From: Michael Hanke Date: Tue, 28 Apr 2009 15:38:18 +0000 (+0200) Subject: Refactored into sphinx, addenum and reblender (separate). X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e21c44a50e6f32ddf033641819960b305bd70b32;p=neurodebian.git Refactored into sphinx, addenum and reblender (separate). --- diff --git a/Makefile b/Makefile index a903a1b..45071d8 100644 --- a/Makefile +++ b/Makefile @@ -1,94 +1,34 @@ -# 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 \ diff --git a/pkgs/fsl.rst b/pkgs/fsl.rst new file mode 100644 index 0000000..440420f --- /dev/null +++ b/pkgs/fsl.rst @@ -0,0 +1,263 @@ +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 ` 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? diff --git a/reblender b/reblender index 7176271..3afd33a 100755 --- a/reblender +++ b/reblender @@ -663,7 +663,7 @@ def writePkgsBy(db, key, value2id, outdir, heading): toc.close() -def writeRst(db, outdir): +def writeRst(db, outdir, addenum_dir=None): createDir(outdir) createDir(os.path.join(outdir, 'pkgs')) @@ -680,8 +680,10 @@ def writeRst(db, outdir): 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) @@ -719,6 +721,9 @@ def prepOptParser(op): 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") @@ -744,7 +749,7 @@ def main(): 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 ') diff --git a/source/.templates/layout.html b/source/.templates/layout.html deleted file mode 100644 index 4e231dc..0000000 --- a/source/.templates/layout.html +++ /dev/null @@ -1,19 +0,0 @@ -{% extends "!layout.html" %} - -{% block extrahead %} - -{% endblock %} - -{% block rootrellink %} -
  • Debian | 
    • -
  • Neuroscience Repository »
    • -
  • Package list
    • -{% endblock %} - -{% block sidebar1 %} -{{ sidebar() }} -{% endblock %} - -{% block sidebar2 %} -{{ sidebar() }} -{% endblock %} diff --git a/source/conf.py b/source/conf.py deleted file mode 100644 index d850bb2..0000000 --- a/source/conf.py +++ /dev/null @@ -1,190 +0,0 @@ -# -*- 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 -# " v 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/. -html_copy_source = False - -# If true, an OpenSearch description file will be output, and all pages will -# contain a 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 diff --git a/source/gpg.rst b/source/gpg.rst deleted file mode 100644 index 43ec2d6..0000000 --- a/source/gpg.rst +++ /dev/null @@ -1,33 +0,0 @@ -.. _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 - `_ - 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). - diff --git a/source/index.rst b/source/index.rst deleted file mode 100644 index 1ad9ceb..0000000 --- a/source/index.rst +++ /dev/null @@ -1,84 +0,0 @@ -*********************************************** - 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 `. - -All other packages are available through the search engine or from the -:ref:`full package 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 - `_ - 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). diff --git a/source/pics/debian-imaging.jpg b/source/pics/debian-imaging.jpg deleted file mode 100644 index bb1dcdf..0000000 Binary files a/source/pics/debian-imaging.jpg and /dev/null differ diff --git a/source/pkgs_addenum/fsl.rst b/source/pkgs_addenum/fsl.rst deleted file mode 100644 index 440420f..0000000 --- a/source/pkgs_addenum/fsl.rst +++ /dev/null @@ -1,263 +0,0 @@ -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 ` 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 | | | | | | |HluÅ¡tík | -+------------+---------------+------+------+---------+------------------+--------+----+--------------+ -|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? diff --git a/source/setup.rst b/source/setup.rst deleted file mode 100644 index 1c6e2e5..0000000 --- a/source/setup.rst +++ /dev/null @@ -1,31 +0,0 @@ -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. - - - diff --git a/sphinx/.templates/layout.html b/sphinx/.templates/layout.html new file mode 100644 index 0000000..4e231dc --- /dev/null +++ b/sphinx/.templates/layout.html @@ -0,0 +1,19 @@ +{% extends "!layout.html" %} + +{% block extrahead %} + +{% endblock %} + +{% block rootrellink %} +
  • Debian | 
    • +
  • Neuroscience Repository »
    • +
  • Package list
    • +{% endblock %} + +{% block sidebar1 %} +{{ sidebar() }} +{% endblock %} + +{% block sidebar2 %} +{{ sidebar() }} +{% endblock %} diff --git a/sphinx/Makefile b/sphinx/Makefile new file mode 100644 index 0000000..fd47aff --- /dev/null +++ b/sphinx/Makefile @@ -0,0 +1,78 @@ +# 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 ' where 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." diff --git a/sphinx/conf.py b/sphinx/conf.py new file mode 100644 index 0000000..d850bb2 --- /dev/null +++ b/sphinx/conf.py @@ -0,0 +1,190 @@ +# -*- 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 +# " v 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/. +html_copy_source = False + +# If true, an OpenSearch description file will be output, and all pages will +# contain a 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 diff --git a/sphinx/gpg.rst b/sphinx/gpg.rst new file mode 100644 index 0000000..43ec2d6 --- /dev/null +++ b/sphinx/gpg.rst @@ -0,0 +1,33 @@ +.. _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 + `_ + 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). + diff --git a/sphinx/index.rst b/sphinx/index.rst new file mode 100644 index 0000000..1ad9ceb --- /dev/null +++ b/sphinx/index.rst @@ -0,0 +1,84 @@ +*********************************************** + 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 `. + +All other packages are available through the search engine or from the +:ref:`full package 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 + `_ + 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). diff --git a/sphinx/pics/debian-imaging.jpg b/sphinx/pics/debian-imaging.jpg new file mode 100644 index 0000000..bb1dcdf Binary files /dev/null and b/sphinx/pics/debian-imaging.jpg differ diff --git a/sphinx/setup.rst b/sphinx/setup.rst new file mode 100644 index 0000000..1c6e2e5 --- /dev/null +++ b/sphinx/setup.rst @@ -0,0 +1,31 @@ +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. + + +