Merge pull request #1297 from effigies/fix/pytest

TEST: Accommodate pytest 8 changes

Author: effigies

nibabel/_compression.py

@@ -17,7 +17,7 @@
 from .optpkg import optional_package
 
 if ty.TYPE_CHECKING:  # pragma: no cover
-    import indexed_gzip  # type: ignore[import-not-found]
+    import indexed_gzip  # type: ignore[import]
     import pyzstd
 
     HAVE_INDEXED_GZIP = True

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -26,7 +26,7 @@
 
 # if memory_profiler is installed, we get memory usage results
 try:
-    from memory_profiler import memory_usage  # type: ignore[import-not-found]
+    from memory_profiler import memory_usage  # type: ignore[import]
 except ImportError:
     memory_usage = None
 

nibabel/cmdline/dicomfs.py

@@ -25,7 +25,7 @@ class dummy_fuse:
 
 
 try:
-    import fuse  # type: ignore[import-not-found]
+    import fuse  # type: ignore[import]
 
     uid = os.getuid()
     gid = os.getgid()

nibabel/gifti/tests/test_gifti.py

@@ -14,7 +14,7 @@
 from ... import load
 from ...fileholders import FileHolder
 from ...nifti1 import data_type_codes
-from ...testing import get_test_data
+from ...testing import deprecated_to, expires, get_test_data
 from .. import (
     GiftiCoordSystem,
     GiftiDataArray,
@@ -275,27 +275,29 @@ def test_labeltable():
     assert len(img.labeltable.labels) == 2
 
 
+@expires('6.0.0')
 def test_metadata():
     md = GiftiMetaData(key='value')
     # Old initialization methods
-    with pytest.warns(DeprecationWarning) as w:
+    with deprecated_to('6.0.0'):
         nvpair = GiftiNVPairs('key', 'value')
     with pytest.warns(FutureWarning) as w:
         md2 = GiftiMetaData(nvpair=nvpair)
     assert len(w) == 1
-    with pytest.warns(DeprecationWarning) as w:
+    with deprecated_to('6.0.0'):
         md3 = GiftiMetaData.from_dict({'key': 'value'})
     assert md == md2 == md3 == {'key': 'value'}
     # .data as a list of NVPairs is going away
-    with pytest.warns(DeprecationWarning) as w:
+    with deprecated_to('6.0.0'):
         assert md.data[0].name == 'key'
+    with deprecated_to('6.0.0'):
         assert md.data[0].value == 'value'
-    assert len(w) == 2
 
 
+@expires('6.0.0')
 def test_metadata_list_interface():
     md = GiftiMetaData(key='value')
-    with pytest.warns(DeprecationWarning):
+    with deprecated_to('6.0.0'):
         mdlist = md.data
     assert len(mdlist) == 1
     assert mdlist[0].name == 'key'
@@ -312,7 +314,7 @@ def test_metadata_list_interface():
     assert md['foo'] == 'bar'
 
     # Append new NVPair
-    with pytest.warns(DeprecationWarning) as w:
+    with deprecated_to('6.0.0'):
         nvpair = GiftiNVPairs('key', 'value')
     mdlist.append(nvpair)
     assert len(mdlist) == 2

nibabel/minc2.py

@@ -163,7 +163,7 @@ class Minc2Image(Minc1Image):
     def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
         # Import of h5py might take awhile for MPI-enabled builds
         # So we are importing it here "on demand"
-        import h5py  # type: ignore[import-not-found]
+        import h5py  # type: ignore[import]
 
         holder = file_map['image']
         if holder.filename is None:

nibabel/spm99analyze.py

@@ -275,7 +275,7 @@ def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
             contents = matf.read()
         if len(contents) == 0:
             return ret
-        import scipy.io as sio  # type: ignore[import-not-found]
+        import scipy.io as sio  # type: ignore[import]
 
         mats = sio.loadmat(BytesIO(contents))
         if 'mat' in mats:  # this overrides a 'M', and includes any flip

nibabel/testing/__init__.py

@@ -233,3 +233,15 @@ def expires(version):
         return lambda x: x
 
     return pytest.mark.xfail(raises=ExpiredDeprecationError)
+
+
+def deprecated_to(version):
+    """Context manager to expect DeprecationWarnings until a given version"""
+    from packaging.version import Version
+
+    from nibabel import __version__ as nbver
+
+    if Version(nbver) < Version(version):
+        return pytest.deprecated_call()
+
+    return nullcontext()

nibabel/tests/test_image_api.py

@@ -48,6 +48,7 @@
     bytesio_filemap,
     bytesio_round_trip,
     clear_and_catch_warnings,
+    deprecated_to,
     expires,
     nullcontext,
 )
@@ -80,10 +81,6 @@
 from .test_parrec import EXAMPLE_IMAGES as PARREC_EXAMPLE_IMAGES
 
 
-def maybe_deprecated(meth_name):
-    return pytest.deprecated_call() if meth_name == 'get_data' else nullcontext()
-
-
 class GenericImageAPI(ValidateAPI):
     """General image validation API"""
 
@@ -194,7 +191,7 @@ def validate_no_slicing(self, imaker, params):
     @expires('5.0.0')
     def validate_get_data_deprecated(self, imaker, params):
         img = imaker()
-        with pytest.deprecated_call():
+        with deprecated_to('5.0.0'):
             data = img.get_data()
         assert_array_equal(np.asanyarray(img.dataobj), data)
 
@@ -246,14 +243,12 @@ def validate_data_interface(self, imaker, params):
                 self._check_array_interface(imaker, meth_name)
             method = getattr(img, meth_name)
             # Data shape is same as image shape
-            with maybe_deprecated(meth_name):
-                assert img.shape == method().shape
+            assert img.shape == method().shape
             # Data ndim is same as image ndim
-            with maybe_deprecated(meth_name):
-                assert img.ndim == method().ndim
+            assert img.ndim == method().ndim
             # Values to get_data caching parameter must be 'fill' or
             # 'unchanged'
-            with maybe_deprecated(meth_name), pytest.raises(ValueError):
+            with pytest.raises(ValueError):
                 method(caching='something')
         # dataobj is read only
         fake_data = np.zeros(img.shape, dtype=img.get_data_dtype())
@@ -277,13 +272,11 @@ def _check_proxy_interface(self, imaker, meth_name):
         assert not img.in_memory
         # Load with caching='unchanged'
         method = getattr(img, meth_name)
-        with maybe_deprecated(meth_name):
-            data = method(caching='unchanged')
+        data = method(caching='unchanged')
         # Still not cached
         assert not img.in_memory
         # Default load, does caching
-        with maybe_deprecated(meth_name):
-            data = method()
+        data = method()
         # Data now cached. in_memory is True if either of the get_data
         # or get_fdata caches are not-None
         assert img.in_memory
@@ -295,36 +288,30 @@ def _check_proxy_interface(self, imaker, meth_name):
         # integers, but lets assume that's not true here.
         assert_array_equal(proxy_data, data)
         # Now caching='unchanged' does nothing, returns cached version
-        with maybe_deprecated(meth_name):
-            data_again = method(caching='unchanged')
+        data_again = method(caching='unchanged')
         assert data is data_again
         # caching='fill' does nothing because the cache is already full
-        with maybe_deprecated(meth_name):
-            data_yet_again = method(caching='fill')
+        data_yet_again = method(caching='fill')
         assert data is data_yet_again
         # changing array data does not change proxy data, or reloaded
         # data
         data[:] = 42
         assert_array_equal(proxy_data, proxy_copy)
         assert_array_equal(np.asarray(img.dataobj), proxy_copy)
-        # It does change the result of get_data
-        with maybe_deprecated(meth_name):
-            assert_array_equal(method(), 42)
+        # It does change the result of get_fdata
+        assert_array_equal(method(), 42)
         # until we uncache
         img.uncache()
         # Which unsets in_memory
         assert not img.in_memory
-        with maybe_deprecated(meth_name):
-            assert_array_equal(method(), proxy_copy)
+        assert_array_equal(method(), proxy_copy)
         # Check caching='fill' does cache data
         img = imaker()
         method = getattr(img, meth_name)
         assert not img.in_memory
-        with maybe_deprecated(meth_name):
-            data = method(caching='fill')
+        data = method(caching='fill')
         assert img.in_memory
-        with maybe_deprecated(meth_name):
-            data_again = method()
+        data_again = method()
         assert data is data_again
         # Check that caching refreshes for new floating point type.
         img.uncache()
@@ -368,17 +355,15 @@ def _check_array_caching(self, imaker, meth_name, caching):
         get_data_func = method if caching is None else partial(method, caching=caching)
         assert isinstance(img.dataobj, np.ndarray)
         assert img.in_memory
-        with maybe_deprecated(meth_name):
-            data = get_data_func()
+        data = get_data_func()
         # Returned data same object as underlying dataobj if using
         # old ``get_data`` method, or using newer ``get_fdata``
         # method, where original array was float64.
         arr_dtype = img.dataobj.dtype
         dataobj_is_data = arr_dtype == np.float64 or method == img.get_data
         # Set something to the output array.
         data[:] = 42
-        with maybe_deprecated(meth_name):
-            get_result_changed = np.all(get_data_func() == 42)
+        get_result_changed = np.all(get_data_func() == 42)
         assert get_result_changed == (dataobj_is_data or caching != 'unchanged')
         if dataobj_is_data:
             assert data is img.dataobj
@@ -387,15 +372,13 @@ def _check_array_caching(self, imaker, meth_name, caching):
             assert_array_equal(np.asarray(img.dataobj), 42)
             # Uncache has no effect
             img.uncache()
-            with maybe_deprecated(meth_name):
-                assert_array_equal(get_data_func(), 42)
+            assert_array_equal(get_data_func(), 42)
         else:
             assert not data is img.dataobj
             assert not np.all(np.asarray(img.dataobj) == 42)
             # Uncache does have an effect
             img.uncache()
-            with maybe_deprecated(meth_name):
-                assert not np.all(get_data_func() == 42)
+            assert not np.all(get_data_func() == 42)
         # in_memory is always true for array images, regardless of
         # cache state.
         img.uncache()
@@ -408,8 +391,7 @@ def _check_array_caching(self, imaker, meth_name, caching):
         if arr_dtype not in float_types:
             return
         for float_type in float_types:
-            with maybe_deprecated(meth_name):
-                data = get_data_func(dtype=float_type)
+            data = get_data_func(dtype=float_type)
             assert (data is img.dataobj) == (arr_dtype == float_type)
 
     def validate_shape(self, imaker, params):

nibabel/tests/test_image_load_save.py

@@ -40,7 +40,7 @@
 from .. import spm99analyze as spm99
 from ..optpkg import optional_package
 from ..spatialimages import SpatialImage
-from ..testing import expires
+from ..testing import deprecated_to, expires
 from ..tmpdirs import InTemporaryDirectory
 from ..volumeutils import native_code, swapped_code
 
@@ -285,7 +285,7 @@ def test_filename_save():
 @expires('5.0.0')
 def test_guessed_image_type():
     # Test whether we can guess the image type from example files
-    with pytest.deprecated_call():
+    with deprecated_to('5.0.0'):
         assert nils.guessed_image_type(pjoin(DATA_PATH, 'example4d.nii.gz')) == Nifti1Image
         assert nils.guessed_image_type(pjoin(DATA_PATH, 'nifti1.hdr')) == Nifti1Pair
         assert nils.guessed_image_type(pjoin(DATA_PATH, 'example_nifti2.nii.gz')) == Nifti2Image

nibabel/tests/test_loadsave.py

@@ -21,7 +21,7 @@
 from ..loadsave import _signature_matches_extension, load, read_img_data
 from ..openers import Opener
 from ..optpkg import optional_package
-from ..testing import expires
+from ..testing import deprecated_to, expires
 from ..tmpdirs import InTemporaryDirectory
 
 _, have_scipy, _ = optional_package('scipy')
@@ -50,14 +50,14 @@ def test_read_img_data():
             fpath = pathlib.Path(fpath)
         img = load(fpath)
         data = img.get_fdata()
-        with pytest.deprecated_call():
+        with deprecated_to('5.0.0'):
             data2 = read_img_data(img)
         assert_array_equal(data, data2)
         # These examples have null scaling - assert prefer=unscaled is the same
         dao = img.dataobj
         if hasattr(dao, 'slope') and hasattr(img.header, 'raw_data_from_fileobj'):
             assert (dao.slope, dao.inter) == (1, 0)
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert_array_equal(read_img_data(img, prefer='unscaled'), data)
         # Assert all caps filename works as well
         with TemporaryDirectory() as tmpdir:
@@ -140,21 +140,21 @@ def test_read_img_data_nifti():
             img = img_class(data, np.eye(4))
             img.set_data_dtype(out_dtype)
             # No filemap => error
-            with pytest.deprecated_call(), pytest.raises(ImageFileError):
+            with deprecated_to('5.0.0'), pytest.raises(ImageFileError):
                 read_img_data(img)
             # Make a filemap
             froot = f'an_image_{i}'
             img.file_map = img.filespec_to_file_map(froot)
             # Trying to read from this filemap will generate an error because
             # we are going to read from files that do not exist
-            with pytest.deprecated_call(), pytest.raises(OSError):
+            with deprecated_to('5.0.0'), pytest.raises(OSError):
                 read_img_data(img)
             img.to_file_map()
             # Load - now the scaling and offset correctly applied
             img_fname = img.file_map['image'].filename
             img_back = load(img_fname)
             data_back = img_back.get_fdata()
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert_array_equal(data_back, read_img_data(img_back))
             # This is the same as if we loaded the image and header separately
             hdr_fname = img.file_map['header'].filename if 'header' in img.file_map else img_fname
@@ -166,16 +166,16 @@ def test_read_img_data_nifti():
             # Unscaled is the same as returned from raw_data_from_fileobj
             with open(img_fname, 'rb') as fobj:
                 unscaled_back = hdr_back.raw_data_from_fileobj(fobj)
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert_array_equal(unscaled_back, read_img_data(img_back, prefer='unscaled'))
             # If we futz with the scaling in the header, the result changes
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert_array_equal(data_back, read_img_data(img_back))
             has_inter = hdr_back.has_data_intercept
             old_slope = hdr_back['scl_slope']
             old_inter = hdr_back['scl_inter'] if has_inter else 0
             est_unscaled = (data_back - old_inter) / old_slope
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 actual_unscaled = read_img_data(img_back, prefer='unscaled')
             assert_almost_equal(est_unscaled, actual_unscaled)
             img_back.header['scl_slope'] = 2.1
@@ -185,10 +185,10 @@ def test_read_img_data_nifti():
             else:
                 new_inter = 0
             # scaled scaling comes from new parameters in header
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert np.allclose(actual_unscaled * 2.1 + new_inter, read_img_data(img_back))
             # Unscaled array didn't change
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert_array_equal(actual_unscaled, read_img_data(img_back, prefer='unscaled'))
             # Check the offset too
             img.header.set_data_offset(1024)
@@ -200,14 +200,14 @@ def test_read_img_data_nifti():
                 fobj.write(b'\x00\x00')
             img_back = load(img_fname)
             data_back = img_back.get_fdata()
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert_array_equal(data_back, read_img_data(img_back))
             img_back.header.set_data_offset(1026)
             # Check we pick up new offset
             exp_offset = np.zeros((data.size,), data.dtype) + old_inter
             exp_offset[:-1] = np.ravel(data_back, order='F')[1:]
             exp_offset = np.reshape(exp_offset, shape, order='F')
-            with pytest.deprecated_call():
+            with deprecated_to('5.0.0'):
                 assert_array_equal(exp_offset, read_img_data(img_back))
             # Delete stuff that might hold onto file references
             del img, img_back, data_back