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