Merge remote branch 'origin'

diff --git a/future/blends/eeglab b/future/blends/eeglab
index 55a95606dc3c9f87434fc3bfb93553d8a9e7a754..58f737d3ff014d478df660195b607e032348b4e2 100644 (file)
--- a/future/blends/eeglab
+++ b/future/blends/eeglab
@@ -1,6 +1,7 @@
 Source: eeglab
 Tasks: debian-science/neuroscience-cognitive,
-          debian-med/imaging
+       debian-science/electrophysiology,
+       debian-med/imaging
 Homepage: http://sccn.ucsd.edu/eeglab
 Responsible: NeuroDebian Team <team@neuro.debian.net>
 Language: C, Matlab/Octave
@@ -8,6 +9,7 @@ Version: 9
 Author: Arnaud Delorme <arno@ucsd.edu>, Scott Makeig <smakeig@ucsd.edu>
 License: GPL-2+
 WNPP: 605739
+Pkg-URL: http://neuro.debian.net
 Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics
 Published-Authors: Delorme A and Makeig S
 Published-In: Journal of Neuroscience Methods 134:9-21

diff --git a/neurodebian.cfg b/neurodebian.cfg
index 5efe97e53e1f395af060057b8f01095b4f83f790..ece9fea625a996a23a256e67f9035e5b8efddd28 100644 (file)
--- a/neurodebian.cfg
+++ b/neurodebian.cfg
@@ -22,7 +22,7 @@ select names = libnifti2 odin mitools afni-atlases python-pyssdh python-networkx
  r-cran-glmnet python-rpy2 python-nibabel-snapshot
  python-sklearn python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab-support
  svgtune rorden-mri-tutorial caret-data python-joblib python-sphinx fail2ban
- python-pandas neurodebian numdiff nuitka
+ python-pandas neurodebian numdiff nuitka pytables
 
 # Information about prospective packages to be imported from taskfiles
 prospective =
@@ -42,6 +42,7 @@ prospective =
 # to be added as an alias as well
 cctools = coop-computing-tools
 mni-icbm152-nlin-2009 = mni-icbm152-nlin-2009a mni-icbm152-nlin-2009b mni-icbm152-nlin-2009c
+eeglab = matlab-eeglab11 eeglab11-sampledata
 fsl = fsl fsl-doc fsl-atlases fsl-possum-data fsl-first-data fsl-feeds fsl-mni152-templates
 fslview = fslview fslview-doc
 python-mvpa = python-mvpa python-mvpa2
@@ -58,6 +59,7 @@ pysurfer = python-surfer
 pyxnat = python-pyxnat
 openwalnut = openwalnut-qt4
 neurodebian = neurodebian-dev neurodebian-desktop neurodebian-keyring neurodebian-popularity-contest neurodebian-guest-additions
+pytables = python-tables
 
 [mirrors]
 au = http://mirror.aarnet.edu.au/pub/neurodebian

diff --git a/sphinx/derivatives.rst b/sphinx/derivatives.rst
new file mode 100644 (file)
index 0000000..588dc76
--- /dev/null
+++ b/sphinx/derivatives.rst
@@ -0,0 +1,78 @@
+.. -*- mode: rst; fill-column: 78 -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+
+.. _chap_derivatives:
+
+*************************
+NeuroDebian "Derivatives"
+*************************
+
+NeuroDebian_ is not a *Linux distribution* in a traditional sense because we
+work within Debian_ project thus not providing our custom installer etc.  But
+we are a Linux-distribution providing a repository of up-to-date builds and
+maintaining a :ref:`chap_vm` deployment of Debian.  Because of the openness
+and modularity of Debian other enthusiasts develop customized derivative
+solutions based to address a particular demand.
+
+This page presents such *derivative* projects which are tuned for particular
+domains of application in neuroscience and rely on NeuroDebian_ as the origin
+for necessary tools.
+
+.. note::
+
+   These projects are not maintained by NeuroDebian_ team.  Please direct all
+   you support inquiries to respective authors/maintainers.
+
+
+Live CD/USB Media
+=================
+
+USB Stick for Computational Neuroscience by Cengiz Günay
+--------------------------------------------------------
+
++---------------------------+-------------------------------------------------------+
+|**Author**                 |Cengiz Günay <cgunay@emory.edu>                        |
++---------------------------+-------------------------------------------------------+
+|**Homepage**               | N/A                                                   |
++---------------------------+-------------------------------------------------------+
+|**Purpose**                | Computational neuroscience tools for course-work      |
++---------------------------+-------------------------------------------------------+
+|**Features**               | - Persistent Storage                                  |
+|                           | - XXX                                                 |
++---------------------------+-------------------------------------------------------+
+|**Pre-installed Software** | NeuroDebian                                           |
+|                           |   Brian (XXX?), XXX                                   |
+|                           | Custom:                                               |
+|                           |   Genesis, Neuron, XPPAUT                             |
++---------------------------+-------------------------------------------------------+
+|**Download**               | http://neuro.debian.net/debian/live/3rd/XXX.iso [2GB] |
++---------------------------+-------------------------------------------------------+
+|**References**             | XXX point to the blog entry whenever is ready         |
++---------------------------+-------------------------------------------------------+
+
+
+Lin4Neuro
+---------
+
+
+Virtual Appliances
+==================
+
+* XNAT
+* MIPAV
+
+
+Cloud Environments
+==================
+
+* NITRC?
+
+
+Cloud Images
+============
+
+* UK Grant project
+* INCF Cloud App?
+
+
+.. include:: link_names.txt

diff --git a/sphinx/index.rst b/sphinx/index.rst
index ab7f745a9fd21d5b5c868d09b371926a294b6280..052c687b563c17809bfae1df20073bd93b7ca4e8 100644 (file)
--- a/sphinx/index.rst
+++ b/sphinx/index.rst
@@ -97,7 +97,7 @@ the terminal you can use :command:`apt-get`::
 Popularity Contest
 ------------------
 
-We would strongly encourage you to participate in the `popularity
+We encourage you to participate in the `popularity
 contest <http://popcon.debian.org>`_ (popcon), which anonymously
 collects the list of packages you installed/use on your system.
 Collecting such statistics is of particular importance for research
@@ -230,6 +230,17 @@ If your are interested in mirroring the repository, please see the :ref:`faq`.
 Publications
 ============
 
+Halchenko, Y.O. & Hanke, M. (2012). `Environments for efficient
+contemporary research in neuroimaging: PyMVPA and NeuroDebian
+<_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
+*Talk given at the University of Pennsylvania School of Medicine*,
+Philadelphia, PA, USA.
+
+Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
+NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
+*Talk given at the Max-Planck-Institute for Human Cognitive and Brain
+Sciences*, Leipzig, Germany.
+
 Hanke, M. (2011). `More than batteries included: NeuroDebian
 <_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
 *Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,

diff --git a/sphinx/proj_matlab.rst b/sphinx/proj_matlab.rst
index a79948343446b676622ccfd60410e0df9e23e776..56d3ac119b38de56e452532bb74f8747241fc6fd 100644 (file)
--- a/sphinx/proj_matlab.rst
+++ b/sphinx/proj_matlab.rst
@@ -41,13 +41,15 @@ with Octave, as well as developing patches to achieve such compatibility.
 Status
 ------
 
-A :ref:`Matlab-support package <pkg_matlab-support>` draft is ready, available
-from NeuroDebian, and has been uploaded to `Debian NEW queue
-<http://ftp-master.debian.org/new.html>`_ .
+A :ref:`Matlab-support package <pkg_matlab-support>` is available starting from
+Debian 7.0 (wheezy) and Ubunty 11.10 (oneiric). Backports for older releases can
+be obtained from NeuroDebian.
 
-Packaging of individual Matlab-based software has started. This includes
-:ref:`SPM <pkg_matlab-spm8>` and :ref:`Fieldtrip <pkg_fieldtrip>` (see
-references_ for more packages). Expanding the coverage is planned.
+Packaging of individual Matlab-based software has started. An
+:ref:`SPM <pkg_matlab-spm8>` package is ready, and a preliminary package of
+:ref:`EEGLAB <pkg_matlab-eeglab11>` is available from NeuroDebian.
+An upcoming :ref:`Fieldtrip <pkg_fieldtrip>` package is work-in-progress (see
+references_ for more packages). Further expansion of the coverage is planned.
 
 .. todo:: Integrating Matlab-based software
 
@@ -57,17 +59,6 @@ references_ for more packages). Expanding the coverage is planned.
      complement :ref:`octave-psychtoolbox-3 <pkg_octave-psychtoolbox-3>`.
    * Create :ref:`matlab-biosig <pkg_matlab-biosig>` to
      complement :ref:`octave-biosig <pkg_octave-biosig>`.
-   * Package `EEGLAB <http://bugs.debian.org/605739>`_.
-
-.. note:: Done:
-
-   * Adapt the packaging of `dynare <http://packages.debian.org/sid/dynare-matlab>`_
-     in Debian to use the new support package. Once this is done and reviewed by
-     its maintainers the support package can be submitted for inclusion into
-     Debian proper.
-   * Upload :ref:`libgdf <pkg_libgdf-dev>` (including :ref:`matlab-gdf
-     <pkg_matlab-gdf>`) to Debian proper as soon as :ref:`matlab-support
-     <pkg_matlab-support>` is accepted
 
 References
 ----------

diff --git a/tools/nd_apachelogs2subscriptionstats b/tools/nd_apachelogs2subscriptionstats
index 6ecc7c73936e4ed8e0a094ebec6c69bf2dfb587d..b39df162fb0799ebcbcc61b19fd3306c3faad3d4 100755 (executable)
--- a/tools/nd_apachelogs2subscriptionstats
+++ b/tools/nd_apachelogs2subscriptionstats
@@ -27,9 +27,9 @@ dt = [('ip', '|S16'),
 def make_figure(data):
     fig = pl.figure(figsize=(14,3))
     ax = fig.add_subplot(121)
-    plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Debian')], title="Debian", ymax=10)
+    plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Debian')], title="Debian", ymax=11)
     ax = fig.add_subplot(122)
-    plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Ubuntu')], title="Ubuntu", ymax=10)
+    plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Ubuntu')], title="Ubuntu", ymax=11)
     fig.autofmt_xdate()
     return fig