`_, New Hampshire, USA.
+
+.. _DebConf10: http://debconf10.debconf.org/
+.. _Dartmouth College: http://www.dartmouth.edu/
:author: Prof. Brian Avants
:affiliation: Research Assistant Professor of Radiology, University of Pennsylvania, Philadelphia, USA
:date: 2010-09-16
- :tags: lofs, practices, standardization, mentorship, dissemination, impact
+ :tags: lofs, practices, standardization, mentorship,
+ dissemination, impact, upstream
: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.
:author: Dr. Matthew Brett
:affiliation: Specialist researcher, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
:date: 2010-09-02
- :tags: lofs, practices, team, sharing
+ :tags: lofs, practices, team, sharing, upstream
:group: Research software projects
[...] 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.
:author: Prof. Gene Cooperman
:affiliation: College of Computer and Information Science, Northeastern University, Boston, USA
:date: 2011-06-21
- :tags: lofs
+ :tags: lofs, upstream
: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.
: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, mentorship
+ :tags: lofs, mentorship, upstream
: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.
:author: Prof. Bruce Fischl
:affiliation: Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA
:date: 2010-09-10
- :tags: lofs, perspective, software distribution
+ :tags: lofs, perspective, software distribution, upstream
:group: Research software projects
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.
:author: Stephan Gerhard
:affiliation: Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
:date: 2011-06-21
- :tags: lofs, support, Debian, open science
+ :tags: lofs, support, Debian, open science, upstream
: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.
:author: Dr. Satrajit Ghosh
:affiliation: Research scientist, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
:date: 2011-06-13
- :tags: lofs, software distribution
+ :tags: lofs, software distribution, upstream
:group: Research software projects
In creating a source repository for distribution of common neuroimaging tools, NeuroDebian has filled a gaping void. It is an incredibly useful resource that we have been relying on at MIT for installation of software.
:author: Valentin Haenel
:affiliation: Psignifit and pyoptical developer, Modellierung Kognitiver Prozesse, Technische Universität, Berlin, Germany
:date: 2010-09-17
- :tags: lofs, reproducibility
+ :tags: lofs, reproducibility, upstream
:group: Research software projects
[ [...] The] only way to conduct reliable and reproducible science is to use open source software [...]. NeuroDebian is by far the most advanced undertaking for such a scientific approach in the neuroscience community.
:author: Dr. Thies Jochimsen
:affiliation: Post-doctoral researcher, Medical Physics Group, Department of Diagnostic and Interventional Radiology, University Hospital Jena, Jena, Germany
:date: 2010-09-02
- :tags: lofs, team, software distribution, mentorship
+ :tags: lofs, team, software distribution, mentorship, upstream
: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.
: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
+ :tags: lofs, vm, contributions, practices, upstream
: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.
:author: Dr. Gabriele Lohmann
:affiliation: Lipsia lead developer, Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
:date: 2010-09-13
- :tags: lofs
+ :tags: lofs, upstream
:group: Research software projects
It [NeuroDebian] has been and continues to be of great value in all of our projects [...]
:author: Valerio Lucio
:affiliation: Manager Information Systems, Center for Brain Imaging, New York University, New York City, USA
:date: 2010-09-01
- :tags: lofs, contributions, Debian
+ :tags: lofs, contributions, Debian, upstream
:group: Research software projects
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
:author: Sebastiaan Mathôt
:affiliation: OpenSesame lead developer, Vrije Universiteit, Amsterdam, The Netherlands
:date: 2011-07-29
- :tags: lofs, software distribution, mentorship, Debian
+ :tags: lofs, software distribution, mentorship, Debian, upstream
: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.
:author: Dr. Eilif Muller
:affiliation: Post-doctoral researcher, Brain Mind Institute, EPFL, Lausanne, Switzerland
:date: 2010-09-09
- :tags: lofs, reproducibility, standardization, breadth
+ :tags: lofs, reproducibility, standardization, breadth, upstream
:group: Research software projects
I am constantly aware that software packaging and supporting user needs on diverse platforms represents a severe burden for developers. The NeuroDebian software platform addresses these problems for a good fraction of production environments in the field, while contributing to research reproducibility through software standardization.
:author: Prof. Jonathan Peirce
:affiliation: School of Psychology, University of Nottingham, Nottingham, UK
:date: 2010-09-06
- :tags: lofs, money, impact
+ :tags: lofs, money, impact, upstream
:group: Research software projects
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.
:author: Dr. Fernando Perez
:affiliation: IPython developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
:date: 2010-09-08
- :tags: lofs, contributions, team
+ :tags: lofs, contributions, team, upstream
: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 [...]
:author: Dr. Ariel Rokem
:affiliation: NiTime developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
:date: 2010-09-15
- :tags: lofs, frontier, contributions, speed, standardization, dissemination
+ :tags: lofs, frontier, contributions, speed, standardization,
+ dissemination, upstream
:group: Research software projects
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.
:author: Prof. Per B. Sederberg
:affiliation: Department of Psychology, Ohio State University, Columbus, Ohio, USA
:date: 2010-09-16
- :tags: lofs, impact, quality
+ :tags: lofs, impact, quality, upstream
: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.
:author: Prof. Stephen M. Smith
:affiliation: Associate Director, Centre for Functional Magnetic, Resonance Imaging of the Brain University of Oxford, Oxford, UK
:date: 2010-09-01
- :tags: lofs, contributions, support, Debian
+ :tags: lofs, contributions, support, Debian, upstream
:group: Research software projects
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.
:author: Dr. Gaël Varoquaux
:affiliation: Parietal project, INRIA, Neurospin research center, Gif sur Yvette, France
:date: 2010-09-01
- :tags: lofs, reproducibility, dissemination
+ :tags: lofs, reproducibility, dissemination, upstream
: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.
[...] 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
+ :author: Dr. Robert Buccigrossi
+ :affiliation: Technical Lead of the NITRC project
:date: 2011-09-22
- :tags: nitrc, ease
- :group: Individual laboratories and researchers
+ :tags: nitrc, ease, cloud, derivatives
+ :group: Research software projects
: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.
--- /dev/null
+Report a bug
+============
+
+If you believe that there is a bug in ``###pkgname###``, we would be grateful if
+you take the time to report it. Only known problems can get fixed!
+
+Here are a few tips to help you report this bug in a way that facilitates its
+resolution.
+
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
+
+ Please double-check the name of the faulty package
+ If you have trouble with a command, you can identify the corresponding package
+ by running this command in a terminal::
+
+ $ dpkg -S `readlink -f $(which COMMAND)`
+
+ where ``COMMAND`` is the name of the command that fails.
+
+ If you believe there is a problem with a file installed on your system you
+ can find the responsible package by running::
+
+ $ dpkg -S FULLPATH
+
+ where ``FULLPATH`` is the complete absolute path of the file.
+
+ Try to reproduce the bug
+ If you cannot reproduce the bug it is likely that the package maintainer
+ also cannot do it. Please make an attempt to find out under which
+ circumstances the faulty behavior occurs. However, if you can't figure it
+ out, please report the bug nevertheless -- maybe someone else can provide
+ the missing information.
+
+ Describe the problem so that the developer can reproduce it
+ That means including every single detail -- not just the "important" ones.
+ What kind of system (hardware/software) are you using? What did you do
+ exactly when the bug hit you?
+
+ Remember: bug reports are not just input for developers, but also help other
+ users to identify whether they are affected by the same problem, and a
+ recommended solution applies to them as well.
+
+ A good bug report is an important service to the community!
+
+ More information on high quality bug reporting is available at:
+ http://raphaelhertzog.com/go/bugreporting/
+
+
+Please email bug reports to the neurodebian-users_ or neurodebian-devel_
+mailing list -- whichever is more appropriate. In rare cases where your
+bug report contains confidential information, please email it directly
+to `team@neuro.debian.net <mailto:team@neuro.debian.net?subject=BUG-###pkgname###:>`_.
+
+If you have evidence that the faulty behavior is not specific to NeuroDebian,
+your bug report is best directed to the developers of the respective software.
+
+.. raw:: html
+
+ <script type="text/javascript">
+ var split = location.search.replace('?', '').split('=')
+ if ( split[0] == 'p' ) {
+ $(document.body).html($(document.body).html().replace('###pkgname###', split[1]));
+ }
+ </script>
+
+.. include:: link_names.txt
--- /dev/null
+First select what kind of operating system you are using, and then choose a
+download server close to you:
+
+.. include:: sources_lists
+
+.. raw:: html
+
+ <div class="nojavascriptinstructions">
+ This form requires javascript. If disabled, incomplete instructions are
+ displayed below</div>
+ <div id="repoconfig">
+ <div class="nojavascriptinstructions">
+ Instructions for Debian-derived systems
+ </div>
+ <p>Select desired components:<br />
+ <table><tr>
+ <td><input type="radio" name="components" value="libre"></td>
+ <td><strong>only</strong> software with guaranteed freedoms<br />
+ <span style=font-size:75%>all packages are
+ <a href="http://www.debian.org/social_contract#guidelines">DSFG</a>-compliant,
+ with permission to use, modify, re-distribute under any condition</span></td></tr>
+ <tr><td><input type="radio" name="components" value="full"></td>
+ <td>all software<br />
+ <span style=font-size:75%>
+ individual packages may have restrictive licenses and you are required to
+ check license-compliance manually
+ </span></td></tr>
+ </table>
+ <div class="reposetup">
+
+You can enable NeuroDebian on your system by simply copying and pasting the
+following two commands into a terminal window. This will add the NeuroDebian
+repository to your native package management system, and you will be able to
+install neuroscience software the same way as any other package.
+
+.. raw:: html
+
+ <pre id="code">
+ After selecting a release the setup code will be shown here.
+ </pre>
+
+Now you can update the package index and you are ready to install packages.
+Simply execute the following command in a terminal::
+
+ sudo apt-get update
+
+You are ready to go -- enjoy NeuroDebian!
+
+.. note::
+
+ Not every package is available for all distributions/releases. For information
+ about which package version is available for which release and architecture,
+ please have a look at the corresponding package pages.
+
+.. raw:: html
+
+ </div> <!-- end reposetup -->
+ </div> <!-- end repoconfig -->
+
+ <div id="vmsetup">
+ <div class="nojavascriptinstructions">
+ Instructions for non-Debian systems
+ </div>
+
+For all non-Debian operating systems we recommend to deploy NeuroDebian as a
+`virtual appliance`_ (virtual machine) -- this will only take a few minutes.
+On all modern hardware (built within
+the last 3-4 years) a virtual appliance is a convenient solution to run
+NeuroDebian simultaneously with the primary operating system -- without
+noticeable performance loss. To start using NeuroDebian:
+
+1. Download this image file:
+
+.. raw:: html
+
+ <div id="vmimagedownload">
+ <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
+ </div>
+
+2. Import this image into VirtualBox_. If you do not have VirtualBox_
+ installed yet, visit the `VirtualBox download page
+ <http://www.virtualbox.org/wiki/Downloads>`_ and get an installer for your
+ system (installers for Windows, Linux, Mac and Solaris are available).
+
+3. Finish the configuration by following :ref:`the instructions on setting up
+ the virtual appliance <chap_vm>`. `[Virtual machine
+ setup video tutorial] <http://www.youtube.com/watch?v=eqfjKV5XaTE>`_
+
+
+
+
+You are ready to go -- enjoy NeuroDebian!
+
+.. note::
+
+ If you want a verified stable (but older) virtual appliances based
+ on `Debian 6.0 (squeeze)`_ release, download one of the image files
+ listed below.
+
+ * `NeuroDebian 6.0.6 image (32bit)
+ <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_i386.ova>`_ [~559MB]
+
+ * `NeuroDebian 6.0.6 image (64bit)
+ <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_amd64.ova>`_ [~576MB]
+
+.. raw:: html
+
+ </div> <!-- end vmsetup -->
+
+.. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
+.. _VirtualBox: http://www.virtualbox.org
+
+.. raw:: html
+
+ <script type="text/javascript">
+ function createvmdownload(rel, mir) {
+ var img_version = '7.0.0';
+ var img_suffix;
+ var base_url;
+ var img_url;
+ var md5sum_url;
+ if (rel == 'win32') {
+ img_suffix = 'i386';
+ } else {
+ img_suffix = 'amd64';
+ };
+ if(mir in mirrors) {
+ base_url = mirrors[mir] + '/vm/';
+ img_url = base_url + 'NeuroDebian_' + img_version + '_' + img_suffix + '.ova';
+ md5sum_url = base_url + 'MD5SUMS';
+ } else {
+ return 'Internal error';
+ };
+ return '<blockquote><a href="' + img_url
+ + '">Virtual applicance image</a> [<a title="Verify image integrity by dowloading this file and running `md5sum -c MD5SUMS`" href="'
+ + md5sum_url
+ + '">MD5SUM</a>, <a title="Verify authenticity of the MD5SUM file by downloading this file and running `gpg –verify MD5SUMS.gpg`" href="'
+ + md5sum_url + '.gpg">MD5SUM.gpg</a>]</blockquote>' ;
+
+ };
+
+ function createrepourl(rel, mir, comp) {
+ if(mir in mirrors) {
+ var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel + "."
+ + mir + "." + comp + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
+ + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
+ return retrepo;
+ }
+
+ };
+
+ function update_by_form() {
+ var rel = $("#release").val();
+ var mir = $("#mirror").val();
+ var comp = $('input[name="components"]:checked').val();
+ if (rel != '' && mir != '') {
+ if (rel in {'win32':'', 'win64':'', 'mac':''}) {
+ $('#vmimagedownload').html(createvmdownload(rel, mir));
+ $('#vmsetup').slideDown();
+ $('#repoconfig').slideUp();
+ } else {
+ $('#vmsetup').slideUp();
+ $('#repoconfig').slideDown();
+ if (comp == undefined) {
+ $('.reposetup').slideUp();
+ } else {
+ $('#code').text(createrepourl(rel, mir, comp));
+ $('.reposetup').slideDown();
+ }
+ };
+ }
+ else
+ {
+ $('#repoconfig').slideUp();
+ $('#vmsetup').slideUp();
+ };
+ };
+
+ $(document).ready(function($) {
+ update_by_form();
+ $('#repoconfig').hide()
+ $('.reposetup').hide();
+ $('#vmsetup').hide()
+ $('#release').change(update_by_form);
+ $('#mirror').change(update_by_form);
+ $('input[name=components]:radio').change(update_by_form);
+ });
+
+ </script>
Testimonials
============
+Here is some feedback we got from the neuroscience community on various
+occasions. On this page it is grouped by its origin (i.e. `research
+institutions`_, `research software projects`_, `individual laboratories and
+researchers`_). Alternatively, you can read testimonials related to specific
+topics:
+
+* :ref:`testimonials_open_science`
+* :ref:`testimonials_standardization`
+* :ref:`testimonials_vm`
+
.. None so far replied
..
.. Organizations
.. :group: Organizations
-By Topic
---------
-
-* :ref:`testimonials_open_science`
-* :ref:`testimonials_standardization`
-* :ref:`testimonials_vm`
-
-
Research Institutions
---------------------
.. not implemented for now
.. :sections: group
+.. quote::
+ :author: Christian Haselgrove
+ :affiliation: Vice President for Neuroinformatics at
+ Neuromorphometrics, Inc; University of Massachusetts Medical School
+ :date: 2013-02-06
+ :tags: email, derivatives, management
+
+ Developing informatics infrastructure often involves building
+ complex systems that require interaction between existing
+ components such as software and atlases. NeuroDebian makes it
+ trivial to manage the components of these systems, freeing me to
+ focus on the novel and important aspects of my work.
+
Research Software Projects
--------------------------
.. quotes::
:group: Research software projects
+
.. quote::
:author: Stephan Gerhard, et al.
:date: 2011-06-06
For proper software packaging and distribution, the NeuroDebian project provides professional expertise and infrastructure.
+.. quote::
+ :author: Chuck Theobald
+ :affiliation: Lewis Center for Neuroimaging, University of Oregon, MRIConvert/mcverter build master and developer
+ :tags: email, impact, software distribution, upstream, dissemination
+ :date: 2013-02-06
+
+ As a system administrator, I support the efforts of a number of
+ researchers who use fMRI analysis software. I was overjoyed to find
+ the NeuroDebian repository, a one-stop shop for nearly every
+ software package the researchers use. The work of the NeuroDebian
+ Team greatly simplifies the task of providing our researchers the
+ best software available, and I consider the repository a vital part
+ of my professional life. As a maintainer on the MRIConvert
+ project, I find that NeuroDebian provides a valuable venue for
+ dissemination of our software. It would not be possible to reach
+ the same wide audience without the NeuroDebian repository.
+
+.. quote::
+ :author: Dr. Kiyotaka Nemoto
+ :affiliation: University of Tsukuba
+ :tags: email, derivatives, time
+ :date: 2013-02-06
+
+ Neurodebian is the best solution for researchers in neuroscience.
+ Everybody should have experienced wasting so much time in just setting
+ up software. With Neurodebian repository, you can easily setup many
+ useful software packages and focus on your research. I recommend this
+ repository to everyone who is interested in using Linux in
+ neuroscience.
+
+.. quote::
+ :author: Dr. Andrew Janke
+ :affiliation: Center for Advanced Imaging, University of Queensland, Australia
+ :date: 2013-02-06
+ :tags: email, upstream, stability, versioning, provenance, vm,
+ reproducibility, collaboration
+
+ We use NeuroDebian on a daily basis as it provides a stable and
+ versioned software base for analysis. This is critical as it allows us
+ to maintain data provenance, something that is often sorely lacking.
+ Our collaborators who don't quite have their heads around Linux yet
+ are pointed to the NeuroDebian Virtual Machine, it allows them to run
+ an identical analysis environment to us regardless of where they are
+ or operating system.
+
+.. quote::
+ :author: Nina Preuss
+ :affiliation: PMP, nitrc.org
+ :date: 2013-02-06
+ :tags: disqus, money, quality, contributions, cloud, derivatives
+
+ NITRC-CE, or the NITRC Computational Environment, on the Amazon
+ Marketplace wouldn't have happened as quickly and thus cost effectively
+ without leveraging NeuroDebian's good works. We appreciate their
+ critical contribution to the neuroimaging compute community.
+
+.. quote::
+ :author: Sebastiaan Mathôt
+ :affiliation: Aix-Marseille université, Laboratoire de Psychologie Cognitive
+ :date: 2013-02-06
+ :tags: email, impact
+
+ For any neuroscientist that relies on open-source software,
+ NeuroDebian is the single most important resource.
+
+.. quote::
+ :author: Sebastian Eichelbaum
+ :affiliation: OpenWalnut project, Image and Signal Processing Group, Institute of Computer Science, University of Leipzig, Germany
+ :date: 2013-02-11
+ :tags: email, breadth, dissemination
+
+ With NeuroDebian we can utilize thousands of tools, providing the foundation for our research. On the other hand, we can provide our tools to a large community easily.
+
+
+.. quote::
+ :author: Francisco Pereira
+ :affiliation: Siemens Corporate Research
+ :date: 2013-02-06
+ :tags: gplus, time
+
+ Thanks to NeuroDebian I now have to spend my time thinking hard about what to do with the tools, rather than leisurely installing them and tracking dependencies.
+
+.. quote::
+ :author: Alexander Wiebel
+ :affiliation: OpenWalnut project, Zuse Institute Berlin (ZIB), Germany
+ :date: 2013-02-19
+ :tags: email, breadth, dissemination
+
+ It is great to have NeuroDebian as a platform to bring our
+ visualization system OpenWalnut to a broad audience together with the large variety of
+ related data analysis tools available in NeuroDebian.
+
+
Individual Laboratories and Researchers
---------------------------------------
VirtualBox, ran AFNI, and generated the files I needed, all within
about an hour and a half. [...] not bad, considering that I know
essentially no Linux/Unix. So here's a big "thanks!" :)
+
+.. quote::
+ :author: Vincent Kersten
+ :affiliation: University Medical Center Utrecht
+ :tags: email, standardization, money, Debian
+ :date: 2013-02-06
+
+ Neurodebian provides us with a consitent way of sotware packaging
+ and upgrades, eliminating tedious compiles and home-brew setups,
+ while seamlessly integrating with the Debian distribution. Excellent
+ and very valuable work, saving costs and difficult to spot
+ errors. High five Michael, Yaroslav and team! Keep them packages
+ coming!
+
+.. quote::
+ :author: Christian Stephan-Otto
+ :affiliation: Neuroimaging Research Group, Parc Sanitari Sant Joan de Deu, Barcelona, Spain
+ :date: 2013-02-06
+ :tags: email, vm, breadth
+
+ Since I started using a NeuroDebian virtual machine on win64 months
+ ago I am relying more and more on its diverse tools, from
+ population-specific template creation to pipelining the analysis of
+ fMRI, DTI and morphology studies. There is a great chance I will
+ end up working exclusively with NeuroDebian!
+
+.. quote::
+ :author: Mathias Goldau
+ :affiliation: Cortical Networks, Max-Planck-Institute for neurological research, Cologne, Germany
+ :date: 2013-02-07
+ :tags: email, time, breadth
+
+ Without NeuroDebian we would have wasted precious time for
+ deploying software, and we wouldn't have tested so many software
+ tools.
+
+.. quote::
+ :author: Joseph Viviano
+ :affiliation: York University, Toronto Canada
+ :date: 2013-02-19
+ :tags: email, reproducibility, versioning, impact
+
+ NeuroDebian not only helped our lab focus on research and producing
+ results with FOSS, it has also made it much easier to maintain
+ version control, facilitating data portability and
+ reproducibility. I see this as the most important current project
+ working towards transparent neuroscientific methods with clear and
+ reproducible results.
+
+.. quote::
+ :author: Dr. Bertram Walter
+ :affiliation: Bender Institute of Neuroimaging, University of Giessen, Germany
+ :date: 2013-02-22
+ :tags: email, money, maintenance, support, quality
+
+ Neurodebian provides not only a platform for neuroscience
+ applications that makes maintenance of collections of tools
+ easy. The staff also gives a very quick support in case of - very
+ rare - problems. Altogether Neurodebian saves a lot of time and
+ money.
--- /dev/null
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _chap_acknowledgements:
+
+****************
+Acknowledgements
+****************
+
+Many people have contributed to NeuroDebian over the years. We thank all
+researchers and programmers that produce scientific tools as free and
+open source software.
+
+We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless
+supply of Italian espresso <coffeeart>`.
+
+.. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
+
+Thanks to the following institutions and individuals for hosting a mirror:
+
+* `Department of Psychological and Brain Sciences at Dartmouth College`_
+ *[us-nh]* (primary mirror)
+* `Department of Experimental Psychology at the University of Magdeburg`_
+ *[de-md]*
+* `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
+* `Paul Ivanov`_ *[us-ca]*
+* `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
+ *[us-tn]*
+* `Australia's research and education network (AARNET)
+ <http://www.aarnet.edu.au>`_ *[au]*
+* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
+* Iaroslav Iurchenko *[ua]*
+* `Nikolaus Valentin Haenel`_ *[de-v]*
+* `INCF G-Node at Ludwig-Maximilians-Universität München <http://www.g-node.org>`_ *[de-m]*
+
+If your are interested in mirroring the repository, please see the :ref:`faq`.
+
+.. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
+.. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
+.. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
+.. _Paul Ivanov: http://www.pirsquared.org
+.. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
+.. _Nikolaus Valentin Haenel: http://haenel.co
+
+.. include:: link_names.txt
NeuroDebian Virtual Machine
===========================
+`Installation`_ | `Working with the virtual machine`_ | `Troubleshooting`_ |
+`What has changed`_
+
.. quotes::
:random: 1
:tags: vm
-For those who are not yet running a Debian-based operation system we offer a
-`virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit
-from a Debian-based research environment on other operating systems.
-This virtual machine initially comes as a compact Debian installation that can,
-once installed, be equipped with a large variety of neuroscience software with
-just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
+For all systems running a non-Debian-based operation system, such as MS Windows
+or Mac OS X, we offer a `virtual machine`_ that can be equipped with a large
+variety of neuroscience software with just a few mouse clicks (e.g. AFNI_,
+FSL_, PyMVPA_).
.. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
-.. _AFNI: http://afni.nimh.nih.gov/afni/
-.. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
-.. _FSL: http://www.fmrib.ox.ac.uk/fsl/
-.. _PyMVPA: http://www.pymvpa.org
-
-
-Downloads
----------
-
-* `NeuroDebian 6.0.6 image (32bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_i386.ova>`_ [~559MB]
-
- *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 6.0.6 image (64bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_amd64.ova>`_ [~576MB]
-
- *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.*
-
-Virtual appliances above carry guest additions for 4.x series of the
-VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2
-virtual appliances:
-
-* `NeuroDebian 6.0.2 image (32bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
-
-* `NeuroDebian 6.0.2 image (64bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
-
-.. note::
-
- This older virtual appliances are distributed as a `zip` file. Please
- extract all files from the `.zip` file, using appropriate software
- for your operating system.
-
-.. 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)
-
- *This webpage offers installers of the VirtualBox application, as well as the
- documentation.*
-
-Changes
--------
-
-6.0.6 -- 01 Oct 2012
-
- * Updated core system to Debian squeeze 6.0.6
-
-6.0.5 -- 10 Nov 2011
-
- * Updated core system to Debian squeeze 6.0.3
- * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
-
- - ``~/host`` is now symlinked to correct path ``/media/sf_host``
- - ``brain`` user is added to ``vboxsf`` group so mounted host
- directories should become readily available
-
- * Root partition size and swap space got doubled in size (40GB
- and 2GB correspondingly). Space is allocated dynamically so
- the actual size of the virtual drive should not grow unless
- you use it
-
-6.0.4 -- 13 Jun 2011
-
- * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
-
-6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
-
- * Updated to Debian squeeze 6.0.1
- * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
- * Appliance is available as a single file (.ova) ready for the import
-
-6.0.2 -- 08 Feb 2011
-
-6.0.1 -- 01 Dec 2010
-Documentation
--------------
-
-The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
+The virtual machine contains an installation of `Debian 7.0 (wheezy)`_ with a
GNOME_ desktop environment. All installed software comes from standard Debian
-packages, or prospective Debian packages from NeuroDebian. This means that all
-contained software is readily available for any system running a Debian
-operating system (or a recent Ubuntu release). The virtual machine can be seen
-as a showcase of what Debian for neuroscience research feels like. Moreover,
-once downloaded this virtual machine can be kept up to date, just as any other
+packages, or prospective Debian packages from NeuroDebian. The virtual machine
+can be seen as a showcase of what Debian for neuroscience research feels like.
+Once downloaded this virtual machine can be kept up to date, just as any other
Debian installation. Using convenient graphical package management tools users
will benefit from security bug fixes provided by the Debian project for the
whole operating system, as well as from software updates for
neuroscience-related packages.
-.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
-.. _GNOME: http://www.gnome.org/
+Even on Debian-based systems this virtual machine is an excellent way to
+maintain an analysis environment that remains identical throughout the lifetime
+of a study and that can be archived alongside acquired data and publications.
+This is a much more practical way than freezing the entire software stack of a
+whole workstation, where it quickly becomes troublesome to combine the desire
+for latest research methodology for new studies and the need for stability for
+ongoing projects.
Installation
~~~~~~~~~~~~
-The following video shows how to get the NeuroDebian virtual machine running
-on your machine. The installation is shown for Mac OS X. It should, however, be
-very similar on a Windows box. If you cannot watch the video, please take a
-look at the written instructions below.
-
-.. raw:: html
+The following instructions demonstrate how to install the NeuroDebian virtual
+machine -- here shown exemplary for Mac OS X, but the procedure is virtually
+identical on a Windows box. There is also a video tutorial at coffee break
+length. `[Virtual machine setup video tutorial]
+<http://www.youtube.com/watch?v=eqfjKV5XaTE>`_.
- <iframe title="YouTube video player"
- class="youtube-player"
- type="text/html"
- width="640"
- height="375"
- src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
- frameborder="0"></iframe>
-
-First download and install a recent version of VirtualBox_. VirtualBox is a
-virtualization software that is freely available for Windows, MacOS X, Solaris,
-and Linux. VirtualBox comes with a comprehensive manual that should answer
-potential questions regarding installation and maintenance.
+If you don't have t already, first download and install a recent version of
+VirtualBox_. VirtualBox is a virtualization software that is freely available
+for Windows, MacOS X, Solaris, and Linux. VirtualBox comes with a comprehensive
+manual that should answer potential questions regarding installation and
+maintenance.
.. _VirtualBox: http://www.virtualbox.org
-Next, download the most recent version of the NeuroDebian virtual machine from
-the Downloads_ section. Start VirtualBox and select "Import Appliance" from the file
-menu.
+Obtain the most recent version of the NeuroDebian virtual machine by visiting
+http://neuro.debian.net and selecting your operating system and a download
+server on the frontpage.
+
+Start VirtualBox and select "Import Appliance" from the file menu.
.. image:: pics/vm_import_app.jpg
.. image:: pics/vm_settings.jpg
-The virtual machine logs yourself in automatically. The name of the virtual
-machine user is `brain` and the password is `neurodebian`. The *root* password
-is also `neurodebian`. In most cases, however, you should not be forced to type
-the password, since `sudo` is configured to work without it.
+The virtual machine logs yourself in automatically. This is the default account:
+
+:user: brain
+:password: neurodebian
+
+:root password: neurodebian
+
+In most cases you should not be forced to type the password, because ``sudo``
+is configured to work without it.
.. note::
Working with the virtual machine
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The next video is a demonstration of some basic desktop integration features.
-It shows how to use the virtual machine in full-screen and seamless mode, shared
-folder access, software installation, as well as suspending and resuming the
-virtual machine.
-
-.. raw:: html
-
- <iframe title="YouTube video player"
- class="youtube-player"
- type="text/html"
- width="640"
- height="375"
- src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
- frameborder="0"></iframe>
+The NeuroDebian virtual machine has very low maintenance demands. We have
+prepared a short video demo that shows most typical procedures that you will
+probably perform while working with NeuroDebian inside a virtual machine:
+use the virtual machine in full-screen and seamless mode, shared folder access,
+software installation, as well as suspending and resuming the
+virtual machine. `[Virtual machine handling video tutorial]
+<http://www.youtube.com/watch?v=OV7fYSEoOeQ>`_
.. _chap_vm_troubleshooting:
Troubleshooting
~~~~~~~~~~~~~~~
-Updating the VM or installing new packages doesn't work.
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
+
+ Updating the VM or installing new packages doesn't work
+ The VM uses as service that tries to figure out the best/closest package
+ repository for you. In some network environments this service might not work
+ well, or not at all. To check if this is a problem, you can modify the
+ respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need
+ to use ``sudo`` for that) and replace the package repository URL with a
+ mirror close to you. A comprehensive list of mirrors is available at:
+ http://www.debian.org/mirror/list
+
+ Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
+ URL. For example, in Canada you might want to change::
+
+ deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
+
+ to::
+
+ deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+
+ Only modify lines that refer to ``geomirror`` (all of them), but do **not**
+ modify entries for ``security.debian.org``.
+
+ Our proxy setup at work prevents APT from downloading packages
+ APT needs to be told how to access the proxy. Talk to your local sysadmin
+ and ask for the proxy's address (maybe a username and password too), as well
+ as the ports for HTTP and FTP proxies. With this information add the
+ following lines in the file, /etc/apt/apt.conf.d/80proxy. This will ensure
+ that after an upgrade changes won't be lost::
+
+ Acquire::http::proxy "http://<username>:<password>@<proxy>:<port>/";
+ Acquire::ftp::proxy "ftp://<username>:<password>@<proxy>:<port>/";
+ Acquire::https::proxy "https://<username>:<password>@<proxy>:<port>/";
+
+ I cannot hear sounds played in the virtual machine
+ By default the sound is muted. To enable playback launch the mixer applet by
+ clicking on the mixer icon in the task bar. Unmute the master volume
+ control. Now click on the "Volume control" to load the channel mixer dialog.
+ Unmute the "Master" and "PCM" channels and raise the volume as desired. You
+ should now be able to hear sounds played within the virtual machines through
+ your host computer's speakers.
+
+ My VM lost mounted host directories after upgrading from VirtualBox from 3.x to 4.x
+ NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
+ 3.x series of VirtualBox and some initial versions of VirtualBox in
+ 4.x series have failed to mount host directories properly.
+ VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
+ series. If you nevertheless want to upgrade guest additions within
+ NeuroDebian VM, please rebuild the version available from the
+ backports::
+
+ sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
+ sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
+ virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+
+ and reboot VM.
+
+ I am still running an older VirtualBox 3.x
+ Download one of the image files listed below. These older releases
+ are distributed as a `zip` file. Please extract all files from the
+ `.zip` file, using appropriate software for your operating system.
+
+ * `NeuroDebian 6.0.2 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
+
+ * `NeuroDebian 6.0.2 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
+
+
+What has changed
+----------------
+
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
- The VM uses as service that tries to figure out the best/closest package
- repository for you. In some network environments this service might not work
- well, or not at all. To check if this is a problem, you can modify the
- respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need to
- use ``sudo`` for that) and replace the package repository URL with a mirror
- close to you. A comprehensive list of mirrors is available at:
- http://www.debian.org/mirror/list
+ 7.0.0 -- 15 May 2013
+ * VM appliance based on the official wheezy release.
+ * Uses xfce4-terminal by default (instead of urxvt/rxvt-unicode as
+ in beta-releases)
- Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
- URL. For example, in Canada you might want to change::
+ 6.999.b4.20130421 -- 22 Apr 2013
+ * Refreshed VM appliance to avoid lengthy initial upgrade
- deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
+ 6.999.b4.20121231 -- 31 Dec 2012
+ * Based on beta 4 release of debian-installer_ for wheezy
+ * Comes with XFCE4_ instead of GNOME_
- to::
+ 6.0.6 -- 01 Oct 2012
+ * Updated core system to Debian squeeze 6.0.6
- deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+ 6.0.5 -- 10 Nov 2011
+ * Updated core system to Debian squeeze 6.0.3
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
- Only modify lines that refer to ``geomirror`` (all of them), but do **not**
- modify entries for ``security.debian.org``.
+ - ``~/host`` is now symlinked to correct path ``/media/sf_host``
+ - ``brain`` user is added to ``vboxsf`` group so mounted host
+ directories should become readily available
-I cannot hear sounds played in the virtual machine.
+ * Root partition size and swap space got doubled in size (40GB
+ and 2GB correspondingly). Space is allocated dynamically so
+ the actual size of the virtual drive should not grow unless
+ you use it
- By default the sound is muted. To enable playback launch the mixer applet by
- clicking on the mixer icon in the task bar. Unmute the master volume control.
- Now click on the "Volume control" to load the channel mixer dialog. Unmute
- the "Master" and "PCM" channels and raise the volume as desired. You should
- now be able to hear sounds played within the virtual machines through your
- host computer's speakers.
+ 6.0.4 -- 13 Jun 2011
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
-I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
-mounted host directories.
+ 6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
+ * Updated to Squeeze 6.0.1
+ * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
+ * Appliance is available as a single file (.ova) ready for the import
- NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
- 3.x series of VirtualBox and some initial versions of VirtualBox in
- 4.x series have failed to mount host directories properly.
- VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
- series. If you nevertheless want to upgrade guest additions within
- NeuroDebian VM, please rebuild the version available from the
- backports::
+ 6.0.2 -- 08 Feb 2011
+ * Minor update
- sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
- sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
- virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+ 6.0.1 -- 01 Dec 2010
+ * Minor update
- and reboot VM.
+.. include:: link_names.txt
interesting:
* :ref:`NeuroDebian news <news>`
-* :ref:`User support <support>`
+* :ref:`User support <chap_contacts>`
* :ref:`Virtual machine tutorial video <chap_vm>`
* :ref:`Known issues and troubleshooting <chap_vm_troubleshooting>`
--- /dev/null
+.. -*- mode: rst; fill-column: 78; indent-tabs-mode: nil -*-
+.. vi: set ft=rst sts=4 ts=4 sw=4 et tw=79:
+ ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+ #
+ # See COPYING file distributed along with the NeuroDebian package for the
+ # copyright and license terms.
+ #
+ ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+
+.. index:: Who is using it?, Publications
+.. _chap_whoisusingit:
+
+****************
+Who Is Using It?
+****************
+
+
+.. only:: html
+
+ If you are using NeuroDebian or have published a study employing it, please
+ leave a comment at the bottom of this page, if you want to be listed here as
+ well.
+
+
+Tools and systems built atop NeuroDebian
+========================================
+
+* ref:`Nemoto et al., BMC Medical Imaging (2011) <NDR+2011>`: Lin4Neuro: a
+ customized Linux distribution ready for neuroimaging analysis.
+
+* ref:`Stoner et al., Frontiers in Neuroinformatics (2012) <SLZ+2011>`:
+ A cloud-based data-sharing and analysis cyberinfrastructure for
+ neuroinformatics.
+
+Articles referring to NeuroDebian
+=================================
+
+* :ref:`Yamazaki et al., NeuralNetworks (2011) <YIO+2012>`: Simulation platform:
+ A cloud-based online simulation environment.
+
+* ref:`Aguirre, NeuroImage (2012) <Agu2012>`: FIASCO, VoxBo, and MEDx: Behind
+ the code.
+
+* ref:`Mathôt et al., Behavioral Research Methods (2012) <MST2012>`: OpenSesame:
+ An open-source, graphical experiment builder for the social sciences.
+
+* ref:`Minervini et al., Image Processing Theory, Tools and Applications (2012)
+ <MDT+2012>`: Mouse neuroimaging phenotyping in the cloud.
+
+* ref:`Galluppi et al., Computing Frontiers (2012) <GDS+2012>`: A hierachical
+ configuration system for a massively parallel neural hardware platform.
+
+* ref:`Cauda et al., NeuroImage (2012) <CCT+2012>`: Meta-analytic clustering of
+ the insular cortex Characterizing the meta-analytic connectivity of the insula
+ when involved in active tasks.
+
+* ref:`Gingnell et al., Psychoneuroendocrinology (2012) <GEF+2012>`: Oral
+ contraceptive use changes brain activity and mood in women with previous
+ negative affect on the pill—A double-blinded, placebo-controlled randomized
+ trial of a levonorgestrel-containing combined oral contraceptive.
+
+* ref:`Gingnell et al., Hormones and Behavior (2012) <GMB+2012>`: Menstrual
+ cycle effects on amygdala reactivity to emotional stimulation in premenstrual
+ dysphoric disorder.
+
+* ref:`Milham, Neuron, (2012) <Mil2012>`: Open Neuroscience Solutions for the
+ Connectome-wide Association Era.
+
+* ref:`Visan, Computer Science Dissertations (2012) <Vis2012>`: Temporal
+ meta-programming: treating time as a spatial dimension.
+
+* ref:`Gerhard et al., Frontiers in Neuroinformatics (2011) <GDL+2011>`: The
+ connectome viewer toolkit: an open source framework to manage, analyze, and
+ visualize connectomes.
+
+* ref:`Soh et al., Journal of Integrative Bioinformatics (2011) <SMT+2011>`:
+ Integrative visualization of temporally varying medical image patterns.
+
+* ref:`Gosh et al., HBM (2010) <GBC+2010>`: Nipype: opensource platform for
+ unified and replicable interaction with existing neuroimaging tools.
+
# extract the original source package
dpkg-source -x $dsc_file $sdir
# note backport in changelog
+# This will create a new changelog entry
+# All subsequent calls to dch should use -a to assure that those entries
+# are appended to the existing entry (otherwise with wheezy new entries will be added)
$bp_dch_cmd -D ${bp_distribution} -l "${bp_version}" "Backported for ${bp_distribution}."
if [ "$bp_update_maintainer" = 1 ]; then
printf "${green}Enabling additional quilt patch series for $bp_distribution.\n${NC}"
fi
cat $sdir/debian/patches/series-$bp_distribution >> $sdir/debian/patches/series
- $bp_dch_cmd "Added 'series-$bp_distribution' in quilt patch series."
+ $bp_dch_cmd -a "Added 'series-$bp_distribution' in quilt patch series."
fi
# look for backport patches
for p in $(ls -1 $sdir/debian/patches/$bp_distribution-dsc-patch* 2> /dev/null || true); do
printf "${green}Applying additional patch $(basename "$p").\n${NC}"
fi
patch -p1 --directory=$sdir < "$p"
- $bp_dch_cmd "Applied additional patch from debian/patches/$(basename "$p")."
+ $bp_dch_cmd -a "Applied additional patch from debian/patches/$(basename "$p")."
done
fi
printf "${green}Modifying debian/control with given instructions.\n${NC}"
fi
bash -c "sed -i $bp_mod_control $sdir/debian/control"
- $bp_dch_cmd "Used following sed expression to modify debian/control:$bp_mod_control."
+ $bp_dch_cmd -a "Used following sed expression to modify debian/control:$bp_mod_control."
fi
# extract final version
# ln -f is used for further robustness
[ ! -L $HOME/host ] && ln -sf /media/sf_host $HOME/host
+# Figure out which version of IPython is available
+ipython_version=$(apt-cache policy ipython 2>/dev/null | sed -ne '/Version table:/ { n;s,^[ \*]*\(.*\) .*,\1,gp}')
+dpkg --compare-versions $ipython_version lt 0.13.1 && ipython=ipython01x || ipython=ipython
+
# TODO: add PyMVPA:
# FALSE "PyMVPA" "python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorial-data" \
# needs -doc and -tutorial-data package
additional components will be installed." \
FALSE "Emacs" "emacs" \
FALSE "Graphics (e.g. GIMP, Inscape)" "gimp,inkscape,svgtune,xzgv,vym" \
-FALSE "Octave" "octave,qtoctave" \
+FALSE "Octave" "qtoctave" \
FALSE "OpenOffice.org" "openoffice.org" \
-FALSE "PyMVPA Tutorial" "ipython01x,python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorialdata,spyder" \
+FALSE "PyMVPA Tutorial" "$ipython,python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorialdata,spyder" \
FALSE "Python: Electrophysiology & Modeling" "python-brian,python-pynn,python-pyentropy,stimfit" \
-FALSE "Python: Neuroimaging" "ipython01x,spyder,nipy-suite,python-mvpa2" \
-FALSE "Python: Scientific stack" "ipython01x,spyder,python-matplotlib,python-pandas,python-sympy" \
+FALSE "Python: Neuroimaging" "$ipython,spyder,nipy-suite,python-mvpa2" \
+FALSE "Python: Scientific stack" "$ipython,spyder,python-matplotlib,python-pandas,python-sympy" \
FALSE "R" "r-recommended" \
FALSE "TeX Live" "texlive" \
FALSE "Adobe Flash browser plugin" "flashplugin-nonfree" \
-FALSE "Sun Java browser plugin" "sun-java6-plugin" \
|| true)
if [ -n "$packages" ]; then
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
-# Create a figure with the NeuroDebian repo subscription stats from the apache logs
-# Requires out put of
-# zgrep "GET /lists/[-a-z\.]\+ HTTP" neuro.debian.net-*access.log* | sed -e 's,[^:]*:\([0-9\.]\+\).*\[\(.*\):.*:.*:.*/lists/\(.*\) HTTP.*,\2;\3;\1,' -e 's,/, ,g'
-# either from a file or on stdin. Needs output filename as the only argument
-
import fileinput
import sys
+import time
from datetime import datetime
-import numpy as np
-import matplotlib
-matplotlib.use('Agg')
-import pylab as pl
-from matplotlib.dates import date2num, num2date
-from matplotlib.dates import YearLocator, MonthLocator, DateFormatter
-from matplotlib.font_manager import FontProperties
-from ConfigParser import SafeConfigParser
-from math import ceil
-
-dt = [('ip', '|S16'),
- ('loc', '|S3'),
- ('suite', '|S20'),
- ('date', float)]
-
-
-def make_figure(data, ymax=None):
- fig = pl.figure(figsize=(14,3))
- distros = ('Debian', 'Ubuntu')
- # Sorting is actually seems to be not needed on Python 2.7
- # which probably returns release codenames in the order as
- # in the config file which is already correct
- # But since our server is still on previous stable release
- # let's sort for now explicitly
- # 9999 for 'nd' == 'sid'
- sorting_ids = dict([(x[0], len(x[1])>2 and float(x[1][2:]) or 9999)
- for x in cfg.items('release backport ids')])
- for idistro, distro in enumerate(distros):
- ax = fig.add_subplot(1, len(distros), idistro+1)
- suites = [code for code in cfg.options('release codenames')
- if cfg.get('release codenames', code).count(distro)]
- # sort suites according to backport ids
- # and in reverse order so the freshiest is on top
- suites = sorted(suites,
- cmp=lambda x,y: cmp(sorting_ids[x], sorting_ids[y]),
- reverse=True)
- plot_datehist(ax, data, 10, suites, title=distro, ymax=ymax)
- fig.autofmt_xdate()
- return fig
-
+import re
+import sets
+import json
+import operator
-def plot_datehist(ax, data, bins, suites, title=None, ymax=None):
- colors=['#ff0088', '#20435C', '#45902C', '#E08720']
- linestyle=['-', '--']
- global_x_max = None
- global_x_min = None
- global_y_max = None
- for i, suite in enumerate(suites):
- dates = data['date'][data['suite'] == suite]
- # history in days
- history_length = dates.max() - dates.min()
- # make approx monthly bins, smaller bins yield spiky curves
- # needs new=True to work with oldish numpy
- (hist, bin_edges) = np.histogram(dates, np.ceil(history_length/30.))
- if False:
- # debug output ;-)
- print dates.min(), num2date(dates.min()), dates.max(), \
- num2date(dates.max()), history_length
- print bin_edges
- if len(bin_edges) < 2:
- # protect against single data point entries by ignoring them
- # wouldn't be able to draw a line anyway ;-)
- continue
- width = bin_edges[1] - bin_edges[0]
- # think lines
- y = hist / width
- global_y_max = max(max(y), global_y_max)
- ax.plot(bin_edges[:-1]+(width/2), y,
- label=suite, color=colors[i%4], linestyle=linestyle[i//4], lw=2)
- # transparent curve shading
- ax.fill_between(bin_edges[:-1]+(width/2), 0, hist / width, alpha=0.2,
- label=suite, color=colors[i%4])
- # figure out axis limits to avoid whitespace in plots
- x_max = bin_edges[-2] + width/2
- x_min = bin_edges[0] + width/2
-
- global_x_max = max(x_max, global_x_max)
- if global_x_min is None or x_min < global_x_min:
- global_x_min = x_min
-
- ax.set_xlim(global_x_min, global_x_max)
- ax.set_ylabel('New subscriptions [1/day]')
- if title:
- ax.set_title(title)
- if not ymax:
- # Always leave significant 5% for improvement ;-)
- ymax = global_y_max * 1.05
- ax.set_ylim(0, ymax)
- # set x-ticks in date
- # see: http://matplotlib.sourceforge.net/examples/api/date_demo.html
- ax.xaxis.set_major_locator(YearLocator())
- ax.xaxis.set_major_formatter(DateFormatter('\n\n%Y'))
- ax.xaxis.set_minor_locator(MonthLocator(interval=2))
- ax.xaxis.set_minor_formatter(DateFormatter('%b'))
- # format the coords message box
- ax.format_xdata = DateFormatter('%Y-%m-%d')
- ax.grid(True)
- # pukes with old matplotlib
- #font = FontProperties()
- #font.set_size = 8
- pl.legend(loc='upper left', #prop=font,
- labelspacing=.2, borderaxespad=.2,
- handletextpad=.2, borderpad=.2)
+releases = {
+ 'etch': 'Debian GNU/Linux 4.0 (etch)',
+ 'lenny': 'Debian GNU/Linux 5.0 (lenny)',
+ 'squeeze': 'Debian GNU/Linux 6.0 (squeeze)',
+ 'wheezy': 'Debian GNU/Linux 7.0 (wheezy)',
+ 'jessie': 'Debian testing (jessie)',
+ 'sid': 'Debian unstable (sid)',
+ 'hardy': 'Ubuntu 08.04 LTS "Hardy Heron" (hardy)',
+ 'jaunty': 'Ubuntu 09.04 "Jaunty Jackalope" (jaunty)',
+ 'karmic': 'Ubuntu 09.10 "Karmic Koala" (karmic)',
+ 'lucid': 'Ubuntu 10.04 LTS "Lucid Lynx" (lucid)',
+ 'maverick': 'Ubuntu 10.10 "Maverick Meerkat" (maverick)',
+ 'natty': 'Ubuntu 11.04 "Natty Narwhal" (natty)',
+ 'oneiric': 'Ubuntu 11.10 "Oneiric Ocelot" (oneiric)',
+ 'precise': 'Ubuntu 12.04 LTS "Precise Pangolin" (precise)',
+ 'quantal': 'Ubuntu 12.10 "Quantal Quetzal" (quantal)',
+ 'raring': 'Ubuntu 13.04 "Raring Ringtail" (raring)',
+ 'saucy': 'Ubuntu 13.10 "Saucy Salamander" (saucy)',
+}
if __name__ == '__main__':
- if not len(sys.argv) > 1:
- print 'Need output filename.'
- sys.exit(1)
- cfg_path="/home/neurodebian/neurodebian.git/neurodebian.cfg"
- #cfg_path="../neurodebian.cfg"
- cfg = SafeConfigParser()
- cfg.read(cfg_path)
- data = []
- for line in fileinput.FileInput(sys.argv[2:], openhook=fileinput.hook_compressed):
- date, list_, ip = line.split(';')
+ data = {}
+ # get the IP, date and target release
+ # the date is truncated to a month/year combo
+ listget = re.compile(r'^([0-9.:]*) .*\[([^:]*).*GET /lists/([a-z]*)')
+ for line in fileinput.FileInput(openhook=fileinput.hook_compressed):
+ match = listget.match(line)
+ if not match:
+ continue
+ addr, date, release = match.groups()
+ if not release in releases:
+ # ignore fantasy names
+ continue
+ date = datetime.strptime(date, '%d/%b/%Y')
+ # truncate to a week
try:
- suite, loc = list_.split('.')
+ date = datetime(date.year, date.month, date.day / 7 * 7 + 1)
except ValueError:
- suite = list_
- loc = ''
- date = datetime.strptime(date, "%d %b %Y")
- data.append((ip.strip(), loc, suite, date2num(date)))
- data = np.array(data, dtype=dt)
- make_figure(data).savefig(sys.argv[1], bbox_inches='tight', dpi=60)
+ # only on Feb28...
+ date = datetime(date.year, date.month, date.day / 7 * 7)
+ # microseconds since epoch
+ date = int(time.mktime(date.timetuple()) * 1000)
+ rstats = data.setdefault(releases[release], {})
+ rtime = rstats.setdefault(date, 0)
+ rtime += 1
+ rstats[date] = rtime
+ data[releases[release]] = rstats
+ # determine the union of all timestamps
+ timestamps = sets.Set()
+ for codename, stats in data.iteritems():
+ timestamps.union_update(stats.keys())
+ export = [{'key': release,
+ 'values': [[ts, float(data[release].setdefault(ts, 0)) / 7]
+ for ts in sorted(timestamps)]}
+ for release in sorted(data)]
+ print json.dumps(export)
#
set -e
-set -u
release=$1
dscfile=$2
exit 1
fi
+set -u
+
upstream_name=${dscfile%%_*}
# To overcome bash desire to claim empty array unbound under 'set -u'
--- /dev/null
+#!/usr/bin/python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+import fileinput
+import sys
+import time
+from datetime import datetime
+import re
+import sets
+import json
+import operator
+
+
+releases = {
+ 'etch': 'Debian GNU/Linux 4.0 (etch)',
+ 'lenny': 'Debian GNU/Linux 5.0 (lenny)',
+ 'squeeze': 'Debian GNU/Linux 6.0 (squeeze)',
+ 'wheezy': 'Debian testing (wheezy)',
+ 'sid': 'Debian unstable (sid)',
+ 'hardy': 'Ubuntu 08.04 LTS "Hardy Heron" (hardy)',
+ 'jaunty': 'Ubuntu 09.04 "Jaunty Jackalope" (jaunty)',
+ 'karmic': 'Ubuntu 09.10 "Karmic Koala" (karmic)',
+ 'lucid': 'Ubuntu 10.04 LTS "Lucid Lynx" (lucid)',
+ 'maverick': 'Ubuntu 10.10 "Maverick Meerkat" (maverick)',
+ 'natty': 'Ubuntu 11.04 "Natty Narwhal" (natty)',
+ 'oneiric': 'Ubuntu 11.10 "Oneiric Ocelot" (oneiric)',
+ 'precise': 'Ubuntu 12.04 LTS "Precise Pangolin" (precise)',
+ 'quantal': 'Ubuntu 12.10 "Quantal Quetzal" (quantal)',
+ 'raring': 'Ubuntu 13.04 "Raring Ringtail" (raring)',
+ 'saucy': 'Ubuntu 13.10 "Saucy Salamander" (saucy)',
+}
+
+def error(msg):
+ sys.stderr.write('E: %s\n' % msg)
+
+def info(msg):
+ # print nothing ATM
+ # sys.stderr.write("I: %s\n" % msg)
+ pass
+
+file_regex = re.compile('.*popcon-(\d{4}-\d{1,2}-\d{1,2})(|.gz)')
+
+def read_popcon_stats(filename, read_packages=True):
+ info("Reading %s" % filename)
+ entry = dict(submissions = None,
+ package = {},
+ release = {},
+ architecture = {})
+
+ for line in fileinput.FileInput(filename, openhook=fileinput.hook_compressed):
+ key, values = [x.strip().lower() for x in line.split(':', 1)]
+ if key == 'package': # most probable
+ if not read_packages:
+ break
+ try:
+ pkg, vote, old, recent, nofiles = values.split()
+ except ValueError:
+ raise ValueError("Failed to split %s" % values)
+ entry[key][pkg] = tuple(int(x) for x in (vote, old, recent, nofiles))
+ elif key in ('release', 'architecture'):
+ kvalue, value = values.split()
+ entry[key][kvalue] = int(value)
+ elif key == 'submissions':
+ entry[key] = int(values)
+ else:
+ raise ValueError("Do not know how to handle line" % line)
+ return entry
+
+if __name__ == '__main__':
+ data = {}
+
+ popcon_versions = {}
+ timestamps = sets.Set()
+
+ for f in sys.argv[1:]:
+ file_reg = file_regex.match(f)
+ if not file_reg:
+ error("Failed to recognize filename %s" % f)
+ continue
+
+ date = time.strptime(file_reg.groups()[0], '%Y-%m-%d')
+ entry = read_popcon_stats(f, read_packages=False)
+
+ date_int = int(time.mktime(date)*1000)
+ # Let's coarsen a bit -- to a week which makes sense anyways
+ # since popcon submissions are spread over a week for balanced
+ # load
+ coarsen_days = 7
+ coarsen = coarsen_days*24*3600*1000
+ # coarsen and place marker at the end of the duration
+ # but not later than today
+ date_int = min((date_int//coarsen + 1)*coarsen,
+ time.time()*1000)
+ for version, count in entry['release'].iteritems():
+ if not version in popcon_versions:
+ popcon_versions[version] = {}
+ popcon_ = popcon_versions[version]
+ popcon_[date_int] = count + popcon_.get(date_int, 0)
+ timestamps.add(date_int)
+
+ versions = sorted([x for x in popcon_versions.keys() if not 'ubuntu' in x]) + \
+ sorted([x for x in popcon_versions.keys() if 'ubuntu' in x])
+
+ # we need to make sure that for every date we have an entry for
+ # every version, otherwise d3 pukes because of ... d3.v2.js:expand
+ export = [{'key': k,
+ 'values': [[date, popcon_versions[k].get(date, 0)/coarsen_days]
+ for date in sorted(list(timestamps))]}
+ for k in versions]
+ print json.dumps(export)
+
--- /dev/null
+#!/usr/bin/python
+#emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
+#ex: set sts=4 ts=4 sw=4 noet:
+"""Script to do rudimentary checks of NeuroDebian mirrors to verify they are in good shape
+"""
+
+
+import sys
+from urllib import urlopen
+from ConfigParser import SafeConfigParser
+
+#cfg_path="/etc/neurodebian/neurodebian.cfg"
+cfg_path="./neurodebian.cfg"
+main_mirror='us-nh'
+
+# read configuration
+cfg = SafeConfigParser()
+cfg.read(cfg_path)
+
+# load information about mirrors
+mirrors = cfg.options('mirrors')
+urls = dict([(x, cfg.get('mirrors', x)) for x in mirrors])
+slave_mirrors = mirrors.pop(mirrors.index(main_mirror))
+
+#if True:
+def fetch_listing(url):
+ """Traverses whole website, obtains listing of all files available
+
+
+ TODO: eventually use scrapy, but stable one has only 0.8 while
+ 0.16 is out... so -- later
+ """
+ print url
+ #url = 'http://neuro.debian.net/debian/dists/dapper/'
+ #url = "http://mirror.aarnet.edu.au/pub/neurodebian/dists/dapper/"
+ parser = etree.HTMLParser()
+ from lxml.html import parse, submit_form, fromstring
+ #page = etree.parse(urlopen('http://neuro.debian.net/debian/dists/dapper/'), parser)
+ #page = objectify.parse(urlopen('http://neuro.debian.net/debian/dists/dapper/'), parser)
+ page = parse(url).getroot()
+
+ #page = fromstring(''.join(urlopen(url).readlines()))
+ #page.make_links_absolute(url)
+
+
+ # go through all rows with links
+ rows = [row for row in page.iter('tr')]
+ res = {}
+ for row in rows:
+ pass
+
+ # do I need parent actually for anything? yes -- time/size
+ # actually -- of no use since presence/presentation heavily varies
+ # across mirrors, so let's not rely on them
+ links = [ (l[0].getparent().getparent(),
+ l[2].endswith('/'),) +
+ l
+ for l in page.iterlinks()
+ if (l[1] == 'href'
+ and not (
+ l[2][0] in ('/', '?')
+ or l[2].startswith('http://')
+ or l[2].startswith('mailto:')
+ )) ]
+
+ for p, isdir, a, _, name, _ in links:
+ print name
+ if isdir:
+ fetch_listing('%s/%s' %
+ (url, name))
+
+if False:
+ for m, url in urls.iteritems():
+ print "Mirror %s" % m
+ fetch_listing(url + '/dists/dapper')
+else:
+ fetch_listing(urls[main_mirror] + '/dists/dapper')
+"""
+au has fancier index pages, so we would need to distil page first more
+"""
apt-get install --no-install-recommends -y \
gnome-core mc evince bash-completion ntpdate file-roller gnome-utils \
- gnome-themes eog vim reportbug \
+ gnome-themes gnome-disk-utility network-manager-gnome eog vim reportbug \
software-center gdebi gedit-plugins gnome-media synaptic menu less libxp6
# Clean-up installed development files which got pulled in for
--- /dev/null
+#!/bin/bash
+
+# play safe
+set -e
+set -u
+
+# Standard Debian install
+
+# prepare on hydra and use debproxy for speed
+
+# have dedicated hard-drives for swap and home
+
+# expert install
+
+# hostname: neurodebian
+# domain: ''
+
+# Needs to be assured since it got reset to debian
+hostname neurodebian # this is not a permanent change
+echo "neurodebian" >| /etc/hostname # make it permanent
+sed -i -e 's/^127\.0\.1\.1.*/127.0.1.1\tneurodebian/g' /etc/hosts
+
+# all file in one partition
+
+# root: not there
+# user: brain
+# pwd: neurodebian
+
+
+# Do a minimal install
+# --------------------
+
+# All files in one partition/
+# just base system, run selection, but no tasks (not even 'Standard system')
+
+# set root password to 'neurodebian' too
+#echo "Set root passwd:"
+#passwd root
+
+apt-get install --no-install-recommends -y etckeeper
+
+# setup etckeeper
+git config --global user.name NeuroDebian
+git config --global user.email nd@localhost
+
+# install new stuff
+# -----------------
+
+# Add sources.list for backports and neurodebian
+wget -O /etc/apt/sources.list.d/neuro.debian.net.list http://neuro.debian.net/lists/wheezy.us-nh
+
+# Development versions (TODO: comment out upon finishing)
+#cat /etc/apt/sources.list.d/neuro.debian.net.list | sed -e 's,/debian ,/debian-devel ,g' \
+# >| /etc/apt/sources.list.d/neuro.debian.net-devel.list
+
+## No backports yet
+## echo "deb http://backports.debian.org/debian-backports wheezy-backports main contrib non-free" > /etc/apt/sources.list.d/backports.debian.org.list
+cat << EOT > /etc/apt/preferences.d/backports.debian.org.pref
+Package: *
+Pin: release a=wheezy-backports
+Pin-Priority: 200
+EOT
+
+apt-get update -y
+# Backports' Release files signed with both ftpmaster and old backports keys
+# That causes APT to spit out a warning, but to not confuse users, lets simply
+# obtain that key if possible
+gpg --keyserver hkp://subkeys.pgp.net --recv-keys 16BA136C && \
+ gpg --export 16BA136C | apt-key add - || :
+
+apt-get install -y --allow-unauthenticated neurodebian-keyring
+apt-get update -y
+
+# to cheat the VM check
+touch /dev/vboxguest
+
+# Assure that corresponding linux headers are installed since otherwise they
+# might not be. There is also a dichotomy between target 686 and installer
+# using 486 build of the kernel. It requires manual build/installation
+# of guest additions for 686 at this point. Hence all the ugly logic below
+cunamer=`uname -r`
+cdarch=${cunamer##*-}
+# We carry 686 only
+[ $cdarch = '486' ] && darch='686-pae' || darch=$cdarch
+apt-get install -y linux-headers-$cdarch
+
+## # Forcefully install guest additions from backports so we are
+## # compatible with VirtualBox 4.x series
+## apt-get install -y -t wheezy-backports virtualbox-ose-guest-dkms \
+## virtualbox-ose-guest-utils virtualbox-ose-guest-x11 \
+## >| /var/log/initial_setup-dkms.log 2>&1
+
+# to get all the rest stuff in recommends
+apt-get install -y dkms neurodebian-guest-additions
+
+if [ "$darch" != "$cdarch" ] ; then
+ # Because DKMS builds for currently running kernel, which during
+ # installation might be a more generic 486, lets force building for 686
+ # and also install necessary headers (will be purged later on anyways)
+ apt-get install -y linux-headers-$darch
+
+ unamer=${cunamer//$cdarch/$darch}
+ # First collect information about installed vb additions
+ vbg=( `dkms status | grep virtualbox | head -n 1 | tr ',' ' '` )
+ echo "I: forcing build and install of guest additions for 686"
+ dkms build -m ${vbg[0]} -v ${vbg[1]} -a i686 -k $unamer \
+ >| /var/log/initial_setup-dkms-686-build.log 2>&1
+ dkms install -m ${vbg[0]} -v ${vbg[1]} -a i686 -k $unamer \
+ >| /var/log/initial_setup-dkms-686-install.log 2>&1
+fi
+
+# Prune DKMS's build -- should be no need to carry it around
+find /var/lib/dkms -iname build | xargs -r rm -rf
+
+# Add brain use into vboxsf group so he gets access to shared folders
+# by default
+adduser brain vboxsf
+
+# assure at the end that we got right modules build in the right location
+find /lib/modules/*$darch -iname vboxsf.ko | grep -q .
+
+# That was for GNOME
+# apt-get install --no-install-recommends -y \
+# gnome-core mc evince bash-completion ntpdate file-roller gnome-utils \
+# gnome-themes gnome-disk-utility network-manager-gnome eog vim reportbug \
+# software-center gdebi gedit-plugins gnome-media synaptic menu less libxp6
+
+apt-get install --no-install-recommends -y \
+ mc evince bash-completion ntpdate file-roller \
+ eog vim reportbug \
+ software-center synaptic menu less libxp6 \
+ task-xfce-desktop lightdm zenity \
+ chromium-browser \
+ sudo neurodebian-desktop update-notifier
+
+# Assure having xfce4 terminal and it being default one
+apt-get install -y xfce4-terminal
+# Do not even try to deal with alternatives -- it will be the one and would puke
+# update-alternatives --set x-terminal-emulator /usr/bin/xfce4-terminal
+
+# XXX last ones are actually pulled it by neurodebian-guest-additions whenever we
+# resolve their destiny ;-) although it might be pooling too much, eg exim4
+
+# Clean-up installed development files which got pulled in for
+# VM guest additions (to build kernel modules via DKMS)
+apt-get purge -y libc6-dev
+dpkg -l | awk '/^ii.*[ \t]linux-headers/{print $2;}' | xargs -r apt-get purge -y
+
+# Gnome optional pulled by gnome-core:
+apt-get purge -y gnome-core evolution-common evolution libevolution
+
+# And utter cleanup
+apt-get -y autoremove
+
+# intermediate cleanup to prevent virtual harddrive from fragmenting too much
+find /var/cache/apt/archives/ -name '*.deb' -delete
+
+# cleanup unwanted stuff
+# video drivers (all but vesa)
+apt-get purge -y --force-yes $(apt-cache search --names-only --installed xserver-xorg-video | grep xserver-xorg-video | cut -d ' ' -f 1,1) xserver-xorg-video-vesa+
+apt-get purge -y brasero freepats
+
+# Seems to be not used by any installed piece
+apt-get purge -y libwebkitgtk-1.0-0
+
+# and whatever is obsolete
+apt-get autoremove --purge -y
+
+# custom config
+# use NeuroDebian website as default homepage
+sed -i -e 's,http://www.debian.org,http://neuro.debian.net,g' /etc/chromium*/master_preferences
+
+# Place default XFCE4 panel config, otherwise a dialog appears
+# Thanks go to cavalier@freenode IRC for the hint
+xfdir=/home/brain/.config/xfce4/xfconf/xfce-perchannel-xml
+mkdir -p $xfdir
+cp /etc/xdg/xfce4/panel/default.xml $xfdir/xfce4-panel.xml
+chown brain.brain -R /home/brain/.config
+
+# reduce grub timeout to speed up boot of VM
+sed -i -e 's/GRUB_TIMEOUT=5/GRUB_TIMEOUT=1/g' /etc/default/grub
+update-grub
+
+# finally configure geomirror for APT and disable deb-src lists
+cp /etc/apt/sources.list /etc/apt/sources.list.orig
+sed -i -e "s,\(deb\(\|-src\) http://\)[^/]*/debian,\1http.debian.net/debian,g" \
+ -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/
--- /dev/null
+#### Contents of the preconfiguration file (for wheezy)
+### Hints:
+### To get a list of current d-i setting keys, run
+### sudo debconf-get-selections --installer
+### on an up-to-date system
+###
+### Localization
+# Locale sets language and country.
+d-i debian-installer/locale string en_US.UTF-8
+d-i debian-installer/language string en
+d-i debian-installer/country string US
+
+# Keyboard selection.
+#d-i console-tools/archs select at
+#d-i console-setup-pc-ekmap/keymap select us
+# Need to set "American English" for "Keymap to use"
+d-i countrychooser/country-name select United States
+# Example for a different keyboard architecture
+#d-i console-keymaps-usb/keymap select mac-usb-us
+#d-i console-keymaps-at/keymap select us
+d-i keyboard-configuration/xkb-keymap select us
+
+### Network configuration
+# netcfg will choose an interface that has link if possible. This makes it
+# skip displaying a list if there is more than one interface.
+d-i netcfg/choose_interface select auto
+
+# To pick a particular interface instead:
+#d-i netcfg/choose_interface select eth1
+
+# If you have a slow dhcp server and the installer times out waiting for
+# it, this might be useful.
+#d-i netcfg/dhcp_timeout string 60
+
+# If you prefer to configure the network manually, uncomment this line and
+# the static network configuration below.
+#d-i netcfg/disable_dhcp boolean true
+
+# If you want the preconfiguration file to work on systems both with and
+# without a dhcp server, uncomment these lines and the static network
+# configuration below.
+#d-i netcfg/dhcp_failed note
+#d-i netcfg/dhcp_options select Configure network manually
+
+# Static network configuration.
+#d-i netcfg/get_nameservers string 192.168.1.1
+#d-i netcfg/get_ipaddress string 192.168.1.42
+#d-i netcfg/get_netmask string 255.255.255.0
+#d-i netcfg/get_gateway string 192.168.1.1
+#d-i netcfg/confirm_static boolean true
+
+# Any hostname and domain names assigned from dhcp take precedence over
+# 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 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
+# change to false to disable asking.
+#d-i hw-detect/load_firmware boolean true
+
+### Network console
+# Use the following settings if you wish to make use of the network-console
+# component for remote installation over SSH. This only makes sense if you
+# intend to perform the remainder of the installation manually.
+#d-i anna/choose_modules string network-console
+#d-i network-console/password password r00tme
+#d-i network-console/password-again password r00tme
+
+### Mirror settings
+# If you select ftp, the mirror/country string does not need to be set.
+#d-i mirror/protocol string ftp
+d-i mirror/country string manual
+d-i mirror/http/hostname string %(MIRROR_HTTP_HOSTNAME)s
+d-i mirror/http/directory string /debian
+#d-i mirror/http/proxy string
+
+# Suite to install.
+d-i mirror/suite string wheezy
+# Suite to use for loading installer components (optional).
+#d-i mirror/udeb/suite string testing
+
+### Clock and time zone setup
+# Controls whether or not the hardware clock is set to UTC.
+d-i clock-setup/utc boolean true
+
+# You may set this to any valid setting for $TZ; see the contents of
+# /usr/share/zoneinfo/ for valid values.
+d-i time/zone string %(TIME_ZONE)s
+
+# Controls whether to use NTP to set the clock during the install
+d-i clock-setup/ntp boolean true
+# NTP server to use. The default is almost always fine here.
+#d-i clock-setup/ntp-server string ntp.example.com
+
+### Partitioning
+# If the system has free space you can choose to only partition that space.
+#d-i partman-auto/init_automatically_partition select biggest_free
+
+# Alternatively, you can specify a disk to partition. The device name must
+# be given in traditional non-devfs format.
+# Note: A disk must be specified, unless the system has only one disk.
+# For example, to use the first SCSI/SATA hard disk:
+d-i partman-auto/disk string /dev/sda
+# In addition, you'll need to specify the method to use.
+# The presently available methods are: "regular", "lvm" and "crypto"
+d-i partman-auto/method string regular
+
+# If one of the disks that are going to be automatically partitioned
+# contains an old LVM configuration, the user will normally receive a
+# warning. This can be preseeded away...
+#d-i partman-lvm/device_remove_lvm boolean true
+# The same applies to pre-existing software RAID array:
+#d-i partman-md/device_remove_md boolean true
+# And the same goes for the confirmation to write the lvm partitions.
+#d-i partman-lvm/confirm boolean true
+
+# You can choose one of the three predefined partitioning recipes:
+# - atomic: all files in one partition
+# - home: separate /home partition
+# - multi: separate /home, /usr, /var, and /tmp partitions
+d-i partman-auto/choose_recipe select atomic
+
+# Or provide a recipe of your own...
+# The recipe format is documented in the file devel/partman-auto-recipe.txt.
+# If you have a way to get a recipe file into the d-i environment, you can
+# just point at it.
+#d-i partman-auto/expert_recipe_file string /hd-media/recipe
+
+# If not, you can put an entire recipe into the preconfiguration file in one
+# (logical) line. This example creates a small /boot partition, suitable
+# swap, and uses the rest of the space for the root partition:
+d-i partman-auto/expert_recipe string \
+ boot-root :: \
+ 10000 40000 1000000000 ext4 \
+ $primary{ } $bootable{ } \
+ method{ format } format{ } \
+ use_filesystem{ } filesystem{ ext4 } \
+ label{NEURODEBIAN} \
+ mountpoint{ / } \
+ . \
+ 2048 2048 2048 linux-swap \
+ method{ swap } format{ } \
+ .
+
+# This makes partman automatically partition without confirmation, provided
+# that you told it what to do using one of the methods above.
+d-i partman/confirm_write_new_label boolean true
+d-i partman/choose_partition select finish
+d-i partman/confirm boolean true
+d-i partman/confirm_nooverwrite boolean true
+
+### Base system installation
+# Select the initramfs generator used to generate the initrd for 2.6 kernels.
+#d-i base-installer/kernel/linux/initramfs-generators string yaird
+
+# The kernel image (meta) package to be installed; "none" can be used if no
+# kernel is to be installed.
+#d-i base-installer/kernel/image string linux-image-2.6-486
+
+### Account setup
+# Skip creation of a root account (normal user account will be able to
+# use sudo).
+#d-i passwd/root-login boolean false
+# Alternatively, to skip creation of a normal user account.
+#d-i passwd/make-user boolean false
+
+# Root password, either in clear text
+d-i passwd/root-password password neurodebian
+d-i passwd/root-password-again password neurodebian
+# or encrypted using an MD5 hash.
+#d-i passwd/root-password-crypted password [MD5 hash]
+
+# To create a normal user account.
+d-i passwd/user-fullname string NeuroDebian User
+d-i passwd/username string brain
+# Normal user's password, either in clear text
+d-i passwd/user-password password neurodebian
+d-i passwd/user-password-again password neurodebian
+# or encrypted using an MD5 hash.
+#d-i passwd/user-password-crypted password [MD5 hash]
+# Create the first user with the specified UID instead of the default.
+d-i passwd/user-uid string 1000
+# XXX no gid?
+
+# 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 floppy video plugdev dip sudo
+
+### Apt setup
+# You can choose to install non-free and contrib software.
+d-i apt-setup/non-free boolean true
+d-i apt-setup/contrib boolean true
+# Uncomment this if you don't want to use a network mirror.
+#d-i apt-setup/use_mirror boolean false
+# Select which update services to use; define the mirrors to be used.
+# Values shown below are the normal defaults.
+d-i apt-setup/services-select multiselect security, volatile
+d-i apt-setup/security_host string security.debian.org
+#d-i apt-setup/volatile_host string volatile.debian.org
+# XXX?
+
+# Additional repositories, local[0-9] available
+#d-i apt-setup/local0/repository string \
+# http://local.server/debian stable main
+#d-i apt-setup/local0/comment string local server
+# XXX our nd?
+#d-i apt-getup/local0/repository string \
+# http://neuro.debian.net/debian data main contrib non-free
+#d-i apt-setup/local0/comment string NeuroDebian data
+#d-i apt-setup/local0/source boolean true
+#d-i apt-getup/local1/repository string \
+# http://neuro.debian.net/debian squeeze main contrib non-free
+#d-i apt-setup/local1/comment string NeuroDebian software
+#d-i apt-setup/local1/source boolean true
+
+
+# URL to the public key of the local repository; you must provide a key or
+# apt will complain about the unauthenticated repository and so the
+# sources.list line will be left commented out
+#d-i apt-setup/local0/key string \
+# http://neuro.debian.net/_static/neuro.debian.net.asc
+
+# By default the installer requires that repositories be authenticated
+# using a known gpg key. This setting can be used to disable that
+# authentication. Warning: Insecure, not recommended.
+#d-i debian-installer/allow_unauthenticated string true
+
+### Package selection
+#tasksel tasksel/first multiselect standard, web-server
+tasksel tasksel/first multiselect
+# If the desktop task is selected, install the kde and xfce desktops
+# instead of the default gnome desktop.
+#tasksel tasksel/desktop multiselect kde, xfce
+
+# Individual additional packages to install
+#d-i pkgsel/include string openssh-server build-essential
+# Whether to upgrade packages after debootstrap.
+# Allowed values: none, safe-upgrade, full-upgrade
+#d-i pkgsel/upgrade select none
+
+# Some versions of the installer can report back on what software you have
+# installed, and what software you use. The default is not to report back,
+# but sending reports helps the project determine what software is most
+# popular and include it on CDs.
+# ND: popcon installed upon initial boot
+popularity-contest popularity-contest/participate boolean false
+
+### Boot loader installation
+# Grub is the default boot loader (for x86). If you want lilo installed
+# instead, uncomment this:
+#d-i grub-installer/skip boolean true
+# To also skip installing lilo, and install no bootloader, uncomment this
+# too:
+#d-i lilo-installer/skip boolean true
+
+# This is fairly safe to set, it makes grub install automatically to the MBR
+# if no other operating system is detected on the machine.
+d-i grub-installer/only_debian boolean true
+
+# This one makes grub-installer install to the MBR if it also finds some other
+# OS, which is less safe as it might not be able to boot that other OS.
+d-i grub-installer/with_other_os boolean false
+
+# Alternatively, if you want to install to a location other than the mbr,
+# uncomment and edit these lines:
+#d-i grub-installer/only_debian boolean false
+#d-i grub-installer/with_other_os boolean false
+#d-i grub-installer/bootdev string (hd0,0)
+# To install grub to multiple disks:
+#d-i grub-installer/bootdev string (hd0,0) (hd1,0) (hd2,0)
+
+# Optional password for grub, either in clear text
+#d-i grub-installer/password password r00tme
+#d-i grub-installer/password-again password r00tme
+# or encrypted using an MD5 hash, see grub-md5-crypt(8).
+#d-i grub-installer/password-crypted password [MD5 hash]
+
+### Finishing up the installation
+# During installations from serial console, the regular virtual consoles
+# (VT1-VT6) are normally disabled in /etc/inittab. Uncomment the next
+# line to prevent this.
+#d-i finish-install/keep-consoles boolean true
+
+# Avoid that last message about the install being complete.
+d-i finish-install/reboot_in_progress note
+
+# This will prevent the installer from ejecting the CD during the reboot,
+# which is useful in some situations.
+#d-i cdrom-detect/eject boolean false
+
+# This is how to make the installer shutdown when finished, but not
+# reboot into the installed system.
+#d-i debian-installer/exit/halt boolean true
+# This will power off the machine instead of just halting it.
+d-i debian-installer/exit/poweroff boolean true
+
+### Preseeding other packages
+# Depending on what software you choose to install, or if things go wrong
+# during the installation process, it's possible that other questions may
+# be asked. You can preseed those too, of course. To get a list of every
+# possible question that could be asked during an install, do an
+# installation, and then run these commands:
+# debconf-get-selections --installer > file
+# debconf-get-selections >> file
+
+
+#### Advanced options
+### Running custom commands during the installation
+# d-i preseeding is inherently not secure. Nothing in the installer checks
+# for attempts at buffer overflows or other exploits of the values of a
+# preconfiguration file like this one. Only use preconfiguration files from
+# trusted locations! To drive that home, and because it's generally useful,
+# here's a way to run any shell command you'd like inside the installer,
+# automatically.
+
+# This first command is run as early as possible, just after
+# preseeding is read.
+#d-i preseed/early_command string anna-install some-udeb
+
+# This command is run just before the install finishes, but when there is
+# still a usable /target directory. You can chroot to /target and use it
+# directly, or use the apt-install and in-target commands to easily install
+# packages and run commands in the target system.
+#d-i preseed/late_command string apt-install zsh; in-target chsh -s /bin/zsh
+#d-i preseed/late_command string wget -O/target/tmp/initial_setup http://git.debian.org/?p=pkg-exppsy/neurodebian.git;a=blob_plain;f=vm/d-i/tools/initial_setup;hb=HEAD; \
+d-i preseed/late_command string wget -O/target/tmp/initial_setup http://%(DI_HTTP_HOSTNAME)s/initial_setup ; \
+ in-target /bin/bash /tmp/initial_setup
+
+# XXX here get/call nd_setupguestos ?
+
# log files
find vbmnt/var/log -type f -delete
# apt lists
-find vbmnt/var/lib/apt -type f -name '*debian*' -o -type f -name '*list*' -delete
+find vbmnt/var/lib/apt -type f -name '*debian*' -o -type f -name '*list*' | xargs -r rm
# user data
# cannot clean all root stuff, because it also contains useful thing (e.g. git setup)
rm -f vbmnt/root/.*history
#emacs: -*- mode: shell-script; c-basic-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
#ex: set sts=4 ts=4 sw=4 noet:
+# fail early
set -eu
-# TODO: arguments later on to become cmdline args
-#iso=debian-squeeze-di-beta1-amd64-businesscard.iso
-iso=debian-6.0.6-${ARCH:=amd64}-businesscard.iso
-di_cd=$(readlink -f $PWD/../../../neurodebian-images/$iso)
-di_host=head1.hydra.dartmouth.edu # where to look for di preseed
-
build_dir=$PWD/build
dist_dir=$PWD/dist
vendor="NeuroDebian"
-vm_version="6.0.6"
+vm_version="7.0.0"
vm_ostype=Debian
vendor_url="http://neuro.debian.net"
product_url="${vendor_url}/vm.html"
+di_port=10100 # port to start webserver on
# 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.
However, by default this virtual machine is also enabled to install additional software from Debian and NeuroDebian repositories that is distributed under more restrictive licenses (e.g. closed-source, non-commercial, research-only). It is the user's responsibility to adhere to the terms and conditions of any particular software that is installed and used in this virtual machine. Copyright and license details for any installed PACKAGE are available in /usr/share/doc/PACKAGE/copyright inside the virtual machine."
+# The defaults to be modified from cmdline
+di_cd=
+# look here for more details about the default IP of the host:
+# # http://www.virtualbox.org/manual/ch09.html#changenat
+mirror_host=10.0.0.1:9999
+di_tz='US/Eastern'
+di_preseed_in=
+
+function usage {
+echo "Usage: $0 [OPTIONS]
+
+Create ND VirtualBox appliance.
+
+Options:
+ -p PRESEED_IN path to preesed.cfg.in file for d-i
+ -i ISO path to debian installation iso file
+ -m MIRROR debian mirror to use for installation
+ -t TIME_ZONE time zone of virtual machine
+ -h Show this help and exit
+"
+}
+
+# Process cmdline
+while getopts "p:i:" OPTION
+do
+ case $OPTION in
+ "p") di_preseed_in="$OPTARG";;
+ "i") di_cd="$OPTARG";;
+ "m") mirror_host="$OPTARG";;
+ "t") di_tz="$OPTARG";;
+ "h") exit 1;;
+ esac
+done
+
+if [ -z "$di_cd" ] ; then
+ echo "You must specify the iso image (-i)" >&2
+ exit 1
+fi
+
+if [ -z "$di_preseed_in" ]; then
+ # deduce release and use corresponding directory here
+ release=$(basename "$di_cd" | cut -d- -f2)
+ di_preseed_in=$(dirname $0)/../d-i/$release/preseed.cfg.in
+ if [ ! -e "$di_preseed_in" ]; then
+ echo "$di_preseed_in is not found. Specify one with -p" >&2
+ exit 2
+ fi
+fi
+
+# Figure out our IP address for VM to reach webserver
+eth=`route | awk '/default/{print $8;}'`
+di_host=`ip addr show dev $eth | sed -ne '/inet /s, *inet \([0-9.]*\)/.*,\1,gp'`
-# Computed settings
-#vm_basepath=
+# Generate preseed file
+# yoh could not escape Python here
+di_preseed=${di_preseed_in%.in}
+python -c "open('$di_preseed', 'w').write(open('$di_preseed_in').read() % {'DI_HTTP_HOSTNAME': '$di_host:$di_port', 'MIRROR_HTTP_HOSTNAME': '$mirror_host', 'TIME_ZONE': '$di_tz'})"
# By default 32bit unless installer image has amd64
# TODO: might need to make more robust?
rm -f ${vm_disk}
}
-clean_buildvm # clean things up
+clean_buildvm >&/dev/null # clean things up
#exit
# Check that no previous VM was left (can happen if previous failures
# type auto url=$di_host
# press Enter"
+# start local web server to serve preseed file
+builtin cd $(dirname ${di_preseed})
+python -m SimpleHTTPServer ${di_port} >&/dev/null &
+di_pid=$!
+builtin cd -
+
+
+
VBoxManage startvm "${vm_name}"
# TODO: see if we could just use virtinst (virt-install tool) to run d-i
# 01 81 \
# 1e 9e 16 96 14 94 18 98 39 b9 16 96 13 93 26 a6 0d 8d 23 a3 15 95 20 a0 13 93 1e 9e \
# 1c 9c # ESCAPE, auto url=hydra, ENTER
-echo "typeGuest \"${vm_name}\" \"&ESC;Wauto url=${di_host}&ENTER;\"" | /usr/lib/virtualbox/vboxshell.py
-
-: "
-oops -- asked either I want to store Partitioning on the disk...
-
-didn't happen before
-"
+echo "typeGuest \"${vm_name}\" \"&ESC;Wauto url=${di_host}|;${di_port}/$(basename ${di_preseed})&ENTER;\"" | /usr/lib/virtualbox/vboxshell.py
# wait for it to finish! -- found no cleaner way :-/
sleep 10
sleep 5
done
+# kill the web server
+kill ${di_pid} || echo "Could not kill the webserver"
+
_info Compacting VDI
sudo ./nd_compactvdi "${vm_disk}"
--- /dev/null
+URxvt.background: black
+URxvt.foreground: white
+URxvt.coursorColor: red
+URxvt.saveLines: 1000
+URxvt.perl-ext: searchable-scrollback<M-s>,tabbed,option-popup,selection
+# workaround for #546527
+URxvt.perl-ext-common: default,-option-popup,-selection-popup
+URxvt.underlineURLs: true
--- /dev/null
+[Desktop Entry]
+Name=Spyke Viewer
+GenericName=Graphical utility for analyzing electrophysiological data
+Exec=nd-autoinstall spykeviewer
+Type=Application
+Terminal=false
+Categories=X-NeuroDebian-Electrophysiology
+Icon=spykeviewer.png
projects / neurodebian.git / commitdiff
