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7 **************************
8 Frequently Asked Questions
9 **************************
13 <div class="expandinstructions">Click on an item to expand it</div>
18 In the course of our own research endeavors |we| have joined forces to
19 develop `PyMVPA -- a Python framework for multivariate pattern analysis of
20 neural data <http://www.pymvpa.org>`_. To conveniently deploy PyMVPA for
21 anyone using Debian-derived distributions this package repository was created
22 initially. Besides the PyMVPA_ project |we| collaborate with the `NiPy team
23 <http://neuroimaging.scipy.org>`_ on various projects, such as NiBabel_ and
24 NiPype_. Quickly NeuroDebian_ became the ultimate integrated environment for
25 all these projects -- and we are constantly working on enriching this
26 environment with as many additional relevant software as possible.
29 Debian, Debian, Debian -- What about Ubuntu?
30 NeuroDebian offers backported binary packages for recent Ubuntu releases
31 whenever possible. However, since Ubuntu (like many other derivatives) uses
32 Debian as its foundation, it is more efficient to spend time maintaining
33 packages in Debian, instead of having to directly contribute to countless
34 child-distributions. After the appearance of new packages in Debian, Ubuntu
35 typically synchronizes them quickly and they become available in the *Ubuntu
36 universe* -- a repository of Debian packages rebuilt for a particular Ubuntu
37 release. We are not constantly rebuilding of all available NeuroDebian
38 packages for new Ubuntu releases. Therefore, you might find some packages
39 temporarily being available for older Ubuntu releases only -- until the point
40 when a new package version is made and gets built for all currently supported
44 How do I get a new neuroscience-related FOSS into (Neuro)Debian?
45 The goal of NeuroDebian is to package neuroscience software for Debian. Hence
46 getting software into NeuroDebian means trying to get it into Debian. There are
47 at least two possibilities to achieve that:
49 * You can approach packaging it yourself. Start by filing an ITP_ (Intent to
50 package) bugreport) and `ask us <team@neuro.debian.net>`_ to mentor your
51 upload to Debian_, if you are not a Debian developer.
53 * `Contact us <team@neuro.debian.net>`_ -- but then it might take a little
54 longer, depending on our current workload and interest in a particular
58 I have heard that some packages are non-free. Will you charge me for them?
59 No. The term :term:`non-free` refers to an archive section. NeuroDebian uses
60 exactly the same `archive sections as Debian proper
61 <http://www.debian.org/doc/debian-policy/ch-archive.html>`_. The *non-free*
62 section contains packages that have certain restrictions regarding **your
63 freedom** to employ them for a particular purpose. In contrast, for packages
64 in the *main* section your are completely free to do whatever and in whatever
65 context you like. Regardless of the actual license or archive section, all
66 packages in NeuroDebian are provided free of charge and under the licensing
67 terms of the original developers.
70 When does a package migrate from NeuroDebian into Debian proper?
71 In short: When it is ready. The longer answer is that there is nothing
72 special to packages in NeuroDebian in comparison to packages conducted
73 elsewhere. Packaging efforts are announced to Debian via ITPs_ and the
74 packaging itself is available in some version control system -- typically in
75 the Git repositories of the `pkg-exppsy group on Debian's Alioth server`_, or
76 another VCS, or on http://mentors.debian.net.
78 The only difference is that a particular package becomes available through the
79 NeuroDebian repository before it has passed all checks for compliance with
80 Debian's standards. But even after a package becomes part of Debian the
81 NeuroDebian repository continues to provide binary packages of new versions
82 for a certain set of Debian and Ubuntu releases (aka backports).
84 .. _ITPs: http://www.debian.org/devel/wnpp
85 .. _pkg-exppsy group on Debian's Alioth server: http://alioth.debian.org/projects/pkg-exppsy/
88 How to create a mirror of the repository?
89 The NeuroDebian repository can be mirrored with rsync. If you are interested
90 in sponsoring storage space and bandwidth for another mirror, please
91 `contact us <team@neuro.debian.net>`_.
94 .. _sec_pkg_authentication:
96 What means "The following signatures couldn't be verified..."?
97 When you start using this repository, you probably get warning messages
100 The following signatures couldn't be verified because
101 the public key is not available.
103 Or you will be asked questions like this over and over::
105 WARNING: The following packages cannot be authenticated!
107 Install these packages without verification [y/N]?
109 This is because your APT installation initially does not know the GPG
110 key that is used to sign the release files of this repository. It is easy to
111 make APT happy again. The simplest way is to install the ``neurodebian-keyring``
112 package that is available from the NeuroDebian repository. Alternatively:
114 1. Get the key. Either download the `repository key from here
115 <_static/neuro.debian.net.asc>`_
116 or fetch it from http://wwwkeys.pgp.net (2649A5A9).
118 2. Now feed the key into APT by invoking::
122 Where `#file#` has to be replaced with the location of the key file you just
123 downloaded. You need to have superuser-privileges to do this (either do it
124 as root or use sudo).
127 Why is NeuroDebian not a Pure Blend?
128 This is in the works, but...
130 There is no need for it to become one, as the existing Debian Pure Blends
131 already offer the desired functionality *within* Debian. Similar to Pure
132 Blends, NeuroDebian's goal is to provide software for neuroscientists using
133 the Debian operating system, and therefore the ultimate goal is to get all
134 relevant software **into Debian**.
136 However, various reasons exist that prevent a particular software from
137 entering Debian. Some are temporary, i.e. a package is already useable, but
138 some technical bits do not meet Debian's standards (yet) or a licensing issue
139 needs to be resolved first. For some software the licensing is so restrictive
140 that it cannot be distributed by Debian, and hence cannot even go into its
141 *non-free* branch. Unfortunately, sometimes these issues cannot be solved to
142 a degree that is acceptable for Debian. For some other packages Debian itself
143 is not ready yet, e.g. huge data packages with neuroscience data (:ref:`with
144 sometimes over 1GB <pkg_fsl-first-data>`).
146 NeuroDebian aims to be a platform that provides a staging area for
147 neuroscience software packages on their way into Debian. All packages are
148 properly registered in the relevant `Debian Pure Blends`_, e.g.
149 `Debian Science Cognitive Neuroscience`_ or `Debian Med Imaging`_. Inside
150 Debian these efforts already provide a suitable framework for this purpose,
151 and hence there is no need to establish yet another one.
153 .. _Debian Pure Blends: http://wiki.debian.org/DebianPureBlends
154 .. _Debian Science Cognitive Neuroscience: http://blends.alioth.debian.org/science/tasks/neuroscience-cognitive
155 .. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
158 I want to help. How do I get involved?
159 We always need people to help maintaining existing packages. If you need
160 some additional software packaged and you want to try it on your own, we would
161 be happy to mentor you. We also have a :ref:`list of ongoing and planned
162 projects <projects>`, each listing a number of tasks that need to be done.
164 If you found something you are interested in, please email the
165 neurodebian-devel_ mailing list and let us know about it. Thanks!
168 How can I cite NeuroDebian?
169 Please cite the following paper:
171 Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
172 next step: An integrated, community-driven computing platform for neuroscience
173 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
174 *Frontiers in Neuroinformatics*, 6:22.
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