Merge remote-tracking branch 'upstream/master' into enh/cifti2

* upstream/master:
  WIP: debugging round trip error
  BF: add requirements.txt to MANIFEST.in
  TST: Add sdist, wheel & requirements INSTALL_TYPEs
  TST: Travis with pydicom > 0.9.9 git commit
  BF: Prepare for pydicom 1.0
  DOC: include all copyright information in greyed box.
  DOC: change URL to numpy docstring style guide (partial fix for #376)
  DOC: fix openhub.net badge (#378), prevent overflow of sidebar content.
  DOC: Add six copyright (#375)
  DOC: remove trailing sentence
  RF: remove doctest string markup
  TST: enable Python 3.5 tests
  RF+API: TripWireError subclasses AttributeError

Author: satra

.travis.yml

@@ -21,11 +21,13 @@ 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
@@ -39,20 +41,37 @@ 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 [ "${COVERAGE}" == "1" ]; then
@@ -61,7 +80,21 @@ before_install:
       fi
 # command to install dependencies
 install:
-    - python setup.py install
+    - |
+      if [ "$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

COPYING

@@ -128,27 +128,29 @@ In ``nibabel/externals/ordereddict.py``
 
 Copied from: https://pypi.python.org/packages/source/o/ordereddict/ordereddict-1.1.tar.gz#md5=a0ed854ee442051b249bfad0f638bbec
 
-Copyright (c) 2009 Raymond Hettinger
-
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation files
-(the "Software"), to deal in the Software without restriction,
-including without limitation the rights to use, copy, modify, merge,
-publish, distribute, sublicense, and/or sell copies of the Software,
-and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-    The above copyright notice and this permission notice shall be
-    included in all copies or substantial portions of the Software.
-
-    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-    HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-    WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-    OTHER DEALINGS IN THE SOFTWARE.
+::
+
+  Copyright (c) 2009 Raymond Hettinger
+
+  Permission is hereby granted, free of charge, to any person
+  obtaining a copy of this software and associated documentation files
+  (the "Software"), to deal in the Software without restriction,
+  including without limitation the rights to use, copy, modify, merge,
+  publish, distribute, sublicense, and/or sell copies of the Software,
+  and to permit persons to whom the Software is furnished to do so,
+  subject to the following conditions:
+
+      The above copyright notice and this permission notice shall be
+      included in all copies or substantial portions of the Software.
+
+      THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+      EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+      OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+      NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+      HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+      WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+      FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+      OTHER DEALINGS IN THE SOFTWARE.
 
 mni_icbm152_t1_tal_nlin_asym_09a
 --------------------------------
@@ -158,6 +160,8 @@ The file ``doc/source/someone.nii.gz`` is a subsampled version of the file
 archive ``mni_icbm152_t1_tal_nlin_asym_09a``.  The original image has the
 following license (where 'softwware' refers to the image):
 
+::
+
     Copyright (C) 1993-2004 Louis Collins, McConnell Brain Imaging Centre,
     Montreal Neurological Institute, McGill University.
 
@@ -209,3 +213,34 @@ the PDDL version 1.0 available at http://opendatacommons.org/licenses/pddl/1.0/
 
 is courtesy of the University of Massachusetts Medical School, also released
 under the PDDL.
+
+
+Six
+--------------------
+
+In ``nibabel/externals/six.py``
+
+Copied from: https://pypi.python.org/packages/source/s/six/six-1.3.0.tar.gz#md5=ec47fe6070a8a64c802363d2c2b1e2ee
+
+::
+
+    Copyright (c) 2010-2013 Benjamin Peterson
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy of
+    this software and associated documentation files (the "Software"), to deal in
+    the Software without restriction, including without limitation the rights to
+    use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+    the Software, and to permit persons to whom the Software is furnished to do so,
+    subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in all
+    copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+    FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+    COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+    IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+

Changelog

@@ -34,6 +34,12 @@ References like "pr/298" refer to github pull request numbers.
     are raising a DataError if the track is truncated when ``strict=True``
     (the default), rather than a TypeError when trying to create the points
     array.
+  * 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)
 

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/_static/nibabel.css

@@ -31,3 +31,8 @@ div.footer {
 div.body {
     background-color: white;
 }
+
+.sphinxsidebarwrapper {
+    /* don't let anything exceed sidebar boundaries */
+    overflow: hidden;
+}

doc/source/_templates/indexsidebar.html

@@ -6,7 +6,7 @@ <h3>Quick links</h3>
     <li><a href="https://mail.python.org/pipermail/neuroimaging">Mailing list archive</a></li>
 </ul>
 
-<script type="text/javascript" src="https://www.ohloh.net/projects/480908/widgets/project_partner_badge"></script>
+<script type='text/javascript' src='https://www.openhub.net/p/nibabel/widgets/project_thin_badge?format=js'></script>
 
 <h3>Search mailing list archive</h3>
 <script type="text/javascript">

doc/source/devel/devguide.rst

@@ -28,7 +28,7 @@ Code Documentation
 
 All documentation should be written using Numpy documentation conventions:
 
-  http://projects.scipy.org/numpy/wiki/CodingStyleGuidelines#docstring-standard
+  https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard
 
 
 Git Repository

doc/source/dicom/dcm2nii_algorithms.rst

@@ -89,7 +89,4 @@ Sort compares two dicom images, call them ``dcm1`` and ``dcm2``.   Tests are:
 
 Next remove repeated values as found in the first step above.
 
-There's a function ``
-
-
 .. include:: ../links_names.txt

nibabel/nicom/dicomwrappers.py

@@ -49,10 +49,13 @@ def wrapper_from_file(file_like, *args, **kwargs):
     dcm_w : ``dicomwrappers.Wrapper`` or subclass
        DICOM wrapper corresponding to DICOM data type
     """
-    import dicom
+    try:
+        from dicom import read_file
+    except ImportError:
+        from pydicom.dicomio import read_file
 
     with ImageOpener(file_like) as fobj:
-        dcm_data = dicom.read_file(fobj, *args, **kwargs)
+        dcm_data = read_file(fobj, *args, **kwargs)
     return wrapper_from_data(dcm_data)
 
 

nibabel/nicom/tests/test_csareader.py

@@ -31,7 +31,10 @@ def test_csa_header_read():
     assert_true(csa.is_mosaic(hdr))
     # Get a shallow copy of the data, lacking the CSA marker
     # Need to do it this way because del appears broken in pydicom 0.9.7
-    from dicom.dataset import Dataset
+    try:
+        from dicom.dataset import Dataset
+    except ImportError:
+        from pydicom.dataset import Dataset
     data2 = Dataset()
     for element in DATA:
         if (element.tag.group, element.tag.elem) != (0x29, 0x10):