]> git.donarmstrong.com Git - neurodebian.git/commitdiff
Merge branch 'master' of git://git.debian.org/pkg-exppsy/neurodebian
authorYaroslav Halchenko <debian@onerussian.com>
Fri, 4 Nov 2011 18:26:38 +0000 (14:26 -0400)
committerYaroslav Halchenko <debian@onerussian.com>
Fri, 4 Nov 2011 18:26:38 +0000 (14:26 -0400)
* 'master' of git://git.debian.org/pkg-exppsy/neurodebian: (66 commits)
  adding neurodebian and its aliased pkgs to neurodebian.cfg
  Boosted policy to 3.9.2 -- no changes
  adjust changelog for release
  nd_adddistall to add to all dists not just nd
  list to email on survey
  recommend ubuntu-keyring (backported) and moved python into recommends
  BF: removing hardcoded for debug purposes $PWD/
  make all leading dirs to aptcache as well
  removed duplicate Suggests:
  NH: little helper to initiate chroots for all supported distros
  BF: time into recommends since used in nd_ scripts
  BF: call apt-key add explicitly for older Ubuntus
  scaled neurodebian_back down to 74% (makes around 260mm width)
  changed "Debian" into white + fixed tiny bits of openlogo which flew away
  reduced size of pocket logo to match already printed size
  reordered dists by age to match Debian ones order
  RF: only suggest virtualbox-ose while installing neurodebian-dev
  NF: nd_rebuildarchive helper to rebuild archive for a new release
  ENH: allow for custom version suffix prefix in backport-dsc
  T-shirt artwork.
  ...

41 files changed:
Makefile
artwork/debian_pocket.svg [new file with mode: 0644]
artwork/neurodebian_back.svg [new file with mode: 0644]
cmdsettings.sh
debian/changelog
debian/control
future/blends/elastix [deleted file]
future/blends/isis [new file with mode: 0644]
future/blends/neo [new file with mode: 0644]
future/blends/pandas [new file with mode: 0644]
future/blends/psychlops [new file with mode: 0644]
future/blends/pymeg [new file with mode: 0644]
future/blends/pysurfer [new file with mode: 0644]
future/blends/pyxnat [deleted file]
future/blends/stabilitycalc [new file with mode: 0644]
neurodebian.cfg
neurodebian/dde.py
sphinx/_static/neurodebian.css
sphinx/blog/2011/2011-09-26_in_the_spotlight.rst [new file with mode: 0644]
sphinx/blog/2011/2011-09-26_spotlight_opensesame.rst [new file with mode: 0644]
sphinx/coffeeart.rst
sphinx/index.rst
sphinx/pics/blog/opensesame_backend.png [new file with mode: 0644]
sphinx/pics/blog/opensesame_stimulus.png [new file with mode: 0644]
sphinx/pics/coffeeart/2011-03-23_13.44.26.jpg [new file with mode: 0644]
sphinx/pics/coffeeart/2011-08-2X.jpg [new file with mode: 0644]
sphinx/pics/coffeeart/2011-09-01_18.48.53.jpg [new file with mode: 0644]
sphinx/projects.rst
sphinx/quotes-nihr01.rst
sphinx/quotes-nitrc.rst
sphinx/sphinxext/feed/__init__.py
survey/NOTES.txt
tools/backport-dsc
tools/nd_adddist
tools/nd_adddistall [new file with mode: 0755]
tools/nd_build
tools/nd_build4allnd
tools/nd_build_testrdepends [new file with mode: 0755]
tools/nd_execute [new file with mode: 0755]
tools/nd_fetch_bdepends [new file with mode: 0755]
tools/nd_rebuildarchive [new file with mode: 0755]

index b18c3107a176a98b3bedf619db7ae03a430084d6..4b9e35a7c432e465bdc0be57ec29b89b60395f49 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -20,7 +20,7 @@ html: pics source
 
 
 clean:
-       -rm html-stamp source-stamp
+       -rm html-stamp source-stamp upload-website-stamp
        $(MAKE) -C artwork clean
 
 
@@ -30,7 +30,7 @@ distclean: clean
 
 source: source-stamp
 source-stamp: build/db.db
-       PYTHONPATH=. python neurodebian/dde.py \
+       PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
                --cfg neurodebian.cfg \
                --db build/db.db \
                --outdir build/src \
@@ -53,7 +53,7 @@ updatedb: removedb removecache build/db.db
 
 build/db.db:
        mkdir -p build
-       PYTHONPATH=. python neurodebian/dde.py \
+       PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
                --cfg neurodebian.cfg \
                --db build/db.db \
                updatedb
@@ -64,6 +64,12 @@ upload-website: html
        rsync -rvzlhp --delete \
         --exclude=debian --exclude=debian-local --exclude=_files \
         --chmod=Dg+s,g+rw $(WWW_DIR) $(WWW_UPLOAD_URI)
+       : # Touch stamp here so we get it updated on every upload
+       touch $@-stamp
+
+# call upload iff .git/index was modified, i.e. new changes got pulled in
+upload-website-stamp: .git/index
+       $(MAKE) upload-website
 
 .PHONY: removedb removecache updatedb upload-website clean distclean pics html
 
diff --git a/artwork/debian_pocket.svg b/artwork/debian_pocket.svg
new file mode 100644 (file)
index 0000000..af98ca7
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index 1dc6a9d4c0833b18b8d57a9c5cc163b639638c4e..3466c7835d60e44383c154fa1d32a8da311aae42 100644 (file)
@@ -7,7 +7,7 @@ buildplace="${cowbuilderroot}/build"
 
 # all cuurently supported dists
 allnddists="nd+debian-lenny nd+debian-squeeze nd+debian-wheezy nd+debian-sid \
-            nd+ubuntu-natty nd+ubuntu-maverick nd+ubuntu-lucid nd+ubuntu-karmic nd+ubuntu-hardy"
+            nd+ubuntu-hardy nd+ubuntu-karmic nd+ubuntu-lucid nd+ubuntu-maverick nd+ubuntu-natty nd+ubuntu-oneiric"
 alldists="$allnddists debian-lenny debian-squeeze debian-wheezy debian-sid"
 
 # default is debian
@@ -22,4 +22,4 @@ if [ "${family#nd+}" = "ubuntu" ]; then
   mirror="http://ubuntu.media.mit.edu/ubuntu"
 fi
 
-if [ ! -d $aptcache ]; then mkdir $aptcache; fi
+if [ ! -d $aptcache ]; then mkdir -p $aptcache; fi
index 0b319c86e60c2dda789ce8f5a3be2dd61b4464ae..9c34af3aa72dfff24802bc7d97f7d6ce0b89ebc3 100644 (file)
@@ -1,3 +1,23 @@
+neurodebian (0.26) unstable; urgency=low
+
+  [ Michael Hanke & Yaroslav Halchenko]
+  * website:
+    - lots of changes: blog, artwork, survey, testimonials, etc.
+  * nd_* tools:
+    - added support for Ubuntu 11.04 -- Oneiric
+    - new tool nd_build_testrdepends to test either upcoming version of a
+      package would break any reverse build-depends
+    - new tool nd_adddistall to generate cow chroots for all distributions
+    - nd_build now returns non-0 code upon any failure to build
+  * VM:
+    - tuned for releasing 6.0.4 -- addressed issue with dkms build of
+      guest additions
+    - NeuroDebian "Welcome Wizard" pulls scipy instead of only numpy for
+      "Scientific Python"
+  * Boosted policy to 3.9.2 -- no changes
+
+ -- Yaroslav Halchenko <debian@onerussian.com>  Mon, 17 Oct 2011 00:10:27 -0400
+
 neurodebian (0.25) unstable; urgency=low
 
   * Various improvements to the webportal.
index 746ea0d4eb4a9e6ab843205c13da9f6389df0e24..03a53c0fe85776697d046fe5776a808af931f698 100644 (file)
@@ -4,7 +4,7 @@ Priority: optional
 Maintainer: NeuroDebian Team <team@neuro.debian.net>
 Uploaders: Michael Hanke <mih@debian.org>, Yaroslav Halchenko <debian@onerussian.com>
 Build-Depends: debhelper (>= 7.0.50~), xcftools, help2man, inkscape, imagemagick, python-html5lib
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
 Homepage: http://neuro.debian.net
 Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/neurodebian.git
 Vcs-Git: git://git.debian.org/git/pkg-exppsy/neurodebian.git
@@ -13,9 +13,9 @@ XS-DM-Upload-Allowed: yes
 
 Package: neurodebian-dev
 Architecture: all
-Depends: ${misc:Depends}, devscripts, cowbuilder, python, neurodebian-keyring
-Recommends: virtualbox-ose, virtualbox-ose-fuse, zerofree, moreutils
-Suggests:
+Depends: ${misc:Depends}, devscripts, cowbuilder, neurodebian-keyring
+Recommends: python, zerofree, moreutils, time, ubuntu-keyring
+Suggests: virtualbox-ose, virtualbox-ose-fuse
 Description: NeuroDebian development tools
  neuro.debian.net sphinx website sources and development tools used by
  NeuroDebian to provide backports for a range of Debian/Ubuntu
diff --git a/future/blends/elastix b/future/blends/elastix
deleted file mode 100644 (file)
index e283283..0000000
+++ /dev/null
@@ -1,22 +0,0 @@
-Source: elastix
-Tasks: debian-med/imaging
-Homepage: http://elastix.isi.uu.nl/index.php
-Author: Stefan Klein,  Marius Staring
-Language: C++
-License: BSD-3
-WNPP: 607030
-Version: 4.4
-Pkg-Description: toolbox for rigid and nonrigid registration of images
- elastix is open source software, based on the well-known Insight
- Segmentation and Registration Toolkit (ITK). The software consists of
- a collection of algorithms that are commonly used to solve (medical)
- image registration problems. The modular design of elastix allows the
- user to quickly configure, test, and compare different registration
- methods for a specific application. A command-line interface enables
- automated processing of large numbers of data sets, by means of
- scripting.
-Published-Title: elastix: a toolbox for intensity based medical image registration
-Published-Authors: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim
-Published-In: IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205
-Published-Year: 2010
-Registration: http://elastix.isi.uu.nl/download.php
diff --git a/future/blends/isis b/future/blends/isis
new file mode 100644 (file)
index 0000000..861c77c
--- /dev/null
@@ -0,0 +1,13 @@
+Source: isis
+Tasks: debian-med/imaging
+Homepage: http://isis-group.github.com/isis/
+Author: Lydia Hellrung (hellrung@cbs.mpg.de) et al.
+Language: C++
+License: GPL-2+
+Version: 0.3.3
+Responsible: NeuroDebian Team <team@neuro.debian.net>
+Pkg-Description: I/O framework for neuroimaging data
+ This framework aids access of and conversion between various established
+ neuro-imaging data formats, like  Nifti, Analyze, DICOM and VISTA. ISIS
+ is extensible with plugins to add support for additional data formats.
+Why: IO layer for Lipsia and maybe soon Odin.
diff --git a/future/blends/neo b/future/blends/neo
new file mode 100644 (file)
index 0000000..afea791
--- /dev/null
@@ -0,0 +1,21 @@
+Source: neo
+Tasks: debian-science/electrophysiology
+Homepage: http://neuralensemble.org/trac/neo
+License: BSD
+Author: Samuel Garcia, Pierre Yger, Luc Estabanez, Andrew Davison, Yury V. Zaytsev
+Language: Python
+Version: 0.1
+Vcs-SVN: https://neuralensemble.org/svn/neo/
+Pkg-Description: IO library for electrophysiological data formats in Python
+ NEO stands for Neural Ensemble Objects and is a project to provide common
+ class names and concepts for dealing with electro-physiological (in vivo
+ and/or simulated) data with the aim of getting OpenElectrophy, NeuroTools,
+ G-node and maybe other projects with similar goals more close together.
+ .
+ In particular Neo provides:
+ .
+  * a set a classes with precise definitions
+  * an IO module that offer a simple API that fit many formats
+  * documentation.
+  * a set of examples like a format convertor
+Remark: Upstream says not worth packaging before v0.2 is released.
diff --git a/future/blends/pandas b/future/blends/pandas
new file mode 100644 (file)
index 0000000..e89e924
--- /dev/null
@@ -0,0 +1,26 @@
+Source: pandas
+Tasks: debian-science/statistics
+Homepage: http://pandas.sourceforge.net
+Author: Wes McKinney <wesmckinn@gmail.com>
+Language: Python, Cython
+License: BSD-3
+Version: 0.4.0
+Pkg-Description: data structures for "relational" or "labeled" data
+ pandas is a Python package providing fast, flexible, and expressive
+ data structures designed to make working with "relational" or
+ "labeled" data both easy and intuitive. It aims to be the fundamental
+ high-level building block for doing practical, real world data
+ analysis in Python. pandas is well suited for many different kinds of
+ data:
+ .
+  - Tabular data with heterogeneously-typed columns, as in an SQL
+    table or Excel spreadsheet
+  - Ordered and unordered (not necessarily fixed-frequency) time
+    series data.
+  - Arbitrary matrix data (homogeneously typed or heterogeneous) with
+    row and column labels
+  - Any other form of observational / statistical data sets. The data
+    actually need not be labeled at all to be placed into a pandas
+    data structure
+Pkg-URL: http://neuro.debian.net/pkgs/cctools.html
+WNPP: 641464
diff --git a/future/blends/psychlops b/future/blends/psychlops
new file mode 100644 (file)
index 0000000..a372872
--- /dev/null
@@ -0,0 +1,14 @@
+Source: psychlops
+Tasks: debian-science/psychophysics
+Homepage: http://psychlops.sourceforge.jp
+Language: C++
+License: GPL
+Version: 1.5.0
+Pkg-Description:
+ Psychlops is a free C++ library to offer the easy way to develop a
+ demonstration of various types of visual stimulus used in the Vision
+ science.
+ .
+ Binary builds are available only for OS X and Windows.  Sources
+ available from sf's SVN:
+ http://sourceforge.jp/projects/psychlops/svn/view/cpp/
diff --git a/future/blends/pymeg b/future/blends/pymeg
new file mode 100644 (file)
index 0000000..aa20147
--- /dev/null
@@ -0,0 +1,15 @@
+Source: pymeg
+Tasks: debian-science/electrophysiology,
+          debian-med/imaging
+Homepage: https://github.com/badbytes/pymeg/wiki
+Author: Dan Collins <quaninux@gmail.com>
+Language: Python
+License: GPL-3
+Version: unknown
+Pkg-Description: suite for analysis of magnetoencephalography (MEG) data
+  PyMEG is a project in Python to do various neuroimaging processing
+  with magnetoencephalography (MEG) data. The purpose of this project,
+  is to create a suite of functions to do MEG analysis in Python.
+Remark: Needs DFSG-ification.
+        According to the author is not yet ready for the use by
+        mortals -- wasn't released yet.
diff --git a/future/blends/pysurfer b/future/blends/pysurfer
new file mode 100644 (file)
index 0000000..22b8483
--- /dev/null
@@ -0,0 +1,18 @@
+Source: pysurfer
+Tasks: debian-science/neuroscience-cognitive, debian-med/imaging
+Homepage: http://pysurfer.github.com/
+Author:  Michael Waskom, Alexandre Gramfort, Scott Burns, Satrajit Gosh
+Language: Python
+License: BSD-3
+Version: 0.1+git....
+WNPP: 641345
+Pkg-Description: visualize Freesurfer's data in Python
+ This is a Python package for visualization and interaction with cortical
+ surface representations of neuroimaging data from Freesurfer. It
+ extends Mayavi’s powerful visualization engine with a high-level interface for
+ working with MRI and MEG data.
+ .
+ PySurfer offers both a command-line interface designed to broadly replicate
+ Freesurfer’s Tksurfer program as well as a Python library for writing scripts
+ to efficiently explore complex datasets.
+Responsible: NeuroDebian Team <team@neuro.debian.net>
diff --git a/future/blends/pyxnat b/future/blends/pyxnat
deleted file mode 100644 (file)
index 554a730..0000000
+++ /dev/null
@@ -1,21 +0,0 @@
-Source: pyxnat
-Tasks: debian-science/neuroscience-cognitive,
-          debian-med/imaging-dev
-Homepage: http://packages.python.org/pyxnat
-Author: Yannick Schwartz <yannick.schwartz@cea.fr>
-Language: Python
-License: BSD
-Version: 0.6.2
-WNPP: 609820
-Pkg-Description: interface to access neuroimaging data on XNAT servers
- XNAT is an extensible database for neuroimaging data.  pyxnat is a
- Python library that relies on the REST API provided by the XNAT
- platform since its 1.4 version. The main objective of pyxnat is to
- ease communications with an XNAT server to plug-in external tools or
- python scripts to process the data. pyxnet features:
- .
-  - resources browsing capabilities
-  - read and write access to resources
-  - complex searches
-  - disk-caching of requested files and resources
-Responsible: NeuroDebian Team <team@neuro.debian.net>
diff --git a/future/blends/stabilitycalc b/future/blends/stabilitycalc
new file mode 100644 (file)
index 0000000..d9043c1
--- /dev/null
@@ -0,0 +1,14 @@
+Source: stabilitycalc
+Tasks: debian-med/imaging
+Homepage: https://github.com/bbfrederick/stabilitycalc
+License: BSD
+Author: Blaise Frederick
+Language: Python
+Version: 0.1
+Pkg-URL: http://neuro.debian.net/pkgs/stabilitycalc.html
+Responsible: NeuroDebian Team <team@neuro.debian.net>
+Vcs-Git: https://github.com/bbfrederick/stabilitycalc.git
+Pkg-Description: evaluate fMRI scanner stability
+ Command-line tools to calculate numerous fMRI scanner stability metrics, based
+ on the FBIRN quality assurance test protocol. Any 4D volumetric timeseries
+ image in NIfTI format is supported input. Output is a rich HTML report.
index 542771093676a4b12cfd552ecdd9f70937418d67..d77fbf23a436f3ec696262d71f6c8d71c16b2845 100644 (file)
@@ -22,6 +22,7 @@ select names = libnifti2 odin mitools afni-atlases python-pyssdh python-networkx
  r-cran-glmnet python-rpy2 python-nibabel-snapshot
  python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab-support
  svgtune rorden-mri-tutorial caret-data python-joblib python-sphinx fail2ban
+ python-pandas neurodebian
 
 # Information about prospective packages to be imported from taskfiles
 prospective =
@@ -43,7 +44,7 @@ cctools = coop-computing-tools
 mni-icbm152-nlin-2009 = mni-icbm152-nlin-2009a mni-icbm152-nlin-2009b mni-icbm152-nlin-2009c
 fsl = fsl fsl-doc fsl-atlases fsl-possum-data fsl-first-data fsl-feeds fsl-mni152-templates
 fslview = fslview fslview-doc
-python-mvpa = python-mvpa python-mvpa-snapshot
+python-mvpa = python-mvpa python-mvpa-snapshot python-mvpa2
 libgiftiio-dev = libgiftiio-dev gifti-bin
 openmeeg-tools = openmeeg-tools libopenmeeg-dev python-openmeeg libopenmeeg1
 libbiosig-dev = libbiosig-dev python-biosig octave-biosig biosig-tools libbiosig0
@@ -52,6 +53,11 @@ 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
 
 [mirrors]
 de = http://apsy.gse.uni-magdeburg.de/debian
@@ -63,7 +69,7 @@ us-tn = http://masi.vuse.vanderbilt.edu/neurodebian
 [mirror names]
 de = Germany (University of Magdeburg)
 gr = Greece (Aristotle University of Thessaloniki)
-us-ca = USA-CA (Paul Ivanov)
+us-ca = USA-CA (Paul Ivanov, California)
 us-nh = USA-NH (Dartmouth College)
 us-tn = USA-TN (Vanderbilt)
 
@@ -80,6 +86,7 @@ releases =
  http://neuro.debian.net/debian/dists/lucid/Release
  http://neuro.debian.net/debian/dists/maverick/Release
  http://neuro.debian.net/debian/dists/natty/Release
+ http://neuro.debian.net/debian/dists/oneiric/Release
  http://neuro.debian.net/debian/dists/etch/Release
  http://neuro.debian.net/debian/dists/lenny/Release
  http://neuro.debian.net/debian/dists/squeeze/Release
@@ -108,7 +115,7 @@ maverick = Ubuntu 10.10 "Maverick Meerkat" (maverick)
 # EOL: October 2012
 natty = Ubuntu 11.04 "Natty Narwhal" (natty)
 # EOL: April 2013
-oneiric = Upcoming Ubuntu 11.10 "Oneiric Ocelot" (oneiric)
+oneiric = Ubuntu 11.10 "Oneiric Ocelot" (oneiric)
 
 [release backport ids]
 # the purpose of these ids is to have version suffixes for backported packages
@@ -157,6 +164,8 @@ nifti-bin = 26
 odin = 153
 python-mvpa = 162
 python-nipype = 325
+python-surfer = 517
+python-pyxnat = 453
 slicer = 50
 spm8 = 24
 voxbo = 73
index 479e96a8c94d8bb3c21b7c1968beb78840154242..442123e253f5370d3ac068d3d0f8046d1b8569c2 100755 (executable)
@@ -512,7 +512,7 @@ def import_dde(cfg, db):
                 if q.has_key('popcon'):
                     db[p]['main']['debian_popcon'] = q['popcon']
                 # if we have debian, need to get ubuntu
-                q = dde_get(query_url + "/packages/prio-ubuntu-natty/%s" % p)
+                q = dde_get(query_url + "/packages/prio-ubuntu-oneiric/%s" % p)
                 if q and q.has_key('popcon'):
                     db[p]['main']['ubuntu_popcon'] = q['popcon']
             else:
index 19fd8cfcbb7fee965f6d16bc6d50a90a6da3e44a..e5e3d06266fc6415acdb3d8381b499c6925846bc 100644 (file)
@@ -380,6 +380,8 @@ div.body p, div.body dd, div.body li {
 
 div.body p.caption {
     text-align: inherit;
+    font-size: 95%;
+    font-style: italic;
 }
 
 div.body td {
diff --git a/sphinx/blog/2011/2011-09-26_in_the_spotlight.rst b/sphinx/blog/2011/2011-09-26_in_the_spotlight.rst
new file mode 100644 (file)
index 0000000..49d6150
--- /dev/null
@@ -0,0 +1,14 @@
+:date: 2011-09-26 15:00:00
+:tags: neuroscience, software, spotlight
+
+In the spotlight ...
+====================
+
+We are about to start a new series of blog posts introducing software packages
+for psychological and neuroscience research. In this series, guest authors can
+present (their) software and highlight interesting features that make it stand
+out from similar solution. This series also is an opportunity to give an
+overview on what software solution exist to solve a particular problem. If you
+are interested in writing about something that you use, wrote, or recommend:
+:ref:`contact us <support>`.
+
diff --git a/sphinx/blog/2011/2011-09-26_spotlight_opensesame.rst b/sphinx/blog/2011/2011-09-26_spotlight_opensesame.rst
new file mode 100644 (file)
index 0000000..8657308
--- /dev/null
@@ -0,0 +1,120 @@
+:date: 2011-09-26 16:00:00
+:tags: neuroscience, software, spotlight, guest post, opensesame, sebastiaan mathot
+:author: Sebastiaan Mathôt
+:author_email: s.mathot@vu.nl
+
+In the spotlight: OpenSesame
+============================
+
+I suspect that many of you will not be familiar with me or my software, so
+let's start with a brief introduction. My name is Sebastiaan Mathôt. I'm the
+lead developer of OpenSesame_, a graphical tool for creating psychological and
+neuroscientific experiments.
+
+About OpenSesame
+----------------
+
+The reason that I started working on OpenSesame, aside from the inherent
+pleasure that a geek like myself derives from developing software, was my
+dissatisfaction with the tools that were available. Not that there's a shortage
+of experiment building software, not at all. And for people with reasonable
+programming skills there are many viable options: MatLab/ Octave in combination
+with the `Psychophysics Toolbox`_, Python in combination with VisionEgg_ or
+PsychoPy_, to name but a few (most of these are, incidentally, available through
+NeuroDebian). But for people with relatively modest programming skills, such as
+most students doing a Bachelor's or Master's project, there aren't that many
+options. In my experience, people will generally end up using a proprietary
+program, such as E-Prime, Inquisit, or what have you. These offer a reasonably
+intuitive graphical interface, but at a price. First, these packages are
+expensive and, due to licensing restrictions, people are frequently unable to
+install them on their personal computers. Second, they are limited in their
+functionality and in their interoperability with other software.
+
+.. figure:: pics/blog/opensesame_stimulus.png
+
+   One of the unique features of OpenSesame is the ability to draw your
+   stimuli. You can combine this what-you-see-is-what-you-get approach with
+   scripting, to easily create flexible stimulus displays.
+
+Therefore, I wanted to develop a graphical environment for building
+experiments, centered around the Python programming language. The idea was to
+give users the type of comprehensive graphical interface that they have come to
+expect from proprietary packages, but for free, and without taking away any of
+the power that Python has to offer. And, almost a year, 12 public releases, and
+more than 10,000 downloads later, the result is OpenSesame!
+
+Back-end independence
+---------------------
+
+In this post I want to highlight one of OpenSesame's features: back-end
+independence. This may sound a bit technical and boring, but it's not. Well...
+maybe a little boring. In fact, it should be a little boring, because it's a
+feature that you're not supposed too notice, unless you need it.
+
+So what do I mean by "back-end independence"? Experiments are all about
+presenting stimuli. Most often visual stimuli on a computer display, sometimes
+sounds, tactile stimuli, etc. From the perspective of a programmer, there are
+many ways to present such stimuli. Put differently, there are many programming
+libraries that you can use.
+
+For example, if you want to write a program that controls a computer display,
+you can use a Python library called PyGame_. PyGame has been designed with
+video-games in mind, but, experiments being conceptually so similar (although
+not typically as entertaining), it is also well suited for creating
+experiments. For this reason, I initially designed OpenSesame around PyGame.
+
+This seemed like a good idea at the time, but there was a huge drawback. If
+people wanted to use OpenSesame, they were forced to use PyGame as well. It was
+a package deal, so if PyGame didn't support a particular feature, neither did
+OpenSesame. That wasn't very nice. And it also wasn't necessary, because there
+was nothing in OpenSesame that inherently required PyGame. It was just an
+arbitrary design choice that I had made at the outset.
+
+So I decided to decouple the "back-end" (i.e., all the functions that had been
+handled by PyGame up to that point) from the rest of OpenSesame. This means
+that the user can now choose which back-end he or she wants to use for
+controlling the display etc. Importantly, OpenSesame continues to function in
+the same way, regardless of which back-end is selected. For users who don't
+care or know what a back-end is, let alone which back-end they prefer, PyGame
+still serves as a default.
+
+.. figure:: pics/blog/opensesame_backend.png
+
+   You can easily select your favorite back-end using the graphical interface.
+   The same experiment can be run, (usually) completely unmodified, using any
+   of the three available back-ends.
+
+So what's the upshot of all this? Right now, the most direct benefit is that
+you can use OpenGL and PsychoPy in your OpenSesame experiments. PsychoPy in
+particular provides lots of functions (drawing Gabor patches etc.) that are
+very convenient when creating experiments. Previously, users couldn't use
+these, because PsychoPy doesn't play nice with PyGame (even though it actually
+uses, or can use, PyGame under the hood). Now they can, so that's a definite
+plus. And in the future I may add more back-ends, depending on popular demand.
+For example, VisionEgg is another library for creating experiments. VisionEgg
+is quite popular and could probably be used as a back-end as well.
+
+This means that users of OpenSesame now have both a comprehensive graphical
+interface and powerful programming libraries at their disposal. They can
+choose. Most of the experiment can usually be created using the GUI, which is
+especially appealing for the less tech-savvy among us. But, for more
+complicated parts, Python scripting can be used and, consequently, users have
+access to a wide range of libraries.
+
+I think that OpenSesame's back-end independence is a nice example (one of many,
+I hasten to add) of how free software can work together. If it hadn't been
+possible to use PsychoPy and OpenGL in OpenSesame, I would have probably ended
+up duplicating lots of functionality. That would have been very time consuming.
+Time that I have now spent on refining other parts of OpenSesame, unique parts
+and not simply duplicates of existing functionality.
+
+And ultimately, I believe that this type of interoperability is why free
+software will continue to grow.
+
+.. _PyGame: http://pygame.org
+.. _PsychoPy: http://psychopy.org/
+.. _VisionEgg: http://www.visionegg.org/
+.. _Psychophysics Toolbox: http://psychtoolbox.org
+.. _OpenSesame: http://www.cogsci.nl/opensesame
+
+
index 294c4df8c828d240c4ee93e812041553202dccdf..03bcc2ba69a037b80e533a7fe9652499e00538d9 100644 (file)
@@ -8,7 +8,20 @@
 Coffee Art
 **********
 
+2011-09-01 18.48.53
+-------------------
+
+.. figure:: /pics/coffeeart/2011-09-01_18.48.53.jpg
+
+2011-08-25 00:00:00
+-------------------
+
+.. figure:: /pics/coffeeart/2011-08-2X.jpg
+
+2011-03-23 13:44:26
+-------------------
 
+.. figure:: /pics/coffeeart/2011-03-23_13.44.26.jpg
 
 2010-10-22 09:58:31
 -------------------
index a0f6c3556b75bae50bde3d7318c04ae4f6654bb7..71177d6a3c361e2378769dd037cec3da03d709cd 100644 (file)
@@ -194,6 +194,16 @@ If your are interested in mirroring the repository, please see the :ref:`faq`.
 Publications
 ============
 
+Hanke, M. (2011). `More than batteries included: NeuroDebian
+<_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
+*Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
+Paris, France.
+
+Halchenko, Y. O. (2011). `Ï€'s in Debian or Scientific Debian: NumPy, SciPy and beyond
+<_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
+*Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
+Paris, France.
+
 Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
 *Frontiers in Neuroinformatics, 5:8*.
diff --git a/sphinx/pics/blog/opensesame_backend.png b/sphinx/pics/blog/opensesame_backend.png
new file mode 100644 (file)
index 0000000..cb202d5
Binary files /dev/null and b/sphinx/pics/blog/opensesame_backend.png differ
diff --git a/sphinx/pics/blog/opensesame_stimulus.png b/sphinx/pics/blog/opensesame_stimulus.png
new file mode 100644 (file)
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@@ -77,6 +77,7 @@ Promotion
   **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
index 3b7a1bdaf000de36a26aa59c57df22af057e5856..d83347362d695fc85afcf59bdf6df0eb7f7c990f 100644 (file)
@@ -1,4 +1,4 @@
-.. Generated on Tue Feb  1 12:05:45 EST 2011
+.. Generated on Sun Oct  2 14:27:59 EDT 2011
 .. Do not edit directly
 
 Quotes from NIH R01 grant proposal letters of recommendation
@@ -10,6 +10,16 @@ Quotes from NIH R01 grant proposal letters of recommendation
 
 
 
+.. quote::
+   :author: Prof. Alfonso Caramazza
+   :affiliation: Director, Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
+   :date: 2011-06-27
+   :tags:  lofs
+   :group: Research institutions
+
+   NeuroDebian is an effective solution to support a heterogeneous working environment. [...] NeuroDebian is useful also for education purpose.
+
+
 .. quote::
    :author: Prof. Thomas J. Grabowski, Jr.
    :affiliation: Director, Integrated Brain Imaging Center, University of Washington, Seattle, Washington, USA
@@ -80,6 +90,46 @@ Quotes from NIH R01 grant proposal letters of recommendation
    NeuroDebian project made our library available to an unprecedented number of users  [...] as a system administrator, I rely on NeuroDebian for setting up and keeping up-to-date the software installed on the numerous clients and servers used by more than 150 scientists
 
 
+.. quote::
+   :author: Prof. Todd F. Heatherton
+   :affiliation: Lincoln Feline Professor, Psychology and Brain Sciences Department
+   :date: 2011-06-22
+   :tags:  lofs, dartmouth, vm
+   :group: Participating institutions
+
+   We have found the NeuroDebian VM so easy to us and so simple to maintain that we're currently in the process of converting some of our workstations to full NeuroDebian installations
+
+
+.. quote::
+   :author: Prof. Peter U. Tse
+   :affiliation: Associate Professor, Psychology and Brain Sciences Department
+   :date: 2007-12-31
+   :tags:  lofs, dartmouth, team
+   :group: Participating institutions
+
+   [...] vibrant NeuroDebian team  [...] has been a great asset to the Psychology and Brain sciences department at Dartmouth. On multiple occasions they have provided support and advice beyond the scope of the NeuroDebian effort, showing their knowledge of methodological developments in the neuroscience field and making us aware of recent technological advances we could benefit from in our research.
+
+
+.. quote::
+   :author: Prof. Stefan Pollmann
+   :affiliation: 
+   :date: 2010-09-02
+   :tags:  lofs, money
+   :group: Participating institutions
+
+   My lab is using NeuroDebian for almost five years now  [...] The minimal maintenance cost allow us to operate our research and computing infrastructure  [...] even without a dedicated system administrator. Consequently, these resources could be invested into scientific personnel instead.
+
+
+.. quote::
+   :author: Prof. Brian Avants
+   :affiliation: Research Assistant Professor of Radiology, University of Pennsylvania, Philadelphia, USA
+   :date: 2010-09-16
+   :tags:  lofs, practices, standartization, mentorship, dissemination, impact
+   :group: Research software projects
+
+   The NeuroDebian team taught me a great deal about how to systematize software development for reliable dissemination [...] This speaks very highly of the deep skillset and commitment to user support represented in the NeuroDebian project, which will have high impact on the field and help standardize both the analysis and the interpretation of neuroimaging data.
+
+
 .. quote::
    :author: Dr. Matthew Brett
    :affiliation: Specialist researcher, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
@@ -90,6 +140,26 @@ Quotes from NIH R01 grant proposal letters of recommendation
    [...] your team are ideally placed to make this system work. I have worked with Yaroslav Halchenko and Michael Hanke.  [...] Their record on working together as a team, and individually, is easy to find, and speaks for itself.  Their demonstrated combination of seemingly inexhaustible energy, openness and skill has been of enormous benefit to our own project and community.  
 
 
+.. quote::
+   :author: Prof. Gene Cooperman
+   :affiliation: College of Computer and Information Science, Northeastern University, Boston, USA
+   :date: 2011-06-21
+   :tags:  lofs
+   :group: Research software projects
+
+   [...] we have benefited from the NeuroDebian team through their mentoring and direct efforts to improve the DMTCP software for wider distribution.
+
+
+.. quote::
+   :author: Sebastian Eichelbaum
+   :affiliation: OpenWalnut project, Image and Signal Processing Group, Institute of Computer Science, University of Leipzig, Germany
+   :date: 2011-06-30
+   :tags:  lofs, mentoring
+   :group: Research software projects
+
+   We are currently preparing our first software-release in NeuroDebian and found it to be easy and straight-forward with a great support.
+
+
 .. quote::
    :author: Prof. Bruce Fischl
    :affiliation: Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA
@@ -100,10 +170,20 @@ Quotes from NIH R01 grant proposal letters of recommendation
    Having FreeSurfer integrated into the Debian operating system by the NeuroDebian team would have enormous benefits for us, and for the thousands of users of FreeSurfer across the world.
 
 
+.. quote::
+   :author: Stephan Gerhard
+   :affiliation: Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
+   :date: 2011-06-21
+   :tags:  lofs, support, Debian, open science
+   :group: Research software projects
+
+   The Debian project provides the scientific community with a truly universal operating system. The breadth and quality of its community-driven development and technical support is superior to many other available commercial alternatives. It provides a sound basis for the open science movement.
+
+
 .. quote::
    :author: Dr. Satrajit Ghosh
    :affiliation: Research scientist, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
-   :date: 2010-09-06
+   :date: 2011-06-13
    :tags:  lofs, software distribution
    :group: Research software projects
 
@@ -130,6 +210,16 @@ Quotes from NIH R01 grant proposal letters of recommendation
    [...] distributing the software via NeuroDebian generates valuable feedback which is indispensable for the development of free software. When working with the NeuroDebian team in the past, I have found their members to be very cooperative,    target-oriented and responsive.
 
 
+.. quote::
+   :author: Mario Kleiner
+   :affiliation: Dipl. Inf., Psychtoolbox lead developer, Department for Cognitive and Computational Psychophysics, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
+   :date: 2011-06-21
+   :tags:  lofs, vm, contributions, practices
+   :group: Research software projects
+
+   We find the approach taken by NeuroDebian and the progress it made so far very pleasant and promising.  [...] The NeuroDebian team helped us to improve the quality of our software and of some of our processes by review, constructive suggestions and even software patches.  The availability of the NeuroDebian Virtual Machine was instrumental for fast porting of the Psychtoolbox to a 64 bit Linux environment.
+
+
 .. quote::
    :author: Dr. Gabriele Lohmann
    :affiliation: Lipsia lead developer, Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
@@ -150,6 +240,16 @@ Quotes from NIH R01 grant proposal letters of recommendation
    The dinifti tool was one of the first to appear in Debian and ever since it's inclusion in the distribution, I have received invaluable feedback from the Debian community 
 
 
+.. quote::
+   :author: Sebastiaan Mathôt
+   :affiliation: OpenSesame lead developer, Vrije Universiteit, Amsterdam, The Netherlands
+   :date: 2011-07-29
+   :tags:  lofs, software distribution, mentorship, Debian
+   :group: Research software projects
+
+   The NeuroDebian team has helped me to make my software (OpenSesame) available to the wider public in a much more professional fashion than I would have been able to do for myself.
+
+
 .. quote::
    :author: Dr. Eilif Muller
    :affiliation: Post-doctoral researcher, Brain Mind Institute, EPFL, Lausanne, Switzerland
@@ -170,6 +270,16 @@ Quotes from NIH R01 grant proposal letters of recommendation
    Having such a group of experts [NeuroDebian developers] that search for open-source software solutions, refine them and then make them trivially easy for users to install and try out is of absolutely invaluable benefit to the research community and to the funding bodies that would, otherwise, be paying much larger sums in commercial software licensing fees.
 
 
+.. quote::
+   :author: Dr. Fernando Perez
+   :affiliation: IPython developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
+   :date: 2010-09-08
+   :tags:  lofs, contributions, team
+   :group: Research software projects
+
+   Their [NeuroDebian developers] commitment to strongly tested, validated and documented tools for computational-based research in neuroscience is exemplary, and we owe them a great debt of gratitude for the contributions they have already made [...] 
+
+
 .. quote::
    :author: Dr. Ariel Rokem
    :affiliation: NiTime developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
@@ -180,6 +290,16 @@ Quotes from NIH R01 grant proposal letters of recommendation
    NeuroDebian is playing a key role in the creation of an ``eco-system'' of open-source solutions for neuroscience  [...] The standards and practices disseminated by the NeuroDebian project allowed me to start using this tool [PsychoPy] efficiently and rapidly and to contribute back to the project within a few months.
 
 
+.. quote::
+   :author: Prof. Per B. Sederberg
+   :affiliation: Department of Psychology, Ohio State University, Columbus, Ohio, USA
+   :date: 2010-09-16
+   :tags:  lofs, impact, quality
+   :group: Research software projects
+
+   [...] NeuroDebian will undoubtedly have a large impact on the quality of neuroscience research, both directly and indirectly, by making almost every known software package related to neuroscience work available in a stable and secure environment and broadening the standard set of techniques researchers can employ. 
+
+
 .. quote::
    :author: Prof. Stephen M. Smith
    :affiliation: Associate Director, Centre for Functional Magnetic, Resonance Imaging of the Brain University of Oxford, Oxford, UK
@@ -190,6 +310,36 @@ Quotes from NIH R01 grant proposal letters of recommendation
    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 â€“ without any additional investment of my lab, but solely due to FSL’s presence in the Debian archive.  
 
 
+.. quote::
+   :author: Dr. Gaël Varoquaux
+   :affiliation: Parietal project, INRIA, Neurospin research center, Gif sur Yvette, France
+   :date: 2010-09-01
+   :tags:  lofs, reproducibility, dissemination
+   :group: Research software projects
+
+   The availability of a common platform [NeuroDebian] for many different neuroimaging software solutions makes it much easier to compare solutions and pick the tool of choice for a given research problem.
+
+
+.. quote::
+   :author: Patrik Andersson
+   :affiliation: Image Sciences Institute, University Medical Center Utrecht, the Netherlands
+   :date: 2011-06-15
+   :tags:  lofs, vm
+   :group: Individual laboratories and researchers
+
+   I have been using NeuroDebian for my work on multivariate classification of fMRI data  [...] It is of great value, because I have access to both Windows and Debian OS on my laptop, where I do all my analysis.
+
+
+.. quote::
+   :author: Prof. Hiroyuki Akama
+   :affiliation: Associate Professor, Graduate School of Decision Science and Technology, Tokyo Institute of Technology, Tokyo, Japan begin{lofquote} I am a heavy user of NeuroDebian-Virtual Machine on Windows 64-bit platform. end{lofquote}
+   :date: 2011-06-15
+   :tags:  lofs, vm
+   :group: Individual laboratories and researchers
+
+   I am a heavy user of NeuroDebian-Virtual Machine on Windows 64-bit platform.
+
+
 .. quote::
    :author: Paolo Avesani
    :affiliation: Neuroinformatics Laboratory, Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
@@ -210,6 +360,16 @@ Quotes from NIH R01 grant proposal letters of recommendation
    Both the software and online support forums provided by NeuroDebian have been invaluable for my machine-learning studies of fMRI data.  
 
 
+.. quote::
+   :author: Prof. Jodene Goldenring Fine
+   :affiliation:  Department of Counseling, Education Psychology, and Special Education, Michigan State University, USA
+   :date: 2011-06-18
+   :tags:  lofs, vm, quality, support, speed
+   :group: Individual laboratories and researchers
+
+   [...] I couldn't believe my great luck when after just an hour or so I had a complete [NeuroDebian] system running and my research was back on track.  [...] Your service and support are critical to keeping researchers effectively working on their research, rather than on maintenance issues that negatively affect our productivity. [...] I was working on versions of AFNI and FSL that were several generations behind  [...] Now I will always be up-to-date. [...] Because I am now running a virtual machine, I can keep my data files [with me].
+
+
 .. quote::
    :author: Scott Gorlin
    :affiliation: Ph.D. student, Department of Brain and Cognitive Science Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
@@ -230,6 +390,16 @@ Quotes from NIH R01 grant proposal letters of recommendation
    [NeuroDebian is] an extremely time saving solution
 
 
+.. quote::
+   :author: Jonas Kubilius
+   :affiliation: Ph.D. student, Laboratories of Biological and Experimental Psychology, K. U. Leuven, Belgium
+   :date: 2011-06-18
+   :tags:  lofs, reproducibility, vm, impact, sharing, open science
+   :group: Individual laboratories and researchers
+
+   [...] NeuroDebian allows both researchers and the public to easily replicate the entire experimental procedure, a feature rendered difficult or often impossible by proprietary software packages that most scientists rely on nowadays.  I have been increasingly using NeuroDebian in a Virtual Machine because Linux operating systems are not supported by the university.  [...] Moreover, powered by NeuroDebian’s openness, I see a reason to publish the full code of our experimental and analysis scripts. [NeuroDebian] makes the goal of open science finally viable.
+
+
 .. quote::
    :author: Kaunitz Lisandro Nicolas
    :affiliation: Center for Mind/Brain sciences -CIMEC-, University of Trento, Trento, Italy
@@ -261,33 +431,33 @@ Quotes from NIH R01 grant proposal letters of recommendation
 
 
 .. quote::
-   :author: Prof. Stefan Pollmann
-   :affiliation: Lehrstuhl für Allgemeine Psychologie, Otto-von-Guericke Universität, Magdeburg, Germany
-   :date: 2010-09-02
-   :tags:  lofs, money
+   :author: Dr. Felipe Picon
+   :affiliation: Child and Adolescent Psychiatrist, Department of Psychiatry of Federal University of Rio Grande do Su, Porto Alegre, RS, Brazil
+   :date: 2011-06-14
+   :tags:  lofs, ease
    :group: Individual laboratories and researchers
 
-   My lab is using NeuroDebian for almost five years now  [...] The minimal maintenance cost allow us to operate our research and computing infrastructure  [...] even without a dedicated system administrator. Consequently, these resources could be invested into scientific personnel instead.
+   We have been relying on NeuroDebian  [...] for our work on Adult ADHD neuroimaging and find it to be very useful.
 
 
 .. quote::
-   :author: Dr. Daqiang Sun
-   :affiliation: Post-doctoral researcher, Department of Psychology, University of California, Los Angeles, USA
-   :date: 2010-09-15
-   :tags:  lofs, speed
+   :author: Dr. Bhavani Shankara Bagepally
+   :affiliation: Department of Psychiatry, National Institute of Mental Health And Neurosciences (NIMHANS), Bangalore, India
+   :date: 2011-06-15
+   :tags:  lofs, ease
    :group: Individual laboratories and researchers
 
-   It [NeuroDebian] is and will continue to be invaluable in our multiple NIH-funded research projects.  NeuroDebian nicely takes care of the burden of software deployment and management on my computers and allows me to concentrate on the imaging analysis itself [...]
+   Neuroscience software  [...] easily available at a single point with hastle free installation and easy updating.
 
 
 .. quote::
-   :author: Dr. Gaël Varoquaux
-   :affiliation: Parietal project, INRIA, Neurospin research center, Gif sur Yvette, France
-   :date: 2010-09-01
-   :tags:  lofs, reproducibility, dissemination
+   :author: Dr. Daqiang Sun
+   :affiliation: Post-doctoral researcher, Department of Psychology, University of California, Los Angeles, USA
+   :date: 2010-09-15
+   :tags:  lofs, speed
    :group: Individual laboratories and researchers
 
-   The availability of a common platform [NeuroDebian] for many different neuroimaging software solutions makes it much easier to compare solutions and pick the tool of choice for a given research problem.
+   It [NeuroDebian] is and will continue to be invaluable in our multiple NIH-funded research projects.  NeuroDebian nicely takes care of the burden of software deployment and management on my computers and allows me to concentrate on the imaging analysis itself [...]
 
 
 .. quote::
@@ -299,46 +469,13 @@ Quotes from NIH R01 grant proposal letters of recommendation
 
    Our research would be considerably more difficult without necessary software solutions transparently provided and supported by the NeuroDebian project.  
 
-.. quote::
-   :author: Patrik Andersson
-   :affiliation: Image Sciences Institute, University Medical Center Utrecht, the Netherlands
-   :date: 2011-06-15
-   :tags: lofs, vm
-   :group: Individual laboratories and researchers
-
-   I have been using NeuroDebian for my work on multivariate classification of fMRI data [...] It is of great value, because I have access to both Windows and Debian OS on my laptop, where I do all my analysis.
-
-.. quote::
-   :author: Dr. Felipe Picon
-   :affiliation: Child and Adolescent Psychiatrist, Department of Psychiatry of Federal University of Rio Grande do Su, Porto Alegre, RS, Brazil
-   :date: 2011-06-15
-   :tags: lofs, ease
-   :group: Individual laboratories and researchers
-
-   We have been relying on NeuroDebian [...] for our work on Adult ADHD neuroimaging and find it to be very useful.
-
-.. quote::
-   :author: Dr. Bhavani Shankara Bagepally
-   :affiliation: Department of Psychiatry, National Institute of Mental Health And Neruosciences (NIMHANS), Bangalore, India
-   :tags: lofs, ease
-   :group: Individual laboratories and researchers
-
-   Neuroscience software [...] easily available at a single point with hastle free installation and easy updating.
 
 .. quote::
    :author: Dr. C. J. Werner
    :affiliation: Clinical and Cognitive Neuroscience, Dept. of Neurology, University Hospital RWTH Aachen, Germany
    :date: 2011-06-15
-   :tags: lofs, vm, teaching
+   :tags:  lofs, vm, teaching, dissemination
    :group: Individual laboratories and researchers
 
    [NeuroDebian] makes my lectures on neuroimaging much more convenient and ``hands-on'' by deploying virtual machines on student's laptops [...] a quick, elegant and cost-free solution, enabling students to work on real fMRI data in no time.
 
-.. quote::
-   :author: Dr. Peter U. Tse
-   :affiliation: Associate Professor, Psychology and Brain Sciences Department, Dartmouth College, Hanover, USA
-   :date: 2011-06-16
-   :tags: lofs, team
-   :group: Individual laboratories and researchers
-
-   [...] vibrant NeuroDebian team [...]  has been a great asset [...] showing their knowledge of methodological developments in the neuroscience field and making us aware of recent technological advances we could benefit from in our research.
index a4e0e6c533603e12541a2e15e760af35d4d0b7ee..7c641ff8ad4c218559cc25b75197eda0fadb86b6 100644 (file)
@@ -20,3 +20,12 @@ Quotes from NITRC project page
    :source: NITRC NeuroDebian reviews
 
    [...] Best part for me is that I can run it in a VM without having to worry about replacing my native OS.
+
+.. quote::
+   :author: Robert Buccigrossi
+   :date: 2011-09-22
+   :tags: nitrc, ease
+   :group: Individual laboratories and researchers
+   :source: NITRC forum: http://www.nitrc.org/forum/message.php?msg_id=5013
+
+   Dr. Halchenko's statement "Discover http://neuro.debian.net and be happy" may sound a bit like a sales pitch, but it is rather good advice.  We have been experimenting with the rapid instantiation of computational environments containing neuroimaging tools from NITRC, and the NeuroDebian repository makes installing and updating the tools through apt-related package managers rather trivial.
index 13706a14f34dd4ba104fdc6cfc29233ff09ac341..751e336c46033a1b6c51efab6d383e46afbb21fa 100644 (file)
@@ -11,6 +11,15 @@ feed_entries = None
 #constant unlikely to occur in a docname and legal as a filename
 MAGIC_SEPARATOR = '---###---'
 
+def parse_date(datestring):
+    try:
+        parser = parse_date.parser
+    except AttributeError:
+        import dateutil.parser
+        parser = dateutil.parser.parser()
+        parse_date.parser = parser
+    return parser.parse(datestring)
+    
 def setup(app):
     """
     see: http://sphinx.pocoo.org/ext/appapi.html
@@ -20,6 +29,7 @@ def setup(app):
     if not isinstance(app, Sphinx): return
     app.add_config_value('feed_base_url', '', 'html')
     app.add_config_value('feed_description', '', 'html')
+    app.add_config_value('feed_filename', 'rss.xml', 'html')
     app.add_config_value('feed_title', '', 'html')
     app.add_config_value('feed_subtitle', '', 'html')
     app.add_config_value('feed_author_name', '', 'html')
@@ -29,47 +39,50 @@ def setup(app):
                          {'all': {'filename': 'rss.xml', 'categories': None}},
                          'html')
     app.connect('html-page-context', create_feed_item)
-    app.connect('html-page-context', inject_feed_url)
     app.connect('build-finished', emit_feed)
     app.connect('builder-inited', create_feed_container)
     app.connect('env-purge-doc', remove_dead_feed_item)
     
 def create_feed_container(app):
     """
-    create lazy filesystem stash for keeping RSS entry fragments, since we don't
-    want to store the entire site in the environment (in fact, even if we did,
-    it wasn't persisting for some reason.)
+    create lazy filesystem stash for keeping RSS entry fragments, since we
+    don't want to store the entire site in the environment (in fact, even if
+    we did, it wasn't persisting for some reason.)
     """
     global feed_entries
     rss_fragment_path = os.path.realpath(os.path.join(app.outdir, '..', 'rss_entry_fragments'))
     feed_entries = FSDict(work_dir=rss_fragment_path)
-    app.builder.env.feed_url = app.config.feed_base_url + '/' + 'feed_container'
+    app.builder.env.feed_url = app.config.feed_base_url + '/' + \
+        app.config.feed_filename
 
 def inject_feed_url(app, pagename, templatename, ctx, doctree):
     #We like to provide our templates with a way to link to the rss output file
     ctx['rss_link'] = app.builder.env.feed_url #app.config.feed_base_url + '/' + app.config.feed_filename
     
+
 def create_feed_item(app, pagename, templatename, ctx, doctree):
     """
     Here we have access to nice HTML fragments to use in, say, an RSS feed.
     We serialize them to disk so that we get them preserved across builds.
+    
+    We also inject useful metadata into the context here.
     """
     global feed_entries
-    import dateutil.parser
     from absolutify_urls import absolutify
-    date_parser = dateutil.parser.parser()
     metadata = app.builder.env.metadata.get(pagename, {})
     
     if 'date' not in metadata:
         return #don't index dateless articles
     try:
-        pub_date = date_parser.parse(metadata['date'])
+        pub_date = parse_date(metadata['date'])
+        app.builder.env.metadata.get(pagename, {})
     except ValueError, exc:
         #probably a nonsensical date
         app.builder.warn('date parse error: ' + str(exc) + ' in ' + pagename)
         return
-        
-    # title, link, description, author_email=None,
+    
+    # RSS item attributes, w/defaults:
+    #     title, link, description, author_email=None,
     #     author_name=None, author_link=None, pubdate=None, comments=None,
     #     unique_id=None, enclosure=None, categories=(), item_copyright=None,
     #     ttl=None,
@@ -98,6 +111,10 @@ def create_feed_item(app, pagename, templatename, ctx, doctree):
     else:
         item['author_email'] = app.config.feed_author_email
     feed_entries[nice_name(pagename, pub_date)] = item    
+    
+    #Now, useful variables to keep in context
+    ctx['rss_link'] = app.builder.env.feed_url 
+    ctx['pub_date'] = pub_date
 
 def remove_dead_feed_item(app, env, docname):
     """
@@ -114,8 +131,12 @@ def emit_feed(app, exc):
     global feed_entries
     import os.path
     
+    title = app.config.feed_title
+    if not title:
+        title = app.config.project
+
     feed_dict = {
-      'title': app.config.feed_title,
+      'title': title,
       'subtitle': app.config.feed_subtitle,
       'link': app.config.feed_base_url,
       'feed_url': app.config.feed_base_url,
index 5cbc04f410eec73a1f3260002446aaf12ef51ba5..77bb86648ca81bda8210204c9b47c9a3c7afc90e 100644 (file)
@@ -5,4 +5,5 @@
   connectionists
   cvnet
   visionlist
+  face-research-list@lists.stir.ac.uk
 
index eb757fcd70a4549c98b705d72c8c4e9ff8fa0070..2cd665cdcbd1c39cf3f2d043b7dffe5203e050b5 100755 (executable)
@@ -11,8 +11,9 @@ backports_dsc_version=0.1
 # Defaults #
 ############
 
-bp_distribution=${BACKPORT_DISTRIBUTION:-lenny-backports}
-bp_version_suffix=${BACKPORT_VERSION_SUFFIX:-bpo50}
+bp_distribution=${BACKPORT_DISTRIBUTION:-squeeze-backports}
+bp_version_prefix=${BACKPORT_VERSION_PREFIX:-~}
+bp_version_suffix=${BACKPORT_VERSION_SUFFIX:-bpo60}
 bp_maintainer_name=${DEBFULLNAME:-unamed}
 bp_maintainer_email=${DEBEMAIL:-unknown}
 bp_update_maintainer=1
@@ -128,9 +129,13 @@ Options:
   ideally indicating the backport target distribution. The resulting package
   version will follow this schema:
 
-  <originalversion>~<suffix>+<digit>
+  <originalversion><prefix><suffix>+<digit>
 
-  e.g.: 1.2.3-4~bpo50+1
+  e.g.: 1.2.3-4~bpo60+1 with default <prefix>=~
+
+-p <string>, --version-prefix <string>
+  Version prefix that will be prepended to the backport version.  By default it
+  is ~ but want to be changed (e.g. to +) for forward-porting to next releases.
 
 --verbose
   Enable additional status messages.
@@ -173,7 +178,10 @@ example setting) can be used to pre-configure backport-dsc:
 bp_distribution="lenny-backports"
   Backport target distribution (see --backport-distribution)
 
-bp_version_suffix="bpo50"
+bp_version_prefix="~"
+  Version suffix (see --version-prefix)
+
+bp_version_suffix="bpo60"
   Version suffix (see --version-suffix)
 
 bp_maintainer_name="Unknown fellow"
@@ -223,7 +231,7 @@ EOT
 # Note that we use `"$@"' to let each command-line parameter expand to a
 # separate word. The quotes around `$@' are essential!
 # We need CLOPTS as the `eval set --' would nuke the return value of getopt.
-CLOPTS=`getopt -o h,d:,s: --long help,verbose-help,version,target-distribution:,version-suffix:,maint-name:,maint-email:,no-color,no-backport-patches,verbose,mod-control:,no-maintainer-update, -n 'backport-dsc' -- "$@"`
+CLOPTS=`getopt -o h,d:,s:,p: --long help,verbose-help,version,target-distribution:,version-suffix:,version-prefix:,maint-name:,maint-email:,no-color,no-backport-patches,verbose,mod-control:,no-maintainer-update, -n 'backport-dsc' -- "$@"`
 
 if [ $? != 0 ] ; then
   echo "Terminating..." >&2
@@ -237,6 +245,7 @@ while true ; do
   case "$1" in
          -d|--target-distribution) shift; bp_distribution=$1; shift;;
          -s|--version-suffix) shift; bp_version_suffix=$1; shift;;
+         -p|--version-prefix) shift; bp_version_prefix=$1; shift;;
          --maint-name) shift; bp_maintainer_name=$1; shift;;
          --maint-email) shift; bp_maintainer_email=$1; shift;;
          --no-maintainer-update) bp_update_maintainer=0; shift;;
@@ -295,7 +304,7 @@ src_version=${src_version%%.dsc}
 wdir=$(mktemp -d -t backport-dsc.XXXXXX)
 sdir=$wdir/${src_name}-${src_version}
 
-bp_version="~${bp_version_suffix}+"
+bp_version="${bp_version_prefix}${bp_version_suffix}+"
 
 
 # setup environment for dpkg
index 94bd35b146afbe1c82e97634c2adf9adb123779a..04f281246969047faaa4748fa0a7acd935f19765 100755 (executable)
@@ -21,6 +21,11 @@ fi
 # common options
 opts="--distribution $dist --debootstrap debootstrap --aptcache $aptcache"
 
+if echo $family | grep -q ubuntu; then
+       # Use ubuntu's keyring since otherwise debootstrap would fail
+       opts+=" --debootstrapopts --keyring=/usr/share/keyrings/ubuntu-archive-keyring.gpg"
+fi
+
 mkdir -p ${cowbuilderroot}/cow
 
 for a in i386 amd64; do
@@ -35,15 +40,23 @@ for a in i386 amd64; do
     cowbuilder --create --basepath ${cow} $opts \
                --components "$components" \
                --mirror "$mirror" \
-               --debootstrapopts --arch --debootstrapopts $a \
+               --debootstrapopts --arch=$a \
                --othermirror "deb http://neuro.debian.net/debian $dist main contrib non-free"
-       # deploy our key manually since archive with package is not yet
-       # available at this point
-       cp --preserve=mode {,${cow}}/etc/apt/trusted.gpg.d/neurodebian-archive-keyring.gpg
+    # deploy our key manually since archive with package is not yet
+    # available at this point
+    mkdir -p ${cow}/etc/apt/trusted.gpg.d
+    cp --preserve=mode {,${cow}}/etc/apt/trusted.gpg.d/neurodebian-archive-keyring.gpg
+    # Old ubuntus might not have capability to ready from that key yet,
+    # so we would need to manually add it
+    if [ $dist = 'karmic' ] || [ $dist = 'hardy' ]; then
+        chroot ${cow} bash -c "apt-get install -y --force-yes gnupg \
+        && /usr/bin/apt-key add /etc/apt/trusted.gpg.d/neurodebian-archive-keyring.gpg \
+        && /usr/bin/apt-get update"
+    fi
   else
     cowbuilder --create --basepath ${cow} $opts \
                --components "$components" \
                --mirror "$mirror" \
-               --debootstrapopts --arch --debootstrapopts $a
+               --debootstrapopts --arch=$a
   fi
 done
diff --git a/tools/nd_adddistall b/tools/nd_adddistall
new file mode 100755 (executable)
index 0000000..bff3cd9
--- /dev/null
@@ -0,0 +1,24 @@
+#!/bin/bash
+# Little helper to bootstrap all ND chroots as specified in
+# /etc/neurodebian/cmdsettings.sh unless a list provided in command line
+
+. /etc/neurodebian/cmdsettings.sh
+
+[ -z "$@" ] && dists="$alldists" || dists="$@"
+
+echo "Initiating creation of chroots for $dists"
+
+set -eu
+
+CMD=
+MSGS="SUMMARY:\n"
+for dist in $dists; do
+        if [ -e "$cowbuilderroot/cow/$dist-amd64.cow" ]; then
+                status=exists
+        else
+                $CMD sudo nd_adddist ${dist%%-*} ${dist#*-} && status=ok || status=failed
+        fi
+        MSGS+=" $(printf '%-30s\\t%s' $dist $status)\n"
+done
+echo -en $MSGS
+
index 562b8aa90a0cf855bda10414b8f34b70326134f9..baf77a8d84cbac2765b172332af47609cacfb038 100755 (executable)
@@ -77,6 +77,8 @@ else
   shift; shift; shift; shift
 fi
 
+# failed will be set to 1 if any build fails
+failed=
 for a in $arch; do
   # default
   options="$opts"
@@ -98,8 +100,7 @@ for a in $arch; do
              --buildresult . \
              --logfile "${buildfile}" \
              $options \
-             "$@" && status='OK' || status='FAILED'
-
+             "$@" && status='OK' || { status='FAILED'; failed=1; }
   timeinfo=$(tail -n 1 "${tsfile}")
   # Update the summary of builds
   touch summary.build                               # Assure existence
@@ -107,3 +108,5 @@ for a in $arch; do
   echo -e "${buildfile}\t$status\t$timeinfo" >> summary.build  # Add current one
   rm -f "${tsfile}"
 done
+# Exit with failure status if any built failed
+[ -z $failed ] || exit 1
index 77e7ce908541a86cf58264748a6dd989af1fff78..466271d778eeb7023074fb9f01c54ac9ddce71a1 100755 (executable)
@@ -22,5 +22,5 @@ for d in $allnddists; do
   drelease=${d##*-}
 
   bpdsc=$(nd_backport $drelease $dscfile | tail -n1 | sed -e 's/^.* //g')
-  nd_build $dfamily $drelease $bpdsc "$@"
+  nd_build $dfamily $drelease $bpdsc "$@" || :
 done
diff --git a/tools/nd_build_testrdepends b/tools/nd_build_testrdepends
new file mode 100755 (executable)
index 0000000..a765ee8
--- /dev/null
@@ -0,0 +1,68 @@
+#!/bin/bash
+
+# no undefined
+set -u
+# no failures
+set -e
+
+CMD=
+#echo
+
+family=$1
+dist=$2
+arch=$3      # limit to 1 for now
+
+dscfile=$4
+dscfilef=$(readlink -f $dscfile)
+dscfilef_base=${dscfilef%%.dsc}
+
+pkg=${dscfile%_*}
+
+#? TODO -- should be a parameter as well?
+
+testdir=${dscfilef_base}_$arch.testrdepends.$family-$dist
+bindir=$testdir/bin
+debdir=$testdir/debs
+srcdir=$testdir/srcs
+oldbuildsdir=$srcdir/old
+newbuildsdir=$srcdir/new
+
+echo "I: Building the new package for $pkg"
+
+mkdir -p $debdir $srcdir $bindir
+$CMD nd_build $family $dist $arch $dscfile --buildresult=$debdir
+
+cd $debdir
+dpkg-scanpackages . >| Packages
+cd - > /dev/null
+
+echo "I: Fetching all bdepends for $pkg in $family $dist under $arch"
+# need first to provide the necessary scripts out there
+cp -p $(dirname $0)/nd_fetch_bdepends $bindir
+$CMD nd_execute $family $dist $arch --bindmounts $testdir $bindir/nd_fetch_bdepends $pkg $srcdir
+
+echo "I: preparing the hook"
+cat << EOF >| $bindir/D00add_custom_repo
+echo 'deb file://$debdir ./' >| /etc/apt/sources.list.d/custom.list
+apt-get update
+EOF
+chmod a+x $bindir/D00add_custom_repo
+
+echo "I: Going throught the packages and testing the builds"
+cd $srcdir
+summary_file=${testdir}.summary
+echo -e "\nTesting builds against $dscfile" >> $summary_file
+for dsc in *.dsc; do
+       echo " I: Building $dsc with native versions"
+       src=${dsc%%_*}
+       dscbase=${dsc%%.dsc}
+       nd_build $family $dist $arch $dsc --buildresult=$oldbuildsdir \
+               && old=ok || old=FAILED
+       mv ${dscbase}_$arch.build $oldbuildsdir
+       echo " I: Building $dsc with new versions"
+       nd_build $family $dist $arch $dsc --buildresult=$newbuildsdir \
+               --hookdir=$bindir --bindmount=$testdir \
+               && new=ok || new="FAILED $newbuildsdir/${dscbase}_$arch.build"
+       mv ${dscbase}_$arch.build $newbuildsdir
+       printf '%-40s\t%5s\t%5s\n' $dsc "$old" "$new" >> $summary_file
+done
diff --git a/tools/nd_execute b/tools/nd_execute
new file mode 100755 (executable)
index 0000000..959b685
--- /dev/null
@@ -0,0 +1,56 @@
+#!/bin/bash
+
+if [ -z "$1" ]; then
+cat << EOT
+Script to log into a particular COW and execute some command.
+
+Synopsis
+--------
+
+  nd_execute <family> <codename> <arch> [cowbuilderopts] command
+
+EOT
+exit 1
+fi
+
+family=$1
+dist=$2
+arch=$3
+bmdir=
+#$4
+
+set -e
+
+if [ -z "$family" ]; then
+  echo "You need to provide a distribution family ('debian', 'ubuntu'); prefix with 'nd+' to enable the NeuroDebian repository."
+  exit 1
+fi
+
+if [ -z "$dist" ]; then
+  echo "You need to provide a distribution codename (e.g. 'lenny', 'squeeze')."
+  exit 1
+fi
+
+if [ -z "$arch" ]; then
+  echo "You need to provide an architecture (e.g. 'i386', 'amd64')."
+  exit 1
+fi
+
+. /etc/neurodebian/cmdsettings.sh
+
+shift; shift; shift; # get rid of those from future use of $@
+
+# common options
+opts="--distribution $dist --aptcache $aptcache --buildplace $buildplace"
+
+
+#if [ -n "bmdir" ]; then
+#  options="$opts --bindmounts $bmdir"
+#else
+  options="$opts"
+#fi
+
+cowbuilder --execute \
+             --basepath ${cowbuilderroot}/cow/${family}-${dist}-${arch}.cow \
+             $options \
+             "$@"
diff --git a/tools/nd_fetch_bdepends b/tools/nd_fetch_bdepends
new file mode 100755 (executable)
index 0000000..ebb5d92
--- /dev/null
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+pkg=$1
+tdir=$2
+
+# provide deb-src by uncommenting
+sed -i -e 's,^#deb-src,deb-src,g' /etc/apt/sources.list
+
+mkdir -p $tdir
+cd $tdir
+apt-get update
+apt-get install -y devscripts dctrl-tools
+build-rdeps $pkg >| build-rdeps.output
+
+# Fetch all the sources
+grep -v -e '^[-A-Z]' -e '^ *$' build-rdeps.output \
+       | tee build-rdeps.list \
+       | while read pkg; do
+       apt-get source --download-only $pkg
+done
diff --git a/tools/nd_rebuildarchive b/tools/nd_rebuildarchive
new file mode 100755 (executable)
index 0000000..a189315
--- /dev/null
@@ -0,0 +1,73 @@
+#!/bin/bash
+
+if [ -z "$1" ]; then
+cat << EOT
+Script to re-build entire archive from one release for another.
+
+Often usecase -- rebuilding for a new Ubuntu brew every 6 months.
+
+Synopsis
+--------
+
+  nd_rebuildarchive old_release new_release
+
+e.g.
+  
+  nd_rebuildarchive natty oneiric
+
+EOT
+exit 1 
+fi
+
+set -eu
+
+old_dist=$1
+dist=$2
+
+# some NeuroDebian variables hardcoded in for now
+repo_server=neuro.debian.net
+repo_user=neurodebian
+repo_toppath=www
+repo_urlpath=debian
+repo_distspath=$repo_toppath/$repo_urlpath/dists
+
+family=nd+ubuntu
+
+list_file="$old_dist-$dist.list"
+summary_file="$old_dist-$dist.summary"
+
+[ -e "$list_file" ] || \
+    ssh -l $repo_user $repo_server cat $repo_distspath/$old_dist/*/source/Sources.gz \
+    | zgrep -e '^\(Package\|Directory\| [a-z0-9]\{32\} [0-9]* \S*.dsc$\)' \
+    | sed -e 's,.* \([^ ][^ ]*\)$,\1,g' | tr '\n' ' '| sed -e 's,\.dsc,.dsc\n,g' \
+    > "$list_file"
+   
+CMD=
+#echo
+dist_id=$(nd_querycfg "release backport ids" "$dist")
+cat $list_file \
+| while read name topdir dscfile; do
+    echo "I: Forwardporting for $dist_id $dscfile"
+
+    [ -e $dscfile ]  \
+       || dget -d http://$repo_server/$repo_urlpath/$topdir/$dscfile || { 
+       echo -e "E: $dscfile\t\tFAILED to fetch" >> $summary_file
+       continue
+    }
+
+    
+    bpdscfile=$(/home/neurodebian/neurodebian/tools/backport-dsc \
+        --target-distribution "$dist" \
+       --no-maintainer-update \
+        --version-prefix "+" \
+        --version-suffix "$dist_id" \
+        "$dscfile" | tail -n1 | sed -e 's/^.* //g')
+
+    echo " I: Building backported dscfile: $bpdscfile"
+
+    $CMD sudo nd_build $family $dist $bpdscfile && {
+       echo -e "I: $bpdscfile\t\tOk" >> $summary_file
+    } || {
+       echo -e "E: $bpdscfile\t\tFAILED to build" >> $summary_file
+    }
+done
\ No newline at end of file