From: Michael Hanke Date: Tue, 23 Nov 2010 18:56:41 +0000 (-0500) Subject: Cleanup. X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8bb724db8558e66f76112e8ba53a1f9cce99b502;p=neurodebian.git Cleanup. --- diff --git a/sphinx/faq.rst b/sphinx/faq.rst index fad5394..956de0e 100644 --- a/sphinx/faq.rst +++ b/sphinx/faq.rst @@ -162,5 +162,5 @@ package that is available from the NeuroDebian repository. Alternatively: as root or use sudo). -.. include:: links_names.rst -.. include:: substitutions.rst +.. include:: link_names.txt +.. include:: substitutions.txt diff --git a/sphinx/gpg.rst b/sphinx/gpg.rst deleted file mode 100644 index 43ec2d6..0000000 --- a/sphinx/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/sphinx/index.rst b/sphinx/index.rst index 0e86f0b..6ed25fa 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -268,13 +268,12 @@ efficient, more open, and more fun .. toctree:: :hidden: + datasets livecd - gpg - setup - links_names - substitutions + vm_welcome quotes-nihr01 quotes-nitrc -.. include:: links_names.rst -.. include:: substitutions.rst + +.. include:: link_names.txt +.. include:: substitutions.txt diff --git a/sphinx/link_names.txt b/sphinx/link_names.txt new file mode 100644 index 0000000..1e76ea7 --- /dev/null +++ b/sphinx/link_names.txt @@ -0,0 +1,161 @@ +.. This (-*- rst -*-) format file contains commonly used link targets + and name substitutions. It may be included in many files, + therefore it should only contain link targets and name + substitutions. Try grepping for "^\.\. _" to find plausible + candidates for this list. + +.. NOTE: reST targets are + __not_case_sensitive__, so only one target definition is needed for + nipy, NIPY, Nipy, etc... + +.. _nipy: http://neuroimaging.scipy.org +.. _nipype: http://nipy.sourceforge.net/nipype +.. _`Brain Imaging Center`: http://bic.berkeley.edu/ +.. _dipy: http://nipy.sourceforge.net/dipy +.. _`dipy github`: http://github.com/Garyfallidis/dipy +.. _nibabel: http://nipy.sourceforge.net/nibabel +.. _dipy: http://nipy.sourceforge.net/dipy + +.. Documentation tools +.. _graphviz: http://www.graphviz.org/ +.. _Sphinx: http://sphinx.pocoo.org/ +.. _`Sphinx reST`: http://sphinx.pocoo.org/rest.html +.. _reST: http://docutils.sourceforge.net/rst.html +.. _docutils: http://docutils.sourceforge.net + +.. Licenses +.. _GPL: http://www.gnu.org/licenses/gpl.html +.. _BSD: http://www.opensource.org/licenses/bsd-license.php +.. _LGPL: http://www.gnu.org/copyleft/lesser.html + +.. Source control +.. _git: http://git-scm.com/ +.. _github: http://github.com +.. _github help: http://help.github.com +.. _msysgit: http://code.google.com/p/msysgit/downloads/list +.. _git-osx-installer: http://code.google.com/p/git-osx-installer/downloads/list +.. _bazaar: http://bazaar-vcs.org/ + +.. Other working process +.. _pynifti: http://niftilib.sourceforge.net/pynifti/ +.. _nifticlibs: http://nifti.nimh.nih.gov +.. _nifti: http://nifti.nimh.nih.gov +.. _`nipy launchpad`: https://launchpad.net/nipy +.. _launchpad: https://launchpad.net/ +.. _`nipy trunk`: https://code.launchpad.net/~nipy-developers/nipy/trunk +.. _`nipy mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel +.. _`nipy bugs`: https://bugs.launchpad.net/nipy +.. _pep8: http://www.python.org/dev/peps/pep-0008/ +.. _`numpy coding style`: http://scipy.org/scipy/numpy/wiki/CodingStyleGuidelines + +.. Code support stuff +.. _pychecker: http://pychecker.sourceforge.net/ +.. _pylint: http://www.logilab.org/project/pylint +.. _pyflakes: http://divmod.org/trac/wiki/DivmodPyflakes +.. _virtualenv: http://pypi.python.org/pypi/virtualenv +.. _flymake: http://flymake.sourceforge.net/ +.. _rope: http://rope.sourceforge.net/ +.. _pymacs: http://pymacs.progiciels-bpi.ca/pymacs.html +.. _ropemacs: http://rope.sourceforge.net/ropemacs.html +.. _ECB: http://ecb.sourceforge.net/ +.. _emacs_python_mode: http://www.emacswiki.org/cgi-bin/wiki/PythonMode +.. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/ +.. _nose: http://somethingaboutorange.com/mrl/projects/nose +.. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html + +.. Other python projects +.. _numpy: http://www.scipy.org/NumPy +.. _scipy: http://www.scipy.org +.. _ipython: http://ipython.scipy.org +.. _`ipython manual`: http://ipython.scipy.org/doc/manual/html +.. _matplotlib: http://matplotlib.sourceforge.net +.. _pythonxy: http://www.pythonxy.com +.. _ETS: http://code.enthought.com/projects/tool-suite.php +.. _`Enthought Tool Suite`: http://code.enthought.com/projects/tool-suite.php +.. _python: http://www.python.org +.. _mayavi: http://mayavi.sourceforge.net/ +.. _sympy: http://code.google.com/p/sympy/ + +.. Python imaging projects +.. _PyMVPA: http://www.pymvpa.org +.. _BrainVISA: http://brainvisa.info +.. _anatomist: http://brainvisa.info +.. _pydicom: http://code.google.com/p/pydicom/ + +.. Not so python imaging projects +.. _matlab: http://www.mathworks.com +.. _spm: http://www.fil.ion.ucl.ac.uk/spm +.. _spm8: http://www.fil.ion.ucl.ac.uk/spm/software/spm8 +.. _eeglab: http://sccn.ucsd.edu/eeglab +.. _AFNI: http://afni.nimh.nih.gov/afni +.. _FSL: http://www.fmrib.ox.ac.uk/fsl +.. _FreeSurfer: http://surfer.nmr.mgh.harvard.edu +.. _voxbo: http://www.voxbo.org +.. _mricron: http://www.cabiatl.com/mricro/mricron +.. _slicer: http://www.slicer.org/ + +.. File formats +.. _DICOM: http://medical.nema.org/ +.. _`wikipedia DICOM`: http://en.wikipedia.org/wiki/Digital_Imaging_and_Communications_in_Medicine +.. _GDCM: http://sourceforge.net/apps/mediawiki/gdcm +.. _`DICOM specs`: ftp://medical.nema.org/medical/dicom/2009/ +.. _`DICOM object definitions`: ftp://medical.nema.org/medical/dicom/2009/09_03pu3.pdf +.. _dcm2nii: http://www.cabiatl.com/mricro/mricron/dcm2nii.html +.. _`mricron install`: http://www.cabiatl.com/mricro/mricron/install.html +.. _dicom2nrrd: http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.4 +.. _Nrrd: http://teem.sourceforge.net/nrrd/format.html + +.. General software +.. _gcc: http://gcc.gnu.org +.. _xcode: http://developer.apple.com/TOOLS/xcode +.. _mingw: http://www.mingw.org +.. _cygwin: http://cygwin.com +.. _macports: http://www.macports.org/ +.. _VTK: http://www.vtk.org/ +.. _ITK: http://www.itk.org/ +.. _swig: http://www.swig.org +.. _NeuroDebian: http://neuro.debian.net +.. _Debian: http://www.debian.org +.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy +.. _`Debian Med`: http://debian-med.alioth.debian.org +.. _`Debian Science`: http://wiki.debian.org/DebianScience + +.. Functional imaging labs +.. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk +.. _FMRIB: http://www.fmrib.ox.ac.uk + +.. Other organizations +.. _enthought: +.. _kitware: http://www.kitware.com +.. _nitrc: http://www.nitrc.org + +.. General information links +.. _`wikipedia FMRI`: http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging +.. _`wikipedia PET`: http://en.wikipedia.org/wiki/Positron_emission_tomography + +.. Mathematical methods +.. _`wikipedia ICA`: http://en.wikipedia.org/wiki/Independent_component_analysis +.. _`wikipedia PCA`: http://en.wikipedia.org/wiki/Principal_component_analysis + +.. Mathematical ideas +.. _`wikipedia spherical coordinate system`: http://en.wikipedia.org/wiki/Spherical_coordinate_system +.. _`mathworld spherical coordinate system`: http://mathworld.wolfram.com/SphericalCoordinates.html +.. _`wikipedia affine`: http://en.wikipedia.org/wiki/Affine_transformation +.. _`wikipedia linear transform`: http://en.wikipedia.org/wiki/Linear_transformation +.. _`wikipedia rotation matrix`: http://en.wikipedia.org/wiki/Rotation_matrix +.. _`wikipedia homogenous coordinates`: http://en.wikipedia.org/wiki/Homogeneous_coordinates +.. _`wikipedia axis angle`: http://en.wikipedia.org/wiki/Axis_angle +.. _`wikipedia Euler angles`: http://en.wikipedia.org/wiki/Euler_angles +.. _`Mathworld Euler angles`: http://mathworld.wolfram.com/EulerAngles.html +.. _`wikipedia quaternion`: http://en.wikipedia.org/wiki/Quaternion +.. _`wikipedia shear matrix`: http://en.wikipedia.org/wiki/Shear_matrix +.. _`wikipedia reflection`: http://en.wikipedia.org/wiki/Reflection_(mathematics) +.. _`wikipedia direction cosine`: http://en.wikipedia.org/wiki/Direction_cosine + +.. Homepages +.. _yoh: http://www.onerussian.com +.. _mih: http://mih.voxindeserto.de + +.. Debian specifics +.. _ITP: http://www.debian.org/devel/wnpp +.. _ITPs: http://www.debian.org/devel/wnpp diff --git a/sphinx/links_names.rst b/sphinx/links_names.rst deleted file mode 100644 index 1e76ea7..0000000 --- a/sphinx/links_names.rst +++ /dev/null @@ -1,161 +0,0 @@ -.. This (-*- rst -*-) format file contains commonly used link targets - and name substitutions. It may be included in many files, - therefore it should only contain link targets and name - substitutions. Try grepping for "^\.\. _" to find plausible - candidates for this list. - -.. NOTE: reST targets are - __not_case_sensitive__, so only one target definition is needed for - nipy, NIPY, Nipy, etc... - -.. _nipy: http://neuroimaging.scipy.org -.. _nipype: http://nipy.sourceforge.net/nipype -.. _`Brain Imaging Center`: http://bic.berkeley.edu/ -.. _dipy: http://nipy.sourceforge.net/dipy -.. _`dipy github`: http://github.com/Garyfallidis/dipy -.. _nibabel: http://nipy.sourceforge.net/nibabel -.. _dipy: http://nipy.sourceforge.net/dipy - -.. Documentation tools -.. _graphviz: http://www.graphviz.org/ -.. _Sphinx: http://sphinx.pocoo.org/ -.. _`Sphinx reST`: http://sphinx.pocoo.org/rest.html -.. _reST: http://docutils.sourceforge.net/rst.html -.. _docutils: http://docutils.sourceforge.net - -.. Licenses -.. _GPL: http://www.gnu.org/licenses/gpl.html -.. _BSD: http://www.opensource.org/licenses/bsd-license.php -.. _LGPL: http://www.gnu.org/copyleft/lesser.html - -.. Source control -.. _git: http://git-scm.com/ -.. _github: http://github.com -.. _github help: http://help.github.com -.. _msysgit: http://code.google.com/p/msysgit/downloads/list -.. _git-osx-installer: http://code.google.com/p/git-osx-installer/downloads/list -.. _bazaar: http://bazaar-vcs.org/ - -.. Other working process -.. _pynifti: http://niftilib.sourceforge.net/pynifti/ -.. _nifticlibs: http://nifti.nimh.nih.gov -.. _nifti: http://nifti.nimh.nih.gov -.. _`nipy launchpad`: https://launchpad.net/nipy -.. _launchpad: https://launchpad.net/ -.. _`nipy trunk`: https://code.launchpad.net/~nipy-developers/nipy/trunk -.. _`nipy mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel -.. _`nipy bugs`: https://bugs.launchpad.net/nipy -.. _pep8: http://www.python.org/dev/peps/pep-0008/ -.. _`numpy coding style`: http://scipy.org/scipy/numpy/wiki/CodingStyleGuidelines - -.. Code support stuff -.. _pychecker: http://pychecker.sourceforge.net/ -.. _pylint: http://www.logilab.org/project/pylint -.. _pyflakes: http://divmod.org/trac/wiki/DivmodPyflakes -.. _virtualenv: http://pypi.python.org/pypi/virtualenv -.. _flymake: http://flymake.sourceforge.net/ -.. _rope: http://rope.sourceforge.net/ -.. _pymacs: http://pymacs.progiciels-bpi.ca/pymacs.html -.. _ropemacs: http://rope.sourceforge.net/ropemacs.html -.. _ECB: http://ecb.sourceforge.net/ -.. _emacs_python_mode: http://www.emacswiki.org/cgi-bin/wiki/PythonMode -.. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/ -.. _nose: http://somethingaboutorange.com/mrl/projects/nose -.. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html - -.. Other python projects -.. _numpy: http://www.scipy.org/NumPy -.. _scipy: http://www.scipy.org -.. _ipython: http://ipython.scipy.org -.. _`ipython manual`: http://ipython.scipy.org/doc/manual/html -.. _matplotlib: http://matplotlib.sourceforge.net -.. _pythonxy: http://www.pythonxy.com -.. _ETS: http://code.enthought.com/projects/tool-suite.php -.. _`Enthought Tool Suite`: http://code.enthought.com/projects/tool-suite.php -.. _python: http://www.python.org -.. _mayavi: http://mayavi.sourceforge.net/ -.. _sympy: http://code.google.com/p/sympy/ - -.. Python imaging projects -.. _PyMVPA: http://www.pymvpa.org -.. _BrainVISA: http://brainvisa.info -.. _anatomist: http://brainvisa.info -.. _pydicom: http://code.google.com/p/pydicom/ - -.. Not so python imaging projects -.. _matlab: http://www.mathworks.com -.. _spm: http://www.fil.ion.ucl.ac.uk/spm -.. _spm8: http://www.fil.ion.ucl.ac.uk/spm/software/spm8 -.. _eeglab: http://sccn.ucsd.edu/eeglab -.. _AFNI: http://afni.nimh.nih.gov/afni -.. _FSL: http://www.fmrib.ox.ac.uk/fsl -.. _FreeSurfer: http://surfer.nmr.mgh.harvard.edu -.. _voxbo: http://www.voxbo.org -.. _mricron: http://www.cabiatl.com/mricro/mricron -.. _slicer: http://www.slicer.org/ - -.. File formats -.. _DICOM: http://medical.nema.org/ -.. _`wikipedia DICOM`: http://en.wikipedia.org/wiki/Digital_Imaging_and_Communications_in_Medicine -.. _GDCM: http://sourceforge.net/apps/mediawiki/gdcm -.. _`DICOM specs`: ftp://medical.nema.org/medical/dicom/2009/ -.. _`DICOM object definitions`: ftp://medical.nema.org/medical/dicom/2009/09_03pu3.pdf -.. _dcm2nii: http://www.cabiatl.com/mricro/mricron/dcm2nii.html -.. _`mricron install`: http://www.cabiatl.com/mricro/mricron/install.html -.. _dicom2nrrd: http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.4 -.. _Nrrd: http://teem.sourceforge.net/nrrd/format.html - -.. General software -.. _gcc: http://gcc.gnu.org -.. _xcode: http://developer.apple.com/TOOLS/xcode -.. _mingw: http://www.mingw.org -.. _cygwin: http://cygwin.com -.. _macports: http://www.macports.org/ -.. _VTK: http://www.vtk.org/ -.. _ITK: http://www.itk.org/ -.. _swig: http://www.swig.org -.. _NeuroDebian: http://neuro.debian.net -.. _Debian: http://www.debian.org -.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy -.. _`Debian Med`: http://debian-med.alioth.debian.org -.. _`Debian Science`: http://wiki.debian.org/DebianScience - -.. Functional imaging labs -.. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk -.. _FMRIB: http://www.fmrib.ox.ac.uk - -.. Other organizations -.. _enthought: -.. _kitware: http://www.kitware.com -.. _nitrc: http://www.nitrc.org - -.. General information links -.. _`wikipedia FMRI`: http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging -.. _`wikipedia PET`: http://en.wikipedia.org/wiki/Positron_emission_tomography - -.. Mathematical methods -.. _`wikipedia ICA`: http://en.wikipedia.org/wiki/Independent_component_analysis -.. _`wikipedia PCA`: http://en.wikipedia.org/wiki/Principal_component_analysis - -.. Mathematical ideas -.. _`wikipedia spherical coordinate system`: http://en.wikipedia.org/wiki/Spherical_coordinate_system -.. _`mathworld spherical coordinate system`: http://mathworld.wolfram.com/SphericalCoordinates.html -.. _`wikipedia affine`: http://en.wikipedia.org/wiki/Affine_transformation -.. _`wikipedia linear transform`: http://en.wikipedia.org/wiki/Linear_transformation -.. _`wikipedia rotation matrix`: http://en.wikipedia.org/wiki/Rotation_matrix -.. _`wikipedia homogenous coordinates`: http://en.wikipedia.org/wiki/Homogeneous_coordinates -.. _`wikipedia axis angle`: http://en.wikipedia.org/wiki/Axis_angle -.. _`wikipedia Euler angles`: http://en.wikipedia.org/wiki/Euler_angles -.. _`Mathworld Euler angles`: http://mathworld.wolfram.com/EulerAngles.html -.. _`wikipedia quaternion`: http://en.wikipedia.org/wiki/Quaternion -.. _`wikipedia shear matrix`: http://en.wikipedia.org/wiki/Shear_matrix -.. _`wikipedia reflection`: http://en.wikipedia.org/wiki/Reflection_(mathematics) -.. _`wikipedia direction cosine`: http://en.wikipedia.org/wiki/Direction_cosine - -.. Homepages -.. _yoh: http://www.onerussian.com -.. _mih: http://mih.voxindeserto.de - -.. Debian specifics -.. _ITP: http://www.debian.org/devel/wnpp -.. _ITPs: http://www.debian.org/devel/wnpp diff --git a/sphinx/setup.rst b/sphinx/setup.rst deleted file mode 100644 index 1c6e2e5..0000000 --- a/sphinx/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/spread.rst b/sphinx/spread.rst index 46c8c17..f09c390 100644 --- a/sphinx/spread.rst +++ b/sphinx/spread.rst @@ -46,5 +46,5 @@ banner by using following HTML code for a corresponding image: -.. include:: links_names.rst -.. include:: substitutions.rst +.. include:: link_names.txt +.. include:: substitutions.txt diff --git a/sphinx/substitutions.rst b/sphinx/substitutions.rst deleted file mode 100644 index ac70f4f..0000000 --- a/sphinx/substitutions.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. Substitutions for the whole doc tree - -.. |team| replace:: :ref:`NeuroDebian team ` -.. |we| replace:: :ref:`we ` -.. |spread| replace:: :ref:`spread the word about NeuroDebian ` -.. |repos| replace:: :ref:`NeuroDebian repositories ` -.. |exppsy| replace:: Experimental Psychology diff --git a/sphinx/substitutions.txt b/sphinx/substitutions.txt new file mode 100644 index 0000000..ac70f4f --- /dev/null +++ b/sphinx/substitutions.txt @@ -0,0 +1,7 @@ +.. Substitutions for the whole doc tree + +.. |team| replace:: :ref:`NeuroDebian team ` +.. |we| replace:: :ref:`we ` +.. |spread| replace:: :ref:`spread the word about NeuroDebian ` +.. |repos| replace:: :ref:`NeuroDebian repositories ` +.. |exppsy| replace:: Experimental Psychology