Merge pull request #424 from matthew-brett/prepare-0.4.1

matthew-brett · web-flow · commit acbf364b0865 · 2017-02-10T13:30:45.000Z
MAINT: updating docs for release
diff --git a/AUTHOR b/AUTHOR
@@ -1,6 +1,7 @@
 Alexis Roche <alexis.roche@gmail.com>
 Ariel Rokem <arokem@gmail.com>
 Bertrand Thirion <bertrand.thirion@inria.fr>
+Benjamin Thyreau
 Brian Hawthrorne
 Ben Cipollini <ben.cipollini@gmail.com>
 Chris Burns <cburns@berkeley.edu>
@@ -14,6 +15,7 @@ Jarrod Millman <jarrod.millman@gmail.com>
 Jean-Baptiste Poline <jbpoline@gmail.com>
 Jonathan Taylor <jonathan.taylor@stanford.edu>
 Matthew Brett <matthew.brett@gmail.com>
+Matteo Visconti dOC <matteo.visconti.gr@dartmouth.edu>
 Merlin Keller
 Michael Waskom
 Mike Trumpis
diff --git a/Changelog b/Changelog
@@ -32,9 +32,30 @@ Abbreviated authors are:
 * JBP - Jean-Baptiste Poline
 * JT - Jonathan Taylor
 
+* 0.4.1 (Monday 6 February 2017)
+
+  Bugfix, refactoring and compatibility release.
+
+  * New discrete cosine transform functions for building basis sets;
+  * Fixes for compatibility with Python 3.6;
+  * Fixes for compatibility with Numpy 1.12 (1.12 no longer allows floating
+    point values for indexing and other places where an integer value is
+    required);
+  * Fixes for compatibility with Sympy 1.0;
+  * Drop compatibility with Python 2.6, 3.2, 3.3;
+  * Add ability to pass plotting arguments to ``plot_anat`` function (Matteo
+    Visconti dOC);
+  * Some helpers for working with OpenFMRI datasets;
+  * Signal upcoming change in return shape from ``make_recarray`` when passing
+    in an array for values. Allow user to select upcoming behavior with
+    keyword argument;
+  * Bug fix for axis selection when using record arrays in numpies <= 1.7.1;
+  * Add flag to allow SpaceTimeRealign to read TR from image headers;
+
 * 0.4.0 (Saturday 18 October 2015)
 
-  * Bugfix, refactoring and compatibility release;
+  Bugfix, refactoring and compatibility release.
+
   * Full port to Python 3 using single code-base;
   * Various fixes for modern numpy, scipy, sympy, nibabel compatibility;
   * Refactor space-time realignment (AR);
@@ -62,7 +83,8 @@ Abbreviated authors are:
 
 * 0.3.0 (Saturday 2 February 2013)
 
-  * Bugfix, refactoring and compatibility release
+  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
@@ -88,7 +110,7 @@ Abbreviated authors are:
 
 * 0.2.0 (Sunday 22 July 2012)
 
-  * The first ever official release
+  The first ever official release.
 
     - > 30 contributors
     - > 6 years in development
diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2006-2015, NIPY Developers
+Copyright (c) 2006-2017, NIPY Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
diff --git a/README.rst b/README.rst
@@ -65,7 +65,7 @@ You can find our sources and single-click downloads:
 * Download the `current development version`_ as a tar/zip file;
 * Downloads of all `available releases`_.
 
-.. _main repository: http://github.com/nipy/nipy
+.. _main repository: https://github.com/nipy/nipy
 .. _Documentation: http://nipy.org/nipy
 .. _current development version: https://github.com/nipy/nipy/archive/master.zip
 .. _available releases: http://pypi.python.org/pypi/nipy
@@ -74,7 +74,12 @@ Tests
 =====
 
 To run nipy's tests, you will need to install the nose_ Python testing
-package.  Then::
+package.  If you are using Python 2.7, you will also need to install the mock_
+testing package - e.g.::
+
+    pip install nose mock
+
+Then::
 
     python -c "import nipy; nipy.test()"
 
@@ -113,6 +118,7 @@ You will probably also like to have:
 .. _matplotlib: http://matplotlib.org
 .. _mayavi: http://code.enthought.com/projects/mayavi/
 .. _nose: http://nose.readthedocs.org/en/latest
+.. _mock: https://pypi.python.org/pypi/mock
 
 License
 =======
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 = '2005-2015, Neuroimaging in Python team'
+copyright = '2005-2017, 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/guidelines/make_release.rst b/doc/devel/guidelines/make_release.rst
@@ -71,7 +71,39 @@ Release checklist
   in a python 2 and python 3 virtualenv.  Review the output in (e.g.)
   ``~/tmp/eg_logs``. The output file ``summary.txt`` will have the pass file
   printout that the ``run_log_examples.py`` script puts onto stdout while
-  running.
+  running.  You can run the examples via the buildbot by triggering builds
+  for:
+
+  * https://nipy.bic.berkeley.edu/builders/nipy-examples-2.7
+  * https://nipy.bic.berkeley.edu/builders/nipy-examples-3.4
+
+  The matching outputs appear at:
+
+  * https://nipy.bic.berkeley.edu/nipy-examples-2.7
+  * https://nipy.bic.berkeley.edu/nipy-examples-3.4
+
+  I use the following commands to get the output to my laptop and review with
+  vim::
+
+    PY_VER=2.7
+    BB_SSH=buildbot@nipy.bic.berkeley.edu
+    scp -r ${BB_SSH}:nibotmi/public_html/nipy-examples-${PY_VER} .
+    cd nipy-examples-${PY_VER}
+    # Delete empty files
+    find . -size 0 -exec rm {} \;
+    # Review stderr; :bd to close buffer once reviewed
+    vim *.stderr
+    # Review stdout
+    vim *.stdout
+    cd ..
+
+  Likewise for::
+
+    PY_VER=3.4
+
+  I also did a by-eye comparison between the 2.7 and 3.4 files with::
+
+    diff -r nipy-examples-2.7 nipy-examples-3.4 | less
 
 * Do a final check on the `nipy buildbot`_
 
diff --git a/doc/users/install_data.rst b/doc/users/install_data.rst
@@ -51,33 +51,35 @@ things from Windows powershell.
 
   Call that directory ``<nipy-user>``.  Let's imagine that, for you, this is
   ``~/.nipy``.
-* If that directory does not exist already, create it, e.g.::
+* Make a subdirectory ``nipy`` in your ``<nipy-user>`` directory.  In
+  Unix you could use::
 
-    mkdir ~/.nipy
+    mkdir -p ~/.nipy/nipy
 
-* Make a directory in ``<nipy-user>`` called ``nipy``, e.g.::
-
-    mkdir ~/.nipy/nipy
+  where the ``-p`` flag tells Unix to make any necessary parent directories.
 
 * Go to http://nipy.org/data-packages
-* Download the latest *nipy-templates* and *nipy-data* packages
-* Unpack both these into some directory, e.g.::
+* Download the latest *nipy-templates* and *nipy-data* packages, to some
+  directory.  You can do this via the GUI, or on the command line (in Unix)::
+
+    cd ~/Downloads
+    curl -OL http://nipy.org/data-packages/nipy-templates-0.2.tar.gz
+    curl -OL http://nipy.org/data-packages/nipy-data-0.2.tar.gz
+
+* Unpack both of these::
 
-    mkdir data
-    cd data
-    tar zxvf ~/Downloads/nipy-data-0.2.tar.gz
-    tar zxvf ~/Downloads/nipy-templates-0.2.tar.gz
+    tar zxvf nipy-data-0.2.tar.gz
+    tar zxvf nipy-templates-0.2.tar.gz
 
 * After you have unpacked the templates, you will have a directory called
   something like ``nipy-templates-0.2``.  In that directory you should see a
   subdirectory called ``templates``.  Copy / move / link the ``templates``
   subdirectory into ``<nipy-user>/nipy``, so you now have a directory
-  ``<nipy-user>/nipy/templates``.  From unpacking the data, you should also have
-  a directory like ``nipy-data-0.2`` with a subdirectory ``data``.  Copy / move
-  / link that ``data`` directory into ``<nipy-user>/nipy`` as well.  For
-  example::
+  ``<nipy-user>/nipy/templates``.  From unpacking the data, you should also
+  have a directory like ``nipy-data-0.2`` with a subdirectory ``data``.  Copy
+  / move / link that ``data`` directory into ``<nipy-user>/nipy`` as well.
+  For example::
 
-    cd data
     cp -r nipy-data-0.2/data ~/.nipy/nipy
     cp -r nipy-templates-0.2/templates ~/.nipy/nipy
 
@@ -89,10 +91,10 @@ things from Windows powershell.
 
     (<nibabel.data.VersionedDatasource object at 0x101f8e410>, <nibabel.data.VersionedDatasource object at 0x10044b110>)
 
-  If it shows ``Bomber`` objects instead, something is wrong.  Go back and check
-  that you have the nipy home directory right, and that you have directories
-  ``<nipy-user>/nipy/data`` and ``<nipy-user>/nipy/templates>``, and that each
-  of these two directories have a file ``config.ini`` in them.
+  If it shows ``Bomber`` objects instead, something is wrong.  Go back and
+  check that you have the nipy home directory right, and that you have
+  directories ``<nipy-user>/nipy/data`` and ``<nipy-user>/nipy/templates>``,
+  and that each of these two directories have a file ``config.ini`` in them.
 
 The more general way
 ====================
diff --git a/nipy/info.py b/nipy/info.py
@@ -91,7 +91,7 @@
 * Download the `current development version`_ as a tar/zip file;
 * Downloads of all `available releases`_.
 
-.. _main repository: http://github.com/nipy/nipy
+.. _main repository: https://github.com/nipy/nipy
 .. _Documentation: http://nipy.org/nipy
 .. _current development version: https://github.com/nipy/nipy/archive/master.zip
 .. _available releases: http://pypi.python.org/pypi/nipy
@@ -100,7 +100,12 @@
 =====
 
 To run nipy's tests, you will need to install the nose_ Python testing
-package.  Then::
+package.  If you are using Python 2.7, you will also need to install the mock_
+testing package - e.g.::
+
+    pip install nose mock
+
+Then::
 
     python -c "import nipy; nipy.test()"
 
@@ -139,6 +144,7 @@
 .. _matplotlib: http://matplotlib.org
 .. _mayavi: http://code.enthought.com/projects/mayavi/
 .. _nose: http://nose.readthedocs.org/en/latest
+.. _mock: https://pypi.python.org/pypi/mock
 
 License
 =======

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-Copyright (c) 2006-2015, NIPY Developers`
	`1`	`+Copyright (c) 2006-2017, NIPY Developers`
`2`	`2`	`All rights reserved.`
`3`	`3`
`4`	`4`	`Redistribution and use in source and binary forms, with or without`