Numpy pre-release breaks setting some arrays writable
Closed this issue · 8 comments
effigies commented
Most likely culprit is numpy/numpy#11739, which was merged 7 days ago.
Example failures:
ERROR: test_load_simple_file (nibabel.streamlines.tests.test_streamlines.TestLoadSave)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/tests/test_streamlines.py", line 152, in test_load_simple_file
lazy_load=lazy_load)
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/__init__.py", line 96, in load
return tractogram_file.load(fileobj, lazy_load=lazy_load)
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/tck.py", line 154, in load
streamlines = ArraySequence(tck_reader)
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/array_sequence.py", line 93, in __init__
self.extend(iterable)
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/array_sequence.py", line 239, in extend
for e in elements:
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/tck.py", line 436, in _read
pts.flags.writeable = True
ValueError: cannot set WRITEABLE flag to True of this array
ERROR: test_load_complex_file_in_big_endian (nibabel.streamlines.tests.test_trk.TestTRK)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/tests/test_trk.py", line 194, in test_load_complex_file_in_big_endian
'complex_trk_big_endian_fname', endian='>')
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/streamlines/tests/test_trk.py", line 109, in trk_with_bytes
trk_struct.flags.writeable = True
ValueError: cannot set WRITEABLE flag to True of this array
ERROR: test_big_offset_exts (nibabel.tests.test_analyze.TestAnalyzeImage)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/tests/test_analyze.py", line 809, in test_big_offset_exts
assert_array_equal(arr, img_back.dataobj)
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/numpy/testing/_private/utils.py", line 873, in assert_array_equal
verbose=verbose, header='Arrays are not equal')
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/numpy/testing/_private/utils.py", line 693, in assert_array_compare
y = array(y, copy=False, subok=True)
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/arrayproxy.py", line 356, in __array__
raw_data = self.get_unscaled()
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/arrayproxy.py", line 351, in get_unscaled
mmap=self._mmap)
File "/home/travis/build/nipy/nibabel/venv/lib/python2.7/site-packages/nibabel/volumeutils.py", line 543, in array_from_file
arr.flags.writeable = True
ValueError: cannot set WRITEABLE flag to True of this array
eric-wieser commented
Why doesn't the readinto path get reached here that bypasses the readonly buffer?
effigies commented
@eric-wieser That error is only hit in the Python 2.7 tests, so it's due to readinto not existing in Py2.
eric-wieser commented
I see readinto here, so it looks like it at least exists in python 2. What object are you passing that's missing that attribute?
matthew-brett commented
@eric-wieser - Python 2.7 hits this path with Bzip2 files.
eric-wieser commented
Can you take a dependency on the bz2file backport, @effigies?
yarikoptic commented
FWIW, this issue hit Debian now as well https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=917680