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