-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-
-# Internal variables.
-SRCDIR = build/src
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(SRCDIR)
-
WWW_UPLOAD_URI = elrond:/home/hanke/public_html/archive
-WWW_DIR = build/html
+WWW_DIR = build/_build/html
-.PHONY: help clean html web pickle htmlhelp latex changes linkcheck
+prep:
+ mkdir -p build/src
+ cp -r sphinx/* build/src
-prep:
- mkdir -p build
- cp -r source/* build/src
+html: prep update-db
+ cd build/src && $(MAKE) html BUILDDIR=$(CURDIR)/build
clean:
-rm -rf build
-html: prep
- mkdir -p build/html build/doctrees
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html
- @echo
- @echo "Build finished. The HTML pages are in build/html."
-
-pickle: prep
- mkdir -p build/pickle build/doctrees
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) build/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-web: pickle
-
-json: prep
- mkdir -p build/json build/doctrees
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) build/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp: prep
- mkdir -p build/htmlhelp build/doctrees
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) build/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in build/htmlhelp."
-
-latex: prep
- mkdir -p build/latex build/doctrees
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) build/latex
- @echo
- @echo "Build finished; the LaTeX files are in build/latex."
- @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
- "run these through (pdf)latex."
-
-changes: prep
- mkdir -p build/changes build/doctrees
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) build/changes
- @echo
- @echo "The overview file is in build/changes."
-
-linkcheck: prep
- mkdir -p build/linkcheck build/doctrees
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) build/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in build/linkcheck/output.txt."
-
update-db:
- rm -f build/db.db
+# -r http://apsy.gse.uni-magdeburg.de/debian/dists/lenny/Release \
+ -r http://apsy.gse.uni-magdeburg.de/debian/dists/squeeze/Release \
+# rm -f build/db.db
./reblender \
--db build/db.db \
--outdir build/src \
+ --pkgaddenum pkgs \
-r http://apsy.gse.uni-magdeburg.de/debian/dists/dapper/Release \
-r http://apsy.gse.uni-magdeburg.de/debian/dists/gutsy/Release \
-r http://apsy.gse.uni-magdeburg.de/debian/dists/hardy/Release \
-r http://apsy.gse.uni-magdeburg.de/debian/dists/intrepid/Release \
-r http://apsy.gse.uni-magdeburg.de/debian/dists/etch/Release \
- -r http://apsy.gse.uni-magdeburg.de/debian/dists/lenny/Release \
- -r http://apsy.gse.uni-magdeburg.de/debian/dists/squeeze/Release \
-r http://apsy.gse.uni-magdeburg.de/debian/dists/sid/Release \
-t svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging \
-t svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/imaging-dev \
--- /dev/null
+Related packages
+================
+
+Since FSL covers a very broad range of analysis techniques the suite is split
+into a number of separate packages to allow a more fine-grained selection of
+the functionality provided by FSL. The following related packages are available:
+
+:ref:`deb_fsl`
+ This packages provides the FSL binaries. This includes everything one needs
+ to run a basic fMRI analysis. However, it is recommend to also at least
+ install the :ref:`fsl-atlases <deb_fsl-atlases>` package.
+
+:ref:`deb_fslview`
+ Almost everybody should install this package.
+
+:ref:`deb_fsl-doc`
+ Contains the FSL documentation in HTML format as included in the official FSL
+ sources. This package should be installed to use the online help capabilities
+ of FSL.
+
+:ref:`deb_fslview-doc`
+ The FSLView documentation in HTML format. This package is necessary for the
+ online help system of FSLView.
+
+:ref:`deb_fsl-atlases`
+ Contains the standard space brain templates and brain atlases. Almost
+ everybody should install this package.
+
+:ref:`deb_fsl-possum-data`
+ This package provides the templates for the MR sequence simulator POSSUM.
+ If one does not use POSSUM this package is not necessary.
+
+:ref:`deb_fsl-first-data`
+ This package provides model data for FIRST subcortical brain segmentation.
+ This package is almost 1GB! It is only required if one wants to use FIRST
+ or run the FSL FEEDS suite.
+
+:ref:`deb_fsl-feeds`
+ This package provides the `FSL Evaluation and Example Data Suite`_. This
+ package performs two functions -- it tests whether the FSL tools are working
+ properly and it provides example data to try running FSL on. Additionally the
+ :command:`fsl-selftest` command is avaliable. This is a little script that
+ runs all tests (or a selected one) in a temporary directory and reports the
+ results. A manpage is included. This package can be used to perform
+ `FSL benchmarks`_.
+
+.. _FSL Evaluation and Example Data Suite: http://www.fmrib.ox.ac.uk/fsl/fsl/feeds.html
+
+
+Report bugs
+===========
+
+If you discover any bugs please report them. The best way to get quick and
+professional help is to post to the `FSL mailing list`_. If you send a
+bugreport please include detailed information about the problem. This should at
+least be a description how the bug can be reproduced as well as information
+concerning you environment (for example the operation system). You might also
+want to have a look at the mailing list archive whether the problem has been
+discovered before.
+
+.. _FSL mailing list: http://www.jiscmail.ac.uk/lists/fsl.html
+
+If you use the package on a Debian system (not Ubuntu) you can simply use the
+:command:`reportbug` tool to send a bug report to the `Debian bug tracking
+system`_. The bug tracker provides a public list of all reported `bugs of FSL`_
+and `bugs of FSLView`_
+
+.. _bugs of FSL: http://bugs.debian.org/src:fsl
+.. _bugs of FSLVIEW: http://bugs.debian.org/src:fslview
+.. _Debian bug tracking system: http://bugs.debian.org
+
+
+Additional information
+======================
+
+Since December 2007 the FSL package is officially part of the non-free
+section of Debian. The latest package version will always be available
+from http://packages.debian.org/sid/fsl in the Debian archive.
+However, this only applies to the packages of the FSL and FSLView
+binaries. FSL data packages (first, possum, atlases and feeds) are not
+yet official Debian packages and will be available from here, as well
+as backports for Debian and recent Ubuntu releases.
+
+.. note::
+
+ Please be sure to `read the information`_ about the differences
+ between the Debian packaging and the official FSL releases.
+
+.. _read the information: http://git.debian.org/?p=pkg-exppsy/fsl.git;a=blob;f=debian/README.Debian;hb=debian"
+
+
+Usage information
+-----------------
+
+FSL requires a config file to be sourced before it can be used. For the Debian
+packages this config file is in `/etc/fsl/fsl.sh`. Open a terminal where you
+want to start FSL and source it like this::
+
+ . /etc/fsl/fsl.sh
+
+Note the dot at the beginning. If you want to have this done automatically, you
+could add those line to e.g. your `$HOME/.bashrc` file (or a corresponding
+config file of another POSIX-compatible shell). Once you have done that, you
+can start using FSL.
+
+
+
+Upgrading from FSL 3.x
+----------------------
+
+The FSL configuration file has changed significantly. Please be sure to
+(re)source it.
+
+.. note::
+
+ There seem to be some remaining incompatibilities of FSL scripts with the
+ *dash* shell. This is the default shell on Ubuntu systems. If you discover any
+ problems, please make sure to read `a related posting on the FSL mailing
+ list`_.
+
+.. _a related posting on the FSL mailing list: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=fsl&T=0&F=&S=&P=19638
+
+
+Building binary packages yourself
+---------------------------------
+
+If no binary packages for your distribution/platform are available, you can
+still build your own. All you need to do is to add this line to your
+`/etc/apt/sources.list`::
+
+ deb-src http://apsy.gse.uni-magdeburg.de/debian #distro# main non-free
+
+Choose the value of `#distro#` like described in the binary package section. Be
+sure to update your package list after that (Remember: :command:`aptitude
+update`). To build FSL packages, do this (no superuser privileges required,
+but you might have to install `apt-src` first)::
+
+ apt-src install fsl
+ apt-src build fsl
+
+Be patient as this will take some time. All packages will be created in the
+directory where the commands are executed. Please note, that you might need to
+download or even compile other packages that FSL depends on.
+
+If you are done, you can install the packages with::
+
+ dpkg -i fsl*.deb
+
+After you have repeated this procedure for the `fslview` source package, you
+should be ready to use FSL.
+
+Advanced: Arch-dependend compiler flags
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you have some experience with compiler flags and you also care for speed,
+you might want to have the FSL binaries optimized for every detail of your
+platform. To take advantage of all special features of your favorite processor
+you can specify custom compiler flags that are used when building binary
+packages from the source package of FSL. To achieve this, simply define them in
+a variable called :envvar:`DEB_ARCH_OPT_FLAGS` in the environment. In its
+simplest form, building an optimized package could be done like this::
+
+ DEB_ARCH_OPT_FLAGS="-march=opteron" apt-src build fsl
+
+Note that not all flags are available with every compiler. The above example
+does not work with the standard compiler of Debian sarge (gcc 3.3) and you
+obviously need an AMD Opteron processor.
+
+
+FSL benchmarks
+--------------
+
+Here is a list of some benchmarking results that demonstrate how fast FSL runs
+on several different platforms and distributions. The :command:`fsl-feeds`
+package is used for benchmarking FSL. The listed time for a complete
+fsl-selftest run is the user time as reported by :command:`time -p`. If you are
+also interested in benchmarking results of the non-Debian FSL distribution, you
+can visit the `FSL-FEEDS timing website`_.
+
+.. _FSL-FEEDS timing website: http://www.fmrib.ox.ac.uk/fsl/feeds/doc/timings.html
+
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Distribution|CPU |Arch. |Memory|Compiler |Flags |Version |Time|Submitted |
++============+===============+======+======+=========+==================+========+====+==============+
+|Ubuntu |Intel Core 2 |x86_64|4GB |gcc 4.1.2| |4.0.2-1 |1377| Jiří Keller |
+|gutsy |Quad Q6700 3Ghz| | | | | | | |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian sid |2x Dual Opteron|amd64 |12GB |gcc 4.1.1| |3.3.7-2 |1560|Yaroslav |
+| |275 2.2 Ghz | | | | | | |Halchenko |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Ubuntu edgy |2x Dual Opteron|i686 |3GB |gcc 4.1.2| |3.3.8-1 |2096|Jeff |
+| |275 2.2 GHz | | | | | | |Stevenson |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian lenny|Intel Core2 |i686 |2GB |gcc 4.3.1| |4.1.0-1 |2108|Michael |
+| |E8400 3Ghz | | | | | | |Hanke |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |Quad Opteron |amd64 |32GB |gcc 3.4.6|-O3 -m64 |3.2b-4 |2152|Antti |
+| |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
+| | | | | |-mfpmath=sse | | | |
+| | | | | |-msse2 | | | |
+| | | | | |-ffast-math | | | |
+| | | | | |-funroll-all-loops| | | |
+| | | | | |-fpeel-loops | | | |
+| | | | | |-ftracer | | | |
+| | | | | |-funswitch-loops | | | |
+| | | | | |-funit-at-a-time | | | |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian lenny|Athlon X2 |amd64 |4GB |gcc 4.3 | |4.0.4-1 |2268|Petr |
+| |4800 2.5 GHz | | | | | | |Hluštík |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Ubuntu |Quad Core2 |amd64 |4GB |gcc 4.1 | |4.0-1 |2500|Vincent |
+|feisty |2.4 GHz | | | | | | |Ferrera |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 -m64 |3.2b-4 |2619|Antti |
+| |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
+| | | | | |-mfpmath=sse | | | |
+| | | | | |-msse2 | | | |
+| | | | | |-ffast-math | | | |
+| | | | | |-funroll-all-loops| | | |
+| | | | | |-fpeel-loops | | | |
+| | | | | |-ftracer | | | |
+| | | | | |-funswitch-loops | | | |
+| | | | | |-funit-at-a-time | | | |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 |3.2b-4 |2652|Antti |
+| |850 2.4 GHz | | | | | | |Korvenoja |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |2x Opteron |amd64 |12GB |gcc 4.1.2| |4.0.2-3 |2847|Michael |
+| |270 2.2 GHz | | | | | | |Hanke |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Ubuntu gutsy|Athlon 64X2 |amd64 |2GB |gcc 4.1.3| |4.0.1 |3605|Nicholas P. |
+| |5200+ 2.6 GHz | | | | | | |Holmes |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+
+.. Template
+ | | | | | | | | | |
+ | | | | | | | | | |
+ +------------+---------------+------+------+---------+------------------+--------+----+--------------+
+
+
+If you want to have your system included in this list, please send an email
+with the logfile of the benchmark. You can run the benchmark (and create the
+logfile) by running (fsl-feeds-3.2beta-3 or higher is required)::
+
+ (time -p fsl-selftest -c) > benchmark.log 2>&1
+
+And include the following information in your message:
+
+* Which distribution are you using?
+
+* CPU-type (as specific as possible)
+
+* How much physical memory has the machine? If you don't know this, send the
+ output of::
+
+ free | head -n2 | tail -n1 | awk '{print $2}' -
+
+* If you compiled the binary packages yourself, which compiler did you use?
+ (hint: `gcc --version`)
+
+* Which custom compiler flags did you use when building the package (if any)?
+
+* Which version of the Debian FSL package was used?
toc.close()
-def writeRst(db, outdir):
+def writeRst(db, outdir, addenum_dir=None):
createDir(outdir)
createDir(os.path.join(outdir, 'pkgs'))
pf.write(genPkgPage(db, p))
# check for doc addons
- if os.path.exists(os.path.join(outdir, 'pkgs_addenum/%s.rst' % p)):
- pf.write('\n\n.. include:: ../pkgs_addenum/%s.rst\n' %p)
+ if addenum_dir is not None:
+ addenum = os.path.join(os.path.abspath(addenum_dir), '%s.rst' % p)
+ if os.path.exists(addenum):
+ pf.write('\n\n.. include:: %s\n' % addenum)
pf.close()
toc.write(' pkgs/%s\n' % p)
action="append", dest="prospective_pkgs",
help="None")
+ op.add_option("--pkgaddenum", action="store", dest="addenum_dir",
+ type="string", default=None, help="None")
+
def main():
op = OptionParser(version="%prog 0.0.1")
if not opts.outdir is None:
dpa.writeSourcesLists(opts.outdir)
- writeRst(dpa, opts.outdir)
+ writeRst(dpa, opts.outdir, opts.addenum_dir)
writePkgsBy(dpa, 'maintainer', maintainer2email, opts.outdir,
'Packages maintained by <ITEM>')
+++ /dev/null
-{% extends "!layout.html" %}
-
-{% block extrahead %}
- <meta name="keywords" content="debian, neuroscience">
-{% endblock %}
-
-{% block rootrellink %}
- <li><a href="http://www.debian.org" target="_blank">Debian</a> | </li>
- <li><a href="{{ pathto('index') }}">Neuroscience Repository</a> »</li>
- <li><a href="{{ pathto('genindex') }}">Package list</a></li>
-{% endblock %}
-
-{% block sidebar1 %}
-{{ sidebar() }}
-{% endblock %}
-
-{% block sidebar2 %}
-{{ sidebar() }}
-{% endblock %}
+++ /dev/null
-# -*- coding: utf-8 -*-
-#
-# Debian Package Repository documentation build configuration file, created by
-# sphinx-quickstart on Sat Mar 28 17:08:58 2009.
-#
-# This file is execfile()d with the current directory set to its containing dir.
-#
-# The contents of this file are pickled, so don't put values in the namespace
-# that aren't pickleable (module imports are okay, they're removed automatically).
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import sys, os
-
-# If your extensions are in another directory, add it here. If the directory
-# is relative to the documentation root, use os.path.abspath to make it
-# absolute, like shown here.
-#sys.path.append(os.path.abspath('.'))
-
-# General configuration
-# ---------------------
-
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = []
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['.templates']
-
-# The suffix of source filenames.
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'Debian Neuroscience Package Repository'
-copyright = u'2009, Michael Hanke'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = ''
-# The full version, including alpha/beta/rc tags.
-release = ''
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-today_fmt = '%B %d, %Y'
-
-# List of documents that shouldn't be included in the build.
-#unused_docs = []
-
-# List of directories, relative to source directory, that shouldn't be searched
-# for source files.
-exclude_trees = ['pkgs_addenum']
-
-# The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-
-# Options for HTML output
-# -----------------------
-
-# The style sheet to use for HTML and HTML Help pages. A file of that name
-# must exist either in Sphinx' static/ path, or in one of the custom paths
-# given in html_static_path.
-html_style = 'default.css'
-
-# The name for this set of Sphinx documents. If None, it defaults to
-# "<project> v<release> documentation".
-html_title = project
-
-# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = "Debian Neuroscience"
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-html_logo = 'pics/debian-imaging.jpg'
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['static']
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-html_use_modindex = False
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, the reST sources are included in the HTML build as _sources/<name>.
-html_copy_source = False
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it. The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'debpkgrepo'
-
-
-# Options for LaTeX output
-# ------------------------
-
-# The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
-
-# The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, document class [howto/manual]).
-latex_documents = [
- ('index', 'DebianPackageRepository.tex', ur'Debian Package Repository Documentation',
- ur'Michael Hanke', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_use_modindex = True
+++ /dev/null
-.. _gpg_signatures:
-
-
-Package authentication
-======================
-
-
-When you start using this repository, you might get warning messages like this::
-
- The following signatures couldn't be verified because
- the public key is not available.`
-
-Or you will be asked questions like this over and over::
-
- WARNING: The following packages cannot be authenticated!
- ...
- Install these packages without verification [y/N]?
-
-This is because your APT installation does not know the GPG key that is used to
-sign the release files of this repository. Making APT happy again is easy:
-
-1. Get the key. Either download the `repository key from here
- <http://apsy.gse.uni-magdeburg.de/debian/apsy.gse.uni-magdeburg.de.asc>`_
- or fetch it from *subkeys.pgp.net*.
-
-2. Now feed the key into APT by invoking::
-
- apt-key add #file#
-
- Where `#file#` has to be replaced with the location of the key file you just
- downloaded. You need to have superuser-privileges to do this (either do it
- as root or use sudo).
-
+++ /dev/null
-***********************************************
- Welcome to the Debian Neuroscience Repository
-***********************************************
-
-This repository provides mostly neuroscience-related packages to be
-used on Debian systems (or a Debian-derivates like Ubuntu). It
-contains both unofficial or prospective packages which are not
-available from the main Debian archive, as well backported or simply
-rebuilt packages also available elsewhere.
-
-This service is provided "as is". There is no guarantee that a package
-works as expected, so use them at your own risk. They might kill your
-system (although that is rather unlikely). You've been warned!
-
-The repository contains both neuroscience-related packages as well as
-general purpose software which is necessary to resolved dependencies, or
-is simply useful in the neuroscience context. The featured neuroscience
-software can be browsed via the repository :ref:`genindex` or through the
-:ref:`maintainer view <bymaintainer>`.
-
-All other packages are available through the search engine or from the
-:ref:`full package list <full_pkg_list>`.
-
-
-How to use this repository
-==========================
-
-The easiest way to use this repository is to download an APT-configuration
-file. Simply click on the name of your target distribution/release and save the
-downloaded file in the `/etc/apt/sources.list.d/` directory on your system
-(depending on the browser, you might have to right-click and choose 'save as').
-Saving files in this directory will require superuser privileges, therefore you
-should probably download the file into a temporary directory and subsequently
-move it into `/etc/apt/sources.list.d/`. APT-configurations are available for
-the following releases:
-
-.. include:: sources_lists
-
-Once this is done, you have to update the package index. Use your favorite
-package manager, e.g. synaptic, adept, or whatever you like. In the terminal
-you can use :command:`aptitude` to achieve the same::
-
- sudo aptitude update
-
-Now, you can proceed to install packages, e.g.::
-
- sudo aptitude install lipsia
-
-.. note::
- Not every package is available for all distributions/releases. For information
- about which package version is available for which release and architecture,
- please have a look at the corresponding package pages.
-
-
-Package authentication
-----------------------
-
-When you start using this repository, you might get warning messages
-like this::
-
- The following signatures couldn't be verified because
- the public key is not available.`
-
-Or you will be asked questions like this over and over::
-
- WARNING: The following packages cannot be authenticated!
- ...
- Install these packages without verification [y/N]?
-
-This is because your APT installation initially does not know the GPG
-key that is used to sign the release files of this repository. Making
-APT happy again is easy:
-
-1. Get the key. Either download the `repository key from here
- <http://apsy.gse.uni-magdeburg.de/debian/apsy.gse.uni-magdeburg.de.asc>`_
- or fetch it from *subkeys.pgp.net*.
-
-2. Now feed the key into APT by invoking::
-
- apt-key add #file#
-
- Where `#file#` has to be replaced with the location of the key file you just
- downloaded. You need to have superuser-privileges to do this (either do it
- as root or use sudo).
+++ /dev/null
-Related packages
-================
-
-Since FSL covers a very broad range of analysis techniques the suite is split
-into a number of separate packages to allow a more fine-grained selection of
-the functionality provided by FSL. The following related packages are available:
-
-:ref:`deb_fsl`
- This packages provides the FSL binaries. This includes everything one needs
- to run a basic fMRI analysis. However, it is recommend to also at least
- install the :ref:`fsl-atlases <deb_fsl-atlases>` package.
-
-:ref:`deb_fslview`
- Almost everybody should install this package.
-
-:ref:`deb_fsl-doc`
- Contains the FSL documentation in HTML format as included in the official FSL
- sources. This package should be installed to use the online help capabilities
- of FSL.
-
-:ref:`deb_fslview-doc`
- The FSLView documentation in HTML format. This package is necessary for the
- online help system of FSLView.
-
-:ref:`deb_fsl-atlases`
- Contains the standard space brain templates and brain atlases. Almost
- everybody should install this package.
-
-:ref:`deb_fsl-possum-data`
- This package provides the templates for the MR sequence simulator POSSUM.
- If one does not use POSSUM this package is not necessary.
-
-:ref:`deb_fsl-first-data`
- This package provides model data for FIRST subcortical brain segmentation.
- This package is almost 1GB! It is only required if one wants to use FIRST
- or run the FSL FEEDS suite.
-
-:ref:`deb_fsl-feeds`
- This package provides the `FSL Evaluation and Example Data Suite`_. This
- package performs two functions -- it tests whether the FSL tools are working
- properly and it provides example data to try running FSL on. Additionally the
- :command:`fsl-selftest` command is avaliable. This is a little script that
- runs all tests (or a selected one) in a temporary directory and reports the
- results. A manpage is included. This package can be used to perform
- `FSL benchmarks`_.
-
-.. _FSL Evaluation and Example Data Suite: http://www.fmrib.ox.ac.uk/fsl/fsl/feeds.html
-
-
-Report bugs
-===========
-
-If you discover any bugs please report them. The best way to get quick and
-professional help is to post to the `FSL mailing list`_. If you send a
-bugreport please include detailed information about the problem. This should at
-least be a description how the bug can be reproduced as well as information
-concerning you environment (for example the operation system). You might also
-want to have a look at the mailing list archive whether the problem has been
-discovered before.
-
-.. _FSL mailing list: http://www.jiscmail.ac.uk/lists/fsl.html
-
-If you use the package on a Debian system (not Ubuntu) you can simply use the
-:command:`reportbug` tool to send a bug report to the `Debian bug tracking
-system`_. The bug tracker provides a public list of all reported `bugs of FSL`_
-and `bugs of FSLView`_
-
-.. _bugs of FSL: http://bugs.debian.org/src:fsl
-.. _bugs of FSLVIEW: http://bugs.debian.org/src:fslview
-.. _Debian bug tracking system: http://bugs.debian.org
-
-
-Additional information
-======================
-
-Since December 2007 the FSL package is officially part of the non-free
-section of Debian. The latest package version will always be available
-from http://packages.debian.org/sid/fsl in the Debian archive.
-However, this only applies to the packages of the FSL and FSLView
-binaries. FSL data packages (first, possum, atlases and feeds) are not
-yet official Debian packages and will be available from here, as well
-as backports for Debian and recent Ubuntu releases.
-
-.. note::
-
- Please be sure to `read the information`_ about the differences
- between the Debian packaging and the official FSL releases.
-
-.. _read the information: http://git.debian.org/?p=pkg-exppsy/fsl.git;a=blob;f=debian/README.Debian;hb=debian"
-
-
-Usage information
------------------
-
-FSL requires a config file to be sourced before it can be used. For the Debian
-packages this config file is in `/etc/fsl/fsl.sh`. Open a terminal where you
-want to start FSL and source it like this::
-
- . /etc/fsl/fsl.sh
-
-Note the dot at the beginning. If you want to have this done automatically, you
-could add those line to e.g. your `$HOME/.bashrc` file (or a corresponding
-config file of another POSIX-compatible shell). Once you have done that, you
-can start using FSL.
-
-
-
-Upgrading from FSL 3.x
-----------------------
-
-The FSL configuration file has changed significantly. Please be sure to
-(re)source it.
-
-.. note::
-
- There seem to be some remaining incompatibilities of FSL scripts with the
- *dash* shell. This is the default shell on Ubuntu systems. If you discover any
- problems, please make sure to read `a related posting on the FSL mailing
- list`_.
-
-.. _a related posting on the FSL mailing list: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=fsl&T=0&F=&S=&P=19638
-
-
-Building binary packages yourself
----------------------------------
-
-If no binary packages for your distribution/platform are available, you can
-still build your own. All you need to do is to add this line to your
-`/etc/apt/sources.list`::
-
- deb-src http://apsy.gse.uni-magdeburg.de/debian #distro# main non-free
-
-Choose the value of `#distro#` like described in the binary package section. Be
-sure to update your package list after that (Remember: :command:`aptitude
-update`). To build FSL packages, do this (no superuser privileges required,
-but you might have to install `apt-src` first)::
-
- apt-src install fsl
- apt-src build fsl
-
-Be patient as this will take some time. All packages will be created in the
-directory where the commands are executed. Please note, that you might need to
-download or even compile other packages that FSL depends on.
-
-If you are done, you can install the packages with::
-
- dpkg -i fsl*.deb
-
-After you have repeated this procedure for the `fslview` source package, you
-should be ready to use FSL.
-
-Advanced: Arch-dependend compiler flags
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-If you have some experience with compiler flags and you also care for speed,
-you might want to have the FSL binaries optimized for every detail of your
-platform. To take advantage of all special features of your favorite processor
-you can specify custom compiler flags that are used when building binary
-packages from the source package of FSL. To achieve this, simply define them in
-a variable called :envvar:`DEB_ARCH_OPT_FLAGS` in the environment. In its
-simplest form, building an optimized package could be done like this::
-
- DEB_ARCH_OPT_FLAGS="-march=opteron" apt-src build fsl
-
-Note that not all flags are available with every compiler. The above example
-does not work with the standard compiler of Debian sarge (gcc 3.3) and you
-obviously need an AMD Opteron processor.
-
-
-FSL benchmarks
---------------
-
-Here is a list of some benchmarking results that demonstrate how fast FSL runs
-on several different platforms and distributions. The :command:`fsl-feeds`
-package is used for benchmarking FSL. The listed time for a complete
-fsl-selftest run is the user time as reported by :command:`time -p`. If you are
-also interested in benchmarking results of the non-Debian FSL distribution, you
-can visit the `FSL-FEEDS timing website`_.
-
-.. _FSL-FEEDS timing website: http://www.fmrib.ox.ac.uk/fsl/feeds/doc/timings.html
-
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Distribution|CPU |Arch. |Memory|Compiler |Flags |Version |Time|Submitted |
-+============+===============+======+======+=========+==================+========+====+==============+
-|Ubuntu |Intel Core 2 |x86_64|4GB |gcc 4.1.2| |4.0.2-1 |1377| Jiří Keller |
-|gutsy |Quad Q6700 3Ghz| | | | | | | |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Debian sid |2x Dual Opteron|amd64 |12GB |gcc 4.1.1| |3.3.7-2 |1560|Yaroslav |
-| |275 2.2 Ghz | | | | | | |Halchenko |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Ubuntu edgy |2x Dual Opteron|i686 |3GB |gcc 4.1.2| |3.3.8-1 |2096|Jeff |
-| |275 2.2 GHz | | | | | | |Stevenson |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Debian lenny|Intel Core2 |i686 |2GB |gcc 4.3.1| |4.1.0-1 |2108|Michael |
-| |E8400 3Ghz | | | | | | |Hanke |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Debian etch |Quad Opteron |amd64 |32GB |gcc 3.4.6|-O3 -m64 |3.2b-4 |2152|Antti |
-| |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
-| | | | | |-mfpmath=sse | | | |
-| | | | | |-msse2 | | | |
-| | | | | |-ffast-math | | | |
-| | | | | |-funroll-all-loops| | | |
-| | | | | |-fpeel-loops | | | |
-| | | | | |-ftracer | | | |
-| | | | | |-funswitch-loops | | | |
-| | | | | |-funit-at-a-time | | | |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Debian lenny|Athlon X2 |amd64 |4GB |gcc 4.3 | |4.0.4-1 |2268|Petr |
-| |4800 2.5 GHz | | | | | | |Hluštík |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Ubuntu |Quad Core2 |amd64 |4GB |gcc 4.1 | |4.0-1 |2500|Vincent |
-|feisty |2.4 GHz | | | | | | |Ferrera |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 -m64 |3.2b-4 |2619|Antti |
-| |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
-| | | | | |-mfpmath=sse | | | |
-| | | | | |-msse2 | | | |
-| | | | | |-ffast-math | | | |
-| | | | | |-funroll-all-loops| | | |
-| | | | | |-fpeel-loops | | | |
-| | | | | |-ftracer | | | |
-| | | | | |-funswitch-loops | | | |
-| | | | | |-funit-at-a-time | | | |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 |3.2b-4 |2652|Antti |
-| |850 2.4 GHz | | | | | | |Korvenoja |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Debian etch |2x Opteron |amd64 |12GB |gcc 4.1.2| |4.0.2-3 |2847|Michael |
-| |270 2.2 GHz | | | | | | |Hanke |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-|Ubuntu gutsy|Athlon 64X2 |amd64 |2GB |gcc 4.1.3| |4.0.1 |3605|Nicholas P. |
-| |5200+ 2.6 GHz | | | | | | |Holmes |
-+------------+---------------+------+------+---------+------------------+--------+----+--------------+
-
-.. Template
- | | | | | | | | | |
- | | | | | | | | | |
- +------------+---------------+------+------+---------+------------------+--------+----+--------------+
-
-
-If you want to have your system included in this list, please send an email
-with the logfile of the benchmark. You can run the benchmark (and create the
-logfile) by running (fsl-feeds-3.2beta-3 or higher is required)::
-
- (time -p fsl-selftest -c) > benchmark.log 2>&1
-
-And include the following information in your message:
-
-* Which distribution are you using?
-
-* CPU-type (as specific as possible)
-
-* How much physical memory has the machine? If you don't know this, send the
- output of::
-
- free | head -n2 | tail -n1 | awk '{print $2}' -
-
-* If you compiled the binary packages yourself, which compiler did you use?
- (hint: `gcc --version`)
-
-* Which custom compiler flags did you use when building the package (if any)?
-
-* Which version of the Debian FSL package was used?
+++ /dev/null
-The packages are available through an APT repository You can either browse the
-archive or add this line to your `/etc/apt/sources.list`::
-
- deb http://apsy.gse.uni-magdeburg.de/debian #distro# #section#
-
-Replace `#distro#` with ..., depending on which distribution you are using.
-Note that not every package is available for all distributions. You need to
-replace #section# with the value(s) corresponding to the package(s) you are
-interested in (get it from the table below). Multiple sections are allowed.
-Please, do not forget to update your package index, e.g. by running apt-get
-update. If no binary packages are available for your distribution, you can
-still download the source packages. Simply add this to your
-`/etc/apt/sources.list` (you have to replace #distro# and #section# as
-described above)::
-
- deb-src http://apsy.gse.uni-magdeburg.de/debian #distro# #section#
-
-After the usual apt-get update you can get and build the packages with e.g.
-apt-src or whatever you like. To build e.g. dicomnifti you can do this: apt-src
-install dicomnifti
-
-This downloads the sources and installs all build-dependencies if necessary.
-You need root-privileges to install the build-dependencies, so apt-src might
-ask for a password. Now invoke: apt-src build dicomnifti
-
-This will build all binary packages which should appear in the current
-directory (if everything worked well). You can now install the packages with
-dpkg.
-
-
-
--- /dev/null
+{% extends "!layout.html" %}
+
+{% block extrahead %}
+ <meta name="keywords" content="debian, neuroscience">
+{% endblock %}
+
+{% block rootrellink %}
+ <li><a href="http://www.debian.org" target="_blank">Debian</a> | </li>
+ <li><a href="{{ pathto('index') }}">Neuroscience Repository</a> »</li>
+ <li><a href="{{ pathto('genindex') }}">Package list</a></li>
+{% endblock %}
+
+{% block sidebar1 %}
+{{ sidebar() }}
+{% endblock %}
+
+{% block sidebar2 %}
+{{ sidebar() }}
+{% endblock %}
--- /dev/null
+# Makefile for Sphinx documentation
+#
+
+# target directory
+BUILDDIR = _build
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html web pickle htmlhelp latex changes linkcheck
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " changes to make an overview over all changed/added/deprecated items"
+ @echo " linkcheck to check all external links for integrity"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ mkdir -p $(BUILDDIR)/html $(BUILDDIR)/doctrees
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+pickle:
+ mkdir -p $(BUILDDIR)/pickle $(BUILDDIR)/doctrees
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+web: pickle
+
+json:
+ mkdir -p $(BUILDDIR)/json $(BUILDDIR)/doctrees
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ mkdir -p $(BUILDDIR)/htmlhelp $(BUILDDIR)/doctrees
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+latex:
+ mkdir -p $(BUILDDIR)/latex $(BUILDDIR)/doctrees
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+ "run these through (pdf)latex."
+
+changes:
+ mkdir -p $(BUILDDIR)/changes $(BUILDDIR)/doctrees
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ mkdir -p $(BUILDDIR)/linkcheck $(BUILDDIR)/doctrees
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
--- /dev/null
+# -*- coding: utf-8 -*-
+#
+# Debian Package Repository documentation build configuration file, created by
+# sphinx-quickstart on Sat Mar 28 17:08:58 2009.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# The contents of this file are pickled, so don't put values in the namespace
+# that aren't pickleable (module imports are okay, they're removed automatically).
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If your extensions are in another directory, add it here. If the directory
+# is relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+#sys.path.append(os.path.abspath('.'))
+
+# General configuration
+# ---------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Debian Neuroscience Package Repository'
+copyright = u'2009, Michael Hanke'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = ''
+# The full version, including alpha/beta/rc tags.
+release = ''
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['pkgs_addenum']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# Options for HTML output
+# -----------------------
+
+# The style sheet to use for HTML and HTML Help pages. A file of that name
+# must exist either in Sphinx' static/ path, or in one of the custom paths
+# given in html_static_path.
+html_style = 'default.css'
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+html_title = project
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = "Debian Neuroscience"
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = 'pics/debian-imaging.jpg'
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+html_use_modindex = False
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, the reST sources are included in the HTML build as _sources/<name>.
+html_copy_source = False
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'debpkgrepo'
+
+
+# Options for LaTeX output
+# ------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, document class [howto/manual]).
+latex_documents = [
+ ('index', 'DebianPackageRepository.tex', ur'Debian Package Repository Documentation',
+ ur'Michael Hanke', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True
--- /dev/null
+.. _gpg_signatures:
+
+
+Package authentication
+======================
+
+
+When you start using this repository, you might get warning messages like this::
+
+ The following signatures couldn't be verified because
+ the public key is not available.`
+
+Or you will be asked questions like this over and over::
+
+ WARNING: The following packages cannot be authenticated!
+ ...
+ Install these packages without verification [y/N]?
+
+This is because your APT installation does not know the GPG key that is used to
+sign the release files of this repository. Making APT happy again is easy:
+
+1. Get the key. Either download the `repository key from here
+ <http://apsy.gse.uni-magdeburg.de/debian/apsy.gse.uni-magdeburg.de.asc>`_
+ or fetch it from *subkeys.pgp.net*.
+
+2. Now feed the key into APT by invoking::
+
+ apt-key add #file#
+
+ Where `#file#` has to be replaced with the location of the key file you just
+ downloaded. You need to have superuser-privileges to do this (either do it
+ as root or use sudo).
+
--- /dev/null
+***********************************************
+ Welcome to the Debian Neuroscience Repository
+***********************************************
+
+This repository provides mostly neuroscience-related packages to be
+used on Debian systems (or a Debian-derivates like Ubuntu). It
+contains both unofficial or prospective packages which are not
+available from the main Debian archive, as well backported or simply
+rebuilt packages also available elsewhere.
+
+This service is provided "as is". There is no guarantee that a package
+works as expected, so use them at your own risk. They might kill your
+system (although that is rather unlikely). You've been warned!
+
+The repository contains both neuroscience-related packages as well as
+general purpose software which is necessary to resolved dependencies, or
+is simply useful in the neuroscience context. The featured neuroscience
+software can be browsed via the repository :ref:`genindex` or through the
+:ref:`maintainer view <bymaintainer>`.
+
+All other packages are available through the search engine or from the
+:ref:`full package list <full_pkg_list>`.
+
+
+How to use this repository
+==========================
+
+The easiest way to use this repository is to download an APT-configuration
+file. Simply click on the name of your target distribution/release and save the
+downloaded file in the `/etc/apt/sources.list.d/` directory on your system
+(depending on the browser, you might have to right-click and choose 'save as').
+Saving files in this directory will require superuser privileges, therefore you
+should probably download the file into a temporary directory and subsequently
+move it into `/etc/apt/sources.list.d/`. APT-configurations are available for
+the following releases:
+
+.. include:: sources_lists
+
+Once this is done, you have to update the package index. Use your favorite
+package manager, e.g. synaptic, adept, or whatever you like. In the terminal
+you can use :command:`aptitude` to achieve the same::
+
+ sudo aptitude update
+
+Now, you can proceed to install packages, e.g.::
+
+ sudo aptitude install lipsia
+
+.. note::
+ Not every package is available for all distributions/releases. For information
+ about which package version is available for which release and architecture,
+ please have a look at the corresponding package pages.
+
+
+Package authentication
+----------------------
+
+When you start using this repository, you might get warning messages
+like this::
+
+ The following signatures couldn't be verified because
+ the public key is not available.`
+
+Or you will be asked questions like this over and over::
+
+ WARNING: The following packages cannot be authenticated!
+ ...
+ Install these packages without verification [y/N]?
+
+This is because your APT installation initially does not know the GPG
+key that is used to sign the release files of this repository. Making
+APT happy again is easy:
+
+1. Get the key. Either download the `repository key from here
+ <http://apsy.gse.uni-magdeburg.de/debian/apsy.gse.uni-magdeburg.de.asc>`_
+ or fetch it from *subkeys.pgp.net*.
+
+2. Now feed the key into APT by invoking::
+
+ apt-key add #file#
+
+ Where `#file#` has to be replaced with the location of the key file you just
+ downloaded. You need to have superuser-privileges to do this (either do it
+ as root or use sudo).
--- /dev/null
+The packages are available through an APT repository You can either browse the
+archive or add this line to your `/etc/apt/sources.list`::
+
+ deb http://apsy.gse.uni-magdeburg.de/debian #distro# #section#
+
+Replace `#distro#` with ..., depending on which distribution you are using.
+Note that not every package is available for all distributions. You need to
+replace #section# with the value(s) corresponding to the package(s) you are
+interested in (get it from the table below). Multiple sections are allowed.
+Please, do not forget to update your package index, e.g. by running apt-get
+update. If no binary packages are available for your distribution, you can
+still download the source packages. Simply add this to your
+`/etc/apt/sources.list` (you have to replace #distro# and #section# as
+described above)::
+
+ deb-src http://apsy.gse.uni-magdeburg.de/debian #distro# #section#
+
+After the usual apt-get update you can get and build the packages with e.g.
+apt-src or whatever you like. To build e.g. dicomnifti you can do this: apt-src
+install dicomnifti
+
+This downloads the sources and installs all build-dependencies if necessary.
+You need root-privileges to install the build-dependencies, so apt-src might
+ask for a password. Now invoke: apt-src build dicomnifti
+
+This will build all binary packages which should appear in the current
+directory (if everything worked well). You can now install the packages with
+dpkg.
+
+
+
projects / neurodebian.git / commitdiff
