fix: resolved conflicts

Author: satra

.gitmodules

@@ -13,3 +13,6 @@
 [submodule "nibabel-data/parrec_oblique"]
 	path = nibabel-data/parrec_oblique
 	url = https://github.com/grlee77/parrec_oblique.git
+[submodule "nibabel-data/nitest-cifti2"]
+	path = nibabel-data/nitest-cifti2
+	url = https://github.com/demianw/nibabel-nitest-cifti2.git

.travis.yml

@@ -24,7 +24,6 @@ env:
         - PYDICOM=1
         - INSTALL_TYPE="setup"
 python:
-    - 2.6
     - 3.3
     - 3.4
     - 3.5
@@ -38,6 +37,10 @@ matrix:
       env:
         - DEPENDS=numpy==1.5.1 PYDICOM=0
     # Absolute minimum dependencies plus oldest MPL
+    # Check these against:
+    # doc/source/installation.rst
+    # requirements.txt
+    # .travis.yml
     - python: 2.7
       env:
         - DEPENDS="numpy==1.5.1 matplotlib==1.3.1" PYDICOM=0

appveyor.yml

@@ -17,6 +17,14 @@ environment:
       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"
+
 install:
   # Install miniconda Python
   - "powershell ./tools/install_python.ps1"
@@ -26,6 +34,13 @@ install:
   # 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)\""

doc/source/installation.rst

@@ -48,11 +48,16 @@ the source from `NiBabel pypi`_ .  Go to the pypi page and select the source
 distribution you want.  Download the distribution, unpack it, and then, from
 the unpacked directory, run::
 
-    python setup.py install
+    pip install .
 
-or (if you need root permission to install on a unix system)::
+If you get permission errors, this may be because ``pip`` is trying to install
+to the system directories.  You can solve this error by using ``sudo``, but we
+strongly suggest you either do an install into your "user" directories, like
+this::
 
-    sudo python setup.py install
+    pip install --user .
+
+or you work inside a virtualenv_.
 
 .. _install_debian:
 
@@ -66,60 +71,56 @@ their repositories. Once this is done, installing NiBabel is::
   apt-get update
   apt-get install python-nibabel
 
-Install from source
-===================
+Install a development version
+=============================
 
-If no installer or package is provided for your platform, you can install
-NiBabel from source.
+If you want to test the latest development version of nibabel, or you'd like to
+help by contributing bug-fixes or new features (excellent!), then this section
+is for you.
 
 Requirements
 ------------
 
-*  Python_ 2.6 or greater
-*  NumPy_ 1.5 or greater
-*  SciPy_ (for full SPM-ANALYZE support)
-*  PyDICOM_ 0.9.7 or greater (for DICOM support)
-*  `Python Imaging Library`_ (for PNG conversion in DICOMFS)
-*  nose_ 0.11 or greater (to run the tests)
-*  sphinx_ (to build the documentation)
+.. check these against:
+    nibabel/info.py
+    requirements.txt
+    .travis.yml
 
-Get the sources
----------------
+*  Python_ 2.7 or greater
+*  NumPy_ 1.5 or greater
+*  SciPy_ (optional, for full SPM-ANALYZE support)
+*  PyDICOM_ 0.9.7 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)
+*  sphinx_ (optional, to build the documentation)
 
-The latest release is always available from `NiBabel pypi`_.
+Get the development sources
+---------------------------
 
-Alternatively, you can download a tarball of the latest development snapshot
-(i.e. the current state of the *master* branch of the NiBabel source code
-repository) from the `NiBabel github`_ page.
+You can download a tarball of the latest development snapshot (i.e. the current
+state of the *master* branch of the NiBabel source code repository) from the
+`NiBabel github`_ page.
 
 If you want to have access to the full NiBabel history and the latest
-development code, do a full clone (aka checkout) of the NiBabel
+development code, do a full clone (AKA checkout) of the NiBabel
 repository::
 
-  git clone git://github.com/nipy/nibabel.git
-
-or::
-
   git clone https://github.com/nipy/nibabel.git
 
-(The first may be faster, the second more likely to work behind a firewall).
-
 Installation
 ------------
 
 Just install the modules by invoking::
 
-  sudo python setup.py install
-
-If sudo is not configured (or even installed) you might have to use
-``su`` instead.
+  pip install .
 
+See :ref:`install-pypi` for advice on what to do for permission errors.
 
 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::
+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)
     [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
@@ -128,8 +129,10 @@ It should look something like this::
     >>>
 
 
-To run the nibabel test suite, from the terminal run ``nosetests nibabel`` or ``python -c "import nibabel; nibabel.test()``.
+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`.
+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

@@ -108,7 +108,7 @@
    https://pip.readthedocs.org/en/latest/installing.html
 .. _twine: https://pypi.python.org/pypi/twine
 .. _datapkg: https://pythonhosted.org/datapkg/
-.. _python imaging library: http://pythonware.com/products/pil/
+.. _python imaging library: https://pypi.python.org/pypi/Pillow
 
 .. Python imaging projects
 .. _PyMVPA: http://www.pymvpa.org

nibabel-data/nitest-cifti2

@@ -27,6 +27,8 @@
 """
 import warnings
 
+import numpy as np
+
 from .volumeutils import array_from_file, apply_read_scaling
 from .fileslice import fileslice
 from .keywordonly import kw_only_meth
@@ -111,8 +113,12 @@ def shape(self):
         return self._shape
 
     @property
-    def is_proxy(self):
-        return True
+    def dtype(self):
+        return self._dtype
+
+    @property
+    def offset(self):
+        return self._offset
 
     @property
     def slope(self):
@@ -123,8 +129,8 @@ def inter(self):
         return self._inter
 
     @property
-    def offset(self):
-        return self._offset
+    def is_proxy(self):
+        return True
 
     def get_unscaled(self):
         ''' Read of data from file
@@ -164,3 +170,10 @@ def is_proxy(obj):
         return obj.is_proxy
     except AttributeError:
         return False
+
+
+def reshape_dataobj(obj, shape):
+    """ Use `obj` reshape method if possible, else numpy reshape function
+    """
+    return (obj.reshape(shape) if hasattr(obj, 'reshape')
+            else np.reshape(obj, shape))

nibabel/arrayproxy.py

@@ -194,7 +194,9 @@ def _check_nan2zero(self, nan2zero):
             raise WriterError('Deprecated `nan2zero` argument to `to_fileobj` '
                               'must be same as class value set in __init__')
         warnings.warn('Please remove `nan2zero` from call to ' '`to_fileobj` '
-                      'and use in instance __init__ instead',
+                      'and use in instance __init__ instead.\n'
+                      '* deprecated in version: 2.0\n'
+                      '* will raise error in version: 4.0\n',
                       DeprecationWarning, stacklevel=3)
 
     def _needs_nan2zero(self):

nibabel/arraywriters.py

@@ -16,11 +16,12 @@
    cifti2
 """
 
-from .parse_cifti2_fast import Cifti2Extension
+from .parse_cifti2 import Cifti2Extension
 from .cifti2 import (Cifti2MetaData, Cifti2Header, Cifti2Image, Cifti2Label,
                      Cifti2LabelTable, Cifti2VertexIndices,
                      Cifti2VoxelIndicesIJK, Cifti2BrainModel, Cifti2Matrix,
                      Cifti2MatrixIndicesMap, Cifti2NamedMap, Cifti2Parcel,
-                     Cifti2Surface, Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ,
-                     Cifti2Vertices, Cifti2Volume, CIFTI_BrainStructures,
-                     Cifti2DenseDataSeries, CIFTI_MODEL_TYPES, load, save)
+                     Cifti2Surface,
+                     Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ,
+                     Cifti2Vertices, Cifti2Volume, CIFTI_BRAIN_STRUCTURES,
+                     Cifti2HeaderError, CIFTI_MODEL_TYPES, load, save)