matthew-brett · jonathan-taylor · Oct 5, 2012 · Oct 10, 2012 · Oct 10, 2012 · Oct 11, 2012
diff --git a/.travis.yml b/.travis.yml
@@ -10,6 +10,7 @@ env:
     - PYTHON=python PYSUF=''
     - PYTHON=python3 PYSUF=3
 install:
+    - sudo apt-get update
     - sudo apt-get install $PYTHON-dev
     - sudo apt-get install $PYTHON-numpy
     - sudo apt-get install $PYTHON-scipy
@@ -22,7 +23,7 @@ install:
     - if [ "${PYSUF}" == "3" ]; then
         git clone git://github.com/sympy/sympy.git _sympy ;
         cd _sympy ;
-        git checkout -b 0.7.2 origin/0.7.2 ;
+        git checkout -b 0.7.2 sympy-0.7.2 ;
         python3 ./bin/use2to3 ;
         cd py3k-sympy ;
         sudo python3 setup.py install ;
@@ -37,4 +38,4 @@ script:
     # Change into an innocuous directory and find tests from installation
     - mkdir for_test
     - cd for_test
-    - $PYTHON ../tools/nipnost `$PYTHON -c "import os; import nipy; print(os.path.dirname(nipy.__file__))"`
+    - $PYTHON ../tools/nipnost -A "not slow" `$PYTHON -c "import os; import nipy; print(os.path.dirname(nipy.__file__))"`
diff --git a/AUTHOR b/AUTHOR
@@ -14,4 +14,5 @@ Mike Trumpis
 Tim Leslie
 Tom Waite
 Virgile Fritsch <[email protected]>
+Yannick Schwartz <[email protected]>
 Yaroslav Halchenko <[email protected]>
diff --git a/Changelog b/Changelog
@@ -22,6 +22,40 @@ The full VCS changelog is available here:
 Releases
 ~~~~~~~~
 
+Abbreviated authors are:
+
+* MB - Matthew Brett
+* BT - Bertrand Thirion
+* AR - Alexis Roche
+* GV - Gaël Varoquaux
+* YH - Yarik Halchenko
+
+* 0.3.0 (Saturday 2 February 2013)
+
+  * Bugfix, refactoring and compatibility release
+  * Addition of EM algorithm for mixed effects analysis (BT)
+  * New high-level GLM class interface (BT)
+  * nipy diagnostic scripts save PCA and tsdifana vectors to npz file
+  * Python 3 compatibility through 3.3 (MB)
+  * Fixes for compatibility with upcoming Numpy 1.7
+  * Fixes to background and axis specification in visualization tools (GV, BT)
+  * Fixes and tests for installed nipy scripts (MB)
+  * Fix to optimization parameters for Realign4D - thanks to `bpinsard`
+  * Fix 0 in affine diagonal for TR=0 in affines by default (MB)
+  * Allow saving of nipy images loaded from nifti files that lack explicit
+    affine (MB)
+  * Allow `slice_order=None` to `FmriRealign4D` when not doing time
+    interpolation (AR); check for valid slice order specification (YR)
+  * Refactoring of quantile routine to move code out of C library (AR)
+  * Fix bug in resampling of unsigned int images (AR)
+  * Custom doctest machinery to work round differences of dtype repr on
+    different platforms, and to skip doctests with optional dependencies (MB)
+  * Script to run examples for testing (MB)
+  * Fix for accidental integer division of frametimes in design matrix
+    generation (Fabian Pedregosa)
+  * Various other fixes and refactorings with thanks from (AR, BT, MB, YR,
+    Yannick Schwartz, Virgile Fritsch)
+
 * 0.2.0 (Sunday 22 July 2012)
 
   * The first ever official release

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2006-2012, NIPY Developers
+Copyright (c) 2006-2013, NIPY Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/Makefile b/Makefile
@@ -101,5 +101,9 @@ tox-stale:
 	# installed)
 	tox -e python25,python26,python27,python32,np-1.2.1
 
+recythonize:
+	# Recythonize all pyx files
+	find . -name "*.pyx" -exec cython -I libcstat/wrapper {} \;
+
 .PHONY: orig-src pylint
 
diff --git a/README.rst b/README.rst
@@ -54,14 +54,14 @@ You can find our sources and single-click downloads:
 .. _main repository: http://github.com/nipy/nipy
 .. _Documentation: http://nipy.org/nipy
 .. _current trunk: http://github.com/nipy/nipy/archives/master
-.. _available releases: http://github.com/nipy/nipy/downloads
+.. _available releases: http://pypi.python.org/pypi/nipy
 
 Dependencies
 ============
 
 To run NIPY, you will need:
 
-* python_ >= 2.5.  We don't yet run on python 3, sad to say.
+* python_ >= 2.5 (tested with 2.5, 2.6, 2.7, 3.2, 3.3)
 * numpy_ >= 1.2
 * scipy_ >= 0.7.0
 * sympy_ >= 0.6.6

diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html
@@ -31,13 +31,13 @@ <h4> Site Navigation </h4>
 <h4> NIPY Community </h4>
   <ul class="simple">
     <li><a class="reference external"
-	href="http://nipy.sourceforge.net/">Community Home</a></li>
+	href="http://nipy.org/">Community Home</a></li>
     <li><a class="reference external"
-	href="http://nipy.sourceforge.net/software/projects/">NIPY Projects</a></li>
+	href="http://nipy.org/software/projects/">NIPY Projects</a></li>
     <li><a class="reference external"
 	href="http://mail.scipy.org/mailman/listinfo/nipy-devel">Mailing List</a></li>
     <li><a class="reference external"
-	href="http://nipy.sourceforge.net/software/license/index.html">License</a></li>
+	href="http://nipy.org/software/license/index.html">License</a></li>
   </ul>
 
 <h4> Github repo </h4>

diff --git a/doc/conf.py b/doc/conf.py
@@ -60,7 +60,7 @@
 project = 'nipy'
 
 #copyright = ':ref:`2005-2010, Neuroimaging in Python team. <nipy-software-license>`'
-copyright = '2005-2012, Neuroimaging in Python team'
+copyright = '2005-2013, Neuroimaging in Python team'
 
 # The default replacements for |version| and |release|, also used in various
 # other places throughout the built documents.

diff --git a/doc/devel/code_discussions/comparisons/vtk_datasets.rst b/doc/devel/code_discussions/comparisons/vtk_datasets.rst
@@ -5,7 +5,7 @@
 Here we describe the VTK dataset model, because of some parallels with
 our own idea of an image object.  The document is from the VTK book - [VTK4]_
 
-See also: 
+See also:
 
 * http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/data.html#vtk-data-structures 
 * http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/auto/example_datasets.html
@@ -45,14 +45,13 @@ refers to, you can identify the element.
 
 >>> pts = vtk.vtkPoints()
 >>> id = pts.InsertNextPoint(0, 0, 0)
->>> id
-0
+>>> id == 0
+True
 >>> id = pts.InsertNextPoint(0, 1, 0)
->>> id
-1
->>> pts.GetPoint(1)
-(0.0, 1.0, 0.0)
-
+>>> id == 1
+True
+>>> pts.GetPoint(1) == (0.0, 1.0, 0.0)
+True
 
 A dataset has one or more points
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -91,8 +90,8 @@ True
 >>> triangle.GetCellType() == VTK_TRIANGLE
 True
 >>> pt_ids = triangle.GetPointIds() # these are default (zeros) at the moment
->>> [pt_ids.GetId(i) for i in range(pt_ids.GetNumberOfIds())]
-[0, 0, 0]
+>>> [pt_ids.GetId(i) for i in range(pt_ids.GetNumberOfIds())] == [0, 0, 0]
+True
 
 Here we set the ids.  The ids refer to the points above.  The system
 does not know this yet, but it will because, later, we are going to