Merge pull request #1159 from effigies/mnt/5.0.0-deprecations

MNT: 5.0.0 deprecations

Author: effigies

nibabel/deprecator.py

@@ -182,8 +182,18 @@ def deprecated_func(*args, **kwargs):
                 warnings.warn(message, warn_class, stacklevel=2)
                 return func(*args, **kwargs)
 
-            deprecated_func.__doc__ = _add_dep_doc(deprecated_func.__doc__,
-                                                   message, TESTSETUP, TESTCLEANUP)
+            keep_doc = deprecated_func.__doc__
+            setup = TESTSETUP
+            cleanup = TESTCLEANUP
+            # After expiration, remove all but the first paragraph.
+            # The details are no longer relevant, but any code will likely
+            # raise exceptions we don't need.
+            if keep_doc and until and self.is_bad_version(until):
+                lines = '\n'.join(line.rstrip() for line in keep_doc.splitlines())
+                keep_doc = lines.split('\n\n', 1)[0]
+                setup = ''
+                cleanup = ''
+            deprecated_func.__doc__ = _add_dep_doc(keep_doc, message, setup, cleanup)
             return deprecated_func
 
         return deprecator

nibabel/testing/__init__.py

@@ -16,6 +16,7 @@
 
 import unittest
 
+import pytest
 import numpy as np
 from numpy.testing import assert_array_equal
 
@@ -223,3 +224,15 @@ def setUp(self):
         if self.__class__.__name__.startswith('_'):
             raise unittest.SkipTest("Base test case - subclass to run")
         super().setUp()
+
+
+def expires(version):
+    "Decorator to mark a test as xfail with ExpiredDeprecationError after version"
+    from packaging.version import Version
+    from nibabel import __version__ as nbver
+    from nibabel.deprecator import ExpiredDeprecationError
+
+    if Version(nbver) < Version(version):
+        return lambda x: x
+
+    return pytest.mark.xfail(raises=ExpiredDeprecationError)

nibabel/tests/test_analyze.py

@@ -716,7 +716,7 @@ def test_default_header(self):
 
     def test_data_hdr_cache(self):
         # test the API for loaded images, such that the data returned
-        # from np.asanyarray(img.dataobj) and img,get_fdata() are not
+        # from np.asanyarray(img.dataobj) and img.get_fdata() are not
         # affected by subsequent changes to the header.
         IC = self.image_class
         # save an image to a file map
@@ -740,14 +740,6 @@ def test_data_hdr_cache(self):
         assert hdr.get_data_dtype() == np.dtype(np.uint8)
         assert_array_equal(img2.get_fdata(), data)
         assert_array_equal(np.asanyarray(img2.dataobj), data)
-        # now check read_img_data function - here we do see the changed
-        # header
-        with pytest.deprecated_call(match="from version: 3.2"):
-            sc_data = read_img_data(img2)
-        assert sc_data.shape == (3, 2, 2)
-        with pytest.deprecated_call(match="from version: 3.2"):
-            us_data = read_img_data(img2, prefer='unscaled')
-        assert us_data.shape == (3, 2, 2)
 
     def test_affine_44(self):
         IC = self.image_class

nibabel/tests/test_api_validators.py

@@ -20,6 +20,8 @@ def meth(self):
                     validator(self, imaker, params)
             meth.__name__ = 'test_' + name[len('validate_'):]
             meth.__doc__ = f'autogenerated test from {klass.__name__}.{name}'
+            if hasattr(validator, 'pytestmark'):
+                meth.pytestmark = validator.pytestmark
             return meth
         for name in dir(klass):
             if not name.startswith('validate_'):

nibabel/tests/test_deprecator.py

@@ -111,11 +111,14 @@ def test_dep_func(self):
                 'foo\n\n* deprecated from version: 1.2\n* Raises '
                 f'{ExpiredDeprecationError} as of version: 1.8\n')
         func = dec('foo', '1.2', '1.8')(func_doc_long)
-        assert (func.__doc__ ==
-                'A docstring\n   \n   foo\n   \n   * deprecated from version: 1.2\n   '
-                f'* Raises {ExpiredDeprecationError} as of version: 1.8\n   \n'
-                f'{indent(TESTSETUP, "   ", lambda x: True)}'
-                f'   Some text\n{indent(TESTCLEANUP, "   ", lambda x: True)}')
+        assert func.__doc__ == f"""\
+A docstring
+
+foo
+
+* deprecated from version: 1.2
+* Raises {ExpiredDeprecationError} as of version: 1.8
+"""
         with pytest.raises(ExpiredDeprecationError):
             func()
 

nibabel/tests/test_image_api.py

@@ -48,7 +48,7 @@
 
 from numpy.testing import assert_almost_equal, assert_array_equal, assert_warns, assert_allclose
 from nibabel.testing import (bytesio_round_trip, bytesio_filemap, assert_data_similar,
-                             clear_and_catch_warnings, nullcontext)
+                             clear_and_catch_warnings, nullcontext, expires)
 from ..tmpdirs import InTemporaryDirectory
 
 from .test_api_validators import ValidateAPI
@@ -170,8 +170,8 @@ def validate_no_slicing(self, imaker, params):
         with pytest.raises(TypeError):
             img[:]
 
+    @expires("5.0.0")
     def validate_get_data_deprecated(self, imaker, params):
-        # Check deprecated header API
         img = imaker()
         with pytest.deprecated_call():
             data = img.get_data()
@@ -209,7 +209,7 @@ class DataInterfaceMixin(GetSetDtypeMixin):
     Use this mixin if your image has a ``dataobj`` property that contains an
     array or an array-like thing.
     """
-    meth_names = ('get_fdata', 'get_data')
+    meth_names = ('get_fdata',)
 
     def validate_data_interface(self, imaker, params):
         # Check get data returns array, and caches
@@ -304,27 +304,6 @@ def _check_proxy_interface(self, imaker, meth_name):
         with maybe_deprecated(meth_name):
             data_again = method()
         assert data is data_again
-        # Check the interaction of caching with get_data, get_fdata.
-        # Caching for `get_data` should have no effect on caching for
-        # get_fdata, and vice versa.
-        # Modify the cached data
-        data[:] = 43
-        # Load using the other data fetch method
-        other_name = set(self.meth_names).difference({meth_name}).pop()
-        other_method = getattr(img, other_name)
-        with maybe_deprecated(other_name):
-            other_data = other_method()
-        # We get the original data, not the modified cache
-        assert_array_equal(proxy_data, other_data)
-        assert not np.all(data == other_data)
-        # We can modify the other cache, without affecting the first
-        other_data[:] = 44
-        with maybe_deprecated(other_name):
-            assert_array_equal(other_method(), 44)
-        with pytest.deprecated_call():
-            assert not np.all(method() == other_method())
-        if meth_name != 'get_fdata':
-            return
         # Check that caching refreshes for new floating point type.
         img.uncache()
         fdata = img.get_fdata()
@@ -558,7 +537,7 @@ def validate_to_from_bytes(self, imaker, params):
                 del img_b
 
     @pytest.fixture(autouse=True)
-    def setup(self, httpserver, tmp_path):
+    def setup_method(self, httpserver, tmp_path):
         """Make pytest fixtures available to validate functions"""
         self.httpserver = httpserver
         self.tmp_path = tmp_path
@@ -788,7 +767,7 @@ class TestMinc1API(ImageHeaderAPI):
 
 class TestMinc2API(TestMinc1API):
 
-    def setup(self):
+    def setup_method(self):
         if not have_h5py:
             raise unittest.SkipTest('Need h5py for these tests')
 

nibabel/tests/test_image_load_save.py

@@ -29,6 +29,7 @@
 from ..volumeutils import native_code, swapped_code
 from ..optpkg import optional_package
 from ..spatialimages import SpatialImage
+from ..testing import expires
 
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 import pytest
@@ -270,6 +271,7 @@ def test_filename_save():
             shutil.rmtree(pth)
 
 
+@expires('5.0.0')
 def test_guessed_image_type():
     # Test whether we can guess the image type from example files
     with pytest.deprecated_call():

nibabel/tests/test_loadsave.py

@@ -14,6 +14,7 @@
 from ..filebasedimages import ImageFileError
 from ..tmpdirs import InTemporaryDirectory, TemporaryDirectory
 from ..openers import Opener
+from ..testing import expires
 
 from ..optpkg import optional_package
 _, have_scipy, _ = optional_package('scipy')
@@ -27,6 +28,7 @@
 data_path = pjoin(dirname(__file__), 'data')
 
 
+@expires("5.0.0")
 def test_read_img_data():
     fnames_test = [
         'example4d.nii.gz',
@@ -120,6 +122,7 @@ def test_signature_matches_extension(tmp_path):
     assert msg == ""
 
 
+@expires("5.0.0")
 def test_read_img_data_nifti():
     shape = (2, 3, 4)
     data = np.random.normal(size=shape)

nibabel/tests/test_onetime.py

@@ -1,7 +1,9 @@
 import pytest
 from nibabel.onetime import auto_attr, setattr_on_read
+from nibabel.testing import expires
 
 
+@expires('5.0.0')
 def test_setattr_on_read():
     with pytest.deprecated_call():
         class MagicProp:
@@ -15,3 +17,17 @@ def a(self):
     assert 'a' in x.__dict__
     # Each call to object() produces a unique object. Verify we get the same one every time.
     assert x.a is obj
+
+
+def test_auto_attr():
+    class MagicProp:
+        @auto_attr
+        def a(self):
+            return object()
+
+    x = MagicProp()
+    assert 'a' not in x.__dict__
+    obj = x.a
+    assert 'a' in x.__dict__
+    # Each call to object() produces a unique object. Verify we get the same one every time.
+    assert x.a is obj

nibabel/tests/test_orientations.py

@@ -20,6 +20,7 @@
                             ornt2axcodes, axcodes2ornt, aff2axcodes)
 
 from ..affines import from_matvec, to_matvec
+from ..testing import expires
 
 
 IN_ARRS = [np.eye(4),
@@ -353,6 +354,7 @@ def test_inv_ornt_aff():
         inv_ornt_aff([[0, 1], [1, -1], [np.nan, np.nan]], (3, 4, 5))
 
 
+@expires('5.0.0')
 def test_flip_axis_deprecation():
     a = np.arange(24).reshape((2, 3, 4))
     axis = 1

nibabel/tests/test_spatialimages.py

@@ -26,7 +26,8 @@
     bytesio_round_trip,
     clear_and_catch_warnings,
     suppress_warnings,
-    memmap_after_ufunc
+    memmap_after_ufunc,
+    expires,
 )
 
 from ..tmpdirs import InTemporaryDirectory
@@ -358,21 +359,13 @@ def test_get_fdata(self):
         assert rt_img.get_fdata() is not out_data
         assert (rt_img.get_fdata() == in_data).all()
 
+    @expires("5.0.0")
     def test_get_data(self):
         # Test array image and proxy image interface
         img_klass = self.image_class
         in_data_template = np.arange(24, dtype=np.int16).reshape((2, 3, 4))
         in_data = in_data_template.copy()
         img = img_klass(in_data, None)
-        # Can't slice into the image object:
-        with pytest.raises(TypeError) as exception_manager:
-            img[0, 0, 0]
-        # Make sure the right message gets raised:
-        assert (str(exception_manager.value) ==
-                "Cannot slice image objects; consider using "
-                "`img.slicer[slice]` to generate a sliced image (see "
-                "documentation for caveats) or slicing image array data "
-                "with `img.dataobj[slice]` or `img.get_fdata()[slice]`")
         assert in_data is img.dataobj
         with pytest.deprecated_call():
             out_data = img.get_data()
@@ -411,6 +404,16 @@ def test_slicer(self):
             in_data = in_data_template.copy().reshape(dshape)
             img = img_klass(in_data, base_affine.copy())
 
+            # Can't slice into the image object:
+            with pytest.raises(TypeError) as exception_manager:
+                img[0, 0, 0]
+            # Make sure the right message gets raised:
+            assert (str(exception_manager.value) ==
+                    "Cannot slice image objects; consider using "
+                    "`img.slicer[slice]` to generate a sliced image (see "
+                    "documentation for caveats) or slicing image array data "
+                    "with `img.dataobj[slice]` or `img.get_fdata()[slice]`")
+
             if not spatial_axes_first(img):
                 with pytest.raises(ValueError):
                     img.slicer
@@ -519,13 +522,9 @@ def test_slicer(self):
                         pass
                     else:
                         sliced_data = in_data[sliceobj]
-                        with pytest.deprecated_call():
-                            assert (sliced_data == sliced_img.get_data()).all()
                         assert (sliced_data == sliced_img.get_fdata()).all()
                         assert (sliced_data == sliced_img.dataobj).all()
                         assert (sliced_data == img.dataobj[sliceobj]).all()
-                        with pytest.deprecated_call():
-                            assert (sliced_data == img.get_data()[sliceobj]).all()
                         assert (sliced_data == img.get_fdata()[sliceobj]).all()