Merge pull request #1141 from effigies/mnt/5.0.0.dev0

MNT: 5.0.0.dev0

Author: effigies

nibabel/__init__.py

@@ -58,10 +58,9 @@
 from .freesurfer import MGHImage
 from .funcs import (squeeze_image, concat_images, four_to_three,
                     as_closest_canonical)
-from .orientations import (io_orientation, orientation_affine,
-                           flip_axis, OrientationError,
+from .orientations import (io_orientation, flip_axis, OrientationError,
                            apply_orientation, aff2axcodes)
-from .imageclasses import class_map, ext_map, all_image_classes
+from .imageclasses import all_image_classes
 from . import mriutils
 from . import streamlines
 from . import viewers

nibabel/arraywriters.py

@@ -34,7 +34,6 @@ def __init__(self, array, out_dtype=None)
 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):
@@ -185,38 +184,22 @@ def finite_range(self):
             self._has_nan = has_nan
         return self._finite_range
 
-    def _check_nan2zero(self, nan2zero):
-        if nan2zero is None:
-            return
-        if nan2zero != self._nan2zero:
-            raise WriterError('Deprecated `nan2zero` argument to `to_fileobj` '
-                              'must be same as class value set in __init__')
-        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 """
         return (self._nan2zero and
                 self._array.dtype.kind in 'fc' and
                 self.out_dtype.kind in 'iu' and
                 self.has_nan)
 
-    def to_fileobj(self, fileobj, order='F', nan2zero=None):
+    def to_fileobj(self, fileobj, order='F'):
         """ Write array into `fileobj`
 
         Parameters
         ----------
         fileobj : file-like object
         order : {'F', 'C'}
             order (Fortran or C) to which to write array
-        nan2zero : {None, True, False}, optional, deprecated
-            Deprecated version of argument to __init__ with same name
         """
-        self._check_nan2zero(nan2zero)
         array_to_file(self._array,
                       fileobj,
                       self._out_dtype,
@@ -362,18 +345,15 @@ def _writing_range(self):
             return mn, mx
         return None, None
 
-    def to_fileobj(self, fileobj, order='F', nan2zero=None):
+    def to_fileobj(self, fileobj, order='F'):
         """ Write array into `fileobj`
 
         Parameters
         ----------
         fileobj : file-like object
         order : {'F', 'C'}
             order (Fortran or C) to which to write array
-        nan2zero : {None, True, False}, optional, deprecated
-            Deprecated version of argument to __init__ with same name
         """
-        self._check_nan2zero(nan2zero)
         mn, mx = self._writing_range()
         array_to_file(self._array,
                       fileobj,
@@ -536,18 +516,15 @@ def _set_inter(self, val):
         self._inter = np.squeeze(self.scaler_dtype.type(val))
     inter = property(_get_inter, _set_inter, None, 'get/set inter')
 
-    def to_fileobj(self, fileobj, order='F', nan2zero=None):
+    def to_fileobj(self, fileobj, order='F'):
         """ Write array into `fileobj`
 
         Parameters
         ----------
         fileobj : file-like object
         order : {'F', 'C'}
             order (Fortran or C) to which to write array
-        nan2zero : {None, True, False}, optional, deprecated
-            Deprecated version of argument to __init__ with same name
         """
-        self._check_nan2zero(nan2zero)
         mn, mx = self._writing_range()
         array_to_file(self._array,
                       fileobj,

nibabel/conftest.py

@@ -1,11 +1,5 @@
 import pytest
 
-# Pre-load deprecated modules to avoid cluttering warnings
-with pytest.deprecated_call():
-    import nibabel.keywordonly
-with pytest.warns(FutureWarning):
-    import nibabel.py3k
-
 # Ignore warning requesting help with nicom
 with pytest.warns(UserWarning):
     import nibabel.nicom

nibabel/dataobj_images.py

@@ -48,13 +48,6 @@ def __init__(self, dataobj, header=None, extra=None, file_map=None):
     def dataobj(self):
         return self._dataobj
 
-    @property
-    @deprecate_with_version('_data attribute not part of public API. '
-                            'please use "dataobj" property instead.',
-                            '2.0', '4.0')
-    def _data(self):
-        return self._dataobj
-
     @deprecate_with_version('get_data() is deprecated in favor of get_fdata(),'
                             ' which has a more predictable return type. To '
                             'obtain get_data() behavior going forward, use '

nibabel/ecat.py

@@ -54,7 +54,6 @@
 from .arraywriters import make_array_writer
 from .wrapstruct import WrapStruct
 from .fileslice import canonical_slicers, predict_shape, slice2outax
-from .deprecated import deprecate_with_version
 
 BLOCK_SIZE = 512
 
@@ -863,14 +862,6 @@ def get_subheaders(self):
         """get access to subheaders"""
         return self._subheader
 
-    @classmethod
-    @deprecate_with_version('from_filespec class method is deprecated.\n'
-                            'Please use the ``from_file_map`` class method '
-                            'instead.',
-                            '2.1', '4.0')
-    def from_filespec(klass, filespec):
-        return klass.from_filename(filespec)
-
     @staticmethod
     def _get_fileholders(file_map):
         """ returns files specific to header and image of the image

nibabel/filebasedimages.py

@@ -15,7 +15,6 @@
 from .filename_parser import (types_filenames, TypesFilenamesError,
                               splitext_addext)
 from .openers import ImageOpener
-from .deprecated import deprecate_with_version
 
 
 class ImageFileError(Exception):
@@ -79,7 +78,6 @@ class FileBasedImage:
 
     methods:
 
-       * get_header() (deprecated, use header property instead)
        * to_filename(fname) - writes data to filename(s) derived from
          ``fname``, where the derivation may differ between formats.
        * to_file_map() - save image to files with which the image is already
@@ -208,15 +206,6 @@ def __getitem__(self, key):
         """
         raise TypeError("Cannot slice image objects.")
 
-    @deprecate_with_version('get_header method is deprecated.\n'
-                            'Please use the ``img.header`` property '
-                            'instead.',
-                            '2.1', '4.0')
-    def get_header(self):
-        """ Get header from image
-        """
-        return self.header
-
     def get_filename(self):
         """ Fetch the image filename
 

nibabel/freesurfer/mghformat.py

@@ -24,7 +24,6 @@
 from ..openers import ImageOpener
 from ..batteryrunners import BatteryRunner, Report
 from ..wrapstruct import LabeledWrapStruct
-from ..deprecated import deprecate_with_version
 
 # mgh header
 # See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
@@ -462,45 +461,6 @@ def diagnose_binaryblock(klass, binaryblock, endianness=None):
         return '\n'.join([report.message
                           for report in reports if report.message])
 
-    class _HeaderData:
-        """ Provide interface to deprecated MGHHeader fields"""
-        def __init__(self, structarr):
-            self._structarr = structarr
-
-        def __getitem__(self, item):
-            sa = self._structarr
-            if item == 'mrparams':
-                return np.hstack((sa['tr'], sa['flip_angle'], sa['te'], sa['ti']))
-            return sa[item]
-
-        def __setitem__(self, item, val):
-            sa = self._structarr
-            if item == 'mrparams':
-                sa['tr'], sa['flip_angle'], sa['te'], sa['ti'] = val
-            else:
-                sa[item] = val
-
-    @property
-    @deprecate_with_version('_header_data is deprecated.\n'
-                            'Please use the _structarr interface instead.\n'
-                            'Note also that some fields have changed name and '
-                            'shape.',
-                            '2.3', '4.0')
-    def _header_data(self):
-        """ Deprecated field-access interface """
-        return self._HeaderData(self._structarr)
-
-    def __getitem__(self, item):
-        if item == 'mrparams':
-            return self._header_data[item]
-        return super(MGHHeader, self).__getitem__(item)
-
-    def __setitem__(self, item, value):
-        if item == 'mrparams':
-            self._header_data[item] = value
-        else:
-            super(MGHHeader, self).__setitem__(item, value)
-
 
 class MGHImage(SpatialImage, SerializableImage):
     """ Class for MGH format image

nibabel/freesurfer/tests/test_mghformat.py

@@ -22,7 +22,6 @@
 from ...volumeutils import sys_is_le
 from ...wrapstruct import WrapStructError
 from ... import imageglobals
-from ...deprecator import ExpiredDeprecationError
 
 
 import pytest
@@ -340,20 +339,6 @@ def test_mghheader_default_structarr():
             MGHHeader.default_structarr(endianness=endianness)
 
 
-def test_deprecated_fields():
-    hdr = MGHHeader()
-    hdr_data = MGHHeader._HeaderData(hdr.structarr)
-
-    # mrparams is the only deprecated field at the moment
-    # Accessing hdr_data is equivalent to accessing hdr, so double all checks,
-    # but expect success on hdr_data['mrparams']
-    with pytest.raises(ExpiredDeprecationError):
-        hdr['mrparams']
-    with pytest.raises(ExpiredDeprecationError):
-        hdr['mrparams'] = [1, 2, 3, 4]
-    assert_array_equal(hdr_data['mrparams'], 0)
-
-
 class TestMGHImage(tsi.TestSpatialImage, tsi.MmapImageMixin):
     """ Apply general image tests to MGHImage
     """

nibabel/gifti/__init__.py

@@ -17,6 +17,5 @@
    gifti
 """
 
-from .giftiio import read, write
 from .gifti import (GiftiMetaData, GiftiNVPairs, GiftiLabelTable, GiftiLabel,
                     GiftiCoordSystem, GiftiDataArray, GiftiImage)