[med-svn] [Git][med-team/nibabel][upstream] New upstream version 4.0.2
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Dec 8 21:06:39 GMT 2022
Étienne Mollier pushed to branch upstream at Debian Med / nibabel
Commits:
3e4459c2 by Étienne Mollier at 2022-12-08T21:19:23+01:00
New upstream version 4.0.2
- - - - -
9 changed files:
- Changelog
- nibabel/_version.py
- nibabel/arraywriters.py
- nibabel/gifti/gifti.py
- nibabel/gifti/tests/test_gifti.py
- nibabel/gifti/tests/test_parse_gifti_fast.py
- nibabel/info.py
- nibabel/tests/test_arraywriters.py
- nibabel/tests/test_removalschedule.py
Changes:
=====================================
Changelog
=====================================
@@ -25,6 +25,22 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
References like "pr/298" refer to github pull request numbers.
+4.0.2 (Wednesday 31 August 2022)
+================================
+
+Bug-fix release in the 4.0.x series.
+
+Bug fixes
+---------
+* Make ``GiftiMetaData.data`` a list proxy, deprecate (pr/1127) (CM, reviewed
+ by Hao-Ting Wang)
+
+Maintenance
+-----------
+* Finalize deprecation of ``ArrayWriter.to_fileobj(nan2zero=...)`` argument
+ (pr/1126) (CM)
+
+
4.0.1 (Saturday 18 June 2022)
=============================
=====================================
nibabel/_version.py
=====================================
@@ -26,9 +26,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: 4.0.1)"
- git_full = "b0b16b811aaf7bb866ca764259c0cd20f8c03950"
- git_date = "2022-06-18 17:52:37 +0100"
+ git_refnames = " (tag: 4.0.2)"
+ git_full = "0efe615554874c8d6c1dd3934e22a91f9ffa297f"
+ git_date = "2022-08-31 09:39:12 -0400"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
nibabel/arraywriters.py
=====================================
@@ -29,13 +29,12 @@ something else to make sense of conversions between float and int, or between
larger ints and smaller.
"""
-import warnings
-
import numpy as np
from .casting import (int_to_float, as_int, int_abs, type_info, floor_exact,
best_float, shared_range)
from .volumeutils import finite_range, array_to_file
+from .deprecator import ExpiredDeprecationError
class WriterError(Exception):
@@ -192,11 +191,12 @@ class ArrayWriter(object):
if 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.\n'
- '* deprecated in version: 2.0\n'
- '* will raise error in version: 4.0\n',
- DeprecationWarning, stacklevel=3)
+ raise ExpiredDeprecationError(
+ 'Please remove `nan2zero` from call to `to_fileobj` '
+ 'and use in instance __init__ instead.\n'
+ '* deprecated in version: 2.0\n'
+ '* Raises ExpiredDeprecationError as of version: 4.0\n'
+ )
def _needs_nan2zero(self):
""" True if nan2zero check needed for writing array """
=====================================
nibabel/gifti/gifti.py
=====================================
@@ -26,6 +26,42 @@ from .util import (array_index_order_codes, gifti_encoding_codes,
from ..deprecated import deprecate_with_version
+class _GiftiMDList(list):
+ """List view of GiftiMetaData object that will translate most operations"""
+ def __init__(self, metadata):
+ self._md = metadata
+ super().__init__(
+ GiftiNVPairs._private_init(k, v, metadata)
+ for k, v in metadata.items()
+ )
+
+ def append(self, nvpair):
+ self._md[nvpair.name] = nvpair.value
+ super().append(nvpair)
+
+ def clear(self):
+ super().clear()
+ self._md.clear()
+
+ def extend(self, iterable):
+ for nvpair in iterable:
+ self.append(nvpair)
+
+ def insert(self, index, nvpair):
+ self._md[nvpair.name] = nvpair.value
+ super().insert(index, nvpair)
+
+ def pop(self, index=-1):
+ nvpair = super().pop(index)
+ nvpair._container = None
+ del self._md[nvpair.name]
+ return nvpair
+
+ def remove(self, nvpair):
+ super().remove(nvpair)
+ del self._md[nvpair.name]
+
+
class GiftiMetaData(CaretMetaData):
""" A sequence of GiftiNVPairs containing metadata for a gifti data array
"""
@@ -72,11 +108,12 @@ class GiftiMetaData(CaretMetaData):
return (), {pair.name: pair.value}
@property
+ @deprecate_with_version(
+ 'The data attribute is deprecated. Use GiftiMetaData object '
+ 'directly as a dict.',
+ '4.0', '6.0')
def data(self):
- warnings.warn(
- "GiftiMetaData.data will be a dict in NiBabel 6.0.",
- FutureWarning, stacklevel=2)
- return [GiftiNVPairs(k, v) for k, v in self._data.items()]
+ return _GiftiMDList(self)
@classmethod
@deprecate_with_version(
@@ -94,7 +131,7 @@ class GiftiMetaData(CaretMetaData):
@property
@deprecate_with_version(
- 'metadata property deprecated. Use GiftiMetadata object '
+ 'metadata property deprecated. Use GiftiMetaData object '
'as dict or pass to dict() for a standard dictionary.',
'4.0', '6.0')
def metadata(self):
@@ -113,9 +150,48 @@ class GiftiNVPairs:
name : str
value : str
"""
+ @deprecate_with_version(
+ 'GiftiNVPairs objects are deprecated. Use the GiftiMetaData object '
+ 'as a dict, instead.',
+ '4.0', '6.0')
def __init__(self, name=u'', value=u''):
- self.name = name
- self.value = value
+ self._name = name
+ self._value = value
+ self._container = None
+
+ @classmethod
+ def _private_init(cls, name, value, md):
+ """Private init method to provide warning-free experience"""
+ with warnings.catch_warnings():
+ warnings.simplefilter('ignore', DeprecationWarning)
+ self = cls(name, value)
+ self._container = md
+ return self
+
+ def __eq__(self, other):
+ if not isinstance(other, GiftiNVPairs):
+ return NotImplemented
+ return self.name == other.name and self.value == other.value
+
+ @property
+ def name(self):
+ return self._name
+
+ @name.setter
+ def name(self, key):
+ if self._container:
+ self._container[key] = self._container.pop(self._name)
+ self._name = key
+
+ @property
+ def value(self):
+ return self._value
+
+ @value.setter
+ def value(self, val):
+ if self._container:
+ self._container[self._name] = val
+ self._value = val
class GiftiLabelTable(xml.XmlSerializable):
=====================================
nibabel/gifti/tests/test_gifti.py
=====================================
@@ -228,7 +228,8 @@ def test_labeltable():
def test_metadata():
md = GiftiMetaData(key='value')
# Old initialization methods
- nvpair = GiftiNVPairs('key', 'value')
+ with pytest.warns(DeprecationWarning) as w:
+ nvpair = GiftiNVPairs('key', 'value')
with pytest.warns(FutureWarning) as w:
md2 = GiftiMetaData(nvpair=nvpair)
assert len(w) == 1
@@ -236,7 +237,7 @@ def test_metadata():
md3 = GiftiMetaData.from_dict({'key': 'value'})
assert md == md2 == md3 == {'key': 'value'}
# .data as a list of NVPairs is going away
- with pytest.warns(FutureWarning) as w:
+ with pytest.warns(DeprecationWarning) as w:
assert md.data[0].name == 'key'
assert md.data[0].value == 'value'
assert len(w) == 2
@@ -245,6 +246,85 @@ def test_metadata():
md.get_metadata()
+def test_metadata_list_interface():
+ md = GiftiMetaData(key='value')
+ with pytest.warns(DeprecationWarning):
+ mdlist = md.data
+ assert len(mdlist) == 1
+ assert mdlist[0].name == 'key'
+ assert mdlist[0].value == 'value'
+
+ # Modify elements in-place
+ mdlist[0].name = 'foo'
+ assert mdlist[0].name == 'foo'
+ assert 'foo' in md
+ assert 'key' not in md
+ assert md['foo'] == 'value'
+ mdlist[0].value = 'bar'
+ assert mdlist[0].value == 'bar'
+ assert md['foo'] == 'bar'
+
+ # Append new NVPair
+ with pytest.warns(DeprecationWarning) as w:
+ nvpair = GiftiNVPairs('key', 'value')
+ mdlist.append(nvpair)
+ assert len(mdlist) == 2
+ assert mdlist[1].name == 'key'
+ assert mdlist[1].value == 'value'
+ assert len(md) == 2
+ assert md == {'foo': 'bar', 'key': 'value'}
+
+ # Clearing empties both
+ mdlist.clear()
+ assert len(mdlist) == 0
+ assert len(md) == 0
+
+ # Extension adds multiple keys
+ with pytest.warns(DeprecationWarning) as w:
+ foobar = GiftiNVPairs('foo', 'bar')
+ mdlist.extend([nvpair, foobar])
+ assert len(mdlist) == 2
+ assert len(md) == 2
+ assert md == {'key': 'value', 'foo': 'bar'}
+
+ # Insertion updates list order, though we don't attempt to preserve it in the dict
+ with pytest.warns(DeprecationWarning) as w:
+ lastone = GiftiNVPairs('last', 'one')
+ mdlist.insert(1, lastone)
+ assert len(mdlist) == 3
+ assert len(md) == 3
+ assert mdlist[1].name == 'last'
+ assert mdlist[1].value == 'one'
+ assert md == {'key': 'value', 'foo': 'bar', 'last': 'one'}
+
+ # Popping returns a pair
+ mypair = mdlist.pop(0)
+ assert isinstance(mypair, GiftiNVPairs)
+ assert mypair.name == 'key'
+ assert mypair.value == 'value'
+ assert len(mdlist) == 2
+ assert len(md) == 2
+ assert 'key' not in md
+ assert md == {'foo': 'bar', 'last': 'one'}
+ # Modifying the pair now does not affect md
+ mypair.name = 'completelynew'
+ mypair.value = 'strings'
+ assert 'completelynew' not in md
+ assert md == {'foo': 'bar', 'last': 'one'}
+ # Check popping from the end (lastone inserted before foobar)
+ lastpair = mdlist.pop()
+ assert len(mdlist) == 1
+ assert len(md) == 1
+ assert md == {'last': 'one'}
+
+ # And let's remove an old pair with a new object
+ with pytest.warns(DeprecationWarning) as w:
+ lastoneagain = GiftiNVPairs('last', 'one')
+ mdlist.remove(lastoneagain)
+ assert len(mdlist) == 0
+ assert len(md) == 0
+
+
def test_gifti_label_rgba():
rgba = np.random.rand(4)
kwargs = dict(zip(['red', 'green', 'blue', 'alpha'], rgba))
=====================================
nibabel/gifti/tests/test_parse_gifti_fast.py
=====================================
@@ -147,7 +147,7 @@ def test_default_types():
# GiftiMetaData
assert_default_types(img.meta)
# GiftiNVPairs - Remove in NIB6
- with pytest.warns(FutureWarning):
+ with pytest.warns(DeprecationWarning):
for nvpair in img.meta.data:
assert_default_types(nvpair)
# GiftiLabelTable
@@ -161,7 +161,7 @@ def test_default_types():
# GiftiMetaData
assert_default_types(darray.meta)
# GiftiNVPairs - Remove in NIB6
- with pytest.warns(FutureWarning):
+ with pytest.warns(DeprecationWarning):
for nvpair in darray.meta.data:
assert_default_types(nvpair)
=====================================
nibabel/info.py
=====================================
@@ -12,7 +12,7 @@ relative imports.
# development (pre-release) version.
_version_major = 4
_version_minor = 0
-_version_micro = 1
+_version_micro = 2
_version_extra = '.dev0'
# Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
=====================================
nibabel/tests/test_arraywriters.py
=====================================
@@ -13,11 +13,11 @@ from ..arraywriters import (SlopeInterArrayWriter, SlopeArrayWriter,
make_array_writer, get_slope_inter)
from ..casting import int_abs, type_info, shared_range, on_powerpc
from ..volumeutils import array_from_file, apply_read_scaling, _dt_min_max
+from ..deprecator import ExpiredDeprecationError
from numpy.testing import assert_array_almost_equal, assert_array_equal
import pytest
-from ..testing import (assert_allclose_safely, suppress_warnings,
- error_warnings)
+from ..testing import assert_allclose_safely, suppress_warnings
FLOAT_TYPES = np.sctypes['float']
@@ -506,12 +506,11 @@ def test_nan2zero():
aw = awt(arr, np.float32, **kwargs)
data_back = round_trip(aw)
assert_array_equal(np.isnan(data_back), [True, False])
- # Deprecation warning for nan2zero as argument to `to_fileobj`
- with error_warnings():
- with pytest.deprecated_call():
- aw.to_fileobj(BytesIO(), 'F', True)
- with pytest.deprecated_call():
- aw.to_fileobj(BytesIO(), 'F', nan2zero=True)
+ # Expired deprecation error for nan2zero as argument to `to_fileobj`
+ with pytest.raises(ExpiredDeprecationError):
+ aw.to_fileobj(BytesIO(), 'F', True)
+ with pytest.raises(ExpiredDeprecationError):
+ aw.to_fileobj(BytesIO(), 'F', nan2zero=True)
# Error if nan2zero is not the value set at initialization
with pytest.raises(WriterError):
aw.to_fileobj(BytesIO(), 'F', False)
@@ -528,12 +527,11 @@ def test_nan2zero():
data_back = round_trip(aw)
astype_res = np.array(np.nan).astype(np.int32)
assert_array_equal(data_back, [astype_res, 99])
- # Deprecation warning for nan2zero as argument to `to_fileobj`
- with error_warnings():
- with pytest.deprecated_call():
- aw.to_fileobj(BytesIO(), 'F', False)
- with pytest.deprecated_call():
- aw.to_fileobj(BytesIO(), 'F', nan2zero=False)
+ # Expired deprecation error for nan2zero as argument to `to_fileobj`
+ with pytest.raises(ExpiredDeprecationError):
+ aw.to_fileobj(BytesIO(), 'F', False)
+ with pytest.raises(ExpiredDeprecationError):
+ aw.to_fileobj(BytesIO(), 'F', nan2zero=False)
# Error if nan2zero is not the value set at initialization
with pytest.raises(WriterError):
aw.to_fileobj(BytesIO(), 'F', True)
=====================================
nibabel/tests/test_removalschedule.py
=====================================
@@ -12,6 +12,8 @@ MODULE_SCHEDULE = [
]
OBJECT_SCHEDULE = [
+ ("7.0.0", [("nibabel.gifti.gifti", "GiftiNVPairs"),
+ ]),
("6.0.0", [("nibabel.loadsave", "guessed_image_type"),
("nibabel.loadsave", "read_img_data"),
("nibabel.orientations", "flip_axis"),
@@ -41,6 +43,7 @@ OBJECT_SCHEDULE = [
ATTRIBUTE_SCHEDULE = [
("7.0.0", [("nibabel.gifti.gifti", "GiftiMetaData", "from_dict"),
("nibabel.gifti.gifti", "GiftiMetaData", "metadata"),
+ ("nibabel.gifti.gifti", "GiftiMetaData", "data"),
]),
("5.0.0", [("nibabel.dataobj_images", "DataobjImage", "get_data"),
("nibabel.freesurfer.mghformat", "MGHHeader", "_header_data"),
@@ -62,6 +65,7 @@ ATTRIBUTE_SCHEDULE = [
("nibabel.ecat", "EcatImage", "from_filespec"),
("nibabel.filebasedimages", "FileBasedImage", "get_header"),
("nibabel.spatialimages", "SpatialImage", "get_affine"),
+ ("nibabel.arraywriters", "ArrayWriter", "_check_nan2zero"),
]),
("4.0.0", [("nibabel.dataobj_images", "DataobjImage", "get_shape"),
("nibabel.filebasedimages", "FileBasedImage", "filespec_to_files"),
View it on GitLab: https://salsa.debian.org/med-team/nibabel/-/commit/3e4459c2fe5ea0509cd504e7f813752a371a8a45
--
View it on GitLab: https://salsa.debian.org/med-team/nibabel/-/commit/3e4459c2fe5ea0509cd504e7f813752a371a8a45
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