8000 MRG: add routine to deprecate with from/to versions by matthew-brett · Pull Request #479 · nipy/nibabel · GitHub
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Merged
merged 8 commits into from
Aug 15, 2016
Merged

MRG: add routine to deprecate with from/to versions #479

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87ac814
NF: add cmp_pkg_version function and test
matthew-brett Aug 11, 2016
b7448eb
NF+TST: add class / function to deprecate with versions
matthew-brett Aug 10, 2016
e8654dc
TST: add test of dev version for deprecation
matthew-brett Aug 12, 2016
09c63da
RF: replace numpy deprecation decorator with ours
matthew-brett Aug 10, 2016
1e35fc4
RF: remove `from_filespec` classmethod
matthew-brett Aug 10, 2016
edbdd2c
RF+TST: specify versions for DeprecationWarnings
matthew-brett Aug 10, 2016
101af68
RF+TST: deprecate `get_affine` method of image
matthew-brett Aug 11, 2016
f82e217
RF+TST: add deprecation to ECAT from_filespec
matthew-brett Aug 11, 2016
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RF: replace numpy deprecation decorator with ours 
Replace `np.deprecate_with_doc` with `deprecate_with_version`.

There are other deprecations around the code-base that could be
signalled with this decorator.
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@matthew-brett
matthew-brett committed Aug 12, 2016
commit 09c63dacdf3f031eb374731eee7980e315411e6b
70 changes: 51 additions & 19 deletions nibabel/gifti/gifti.py
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Expand Up @@ -14,7 +14,6 @@
from __future__ import division, print_function, absolute_import

import sys
import warnings

import numpy as np

Expand All @@ -23,6 +22,7 @@
from ..nifti1 import data_type_codes, xform_codes, intent_codes
from .util import (array_index_order_codes, gifti_encoding_codes,
gifti_endian_codes, KIND2FMT)
from ..deprecated import deprecate_with_version

# {en,de}codestring in deprecated in Python3, but
# {en,de}codebytes not available in Python2.
Expand All @@ -47,7 +47,10 @@ def from_dict(klass, data_dict):
meda.data.append(nv)
return meda

@np.deprecate_with_doc("Use the metadata property instead.")
@deprecate_with_version(
'get_metadata method deprecated. '
"Use the metadata property instead."
'2.1', '4.0')
def get_metadata(self):
return self.metadata

Expand Down Expand Up @@ -156,7 +159,10 @@ def __init__(self, key=0, red=None, green=None, blue=None, alpha=None):
self.blue = blue
self.alpha = alpha

@np.deprecate_with_doc("Use the rgba property instead.")
@deprecate_with_version(
'get_rgba method deprecated. '
"Use the rgba property instead."
'2.1', '4.0')
def get_rgba(self):
return self.rgba

Expand Down Expand Up @@ -249,7 +255,9 @@ def print_summary(self):
print('Affine Transformation Matrix: \n', self.xform)


@np.deprecate_with_doc("This is an internal API that will be discontinued.")
@deprecate_with_version(
"data_tag is an internal API that will be discontinued.",
'2.1', '4.0')
def data_tag(dataarray, encoding, datatype, ordering):
class DataTag(xml.XmlSerializable):

Expand Down Expand Up @@ -371,16 +379,20 @@ def num_dim(self):

# Setter for backwards compatibility with pymvpa
@num_dim.setter
@deprecate_with_version(
"num_dim will be read-only in future versions of nibabel",
'2.1', '4.0')
def num_dim(self, value):
warnings.warn(
"num_dim will be read-only in future versions of nibabel",
DeprecationWarning, stacklevel=2)
if value != len(self.dims):
raise ValueError('num_dim value {0} != number of dimensions '
'len(self.dims) {1}'
.format(value, len(self.dims)))

@classmethod
@deprecate_with_version(
'from_array method is deprecated. '
'Please use GiftiDataArray constructor instead.',
'2.1', '4.0')
def from_array(klass,
darray,
intent="NIFTI_INTENT_NONE",
Expand Down Expand Up @@ -419,10 +431,6 @@ def from_array(klass,
-------
da : instance of our own class
"""
warnings.warn(
"Please use GiftiDataArray constructor instead of from_array "
"class method",
DeprecationWarning, stacklevel=2)
return klass(data=darray,
intent=intent,
datatype=datatype,
Expand Down Expand Up @@ -463,7 +471,10 @@ def _to_xml_element(self):

return data_array

@np.deprecate_with_doc("Use the to_xml() function instead.")
@deprecate_with_version(
'to_xml_open method deprecated. '
'Use the to_xml() function instead.',
'2.1', '4.0')
def to_xml_open(self):
out = """<DataArray Intent="%s"
\tDataType="%s"
Expand All @@ -487,7 +498,10 @@ def to_xml_open(self):
self.ext_offset,
)

@np.deprecate_with_doc("Use the to_xml() function instead.")
@deprecate_with_version(
'to_xml_close method deprecated. '
'Use the to_xml() function instead.',
'2.1', '4.0')
def to_xml_close(self):
return "</DataArray>\n"

Expand All @@ -507,7 +521,10 @@ def print_summary(self):
print('Coordinate System:')
print(self.coordsys.print_summary())

@np.deprecate_with_doc("Use the metadata property instead.")
@deprecate_with_version(
'get_metadata method deprecated. '
"Use the metadata property instead."
'2.1', '4.0')
def get_metadata(self):
return self.meta.metadata

Expand Down Expand Up @@ -591,11 +608,17 @@ def labeltable(self, labeltable):
raise TypeError("Not a valid GiftiLabelTable instance")
self._labeltable = labeltable

@np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
@deprecate_with_version(
'set_labeltable method deprecated. '
"Use the gifti_img.labeltable property instead.",
'2.1', '4.0')
def set_labeltable(self, labeltable):
self.labeltable = labeltable

@np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
@deprecate_with_version(
'get_labeltable method deprecated. '
"Use the gifti_img.labeltable property instead.",
'2.1', '4.0')
def get_labeltable(self):
return self.labeltable

Expand All @@ -615,11 +638,17 @@ def meta(self, meta):
raise TypeError("Not a valid GiftiMetaData instance")
self._meta = meta

@np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
@deprecate_with_version(
'set_meta method deprecated. '
"Use the gifti_img.meta property instead.",
'2.1', '4.0')
def set_metadata(self, meta):
self.meta = meta

@np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
@deprecate_with_version(
'get_meta method deprecated. '
"Use the gifti_img.meta property instead.",
'2.1', '4.0')
def get_meta(self):
return self.meta

Expand Down Expand Up @@ -651,7 +680,10 @@ def get_arrays_from_intent(self, intent):
it = intent_codes.code[intent]
return [x for x in self.darrays if x.intent == it]

@np.deprecate_with_doc("Use get_arrays_from_intent instead.")
@deprecate_with_version(
'getArraysFromIntent method deprecated. '
"Use get_arrays_from_intent instead.",
'2.1', '4.0')
def getArraysFromIntent(self, intent):
return self.get_arrays_from_intent(intent)

Expand Down
10 changes: 7 additions & 3 deletions nibabel/gifti/giftiio.py
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Expand Up @@ -10,10 +10,12 @@
# Stephan Gerhard, Oktober 2010
##############

import numpy as np
from ..deprecated import deprecate_with_version


@np.deprecate_with_doc("Use nibabel.load() instead.")
@deprecate_with_version('giftiio.read function deprecated. '
"Use nibabel.load() instead.",
'2.1', '4.0')
def read(filename):
""" Load a Gifti image from a file

Expand All @@ -31,7 +33,9 @@ def read(filename):
return load(filename)


@np.deprecate_with_doc("Use nibabel.save() instead.")
@deprecate_with_version('giftiio.write function deprecated. '
"Use nibabel.load() instead.",
'2.1', '4.0')
def write(image, filename):
""" Save the current image to a new file

Expand Down
9 changes: 7 additions & 2 deletions nibabel/gifti/parse_gifti_fast.py
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Expand Up @@ -24,6 +24,7 @@
gifti_endian_codes)
from ..nifti1 import data_type_codes, xform_codes, intent_codes
from ..xmlutils import XmlParser
from ..deprecated import deprecate_with_version


class GiftiParseError(ExpatError):
Expand Down Expand Up @@ -342,7 +343,9 @@ def pending_data(self):

class Outputter(GiftiImageParser):

@np.deprecate_with_doc("Use GiftiImageParser instead.")
@deprecate_with_version('Outputter class deprecated. '
"Use GiftiImageParser instead.",
'2.1', '4.0')
def __init__(self):
super(Outputter, self).__init__()

Expand All @@ -351,6 +354,8 @@ def initialize(self):
self.__init__()


@np.deprecate_with_doc("Use GiftiImageParser.parse() instead.")
@deprecate_with_version('parse_gifti_file deprecated. '
"Use GiftiImageParser.parse() instead.",
'2.1', '4.0')
def parse_gifti_file(fname=None, fptr=None, buffer_size=None):
GiftiImageParser(buffer_size=buffer_size).parse(fname=fname, fptr=fptr)
20 changes: 16 additions & 4 deletions nibabel/gifti/tests/test_gifti.py
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Expand Up @@ -206,17 +206,29 @@ def test_labeltable():
img.labeltable = new_table
assert_equal(len(img.labeltable.labels), 2)

# Test deprecations
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
newer_table = GiftiLabelTable()
newer_table.labels += ['test', 'me', 'again']
img.set_labeltable(newer_table)
assert_equal(len(w), 1)
assert_equal(len(img.get_labeltable().labels), 3)
assert_equal(len(w), 2)


def test_metadata():
nvpair = GiftiNVPairs('key', 'value')
da = GiftiMetaData(nvpair=nvpair)
assert_equal(da.data[0].name, 'key')
assert_equal(da.data[0].value, 'value')
md = GiftiMetaData(nvpair=nvpair)
assert_equal(md.data[0].name, 'key')
assert_equal(md.data[0].value, 'value')
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
assert_equal(md.get_metadata(), dict(key='value'))
assert_equal(len(w), 1)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
assert_equal(len(w), 2)


def test_gifti_label_rgba():
Expand Down
10 changes: 7 additions & 3 deletions nibabel/gifti/tests/test_giftiio.py
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Expand Up @@ -11,7 +11,8 @@

from nose.tools import (assert_true, assert_false, assert_equal,
assert_raises)
from ...testing import clear_and_catch_warnings
from nibabel.testing import clear_and_catch_warnings
from nibabel.tmpdirs import InTemporaryDirectory


from .test_parse_gifti_fast import (DATA_FILE1, DATA_FILE2, DATA_FILE3,
Expand All @@ -29,7 +30,10 @@ def setUp(self):
def test_read_deprecated():
with clear_and_catch_warnings() as w:
warnings.simplefilter('always', DeprecationWarning)
from nibabel.gifti.giftiio import read
from nibabel.gifti.giftiio import read, write

read(DATA_FILE1)
img = read(DATA_FILE1)
assert_equal(len(w), 1)
with InTemporaryDirectory():
write(img, 'test.gii')
assert_equal(len(w), 2)
20 changes: 11 additions & 9 deletions nibabel/loadsave.py
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Expand Up @@ -11,14 +11,14 @@

import os.path as op
import numpy as np
import warnings

from .filename_parser import splitext_addext
from .openers import ImageOpener
from .filebasedimages import ImageFileError
from .imageclasses import all_image_classes
from .arrayproxy import is_proxy
from .py3k import FileNotFoundError
from .deprecated import deprecate_with_version


def load(filename, **kwargs):
Expand Down Expand Up @@ -48,7 +48,9 @@ def load(filename, **kwargs):
filename)


@np.deprecate
@deprecate_with_version('guessed_image_type deprecated.'
'2.1',
'4.0')
def guessed_image_type(filename):
""" Guess image type from file `filename`

Expand All @@ -62,8 +64,6 @@ def guessed_image_type(filename):
image_class : class
Class corresponding to guessed image type
"""
warnings.warn('guessed_image_type is deprecated', DeprecationWarning,
stacklevel=2)
sniff = None
for image_klass in all_image_classes:
is_valid, sniff = image_klass.path_maybe_image(filename, sniff)
Expand Down Expand Up @@ -124,8 +124,10 @@ def save(img, filename):
converted.to_filename(filename)


@np.deprecate_with_doc('Please use ``img.dataobj.get_unscaled()`` '
'instead')
@deprecate_with_version('read_img_data deprecated.'
'Please use ``img.dataobj.get_unscaled()`` instead.'
'2.0.1',
'4.0')
def read_img_data(img, prefer='scaled'):
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This function also has a docstring deprecation notice.

""" Read data from image associated with files

Expand Down Expand Up @@ -210,7 +212,9 @@ def read_img_data(img, prefer='scaled'):
return hdr.raw_data_from_fileobj(fileobj)


@np.deprecate
@deprecate_with_version('which_analyze_type deprecated.'
'2.1',
'4.0')
def which_analyze_type(binaryblock):
""" Is `binaryblock` from NIfTI1, NIfTI2 or Analyze header?

Expand Down Expand Up @@ -238,8 +242,6 @@ def which_analyze_type(binaryblock):
* if ``sizeof_hdr`` is 348 or byteswapped 348 assume Analyze
* Return None
"""
warnings.warn('which_analyze_type is deprecated', DeprecationWarning,
stacklevel=2)
from .nifti1 import header_dtype
hdr_struct = np.ndarray(shape=(), dtype=header_dtype, buffer=binaryblock)
bs_hdr_struct = hdr_struct.byteswap()
Expand Down
7 changes: 6 additions & 1 deletion nibabel/orientations.py
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Expand Up @@ -13,6 +13,8 @@
import numpy as np
import numpy.linalg as npl

from .deprecated import deprecate_with_version


class OrientationError(Exception):
pass
Expand Down Expand Up @@ -228,7 +230,10 @@ def inv_ornt_aff(ornt, shape):
return np.dot(undo_flip, undo_reorder)


@np.deprecate_with_doc("Please use inv_ornt_aff instead")
@deprecate_with_version('orientation_affine deprecated. '
'Please use inv_ornt_aff instead'
'1.3',
'3.0')
def orientation_affine(ornt, shape):
return inv_ornt_aff(ornt, shape)

Expand Down
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