Merge branch 'master' into orthoview_vlim

Author: effigies

.gitignore

@@ -16,6 +16,7 @@
 .project
 .pydevproject
 *.py.orig
+.DS_Store
 
 # Not sure what the next one is for
 *.kpf

.mailmap

@@ -29,6 +29,7 @@ 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 <markiewicz@stanford.edu>
+Chris Markiewicz <effigies@gmail.com> Chris Markiewicz <markiewicz@stanford.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

@@ -4,11 +4,10 @@
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
 
+dist: xenial
+sudo: true
 language: python
 
-# Run jobs on container-based infrastructure, can be overridden per job
-sudo: false
-
 cache:
   directories:
     - $HOME/.cache/pip
@@ -22,11 +21,14 @@ env:
         - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
         - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
 python:
-    - 3.4
     - 3.5
     - 3.6
+    - 3.7
 matrix:
   include:
+    - python: 3.4
+      dist: trusty
+      sudo: false
     - python: 2.7
       env:
         - COVERAGE=1

COPYING

@@ -121,36 +121,40 @@ Sphinx 0.6 doesn't work properly.
   OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
   DAMAGE.
 
-Ordereddict
+OrderedSet
 -----------
 
-In ``nibabel/externals/ordereddict.py``
+In ``nibabel/externals/oset.py``
 
-Copied from: https://pypi.python.org/packages/source/o/ordereddict/ordereddict-1.1.tar.gz#md5=a0ed854ee442051b249bfad0f638bbec
+Copied from: https://files.pythonhosted.org/packages/d6/b1/a49498c699a3fda5d635cc1fa222ffc686ea3b5d04b84a3166c4cab0c57b/oset-0.1.3.tar.gz
 
 ::
 
-  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, and others All rights reserved.
+
+    Package structured based on the one developed to odict Copyright (c) 2010, BlueDynamics Alliance, Austria
+
+    - Redistributions of source code must retain the above copyright notice, this
+      list of conditions and the following disclaimer.
+
+    - Redistributions in binary form must reproduce the above copyright notice, this
+      list of conditions and the following disclaimer in the documentation and/or
+      other materials provided with the distribution.
+
+    - Neither the name of the BlueDynamics Alliance nor the names of its
+      contributors may be used to endorse or promote products derived from this
+      software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY BlueDynamics Alliance AS IS AND ANY EXPRESS OR
+    IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+    SHALL BlueDynamics Alliance BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+    PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+    BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+    IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+    OF SUCH DAMAGE.
 
 mni_icbm152_t1_tal_nlin_asym_09a
 --------------------------------

Changelog

@@ -20,29 +20,105 @@ Nibabel releases
 
 Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
 Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan
-Gerhard (SG) and Eric Larson (EL).
+Gerhard (SG), Eric Larson (EL), Yaroslav Halchenko (YOH) and Chris Cheng (CC).
 
 References like "pr/298" refer to github pull request numbers.
 
-Upcoming Release
-================
+2.3.1 (Tuesday 16 October 2018)
+===============================
+
+New features
+------------
+* ``nib-diff`` command line tool for comparing image files (pr/617, pr/672,
+  pr/678) (CC, reviewed by YOH, Pradeep Raamana and CM)
+
+Enhancements
+------------
+* Speed up reading of numeric arrays in CIFTI2 (pr/655) (Michiel Cottaar,
+  reviewed by CM)
+* Add ``ndim`` property to ``ArrayProxy`` and ``DataobjImage`` (pr/674) (CM,
+  reviewed by MB)
+
+Bug fixes
+---------
+* Deterministic deduction of slice ordering in degenerate cases (pr/647)
+  (YOH, reviewed by CM)
+* Allow 0ms TR in MGH files (pr/653) (EL, reviewed by CM)
+* Allow for PPC64 little-endian long doubles (pr/658) (MB, reviewed by CM)
+* Correct construction of FreeSurfer annotation labels (pr/666) (CM, reviewed
+  by EL, Paul D. McCarthy)
+* Fix logic for persisting filehandles with indexed-gzip (pr/679) (Paul D.
+  McCarthy, reviewed by CM)
+
+Maintenance
+-----------
+* Fix semantic error in coordinate systems documentation (pr/646) (Ariel
+  Rokem, reviewed by CM, MB)
+* Test on Python 3.7, minor associated fixes (pr/651) (CM, reviewed by Gregory
+  R. Lee, MB)
+
+2.3 (Tuesday 12 June 2018)
+==========================
 
 New features
 ------------
+* TRK <=> TCK streamlines conversion CLI tools (pr/606) (MC, reviewed by CM)
 * Image slicing for SpatialImages (pr/550) (CM)
 
 Enhancements
 ------------
 * Simplfiy MGHImage and add footer fields (pr/569) (CM, reviewed by MB)
+* Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul
+  McCarthy, reviewed by MB, CM)
+* Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy,
+  reviewed by CM, MB)
+* Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves,
+  reviewed by CM, Satra Ghosh, MB, Tim Coalson)
+* Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed
+  by CM, MB)
+* Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri
+  Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko)
+* Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release
+  filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB)
 
 Bug fixes
 ---------
+* Preserve first point of `LazyTractogram` (pr/588) (MC, reviewed by Nil
+  Goyette, CM, MB)
+* Stop adding extraneous metadata padding (pr/593) (Jon Stutters, reviewed by
+  CM, MB)
+* Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan,
+  MB, reviewed by MB, MC, CM)
+* Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB)
+* Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro,
+  reviewed by MC, MB, Eleftherios Garyfallidis, CM)
+* Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk,
+  reviewed by MB, CM)
+* Do not crash on non-``ImportError`` failures in optional imports (pr/618)
+  (Yaroslav Halchenko, reviewed by CM)
+* Return original array from ``get_fdata`` for array image, if no cast
+  required (pr/638, MB, reviewed by CM)
 
 Maintenance
 -----------
+* Use SSH address to use key-based auth (pr/587) (CM, reviewed by MB)
+* Fix doctests for numpy 1.14 array printing (pr/591) (MB, reviewed by CM)
+* Refactor for pydicom 1.0 API changes (pr/599) (MB, reviewed by CM)
+* Increase test coverage, remove unreachable code (pr/602) (CM, reviewed by 
+  Yaroslav Halchenko, MB)
+* Move ``nib-ls`` and other programs to a new cmdline module (pr/601, pr/615)
+  (Chris Cheng, reviewed by MB, Yaroslav Halchenko)
+* Remove deprecated numpy indexing (EL, reviewed by CM)
+* Update documentation to encourage ``get_fdata`` over ``get_data`` (pr/637,
+  MB, reviewed by CM)
 
 API changes and deprecations
 ----------------------------
+* Support for ``keep_file_open = 'auto'`` as a parameter to ``Opener()`` will
+  be deprecated in 2.4, for removal in 3.0. Accordingly, support for
+  ``openers.KEEP_FILE_OPEN_DEFAULT = 'auto'`` will be dropped on the same
+  schedule.
+* Drop-in support for ``indexed_gzip < 0.7`` has been removed.
 
 
 2.2.1 (Wednesday 22 November 2017)

appveyor.yml

@@ -12,6 +12,8 @@ environment:
     - PYTHON: C:\Python35-x64
     - PYTHON: C:\Python36
     - PYTHON: C:\Python36-x64
+    - PYTHON: C:\Python37
+    - PYTHON: C:\Python37-x64
 
 install:
   # Prepend newly installed Python to the PATH of this build (this cannot be
@@ -20,8 +22,7 @@ install:
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
-  - pip install numpy scipy matplotlib nose h5py mock
-  - pip install pydicom
+  - pip install numpy scipy matplotlib nose h5py mock pydicom
   - pip install .
   - SET NIBABEL_DATA_DIR=%CD%\nibabel-data