Merge remote branch 'nipy/master'

Conflicts:
	doc/source/manual.rst

Author: mih

doc/source/index.rst

@@ -18,6 +18,7 @@ Documentation
 * :ref:`Developer discussions <chap_devdiscuss>` (arcane discussions about code
   design)
 * :ref:`Development Changelog <changelog>` (see what has changed)
+* :ref:`DICOM concepts <dicom>` (details about implementing DICOM reading)
 * :ref:`genindex` (access by keywords)
 * :ref:`search` (online and offline full-text search)
 

doc/source/installation.rst

@@ -13,18 +13,40 @@
 Installation
 ************
 
-It should be easy to get NiBabel running on any system. For the most popular
-platforms and operating systems there are binary packages provided in the
-respective native packaging format (DEB, RPM or installers). On all other
-systems NiBabel has to be compiled from source -- which should also be pretty
-straightforward.
+NiBabel is a pure python package at the moment, and it should be easy to get
+NiBabel running on any system. For the most popular platforms and operating
+systems there should be packages in the respective native packaging format
+(DEB, RPM or installers). On other systems you can install NiBabel using
+``easy_install`` or by downloading the source package and running the usual
+``python setup.py install``.
 
-To run all of the tests, you may need some extra data packages - see
-:ref:`installing-data`. 
+.. This remark below is not yet true; comment to avoid confusion
+   To run all of the tests, you may need some extra data packages - see
+   :ref:`installing-data`.
 
 Installer and packages
 ======================
 
+.. _install_pypi:
+
+The python package index
+------------------------
+
+NiBabel is available via `pypi`_.  If you already have setuptools_ or
+distribute_ installed, you can run::
+
+    easy_install nibabel
+
+to download nibabel and its dependencies.  Alternatively go to the `nibabel
+pypi`_ page and select the source distribution you want.  Download the
+distribution, unpack it, and then, from the unpacked directory, run::
+
+    python setup.py install
+
+or (if you need root permission to install on a unix system)::
+
+    sudo python setup.py install
+
 .. _install_debian:
 
 Debian/Ubuntu
@@ -37,21 +59,23 @@ installing NiBabel is::
   apt-get update
   apt-get install python-nibabel
 
-.. _NeuroDebian package: http://neuro.debian.net/pkgs/python-nibabel-snapshot.html
-
-
+.. _NeuroDebian package: http://neuro.debian.net/pkgs/python-nibabel.html
 
 Install from source
 ===================
 
 If no installer or package is provided for your platfom, you can install
-NiBabel from source. It needs a few things to run properly:
+NiBabel from source.
 
-*  Python_ 2.5 or greater
-*  NumPy_
-*  SciPy_ (for SPM-ANALYZE support)
-*  PyDICOM_ (for DICOM support)
+Requirements
+------------
 
+*  Python_ 2.5 or greater
+*  NumPy_ 1.2 or greater
+*  SciPy_ (for full SPM-ANALYZE support)
+*  PyDICOM_ 0.9.5 or greater (for DICOM support)
+*  nose_ 0.11 or greater (to run the tests)
+*  sphinx_ (to build the documentation)
 
 Get the sources
 ---------------
@@ -66,8 +90,13 @@ If you want to have access to the full NiBabel history and the latest
 development code, do a full clone (aka checkout) of the NiBabel
 repository::
 
+  git clone git://github.com/nipy/nibabel.git
+
+or::
+
   git clone http://github.com/nipy/nibabel.git
 
+(The first will be faster, the second more likely to work behind a firewall).
 
 Installation
 ------------

doc/source/links_names.txt

@@ -1,19 +1,32 @@
-.. This (-*- rst -*-) format file contains commonly used link targets
+.. -*- rst -*-
+.. vim: ft=rst
+
+.. 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://nipy.org
+.. nibabel
+.. _nibabel: http://nipy.org/nibabel
+.. _`nibabel github`: http://github.com/nipy/nibabel
+.. _`nibabel mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
+.. _nibabel pypi: http://pypi.python.org/pypi/nibabel
+
+.. other related projects
+.. _nipy community: http://nipy.org
+.. _nipy: http://nipy.org/nipy
 .. _`Brain Imaging Center`: http://bic.berkeley.edu/
 .. _dipy: http://nipy.org/dipy
 .. _`dipy github`: http://github.com/Garyfallidis/dipy
-.. _nibabel: http://nipy.sourceforge.net/nibabel
-.. _nipy development guidelines: http://nipy.sourceforge.net/devel
+.. _nibabel: http://nipy.org/nibabel
+.. _nipy development guidelines: http://nipy.org/devel
+.. _`nipy github`: http://github.com/nipy/nipy
 
 .. Documentation tools
 .. _graphviz: http://www.graphviz.org/
@@ -28,6 +41,9 @@
 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
 .. _MIT License: http://www.opensource.org/licenses/mit-license.php
 
+.. Installation
+.. _pypi: http://pypi.python.org/pypi
+
 .. Working process
 .. _pynifti: http://niftilib.sourceforge.net/pynifti/
 .. _nifticlibs: http://nifti.nimh.nih.gov
@@ -36,10 +52,9 @@
 .. _sourceforge: http://nipy.sourceforge.net/
 .. _`nipy launchpad`: https://launchpad.net/nipy
 .. _launchpad: https://launchpad.net/
-.. _`nipy trunk`: https://code.launchpad.net/~nipy-developers/nipy/trunk
+.. _`nipy trunk`: http://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
-.. _nibabel github: http://github.com/hanke/nibabel
 .. _sourceforge download page: http://sourceforge.net/projects/nipy/files
 
 .. Code support stuff
@@ -65,6 +80,8 @@
 .. _numpy: http://www.scipy.org/NumPy
 .. _scipy: http://www.scipy.org
 .. _ipython: http://ipython.scipy.org
+.. _`ipython github`: http://github.com/ipython/ipython
+.. _`ipython mailing list`: http://mail.scipy.org/mailman/listinfo/IPython-dev
 .. _`ipython manual`: http://ipython.scipy.org/doc/manual/html
 .. _matplotlib: http://matplotlib.sourceforge.net
 .. _pythonxy: http://www.pythonxy.com
@@ -76,6 +93,7 @@
 .. _sympy: http://code.google.com/p/sympy/
 .. _networkx: http://networkx.lanl.gov/
 .. _setuptools: http://pypi.python.org/pypi/setuptools
+.. _distribute: http://packages.python.org/distribute
 
 .. Python imaging projects
 .. _PyMVPA: http://www.pymvpa.org
@@ -124,6 +142,7 @@
 .. _enthought: <http://www.enthought.com>
 .. _kitware: http://www.kitware.com
 .. _NeuroDebian: http://neuro.debian.net
+.. _nitrc: http://www.nitrc.org
 
 .. General information links
 .. _`wikipedia FMRI`: http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging

doc/source/manual.rst

@@ -9,6 +9,5 @@ NiBabel Manual
   installation
   gettingstarted
   installing_data
-  dicom/dicom
   legal
   changelog