Merge pull request #852 from effigies/mnt/deprecations

MNT: Scheduled removals for 3.0

Author: effigies

nibabel/__init__.py

@@ -78,9 +78,6 @@ def teardown_package():
 from .minc2 import Minc2Image
 from .cifti2 import Cifti2Header, Cifti2Image
 from .gifti import GiftiImage
-# Deprecated backwards compatiblity for MINC1
-from .deprecated import ModuleProxy as _ModuleProxy
-minc = _ModuleProxy('nibabel.minc')
 from .minc1 import MincImage
 from .freesurfer import MGHImage
 from .funcs import (squeeze_image, concat_images, four_to_three,
@@ -89,6 +86,7 @@ def teardown_package():
                            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

nibabel/analyze.py

@@ -939,7 +939,7 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------

nibabel/arrayproxy.py

@@ -27,7 +27,6 @@
 """
 from contextlib import contextmanager
 from threading import RLock
-import warnings
 
 import numpy as np
 
@@ -48,15 +47,13 @@
 
 If this flag is set to ``True``, a single file handle is created and used. If
 ``False``, a new file handle is created every time the image is accessed.
-If this flag is set to ``'auto'``, a ``DeprecationWarning`` will be raised, which
-will become a ``ValueError`` in nibabel 3.0.0.
 
 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'`` will be removed
+             behaviour in version 2.4.1. Support for ``'auto'`` was removed
              in version 3.0.0.
 """
 KEEP_FILE_OPEN_DEFAULT = False
@@ -102,7 +99,7 @@ def __init__(self, file_like, spec, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------
@@ -239,14 +236,14 @@ def _should_keep_file_open(self, file_like, keep_file_open):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will be removed in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------
 
         file_like : object
             File-like object or filename, as passed to ``__init__``.
-        keep_file_open : { 'auto', True, False }
+        keep_file_open : { True, False }
             Flag as passed to ``__init__``.
 
         Returns
@@ -259,23 +256,17 @@ def _should_keep_file_open(self, file_like, keep_file_open):
         """
         if keep_file_open is None:
             keep_file_open = KEEP_FILE_OPEN_DEFAULT
-            if keep_file_open == 'auto':
-                warnings.warn("Setting nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT to 'auto' is "
-                              "deprecated and will become an error in v3.0.", DeprecationWarning)
-        if keep_file_open == 'auto':
-            warnings.warn("A value of 'auto' for keep_file_open is deprecated and will become an "
-                          "error in v3.0. You probably want False.", DeprecationWarning)
+            if keep_file_open not in (True, False):
+                raise ValueError("nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT must be boolean. "
+                                 "Found: {}".format(keep_file_open))
         elif keep_file_open not in (True, False):
-            raise ValueError('keep_file_open should be one of {None, True, False}')
+            raise ValueError('keep_file_open must be one of {None, True, False}')
 
         # file_like is a handle - keep_file_open is irrelevant
         if hasattr(file_like, 'read') and hasattr(file_like, 'seek'):
             return False, False
         # if the file is a gzip file, and we have_indexed_gzip,
         have_igzip = openers.HAVE_INDEXED_GZIP and file_like.endswith('.gz')
-        # XXX Remove in v3.0
-        if keep_file_open == 'auto':
-            return have_igzip, have_igzip
 
         persist_opener = keep_file_open or have_igzip
         return keep_file_open, persist_opener

nibabel/brikhead.py

@@ -227,7 +227,7 @@ def __init__(self, file_like, header, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------
@@ -511,7 +511,7 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------

nibabel/checkwarns.py

@@ -421,7 +421,7 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------
@@ -459,7 +459,7 @@ def from_filename(klass, filename, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------

nibabel/dataobj_images.py

@@ -20,10 +20,10 @@ class ModuleProxy(object):
 
     ::
         arr = np.arange(24).reshape((2, 3, 4))
-        minc = ModuleProxy('nibabel.minc')
-        minc_image = minc.Minc1Image(arr, np.eye(4))
+        nifti1 = ModuleProxy('nibabel.nifti1')
+        nifti1_image = nifti1.Nifti1Image(arr, np.eye(4))
 
-    So, the ``minc`` object is a proxy that will import the required module
+    So, the ``nifti1`` object is a proxy that will import the required module
     when you do attribute access and return the attributes of the imported
     module.
     """

nibabel/deprecated.py

@@ -543,7 +543,7 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------

nibabel/freesurfer/mghformat.py

@@ -250,7 +250,7 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
 
         .. deprecated:: 2.4.1
             ``keep_file_open='auto'`` is redundant with `False` and has
-            been deprecated. It will raise an error in nibabel 3.0.
+            been deprecated. It raises an error as of nibabel 3.0.
 
         Parameters
         ----------

nibabel/minc.py

@@ -372,8 +372,6 @@ def test_keep_file_open_true_false_invalid():
     # False     | True             | True                | True
     # True      | False            | True                | n/a
     # True      | True             | True                | False
-    # 'auto'    | False            | False               | n/a
-    # 'auto'    | True             | True                | False
     #
     # Each test tuple contains:
     #  - file type - gzipped ('gz') or not ('bin'), or an open file handle
@@ -388,26 +386,18 @@ def test_keep_file_open_true_false_invalid():
         ('open', False,  True,  False, False),
         ('open', True,   False, False, False),
         ('open', True,   True,  False, False),
-        ('open', 'auto', False, False, False),
-        ('open', 'auto', True,  False, False),
         # non-gzip file - have_igzip is irrelevant, decision should be made
         # solely from kfo flag
         ('bin', False,  False, False, False),
         ('bin', False,  True,  False, False),
         ('bin', True,   False, True,  True),
         ('bin', True,   True,  True,  True),
-        ('bin', 'auto', False, False, False),
-        ('bin', 'auto', True,  False, False),
-        # gzip file. If igzip is present, we persist the ImageOpener. If kfo
-        # is 'auto':
-        #  - if igzip is present, kfo -> True
-        #  - otherwise, kfo -> False
+        # gzip file. If igzip is present, we persist the ImageOpener.
         ('gz', False,  False, False, False),
         ('gz', False,  True,  True,  False),
         ('gz', True,   False, True,  True),
         ('gz', True,   True,  True,  True),
-        ('gz', 'auto', False, False, False),
-        ('gz', 'auto', True,  True,  True)]
+        ]
 
     dtype = np.float32
     data  = np.arange(1000, dtype=dtype).reshape((10, 10, 10))
@@ -477,12 +467,14 @@ def test_keep_file_open_true_false_invalid():
         fname = 'testdata'
         with open(fname, 'wb') as fobj:
             fobj.write(data.tostring(order='F'))
-        with assert_raises(ValueError):
-            ArrayProxy(fname, ((10, 10, 10), dtype), keep_file_open=55)
-        with assert_raises(ValueError):
-            ArrayProxy(fname, ((10, 10, 10), dtype), keep_file_open='autob')
-        with assert_raises(ValueError):
-            ArrayProxy(fname, ((10, 10, 10), dtype), keep_file_open='cauto')
+
+        for invalid_kfo in (55, 'auto', 'cauto'):
+            with assert_raises(ValueError):
+                ArrayProxy(fname, ((10, 10, 10), dtype),
+                           keep_file_open=invalid_kfo)
+            with patch_keep_file_open_default(invalid_kfo):
+                with assert_raises(ValueError):
+                    ArrayProxy(fname, ((10, 10, 10), dtype))
 
 
 def test_pickle_lock():

nibabel/spm99analyze.py

@@ -104,30 +104,10 @@ def test_old_namespace():
     # Check warnings raised
     arr = np.arange(24).reshape((2, 3, 4))
     aff = np.diag([2, 3, 4, 1])
-    with clear_and_catch_warnings() as warns:
-        warnings.simplefilter('always', DeprecationWarning)
-        # Top level import.
-        # This import does not trigger an import of the minc.py module, because
-        # it's the proxy object.
-        from .. import minc
-        assert_equal(warns, [])
-        # If there was a previous import it will be module, otherwise it will be
-        # a proxy
-        previous_import = isinstance(minc, types.ModuleType)
-        if not previous_import:
-            assert_true(isinstance(minc, ModuleProxy))
-        old_minc1image = minc.Minc1Image  # just to check it works
-        # There may or may not be a warning raised on accessing the proxy,
-        # depending on whether the minc.py module is already imported in this
-        # test run.
-        if not previous_import:
-            assert_equal(warns.pop(0).category, DeprecationWarning)
 
     with clear_and_catch_warnings() as warns:
         from .. import Minc1Image, MincImage
         assert_equal(warns, [])
-        # The import from old module is the same as that from new
-        assert_true(old_minc1image is Minc1Image)
         # But the old named import, imported from new, is not the same
         assert_false(Minc1Image is MincImage)
         assert_equal(warns, [])