Merge branch 'master' into debian

* master:
  DOC: Final pass through docs. Added NEWS section to frontpage.
  RF: Removed duplicate classifier from warehouse and minor doc typo fix.
  BF: SMLR in pylab_2d was plotting reverse answer.

doc/examples/clfs_examples.py

@@ -7,7 +7,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Examples demonstrating varioius classifiers on different datasets"""
+"""Examples demonstrating various classifiers on different datasets"""
 
 from mvpa.suite import *
 

doc/examples/pylab_2d.py

@@ -83,7 +83,7 @@
         # get out the values used for the prediction
         res = N.asarray(clf.values)
     elif c == 'SMLR':
-        res = N.asarray(clf.values[:, 0])
+        res = N.asarray(clf.values[:, 1])
     else:
         # get the probabilities from the svm
         res = N.asarray([(q[1][1] - q[1][0] + 1) / 2

doc/faq.txt

@@ -19,6 +19,7 @@ Frequently Asked Questions
 General
 =======
 
+.. index:: optimization
 
 It is sloooooow. What can I do?
 -------------------------------
@@ -66,6 +67,8 @@ I feel like I want to contribute something, do you mind?
   the PyMVPA mailing list.
 
 
+.. index:: Git, development
+
 I want to develop a new feature for PyMVPA. How can I do it efficiently?
 ------------------------------------------------------------------------
 
@@ -138,6 +141,7 @@ The manual is quite insufficient. When will you improve it?
 Data preprocessing
 ==================
 
+.. index:: invariant features
 
 Is there an easy way to remove invariant features from a dataset?
 -----------------------------------------------------------------
@@ -152,6 +156,8 @@ Is there an easy way to remove invariant features from a dataset?
   `removeInvariantFeatures()` that strips such features from a dataset.
 
 
+.. index:: block-averaging
+
 How can I do block-averaging of my block-design fMRI dataset?
 -------------------------------------------------------------
 
@@ -182,6 +188,7 @@ How can I do block-averaging of my block-design fMRI dataset?
 Data analysis
 =============
 
+.. index:: feature selection, feature_ids
 
 How do I know which features were finally selected by a classifier doing feature selection?
 -------------------------------------------------------------------------------------------

doc/index.txt

@@ -26,6 +26,15 @@ Alioth_, a service that is kindly provided by the `Debian project`_.
 .. _Debian project: http://www.debian.org
 
 
+News
+====
+
+  PyMVPA 0.3 is out [18 Aug 2008]
+
+    It contains a number of new features (additional mappers, initial support
+    for plotting, more examples, ...), bugfixes and improved documentation. See
+    the :ref:`changelog <changelog>` for details.
+
 
 Documentation
 =============
@@ -37,7 +46,7 @@ Documentation
   code)
 * `API Reference`_ (comprehensive and up-to-date information about the details
   of the implementation)
-* :ref:`FAQ <faq>`
+* :ref:`FAQ <faq>` (short answers to common problems)
 * :ref:`genindex` (access by keywords)
 * :ref:`search` (online and offline full-text search)
 

doc/installation.txt

@@ -15,12 +15,16 @@ Installation
 
 This section covers the necessary steps to install and run PyMVPA. It contains
 a comprehensive list of software dependencies, as well as recommendation for
-additional software packages that further enhance the functionality provided by PyMVPA.
+additional software packages that further enhance the functionality provided by
+PyMVPA.
 
 
 Dependencies
 ============
 
+
+.. index:: required software, NumPy
+
 Must Have
 ---------
 
@@ -38,7 +42,7 @@ The following software packages are required or PyMVPA will not work at all.
 .. _NumPy: http://numpy.scipy.org/
 .. _ctypes: http://python.net/crew/theller/ctypes/
 
-.. index:: recommendations, SciPy, PyNIfTI, Shogun, R, RPy
+.. index:: recommended software, SciPy, PyNIfTI, Shogun, R, RPy
 
 
 Strong Recommendations
@@ -71,7 +75,7 @@ recommended to install these packages as well.
 .. _R: http://www.r-project.org
 
 
-.. index:: suggestions, IPython, FSL, AFNI, LIBSVM
+.. index:: suggested software, IPython, FSL, AFNI, LIBSVM, matplotlib, hlcuster
 
 
 Suggestions
@@ -173,7 +177,7 @@ package.
 .. _repository at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
 .. _package repository instructions: http://apsy.gse.uni-magdeburg.de/main/index.psp?sec=1&page=hanke/debian&lang=en
 
-
+.. index:: Windows, Windows installer
 .. _install_win:
 
 
@@ -202,12 +206,14 @@ Import the mvpa module, which should cause no error messages.
   >>>
 
 Although you have a working installation already, most likely you want to
-install some additional software. First and foremost install SciPy_ -- download from the same page where you also got the NumPy installer.
+install some additional software. First and foremost install SciPy_ -- download
+from the same page where you also got the NumPy installer.
 
 If you want to use PyMVPA to analyze fMRI datasets, you probably also want to
 install PyNIfTI_. Download the corresponding installer from the website of the
 `NIfTI libraries`_ and install it. PyNIfTI does not come with the required
-`zlib` library, so you also need to download and install it. A binary installer is available from the `GnuWin32 project`_. Install it in some arbitrary folder
+`zlib` library, so you also need to download and install it. A binary installer
+is available from the `GnuWin32 project`_. Install it in some arbitrary folder
 (just the binaries nothing else), find the `zlib1.dll` file in the `bin`
 subdirectory and move it in the Windows `system32` directory. Verify that it
 works by importing the `nifti` module in Python.
@@ -228,7 +234,7 @@ which are shipped with the source code in the `doc/examples` directory.
 .. _NIfTI libraries: http://niftilib.sourceforge.net/
 .. _GnuWin32 project: http://gnuwin32.sourceforge.net/
 
-
+.. index:: OpenSUSE
 .. _install_suse:
 
 
@@ -275,7 +281,7 @@ snapshot_ (i.e. the current state of the *master* branch of the PyMVPA source
 code repository).
 
 .. _snapshot:  http://git.debian.org/?p=pkg-exppsy/pymvpa.git;a=snapshot;h=refs/heads/master;sf=tgz
-.. index:: Git repository
+.. index:: Git, Git repository
 
 If you want to have access to both, the full PyMVPA history and the latest
 development code, you can use the PyMVPA Git_ repository, which is publicly
@@ -294,6 +300,8 @@ working directory, that contains the PyMVPA repository.
 
 .. _Git: http://git.or.cz/
 
+.. index:: build instructions
+
 
 Build it (General instructions)
 -------------------------------
@@ -382,7 +390,7 @@ extension and therefore also requires the patched LIBSVM version and SWIG to be
 available.
 
 
-.. index:: citation, PyMVPA poster
+.. index:: building on Windows
 
 
 Building on Windows Systems
@@ -436,6 +444,7 @@ as described :ref:`above <install_win>`.
 .. _MSYS: http://www.mingw.org/msys.shtml
 
 
+.. index:: OpenSUSE
 .. _build_suse:
 
 

doc/intro.txt

@@ -151,9 +151,7 @@ faster and easier than it has ever been before.
 .. _Per B. Sederberg: http://www.princeton.edu/~persed/
 
 
-.. _requirements:
-.. index:: requirements
-
+.. index:: citation, PyMVPA poster
 
 How to cite PyMVPA
 ==================

doc/matlab.txt

@@ -20,6 +20,7 @@ Matlab and NumPy`_.
 
 .. _basic comparison of Matlab and NumPy: http://www.scipy.org/NumPy_for_Matlab_Users
 
+.. index:: MVPA toolbox for Matlab
 
 It would be nice to have some guidelines on how to use PyMVPA for users who are
 already familiar with the `Matlab MVPA toolbox`_. If you are using both

mvpa/clfs/warehouse.py

@@ -289,7 +289,6 @@ def items(self):
 # GPR
 clfs += GPR(kernel=KernelLinear(), descr="GPR(kernel='linear')")
 clfs += GPR(kernel=KernelSquaredExponential(), descr="GPR(kernel='sqexp')")
-clfs += BLR(descr="BLR()")
 
 # BLR
 clfs += BLR(descr="BLR()")