1 .. -*- mode: rst; fill-column: 78 -*-
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7 **************************
8 Frequently Asked Questions
9 **************************
14 In the course of our own research endeavors |we| have joined forces to
15 develop `PyMVPA -- a Python framework for multivariate pattern analysis of
16 neural data <http://www.pymvpa.org>`_. To conveniently deploy PyMVPA for
17 anyone using Debian-derived distributions this package repository was created
18 initially. Besides the PyMVPA_ project |we| collaborate with the `NiPy team
19 <http://neuroimaging.scipy.org>`_ on various projects, such as NiBabel_ and
20 NiPype_. Quickly NeuroDebian_ became the ultimate integrated environment for
21 all these projects -- and we are constantly working on enriching this
22 environment with as many additional relevant software as possible.
25 Why is NeuroDebian not a Pure Blend?
26 ------------------------------------
28 Because there is no need for it to become one, as the existing Debian Pure
29 Blends already offer the desired functionality *within* Debian. Similar to
30 Pure Blends, NeuroDebian's goal is to provide software for neuroscientists
31 using the Debian operating system, and therefore the ultimate goal is to get
32 all relevant software **into Debian**.
34 However, various reasons exist that prevent a particular software from
35 entering Debian. Some are temporary, i.e. a package is already useable, but
36 some technical bits do not meet Debian's standards (yet) or a licensing issue
37 needs to be resolved first. For some software the licensing is so restrictive
38 that it cannot be distributed by Debian, and hence cannot even go into its
39 *non-free* branch. Unfortunately, sometimes these issues cannot be solved to
40 a degree that is acceptable for Debian. For some other packages Debian itself
41 is not ready yet, e.g. huge data packages with neuroscience data (:ref:`with
42 sometimes over 1GB <pkg_fsl-first-data>`).
44 NeuroDebian aims to be a platform that provides a staging area for
45 neuroscience software packages on their way into Debian. All packages are
46 properly registered in the relevant `Debian Pure Blends`_, e.g.
47 `Debian Science Cognitive Neuroscience`_ or `Debian Med Imaging`_. Inside
48 Debian these efforts already provide a suitable framework for this purpose,
49 and hence there is no need to establish yet another one.
51 .. _Debian Pure Blends: http://wiki.debian.org/DebianPureBlends
52 .. _Debian Science Cognitive Neuroscience: http://blends.alioth.debian.org/science/tasks/neuroscience-cognitive
53 .. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
56 I want to help. How do I get involved?
57 --------------------------------------
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 ----------------------------------------------------------------
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 Debian, Debian, Debian -- What about Ubuntu?
89 --------------------------------------------
91 NeuroDebian offers backported binary packages for recent Ubuntu releases
92 whenever possible. However, since Ubuntu (like many other derivatives) uses
93 Debian as its foundation, it is more efficient to spend time maintaining
94 packages in Debian, instead of having to directly contribute to countless
95 child-distributions. After the appearance of new packages in Debian, Ubuntu
96 typically synchronizes them quickly and they become available in the *Ubuntu
97 universe* -- a repository of Debian packages rebuilt for a particular Ubuntu
98 release. We are not constantly rebuilding of all available NeuroDebian
99 packages for new Ubuntu releases. Therefore, you might find some packages
100 temporarily being available for older Ubuntu releases only -- until the point
101 when a new package version is made and gets built for all currently supported
105 How to create a mirror of the repository?
106 -----------------------------------------
108 The NeuroDebian repository can be mirrored with rsync. If you are interested
109 in sponsoring storage space and bandwidth for another mirror, please
110 `contact us <team@neuro.debian.net>`_.
113 How do I get a new neuroscience-related FOSS into (Neuro)Debian?
114 ----------------------------------------------------------------
116 The goal of NeuroDebian is to package neuroscience software for Debian. Hence
117 getting software into NeuroDebian means trying to get it into Debian. There are
118 at least two possibilities to achieve that:
120 * You can approach packaging it yourself. Start by filing an ITP_ (Intent to
121 package) bugreport) and `ask us <team@neuro.debian.net>`_ to mentor your
122 upload to Debian_, if you are not a Debian developer.
124 * `Contact us <team@neuro.debian.net>`_ -- but then it might take a little
125 longer, depending on our current workload and interest in a particular
129 I have heard that some packages are non-free. Will you charge me for them?
130 --------------------------------------------------------------------------
132 No. The term :term:`non-free` refers to an archive section. NeuroDebian uses
133 exactly the same `archive sections as Debian proper
134 <http://www.debian.org/doc/debian-policy/ch-archive.html>`_. The *non-free*
135 section contains packages that have certain restrictions regarding **your
136 freedom** to employ them for a particular purpose. In contrast, for packages
137 in the *main* section your are completely free to do whatever and in whatever
138 context you like. Regardless of the actual license or archive section, all
139 packages in NeuroDebian are provided free of charge and under the licensing
140 terms of the original developers.
142 .. _sec_pkg_authentication:
144 What means "The following signatures couldn't be verified..."?
145 --------------------------------------------------------------
147 When you start using this repository, you probably get warning messages
150 The following signatures couldn't be verified because
151 the public key is not available.
153 Or you will be asked questions like this over and over::
155 WARNING: The following packages cannot be authenticated!
157 Install these packages without verification [y/N]?
159 This is because your APT installation initially does not know the GPG
160 key that is used to sign the release files of this repository. It is easy to
161 make APT happy again. The simplest way is to install the ``neurodebian-keyring``
162 package that is available from the NeuroDebian repository. Alternatively:
164 1. Get the key. Either download the `repository key from here
165 <_static/neuro.debian.net.asc>`_
166 or fetch it from http://wwwkeys.pgp.net (2649A5A9).
168 2. Now feed the key into APT by invoking::
172 Where `#file#` has to be replaced with the location of the key file you just
173 downloaded. You need to have superuser-privileges to do this (either do it
174 as root or use sudo).
177 How can I cite NeuroDebian?
178 ---------------------------
180 Please cite the following paper:
182 Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
183 next step: An integrated, community-driven computing platform for neuroscience
184 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
185 *Frontiers in Neuroinformatics*, 6:22.
188 .. include:: link_names.txt
189 .. include:: substitutions.txt