MNT: Complete various GIFTI removals

Author: effigies

nibabel/gifti/gifti.py

@@ -122,13 +122,6 @@ def data(self):
     def from_dict(klass, data_dict):
         return klass(data_dict)
 
-    @deprecate_with_version(
-        'get_metadata method deprecated. '
-        "Use the metadata property instead.",
-        '2.1', '4.0')
-    def get_metadata(self):
-        return dict(self)
-
     @property
     @deprecate_with_version(
         'metadata property deprecated. Use GiftiMetaData object '
@@ -274,13 +267,6 @@ def __repr__(self):
         r, g, b, a = chars.astype('u1')
         return f'<GiftiLabel {self.key}="#{r:02x}{g:02x}{b:02x}{a:02x}">'
 
-    @deprecate_with_version(
-        'get_rgba method deprecated. '
-        "Use the rgba property instead.",
-        '2.1', '4.0')
-    def get_rgba(self):
-        return self.rgba
-
     @property
     def rgba(self):
         """ Returns RGBA as tuple """
@@ -488,68 +474,6 @@ def __repr__(self):
     def num_dim(self):
         return len(self.dims)
 
-    # 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):
-        if value != len(self.dims):
-            raise ValueError(f'num_dim value {value} != number of '
-                             f'dimensions len(self.dims) {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",
-                   datatype=None,
-                   encoding="GIFTI_ENCODING_B64GZ",
-                   endian=sys.byteorder,
-                   coordsys=None,
-                   ordering="C",
-                   meta=None):
-        """ Creates a new Gifti data array
-
-        Parameters
-        ----------
-        darray : ndarray
-            NumPy data array
-        intent : string
-            NIFTI intent code, see nifti1.intent_codes
-        datatype : None or string, optional
-            NIFTI data type codes, see nifti1.data_type_codes
-            If None, the datatype of the NumPy array is taken.
-        encoding : string, optionaal
-            Encoding of the data, see util.gifti_encoding_codes;
-            default: GIFTI_ENCODING_B64GZ
-        endian : string, optional
-            The Endianness to store the data array.  Should correspond to the
-            machine endianness.  default: system byteorder
-        coordsys : GiftiCoordSystem, optional
-            If None, a identity transformation is taken.
-        ordering : string, optional
-            The ordering of the array. see util.array_index_order_codes;
-            default: RowMajorOrder - C ordering
-        meta : None or dict, optional
-            A dictionary for metadata information.  If None, gives empty dict.
-
-        Returns
-        -------
-        da : instance of our own class
-        """
-        return klass(data=darray,
-                     intent=intent,
-                     datatype=datatype,
-                     encoding=encoding,
-                     endian=endian,
-                     coordsys=coordsys,
-                     ordering=ordering,
-                     meta=meta)
-
     def _to_xml_element(self):
         # fix endianness to machine endianness
         self.endian = gifti_endian_codes.code[sys.byteorder]
@@ -580,40 +504,6 @@ def _to_xml_element(self):
 
         return data_array
 
-    @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"
-\tArrayIndexingOrder="%s"
-\tDimensionality="%s"
-%s\tEncoding="%s"
-\tEndian="%s"
-\tExternalFileName="%s"
-\tExternalFileOffset="%d">\n"""
-        di = ""
-        for i, n in enumerate(self.dims):
-            di = di + f'\tDim{i}="{n}\"\n'
-        return out % (intent_codes.niistring[self.intent],
-                      data_type_codes.niistring[self.datatype],
-                      array_index_order_codes.label[self.ind_ord],
-                      str(self.num_dim),
-                      str(di),
-                      gifti_encoding_codes.specs[self.encoding],
-                      gifti_endian_codes.specs[self.endian],
-                      self.ext_fname,
-                      self.ext_offset,
-                      )
-
-    @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"
-
     def print_summary(self):
         print('Intent: ', intent_codes.niistring[self.intent])
         print('DataType: ', data_type_codes.niistring[self.datatype])
@@ -630,13 +520,6 @@ def print_summary(self):
             print('Coordinate System:')
             print(self.coordsys.print_summary())
 
-    @deprecate_with_version(
-        'get_metadata method deprecated. '
-        "Use the metadata property instead.",
-        '2.1', '4.0')
-    def get_metadata(self):
-        return dict(self.meta)
-
     @property
     def metadata(self):
         """ Returns metadata as dictionary """
@@ -718,20 +601,6 @@ def labeltable(self, labeltable):
             raise TypeError("Not a valid GiftiLabelTable instance")
         self._labeltable = labeltable
 
-    @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
-
-    @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
-
     @property
     def meta(self):
         return self._meta
@@ -748,20 +617,6 @@ def meta(self, meta):
             raise TypeError("Not a valid GiftiMetaData instance")
         self._meta = meta
 
-    @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
-
-    @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
-
     def add_gifti_data_array(self, dataarr):
         """ Adds a data array to the GiftiImage
 
@@ -925,13 +780,6 @@ def agg_data(self, intent_code=None):
 
         return all_data
 
-    @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)
-
     def print_summary(self):
         print('----start----')
         print('Source filename: ', self.get_filename())

nibabel/gifti/tests/test_gifti.py

@@ -14,7 +14,6 @@
                 GiftiCoordSystem)
 from ...nifti1 import data_type_codes
 from ...fileholders import FileHolder
-from ...deprecator import ExpiredDeprecationError
 
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 import pytest
@@ -182,32 +181,6 @@ def test_dataarray_init():
     assert gda(ext_offset=12).ext_offset == 12
 
 
-def test_dataarray_from_array():
-    with pytest.raises(ExpiredDeprecationError):
-        GiftiDataArray.from_array(np.ones((3, 4)))
-
-
-def test_to_xml_open_close_deprecations():
-    # Smoke test on deprecated functions
-    da = GiftiDataArray(np.ones((1,)), 'triangle')
-    with pytest.raises(ExpiredDeprecationError):
-        da.to_xml_open()
-    with pytest.raises(ExpiredDeprecationError):
-        da.to_xml_close()
-
-
-def test_num_dim_deprecation():
-    da = GiftiDataArray(np.ones((2, 3, 4)))
-    # num_dim is property, set automatically from len(da.dims)
-    assert da.num_dim == 3
-    # setting num_dim to correct value is deprecated
-    with pytest.raises(ExpiredDeprecationError):
-        da.num_dim = 3
-    # setting num_dim to incorrect value is also deprecated
-    with pytest.raises(ExpiredDeprecationError):
-        da.num_dim = 4
-
-
 def test_labeltable():
     img = GiftiImage()
     assert len(img.labeltable.labels) == 0
@@ -217,12 +190,6 @@ def test_labeltable():
     img.labeltable = new_table
     assert len(img.labeltable.labels) == 2
 
-    # Test deprecations
-    with pytest.raises(ExpiredDeprecationError):
-        newer_table = GiftiLabelTable()
-        newer_table.labels += ['test', 'me', 'again']
-        img.set_labeltable(newer_table)
-
 
 def test_metadata():
     md = GiftiMetaData(key='value')
@@ -240,9 +207,6 @@ def test_metadata():
         assert md.data[0].name == 'key'
         assert md.data[0].value == 'value'
     assert len(w) == 2
-    # Test deprecation
-    with pytest.raises(ExpiredDeprecationError):
-        md.get_metadata()
 
 
 def test_metadata_list_interface():
@@ -347,10 +311,6 @@ def assign_rgba(gl, val):
     pytest.raises(ValueError, assign_rgba, gl3, rgba[:2])
     pytest.raises(ValueError, assign_rgba, gl3, rgba.tolist() + rgba.tolist())
 
-    # Test deprecation
-    with pytest.raises(ExpiredDeprecationError):
-        gl3.get_rgba()
-
     # Test default value
     gl4 = GiftiLabel()
     assert len(gl4.rgba) == 4

nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -185,18 +185,6 @@ def test_load_metadata():
         assert img.version == '1.0'
 
 
-def test_metadata_deprecations():
-    img = load(datafiles[0])
-    me = img.meta
-
-    # Test deprecation
-    with pytest.raises(ExpiredDeprecationError):
-        img.get_meta()
-
-    with pytest.raises(ExpiredDeprecationError):
-        img.set_metadata(me)
-
-
 def test_load_dataarray1():
     img1 = load(DATA_FILE1)
     # Round trip
@@ -319,9 +307,6 @@ def test_load_getbyintent():
     da = img.get_arrays_from_intent("NIFTI_INTENT_POINTSET")
     assert len(da) == 1
 
-    with pytest.raises(ExpiredDeprecationError):
-        img.getArraysFromIntent("NIFTI_INTENT_POINTSET")
-
     da = img.get_arrays_from_intent("NIFTI_INTENT_TRIANGLE")
     assert len(da) == 1
 
@@ -349,18 +334,6 @@ def test_load_labeltable():
         assert img.labeltable.labels[1].alpha == 1
 
 
-def test_labeltable_deprecations():
-    img = load(DATA_FILE6)
-    lt = img.labeltable
-
-    # Test deprecation
-    with pytest.raises(ExpiredDeprecationError):
-        img.get_labeltable()
-
-    with pytest.raises(ExpiredDeprecationError):
-        img.set_labeltable(lt)
-
-
 def test_parse_dataarrays():
     fn = 'bad_daa.gii'
     img = gi.GiftiImage()

nibabel/tests/test_removalschedule.py

@@ -47,7 +47,6 @@
     ]),
     ("5.0.0", [("nibabel.dataobj_images", "DataobjImage", "get_data"),
                ("nibabel.freesurfer.mghformat", "MGHHeader", "_header_data"),
-               ("nibabel.gifti.gifti", "GiftiDataArray", "num_dim"),
                ("nibabel.gifti.gifti", "GiftiDataArray", "from_array"),
                ("nibabel.gifti.gifti", "GiftiDataArray", "to_xml_open"),
                ("nibabel.gifti.gifti", "GiftiDataArray", "to_xml_close"),
@@ -57,7 +56,6 @@
                ("nibabel.gifti.gifti", "GiftiImage", "get_metadata"),
                ("nibabel.gifti.gifti", "GiftiImage", "set_metadata"),
                ("nibabel.gifti.gifti", "GiftiImage", "getArraysFromIntent"),
-               ("nibabel.gifti.gifti", "GiftiImage", "getArraysFromIntent"),
                ("nibabel.gifti.gifti", "GiftiMetaData", "get_metadata"),
                ("nibabel.gifti.gifti", "GiftiLabel", "get_rgba"),
                ("nibabel.nicom.dicomwrappers", "Wrapper", "get_affine"),