]> git.donarmstrong.com Git - neurodebian.git/commitdiff
Merge remote branch 'neurolego/master'
authorYaroslav Halchenko <debian@onerussian.com>
Sat, 30 Oct 2010 14:45:13 +0000 (10:45 -0400)
committerYaroslav Halchenko <debian@onerussian.com>
Sat, 30 Oct 2010 14:45:13 +0000 (10:45 -0400)
* neurolego/master:
  updated ascii dump of neuro.debian.net.asc key

53 files changed:
artwork/.gitignore
artwork/brochure/Makefile
artwork/brochure/brochure_debian-neurodebian.tex
artwork/distro-dev.svg [new file with mode: 0644]
cmdsettings.sh
debian/changelog
debian/control
debian/neurodebian-keyring.install [new file with mode: 0644]
debian/neurodebian-keyring.postinst [new file with mode: 0644]
keys/neurodebian-archive-keyring.gpg [new file with mode: 0644]
neurodebian.cfg
sandbox/proposal_regressiontestframwork.moin
sphinx/_static/neurodebian.css
sphinx/_templates/layout.html
sphinx/_templates/page.html [new file with mode: 0644]
sphinx/coffeeart.rst [new file with mode: 0644]
sphinx/conf.py
sphinx/faq.rst
sphinx/index.rst
sphinx/pics/coffeeart/2010-10-22_09.58.31.jpg [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6647.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6666.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6671.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6681.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6685.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6692.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6712.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6719.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6725.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6727.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6769.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6773.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6778.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6790.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6791.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6794.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6795.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6800.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6802.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6806.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6808.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6835.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6863.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6869_.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6870.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6881.JPG [new file with mode: 0644]
sphinx/pics/coffeeart/IMG_6882.JPG [new file with mode: 0644]
sphinx/quotes-nihr01.rst [new file with mode: 0644]
sphinx/quotes-nitrc.rst [new file with mode: 0644]
sphinx/sphinxext/__init__.py [new file with mode: 0644]
sphinx/sphinxext/quote.py [new file with mode: 0644]
sphinx/testimonials.rst [new file with mode: 0644]
sphinx/vm.rst

index 24659ec70c9f43b88a18420b2452fefcd3d23b7d..da45240c173d966a3ff0ba6134fae67ac4d412e0 100644 (file)
@@ -6,3 +6,4 @@ usage_worldmap.png
 logo_tuned/fmri.pdf
 logo_tuned/label.pdf
 openlogo.pdf
+distro-dev.pdf
index f7e6dba98d430ab878635c05a804c99a299853cc..423456cddd9185d1a1133c23d505a774016cf6d6 100644 (file)
@@ -1,7 +1,7 @@
 include LaTeX.mk
 
-all: pics
+all:: pics
 
 .PHONY: pics
 pics:
-       @$(MAKE) -C ../ logo_tuned/label.pdf openlogo.pdf
+       @$(MAKE) -C ../ logo_tuned/label.pdf openlogo.pdf distro-dev.pdf
index e734cfcec9be91f2ca93edcf24f72d861c7301ee..b64fed5d63a502395253918f9381f284f1fa3937 100644 (file)
  {../}
 }
 
+\usepackage{enumitem}           % useful for control of listings
+
 \pagestyle{empty}
 \begin{document}
 
-% DEBIAN
+%%
+%% DEBIAN
+%%
 \begin{multicols}{3}    % 3 columns
 
 \begin{center}
 \includegraphics[width=0.5\columnwidth]{openlogo}
 
 \url{http://www.debian.org}
+\section*{Debian GNU/Linux}
+\subsection*{The Universal Operating System}
 \end{center}
 
+\section*{Reasons to choose Debian}
+\paragraph{It is maintained by its users}
+If something needs to be fixed or improved, we just do it.
 
-buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga duga
-\columnbreak
+\paragraph{Unparalleled support}
 
-buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga duga
-\columnbreak
+Mail sent to the mailing lists often gets answers within 15 minutes (or less),
+for free, and by the people who developed it. Compare that to typical phone
+support: hours spent on the phone, for money, only to get someone who doesn't
+know the system well enough to even understand your question.
+
+\paragraph{You wouldn't be alone in your choice}
+
+A wide range of organizations and individuals use Debian. See our Who's Using
+Debian? page for a description of some high-profile sites which use Debian, and
+have chosen to submit a short description of how they use Debian and why.
+
+\paragraph{The best packaging system in the world.}
+
+Tired of old files from software three versions old cluttering your system? Or
+installing a piece of software only to find it causes your system to crash
+because of software conflicts? Dpkg, Debian's endured packaging system, takes
+care of these issues for you.
+
+\paragraph{Easy installation}
+
+If you have heard that GNU/Linux is difficult to install, then you haven't
+tried Debian lately. We are constantly improving the installation process. You
+can do the installation directly from CD, DOS, floppies or even over the
+network.
+
+\paragraph{Incredible amounts of software}
+
+Debian comes with over 25000 different pieces of software. Every bit of it is
+free. If you have proprietary software that runs under GNU/Linux, you can still
+use it - in fact, there may even be an installer in Debian that will
+automatically install and set up everything for you.
+
+\paragraph{Packages well integrated}
+
+Debian surpasses all other distributions in how well its packages are
+integrated. Since all software is packaged by a coherent group, not only can
+all packages be found at a single site, but you can be assured that we have
+already worked out all issues regarding complicated dependencies. While we feel
+that the deb format has some advantages over the rpm format, it is the
+integration between the packages that makes a Debian system more robust.
+
+\paragraph{Source code}
+
+If you are a software developer, you will appreciate the fact that there are
+hundreds of development tools and languages, plus millions of lines of source
+code in the base system. All of the software in the main distribution meets the
+criteria of the Debian Free Software Guidelines (DFSG). This means that you can
+freely use this code to study from, or to incorporate into new free software
+projects. There are also plenty of tools and code suitable for use in
+proprietary projects.
+
+\paragraph{Easy upgrades}
+
+Due to our packaging system, upgrading to a new version of Debian is a snap.
+Just run apt-get update ; apt-get dist-upgrade (or aptitude update; aptitude
+dist-upgrade in newer releases) and you can upgrade from a CD in a matter of
+minutes or point apt at one of the over 300 Debian mirrors and upgrade over the
+net.
+
+\rotatebox{90}{\includegraphics[height=.9\columnwidth]{distro-dev}}
+\rotatebox{90}{Description}
+
+\paragraph{Multiple architectures and kernels}
+
+Currently Debian supports an impressive number of CPU architectures: alpha,
+amd64, armel, hppa, i386, ia64, mips, mipsel, powerpc, s390, and sparc. It also
+runs on GNU Hurd and FreeBSD kernels besides Linux, and with the debootstrap
+utility you will be hard-pressed to find a device that can't run Debian.
+
+\paragraph{Bug tracking system}
+
+Debian's bug tracking system is publicly available. We don't try to hide the
+fact that software doesn't always work the way users want. Users are encouraged
+to submit bug reports and are notified when and why the bug was closed. This
+system allows Debian to respond to problems quickly and honestly.
+
+
+
+\section*{Acknowledgements}
 
-buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga duga
-\columnbreak
 \end{multicols}
 
 
 \pagebreak
-
-% NEURODEBIAN
+%%
+%% NeuroDEBIAN
+%%
 \begin{multicols}{3}    % 3 columns
 
 \begin{center}
-
 \noindent
+\vspace{-3em}
 \includegraphics[width=\columnwidth]{logo_tuned/label}
 
 \url{http://neuro.debian.net}
+\section*{NeuroDebian Project}
+\subsection*{The Universal Research Environment}
+
+
 \end{center}
 
 \section*{What is NeuroDebian}
@@ -62,7 +150,7 @@ buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dug
 Icons for FSL, Caret, AFNI, etc
 
 
-\columnbreak
+%\columnbreak
 
 \section*{How to get NeuroDebian}
 
@@ -77,20 +165,52 @@ buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dug
 sdflkj
 slkdjf
 
-\columnbreak
+%\columnbreak
 
 \section*{Who is using NeuroDebian}
 
 \noindent
-\includegraphics[width=\columnwidth]{usage_worldmap}
+%\includegraphics[width=\columnwidth]{usage_worldmap}
 
 buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga duga
 
+
+\section*{Future\ldots}
+
+\begin{description}[leftmargin=1em]
+
+\item[Wider coverage]:\\
+  BioSig, NEURON, FreeSurfer, etc.
+
+\item[Assured interoperability]:\\
+  Intergration- and regression- testing
+
+\item[Snapshotting]
+
+\item[Data as 1st class citizen]
+
+\item[Universal Availability]:\\
+  \begin{itemize}
+  \item New versions of Virtual Appliance
+  \item Cloud computing images
+  \end{itemize}
+
+\end{description}
+
+
 \section*{Endorsements}
 
 some quotes from letters of support
 
-\columnbreak
+
+\section*{Acknowledgements}
+
+We are grateful to all Debian developers and contributors for the
+development of Debian OS, and to Prof. Jim Haxby (PBS Department,
+Dartmouth College) for his continued support and endless supply of
+Italian espresso.
+
+%\columnbreak
 \end{multicols}
 
 
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+       x="0"
+       y="0"
+       xlink:href="#use5948"
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+       x="0"
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+       height="354.33069" />
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+       x="0"
+       y="0"
+       xlink:href="#use5950"
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+    <use
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+       xlink:href="#use5948"
+       y="0"
+       x="0" />
+    <use
+       height="354.33069"
+       width="637.79529"
+       transform="matrix(1,0,0,-1,19.106808,293.1062)"
+       id="use6003"
+       xlink:href="#use5952"
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+       x="0" />
+    <path
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+       sodipodi:cx="53.5"
+       id="use6005"
+       style="font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:125%;writing-mode:lr-tb;text-anchor:start;fill:#ffcc00;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:2;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0;display:inline;font-family:DejaVu Sans;-inkscape-font-specification:DejaVu Sans"
+       sodipodi:type="arc"
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+       height="354.33069"
+       width="637.79529"
+       transform="translate(-3.434204,-139.35821)"
+       id="use6019"
+       xlink:href="#use5948"
+       y="0"
+       x="0" />
+  </g>
+</svg>
index 3ba5d1d20c901deb359d9755fd153b5bf573230f..7ffff037862658379ed21f275f2dd48a060a1f67 100644 (file)
@@ -18,7 +18,7 @@ mirror="http://debian.lcs.mit.edu/debian"
 # overwrite necessary bits for ubuntu
 if [ "${family#nd+}" = "ubuntu" ]; then
   aptcache="${cowbuilderroot}/ubuntu_aptcache"
-  components="main universe"
+  components="main universe multiverse"
   mirror="http://ubuntu.media.mit.edu/ubuntu"
 fi
 
index ff699d68cbed1d7acd4acd16e1a4f03c43208852..6d4e290a86e7929ebba7e829409f4044048414aa 100644 (file)
@@ -1,5 +1,5 @@
-neurodebian (1.0) squeeze; urgency=low
+neurodebian (0.3) squeeze; urgency=low
 
   * Initial release.
 
- -- Michael Hanke <michael.hanke@gmail.com>  Sun, 01 Aug 2010 14:01:07 -0400
+ -- Michael Hanke <michael.hanke@gmail.com>  Fri, 29 Oct 2010 10:31:03 -0400
index dc6434f8e8577f08b635580d6c104d038060507e..9917fe214ac2cecefc8317055c396c5f9dfb659a 100644 (file)
@@ -11,14 +11,6 @@ Vcs-Git: git://git.debian.org/git/pkg-exppsy/neurodebian.git
 XS-DM-Upload-Allowed: yes
 
 
-Package: neurodebian
-Architecture: all
-Depends: ${misc:Depends}, zenity
-Suggests:
-Description: neuroscience research environment
- Pacifier
-
-
 Package: neurodebian-dev
 Architecture: all
 Depends: ${misc:Depends}, devscripts, cowbuilder, python
@@ -30,28 +22,28 @@ Description: NeuroDebian development tools
 
 Package: neurodebian-desktop
 Architecture: all
-Depends: ${misc:Depends}, ssh-askpass-gnome | ssh-askpass, desktop-base, gnome-icon-themes
+Depends: ${misc:Depends}, ssh-askpass-gnome | ssh-askpass, desktop-base, gnome-icon-theme
 Suggests:
 Description: neuroscience research environment
  Pacifier
 
 
-Package: neurodebian-trailer
+Package: neurodebian-keyring
 Architecture: all
 Depends: ${misc:Depends}
-Suggests:
-Description: neuroscience research environment
- Pacifier
+Description: GnuPG archive keys of the NeuroDebian archive
+ The NeuroDebian project digitally signs its Release files. This package
+ contains the archive keys used for that.
 
 
 Package: neurodebian-guest-additions
 Architecture: all
-Depends: ${misc:Depends}, sudo, virtualbox-ose-guest-utils, virtualbox-ose-guest-x11, virtualbox-ose-guest-dkms, neurodebian-desktop, gdm
+Depends: ${misc:Depends}, sudo, virtualbox-ose-guest-utils, virtualbox-ose-guest-x11, virtualbox-ose-guest-dkms, neurodebian-desktop, gdm, update-manager-gnome, update-notifier
 Recommends: chromium-browser
 Suggests:
 Description: add-ons and configuration for the NeuroDebian virtual machine
  This package configures a Debian installation as a guest operating system
  in a VirtualBox-based virtual machine for NeuroDebian.
  .
- Do not install this package unless you know what you are doing! For example,
+ DO NOT install this package unless you know what you are doing! For example,
  installation of this package relaxes several security mechanisms.
diff --git a/debian/neurodebian-keyring.install b/debian/neurodebian-keyring.install
new file mode 100644 (file)
index 0000000..ab98d0d
--- /dev/null
@@ -0,0 +1 @@
+keys/neurodebian-archive-keyring.gpg etc/apt/trusted.gpg.d/
diff --git a/debian/neurodebian-keyring.postinst b/debian/neurodebian-keyring.postinst
new file mode 100644 (file)
index 0000000..2ce7600
--- /dev/null
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+set -e
+
+if which apt-key > /dev/null; then
+    apt-key update
+fi
+
+#DEBHELPER#
diff --git a/keys/neurodebian-archive-keyring.gpg b/keys/neurodebian-archive-keyring.gpg
new file mode 100644 (file)
index 0000000..3488e38
Binary files /dev/null and b/keys/neurodebian-archive-keyring.gpg differ
index a75d88715baccb0992288ddcb95ff05c567e494e..db95dbac09cef852f7d30ca2128cce0800bd2fb8 100644 (file)
@@ -28,7 +28,7 @@ prospective =
 # package names -- if the original name should appear in the package list it has
 # to be added as an alias as well
 mni-icbm152-nlin-2009 = mni-icbm152-nlin-2009a mni-icbm152-nlin-2009b mni-icbm152-nlin-2009c
-fsl = fsl fsl-doc fsl-atlases fsl-possum-data fsl-first-data fsl-feeds
+fsl = fsl fsl-doc fsl-atlases fsl-possum-data fsl-first-data fsl-feeds fsl-mni152-templates
 fslview = fslview fslview-doc
 python-mvpa = python-mvpa python-mvpa-snapshot
 libgiftiio-dev = libgiftiio-dev gifti-bin
@@ -38,6 +38,7 @@ libbiosig-dev = libbiosig-dev python-biosig octave-biosig biosig-tools libbiosig
 [mirrors]
 de = http://apsy.gse.uni-magdeburg.de/debian
 gr = http://neurobot.bio.auth.gr/neurodebian
+us-ca = http://neurodeb.pirsquared.org
 us-nh = http://neuro.debian.net/debian
 us-tn = http://masi.vuse.vanderbilt.edu/neurodebian
 
@@ -77,6 +78,7 @@ 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 = Upcoming Ubuntu 11.04 "Natty Narwhal" (natty)
 
 [release backport ids]
 # the purpose of these ids is to have version suffixes for backported packages
index 292cc27db008b6efce54783592027b348c33f20a..f93569b9cc1b61dfeb8d1a674aeb0adf166d31d0 100644 (file)
@@ -1,33 +1,44 @@
 ## This will eventually do to wiki.debian.org/RegressionTestFramework
 
  * '''Created''': <<Date(2010-10-07)>>
- * '''Contributors''': NeuroDebian
+ * '''Contributors''': MichaelHanke
  * '''Packages affected''': 
  * '''See also''': 
 
 == Summary ==
 
-This specification describes the way we would like Debian specifications to be
-written. It takes the form of a specification itself.
+This specification describes conventions and tools that allow Debian to
+distribute and run regression test batteries developed by upstream or
+Debian developers in a uniform fashion.
 
 == Rationale ==
 
-As we develop new ideas for features in Debian, it's important to be able to
-communicate them clearly. This serves the purpose of making it clear what the
-feature is about, and allowing people to evolve an implementation strategy for
-it. 
-
-Publishing this content gives our community a chance to participate in the
-discussion and design of a feature, and increases the chance that community
-members will feel confident enough to start work on the implementation of the
-feature. 
-
-A good specification also allows community members who were not physically
-present at meetings discussing a topic to participate in the implementation of
-the spec.
-
-Bottom line: the better your spec, the better the chances that your ideas will
-clearly understood by every contributor that might help.
+Ideally software packaged for Debian comes with an exhaustive test suite that
+can be used to determine whether this software works as expected on the Debian
+platform. However, especially for complex software, these test suites are often
+resource hungry (CPU time, memory, diskspace, network bandwidth) and cannot be
+ran at package build time by buildds. Consequently, test suites are only
+utilized by the packager on a particular machine, before uploading a new version
+to the archive.
+
+However, Debian is an integrated system and packaged software is typically made
+to rely on functionality provided by other Debian packages (e.g. shared
+libraries) instead of shipping duplicates with different versions in every
+package -- for many good reasons. Unfortunately, there is also a downside to
+this: Debian packages often use 3rd-party tools with different versions than
+those tested by upstream, and moreover, the actual versions might change
+frequently between to subsequent uploads of a package.  Currently a change in a
+dependency that introduces an incompatibility cannot be detected reliably
+(before users have filed a bug report) -- even if upstream provides a testsuite
+that would have caught the breakage. Although there are archive-wide QA efforts
+(e.g. constantly rebuilding all packages) these tests can only detect API/ABI
+breakage or functionality tested during build-time checks -- they are not
+exhaustive for the aforementioned reasons.
+
+This is a proposal to, first of all, package upstream test suites in a way that
+they can be used to run expensive archive-wide QA tests. However, this is also
+a proposal to establish means to test interactions of software from multiple
+Debian packages and test proper, continued, integration into the Debian system.
 
 == Use Cases ==
 
index 69086be643b395e5bbdb131e5948da2551057600..799714d5a602d28d82af050131b612d21796f135 100644 (file)
@@ -660,6 +660,44 @@ img.logo {
     border: 0;
 }
 
+
+/* Epigraphs */
+
+blockquote.epigraph {
+       margin: 1em 0;
+    padding: 0 2em 0 2em;
+    background-color: #faf2e9;
+    border-top: 1px solid #ad7a35;
+    border-bottom: 1px solid #ad7a35;
+    font-style: italic;
+}
+
+blockquote.epigraph p {
+    margin: 0.2em 0 0.2em 0;
+       font-size: 90%;
+}
+
+p.attribution {
+       padding: 0.2em 0 0 1em;
+       font-size: 80%;
+    font-style: normal;
+}
+
+p.attribution span.author {
+    margin: 0;
+    font-weight: bold;
+}
+
+p.attribution span.date {
+       font-size: 90%;
+}
+
+p.attribution span.affiliation, span.source {
+       font-size: 90%;
+       padding: 0 0 0 25px;
+       display: block;
+}
+
 /* :::: PRINT :::: */
 @media print {
     div.document,
index 9e6eb5436353217c3160f7028e1863e79362cf1c..98406af6902966acec550a9ae342929b429a4269 100644 (file)
@@ -5,11 +5,16 @@
 {% endblock %}
 
 {% block rootrellink %}
-  <li><a href="http://www.debian.org" target="_blank">Debian</a> |&nbsp;</li>
-  <li><a href="{{ pathto('index') }}">Neuroscience Repository</a> |&nbsp;</li>
+  <li><a href="http://www.debian.org" target="_blank">Debian</a> ||&nbsp;</li>
+  <li><a href="{{ pathto('index') }}">Neuroscience Repository</a> :&nbsp;</li>
   <li><a href="{{ pathto('pkgs') }}">Software</a> |&nbsp;</li>
   <li><a href="{{ pathto('datasets') }}">Datasets</a> |&nbsp;</li>
   <li><a href="{{ pathto('faq') }}">FAQ</a> |&nbsp;</li>
+  <li><a href="{{ pathto('testimonials') }}">Testimonials</a> &nbsp;</li>
+{% endblock %}
+
+{% block relbaritems %}
+<li class="right"><a href="#disqus_thread">Comments</a>&nbsp;|</li>
 {% endblock %}
 
 {% block sidebar1 %}{% endblock %}
diff --git a/sphinx/_templates/page.html b/sphinx/_templates/page.html
new file mode 100644 (file)
index 0000000..967a0a2
--- /dev/null
@@ -0,0 +1,31 @@
+{% extends "basic/page.html" %}
+
+{% block body %}
+<!-- HEADNOTES -->
+{{ super() }}
+
+
+<h2>Comments</h2>
+<div id="disqus_thread"></div>
+<script type="text/javascript">
+  /**
+    * var disqus_identifier; [Optional but recommended: Define a unique identifier (e.g. post id or slug) for this thread] 
+    */
+  (function() {
+   var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
+   dsq.src = 'http://neurodebian.disqus.com/embed.js';
+   (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
+  })();
+</script>
+<noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript=neurodebian">comments powered by Disqus.</a></noscript>
+<a href="http://disqus.com" class="dsq-brlink">blog comments powered by <span class="logo-disqus">Disqus</span></a>
+
+<script type="text/javascript">
+var disqus_shortname = 'neurodebian';
+(function () {
+  var s = document.createElement('script'); s.async = true;
+  s.src = 'http://disqus.com/forums/neurodebian/count.js';
+  (document.getElementsByTagName('HEAD')[0] || document.getElementsByTagName('BODY')[0]).appendChild(s);
+}());
+</script>
+{% endblock %}
diff --git a/sphinx/coffeeart.rst b/sphinx/coffeeart.rst
new file mode 100644 (file)
index 0000000..684b4bd
--- /dev/null
@@ -0,0 +1,231 @@
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+
+.. _coffeeart:
+
+**********
+Coffee Art
+**********
+
+
+2009-09-28 07:46:08
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6647.JPG
+
+
+
+
+2009-10-08 15:09:32
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6666.JPG
+
+
+
+
+2009-10-20 18:20:04
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6671.JPG
+
+
+
+
+2009-11-05 19:46:26
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6681.JPG
+
+
+
+
+2009-11-10 12:57:41
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6685.JPG
+
+
+
+
+2009-11-17 10:25:01
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6692.JPG
+
+
+
+
+2009-12-03 09:37:24
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6712.JPG
+
+
+
+
+2009-12-03 18:31:35
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6719.JPG
+
+
+
+
+2009-12-08 15:50:46
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6725.JPG
+
+
+
+
+2009-12-10 10:43:18
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6727.JPG
+
+
+
+
+2009-12-31 12:38:28
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6769.JPG
+
+
+
+
+2010-01-23 13:04:58
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6773.JPG
+
+
+
+
+2010-02-03 12:32:42
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6778.JPG
+
+
+
+
+2010-02-09 14:08:10
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6790.JPG
+
+
+
+
+2010-02-12 12:47:08
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6791.JPG
+
+
+
+
+2010-02-17 10:15:11
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6794.JPG
+
+
+
+
+2010-02-17 16:26:50
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6795.JPG
+
+
+
+
+2010-02-18 11:39:11
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6800.JPG
+
+
+
+
+2010-02-18 11:40:55
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6802.JPG
+
+
+
+
+2010-02-23 15:45:32
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6806.JPG
+
+
+
+
+2010-02-25 13:24:49
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6808.JPG
+
+
+
+
+2010-04-06 07:36:12
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6835.JPG
+
+
+
+
+2010-06-23 10:06:25
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6863.JPG
+
+
+
+
+2010-07-14 13:55:50
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6869_.JPG
+
+
+
+
+2010-07-19 10:24:53
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6870.JPG
+
+
+
+
+2010-07-26 11:26:45
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6881.JPG
+
+
+
+
+2010-08-13 13:01:32
+-------------------
+
+.. figure:: /pics/coffeeart/IMG_6882.JPG
+
+
+
+2010-10-22 09:58:31
+-------------------
+
+.. figure:: /pics/coffeeart/2010-10-22_09.58.31.jpg
+
index 698c32dcdf683a19618551baa0ebcf011cd9b469..0bdb259ebf9ac12af4881eb2832e2664b9ac4a71 100644 (file)
@@ -41,7 +41,9 @@ def artworkdir():
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = []
+#extensions = []
+sys.path.append(os.path.abspath('.'))
+extensions = ['sphinxext.quote']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
index a30be4d891bdd0963abb813364619b6e526dd35a..7c9c637c7861524f1ab24b7d1c66bb2185b95150 100644 (file)
@@ -1,11 +1,5 @@
 .. -*- mode: rst; fill-column: 78 -*-
 .. ex: set sts=4 ts=4 sw=4 et tw=79:
-  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-  #
-  #   See COPYING file distributed along with the PyMVPA package for the
-  #   copyright and license terms.
-  #
-  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
 
 .. _faq:
@@ -133,6 +127,39 @@ I have heard that some packages are non-free. Will you charge me for them?
   packages in NeuroDebian are provided free of charge and under the licensing
   terms of the original developers.
 
+.. _sec_pkg_authentication:
+
+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.
+
+Or you will be asked questions like this over and over::
+
+  WARNING: The following packages cannot be authenticated!
+  ...
+  Install these packages without verification [y/N]?
+
+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:
+
+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).
+
 
 .. include:: links_names.rst
 .. include:: substitutions.rst
index 9c61985c217e0cf193561c0272fd537fc3aa8d88..4406164d9c49f1b72a67472390e59e1ce24eaa38 100644 (file)
@@ -4,18 +4,23 @@
  Welcome to the Debian Neuroscience Repository
 ***********************************************
 
+.. quotes::
+   :random: 1
+
 This repository provides mostly neuroscience-related packages to be used on
 Debian_ systems (or Debian-derivatives like Ubuntu_). It contains both unofficial
 or prospective packages which are not (yet) available from the main Debian_
 archive, as well as backported or simply rebuilt packages also available
 elsewhere. Please see the :ref:`faq` for more information about the goals of
-this project.
+this project, and :ref:`read what people say about it <testimonials>`.
+If you appreciate this service, please |spread|.
+
+.. note::
 
-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.
+  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 |spread|, if you like it.
 
 .. raw:: html
 
@@ -38,7 +43,7 @@ News
  new TWTR.Widget({
    version: 2,
    type: 'profile',
-   rpp: 10,
+   rpp: 15,
    interval: 6000,
    width: 'auto',
    height: 150,
@@ -92,18 +97,20 @@ releases and repository mirrors:
   Thanks to the following institutions and individuals for hosting a mirror:
 
   * `Department of Psychological and Brain Sciences at Dartmouth College`_
-    `[us-nh]` (primary mirror)
+    *[us-nh]* (primary mirror)
   * `Department of Experimental Psychology at the University of Magdeburg`_
-    `[de]`
-  * `Neurobot at Aristotle University of Thessaloniki, Greece`_ `[gr]`
+    *[de]*
+  * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
+  * `Paul Ivanov`_ *[us-ca]*
   * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
-    `[us-tn]`
+    *[us-tn]*
 
   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
 
 Once this is done, you have to update the package index. Use your favorite
@@ -121,45 +128,21 @@ Now, you can proceed to install packages, e.g.::
   about which package version is available for which release and architecture,
   please have a look at the corresponding package pages.
 
-
-Package authentication
-----------------------
-
-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.
-
-Or you will be asked questions like this over and over::
-
-  WARNING: The following packages cannot be authenticated!
-  ...
-  Install these packages without verification [y/N]?
-
-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:
-
-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).
+After this initial setup you probably also want to configure your package
+manager to recognize the NeuroDebian archive key. With this key the package
+manager can verify that packages haven't been modified and are identical with
+the ones in the main NeuroDebian archive, regardless of which mirror you
+downloaded them from. The NeuroDebian key id is **2649A5A9**. If you need further
+help setting up package authentication, please take a look at
+:ref:`corresponding FAQ <sec_pkg_authentication>`.
 
 
 .. _chap_installation:
 
-Installation
-============
+Ways to use NeuroDebian
+=======================
 
-Virtual Machine
+Virtual machine
 ---------------
 
 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
@@ -172,8 +155,8 @@ purpose of teaching a neuroimaging data analysis course in a multipurpose
 computer lab.
 
 
-Debian
-------
+Debian installation
+-------------------
 
 Having been exposed to the wonders of NeuroDebian_ you are no longer
 satisfied with your previous choice of operating system?  We would
@@ -186,7 +169,7 @@ hardware architecture and then simply add |repos|.
 .. _chap_team:
 
 
-The Team
+The team
 ========
 
 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
@@ -231,6 +214,42 @@ communication channels within the NeuroDebian community
 .. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream
 
 
+Acknowledgements
+================
+
+We are grateful to Jim Haxby for his continued support and :ref:`endless supply of
+Italian espresso <coffeeart>`.
+
+
+Publications
+============
+
+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? *Poster to be presented at the anual 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/
+
+
 .. toctree::
    :hidden:
 
@@ -238,6 +257,8 @@ communication channels within the NeuroDebian community
    pkgs
    spread
    vm
+   coffeeart
+   testimonials
 
 .. probably should be purged altogether
 .. toctree::
@@ -248,6 +269,8 @@ communication channels within the NeuroDebian community
    setup
    links_names
    substitutions
+   quotes-nihr01
+   quotes-nitrc
 
 .. include:: links_names.rst
 .. include:: substitutions.rst
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+.. Generated on Fri Oct 22 13:05:28 EDT 2010
+.. Do not edit directly
+
+.. quote::
+   :author: Prof. Thomas J. Grabowski, Jr.
+   :affiliation: Director, Integrated Brain Imaging Center, University of Washington, Seattle, Washington, USA
+   :date: 2010-09-16
+   :tags:  lofs, speed, frontier
+   :group: Research institutions
+
+   [...] software for neuroimage processing evolves rapidly and heterogeneously. It is a challenge for research organizations to remain current  [...] In this context we have begun to use the NeuroDebian repository  [...] We hope that this service will continue with an expanded scope  [...]
+
+
+.. quote::
+   :author: Prof. Daniel Y. Kimberg
+   :affiliation: Core Director, Data Processing Facility, Center for Functional Neuroimaging, University of Pennsylvania, Philadelphia, USA
+   :date: 2010-09-08
+   :tags:  lofs, software distribution, quality, reproducibility, practices, impact
+   :group: Research institutions
+
+   The approach taken with NeuroDebian is plainly the most appropriate approach to software distribution for the dominant platform in brain image analysis, and I have great confidence that this project will be a major asset to the neuroscience community in facilitating the distribution of stable software, improving the reliability and replicability of analyses, and in helping to improve software development practices.
+
+
+.. quote::
+   :author: Prof. Bennett Landman
+   :affiliation: Director of the Center for Computational Imaging, Vanderbilt University Institute of Image Science, Nashville, Tennessee, USA
+   :date: 2010-08-31
+   :tags:  lofs, software distribution, quality
+   :group: Research institutions
+
+   NeuroDebian provides an excellent platform for software distribution [...]
+
+
+.. quote::
+   :author: Prof. Barak A. Pearlmutter
+   :affiliation: Hamilton Institute, NUI Maynooth, Co. Kildare, Ireland
+   :date: 2010-09-07
+   :tags:  lofs, software distribution, sharing, money, speed
+   :group: Research institutions
+
+   Having common software stacks makes sharing much easier, potentially (and silently) saving enormous amounts of money and effort and dramatically increasing efficiently and productivity in not one, but many labs. NeuroDebian is of particular utility in these regards.  
+
+
+.. quote::
+   :author: Prof. Russell A. Poldrack
+   :affiliation: Director, Imaging Research Center, University of Texas at Austin, Texas, USA
+   :date: 2010-08-31
+   :tags:  lofs, breadth, impact
+   :group: Research institutions
+
+   I think that the idea of a common platform that supports a broad range of computational needs for neuroscientists is wonderful, and I am very impressed with the work that you have done so far in the NeuroDebian project.  
+
+
+.. quote::
+   :author: Dr. Bertrand Thirion
+   :affiliation: Head of the Parietal research group at Neurospin, Gif sur Yvette, France
+   :date: 2010-09-08
+   :tags:  lofs, breadth
+   :group: Research institutions
+
+   [NeuroDebian is] extremely useful in providing state of the art solutions to numerous standard problems encountered in the analysis of our complex data.
+
+
+.. quote::
+   :author: Tiziano Zito
+   :affiliation: IT system administrator, Bernstein Center for Computational Neuroscience, Berlin, Germany
+   :date: 2010-09-02
+   :tags:  lofs, software distribution, frontier
+   :group: Research institutions
+
+   NeuroDebian project made our library available to an unprecedented number of users  [...] as a system administrator, I rely on NeuroDebian for setting up and keeping up-to-date the software installed on the numerous clients and servers used by more than 150 scientists
+
+
+.. quote::
+   :author: Dr. Matthew Brett
+   :affiliation: Specialist researcher, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
+   :date: 2010-09-02
+   :tags:  lofs, practices, team, sharing
+   :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.  
+
+
+.. quote::
+   :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
+   :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.
+
+
+.. quote::
+   :author: Dr. Satrajit Ghosh
+   :affiliation: Research scientist, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
+   :date: 2010-09-06
+   :tags:  lofs, software distribution
+   :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.
+
+
+.. quote::
+   :author: Valentin Haenel
+   :affiliation: Psignifit and pyoptical developer, Modellierung Kognitiver Prozesse, Technische Universität, Berlin, Germany
+   :date: 2010-09-17
+   :tags:  lofs, reproducibility
+   :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.
+
+
+.. quote::
+   :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
+   :group: Research software projects
+
+   [...] distributing the software via NeuroDebian generates valuable feedback which is indispensable for the development of free software. When working with the NeuroDebian team in the past, I have found their members to be very cooperative,    target-oriented and responsive.
+
+
+.. quote::
+   :author: 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
+   :group: Research software projects
+
+   It [NeuroDebian] has been and continues to be of great value in all of our projects [...]
+
+
+.. quote::
+   :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
+   :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 
+
+
+.. quote::
+   :author: Dr. Eilif Muller
+   :affiliation: Post-doctoral researcher, Brain Mind Institute, EPFL, Lausanne, Switzerland
+   :date: 2010-09-09
+   :tags:  lofs, reproducibility, standartization, breadth
+   :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.  
+
+
+.. quote::
+   :author: Prof. Jonathan Peirce
+   :affiliation: School of Psychology, University of Nottingham, Nottingham, UK
+   :date: 2010-09-06
+   :tags:  lofs, money, impact
+   :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.
+
+
+.. quote::
+   :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, standartization, dissemination
+   :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.
+
+
+.. quote::
+   :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
+   :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.  
+
+
+.. quote::
+   :author: Paolo Avesani
+   :affiliation: Neuroinformatics Laboratory, Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
+   :date: 2010-09-15
+   :tags:  lofs, money
+   :group: Individual laboratories and researchers
+
+   It [NeuroDebian] is of great advantage for the management of the computers of the lab because NeuroDebian allows to reduce the system administration costs.
+
+
+.. quote::
+   :author: John A. Clithero
+   :affiliation: Ph.D. student, Center for Cognitive Neuroscience, Duke University, Durham, North Carolina, USA
+   :date: 2010-09-08
+   :tags:  lofs, support
+   :group: Individual laboratories and researchers
+
+   Both the software and online support forums provided by NeuroDebian have been invaluable for my machine-learning studies of fMRI data.  
+
+
+.. quote::
+   :author: Scott Gorlin
+   :affiliation: Ph.D. student, Department of Brain and Cognitive Science Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
+   :date: 2010-09-16
+   :tags:  lofs, speed, quality
+   :group: Individual laboratories and researchers
+
+   I am writing this letter in support of the NeuroDebian team, whose efforts at producing high-quality free, open-source software have been invaluable to my graduate research.  
+
+
+.. quote::
+   :author: Dr. Attila Krajcsi
+   :affiliation: Lecturer, Cognitive Psychology Department, Eötvös University, Hungary
+   :date: 2010-09-06
+   :tags:  lofs, speed
+   :group: Individual laboratories and researchers
+
+   [NeuroDebian is] an extremely time saving solution
+
+
+.. quote::
+   :author: Kaunitz Lisandro Nicolas
+   :affiliation: Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
+   :date: 2010-09-09
+   :tags:  lofs
+   :group: Individual laboratories and researchers
+
+   [We] find it [NeuroDebian] to be the best tool for running classifiers on our neuroimaging data (EEG and MEG).
+
+
+.. quote::
+   :author: Dr. Emanuele Olivetti
+   :affiliation: Center for Information Technology, Bruno Kessler Foundation, Trento, Italy
+   :date: 2010-09-09
+   :tags:  lofs, speed
+   :group: Individual laboratories and researchers
+
+   NeuroDebian has a major impact within our laboratory as quick and rich research environment for all our projects.
+
+
+.. quote::
+   :author: Dr. Giuseppe Pagnoni
+   :affiliation: Dipartimento di Scienze Biomediche, Università degli studi di Modena e Reggio Emilia, Modena, Italy
+   :date: 2010-09-07
+   :tags:  lofs
+   :group: Individual laboratories and researchers
+
+   We consider NeuroDebian to be a truly commendable effort and an invaluable asset for the neuroimaging community.  
+
+
+.. quote::
+   :author: Prof. Stefan Pollmann
+   :affiliation: Lehrstuhl für Allgemeine Psychologie, Otto-von-Guericke Universität, Magdeburg, Germany
+   :date: 2010-09-02
+   :tags:  lofs, money
+   :group: Individual laboratories and researchers
+
+   My lab is using NeuroDebian for almost five years now  [...] The minimal maintenance cost allow us to operate our research and computing infrastructure  [...] even without a dedicated system administrator. Consequently, these resources could be invested into scientific personnel instead.
+
+
+.. quote::
+   :author: Dr. Daqiang Sun
+   :affiliation: Post-doctoral researcher, Department of Psychology, University of California, Los Angeles, USA
+   :date: 2010-09-15
+   :tags:  lofs, speed
+   :group: Individual laboratories and researchers
+
+   It [NeuroDebian] is and will continue to be invaluable in our multiple NIH-funded research projects.  NeuroDebian nicely takes care of the burden of software deployment and management on my computers and allows me to concentrate on the imaging analysis itself [...]
+
+
+.. quote::
+   :author: Dr. Gaël Varoquaux
+   :affiliation: Parietal project, INRIA, Neurospin research center, Gif sur Yvette, France
+   :date: 2010-09-01
+   :tags:  lofs, reproducibility, dissemination
+   :group: Individual laboratories and researchers
+
+   The availability of a common platform [NeuroDebian] for many different neuroimaging software solutions makes it much easier to compare solutions and pick the tool of choice for a given research problem.
+
+
+.. quote::
+   :author: Dr. Roberto Viviani
+   :affiliation: Department of Psychiatry and Psychotherapy III, University of Ulm, Germany
+   :date: 2010-09-15
+   :tags:  lofs, dissemination
+   :group: Individual laboratories and researchers
+
+   Our research would be considerably more difficult without necessary software solutions transparently provided and supported by the NeuroDebian project.  
+
diff --git a/sphinx/quotes-nitrc.rst b/sphinx/quotes-nitrc.rst
new file mode 100644 (file)
index 0000000..5628804
--- /dev/null
@@ -0,0 +1,19 @@
+.. Selected quotes from NITRC portal
+
+.. quote::
+   :author: Anonymous
+   :date: 2010-05-05
+   :tags:  nitrc, vm, ease, breadth
+   :group: Individual laboratories and researchers
+   :source: NITRC NeuroDebian reviews
+
+   brilliant! as promised, all problems are [on their way to being] solved. (well, at least in so far as neuroscience is concerned :) very cool and as pointed out, NeuroDebian lets you try out all the cool toys of neuroscience research with a very straightforward ease of use (esp. with the virtual machine). very nice...keep up the good work!
+
+.. quote::
+   :author: Anonymous
+   :date: 2010-05-05
+   :tags:  nitrc, vm
+   :group: Individual laboratories and researchers
+   :source: NITRC NeuroDebian reviews
+
+   [...] Best part for me is that I can run it in a VM without having to worry about replacing my native OS.
diff --git a/sphinx/sphinxext/__init__.py b/sphinx/sphinxext/__init__.py
new file mode 100644 (file)
index 0000000..e69de29
diff --git a/sphinx/sphinxext/quote.py b/sphinx/sphinxext/quote.py
new file mode 100644 (file)
index 0000000..f42d23f
--- /dev/null
@@ -0,0 +1,261 @@
+#emacs: -*- coding: utf-8; mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: t -*-
+#ex: set sts=4 ts=4 sw=4 et:
+"""
+   ext.quote
+   ~~~~~~~~~
+
+   Collect and render individual quotes (quote directive) or
+   selections (quotes directive) of quotes.
+
+   Example::
+
+      .. quote::
+         :author: Dr. Joe Black
+                :affiliation: Someone important, somewhere nice
+                :date: 1990-01-01
+                :tags: software, Debian, sphinx
+                :group: Research software projects
+
+            quote.py is a wonderful extension
+
+         .. quotes::
+            :random: 1
+                :tags: sphinx
+
+
+   :copyright: Copyright 2010 Yaroslav O. Halchenko
+   :license: BSD
+
+   Based on todo.py extension from sphinx:
+   :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
+   :license: BSD, see LICENSE for details.
+
+"""
+
+import operator
+from random import sample
+
+from docutils import nodes
+from docutils.parsers.rst import directives, Directive
+from docutils.parsers.rst.directives import body
+
+from sphinx.environment import NoUri
+from sphinx.util.compat import Directive, make_admonition
+
+
+class quote_node(nodes.Body, nodes.Element): pass
+class quotes(nodes.General, nodes.Element): pass
+
+def _info(msg):
+       # print "I: ", msg
+       pass
+
+def _prep_tags(options):
+       """Extract tags listed in a string"""
+       options['tags'] = set((x.strip()
+                                                  for x in
+                                                  options.get('tags', '').split(',')))
+
+class Quote(Directive):
+    """
+    A quote entry, displayed (if configured) in the form of an admonition.
+    """
+
+    has_content = True
+    required_arguments = 0
+    optional_arguments = 0
+    final_argument_whitespace = False
+       option_spec = {
+               'author': directives.unchanged,
+               'affiliation': directives.unchanged,
+               'date': directives.unchanged,
+               'group': directives.unchanged,
+               'tags': directives.unchanged,   # list of tags per quote
+               'source': directives.unchanged}
+
+    def run(self):
+        state = self.state
+        env = self.state.document.settings.env
+        options = self.options
+               if hasattr(env, 'new_serialno'):
+                       targetid = 'index-%s' % env.new_serialno('index')
+               else:
+                       targetid = "index-%s" % env.index_num
+        targetnode = nodes.target('', '', ids=[targetid])
+               targetnode['classes'] = ['epigraph']
+
+        node = quote_node()
+               node += nodes.block_quote(
+                       '',
+                       nodes.paragraph('', '\n'.join(self.content), classes=['text']))
+               #state.nested_parse(self.content, self.content_offset, node)
+
+        for element in node:
+            if isinstance(element, nodes.block_quote):
+                element['classes'] += ['epigraph']
+
+               signode = [nodes.attribution('--', '--')]
+               # Embed all components within attributions
+               siglb = nodes.line_block('')
+               # Pre-format some
+               if 'date' in options:
+                       options['date'] = '[%(date)s]' % options
+               if 'source' in options:
+                       options['source'] = 'Source: %(source)s' % options
+               for el in ['author', 'date', 'affiliation', 'source']:
+                       if el in options:
+                               siglb += [nodes.inline('', '  '+options[el], classes=[el])]
+               signode[0].extend(siglb)
+               node[0].extend(signode)
+               node.line = self.lineno
+               # tune up options
+               _prep_tags(self.options)
+               node.options = options
+        return [targetnode] + [node]
+
+
+
+def process_quotes(app, doctree):
+    # collect all quotes in the environment
+    # this is not done in the directive itself because it some transformations
+    # must have already been run, e.g. substitutions
+       _info("process_quotes")
+
+    env = app.builder.env
+    if not hasattr(env, 'quote_all_quotes'):
+        env.quote_all_quotes = []
+    for node in doctree.traverse(quote_node):
+        try:
+            targetnode = node.parent[node.parent.index(node) - 1]
+            if not isinstance(targetnode, nodes.target):
+                raise IndexError
+        except IndexError:
+            targetnode = None
+        env.quote_all_quotes.append({
+            'docname': env.docname,
+            'lineno': node.line,
+            'quote': node, #.deepcopy(),
+            'target': targetnode,
+        })
+
+
+class Quotes(Directive):
+    """
+    A list of all quote entries.
+    """
+
+    has_content = False
+    required_arguments = 0
+    optional_arguments = 0
+    final_argument_whitespace = False
+       option_spec = {
+               'random': directives.positive_int, # how many to randomly output
+               'group': directives.unchanged,     # what group to show
+               'tags': directives.unchanged,   # list of tags to be matched
+               # 'sections': lambda a: directives.choice(a, ('date', 'group'))
+               }
+
+    def run(self):
+        # Simply insert an empty quotes node which will be replaced later
+        # when process_quote_nodes is called
+               res = quotes('')
+               # tags which must be matched
+               if 'tags' in self.options:
+                       _prep_tags(self.options)
+               res.options = self.options
+               _info("Run Quotes %s" % res)
+        return [res]
+
+
+
+def process_quote_nodes(app, doctree, fromdocname):
+    # Replace all quotes nodes with a list of the collected quotes.
+    # Augment each quote with a backlink to the original location.
+    env = app.builder.env
+
+    if not hasattr(env, 'quote_all_quotes'):
+        env.quote_all_quotes = []
+
+       #_info("process_quote_nodes '%s' %i"
+       #         % (fromdocname, len(env.quote_all_quotes)))
+
+    for node in doctree.traverse(quotes):
+
+        content = []
+               filters = []
+               loptions = node.options
+
+               # Filter by tags?
+               if 'tags' in loptions:
+                       ltags = loptions['tags']
+                       filters.append(
+                               lambda quote: set.issuperset(
+                                       quote.options['tags'], ltags))
+               # Filter by group?
+               if 'group' in loptions:
+                       loptions['group']
+                       filters.append(
+                               lambda quote:
+                               quote.options.get('group', '') == loptions['group'])
+
+        for quote_info in env.quote_all_quotes:
+            quote_entry = quote_info['quote']
+                       if not reduce(operator.__and__,
+                                                 [f(quote_entry) for f in filters],
+                                                 True):
+                               continue
+
+            # Insert into the quotes
+            content.append(quote_entry)
+            ## content.append(para)
+
+               # Handle additional quotes options
+
+               # Select a limited number of random samples
+               if loptions.get('random', None):
+                       # Randomly select desired number of quotes
+                       content = sample(content, loptions['random'])
+
+               # Group items into sections and intersperse the list
+               # with section nodes
+               if loptions.get('sections', None):
+                       raise NotImplementedError
+                       term = loptions['sections']
+                       terms = [q.options.get(term, None) for q in content]
+                       terms = list(set([x for x in terms if x]))
+                       # Simply sort according to what to group on,
+                       # and then insert sections?
+                       section = nodes.section('')
+                       section.extend(nodes.title('', 'XXX'))
+                       section += content[:2]
+                       section.parent = content[0].parent
+                       content = [ section ]
+
+               # Substitute with the content
+        node.replace_self(content)
+
+
+
+def purge_quotes(app, env, docname):
+    if not hasattr(env, 'quote_all_quotes'):
+        return
+       _info("purge_quotes")
+    env.quote_all_quotes = [quote for quote in env.quote_all_quotes
+                          if quote['docname'] != docname]
+
+
+def quotes_noop(self, node):
+       pass
+
+def setup(app):
+    app.add_node(quotes)
+    app.add_node(quote_node,
+                 html=(quotes_noop, quotes_noop),
+                 latex=(quotes_noop, quotes_noop),
+                 text=(quotes_noop, quotes_noop))
+
+    app.add_directive('quote', Quote)
+    app.add_directive('quotes', Quotes)
+    app.connect('doctree-read', process_quotes)
+    app.connect('doctree-resolved', process_quote_nodes)
+    app.connect('env-purge-doc', purge_quotes)
diff --git a/sphinx/testimonials.rst b/sphinx/testimonials.rst
new file mode 100644 (file)
index 0000000..ba6fc32
--- /dev/null
@@ -0,0 +1,46 @@
+.. _testimonials:
+
+Testimonials
+============
+
+.. None so far replied
+..
+.. Organizations
+.. -------------
+..
+.. .. quotes::
+..    :group: Organizations
+
+
+Research Institutions
+---------------------
+
+.. quotes::
+   :group: Research institutions
+
+..   not implemented for now
+..   :sections: group
+
+
+Research Software Projects
+--------------------------
+
+.. quotes::
+   :group: Research software projects
+
+
+Individual Laboratories and Researchers
+---------------------------------------
+
+.. quotes::
+   :group: Individual laboratories and researchers
+
+
+.. quote::
+   :author: Prof. Petr Hlustik
+   :affiliation: Departments of Neurology and Radiology, Palacky University School of Medicine and University Hospital, Olomouc, Czech Republic
+   :date: 2010-10-11
+   :tags: breadth
+
+   [...] those wonderful tools in Debian Neuro [...] make my life as a
+   researcher who also maintains a bunch of Debian boxes so much easier.
index 1a0f90b72758185ce57fe0240dd082fe0ec12ff5..cb20678b842054b97e4169e2aa2170b10a19e5f8 100644 (file)
@@ -3,6 +3,10 @@
 NeuroDebian Virtual Machine
 ===========================
 
+.. quotes::
+   :random: 1
+   :tags: vm
+
 Those, who are not yet running a Debian-based operating system, but are already
 tired of fiddling with dozens of neuro-software packages, can get a glimpse of
 neuroscience research in a Debian environment via a `virtual machine`_.