Merge branch 'maint/4.0.x'

Author: effigies

Changelog

@@ -25,13 +25,30 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+4.0.1 (Saturday 18 June 2022)
+=============================
+
+Bug-fix release in the 4.0.x series.
+
+Bug fixes
+---------
+* Finalize 4.0 deprecations, converting tests expecting ``DeprecationWarning`` to
+  expected ``ExpiredDeprecationError`` (pr/1117) (CM)
+
+Maintenance
+-----------
+* Suppress new numpy warning on nan-to-int cast (pr/1118) (CM, reviewed by MB)
+
+
 4.0.0 (Saturday 18 June 2022)
 =============================
 
 New feature release in the 4.0.x series.
 
 New features
 ------------
+* ``nib-convert`` CLI tool to make image type and data dtype conversion accessible
+  via the command line. (pr/1113) (CM, reviewed by Ariel Rokem)
 * Add ``'mask'``, ``'compat'`` and ``'smallest'`` dtype aliases to NIfTI images
   to allow for dtype specifications that can depend on the contents of the data.
   ``'mask'`` is a synonym for ``uint8``. ``'compat'`` will find the nearest

nibabel/freesurfer/tests/test_mghformat.py

@@ -22,6 +22,7 @@
 from ...volumeutils import sys_is_le
 from ...wrapstruct import WrapStructError
 from ... import imageglobals
+from ...deprecator import ExpiredDeprecationError
 
 
 import pytest
@@ -344,42 +345,13 @@ def test_deprecated_fields():
     hdr_data = MGHHeader._HeaderData(hdr.structarr)
 
     # mrparams is the only deprecated field at the moment
-    # Accessing hdr_data is equivalent to accessing hdr, so double all checks
-    with pytest.deprecated_call(match="from version: 2.3"):
-        assert_array_equal(hdr['mrparams'], 0)
-    assert_array_equal(hdr_data['mrparams'], 0)
-
-    with pytest.deprecated_call(match="from version: 2.3"):
+    # Accessing hdr_data is equivalent to accessing hdr, so double all checks,
+    # but expect success on hdr_data['mrparams']
+    with pytest.raises(ExpiredDeprecationError):
+        hdr['mrparams']
+    with pytest.raises(ExpiredDeprecationError):
         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
-    assert hdr['ti'] == 4
-    assert hdr['fov'] == 0
-    assert_array_almost_equal(hdr_data['mrparams'], [1, 2, 3, 4])
-    assert hdr_data['tr'] == 1
-    assert hdr_data['flip_angle'] == 2
-    assert hdr_data['te'] == 3
-    assert hdr_data['ti'] == 4
-    assert hdr_data['fov'] == 0
-
-    hdr['tr'] = 5
-    hdr['flip_angle'] = 6
-    hdr['te'] = 7
-    hdr['ti'] = 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
-    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])
+    assert_array_equal(hdr_data['mrparams'], 0)
 
 
 class TestMGHImage(tsi.TestSpatialImage, tsi.MmapImageMixin):

nibabel/gifti/tests/test_gifti.py

@@ -15,10 +15,11 @@
 from ..gifti import data_tag
 from ...nifti1 import data_type_codes
 from ...fileholders import FileHolder
+from ...deprecator import ExpiredDeprecationError
 
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 import pytest
-from ...testing import clear_and_catch_warnings, test_data
+from ...testing import test_data
 from .test_parse_gifti_fast import (DATA_FILE1, DATA_FILE2, DATA_FILE3,
                                     DATA_FILE4, DATA_FILE5, DATA_FILE6)
 import itertools
@@ -183,46 +184,29 @@ def test_dataarray_init():
 
 
 def test_dataarray_from_array():
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
-        da = GiftiDataArray.from_array(np.ones((3, 4)))
-        assert len(w) == 1
-        for dt_code in data_type_codes.value_set():
-            data_type = data_type_codes.type[dt_code]
-            if data_type is np.void:  # not supported
-                continue
-            arr = np.zeros((10, 3), dtype=data_type)
-            da = GiftiDataArray.from_array(arr, 'triangle')
-            assert da.datatype == data_type_codes[arr.dtype]
-            bs_arr = arr.byteswap().newbyteorder()
-            da = GiftiDataArray.from_array(bs_arr, 'triangle')
-            assert da.datatype == data_type_codes[arr.dtype]
+    with pytest.raises(ExpiredDeprecationError):
+        GiftiDataArray.from_array(np.ones((3, 4)))
 
 
 def test_to_xml_open_close_deprecations():
     # Smoke test on deprecated functions
     da = GiftiDataArray(np.ones((1,)), 'triangle')
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
-        assert isinstance(da.to_xml_open(), str)
-        assert len(w) == 1
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('once', category=DeprecationWarning)
-        assert isinstance(da.to_xml_close(), str)
-        assert len(w) == 1
+    with pytest.raises(ExpiredDeprecationError):
+        da.to_xml_open()
+    with pytest.raises(ExpiredDeprecationError):
+        da.to_xml_close()
 
 
 def test_num_dim_deprecation():
     da = GiftiDataArray(np.ones((2, 3, 4)))
     # num_dim is property, set automatically from len(da.dims)
     assert da.num_dim == 3
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
-        # OK setting num_dim to correct value, but raises DeprecationWarning
+    # setting num_dim to correct value is deprecated
+    with pytest.raises(ExpiredDeprecationError):
         da.num_dim = 3
-        assert len(w) == 1
-        # Any other value gives a ValueError
-        pytest.raises(ValueError, setattr, da, 'num_dim', 4)
+    # setting num_dim to incorrect value is also deprecated
+    with pytest.raises(ExpiredDeprecationError):
+        da.num_dim = 4
 
 
 def test_labeltable():
@@ -235,14 +219,10 @@ def test_labeltable():
     assert len(img.labeltable.labels) == 2
 
     # Test deprecations
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
+    with pytest.raises(ExpiredDeprecationError):
         newer_table = GiftiLabelTable()
         newer_table.labels += ['test', 'me', 'again']
         img.set_labeltable(newer_table)
-        assert len(w) == 1
-        assert len(img.get_labeltable().labels) == 3
-        assert len(w) == 2
 
 
 def test_metadata():
@@ -261,14 +241,8 @@ def test_metadata():
         assert md.data[0].value == 'value'
     assert len(w) == 2
     # Test deprecation
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
-        assert md.get_metadata() == dict(key='value')
-        assert len(w) == 1
-        assert md.metadata == dict(key='value')
-        assert len(w) == 2
-        assert len(GiftiDataArray().get_metadata()) == 0
-        assert len(w) == 3
+    with pytest.raises(ExpiredDeprecationError):
+        md.get_metadata()
 
 
 def test_gifti_label_rgba():
@@ -295,10 +269,8 @@ def assign_rgba(gl, val):
     pytest.raises(ValueError, assign_rgba, gl3, rgba.tolist() + rgba.tolist())
 
     # Test deprecation
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('once', category=DeprecationWarning)
-        assert kwargs['red'] == gl3.get_rgba()[0]
-        assert len(w) == 1
+    with pytest.raises(ExpiredDeprecationError):
+        gl3.get_rgba()
 
     # Test default value
     gl4 = GiftiLabel()
@@ -325,10 +297,8 @@ def test_gifti_coord():
 
 
 def test_data_tag_deprecated():
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('once', category=DeprecationWarning)
+    with pytest.raises(ExpiredDeprecationError):
         data_tag(np.array([]), 'ASCII', '%i', 1)
-        assert len(w) == 1
 
 
 def test_gifti_round_trip():

nibabel/gifti/tests/test_giftiio.py

@@ -7,16 +7,19 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 
+from ..gifti import GiftiImage
 from ..giftiio import read, write
 from .test_parse_gifti_fast import DATA_FILE1
+from ...deprecator import ExpiredDeprecationError
 
 import pytest
 
 
 def test_read_deprecated(tmp_path):
-    with pytest.deprecated_call():
-        img = read(DATA_FILE1)
+    with pytest.raises(ExpiredDeprecationError):
+        read(DATA_FILE1)
 
+    img = GiftiImage.from_filename(DATA_FILE1)
     fname = tmp_path / 'test.gii'
-    with pytest.deprecated_call():
+    with pytest.raises(ExpiredDeprecationError):
         write(img, fname)

nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -22,6 +22,7 @@
 from ...loadsave import load, save
 from ...nifti1 import xform_codes
 from ...tmpdirs import InTemporaryDirectory
+from ...deprecator import ExpiredDeprecationError
 
 from numpy.testing import assert_array_almost_equal
 
@@ -48,8 +49,8 @@
 
 DATA_FILE1_darr1 = np.array(
     [[-16.07201, -66.187515, 21.266994],
-        [-16.705893, -66.054337, 21.232786],
-        [-17.614349, -65.401642, 21.071466]])
+     [-16.705893, -66.054337, 21.232786],
+     [-17.614349, -65.401642, 21.071466]])
 DATA_FILE1_darr2 = np.array([0, 1, 2])
 
 DATA_FILE2_darr1 = np.array([[0.43635699],
@@ -189,14 +190,11 @@ def test_metadata_deprecations():
     me = img.meta
 
     # Test deprecation
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('once', category=DeprecationWarning)
-        assert me == img.get_meta()
+    with pytest.raises(ExpiredDeprecationError):
+        img.get_meta()
 
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('once', category=DeprecationWarning)
+    with pytest.raises(ExpiredDeprecationError):
         img.set_metadata(me)
-    assert me == img.meta
 
 
 def test_load_dataarray1():
@@ -321,12 +319,8 @@ def test_load_getbyintent():
     da = img.get_arrays_from_intent("NIFTI_INTENT_POINTSET")
     assert len(da) == 1
 
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('once', category=DeprecationWarning)
-        da = img.getArraysFromIntent("NIFTI_INTENT_POINTSET")
-        assert len(da) == 1
-        assert len(w) == 1
-        w[0].category == DeprecationWarning
+    with pytest.raises(ExpiredDeprecationError):
+        img.getArraysFromIntent("NIFTI_INTENT_POINTSET")
 
     da = img.get_arrays_from_intent("NIFTI_INTENT_TRIANGLE")
     assert len(da) == 1
@@ -360,16 +354,11 @@ def test_labeltable_deprecations():
     lt = img.labeltable
 
     # Test deprecation
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
-        assert lt == img.get_labeltable()
-        assert len(w) == 1
+    with pytest.raises(ExpiredDeprecationError):
+        img.get_labeltable()
 
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
+    with pytest.raises(ExpiredDeprecationError):
         img.set_labeltable(lt)
-        assert len(w) == 1
-    assert lt == img.labeltable
 
 
 def test_parse_dataarrays():
@@ -395,16 +384,11 @@ def test_parse_dataarrays():
 def test_parse_deprecated():
 
     # Test deprecation
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
-        op = Outputter()
-        assert len(w) == 1
-        op.initialize()  # smoke test--no error.
-
-    with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('always', category=DeprecationWarning)
-        pytest.raises(ValueError, parse_gifti_file)
-        assert len(w) == 1
+    with pytest.raises(ExpiredDeprecationError):
+        Outputter()
+
+    with pytest.raises(ExpiredDeprecationError):
+        parse_gifti_file()
 
 
 def test_parse_with_buffersize():

nibabel/nicom/tests/test_dicomwrappers.py

@@ -13,6 +13,7 @@
 from .. import dicomwrappers as didw
 from .. import dicomreaders as didr
 from ...volumeutils import endian_codes
+from ...deprecator import ExpiredDeprecationError
 
 import pytest
 from unittest import TestCase
@@ -631,8 +632,8 @@ def test_affine(self):
         # Make sure we find orientation/position/spacing info
         dw = didw.wrapper_from_file(DATA_FILE_4D)
         aff = dw.affine
-        with pytest.deprecated_call():
-            assert np.array_equal(dw.get_affine(), aff)
+        with pytest.raises(ExpiredDeprecationError):
+            dw.get_affine()
 
     @dicom_test
     def test_data_real(self):

nibabel/streamlines/tests/test_array_sequence.py

@@ -10,6 +10,7 @@
 from numpy.testing import assert_array_equal
 
 from ..array_sequence import ArraySequence, is_array_sequence, concatenate
+from ...deprecator import ExpiredDeprecationError
 
 
 SEQ_DATA = {}
@@ -96,7 +97,7 @@ def test_creating_arraysequence_from_list(self):
 
     def test_deprecated_data_attribute(self):
         seq = ArraySequence(SEQ_DATA['data'])
-        with pytest.deprecated_call(match="from version: 3.0"):
+        with pytest.raises(ExpiredDeprecationError):
             seq.data
 
     def test_creating_arraysequence_from_generator(self):