Merge pull request #949 from effigies/test/reduce_warnings

TEST: Suppress expected warnings

Author: effigies

.travis.yml

@@ -147,7 +147,7 @@ script:
           mkdir for_testing
           cd for_testing
           cp ../.coveragerc .
-          pytest --doctest-modules --cov nibabel -v --pyargs nibabel
+          pytest --doctest-modules --doctest-plus --cov nibabel -v --pyargs nibabel
       else
           false
       fi

nibabel/casting.py

@@ -4,6 +4,7 @@
 casting.  Others work round numpy casting to and from python ints
 """
 
+import warnings
 from numbers import Integral
 from platform import processor, machine
 
@@ -349,8 +350,9 @@ def _check_maxexp(np_type, maxexp):
     dt = np.dtype(np_type)
     np_type = dt.type
     two = np_type(2).reshape((1,))  # to avoid upcasting
-    return (np.isfinite(two ** (maxexp - 1)) and
-            not np.isfinite(two ** maxexp))
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", RuntimeWarning)  # Expected overflow warning
+        return np.isfinite(two ** (maxexp - 1)) and not np.isfinite(two ** maxexp)
 
 
 def as_int(x, check=True):

nibabel/cifti2/cifti2.py

@@ -1492,7 +1492,7 @@ def update_headers(self):
 
         >>> import numpy as np
         >>> data = np.zeros((2,3,4))
-        >>> img = Cifti2Image(data)
+        >>> img = Cifti2Image(data)  # doctest: +IGNORE_WARNINGS
         >>> img.shape == (2, 3, 4)
         True
         >>> img.update_headers()

nibabel/conftest.py

@@ -0,0 +1,13 @@
+import pytest
+
+# 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
+
+# Ignore warning requesting help with nicom
+with pytest.warns(UserWarning):
+    import nibabel.nicom

nibabel/deprecator.py

@@ -7,6 +7,26 @@
 
 _LEADING_WHITE = re.compile(r'^(\s*)')
 
+TESTSETUP = """
+
+.. testsetup::
+
+    >>> import pytest
+    >>> import warnings
+    >>> _suppress_warnings = pytest.deprecated_call()
+    >>> _ = _suppress_warnings.__enter__()
+
+"""
+
+TESTCLEANUP = """
+
+.. testcleanup::
+
+    >>> warnings.warn("Avoid error if no doctests to run...", DeprecationWarning)
+    >>> _ = _suppress_warnings.__exit__(None, None, None)
+
+"""
+
 
 class ExpiredDeprecationError(RuntimeError):
     """ Error for expired deprecation
@@ -25,7 +45,7 @@ def _ensure_cr(text):
     return text.rstrip() + '\n'
 
 
-def _add_dep_doc(old_doc, dep_doc):
+def _add_dep_doc(old_doc, dep_doc, setup='', cleanup=''):
     """ Add deprecation message `dep_doc` to docstring in `old_doc`
 
     Parameters
@@ -56,8 +76,11 @@ def _add_dep_doc(old_doc, dep_doc):
         # nothing following first paragraph, just append message
         return old_doc + '\n' + dep_doc
     indent = _LEADING_WHITE.match(old_lines[next_line]).group()
+    setup_lines = [indent + L for L in setup.splitlines()]
     dep_lines = [indent + L for L in [''] + dep_doc.splitlines() + ['']]
-    return '\n'.join(new_lines + dep_lines + old_lines[next_line:]) + '\n'
+    cleanup_lines = [indent + L for L in cleanup.splitlines()]
+    return '\n'.join(new_lines + dep_lines + setup_lines +
+                     old_lines[next_line:] + cleanup_lines + [''])
 
 
 class Deprecator(object):
@@ -160,7 +183,7 @@ def deprecated_func(*args, **kwargs):
                 return func(*args, **kwargs)
 
             deprecated_func.__doc__ = _add_dep_doc(deprecated_func.__doc__,
-                                                   message)
+                                                   message, TESTSETUP, TESTCLEANUP)
             return deprecated_func
 
         return deprecator

nibabel/freesurfer/tests/test_io.py

@@ -86,16 +86,15 @@ def test_geometry():
 
         # now write an incomplete file
         write_geometry(surf_path, coords, faces)
-        with clear_and_catch_warnings() as w:
-            warnings.filterwarnings('always', category=DeprecationWarning)
+        with pytest.warns(UserWarning) as w:
             read_geometry(surf_path, read_metadata=True)
-
         assert any('volume information contained' in str(ww.message) for ww in w)
         assert any('extension code' in str(ww.message) for ww in w)
+
         volume_info['head'] = [1, 2]
-        with clear_and_catch_warnings() as w:
+        with pytest.warns(UserWarning, match="Unknown extension"):
             write_geometry(surf_path, coords, faces, create_stamp, volume_info)
-        assert any('Unknown extension' in str(ww.message) for ww in w)
+
         volume_info['a'] = 0
         with pytest.raises(ValueError):
             write_geometry(surf_path, coords, faces, create_stamp, volume_info)
@@ -266,10 +265,9 @@ def test_write_annot_fill_ctab():
         # values back.
         badannot = (10 * np.arange(nlabels, dtype=np.int32)).reshape(-1, 1)
         rgbal = np.hstack((rgba, badannot))
-        with clear_and_catch_warnings() as w:
+        with pytest.warns(UserWarning,
+                          match=f'Annotation values in {annot_path} will be incorrect'):
             write_annot(annot_path, labels, rgbal, names, fill_ctab=False)
-        assert any(f'Annotation values in {annot_path} will be incorrect' == str(ww.message)
-                   for ww in w)
         labels2, rgbal2, names2 = read_annot(annot_path, orig_ids=True)
         names2 = [n.decode('ascii') for n in names2]
         assert np.all(np.isclose(rgbal2[:, :4], rgba))

nibabel/freesurfer/tests/test_mghformat.py

@@ -345,11 +345,14 @@ def test_deprecated_fields():
 
     # mrparams is the only deprecated field at the moment
     # Accessing hdr_data is equivalent to accessing hdr, so double all checks
-    assert_array_equal(hdr['mrparams'], 0)
+    with pytest.deprecated_call(match="from version: 2.3"):
+        assert_array_equal(hdr['mrparams'], 0)
     assert_array_equal(hdr_data['mrparams'], 0)
 
-    hdr['mrparams'] = [1, 2, 3, 4]
-    assert_array_almost_equal(hdr['mrparams'], [1, 2, 3, 4])
+    with pytest.deprecated_call(match="from version: 2.3"):
+        hdr['mrparams'] = [1, 2, 3, 4]
+    with pytest.deprecated_call(match="from version: 2.3"):
+        assert_array_almost_equal(hdr['mrparams'], [1, 2, 3, 4])
     assert hdr['tr'] == 1
     assert hdr['flip_angle'] == 2
     assert hdr['te'] == 3
@@ -366,14 +369,16 @@ def test_deprecated_fields():
     hdr['flip_angle'] = 6
     hdr['te'] = 7
     hdr['ti'] = 8
-    assert_array_almost_equal(hdr['mrparams'], [5, 6, 7, 8])
+    with pytest.deprecated_call(match="from version: 2.3"):
+        assert_array_almost_equal(hdr['mrparams'], [5, 6, 7, 8])
     assert_array_almost_equal(hdr_data['mrparams'], [5, 6, 7, 8])
 
     hdr_data['tr'] = 9
     hdr_data['flip_angle'] = 10
     hdr_data['te'] = 11
     hdr_data['ti'] = 12
-    assert_array_almost_equal(hdr['mrparams'], [9, 10, 11, 12])
+    with pytest.deprecated_call(match="from version: 2.3"):
+        assert_array_almost_equal(hdr['mrparams'], [9, 10, 11, 12])
     assert_array_almost_equal(hdr_data['mrparams'], [9, 10, 11, 12])
 
 

nibabel/keywordonly.py

@@ -4,7 +4,7 @@
 from functools import wraps
 import warnings
 
-warnings.warn("We will remove this module from nibabel 5.0. "
+warnings.warn("We will remove the 'keywordonly' module from nibabel 5.0. "
               "Please use the built-in Python `*` argument to ensure "
               "keyword-only parameters (see PEP 3102).",
               DeprecationWarning,

nibabel/loadsave.py

@@ -55,9 +55,7 @@ def load(filename, **kwargs):
     raise ImageFileError(f'Cannot work out file type of "{filename}"')
 
 
-@deprecate_with_version('guessed_image_type deprecated.'
-                        '2.1',
-                        '4.0')
+@deprecate_with_version('guessed_image_type deprecated.', '3.2', '5.0')
 def guessed_image_type(filename):
     """ Guess image type from file `filename`
 
@@ -149,10 +147,10 @@ def save(img, filename):
     converted.to_filename(filename)
 
 
-@deprecate_with_version('read_img_data deprecated.'
-                        'Please use ``img.dataobj.get_unscaled()`` instead.'
-                        '2.0.1',
-                        '4.0')
+@deprecate_with_version('read_img_data deprecated. '
+                        'Please use ``img.dataobj.get_unscaled()`` instead.',
+                        '3.2',
+                        '5.0')
 def read_img_data(img, prefer='scaled'):
     """ Read data from image associated with files
 
@@ -236,9 +234,7 @@ def read_img_data(img, prefer='scaled'):
         return hdr.raw_data_from_fileobj(fileobj)
 
 
-@deprecate_with_version('which_analyze_type deprecated.'
-                        '2.1',
-                        '4.0')
+@deprecate_with_version('which_analyze_type deprecated.', '3.2', '4.0')
 def which_analyze_type(binaryblock):
     """ Is `binaryblock` from NIfTI1, NIfTI2 or Analyze header?
 

nibabel/nicom/ascconv.py

@@ -205,7 +205,7 @@ def parse_ascconv(ascconv_str, str_delim='"'):
     attrs, content = ASCCONV_RE.match(ascconv_str).groups()
     attrs = OrderedDict((tuple(x.split('=')) for x in attrs.split()))
     # Normalize string start / end markers to something Python understands
-    content = content.replace(str_delim, '"""')
+    content = content.replace(str_delim, '"""').replace("\\", "\\\\")
     # Use Python's own parser to parse modified ASCCONV assignments
     tree = ast.parse(content)
 

nibabel/nicom/dicomreaders.py

@@ -32,7 +32,7 @@ def mosaic_to_nii(dcm_data):
     if not dcm_w.is_mosaic:
         raise DicomReadError('data does not appear to be in mosaic format')
     data = dcm_w.get_data()
-    aff = np.dot(DPCS_TO_TAL, dcm_w.get_affine())
+    aff = np.dot(DPCS_TO_TAL, dcm_w.affine)
     return Nifti1Image(data, aff)
 
 
@@ -106,7 +106,7 @@ def read_mosaic_dir(dicom_path,
             g = dcm_w.b_vector
         b_values.append(b)
         gradients.append(g)
-    affine = np.dot(DPCS_TO_TAL, dcm_w.get_affine())
+    affine = np.dot(DPCS_TO_TAL, dcm_w.affine)
     return (np.concatenate(arrays, -1),
             affine,
             np.array(b_values),

nibabel/nicom/tests/test_dicomreaders.py

@@ -20,7 +20,7 @@
 @dicom_test
 def test_read_dwi():
     img = didr.mosaic_to_nii(DATA)
-    arr = img.get_data()
+    arr = img.get_fdata()
     assert arr.shape == (128, 128, 48)
     assert_array_almost_equal(img.affine, EXPECTED_AFFINE)
 

nibabel/nicom/tests/test_dicomwrappers.py

@@ -660,13 +660,14 @@ def test_data_derived_shape(self):
         # Test 4D diffusion data with an additional trace volume included
         # Excludes the trace volume and generates the correct shape
         dw = didw.wrapper_from_file(DATA_FILE_4D_DERIVED)
-        assert dw.image_shape == (96, 96, 60, 33)
+        with pytest.warns(UserWarning, match="Derived images found and removed"):
+            assert dw.image_shape == (96, 96, 60, 33)
 
     @dicom_test
     @needs_nibabel_data('nitest-dicom')
     def test_data_unreadable_private_headers(self):
         # Test CT image with unreadable CSA tags
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Error while attempting to read CSA header"):
             dw = didw.wrapper_from_file(DATA_FILE_CT)
         assert dw.image_shape == (512, 571)
 

nibabel/processing.py

@@ -300,7 +300,7 @@ def smooth_image(img,
         fwhm = np.zeros((n_dim,))
         fwhm[:3] = fwhm_scalar
     # Voxel sizes
-    RZS = img.affine[:-1, :n_dim]
+    RZS = img.affine[:, :n_dim]
     vox = np.sqrt(np.sum(RZS ** 2, 0))
     # Smoothing in terms of voxels
     vox_fwhm = fwhm / vox

nibabel/streamlines/tests/test_array_sequence.py

@@ -94,13 +94,18 @@ def test_creating_arraysequence_from_list(self):
         check_arr_seq(ArraySequence(iter(SEQ_DATA['data']), buffer_size),
                       SEQ_DATA['data'])
 
+    def test_deprecated_data_attribute(self):
+        seq = ArraySequence(SEQ_DATA['data'])
+        with pytest.deprecated_call(match="from version: 3.0"):
+            seq.data
+
     def test_creating_arraysequence_from_generator(self):
         gen_1, gen_2 = itertools.tee((e for e in SEQ_DATA['data']))
         seq = ArraySequence(gen_1)
         seq_with_buffer = ArraySequence(gen_2, buffer_size=256)
 
         # Check buffer size effect
-        assert seq_with_buffer.data.shape == seq.data.shape
+        assert seq_with_buffer.get_data().shape == seq.get_data().shape
         assert seq_with_buffer._buffer_size > seq._buffer_size
 
         # Check generator result