renaming links_names to have .rst suffix + adding substitutions

diff --git a/sphinx/links_names.rst b/sphinx/links_names.rst
new file mode 100644 (file)
index 0000000..09da4bb
--- /dev/null
+++ b/sphinx/links_names.rst
@@ -0,0 +1,154 @@
+.. 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
+.. _`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: :ref:`welcome`
+.. _Debian: http://www.debian.org
+.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy
+
+.. Functional imaging labs
+.. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk
+.. _FMRIB: http://www.fmrib.ox.ac.uk
+
+.. Other organizations
+.. _enthought: <http://www.enthought.com>
+.. _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

diff --git a/sphinx/links_names.txt b/sphinx/links_names.txt
deleted file mode 100644 (file)
index 09da4bb..0000000
--- a/sphinx/links_names.txt
+++ /dev/null
@@ -1,154 +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
-.. _`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: :ref:`welcome`
-.. _Debian: http://www.debian.org
-.. _exppsy: http://alioth.debian.org/projects/pkg-exppsy
-
-.. Functional imaging labs
-.. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk
-.. _FMRIB: http://www.fmrib.ox.ac.uk
-
-.. Other organizations
-.. _enthought: <http://www.enthought.com>
-.. _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

diff --git a/sphinx/substitutions.rst b/sphinx/substitutions.rst
new file mode 100644 (file)
index 0000000..0db563e
--- /dev/null
+++ b/sphinx/substitutions.rst
@@ -0,0 +1,4 @@
+.. Substitutions for the whole doc tree
+
+.. |team| replace:: :ref:`chap_team`
+.. |repos| replace:: :ref:`repository_howto`