Merge remote-tracking branch 'nibabel/master' into nf-nib-diff

 Conflicts: generally took master version of the functions
	bin/nib-ls
	nibabel/cmdline/__init__.py
	nibabel/cmdline/ls.py -- chose nf-nib-diff version of main with args being passed
	nibabel/cmdline/utils.py

Author: chrispycheng

.coveragerc

@@ -5,5 +5,4 @@ include = */nibabel/*, */nisext/*
 omit =
     */externals/*
     */benchmarks/*
-    */ast.py
-    */codegen.py
+    */tests/*

.mailmap

@@ -40,3 +40,4 @@ Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
 Jasper J.F. van den Bosch <[email protected]> Jasper <[email protected]>
 Gregory R. Lee <[email protected]> Gregory R. Lee <[email protected]>
 Demian Wassermann <[email protected]> Demian Wassermann <[email protected]>
+Paul McCarthy <[email protected]> Paul McCarthy <[email protected]>

.travis.yml

@@ -14,9 +14,8 @@ cache:
     - $HOME/.cache/pip
 env:
     global:
-        - DEPENDS="six numpy scipy matplotlib h5py pillow"
+        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom"
         - OPTIONAL_DEPENDS=""
-        - PYDICOM=1
         - INSTALL_TYPE="setup"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
@@ -34,27 +33,23 @@ matrix:
     # Absolute minimum dependencies
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1"
     # Absolute minimum dependencies plus oldest MPL
     # Check these against:
     # nibabel/info.py
     # doc/source/installation.rst
     # requirements.txt
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1"
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1 pydicom==0.9.7 pillow==2.6"
-    # test against numpy 1.7
-    - python: 2.7
-      env:
-        - DEPENDS="numpy==1.7.1"
-    # pydicom 1.0 (currently unreleased)
-    - python: 2.7
+        - DEPENDS="numpy==1.7.1 pydicom==0.9.9 pillow==2.6"
+    # pydicom master branch
+    - python: 3.5
       env:
-        - PYDICOM="v1.0"
+        - DEPENDS="numpy git+https://github.com/pydicom/pydicom.git@master"
     # test 2.7 against pre-release builds of everything
     - python: 2.7
       env:
@@ -102,14 +97,6 @@ before_install:
     - pip install -U pip wheel  # needed at one point
     - retry pip install nose flake8 mock  # always
     - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
-    # pydicom <= 0.9.8 doesn't install on python 3
-    - if [ "${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
       pip install coverage;
       pip install coveralls;

Changelog

@@ -24,6 +24,25 @@ Gerhard (SG) and Eric Larson (EL).
 
 References like "pr/298" refer to github pull request numbers.
 
+2.2.1 (Wednesday 22 November 2017)
+==================================
+
+Bug fixes
+---------
+
+* Set L/R labels in orthoview correctly (pr/564) (CM)
+* Defer use of ufunc / memmap test - allows "freezing" (pr/572) (MB, reviewed
+  by Satra Ghosh)
+* Fix doctest failures with pre-release numpy (pr/582) (MB, reviewed by CM)
+
+Maintenance
+-----------
+
+* Update documentation around NIfTI qform/sform codes (pr/576) (Paul McCarthy,
+  reviewed by MB, CM) + (pr/580) (Bennet Fauber, reviewed by Paul McCarthy)
+* Skip precision test on macOS, newer numpy (pr/583) (MB, reviewed by CM)
+* Simplify AppVeyor script, removing conda (pr/584) (MB, reviewed by CM)
+
 2.2 (Friday 13 October 2017)
 ============================
 

appveyor.yml

@@ -1,60 +1,34 @@
 # vim ft=yaml
 # CI on Windows via appveyor
-# This file was based on Olivier Grisel's python-appveyor-demo
 
 environment:
 
   matrix:
-    - PYTHON: "C:\\Python27-conda32"
-      PYTHON_VERSION: "2.7"
-      PYTHON_ARCH: "32"
-
-    - PYTHON: "C:\\Python34-conda32"
-      PYTHON_VERSION: "3.4"
-      PYTHON_ARCH: "32"
-
-    - PYTHON: "C:\\Python34-conda64"
-      PYTHON_VERSION: "3.4"
-      PYTHON_ARCH: "64"
-
-    - PYTHON: "C:\\Python35-conda64"
-      PYTHON_VERSION: "3.5"
-      PYTHON_ARCH: "64"
-
-    - PYTHON: "C:\\Python35-conda32"
-      PYTHON_VERSION: "3.5"
-      PYTHON_ARCH: "32"
+    - PYTHON: C:\Python27
+    - PYTHON: C:\Python27-x64
+    - PYTHON: C:\Python34
+    - PYTHON: C:\Python34-x64
+    - PYTHON: C:\Python35
+    - PYTHON: C:\Python35-x64
+    - PYTHON: C:\Python36
+    - PYTHON: C:\Python36-x64
 
 install:
-  # Install miniconda Python
-  - "powershell ./tools/install_python.ps1"
-
   # Prepend newly installed Python to the PATH of this build (this cannot be
   # done from inside the powershell script as it would require to restart
   # the parent CMD process).
-  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-
-  # Set up a conda environment:
-  - conda config --set always_yes yes
-  - conda update -q conda
-  - conda info -a
-  - conda create -q -n test-environment python=%PYTHON_VERSION%
-  - activate test-environment
-
-  # Check that we have the expected version and architecture for Python
-  - "python --version"
-  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+  - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
 
   # Install the dependencies of the project.
-  - "conda install --yes --quiet numpy scipy matplotlib nose h5py mock"
-  - "pip install pydicom"
-  - "python setup.py install"
-  - "SET NIBABEL_DATA_DIR=%CD%\\nibabel-data"
+  - pip install numpy scipy matplotlib nose h5py mock
+  - pip install pydicom
+  - pip install .
+  - SET NIBABEL_DATA_DIR=%CD%\nibabel-data
 
 build: false  # Not a C# project, build stuff at the test step instead.
 
 test_script:
   # Change into an innocuous directory and find tests from installation
-  - "mkdir for_testing"
-  - "cd for_testing"
-  - "nosetests --with-doctest nibabel"
+  - mkdir for_testing
+  - cd for_testing
+  - nosetests --with-doctest nibabel

bin/nib-ls

@@ -13,5 +13,6 @@ Output a summary table for neuroimaging files (resolution, dimensionality, etc.)
 
 from nibabel.cmdline.ls import main
 
+
 if __name__ == '__main__':
     main()

doc/source/coordinate_systems.rst

@@ -104,7 +104,7 @@ middle voxel in the EPI data array like this:
     (26, 30, 16)
     >>> center_vox_value = epi_img_data[center_i, center_j, center_k]
     >>> center_vox_value
-    81.549287796020508
+    81.5492877960205...
 
 The values (26, 30, 16) are indices into the data array ``epi_img_data``. (26,
 30, 16) is therefore a 'voxel coordinate' - a coordinate into the voxel array.
@@ -776,7 +776,7 @@ center of the EPI image?
     :nofigs:
 
     >>> apply_affine(epi_vox2anat_vox, epi_vox_center)
-    array([ 28.364,  31.562,  36.165])
+    array([28.364, 31.562, 36.165])
 
 The voxel coordinate of the center voxel of the anatomical image is:
 
@@ -786,7 +786,7 @@ The voxel coordinate of the center voxel of the anatomical image is:
 
     >>> anat_vox_center = (np.array(anat_img_data.shape) - 1) / 2.
     >>> anat_vox_center
-    array([ 28. ,  33. ,  27.5])
+    array([28. , 33. , 27.5])
 
 The voxel location in the anatomical image that matches the center voxel of
 the EPI image is nearly exactly half way across the first axis, a voxel or two

doc/source/image_orientation.rst

@@ -53,10 +53,10 @@ Here is the affine (to two digits decimal precision):
 
 >>> np.set_printoptions(precision=2, suppress=True)
 >>> img.affine
-array([[  -2.  ,    0.  ,    0.  ,  117.86],
-       [  -0.  ,    1.97,   -0.36,  -35.72],
-       [   0.  ,    0.32,    2.17,   -7.25],
-       [   0.  ,    0.  ,    0.  ,    1.  ]])
+array([[ -2.  ,   0.  ,   0.  , 117.86],
+       [ -0.  ,   1.97,  -0.36, -35.72],
+       [  0.  ,   0.32,   2.17,  -7.25],
+       [  0.  ,   0.  ,   0.  ,   1.  ]])
 
 What are the orientations of the voxel axes here?
 

doc/source/index.rst

@@ -79,6 +79,7 @@ contributed code and discussion (in rough order of appearance):
 * Venky Reddy
 * Mark Hymers
 * Jasper J.F. van den Bosch
+* Bennet Fauber
 
 License reprise
 ===============

doc/source/installation.rst

@@ -90,7 +90,7 @@ Requirements
 *  NumPy_ 1.7.1 or greater
 *  Six_ 1.3 or greater
 *  SciPy_ (optional, for full SPM-ANALYZE support)
-*  PyDICOM_ 0.9.7 or greater (optional, for DICOM support)
+*  PyDICOM_ 0.9.9 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)
 *  nose_ 0.11 or greater (optional, to run the tests)
 *  mock_ (optional, to run the tests)