Merge pull request #708 from nipy/rel/2.3.2

REL: 2.3.2

Author: effigies

.travis.yml

@@ -96,7 +96,7 @@ before_install:
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install -U pip wheel  # needed at one point
+    - pip install -U pip setuptools>=27.0 wheel
     - retry pip install nose flake8 mock  # always
     - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
     - if [ "${COVERAGE}" == "1" ]; then

Changelog

@@ -24,6 +24,45 @@ Gerhard (SG), Eric Larson (EL), Yaroslav Halchenko (YOH) and Chris Cheng (CC).
 
 References like "pr/298" refer to github pull request numbers.
 
+2.3.2 (Wedmesday 2 January 2019)
+================================
+
+Enhancements
+------------
+* Enable toggling crosshair with ``Ctrl-x`` in ``OrthoSlicer3D`` viewer (pr/701)
+  (Miguel Estevan Moreno, reviewed by CM)
+
+Bug fixes
+---------
+* Read .PAR files corresponding to ADC maps (pr/685) (Gregory R. Lee, reviewed
+  by CM)
+* Increase maximum number of items read from Siemens CSA format (Igor Solovey,
+  reviewed by CM, MB)
+* Check boolean dtypes with ``numpy.issubdtype(..., np.bool_)`` (pr/707)
+  (Jon Haitz Legarreta Gorroño, reviewed by CM)
+
+Maintenance
+-----------
+* Fix small typos in parrec2nii help text (pr/682) (Thomas Roos, reviewed by
+  MB)
+* Remove deprecated calls to ``numpy.asscalar`` (pr/686) (CM, reviewed by
+  Gregory R. Lee)
+* Update QA directives to accommodate Flake8 3.6 (pr/695) (CM)
+* Update DOI links to use ``https://doi.org`` (pr/703) (Katrin Leinweber,
+  reviewed by CM)
+* Remove deprecated calls to ``numpy.fromstring`` (pr/700) (Ariel Rokem,
+  reviewed by CM, MB)
+* Drop ``distutils`` support, require ``bz2file`` for Python 2.7 (pr/700)
+  (CM, reviewed by MB)
+* Replace mutable ``bytes`` hack, disabled in numpy pre-release, with
+  ``bytearray``/``readinto`` strategy (pr/700) (Ariel Rokem, CM, reviewed by
+  CM, MB)
+
+API changes and deprecations
+----------------------------
+* Add ``Opener.readinto`` method to read file contents into pre-allocated buffers
+  (pr/700) (Ariel Rokem, reviewed by CM, MB)
+
 2.3.1 (Tuesday 16 October 2018)
 ===============================
 

appveyor.yml

@@ -22,6 +22,7 @@ install:
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
+  - python -m pip install --upgrade pip setuptools wheel
   - pip install numpy scipy matplotlib nose h5py mock pydicom
   - pip install .
   - SET NIBABEL_DATA_DIR=%CD%\nibabel-data

doc/source/conf.py

@@ -87,7 +87,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2018, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
+copyright = u'2006-2019, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/devel/make_release.rst

@@ -301,7 +301,7 @@ Release checklist
   text for adding a DOI badge in various formats. Copy the DOI Markdown text.
   The markdown will look something like this::
 
-    [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.60847.svg)](http://dx.doi.org/10.5281/zenodo.60847)
+    [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.60847.svg)](https://doi.org/10.5281/zenodo.60847)
 
   Go back to the Github release page for this release, click "Edit release".
   and copy the DOI into the release notes.  Click "Update release".

doc/source/index.rst

@@ -87,6 +87,11 @@ contributed code and discussion (in rough order of appearance):
 * Mathias Goncalves
 * Jakub Kaczmarzyk
 * Dimitri Papadopoulos Orfanos
+* Miguel Estevan Moreno
+* Thomas Roos
+* Igor Solovey
+* Jon Haitz Legarreta Gorroño
+* Katrin Leinweber
 
 License reprise
 ===============

nibabel/affines.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 from six.moves import reduce
-from .testing import setup_test  # flake8: noqa F401
+from .testing import setup_test  # noqa
 
 
 class AffineError(ValueError):

nibabel/analyze.py

@@ -1057,10 +1057,8 @@ def to_file_map(self, file_map=None):
         # Store consumable values for later restore
         offset = hdr.get_data_offset()
         # Scalars of slope, offset to get immutable values
-        slope = (np.asscalar(hdr['scl_slope']) if hdr.has_data_slope
-                 else np.nan)
-        inter = (np.asscalar(hdr['scl_inter']) if hdr.has_data_intercept
-                 else np.nan)
+        slope = hdr['scl_slope'].item() if hdr.has_data_slope else np.nan
+        inter = hdr['scl_inter'].item() if hdr.has_data_intercept else np.nan
         # Check whether to calculate slope / inter
         scale_me = np.all(np.isnan((slope, inter)))
         if scale_me:

nibabel/casting.py

@@ -8,7 +8,7 @@
 from platform import processor, machine
 
 import numpy as np
-from .testing import setup_test  # flake8: noqa F401
+from .testing import setup_test  # noqa
 
 
 class CastingError(Exception):
@@ -268,7 +268,7 @@ def type_info(np_type):
         # 80) but in calculations nexp in fact appears to be 11 as for float64
         ret.update(dict(width=width))
         return ret
-    if vals == (105, 11, 16): # correctly detected double double
+    if vals == (105, 11, 16):  # correctly detected double double
         ret.update(dict(nmant=nmant, nexp=nexp, width=width))
         return ret
     # Oh dear, we don't recognize the type information.  Try some known types

nibabel/cifti2/tests/test_cifti2.py

@@ -58,7 +58,7 @@ def test_cifti2_metadata():
     assert_equal(md.data, dict(metadata_test))
 
     assert_equal(list(iter(md)), list(iter(collections.OrderedDict(metadata_test))))
-    
+
     md.update({'a': 'aval', 'b': 'bval'})
     assert_equal(md.data, dict(metadata_test))
 
@@ -310,7 +310,7 @@ def test_matrix():
 
     assert_raises(ci.Cifti2HeaderError, m.insert, 0, mim_none)
     assert_equal(m.mapped_indices, [])
-   
+
     h = ci.Cifti2Header(matrix=m)
     assert_equal(m.mapped_indices, [])
     m.insert(0, mim_0)