Merge remote branch 'alioth/master'

* alioth/master:
  Add Ohloh user button.
  Some explainations for downloads
  Mention the neurodebian-keyring package.
  Put videos on the VM page (and give some love to it).
  Use DDE data from the latest ubuntu dev-version.
  Link the poster.
  Properly add dangling package found on server.
  Use new electrophysiology task

diff --git a/neurodebian.cfg b/neurodebian.cfg
index ed52527dcf5d99bd64437980fc38e1032ead150e..45f38a6dbb132bc2884382e709d24cab7543bea1 100644 (file)
--- a/neurodebian.cfg
+++ b/neurodebian.cfg
@@ -5,6 +5,7 @@ pkgquery_url = http://dde.debian.net/dde/q/udd
 # Packages listed in the following taskfiles will be featured on the website
 # _if_ they are also present in the repository
 select taskfiles =
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-electrophysiology
  svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-cognitive
  svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-datasets
  svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging
@@ -14,10 +15,11 @@ select taskfiles =
 # package names
 select names = libnifti2 odin mitools afni-atlases python-pyssdh python-networkx
  r-cran-glmnet python-rpy2 python-nibabel-snapshot
- python-scikits-learn python-mdp python-mlpy python-openpyxl
+ python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev
 
 # Information about prospective packages to be imported from taskfiles
 prospective =
+ svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-electrophysiology
  svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-cognitive
  svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-datasets
  svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging

diff --git a/neurodebian/dde.py b/neurodebian/dde.py
index bb8903666e3ca163921cf55e23e54e08acacccc6..e2084e430a45b6a941680bc02e2bbe3fdf21b4b3 100755 (executable)
--- a/neurodebian/dde.py
+++ b/neurodebian/dde.py
@@ -500,7 +500,7 @@ 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-lucid/%s" % p)
+                q = dde_get(query_url + "/packages/prio-ubuntu-natty/%s" % p)
                 if q and q.has_key('popcon'):
                     db[p]['main']['ubuntu_popcon'] = q['popcon']
             else:

diff --git a/sphinx/_static/ohloh_iuseit.png b/sphinx/_static/ohloh_iuseit.png
new file mode 100644 (file)
index 0000000..ff93956
Binary files /dev/null and b/sphinx/_static/ohloh_iuseit.png differ

diff --git a/sphinx/_templates/layout.html b/sphinx/_templates/layout.html
index df8252d0d04c06fefb060f00df591a3a7153a6c8..7d4533a423caef04cf9b80e190cccec09c069358 100644 (file)
--- a/sphinx/_templates/layout.html
+++ b/sphinx/_templates/layout.html
@@ -26,6 +26,9 @@
 
 {% block sidebarsearch %}
 {{ super() }}
+
+<p><a href="https://www.ohloh.net/stack_entries/new?project_id=neurodebian&ref=sample"><img
+src="{{ pathto('_static/ohloh_iuseit.png', 1) }}" border="0" alt="Click to get yourself listed as a NeuroDebian user" /></a></p>
 <p><a href="http://www.nitrc.org/projects/neurodebian"><img
 src="{{ pathto('_static/nitrc_listed.png', 1) }}" border="0" alt="NITRC-listed" /></a></p>
 {% endblock %}

diff --git a/sphinx/faq.rst b/sphinx/faq.rst
index 7c9c637c7861524f1ab24b7d1c66bb2185b95150..fad53945ff76ebd8545ed6205c4edd2cc7f6e479 100644 (file)
--- a/sphinx/faq.rst
+++ b/sphinx/faq.rst
@@ -146,7 +146,8 @@ Or you will be asked questions like this over and over::
 
 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:
+make APT happy again. The simplest way is to install the ``neurodebian-keyring``
+package that is available from the NeuroDebian repository. Alternatively:
 
 1. Get the key. Either download the `repository key from here
    <_static/neuro.debian.net.asc>`_

diff --git a/sphinx/index.rst b/sphinx/index.rst
index 8e2380af337427124becf94e76803887beb7efc9..0e86f0b4f473017fcd24d057b02f68c723420058 100644 (file)
--- a/sphinx/index.rst
+++ b/sphinx/index.rst
@@ -228,9 +228,9 @@ 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.
+(2010). `Having trouble getting your Nature paper? Maybe you are not using the
+right tools? <_files/NeuroDebian_SfN2010.png>`_ *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>`_.

diff --git a/sphinx/vm.rst b/sphinx/vm.rst
index a60dcc4444cfcae621adfe3eb761d9849af1e740..da675301d9e0b44a992b420a172e5c510522d093 100644 (file)
--- a/sphinx/vm.rst
+++ b/sphinx/vm.rst
@@ -8,7 +8,7 @@ NeuroDebian Virtual Machine
    :tags: vm
 
 For those who are not yet running a Debian-based operation system we offer a
-`virtual machine`_ that can be used with `VirtualBox`_ to allow users to benefit
+`virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit
 from a Debian-based research environment on other operating systems.
 This virtual machine initially comes as a compact Debian installation that can,
 once installed, be equipped with a large variety of neuroscience software with
@@ -24,13 +24,63 @@ just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
 Downloads
 ---------
 
-* `NeuroDebian 6.0.0 image (amd64)
+* NeuroDebian 6.0.0 image (32bit) [coming soon; leave a comment below if you
+  need it urgently]
+
+  *This image should work on virtually all systems that are supported by*
+  VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
+  is not compatible with a host machine.*
+
+* `NeuroDebian 6.0.0 image (64bit)
   <http://neuro.debian.net/debian/vm/neurodebian_6.0.0_amd64.zip>`_ [~570MB]
+
+  *This image only works on 64bit host machines with active hardware
+  virtualization support. The should include all recent Apple hardware and most
+  64bit Windows systems.*
+
 * `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
   Solaris)
 
+  *This webpage offers installers of the VirtualBox application, as well as the
+  documentation.*
+
+
+Documentation
+-------------
+
+The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
+GNOME_ desktop environment. All installed software comes from standard Debian
+packages, or prospective Debian packages from NeuroDebian. This means that all
+contained software is readily available for any system running a Debian
+operating system (or a recent Ubuntu release). The virtual machine can be seen
+as a showcase of what Debian for neuroscience research feels like. Moreover,
+once downloaded this virtual machine can be kept up to date, just as any other
+Debian installation. Using convenient graphical package management tools users
+will benefit from security bug fixes provided by the Debian project for the
+whole operating system, as well as from software updates for
+neuroscience-related packages.
+
+.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
+.. _GNOME: http://www.gnome.org/
+
+
 Installation
-------------
+~~~~~~~~~~~~
+
+The following video shows how to get the NeuroDebian virtual machine running
+on your machine. The installation is shown for Mac OS X. It should, however, be
+very similar on a Windows box. If you cannot watch the video, please take a
+look at the written instructions below.
+
+.. raw:: html
+
+  <iframe title="YouTube video player"
+          class="youtube-player"
+          type="text/html"
+          width="640"
+          height="375"
+          src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
+          frameborder="0"></iframe>
 
 First download and install a recent version of VirtualBox_. VirtualBox is a
 virtualization software that is freely available for Windows, MacOS X, Solaris,
@@ -40,65 +90,53 @@ potential questions regarding installation and maintenance.
 .. _VirtualBox: http://www.virtualbox.org
 
 Next, download the most recent version of the NeuroDebian virtual machine from
-the `download page`_ (about 1GB download size). The machine is distributed as a
-`tar` file. Please extract this file, using appropriate software for your
-operating system. Every Linux system comes with the `tar` commandline utility,
-and potentially other graphical archivers that can extract this format. MacOS X
-users can simply double-click such file to extract it. Windows users can extract
-it with, for example, 7zip_.
-
-Once extracted, you'll find a directory with three files. Now start VirtualBox,
-and select "Import Appliance" from the file menu.
-
-.. _download page: http://neuro.debian.net/debian/vm
-.. _7zip: http://www.7-zip.org/
+the Downloads_ section. The machine is distributed as a zip file. Please
+extract this file, using appropriate software for your operating system.
+Once extracted, start VirtualBox and select "Import Appliance" from the file
+menu.
 
 .. image:: pics/vm_import_app.jpg
 
-Next dialog will ask you to choose a virtual machine. Please navigate to the
-extracted NeuroDebian download and select the `NeuroDebian.ovf` file.
+The next dialog will ask you to choose a virtual machine. Please navigate to the
+extracted NeuroDebian download and select the `.ovf` file.
 
 .. image:: pics/vm_import_wizard.jpg
 
-You can finish importing of NeuroDebian by clicking on *next* a couple of times. There
-is no need to change anything, as we will get through the settings in a second.
-Importing of the virtual machine will take a short while, as it is distributed in
-a compressed format that now gets extracted (total extracted size about 3.5
-GB).  Once imported, the NeuroDebian virtual machine will appear in the list of
-available machines. Do **not** start it yet, but select NeuroDebian and hit the
-*Settings* button. In the following dialog you'll have a chance to configure
-the machine. You can assign the amount of RAM that should be made available to
-it (for serious fMRI data processing, please allow at least 2 GB). If you have
-a recent computer with multiple CPU cores, you can also decide how many cores
-should be used by the virtual machine. If you have a large screen you should
-increase the display memory to 32 MB in the *Display* settings.
+You can finish importing of NeuroDebian by clicking on *next* a couple of
+times.  There is no need to change anything, as we will get through the
+settings in a second.  Importing of the virtual machine will take a short
+while, as it is distributed in a compressed format that now gets extracted
+(total extracted size about 2 GB).  Once imported, the NeuroDebian virtual
+machine will appear in the list of available machines. Do **not** start it yet,
+but select NeuroDebian and hit the *Settings* button. In the following dialog
+you'll have a chance to configure the machine. You can assign the amount of RAM
+that should be made available to it (for serious fMRI data processing, please
+allow at least 2 GB). If you have a recent computer with multiple CPU cores,
+you can also decide how many cores should be used by the virtual machine. If
+you have a large screen you should increase the display memory to 32 MB in the
+*Display* settings.
 
 .. image:: pics/vm_add_host_folder.jpg
 
 However, most important is the *Shared Folders* setup. Shared folders allow the
 virtual machine to access the local harddrive of the host computer. This is an
 easy way to access data on the computer without duplicating it or using the
-network to access it. The virtual machine is preconfigured to access a shared folder named
-labeled "host".  Click on the *add* button to select a folder that shall be
-accessible by the machine (e.g. your home directory) and put "host" as the
-folder name. Note, the folder name is simply a label. Your directory will not
-be renamed.
+network to access it. The virtual machine is preconfigured to access a shared
+folder named labeled "host".  Click on the *add* button to select a folder that
+shall be accessible by the machine (e.g. your home directory) and put "host" as
+the folder name. Note, the folder name is simply a label. Your directory will
+not be renamed.
 
 .. image:: pics/vm_host_folder.jpg
 
 Finally, close the settings dialog. You have now completed the setup, and you
 can start the virtual machine by hitting the *Start* button. A new window will
 appear showing the boot process. After a short while the NeuroDebian desktop
-will appear. You can now explore the system. The virtual machine is connected
+will appear, and a setup wizard will guide your through the final steps of the
+configuration. You can now explore the system. The virtual machine is connected
 with your host computer, and shares its Internet connection. Via this
 connection you can update the contained software packages at any time.
 
-.. warning::
-
-  VirtualBox might offer you to upgrade the "guest additions" to version 3.1.2.
-  Do **not** do this, since that version is broken, and after the upgrade you
-  will now longer be able to use the mouse inside the virtual machine.
-
 .. image:: pics/vm_settings.jpg
 
 The virtual machine logs yourself in automatically. The name of the virtual
@@ -106,43 +144,39 @@ machine user is `brain` and the password is `neurodebian`. The *root* password
 is also `neurodebian`. In most cases, however, you should not be forced to type
 the password, since `sudo` is configured to work without it.
 
-Enjoy!
+.. note::
 
+  For increased security you might want to change the default password. You can
+  do so by opening a terminal window and running the ``passwd`` command.
 
 
-Details
--------
-
-The virtual machine contains an installation of `Debian 5.0 (lenny)`_ with a
-GNOME_ desktop environment. All installed software comes from standard Debian
-packages, or prospective Debian packages from NeuroDebian -- no custom
-installations whatsoever. This means that all contained software is readily
-available for any system running a Debian operating system (or a recent Ubuntu
-release). The virtual machine can be seen as a showcase of what Debian for
-neuroscience research feels like. Moreover, once downloaded this virtual
-machine can be kept up to date, just as any other Debian installation. Using
-convenient graphical package management tools users will benefit from security
-bugfixes provided by the Debian project for the whole operating system, as well
-as from software updates for neuroscience-related packages.
-
-.. _Debian 5.0 (lenny): http://www.debian.org/releases/stable
-.. _GNOME: http://www.gnome.org/
+Working with the virtual machine
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+The next video is a demonstration of some basic desktop integration features.
+It shows how to use the virtual machine in full-screen and seamless mode, shared
+folder access, software installation, as well as suspending and resuming the
+virtual machine.
 
+.. raw:: html
 
-Troubleshooting
----------------
-
-There is no network connectivity.
+  <iframe title="YouTube video player"
+          class="youtube-player"
+          type="text/html"
+          width="640"
+          height="375"
+          src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
+          frameborder="0"></iframe>
 
-  If the virtual machine cannot access the internet, but the host computer can,
-  it might be necessary to re-establish the network connection. To do this,
-  please click on the `network manager` icon in the virtual machine's system
-  tray (upper right corner of the desktop) and select `Wired Network`. After a
-  few seconds the network should become available.
 
+Troubleshooting
+~~~~~~~~~~~~~~~
 
 I cannot hear sounds played in the virtual machine.
 
-  Sorry, but audio is not (yet) preconfigured properly. If you want to have that
-  fixed, please drop us a note.
+  By default the sound is muted. To enable playback launch the mixer applet by
+  clicking on the mixer icon in the task bar. Unmute the master volume control.
+  Now click on the "Volume control" to load the channel mixer dialog. Unmute
+  the "Master" and "PCM" channels and raise the volume as desired. You should
+  now be able to hear sounds played within the virtual machines through your
+  host computer's speakers.