Resolve conflicts from #479

nibabel/arraywriters.py

@@ -194,7 +194,9 @@ def _check_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',
+                      'and use in instance __init__ instead.\n'
+                      '* deprecated in version: 2.0\n'
+                      '* will raise error in version: 4.0\n',
                       DeprecationWarning, stacklevel=3)
 
     def _needs_nan2zero(self):

nibabel/cifti2/tests/test_cifti2.py

@@ -6,15 +6,9 @@
 import numpy as np
 
 from nibabel import cifti2 as ci
-from nibabel.nifti1 import data_type_codes, intent_codes
 from nibabel.nifti2 import Nifti2Header
-
-from nibabel import cifti2 as ci
 from nibabel.cifti2.cifti2 import _float_01
 
-from numpy.testing import (assert_array_almost_equal,
-                           assert_array_equal)
-
 from nose.tools import assert_true, assert_equal, assert_raises, assert_is_none
 
 from nibabel.tests.test_dataobj_images import TestDataobjAPI as _TDA

nibabel/dataobj_images.py

@@ -8,11 +8,10 @@
 * has an attribute or property ``shape``.
 """
 
-import warnings
-
 import numpy as np
 
 from .filebasedimages import FileBasedImage
+from .deprecated import deprecate_with_version
 
 
 class DataobjImage(FileBasedImage):
@@ -49,11 +48,10 @@ 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):
-        warnings.warn('Please use ``dataobj`` instead of ``_data``; '
-                      'We will remove this wrapper for ``_data`` soon',
-                      FutureWarning,
-                      stacklevel=2)
         return self._dataobj
 
     def get_data(self, caching='fill'):
@@ -231,12 +229,11 @@ def uncache(self):
     def shape(self):
         return self._dataobj.shape
 
+    @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
-
-        This function deprecated; please use the ``shape`` property instead
         """
-        warnings.warn('Please use the shape property instead of get_shape',
-                      DeprecationWarning,
-                      stacklevel=2)
         return self.shape

nibabel/deprecated.py

@@ -1,8 +1,11 @@
-""" Module to help with deprecating classes and modules
+""" Module to help with deprecating objects and classes
 """
 
 import warnings
 
+from .deprecator import Deprecator
+from .info import cmp_pkg_version
+
 
 class ModuleProxy(object):
     """ Proxy for module that may not yet have been imported
@@ -63,3 +66,18 @@ def __init__(self, *args, **kwargs):
                       FutureWarning,
                       stacklevel=2)
         super(FutureWarningMixin, self).__init__(*args, **kwargs)
+
+
+class VisibleDeprecationWarning(UserWarning):
+    """ Deprecation warning that will be shown by default
+
+    Python >= 2.7 does not show standard DeprecationWarnings by default:
+
+    http://docs.python.org/dev/whatsnew/2.7.html#the-future-for-python-2-x
+
+    Use this class for cases where we do want to show deprecations by default.
+    """
+    pass
+
+
+deprecate_with_version = Deprecator(cmp_pkg_version)

nibabel/deprecator.py

@@ -0,0 +1,168 @@
+""" Class for recording and reporting deprecations
+"""
+
+import functools
+import warnings
+import re
+
+_LEADING_WHITE = re.compile('^(\s*)')
+
+
+class ExpiredDeprecationError(RuntimeError):
+    """ Error for expired deprecation
+
+    Error raised when a called function or method has passed out of its
+    deprecation period.
+    """
+    pass
+
+
+def _ensure_cr(text):
+    """ Remove trailing whitespace and add carriage return
+
+    Ensures that `text` always ends with a carriage return
+    """
+    return text.rstrip() + '\n'
+
+
+def _add_dep_doc(old_doc, dep_doc):
+    """ Add deprecation message `dep_doc` to docstring in `old_doc`
+
+    Parameters
+    ----------
+    old_doc : str
+        Docstring from some object.
+    dep_doc : str
+        Deprecation warning to add to top of docstring, after initial line.
+
+    Returns
+    -------
+    new_doc : str
+        `old_doc` with `dep_doc` inserted after any first lines of docstring.
+    """
+    dep_doc = _ensure_cr(dep_doc)
+    if not old_doc:
+        return dep_doc
+    old_doc = _ensure_cr(old_doc)
+    old_lines = old_doc.splitlines()
+    new_lines = []
+    for line_no, line in enumerate(old_lines):
+        if line.strip():
+            new_lines.append(line)
+        else:
+            break
+    next_line = line_no + 1
+    if next_line >= len(old_lines):
+        # nothing following first paragraph, just append message
+        return old_doc + '\n' + dep_doc
+    indent = _LEADING_WHITE.match(old_lines[next_line]).group()
+    dep_lines = [indent + L for L in [''] + dep_doc.splitlines() + ['']]
+    return '\n'.join(new_lines + dep_lines + old_lines[next_line:]) + '\n'
+
+
+class Deprecator(object):
+    """ Class to make decorator marking function or method as deprecated
+
+    The decorated function / method will:
+
+    * Raise the given `warning_class` warning when the function / method gets
+      called, up to (and including) version `until` (if specified);
+    * Raise the given `error_class` error when the function / method gets
+      called, when the package version is greater than version `until` (if
+      specified).
+
+    Parameters
+    ----------
+    version_comparator : callable
+        Callable accepting string as argument, and return 1 if string
+        represents a higher version than encoded in the `version_comparator`, 0
+        if the version is equal, and -1 if the version is lower.  For example,
+        the `version_comparator` may compare the input version string to the
+        current package version string.
+    warn_class : class, optional
+        Class of warning to generate for deprecation.
+    error_class : class, optional
+        Class of error to generate when `version_comparator` returns 1 for a
+        given argument of ``until`` in the ``__call__`` method (see below).
+    """
+
+    def __init__(self,
+                 version_comparator,
+                 warn_class=DeprecationWarning,
+                 error_class=ExpiredDeprecationError):
+        self.version_comparator = version_comparator
+        self.warn_class = warn_class
+        self.error_class = error_class
+
+    def is_bad_version(self, version_str):
+        """ Return True if `version_str` is too high
+
+        Tests `version_str` with ``self.version_comparator``
+
+        Parameters
+        ----------
+        version_str : str
+            String giving version to test
+
+        Returns
+        -------
+        is_bad : bool
+            True if `version_str` is for version below that expected by
+            ``self.version_comparator``, False otherwise.
+        """
+        return self.version_comparator(version_str) == -1
+
+    def __call__(self, message, since='', until='',
+                 warn_class=None, error_class=None):
+        """ Return decorator function function for deprecation warning / error
+
+        Parameters
+        ----------
+        message : str
+            Message explaining deprecation, giving possible alternatives.
+        since : str, optional
+            Released version at which object was first deprecated.
+        until : str, optional
+            Last released version at which this function will still raise a
+            deprecation warning.  Versions higher than this will raise an
+            error.
+        warn_class : None or class, optional
+            Class of warning to generate for deprecation (overrides instance
+            default).
+        error_class : None or class, optional
+            Class of error to generate when `version_comparator` returns 1 for a
+            given argument of ``until`` (overrides class default).
+
+        Returns
+        -------
+        deprecator : func
+            Function returning a decorator.
+        """
+        warn_class = warn_class if warn_class else self.warn_class
+        error_class = error_class if error_class else self.error_class
+        messages = [message]
+        if (since, until) != ('', ''):
+            messages.append('')
+        if since:
+            messages.append('* deprecated from version: ' + since)
+        if until:
+            messages.append('* {} {} as of version: {}'.format(
+                "Raises" if self.is_bad_version(until) else "Will raise",
+                error_class,
+                until))
+        message = '\n'.join(messages)
+
+        def deprecator(func):
+
+            @functools.wraps(func)
+            def deprecated_func(*args, **kwargs):
+                if until and self.is_bad_version(until):
+                    raise error_class(message)
+                warnings.warn(message, warn_class, stacklevel=2)
+                return func(*args, **kwargs)
+
+            deprecated_func.__doc__ = _add_dep_doc(deprecated_func.__doc__,
+                                                   message)
+            return deprecated_func
+
+        return deprecator

nibabel/ecat.py

@@ -53,6 +53,7 @@
 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
 
@@ -846,6 +847,10 @@ def get_subheaders(self):
         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)