Merge pull request #980 from effigies/mnt/deprecations

MNT: Remove modules, objects and attributes deprecated in 3.0

Author: effigies

nibabel/__init__.py

@@ -55,16 +55,13 @@
 from .minc2 import Minc2Image
 from .cifti2 import Cifti2Header, Cifti2Image
 from .gifti import GiftiImage
-from .minc1 import MincImage
 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,
                            apply_orientation, aff2axcodes)
 from .imageclasses import class_map, ext_map, all_image_classes
-from .deprecated import ModuleProxy as _ModuleProxy
-trackvis = _ModuleProxy('nibabel.trackvis')
 from . import mriutils
 from . import streamlines
 from . import viewers

nibabel/analyze.py

@@ -932,10 +932,6 @@ def set_data_dtype(self, dtype):
     def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
         """ Class method to create image from mapping in ``file_map``
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
         file_map : dict

nibabel/arrayproxy.py

@@ -30,7 +30,6 @@
 
 import numpy as np
 
-from .deprecated import deprecate_with_version
 from .volumeutils import array_from_file, apply_read_scaling
 from .fileslice import fileslice, canonical_slicers
 from . import openers
@@ -50,10 +49,6 @@
 If this is set to any other value, attempts to create an ``ArrayProxy`` without
 specifying the ``keep_file_open`` flag will result in a ``ValueError`` being
 raised.
-
-.. warning:: Setting this flag to a value of ``'auto'`` became deprecated
-             behaviour in version 2.4.1. Support for ``'auto'`` was removed
-             in version 3.0.0.
 """
 KEEP_FILE_OPEN_DEFAULT = False
 
@@ -90,15 +85,10 @@ class ArrayProxy(object):
     """
     # Assume Fortran array memory layout
     order = 'F'
-    _header = None
 
     def __init__(self, file_like, spec, *, mmap=True, keep_file_open=None):
         """Initialize array proxy instance
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
         file_like : object
@@ -146,8 +136,6 @@ def __init__(self, file_like, spec, *, mmap=True, keep_file_open=None):
                    spec.get_data_offset(),
                    1. if slope is None else slope,
                    0. if inter is None else inter)
-            # Reference to original header; we will remove this soon
-            self._header = spec.copy()
         elif 2 <= len(spec) <= 5:
             optional = (0, 1., 0.)
             par = spec + optional[len(spec) - 2:]
@@ -232,10 +220,6 @@ def _should_keep_file_open(self, file_like, keep_file_open):
            In this case, file handle management is delegated to the
            ``indexed_gzip`` library.
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
 
@@ -269,11 +253,6 @@ def _should_keep_file_open(self, file_like, keep_file_open):
         persist_opener = keep_file_open or have_igzip
         return keep_file_open, persist_opener
 
-    @property
-    @deprecate_with_version('ArrayProxy.header deprecated', '2.2', '3.0')
-    def header(self):
-        return self._header
-
     @property
     def shape(self):
         return self._shape

nibabel/benchmarks/bench_streamlines.py

@@ -221,10 +221,6 @@ def __init__(self, file_like, header, *, mmap=True, keep_file_open=None):
         """
         Initialize AFNI array proxy
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
         file_like : file-like object
@@ -504,10 +500,6 @@ def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
         """
         Creates an AFNIImage instance from `file_map`
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
         file_map : dict

nibabel/brikhead.py

@@ -3,8 +3,6 @@
 # Pre-load deprecated modules to avoid cluttering warnings
 with pytest.deprecated_call():
     import nibabel.keywordonly
-with pytest.deprecated_call():
-    import nibabel.trackvis
 with pytest.warns(FutureWarning):
     import nibabel.py3k
 

nibabel/conftest.py

@@ -404,23 +404,10 @@ def shape(self):
     def ndim(self):
         return self._dataobj.ndim
 
-    @deprecate_with_version('get_shape method is deprecated.\n'
-                            'Please use the ``img.shape`` property '
-                            'instead.',
-                            '1.2', '3.0')
-    def get_shape(self):
-        """ Return shape for image
-        """
-        return self.shape
-
     @classmethod
     def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
         """ Class method to create image from mapping in ``file_map``
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
         file_map : dict
@@ -454,10 +441,6 @@ def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
     def from_filename(klass, filename, *, mmap=True, keep_file_open=None):
         """Class method to create image from filename `filename`
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
         filename : str

nibabel/dataobj_images.py

@@ -159,9 +159,9 @@ class FileBasedImage(object):
     itself back to the files pointed to in ``file_map``.  When a file holder
     holds active file-like objects, then these may be affected by the
     initial file read; in this case, the contains file-like objects need to
-    carry the position at which a write (with ``to_files``) should place the
+    carry the position at which a write (with ``to_file_map``) should place the
     data.  The ``file_map`` contents should therefore be such, that this will
-    work:
+    work.
     """
     header_class = FileBasedHeader
     _meta_sniff_len = 0
@@ -263,14 +263,6 @@ def from_filename(klass, filename):
     def from_file_map(klass, file_map):
         raise NotImplementedError
 
-    @classmethod
-    @deprecate_with_version('from_files class method is deprecated.\n'
-                            'Please use the ``from_file_map`` class method '
-                            'instead.',
-                            '1.0', '3.0')
-    def from_files(klass, file_map):
-        return klass.from_file_map(file_map)
-
     @classmethod
     def filespec_to_file_map(klass, filespec):
         """ Make `file_map` for this class from filename `filespec`
@@ -307,14 +299,6 @@ def filespec_to_file_map(klass, filespec):
             file_map[key] = FileHolder(filename=fname)
         return file_map
 
-    @classmethod
-    @deprecate_with_version('filespec_to_files class method is deprecated.\n'
-                            'Please use the "filespec_to_file_map" class '
-                            'method instead.',
-                            '1.0', '3.0')
-    def filespec_to_files(klass, filespec):
-        return klass.filespec_to_file_map(filespec)
-
     def to_filename(self, filename):
         """ Write image to files implied by filename string
 
@@ -332,21 +316,9 @@ def to_filename(self, filename):
         self.file_map = self.filespec_to_file_map(filename)
         self.to_file_map()
 
-    @deprecate_with_version('to_filespec method is deprecated.\n'
-                            'Please use the "to_filename" method instead.',
-                            '1.0', '3.0')
-    def to_filespec(self, filename):
-        self.to_filename(filename)
-
     def to_file_map(self, file_map=None):
         raise NotImplementedError
 
-    @deprecate_with_version('to_files method is deprecated.\n'
-                            'Please use the "to_file_map" method instead.',
-                            '1.0', '3.0')
-    def to_files(self, file_map=None):
-        self.to_file_map(file_map)
-
     @classmethod
     def make_file_map(klass, mapping=None):
         """ Class method to make files holder for this image type

nibabel/filebasedimages.py

@@ -537,10 +537,6 @@ def filespec_to_file_map(klass, filespec):
     def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
         """ Class method to create image from mapping in ``file_map``
 
-        .. deprecated:: 2.4.1
-            ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It raises an error as of nibabel 3.0.
-
         Parameters
         ----------
         file_map : dict

nibabel/freesurfer/mghformat.py

@@ -17,8 +17,6 @@
 from .spatialimages import SpatialHeader, SpatialImage
 from .fileslice import canonical_slicers
 
-from .deprecated import deprecate_with_version
-
 _dt_dict = {
     ('b', 'unsigned'): np.uint8,
     ('b', 'signed__'): np.int8,
@@ -342,16 +340,3 @@ def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
 
 
 load = Minc1Image.load
-
-
-# Backwards compatibility
-@deprecate_with_version('MincFile is deprecated; please use Minc1File instead',
-                        since='2.0.0', until='3.0.0', warn_class=FutureWarning)
-class MincFile(Minc1File):
-    pass
-
-
-@deprecate_with_version('MincImage is deprecated; please use Minc1Image instead',
-                        since='2.0.0', until='3.0.0', warn_class=FutureWarning)
-class MincImage(Minc1Image):
-    pass