Merge pull request #377 from effigies/candidate2.0.2

REL: Bugfix release 2.0.2

Author: effigies

.mailmap

@@ -29,3 +29,5 @@ Basile Pinsard <basile.pinsard@gmail.com> bpinsard <bpinsard@imed.jussieu.fr>
 Nguyen, Ly <nguyen60@seattleu.edu> lxn2 <lxn2@uw.edu>
 Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
+Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@gmail.com>
+Chris Markiewicz <effigies@gmail.com> Chris Johnson <effigies@bu.edu>

.travis.yml

@@ -8,11 +8,13 @@ env:
     global:
         - DEPENDS="numpy scipy matplotlib h5py"
         - PYDICOM=1
+        - INSTALL_TYPE="setup"
 python:
     - 2.6
     - 3.2
     - 3.3
     - 3.4
+    - 3.5
 matrix:
   include:
     - python: 2.7
@@ -26,20 +28,37 @@ matrix:
     - python: 2.7
       env:
         - DEPENDS="numpy==1.5.1 pydicom==0.9.7"
+    # pydicom 1.0 (currently unreleased)
+    - python: 2.7
+      env:
+        - PYDICOM="v1.0"
     # Documentation doctests
     - python: 2.7
       env:
         - DOC_DOC_TEST=1
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=sdist
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=wheel
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=requirements
 before_install:
+    - source tools/travis_tools.sh
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install nose # always
-    - pip install --no-index -f http://travis-wheels.scikit-image.org $DEPENDS
+    - pip install -U pip  # upgrade to latest pip to find 3.5 wheels
+    - retry pip install nose # always
+    - wheelhouse_pip_install $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
         if [ "$PYDICOM" == "1" ]; then
             pip install pydicom;
+        elif [ "$PYDICOM" == "v1.0" ]; then
+            pip install git+https://github.com/darcymason/pydicom.git@43f278444d5cb2e4648135d3edcd430c363c6975;
         fi
       fi
     - if [ "${COVERAGE}" == "1" ]; then
@@ -51,7 +70,21 @@ before_install:
       fi
 # command to install dependencies
 install:
-    - python setup.py install
+    - |
+      if [ "$INSTALL_TYPE" == "setup" ]; then
+          python setup.py install
+      elif [ "$INSTALL_TYPE" == "sdist" ]; then
+          python setup_egg.py egg_info  # check egg_info while we're here
+          python setup_egg.py sdist
+          wheelhouse_pip_install dist/*.tar.gz
+      elif [ "$INSTALL_TYPE" == "wheel" ]; then
+          pip install wheel
+          python setup_egg.py bdist_wheel
+          wheelhouse_pip_install dist/*.whl
+      elif [ "$INSTALL_TYPE" == "requirements" ]; then
+          wheelhouse_pip_install -r requirements.txt
+          python setup.py install
+      fi
     # Point to nibabel data directory
     - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 # command to run tests, e.g. python setup.py test

Changelog

@@ -24,6 +24,25 @@ and Stephan Gerhard (SG).
 
 References like "pr/298" refer to github pull request numbers.
 
+* 2.0.2 (Monday 23 November 2015)
+
+  * Fix for integer overflow on large images (pr/325) (MB);
+  * Fix for Freesurfer nifti files with unusual dimensions (pr/332) (Chris
+    Markiewicz);
+  * Fix typos on benchmarks and tests (pr/336, pr/340, pr/347) (Chris
+    Markiewicz);
+  * Fix Windows install script (pr/339) (MB);
+  * Support for Python 3.5 (pr/363) (MB) and numpy 1.10 (pr/358) (Chris
+    Markiewicz);
+  * Update pydicom imports to permit version 1.0 (pr/379) (Chris Markiewicz);
+  * Workaround for Python 3.5.0 gzip regression (pr/383) (Ben Cipollini).
+  * tripwire.TripWire object now raises subclass of AttributeError when trying
+    to get an attribute, rather than a direct subclass of Exception.  This
+    prevents Python 3.5 triggering the tripwire when doing inspection prior to
+    running doctests.
+  * Minor API change for tripwire.TripWire object; code that checked for
+    AttributeError will now also catch TripWireError.
+
 * 2.0.1 (Saturday 27 June 2015)
 
   Contributions from Ben Cipollini, Chris Markiewicz, Alexandre Gramfort,

MANIFEST.in

@@ -1,5 +1,5 @@
 include AUTHOR COPYING Makefile* MANIFEST.in setup* README.*
-include Changelog TODO
+include Changelog TODO requirements.txt
 recursive-include doc *
 recursive-include bin *
 recursive-include tools *

doc/source/devel/advanced_testing.rst

@@ -0,0 +1,32 @@
+.. -*- mode: rst -*-
+.. ex: set sts=4 ts=4 sw=4 et tw=79:
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+  #
+  #   See COPYING file distributed along with the NiBabel package for the
+  #   copyright and license terms.
+  #
+  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+.. _advanced_testing:
+
+************
+Advanced Testing
+************
+
+Setup
+-----
+
+Before running advanced tests, please update all submodules of nibabel, by running ``git submodule update --init``
+
+
+Long-running tests
+------------------
+
+Long-running tests are not enabled by default, and can be resource-intensive. To run these tests:
+
+* Set environment variable ``NIPY_EXTRA_TESTS=slow``
+* Run ``nosetests``.
+
+Note that some tests may require a machine with >4GB of RAM.
+
+.. include:: ../links_names.txt

doc/source/devel/index.rst

@@ -14,3 +14,4 @@ Developer documentation page
     add_image_format
     devdiscuss
     make_release
+    advanced_testing

doc/source/devel/make_release.rst

@@ -130,11 +130,9 @@ Release checklist
 * Check on different platforms, particularly windows and PPC. Look at the
   `nipy buildbot`_ automated test runs for this.
 
-* Check the documentation doctests::
+* Check the documentation doctests (forcing Python 2)::
 
-    cd doc
-    make doctest
-    cd ..
+    make -C doc doctest SPHINXBUILD="python $(which sphinx-build)"
 
   This should also be tested by `nibabel on travis`_.
 

doc/source/index.rst

@@ -47,7 +47,7 @@ contributed code and discussion (in rough order of appearance):
 * Bago Amirbekian
 * Brendan Moloney
 * Félix C. Morency
-* Chris Johnson
+* Chris Markiewicz
 * JB Poline
 * Nolan Nichols
 * Nguyen, Ly
@@ -61,8 +61,7 @@ contributed code and discussion (in rough order of appearance):
 * Demian Wassermann
 * Philippe Gervais
 * Justin Lecher
-* Ben Cippolini
-* Chris Markiewicz
+* `Ben Cipollini`_
 * Clemens C. C. Bauer
 
 License reprise

doc/source/installation.rst

@@ -114,7 +114,11 @@ Just install the modules by invoking::
 If sudo is not configured (or even installed) you might have to use
 ``su`` instead.
 
-Now fire up Python and try importing the module to see if everything is fine.
+
+Validating your install
+-----------------------
+
+For a basic test of your installation, fire up Python and try importing the module to see if everything is fine.
 It should look something like this::
 
     Python 2.7.8 (v2.7.8:ee879c0ffa11, Jun 29 2014, 21:07:35)
@@ -123,4 +127,9 @@ It should look something like this::
     >>> import nibabel
     >>>
 
+
+To run the nibabel test suite, from the terminal run ``nosetests nibabel`` or ``python -c "import nibabel; nibabel.test()``.
+
+To run an extended test suite that validates ``nibabel`` for long-running and resource-intensive cases, please see :ref:`advanced_testing`.
+
 .. include:: links_names.txt

doc/source/links_names.txt

@@ -5,7 +5,7 @@
    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.  
+   candidates for this list.
 
 
 .. NOTE: reST targets are
@@ -233,6 +233,7 @@
 .. _Michael Hanke: http://mih.voxindeserto.de
 .. _Gaël Varoquaux: http://gael-varoquaux.info/
 .. _Stephan Gerhard: http://www.unidesign.ch
+.. _Ben Cipollini: http://bcipolli.github.io/
 
 .. Substitutions
 .. |emdash| unicode:: U+02014