diff --git a/.travis.yml b/.travis.yml index 3545a5f573..b4c0cf5ee8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -20,7 +20,7 @@ addons: - libatlas-base-dev env: global: - - DEPENDS="numpy scipy matplotlib h5py pillow" + - DEPENDS="six numpy scipy matplotlib h5py pillow" - PYDICOM=1 - INSTALL_TYPE="setup" - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com" @@ -37,7 +37,7 @@ matrix: # Absolute minimum dependencies - python: 2.7 env: - - DEPENDS=numpy==1.6.0 PYDICOM=0 + - DEPENDS="numpy==1.6.0" PYDICOM=0 # Absolute minimum dependencies plus oldest MPL # Check these against: # nibabel/info.py diff --git a/bin/nib-ls b/bin/nib-ls index 1a687c25ad..fe8007d917 100755 --- a/bin/nib-ls +++ b/bin/nib-ls @@ -19,11 +19,9 @@ import numpy as np import nibabel as nib from math import ceil -from collections import defaultdict from optparse import OptionParser, Option from io import StringIO from nibabel.py3k import asunicode -from nibabel.externals.six.moves import xrange __author__ = 'Yaroslav Halchenko' __copyright__ = 'Copyright (c) 2011-2016 Yaroslav Halchenko ' \ diff --git a/doc/source/installation.rst b/doc/source/installation.rst index 6b53841c05..9c18dfe3ee 100644 --- a/doc/source/installation.rst +++ b/doc/source/installation.rst @@ -88,6 +88,7 @@ Requirements * Python_ 2.7, or >= 3.4 * NumPy_ 1.6 or greater +* Six_ 1.3 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) diff --git a/nibabel/affines.py b/nibabel/affines.py index 3a41bce972..6deab93ad3 100644 --- a/nibabel/affines.py +++ b/nibabel/affines.py @@ -5,7 +5,7 @@ import numpy as np -from .externals.six.moves import reduce +from six.moves import reduce class AffineError(ValueError): diff --git a/nibabel/benchmarks/bench_load_save.py b/nibabel/benchmarks/bench_load_save.py index 95efa22294..c2ee68578a 100644 --- a/nibabel/benchmarks/bench_load_save.py +++ b/nibabel/benchmarks/bench_load_save.py @@ -19,7 +19,7 @@ import numpy as np -from ..externals.six import BytesIO +from io import BytesIO from .. import Nifti1Image diff --git a/nibabel/benchmarks/bench_streamlines.py b/nibabel/benchmarks/bench_streamlines.py index 3928fcfd4d..c076657d27 100644 --- a/nibabel/benchmarks/bench_streamlines.py +++ b/nibabel/benchmarks/bench_streamlines.py @@ -17,7 +17,7 @@ import numpy as np -from nibabel.externals.six.moves import zip +from six.moves import zip from nibabel.tmpdirs import InTemporaryDirectory from numpy.testing import assert_array_equal diff --git a/nibabel/data.py b/nibabel/data.py index e6e191901b..2a53f15f64 100644 --- a/nibabel/data.py +++ b/nibabel/data.py @@ -8,7 +8,7 @@ from os.path import join as pjoin import glob import sys -from .externals.six.moves import configparser +from six.moves import configparser from distutils.version import LooseVersion from .environment import get_nipy_user_dir, get_nipy_system_dir diff --git a/nibabel/dft.py b/nibabel/dft.py index 1efbca06b8..fc9e7fccd6 100644 --- a/nibabel/dft.py +++ b/nibabel/dft.py @@ -22,7 +22,7 @@ import numpy -from .externals.six import BytesIO +from six import BytesIO from .nifti1 import Nifti1Header diff --git a/nibabel/eulerangles.py b/nibabel/eulerangles.py index e633a6a22c..eac1c046ed 100644 --- a/nibabel/eulerangles.py +++ b/nibabel/eulerangles.py @@ -85,7 +85,7 @@ import math -from .externals.six.moves import reduce +from six.moves import reduce import numpy as np diff --git a/nibabel/externals/__init__.py b/nibabel/externals/__init__.py index 7eebe865dc..4c31772bb5 100644 --- a/nibabel/externals/__init__.py +++ b/nibabel/externals/__init__.py @@ -1,5 +1,5 @@ # init for externals package -try: - from collections import OrderedDict -except ImportError: # < Python 2.7 - from .ordereddict import OrderedDict +from collections import OrderedDict + +from ..deprecated import ModuleProxy as _ModuleProxy +six = _ModuleProxy('nibabel.externals.six') diff --git a/nibabel/externals/netcdf.py b/nibabel/externals/netcdf.py index 06375f8bdd..24b17706b8 100644 --- a/nibabel/externals/netcdf.py +++ b/nibabel/externals/netcdf.py @@ -35,13 +35,13 @@ from operator import mul from mmap import mmap, ACCESS_READ -import numpy as np +import numpy as np # noqa from ..py3k import asbytes, asstr from numpy import fromstring, ndarray, dtype, empty, array, asarray from numpy import little_endian as LITTLE_ENDIAN from functools import reduce -from .six import integer_types +from six import integer_types ABSENT = b'\x00\x00\x00\x00\x00\x00\x00\x00' diff --git a/nibabel/externals/ordereddict.py b/nibabel/externals/ordereddict.py deleted file mode 100644 index 66086c09b4..0000000000 --- a/nibabel/externals/ordereddict.py +++ /dev/null @@ -1,132 +0,0 @@ -# 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. - -# Allow Python3 to import module even though broken -# The following import checks are a modification from the original ordereddict -try: - from UserDict import DictMixin -except ImportError: - pass -else: - class OrderedDict(dict, DictMixin): - - def __init__(self, *args, **kwds): - if len(args) > 1: - raise TypeError('expected at most 1 arguments, got %d' % len(args)) - try: - self.__end - except AttributeError: - self.clear() - self.update(*args, **kwds) - - def clear(self): - self.__end = end = [] - end += [None, end, end] # sentinel node for doubly linked list - self.__map = {} # key --> [key, prev, next] - dict.clear(self) - - def __setitem__(self, key, value): - if key not in self: - end = self.__end - curr = end[1] - curr[2] = end[1] = self.__map[key] = [key, curr, end] - dict.__setitem__(self, key, value) - - def __delitem__(self, key): - dict.__delitem__(self, key) - key, prev, next = self.__map.pop(key) - prev[2] = next - next[1] = prev - - def __iter__(self): - end = self.__end - curr = end[2] - while curr is not end: - yield curr[0] - curr = curr[2] - - def __reversed__(self): - end = self.__end - curr = end[1] - while curr is not end: - yield curr[0] - curr = curr[1] - - def popitem(self, last=True): - if not self: - raise KeyError('dictionary is empty') - if last: - key = reversed(self).next() - else: - key = iter(self).next() - value = self.pop(key) - return key, value - - def __reduce__(self): - items = [[k, self[k]] for k in self] - tmp = self.__map, self.__end - del self.__map, self.__end - inst_dict = vars(self).copy() - self.__map, self.__end = tmp - if inst_dict: - return (self.__class__, (items,), inst_dict) - return self.__class__, (items,) - - def keys(self): - return list(self) - - setdefault = DictMixin.setdefault - update = DictMixin.update - pop = DictMixin.pop - values = DictMixin.values - items = DictMixin.items - iterkeys = DictMixin.iterkeys - itervalues = DictMixin.itervalues - iteritems = DictMixin.iteritems - - def __repr__(self): - if not self: - return '%s()' % (self.__class__.__name__,) - return '%s(%r)' % (self.__class__.__name__, self.items()) - - def copy(self): - return self.__class__(self) - - @classmethod - def fromkeys(cls, iterable, value=None): - d = cls() - for key in iterable: - d[key] = value - return d - - def __eq__(self, other): - if isinstance(other, OrderedDict): - if len(self) != len(other): - return False - for p, q in zip(self.items(), other.items()): - if p != q: - return False - return True - return dict.__eq__(self, other) - - def __ne__(self, other): - return not self == other diff --git a/nibabel/externals/six.py b/nibabel/externals/six.py index b23166effd..77e656cd67 100644 --- a/nibabel/externals/six.py +++ b/nibabel/externals/six.py @@ -1,405 +1,12 @@ -"""Utilities for writing code that runs on Python 2 and 3""" +""" Shim allowing some grace time for removal of six.py copy """ +# Remove around version 4.0 +from __future__ import absolute_import -# 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. +import warnings -import operator -import sys -import types +warnings.warn("We no longer carry a copy of the 'six' package in nibabel; " + "Please import the 'six' package directly", + FutureWarning, + stacklevel=2) -__author__ = "Benjamin Peterson " -__version__ = "1.3.0" - - -# True if we are running on Python 3. -PY3 = sys.version_info[0] == 3 - -if PY3: - string_types = str, - integer_types = int, - class_types = type, - text_type = str - binary_type = bytes - - MAXSIZE = sys.maxsize -else: - string_types = basestring, - integer_types = (int, long) - class_types = (type, types.ClassType) - text_type = unicode - binary_type = str - - if sys.platform.startswith("java"): - # Jython always uses 32 bits. - MAXSIZE = int((1 << 31) - 1) - else: - # It's possible to have sizeof(long) != sizeof(Py_ssize_t). - class X(object): - def __len__(self): - return 1 << 31 - try: - len(X()) - except OverflowError: - # 32-bit - MAXSIZE = int((1 << 31) - 1) - else: - # 64-bit - MAXSIZE = int((1 << 63) - 1) - del X - - -def _add_doc(func, doc): - """Add documentation to a function.""" - func.__doc__ = doc - - -def _import_module(name): - """Import module, returning the module after the last dot.""" - __import__(name) - return sys.modules[name] - - -class _LazyDescr(object): - - def __init__(self, name): - self.name = name - - def __get__(self, obj, tp): - result = self._resolve() - setattr(obj, self.name, result) - # This is a bit ugly, but it avoids running this again. - delattr(tp, self.name) - return result - - -class MovedModule(_LazyDescr): - - def __init__(self, name, old, new=None): - super(MovedModule, self).__init__(name) - if PY3: - if new is None: - new = name - self.mod = new - else: - self.mod = old - - def _resolve(self): - return _import_module(self.mod) - - -class MovedAttribute(_LazyDescr): - - def __init__(self, name, old_mod, new_mod, old_attr=None, new_attr=None): - super(MovedAttribute, self).__init__(name) - if PY3: - if new_mod is None: - new_mod = name - self.mod = new_mod - if new_attr is None: - if old_attr is None: - new_attr = name - else: - new_attr = old_attr - self.attr = new_attr - else: - self.mod = old_mod - if old_attr is None: - old_attr = name - self.attr = old_attr - - def _resolve(self): - module = _import_module(self.mod) - return getattr(module, self.attr) - - - -class _MovedItems(types.ModuleType): - """Lazy loading of moved objects""" - - -_moved_attributes = [ - MovedAttribute("cStringIO", "cStringIO", "io", "StringIO"), - MovedAttribute("filter", "itertools", "builtins", "ifilter", "filter"), - MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"), - MovedAttribute("map", "itertools", "builtins", "imap", "map"), - MovedAttribute("reload_module", "__builtin__", "imp", "reload"), - MovedAttribute("reduce", "__builtin__", "functools"), - MovedAttribute("StringIO", "StringIO", "io"), - MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"), - MovedAttribute("zip", "itertools", "builtins", "izip", "zip"), - MovedAttribute("zip_longest", "itertools", "itertools", "izip_longest", "zip_longest"), - - MovedModule("builtins", "__builtin__"), - MovedModule("configparser", "ConfigParser"), - MovedModule("copyreg", "copy_reg"), - MovedModule("http_cookiejar", "cookielib", "http.cookiejar"), - MovedModule("http_cookies", "Cookie", "http.cookies"), - MovedModule("html_entities", "htmlentitydefs", "html.entities"), - MovedModule("html_parser", "HTMLParser", "html.parser"), - MovedModule("http_client", "httplib", "http.client"), - MovedModule("email_mime_multipart", "email.MIMEMultipart", "email.mime.multipart"), - MovedModule("email_mime_text", "email.MIMEText", "email.mime.text"), - MovedModule("email_mime_base", "email.MIMEBase", "email.mime.base"), - MovedModule("BaseHTTPServer", "BaseHTTPServer", "http.server"), - MovedModule("CGIHTTPServer", "CGIHTTPServer", "http.server"), - MovedModule("SimpleHTTPServer", "SimpleHTTPServer", "http.server"), - MovedModule("cPickle", "cPickle", "pickle"), - MovedModule("queue", "Queue"), - MovedModule("reprlib", "repr"), - MovedModule("socketserver", "SocketServer"), - MovedModule("tkinter", "Tkinter"), - MovedModule("tkinter_dialog", "Dialog", "tkinter.dialog"), - MovedModule("tkinter_filedialog", "FileDialog", "tkinter.filedialog"), - MovedModule("tkinter_scrolledtext", "ScrolledText", "tkinter.scrolledtext"), - MovedModule("tkinter_simpledialog", "SimpleDialog", "tkinter.simpledialog"), - MovedModule("tkinter_tix", "Tix", "tkinter.tix"), - MovedModule("tkinter_constants", "Tkconstants", "tkinter.constants"), - MovedModule("tkinter_dnd", "Tkdnd", "tkinter.dnd"), - MovedModule("tkinter_colorchooser", "tkColorChooser", - "tkinter.colorchooser"), - MovedModule("tkinter_commondialog", "tkCommonDialog", - "tkinter.commondialog"), - MovedModule("tkinter_tkfiledialog", "tkFileDialog", "tkinter.filedialog"), - MovedModule("tkinter_font", "tkFont", "tkinter.font"), - MovedModule("tkinter_messagebox", "tkMessageBox", "tkinter.messagebox"), - MovedModule("tkinter_tksimpledialog", "tkSimpleDialog", - "tkinter.simpledialog"), - MovedModule("urllib_robotparser", "robotparser", "urllib.robotparser"), - MovedModule("winreg", "_winreg"), -] -for attr in _moved_attributes: - setattr(_MovedItems, attr.name, attr) -del attr - -moves = sys.modules[__name__ + ".moves"] = _MovedItems("moves") - - -def add_move(move): - """Add an item to six.moves.""" - setattr(_MovedItems, move.name, move) - - -def remove_move(name): - """Remove item from six.moves.""" - try: - delattr(_MovedItems, name) - except AttributeError: - try: - del moves.__dict__[name] - except KeyError: - raise AttributeError("no such move, %r" % (name,)) - - -if PY3: - _meth_func = "__func__" - _meth_self = "__self__" - - _func_closure = "__closure__" - _func_code = "__code__" - _func_defaults = "__defaults__" - _func_globals = "__globals__" - - _iterkeys = "keys" - _itervalues = "values" - _iteritems = "items" - _iterlists = "lists" -else: - _meth_func = "im_func" - _meth_self = "im_self" - - _func_closure = "func_closure" - _func_code = "func_code" - _func_defaults = "func_defaults" - _func_globals = "func_globals" - - _iterkeys = "iterkeys" - _itervalues = "itervalues" - _iteritems = "iteritems" - _iterlists = "iterlists" - - -try: - advance_iterator = next -except NameError: - def advance_iterator(it): - return it.next() -next = advance_iterator - - -try: - callable = callable -except NameError: - def callable(obj): - return any("__call__" in klass.__dict__ for klass in type(obj).__mro__) - - -if PY3: - def get_unbound_function(unbound): - return unbound - - Iterator = object -else: - def get_unbound_function(unbound): - return unbound.im_func - - class Iterator(object): - - def next(self): - return type(self).__next__(self) - - callable = callable -_add_doc(get_unbound_function, - """Get the function out of a possibly unbound function""") - - -get_method_function = operator.attrgetter(_meth_func) -get_method_self = operator.attrgetter(_meth_self) -get_function_closure = operator.attrgetter(_func_closure) -get_function_code = operator.attrgetter(_func_code) -get_function_defaults = operator.attrgetter(_func_defaults) -get_function_globals = operator.attrgetter(_func_globals) - - -def iterkeys(d, **kw): - """Return an iterator over the keys of a dictionary.""" - return iter(getattr(d, _iterkeys)(**kw)) - -def itervalues(d, **kw): - """Return an iterator over the values of a dictionary.""" - return iter(getattr(d, _itervalues)(**kw)) - -def iteritems(d, **kw): - """Return an iterator over the (key, value) pairs of a dictionary.""" - return iter(getattr(d, _iteritems)(**kw)) - -def iterlists(d, **kw): - """Return an iterator over the (key, [values]) pairs of a dictionary.""" - return iter(getattr(d, _iterlists)(**kw)) - - -if PY3: - def b(s): - return s.encode("latin-1") - def u(s): - return s - if sys.version_info[1] <= 1: - def int2byte(i): - return bytes((i,)) - else: - # This is about 2x faster than the implementation above on 3.2+ - int2byte = operator.methodcaller("to_bytes", 1, "big") - import io - StringIO = io.StringIO - BytesIO = io.BytesIO -else: - def b(s): - return s - def u(s): - return unicode(s, "unicode_escape") - int2byte = chr - import StringIO - StringIO = BytesIO = StringIO.StringIO -_add_doc(b, """Byte literal""") -_add_doc(u, """Text literal""") - - -if PY3: - import builtins - exec_ = getattr(builtins, "exec") - - - def reraise(tp, value, tb=None): - if value.__traceback__ is not tb: - raise value.with_traceback(tb) - raise value - - - print_ = getattr(builtins, "print") - del builtins - -else: - def exec_(_code_, _globs_=None, _locs_=None): - """Execute code in a namespace.""" - if _globs_ is None: - frame = sys._getframe(1) - _globs_ = frame.f_globals - if _locs_ is None: - _locs_ = frame.f_locals - del frame - elif _locs_ is None: - _locs_ = _globs_ - exec("""exec _code_ in _globs_, _locs_""") - - - exec_("""def reraise(tp, value, tb=None): - raise tp, value, tb -""") - - - def print_(*args, **kwargs): - """The new-style print function.""" - fp = kwargs.pop("file", sys.stdout) - if fp is None: - return - def write(data): - if not isinstance(data, basestring): - data = str(data) - fp.write(data) - want_unicode = False - sep = kwargs.pop("sep", None) - if sep is not None: - if isinstance(sep, unicode): - want_unicode = True - elif not isinstance(sep, str): - raise TypeError("sep must be None or a string") - end = kwargs.pop("end", None) - if end is not None: - if isinstance(end, unicode): - want_unicode = True - elif not isinstance(end, str): - raise TypeError("end must be None or a string") - if kwargs: - raise TypeError("invalid keyword arguments to print()") - if not want_unicode: - for arg in args: - if isinstance(arg, unicode): - want_unicode = True - break - if want_unicode: - newline = unicode("\n") - space = unicode(" ") - else: - newline = "\n" - space = " " - if sep is None: - sep = space - if end is None: - end = newline - for i, arg in enumerate(args): - if i: - write(sep) - write(arg) - write(end) - -_add_doc(reraise, """Reraise an exception.""") - - -def with_metaclass(meta, base=object): - """Create a base class with a metaclass.""" - return meta("NewBase", (base,), {}) +from six import * # noqa diff --git a/nibabel/externals/tests/test_ordereddict.py b/nibabel/externals/tests/test_ordereddict.py deleted file mode 100644 index df77b3aeb2..0000000000 --- a/nibabel/externals/tests/test_ordereddict.py +++ /dev/null @@ -1,21 +0,0 @@ -# Test ordered dict loading - -from os.path import dirname, relpath, realpath -import sys -import inspect - -from .. import OrderedDict - -from nose.tools import assert_equal, assert_true - -MY_PATH = dirname(realpath(__file__)) - -def test_right_version(): - # If Python < 2.7, use our own copy, else use system copy - if sys.version_info[:2] < (2, 7): - class_path = realpath(inspect.getfile(OrderedDict)) - rel_dir = dirname(relpath(class_path, MY_PATH)) - assert_equal(rel_dir, '..') - else: - import collections - assert_true(collections.OrderedDict is OrderedDict) diff --git a/nibabel/externals/tests/test_six.py b/nibabel/externals/tests/test_six.py new file mode 100644 index 0000000000..35db2ca851 --- /dev/null +++ b/nibabel/externals/tests/test_six.py @@ -0,0 +1,33 @@ +""" Test we are deprecating externals.six import +""" + +import warnings +import types + +from nose.tools import assert_true, assert_equal + +from nibabel.deprecated import ModuleProxy + + +def test_old_namespace(): + with warnings.catch_warnings(record=True) as warns: + # Top level import. + # This import does not trigger an import of the six.py module, because + # it's the proxy object. + from nibabel.externals import six + assert_equal(warns, []) + # If there was a previous import it will be module, otherwise it will be + # a proxy. + previous_import = isinstance(six, types.ModuleType) + if not previous_import: + assert_true(isinstance(six, ModuleProxy)) + shim_BytesIO = six.BytesIO # just to check it works + # There may or may not be a warning raised on accessing the proxy, + # depending on whether the externals.six.py module is already imported + # in this test run. + if not previous_import: + assert_equal(warns.pop(0).category, FutureWarning) + from six import BytesIO + assert_equal(warns, []) + # The import from old module is the same as that from new + assert_true(shim_BytesIO is BytesIO) diff --git a/nibabel/filebasedimages.py b/nibabel/filebasedimages.py index 5e5d22fee7..3517845137 100644 --- a/nibabel/filebasedimages.py +++ b/nibabel/filebasedimages.py @@ -8,7 +8,7 @@ ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## ''' Common interface for any image format--volume or surface, binary or xml.''' -from .externals.six import string_types +from six import string_types from .fileholders import FileHolder from .filename_parser import (types_filenames, TypesFilenamesError, splitext_addext) diff --git a/nibabel/fileslice.py b/nibabel/fileslice.py index a0c28b68bd..ee72b83c99 100644 --- a/nibabel/fileslice.py +++ b/nibabel/fileslice.py @@ -6,7 +6,7 @@ from numbers import Integral from mmap import mmap -from .externals.six.moves import reduce +from six.moves import reduce import numpy as np diff --git a/nibabel/freesurfer/io.py b/nibabel/freesurfer/io.py index 127a4acf8b..970d7adc6e 100644 --- a/nibabel/freesurfer/io.py +++ b/nibabel/freesurfer/io.py @@ -7,8 +7,8 @@ import getpass import time -from ..externals import OrderedDict -from ..externals.six.moves import xrange +from collections import OrderedDict +from six.moves import xrange from ..openers import Opener diff --git a/nibabel/freesurfer/tests/test_mghformat.py b/nibabel/freesurfer/tests/test_mghformat.py index 9683148e5f..2fb9ecf0d4 100644 --- a/nibabel/freesurfer/tests/test_mghformat.py +++ b/nibabel/freesurfer/tests/test_mghformat.py @@ -13,7 +13,7 @@ import numpy as np -from ...externals.six import BytesIO +from six import BytesIO from .. import load, save from ...openers import ImageOpener from ..mghformat import MGHHeader, MGHError, MGHImage diff --git a/nibabel/gifti/parse_gifti_fast.py b/nibabel/gifti/parse_gifti_fast.py index 234c8dc0a1..4cdbd3d768 100644 --- a/nibabel/gifti/parse_gifti_fast.py +++ b/nibabel/gifti/parse_gifti_fast.py @@ -12,7 +12,7 @@ import sys import warnings import zlib -from ..externals.six import StringIO +from io import StringIO from xml.parsers.expat import ExpatError import numpy as np diff --git a/nibabel/gifti/tests/test_gifti.py b/nibabel/gifti/tests/test_gifti.py index 3c7bcdaca0..f1285d441d 100644 --- a/nibabel/gifti/tests/test_gifti.py +++ b/nibabel/gifti/tests/test_gifti.py @@ -7,7 +7,7 @@ import numpy as np import nibabel as nib -from nibabel.externals.six import string_types +from six import string_types from nibabel.gifti import (GiftiImage, GiftiDataArray, GiftiLabel, GiftiLabelTable, GiftiMetaData, GiftiNVPairs, GiftiCoordSystem) diff --git a/nibabel/info.py b/nibabel/info.py index 5a55e12fec..956361f13d 100644 --- a/nibabel/info.py +++ b/nibabel/info.py @@ -188,6 +188,7 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__): # .travis.yml NUMPY_MIN_VERSION = '1.6.0' PYDICOM_MIN_VERSION = '0.9.7' +SIX_MIN_VERSION = '1.3' # Main setup parameters NAME = 'nibabel' diff --git a/nibabel/optpkg.py b/nibabel/optpkg.py index f0b6988d7c..794960ddc3 100644 --- a/nibabel/optpkg.py +++ b/nibabel/optpkg.py @@ -1,7 +1,7 @@ """ Routines to support optional packages """ from distutils.version import LooseVersion -from .externals.six import string_types, callable +from six import string_types try: import nose diff --git a/nibabel/parrec.py b/nibabel/parrec.py index c9c1568941..1819b257ef 100644 --- a/nibabel/parrec.py +++ b/nibabel/parrec.py @@ -129,7 +129,7 @@ import re from io import StringIO from locale import getpreferredencoding -from nibabel.externals import OrderedDict +from collections import OrderedDict from .keywordonly import kw_only_meth from .spatialimages import SpatialHeader, SpatialImage diff --git a/nibabel/py3k.py b/nibabel/py3k.py index f896368fa9..1c3300ac91 100644 --- a/nibabel/py3k.py +++ b/nibabel/py3k.py @@ -1,9 +1,9 @@ """ Python 3 compatibility tools. -Copied from numpy/compat/py3k +Copied from numpy/compat/py3k. -Please prefer the routines in externals/six.py when possible +Please prefer the routines in the six module when possible. BSD license """ diff --git a/nibabel/spm99analyze.py b/nibabel/spm99analyze.py index bb92305d18..b0df20f553 100644 --- a/nibabel/spm99analyze.py +++ b/nibabel/spm99analyze.py @@ -10,7 +10,7 @@ import warnings import numpy as np -from .externals.six import BytesIO +from six import BytesIO from .spatialimages import HeaderDataError, HeaderTypeError diff --git a/nibabel/streamlines/__init__.py b/nibabel/streamlines/__init__.py index 8ba95a41af..b0a6b744bb 100644 --- a/nibabel/streamlines/__init__.py +++ b/nibabel/streamlines/__init__.py @@ -2,7 +2,7 @@ """ import os import warnings -from ..externals.six import string_types +from six import string_types from .header import Field from .array_sequence import ArraySequence diff --git a/nibabel/streamlines/tests/test_streamlines.py b/nibabel/streamlines/tests/test_streamlines.py index c2f1c066d3..5f38e3979a 100644 --- a/nibabel/streamlines/tests/test_streamlines.py +++ b/nibabel/streamlines/tests/test_streamlines.py @@ -6,7 +6,7 @@ from os.path import join as pjoin import nibabel as nib -from nibabel.externals.six import BytesIO +from six import BytesIO from nibabel.tmpdirs import InTemporaryDirectory from nibabel.testing import data_path diff --git a/nibabel/streamlines/tests/test_tractogram.py b/nibabel/streamlines/tests/test_tractogram.py index fef38c513e..e970dd1d11 100644 --- a/nibabel/streamlines/tests/test_tractogram.py +++ b/nibabel/streamlines/tests/test_tractogram.py @@ -10,7 +10,7 @@ from nibabel.testing import clear_and_catch_warnings from nose.tools import assert_equal, assert_raises, assert_true from numpy.testing import assert_array_equal, assert_array_almost_equal -from nibabel.externals.six.moves import zip +from six.moves import zip from .. import tractogram as module_tractogram from ..tractogram import TractogramItem, Tractogram, LazyTractogram diff --git a/nibabel/streamlines/tests/test_trk.py b/nibabel/streamlines/tests/test_trk.py index f890021689..eeed4cf505 100644 --- a/nibabel/streamlines/tests/test_trk.py +++ b/nibabel/streamlines/tests/test_trk.py @@ -4,7 +4,7 @@ import numpy as np from os.path import join as pjoin -from nibabel.externals.six import BytesIO +from six import BytesIO from nibabel.testing import data_path from nibabel.testing import clear_and_catch_warnings, assert_arr_dict_equal diff --git a/nibabel/streamlines/tractogram_file.py b/nibabel/streamlines/tractogram_file.py index a1dc4e83fb..037d25f1ff 100644 --- a/nibabel/streamlines/tractogram_file.py +++ b/nibabel/streamlines/tractogram_file.py @@ -1,7 +1,7 @@ """ Define abstract interface for Tractogram file classes """ from abc import ABCMeta, abstractmethod -from nibabel.externals.six import with_metaclass +from six import with_metaclass from .header import Field diff --git a/nibabel/testing/__init__.py b/nibabel/testing/__init__.py index 2200b25182..2c6574da97 100644 --- a/nibabel/testing/__init__.py +++ b/nibabel/testing/__init__.py @@ -26,7 +26,7 @@ except ImportError: pass -from nibabel.externals.six.moves import zip_longest +from six.moves import zip_longest # set path to example data data_path = abspath(pjoin(dirname(__file__), '..', 'tests', 'data')) diff --git a/nibabel/tests/test_analyze.py b/nibabel/tests/test_analyze.py index 17e7b07719..da89808e4f 100644 --- a/nibabel/tests/test_analyze.py +++ b/nibabel/tests/test_analyze.py @@ -20,7 +20,7 @@ import numpy as np -from ..externals.six import BytesIO, StringIO +from six import BytesIO, StringIO from ..spatialimages import (HeaderDataError, HeaderTypeError, supported_np_types) from ..analyze import AnalyzeHeader, AnalyzeImage diff --git a/nibabel/tests/test_api_validators.py b/nibabel/tests/test_api_validators.py index f2dcaa3623..affa89d3e3 100644 --- a/nibabel/tests/test_api_validators.py +++ b/nibabel/tests/test_api_validators.py @@ -2,7 +2,7 @@ """ from __future__ import division, print_function, absolute_import -from ..externals.six import with_metaclass +from six import with_metaclass from nose.tools import assert_equal diff --git a/nibabel/tests/test_arrayproxy.py b/nibabel/tests/test_arrayproxy.py index abc7856623..86f7c7f9b5 100644 --- a/nibabel/tests/test_arrayproxy.py +++ b/nibabel/tests/test_arrayproxy.py @@ -12,7 +12,7 @@ import warnings -from ..externals.six import BytesIO +from six import BytesIO from ..tmpdirs import InTemporaryDirectory import numpy as np diff --git a/nibabel/tests/test_arraywriters.py b/nibabel/tests/test_arraywriters.py index 2f06f3a682..79c3a86088 100644 --- a/nibabel/tests/test_arraywriters.py +++ b/nibabel/tests/test_arraywriters.py @@ -10,7 +10,7 @@ import itertools import numpy as np -from ..externals.six import BytesIO +from six import BytesIO from ..arraywriters import (SlopeInterArrayWriter, SlopeArrayWriter, WriterError, ScalingError, ArrayWriter, make_array_writer, get_slope_inter) diff --git a/nibabel/tests/test_batteryrunners.py b/nibabel/tests/test_batteryrunners.py index 8f1710f779..71cbbba072 100644 --- a/nibabel/tests/test_batteryrunners.py +++ b/nibabel/tests/test_batteryrunners.py @@ -9,7 +9,7 @@ ''' Tests for BatteryRunner and Report objects ''' -from ..externals.six import StringIO +from six import StringIO import logging diff --git a/nibabel/tests/test_dft.py b/nibabel/tests/test_dft.py index 9a164549a9..b350d6bdc9 100644 --- a/nibabel/tests/test_dft.py +++ b/nibabel/tests/test_dft.py @@ -3,7 +3,7 @@ import os from os.path import join as pjoin, dirname -from ..externals.six import BytesIO +from six import BytesIO from ..testing import suppress_warnings import numpy as np diff --git a/nibabel/tests/test_fileholders.py b/nibabel/tests/test_fileholders.py index 0069eef36a..47b6072a80 100644 --- a/nibabel/tests/test_fileholders.py +++ b/nibabel/tests/test_fileholders.py @@ -1,7 +1,7 @@ """ Testing fileholders """ -from ..externals.six import BytesIO +from six import BytesIO from ..fileholders import FileHolder diff --git a/nibabel/tests/test_files_interface.py b/nibabel/tests/test_files_interface.py index 788be6a31a..765e4410f2 100644 --- a/nibabel/tests/test_files_interface.py +++ b/nibabel/tests/test_files_interface.py @@ -13,7 +13,7 @@ import numpy as np from .. import Nifti1Image, Nifti1Pair, MGHImage, all_image_classes -from ..externals.six import BytesIO +from six import BytesIO from ..fileholders import FileHolderError from ..spatialimages import SpatialImage diff --git a/nibabel/tests/test_image_api.py b/nibabel/tests/test_image_api.py index e86b8c8ea7..a76cb2737b 100644 --- a/nibabel/tests/test_image_api.py +++ b/nibabel/tests/test_image_api.py @@ -24,7 +24,7 @@ import warnings from functools import partial -from ..externals.six import string_types +from six import string_types import numpy as np diff --git a/nibabel/tests/test_image_load_save.py b/nibabel/tests/test_image_load_save.py index d43d1ee581..6960bb9c81 100644 --- a/nibabel/tests/test_image_load_save.py +++ b/nibabel/tests/test_image_load_save.py @@ -8,7 +8,7 @@ ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## ''' Tests for loader function ''' from __future__ import division, print_function, absolute_import -from ..externals.six import BytesIO +from six import BytesIO import shutil from os.path import dirname, join as pjoin diff --git a/nibabel/tests/test_nifti1.py b/nibabel/tests/test_nifti1.py index 6aab35aff0..a4b5ab98ab 100644 --- a/nibabel/tests/test_nifti1.py +++ b/nibabel/tests/test_nifti1.py @@ -18,7 +18,7 @@ from nibabel.affines import from_matvec from nibabel.casting import type_info, have_binary128 from nibabel.eulerangles import euler2mat -from nibabel.externals.six import BytesIO +from six import BytesIO from nibabel.nifti1 import (load, Nifti1Header, Nifti1PairHeader, Nifti1Image, Nifti1Pair, Nifti1Extension, Nifti1DicomExtension, Nifti1Extensions, data_type_codes, extension_codes, diff --git a/nibabel/tests/test_proxy_api.py b/nibabel/tests/test_proxy_api.py index 7825f7faff..b6fd1a004c 100644 --- a/nibabel/tests/test_proxy_api.py +++ b/nibabel/tests/test_proxy_api.py @@ -35,7 +35,7 @@ import numpy as np -from ..externals.six import string_types +from six import string_types from ..volumeutils import apply_read_scaling from ..analyze import AnalyzeHeader from ..spm99analyze import Spm99AnalyzeHeader diff --git a/nibabel/tests/test_round_trip.py b/nibabel/tests/test_round_trip.py index f60c9e9362..c6ba5ead96 100644 --- a/nibabel/tests/test_round_trip.py +++ b/nibabel/tests/test_round_trip.py @@ -5,7 +5,7 @@ import numpy as np -from ..externals.six import BytesIO +from six import BytesIO from .. import Nifti1Image, Nifti1Header from ..spatialimages import HeaderDataError, supported_np_types from ..arraywriters import ScalingError diff --git a/nibabel/tests/test_scaling.py b/nibabel/tests/test_scaling.py index 0d7395fb88..3a201db699 100644 --- a/nibabel/tests/test_scaling.py +++ b/nibabel/tests/test_scaling.py @@ -11,7 +11,7 @@ import numpy as np -from ..externals.six import BytesIO +from six import BytesIO from ..volumeutils import (calculate_scale, scale_min_max, finite_range, apply_read_scaling, array_to_file, array_from_file) from ..casting import type_info diff --git a/nibabel/tests/test_spatialimages.py b/nibabel/tests/test_spatialimages.py index 75c4f6e535..80b79c5318 100644 --- a/nibabel/tests/test_spatialimages.py +++ b/nibabel/tests/test_spatialimages.py @@ -14,7 +14,7 @@ import numpy as np -from ..externals.six import BytesIO +from six import BytesIO from ..spatialimages import (SpatialHeader, SpatialImage, HeaderDataError, Header, ImageDataError) diff --git a/nibabel/tests/test_spm99analyze.py b/nibabel/tests/test_spm99analyze.py index f810fb659e..e1be6200fb 100644 --- a/nibabel/tests/test_spm99analyze.py +++ b/nibabel/tests/test_spm99analyze.py @@ -10,7 +10,7 @@ import numpy as np import itertools -from ..externals.six import BytesIO +from six import BytesIO from numpy.testing import assert_array_equal, assert_array_almost_equal, dec diff --git a/nibabel/tests/test_trackvis.py b/nibabel/tests/test_trackvis.py index 1a240957ab..2e3f0a8adb 100644 --- a/nibabel/tests/test_trackvis.py +++ b/nibabel/tests/test_trackvis.py @@ -5,7 +5,7 @@ import numpy as np -from ..externals.six import BytesIO +from six import BytesIO from .. import trackvis as tv from ..orientations import aff2axcodes from ..volumeutils import native_code, swapped_code diff --git a/nibabel/tests/test_utils.py b/nibabel/tests/test_utils.py index f9b7fda632..cf14239f8e 100644 --- a/nibabel/tests/test_utils.py +++ b/nibabel/tests/test_utils.py @@ -12,7 +12,7 @@ import os from os.path import exists -from ..externals.six import BytesIO +from six import BytesIO import tempfile import warnings import functools diff --git a/nibabel/tests/test_wrapstruct.py b/nibabel/tests/test_wrapstruct.py index a2f1d6c2de..5ea346dab9 100644 --- a/nibabel/tests/test_wrapstruct.py +++ b/nibabel/tests/test_wrapstruct.py @@ -26,7 +26,7 @@ import logging import numpy as np -from ..externals.six import BytesIO, StringIO +from six import BytesIO, StringIO from ..wrapstruct import WrapStructError, WrapStruct, LabeledWrapStruct from ..batteryrunners import Report diff --git a/nisext/sexts.py b/nisext/sexts.py index da1c056418..b0d34348e5 100644 --- a/nisext/sexts.py +++ b/nisext/sexts.py @@ -265,3 +265,32 @@ def run(self): continue with open(bat_file, 'wt') as fobj: fobj.write(bat_contents) + + +class Bunch(object): + def __init__(self, vars): + for key, name in vars.items(): + if key.startswith('__'): + continue + self.__dict__[key] = name + + +def read_vars_from(ver_file): + """ Read variables from Python text file + + Parameters + ---------- + ver_file : str + Filename of file to read + + Returns + ------- + info_vars : Bunch instance + Bunch object where variables read from `ver_file` appear as + attributes + """ + # Use exec for compabibility with Python 3 + ns = {} + with open(ver_file, 'rt') as fobj: + exec(fobj.read(), ns) + return Bunch(ns) diff --git a/requirements.txt b/requirements.txt index 28c0ee779a..4faf1a105c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,4 +5,5 @@ # .travis.yml # doc/source/installation.rst -numpy>=1.5.1 +six>=1.3 +numpy>=1.6 diff --git a/setup.py b/setup.py index 5e9bf51c29..4d3c088fb4 100755 --- a/setup.py +++ b/setup.py @@ -29,13 +29,13 @@ from distutils.core import setup # Commit hash writing, and dependency checking -from nisext.sexts import get_comrec_build, package_check, install_scripts_bat +from nisext.sexts import (get_comrec_build, package_check, install_scripts_bat, + read_vars_from) cmdclass = {'build_py': get_comrec_build('nibabel'), 'install_scripts': install_scripts_bat} -# Get version and release info, which is all stored in nibabel/info.py -ver_file = os.path.join('nibabel', 'info.py') -exec(open(ver_file).read()) +# Get project related strings. +INFO = read_vars_from(pjoin('nibabel', 'info.py')) # Prepare setuptools args if 'setuptools' in sys.modules: @@ -53,31 +53,32 @@ pkg_chk = package_check # Do dependency checking -pkg_chk('numpy', NUMPY_MIN_VERSION) +pkg_chk('numpy', INFO.NUMPY_MIN_VERSION) +pkg_chk('six', INFO.SIX_MIN_VERSION) custom_pydicom_messages = {'missing opt': 'Missing optional package "%s"' ' provided by package "pydicom"' } pkg_chk('dicom', - PYDICOM_MIN_VERSION, + INFO.PYDICOM_MIN_VERSION, optional='dicom', messages = custom_pydicom_messages) def main(**extra_args): - setup(name=NAME, - maintainer=MAINTAINER, - maintainer_email=MAINTAINER_EMAIL, - description=DESCRIPTION, - long_description=LONG_DESCRIPTION, - url=URL, - download_url=DOWNLOAD_URL, - license=LICENSE, - classifiers=CLASSIFIERS, - author=AUTHOR, - author_email=AUTHOR_EMAIL, - platforms=PLATFORMS, - version=VERSION, - requires=REQUIRES, - provides=PROVIDES, + setup(name=INFO.NAME, + maintainer=INFO.MAINTAINER, + maintainer_email=INFO.MAINTAINER_EMAIL, + description=INFO.DESCRIPTION, + long_description=INFO.LONG_DESCRIPTION, + url=INFO.URL, + download_url=INFO.DOWNLOAD_URL, + license=INFO.LICENSE, + classifiers=INFO.CLASSIFIERS, + author=INFO.AUTHOR, + author_email=INFO.AUTHOR_EMAIL, + platforms=INFO.PLATFORMS, + version=INFO.VERSION, + requires=INFO.REQUIRES, + provides=INFO.PROVIDES, packages = ['nibabel', 'nibabel.externals', 'nibabel.externals.tests',