TEST: Suppress deprecation warnings from pytest and numpy

Author: effigies

nibabel/nicom/tests/test_dicomwrappers.py

@@ -361,10 +361,10 @@ def test_assert_parallel():
 
 @dicom_test
 def test_decimal_rescale():
-    # Test that we don't get back a data array with dtype np.object when our
+    # Test that we don't get back a data array with dtype object when our
     # rescale slope is a decimal
     dw = didw.wrapper_from_file(DATA_FILE_DEC_RSCL)
-    assert dw.get_data().dtype != np.object
+    assert dw.get_data().dtype != np.dtype(object)
 
 
 def fake_frames(seq_name, field_name, value_seq):

nibabel/streamlines/tests/test_streamlines.py

@@ -2,6 +2,7 @@
 import unittest
 import tempfile
 import numpy as np
+import warnings
 
 import pytest
 
@@ -12,7 +13,7 @@
 from nibabel.tmpdirs import InTemporaryDirectory
 from numpy.compat.py3k import asbytes
 
-from nibabel.testing import data_path
+from nibabel.testing import data_path, error_warnings, clear_and_catch_warnings
 
 from .test_tractogram import assert_tractogram_equal
 from ..tractogram import Tractogram, LazyTractogram
@@ -142,7 +143,7 @@ def test_load_empty_file(self):
                 else:
                     assert type(tfile.tractogram), LazyTractogram
 
-                with pytest.warns(Warning if lazy_load else None):
+                with pytest.warns(Warning) if lazy_load else error_warnings():
                     assert_tractogram_equal(tfile.tractogram,
                                             DATA['empty_tractogram'])
 
@@ -158,7 +159,7 @@ def test_load_simple_file(self):
                 else:
                     assert type(tfile.tractogram), LazyTractogram
 
-                with pytest.warns(Warning if lazy_load else None):
+                with pytest.warns(Warning) if lazy_load else error_warnings():
                     assert_tractogram_equal(tfile.tractogram,
                                             DATA['simple_tractogram'])
 
@@ -184,7 +185,7 @@ def test_load_complex_file(self):
                     data = DATA['data_per_streamline']
                     tractogram.data_per_streamline = data
 
-                with pytest.warns(Warning if lazy_load else None):
+                with pytest.warns(Warning) if lazy_load else error_warnings():
                     assert_tractogram_equal(tfile.tractogram,
                                             tractogram)
 
@@ -244,7 +245,8 @@ def test_save_complex_file(self):
                     ((not cls.SUPPORTS_DATA_PER_POINT) +
                      (not cls.SUPPORTS_DATA_PER_STREAMLINE))
 
-                with pytest.warns(Warning if nb_expected_warnings else None) as w:
+                with clear_and_catch_warnings() as w:
+                    warnings.simplefilter('always')
                     nib.streamlines.save(complex_tractogram, filename)
                 assert len(w) == nb_expected_warnings
 

nibabel/streamlines/tests/test_tck.py

@@ -15,7 +15,7 @@
 
 import pytest
 from numpy.testing import assert_array_equal
-from ...testing import data_path
+from ...testing import data_path, error_warnings
 from .test_tractogram import assert_tractogram_equal
 
 DATA = {}
@@ -47,13 +47,13 @@ class TestTCK(unittest.TestCase):
     def test_load_empty_file(self):
         for lazy_load in [False, True]:
             tck = TckFile.load(DATA['empty_tck_fname'], lazy_load=lazy_load)
-            with pytest.warns(Warning if lazy_load else None):
+            with pytest.warns(Warning) if lazy_load else error_warnings():
                 assert_tractogram_equal(tck.tractogram, DATA['empty_tractogram'])
 
     def test_load_simple_file(self):
         for lazy_load in [False, True]:
             tck = TckFile.load(DATA['simple_tck_fname'], lazy_load=lazy_load)
-            with pytest.warns(Warning if lazy_load else None):
+            with pytest.warns(Warning) if lazy_load else error_warnings():
                 assert_tractogram_equal(tck.tractogram, DATA['simple_tractogram'])
 
         # Force TCK loading to use buffering.
@@ -88,7 +88,7 @@ def test_load_simple_file_in_big_endian(self):
         for lazy_load in [False, True]:
             tck = TckFile.load(DATA['simple_tck_big_endian_fname'],
                                lazy_load=lazy_load)
-            with pytest.warns(Warning if lazy_load else None):
+            with pytest.warns(Warning) if lazy_load else error_warnings():
                 assert_tractogram_equal(tck.tractogram, DATA['simple_tractogram'])
             assert tck.header['datatype'] == 'Float32BE'
 

nibabel/streamlines/tests/test_trk.py

@@ -8,7 +8,7 @@
 from io import BytesIO
 
 import pytest
-from ...testing import data_path, clear_and_catch_warnings, assert_arr_dict_equal
+from ...testing import data_path, clear_and_catch_warnings, assert_arr_dict_equal, error_warnings
 from numpy.testing import assert_array_equal
 
 from .test_tractogram import assert_tractogram_equal
@@ -87,19 +87,19 @@ class TestTRK(unittest.TestCase):
     def test_load_empty_file(self):
         for lazy_load in [False, True]:
             trk = TrkFile.load(DATA['empty_trk_fname'], lazy_load=lazy_load)
-            with pytest.warns(Warning if lazy_load else None):
+            with pytest.warns(Warning) if lazy_load else error_warnings():
                 assert_tractogram_equal(trk.tractogram, DATA['empty_tractogram'])
 
     def test_load_simple_file(self):
         for lazy_load in [False, True]:
             trk = TrkFile.load(DATA['simple_trk_fname'], lazy_load=lazy_load)
-            with pytest.warns(Warning if lazy_load else None):
+            with pytest.warns(Warning) if lazy_load else error_warnings():
                 assert_tractogram_equal(trk.tractogram, DATA['simple_tractogram'])
 
     def test_load_complex_file(self):
         for lazy_load in [False, True]:
             trk = TrkFile.load(DATA['complex_trk_fname'], lazy_load=lazy_load)
-            with pytest.warns(Warning if lazy_load else None):
+            with pytest.warns(Warning) if lazy_load else error_warnings():
                 assert_tractogram_equal(trk.tractogram, DATA['complex_tractogram'])
 
     def trk_with_bytes(self, trk_key='simple_trk_fname', endian='<'):
@@ -199,7 +199,7 @@ def test_load_complex_file_in_big_endian(self):
         for lazy_load in [False, True]:
             trk = TrkFile.load(DATA['complex_trk_big_endian_fname'],
                                lazy_load=lazy_load)
-            with pytest.warns(Warning if lazy_load else None):
+            with pytest.warns(Warning) if lazy_load else error_warnings():
                 assert_tractogram_equal(trk.tractogram, DATA['complex_tractogram'])
 
     def test_tractogram_file_properties(self):

nibabel/tests/test_volumeutils.py

@@ -55,7 +55,8 @@
                            assert_array_equal)
 import pytest
 
-from nibabel.testing import nullcontext, assert_dt_equal, assert_allclose_safely, suppress_warnings
+from nibabel.testing import (assert_dt_equal, assert_allclose_safely,
+                             suppress_warnings, error_warnings)
 
 pyzstd, HAVE_ZSTD, _ = optional_package("pyzstd")
 
@@ -623,7 +624,7 @@ def test_a2f_bad_scaling():
             (0, np.nan, -np.inf, np.inf)):
         arr = np.ones((2,), dtype=in_type)
         fobj = BytesIO()
-        cm = nullcontext()
+        cm = error_warnings()
         if (np.issubdtype(in_type, np.complexfloating) and
                 not np.issubdtype(out_type, np.complexfloating)):
             cm = pytest.warns(np.ComplexWarning)
@@ -674,37 +675,37 @@ def test_a2f_nan2zero_range():
         warn_type = np.ComplexWarning if np.issubdtype(dt, np.complexfloating) else None
         # No errors from explicit thresholding
         # mn thresholding excluding zero
-        with pytest.warns(warn_type):
+        with pytest.warns(warn_type) if warn_type else error_warnings():
             assert_array_equal([1, 1, 1, 0],
                                write_return(arr, fobj, np.int8, mn=1))
         # mx thresholding excluding zero
-        with pytest.warns(warn_type):
+        with pytest.warns(warn_type) if warn_type else error_warnings():
             assert_array_equal([-1, -1, -1, 0],
                                write_return(arr, fobj, np.int8, mx=-1))
         # Errors from datatype threshold after scaling
-        with pytest.warns(warn_type):
+        with pytest.warns(warn_type) if warn_type else error_warnings():
             back_arr = write_return(arr, fobj, np.int8, intercept=128)
         assert_array_equal([-128, -128, -127, -128], back_arr)
         with pytest.raises(ValueError):
             write_return(arr, fobj, np.int8, intercept=129)
         with pytest.raises(ValueError):
             write_return(arr_no_nan, fobj, np.int8, intercept=129)
         # OK with nan2zero false, but we get whatever nan casts to
-        with pytest.warns(warn_type):
+        with pytest.warns(warn_type) if warn_type else error_warnings():
             nan_cast = np.array(np.nan, dtype=dt).astype(np.int8)
-        with pytest.warns(warn_type):
+        with pytest.warns(warn_type) if warn_type else error_warnings():
             back_arr = write_return(arr, fobj, np.int8, intercept=129, nan2zero=False)
         assert_array_equal([-128, -128, -128, nan_cast], back_arr)
         # divslope
-        with pytest.warns(warn_type):
+        with pytest.warns(warn_type) if warn_type else error_warnings():
             back_arr = write_return(arr, fobj, np.int8, intercept=256, divslope=2)
         assert_array_equal([-128, -128, -128, -128], back_arr)
         with pytest.raises(ValueError):
             write_return(arr, fobj, np.int8, intercept=257.1, divslope=2)
         with pytest.raises(ValueError):
             write_return(arr_no_nan, fobj, np.int8, intercept=257.1, divslope=2)
         # OK with nan2zero false
-        with pytest.warns(warn_type):
+        with pytest.warns(warn_type) if warn_type else error_warnings():
             back_arr = write_return(arr, fobj, np.int8,
                                     intercept=257.1, divslope=2, nan2zero=False)
         assert_array_equal([-128, -128, -128, nan_cast], back_arr)