Merge pull request #787 from effigies/maint/purge_python2

MAINT: Require Python >= 3.5, purge Python 2 compatibility

.travis.yml

@@ -22,76 +22,59 @@ env:
         - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
         - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
 python:
-    - 3.5
     - 3.6
     - 3.7
 matrix:
   include:
-    - python: 3.4
-      dist: trusty
-      sudo: false
     # Absolute minimum dependencies
-    - python: 2.7
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8 setuptools==30.3.0"
+        - DEPENDS="-r min-requirements.txt setuptools==30.3.0"
     # Absolute minimum dependencies
-    - python: 2.7
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8"
+        - DEPENDS="-r min-requirements.txt"
         - CHECK_TYPE="import"
     # Absolute minimum dependencies plus oldest MPL
     # Check these against:
     # nibabel/info.py
     # doc/source/installation.rst
     # requirements.txt
-    - python: 2.7
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8 matplotlib==1.3.1"
+        - DEPENDS="-r min-requirements.txt matplotlib==1.3.1"
     # Minimum pydicom dependency
-    - python: 2.7
+    - python: 3.5
       env:
-        - DEPENDS="numpy==1.8 pydicom==0.9.9 pillow==2.6"
+        - DEPENDS="-r min-requirements.txt pydicom==0.9.9 pillow==2.6"
     # pydicom master branch
     - python: 3.5
       env:
         - DEPENDS="numpy git+https://github.com/pydicom/pydicom.git@master"
-    # test 2.7 against pre-release builds of everything
-    - python: 2.7
-      env:
-        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     # test 3.5 against pre-release builds of everything
     - python: 3.5
       env:
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
-    - python: 2.7
+    - python: 3.5
       env:
         - INSTALL_TYPE=sdist
-    - python: 2.7
+    - python: 3.5
       env:
         - INSTALL_TYPE=wheel
-    - python: 2.7
+    - python: 3.5
       env:
         - INSTALL_TYPE=requirements
-    - python: 2.7
+    - python: 3.5
       env:
         - INSTALL_TYPE=archive
-    - python: 2.7
-      env:
-        - CHECK_TYPE="style"
     - python: 3.5
       env:
         - CHECK_TYPE="style"
     # Documentation doctests
-    - python: 2.7
-      env:
-        - CHECK_TYPE="doc_doctests"
     - python: 3.5
       env:
         - CHECK_TYPE="doc_doctests"
     # Run tests with indexed_gzip present
-    - python: 2.7
-      env:
-        - OPTIONAL_DEPENDS="indexed_gzip"
     - python: 3.5
       env:
         - OPTIONAL_DEPENDS="indexed_gzip"

COPYING

@@ -218,34 +218,3 @@ 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.
-
-

doc/source/installation.rst

@@ -81,14 +81,10 @@ is for you.
 Requirements
 ------------
 
-.. check these against:
-    nibabel/info.py
-    requirements.txt
-    .travis.yml
-
-*  Python_ 2.7, or >= 3.4
-*  NumPy_ 1.8 or greater
-*  Six_ 1.3 or greater
+.. check these against setup.cfg
+
+*  Python_ 3.5.1 or greater
+*  NumPy_ 1.12 or greater
 *  SciPy_ (optional, for full SPM-ANALYZE support)
 *  PyDICOM_ 0.9.9 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)

doc/source/scripts/make_coord_examples.py

@@ -15,7 +15,6 @@
 * someones_epi.nii.gz (pretend single EPI volume)
 * someones_anatomy.nii.gz (pretend single subject structural)
 """
-from __future__ import division, print_function
 
 import math
 

doc/tools/build_modref_templates.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 """Script to auto-generate our API docs.
 """
-from __future__ import print_function, division
 
 # stdlib imports
 import sys

min-requirements.txt

@@ -0,0 +1,2 @@
+# Auto-generated by tools/update_requirements.py
+numpy ==1.12

nibabel/affines.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from six.moves import reduce
+from functools import reduce
 
 
 class AffineError(ValueError):

nibabel/arraywriters.py

@@ -28,7 +28,6 @@ def __init__(self, array, out_dtype=None)
 something else to make sense of conversions between float and int, or between
 larger ints and smaller.
 """
-from __future__ import division, absolute_import
 
 import warnings
 

nibabel/benchmarks/bench_array_to_file.py

@@ -13,7 +13,6 @@
 
     nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_load_save.py
 """
-from __future__ import division, print_function
 
 import sys
 from io import BytesIO  # NOQA

nibabel/benchmarks/bench_fileslice.py

@@ -11,7 +11,6 @@
 
     nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_fileslice.py
 """
-from __future__ import division, print_function
 
 import sys
 from timeit import timeit

nibabel/benchmarks/bench_finite_range.py

@@ -13,7 +13,6 @@
 
     nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_finite_range
 """
-from __future__ import division, print_function
 
 import sys
 

nibabel/benchmarks/bench_load_save.py

@@ -13,7 +13,6 @@
 
     nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_load_save.py
 """
-from __future__ import division, print_function
 
 import sys
 

nibabel/benchmarks/bench_streamlines.py

@@ -13,11 +13,9 @@
 
     nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_streamlines.py
 """
-from __future__ import division, print_function
 
 import numpy as np
 
-from six.moves import zip
 from nibabel.tmpdirs import InTemporaryDirectory
 
 from numpy.testing import assert_array_equal

nibabel/benchmarks/butils.py

@@ -1,6 +1,5 @@
 """ Benchmarking utilities
 """
-from __future__ import print_function, division
 
 from .. import get_info
 

nibabel/brikhead.py

@@ -27,14 +27,12 @@
 am aware) always be >= 1. This permits sub-brick indexing common in AFNI
 programs (e.g., example4d+orig'[0]').
 """
-from __future__ import print_function, division
 
 from copy import deepcopy
 import os
 import re
 
 import numpy as np
-from six import string_types
 
 from .arrayproxy import ArrayProxy
 from .fileslice import strided_scalar
@@ -204,7 +202,7 @@ def parse_AFNI_header(fobj):
     [1, 1, 1]
     """
     # edge case for being fed a filename instead of a file object
-    if isinstance(fobj, string_types):
+    if isinstance(fobj, str):
         with open(fobj, 'rt') as src:
             return parse_AFNI_header(src)
     # unpack variables in HEAD file

nibabel/checkwarns.py

@@ -8,7 +8,6 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 ''' Contexts for *with* statement allowing checks for warnings
 '''
-from __future__ import division, print_function
 
 import warnings
 

nibabel/cifti2/cifti2.py

@@ -16,13 +16,8 @@
 
     http://www.nitrc.org/projects/cifti
 '''
-from __future__ import division, print_function, absolute_import
 import re
-try:
-    from collections.abc import MutableSequence, MutableMapping, Iterable
-except ImportError:
-    # PY2 compatibility
-    from collections import MutableSequence, MutableMapping, Iterable
+from collections.abc import MutableSequence, MutableMapping, Iterable
 from collections import OrderedDict
 from .. import xmlutils as xml
 from ..filebasedimages import FileBasedHeader

nibabel/cifti2/cifti2_axes.py

@@ -120,7 +120,6 @@
 """
 import numpy as np
 from . import cifti2
-from six import string_types, add_metaclass, integer_types
 from operator import xor
 import abc
 
@@ -173,8 +172,7 @@ def to_header(axes):
     return cifti2.Cifti2Header(matrix)
 
 
-@add_metaclass(abc.ABCMeta)
-class Axis(object):
+class Axis(abc.ABC):
     """
     Abstract class for any object describing the rows or columns of a CIFTI-2 vector/matrix
 
@@ -289,7 +287,7 @@ def __init__(self, name, voxel=None, vertex=None, affine=None,
         else:
             self.vertex = np.asanyarray(vertex, dtype=int)
 
-        if isinstance(name, string_types):
+        if isinstance(name, str):
             name = [self.to_cifti_brain_structure_name(name)] * self.vertex.size
         self.name = np.asanyarray(name, dtype='U')
 
@@ -505,7 +503,7 @@ def to_cifti_brain_structure_name(name):
         """
         if name in cifti2.CIFTI_BRAIN_STRUCTURES:
             return name
-        if not isinstance(name, string_types):
+        if not isinstance(name, str):
             if len(name) == 1:
                 structure = name[0]
                 orientation = 'both'
@@ -589,7 +587,7 @@ def volume_shape(self, value):
             value = tuple(value)
             if len(value) != 3:
                 raise ValueError("Volume shape should be a tuple of length 3")
-            if not all(isinstance(v, integer_types) for v in value):
+            if not all(isinstance(v, int) for v in value):
                 raise ValueError("All elements of the volume shape should be integers")
         self._volume_shape = value
 
@@ -679,9 +677,9 @@ def __getitem__(self, item):
 
         Otherwise returns a new BrainModelAxis
         """
-        if isinstance(item, integer_types):
+        if isinstance(item, int):
             return self.get_element(item)
-        if isinstance(item, string_types):
+        if isinstance(item, str):
             raise IndexError("Can not index an Axis with a string (except for ParcelsAxis)")
         return self.__class__(self.name[item], self.voxel[item], self.vertex[item],
                               self.affine, self.volume_shape, self.nvertices)
@@ -914,7 +912,7 @@ def volume_shape(self, value):
             value = tuple(value)
             if len(value) != 3:
                 raise ValueError("Volume shape should be a tuple of length 3")
-            if not all(isinstance(v, integer_types) for v in value):
+            if not all(isinstance(v, int) for v in value):
                 raise ValueError("All elements of the volume shape should be integers")
         self._volume_shape = value
 
@@ -989,14 +987,14 @@ def __getitem__(self, item):
         - `string`: 2-element tuple of (parcel voxels, parcel vertices
         - other object that can index 1D arrays: new Parcel axis
         """
-        if isinstance(item, string_types):
+        if isinstance(item, str):
             idx = np.where(self.name == item)[0]
             if len(idx) == 0:
                 raise IndexError("Parcel %s not found" % item)
             if len(idx) > 1:
                 raise IndexError("Multiple parcels with name %s found" % item)
             return self.voxels[idx[0]], self.vertices[idx[0]]
-        if isinstance(item, integer_types):
+        if isinstance(item, int):
             return self.get_element(item)
         return self.__class__(self.name[item], self.voxels[item], self.vertices[item],
                               self.affine, self.volume_shape, self.nvertices)
@@ -1125,7 +1123,7 @@ def __add__(self, other):
         )
 
     def __getitem__(self, item):
-        if isinstance(item, integer_types):
+        if isinstance(item, int):
             return self.get_element(item)
         return self.__class__(self.name[item], self.meta[item])
 
@@ -1270,7 +1268,7 @@ def __add__(self, other):
         )
 
     def __getitem__(self, item):
-        if isinstance(item, integer_types):
+        if isinstance(item, int):
             return self.get_element(item)
         return self.__class__(self.name[item], self.label[item], self.meta[item])
 
@@ -1437,7 +1435,7 @@ def __getitem__(self, item):
                 nelements = 0
             return SeriesAxis(idx_start * self.step + self.start, self.step * step,
                               nelements, self.unit)
-        elif isinstance(item, integer_types):
+        elif isinstance(item, int):
             return self.get_element(item)
         raise IndexError('SeriesAxis can only be indexed with integers or slices '
                          'without breaking the regular structure')

nibabel/cifti2/parse_cifti2.py

@@ -6,7 +6,6 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-from __future__ import division, print_function, absolute_import
 
 from distutils.version import LooseVersion