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tests failing with numpy-1.10 #4247
Description
==================================================================== test session starts ====================================================================
platform linux -- Python 3.4.3 -- py-1.4.30 -- pytest-2.7.3 -- /usr/bin/python3.4
/usr/lib64/python3.4/importlib/_bootstrap.py:321: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
return f(*args, **kwds)
rootdir: /var/tmp/portage/dev-python/astropy-1.0.5/work/astropy-1.0.5, inifile: setup.cfg
plugins: cov, pythonpath, catchlog
Running tests with Astropy version 1.0.5.
Running tests in astropy/io/fits/tests/test_checksum.py astropy/io/fits/tests/test_connect.py.
Platform: Linux-4.1.9-lh-x86_64-Intel-R-_Core-TM-_i7-2600_CPU_@_3.40GHz-with-gentoo-2.2
Executable: /usr/bin/python3.4
Full Python Version:
3.4.3 (default, Aug 21 2015, 10:51:23)
[GCC 4.9.3]
encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
byteorder: little
float info: dig: 15, mant_dig: 15
Numpy: 1.10.1
Scipy: 0.16.0
Matplotlib: 1.4.3
h5py: 2.5.0
collected 46 items
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_sample_file PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_image_create PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_nonstandard_checksum PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_scaled_data PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_scaled_data_auto_rescale PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_uint16_data PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_groups_hdu_data FAILED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_binary_table_data FAILED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_variable_length_table_data FAILED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_ascii_table_data PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_compressed_image_data PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_compressed_image_data_int16 FAILED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_compressed_image_data_float32 /usr/lib64/python3.4/site-packages/py/_code/source.py:348: ResourceWarning: unclosed file <_io.FileIO name='/tmp/.private/justin/fits-test-v3agys4z/tmp.fits' mode='wb'>
astnode = compile(content, "source", "exec", 1024) # 1024 for AST
/usr/lib64/python3.4/site-packages/py/_code/source.py:348: ResourceWarning: unclosed file <_io.FileIO name='/tmp/.private/justin/fits-test-36tp_7at/tmp.fits' mode='wb'>
astnode = compile(content, "source", "exec", 1024) # 1024 for AST
FAILED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_open_with_no_keywords PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_append PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_writeto_convenience PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_hdu_writeto PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_hdu_writeto_existing PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_datasum_only PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_open_update_mode_preserve_checksum PASSED
astropy/io/fits/tests/test_checksum.py::TestChecksumFunctions::test_open_update_mode_update_checksum FAILED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_simple PASSED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_simple_meta PASSED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_simple_meta_conflicting PASSED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_simple_noextension PASSED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_with_units PASSED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_masked PASSED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_masked_nan PASSED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_read_from_fileobj FAILED
astropy/io/fits/tests/test_connect.py::TestSingleTable::test_read_with_nonstandard_units PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read FAILED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_with_hdu_0 PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_with_hdu_1[1] FAILED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_with_hdu_1[first] FAILED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_with_hdu_2[2] PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_with_hdu_2[second] PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_from_hdulist PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_from_hdulist_with_hdu_0 PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_from_hdulist_with_hdu_1[1] PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_from_hdulist_with_hdu_1[first] PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_from_hdulist_with_hdu_2[2] PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_from_hdulist_with_hdu_2[second] PASSED
astropy/io/fits/tests/test_connect.py::TestMultipleHDU::test_read_from_single_hdu PASSED
astropy/io/fits/tests/test_connect.py::test_masking_regression_1795 PASSED
astropy/io/fits/tests/test_connect.py::test_scale_error PASSED
astropy/io/fits/tests/test_connect.py::test_bool_column PASSED
========================================================================= FAILURES ==========================================================================
________________________________________________________ TestChecksumFunctions.test_groups_hdu_data _________________________________________________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x2b5c640f48d0>
def test_groups_hdu_data(self):
imdata = np.arange(100.0)
imdata.shape = (10, 1, 1, 2, 5)
pdata1 = np.arange(10) + 0.1
pdata2 = 42
x = fits.hdu.groups.GroupData(imdata, parnames=[str('abc'), str('xyz')],
pardata=[pdata1, pdata2], bitpix=-32)
hdu = fits.GroupsHDU(x)
> hdu.writeto(self.temp('tmp.fits'), clobber=True, checksum=True)
astropy/io/fits/tests/test_checksum.py:156:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
astropy/io/fits/hdu/base.py:450: in writeto
checksum=checksum)
astropy/io/fits/hdu/hdulist.py:680: in writeto
hdu._prewriteto(checksum=checksum)
astropy/io/fits/hdu/image.py:539: in _prewriteto
return super(_ImageBaseHDU, self)._prewriteto(checksum, inplace)
astropy/io/fits/hdu/base.py:568: in _prewriteto
self._update_checksum(checksum)
astropy/io/fits/hdu/base.py:625: in _update_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1403: in add_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1353: in add_datasum
cs = self._calculate_datasum(blocking)
astropy/io/fits/hdu/groups.py:530: in _calculate_datasum
blocking=blocking)
astropy/io/fits/hdu/base.py:1609: in _compute_checksum
sum32 = self._compute_hdu_checksum(data[i:i + length], sum32)
astropy/io/fits/hdu/groups.py:211: in __getitem__
out = super(GroupData, self).__getitem__(key)
astropy/io/fits/fitsrec.py:486: in __getitem__
out = self.view(np.recarray).__getitem__(key).view(subtype)
astropy/io/fits/hdu/groups.py:204: in __array_finalize__
super(GroupData, self).__array_finalize__(obj)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("recarray has no attribute _nfields") raised in repr()] GroupData object at 0x2b5c640e46d8>
obj = array([ 61, 204, 204, 205, 66, 40, 0, 0, 0, 0, 0, 0, 63,
128, 0, 0, 64, 0, 0, 0, 64,...66, 190, 0, 0, 66, 192, 0, 0,
66, 194, 0, 0, 66, 196, 0, 0, 66, 198, 0, 0], dtype=uint8)
def __array_finalize__(self, obj):
if obj is None:
return
if isinstance(obj, FITS_rec):
self._converted = obj._converted
self._heapoffset = obj._heapoffset
self._heapsize = obj._heapsize
self._coldefs = obj._coldefs
self._nfields = obj._nfields
self._gap = obj._gap
self._uint = obj._uint
else:
# This will allow regular ndarrays with fields, rather than
# just other FITS_rec objects
> self._nfields = len(obj.dtype.names)
E TypeError: object of type 'NoneType' has no len()
astropy/io/fits/fitsrec.py:249: TypeError
_______________________________________________________ TestChecksumFunctions.test_binary_table_data ________________________________________________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x2b5c5f5b9080>
def test_binary_table_data(self):
a1 = np.array(['NGC1001', 'NGC1002', 'NGC1003'])
a2 = np.array([11.1, 12.3, 15.2])
col1 = fits.Column(name='target', format='20A', array=a1)
col2 = fits.Column(name='V_mag', format='E', array=a2)
cols = fits.ColDefs([col1, col2])
tbhdu = fits.BinTableHDU.from_columns(cols)
> tbhdu.writeto(self.temp('tmp.fits'), clobber=True, checksum=True)
astropy/io/fits/tests/test_checksum.py:171:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
astropy/io/fits/hdu/base.py:1754: in writeto
checksum=checksum)
astropy/io/fits/hdu/hdulist.py:680: in writeto
hdu._prewriteto(checksum=checksum)
astropy/io/fits/hdu/table.py:527: in _prewriteto
return super(_TableBaseHDU, self)._prewriteto(checksum, inplace)
astropy/io/fits/hdu/base.py:568: in _prewriteto
self._update_checksum(checksum)
astropy/io/fits/hdu/base.py:625: in _update_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1403: in add_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1353: in add_datasum
cs = self._calculate_datasum(blocking)
astropy/io/fits/hdu/table.py:834: in _calculate_datasum
return self._calculate_datasum_with_heap(blocking)
astropy/io/fits/hdu/table.py:804: in _calculate_datasum_with_heap
csum = self._compute_checksum(dout, blocking=blocking)
astropy/io/fits/hdu/base.py:1609: in _compute_checksum
sum32 = self._compute_hdu_checksum(data[i:i + length], sum32)
astropy/io/fits/fitsrec.py:486: in __getitem__
out = self.view(np.recarray).__getitem__(key).view(subtype)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("recarray has no attribute _nfields") raised in repr()] FITS_rec object at 0x2b5c64a90908>
obj = array([ 78, 71, 67, 49, 48, 48, 49, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 154,...48, 48, 51, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 51, 51, 115, 65], dtype=uint8)
def __array_finalize__(self, obj):
if obj is None:
return
if isinstance(obj, FITS_rec):
self._converted = obj._converted
self._heapoffset = obj._heapoffset
self._heapsize = obj._heapsize
self._coldefs = obj._coldefs
self._nfields = obj._nfields
self._gap = obj._gap
self._uint = obj._uint
else:
# This will allow regular ndarrays with fields, rather than
# just other FITS_rec objects
> self._nfields = len(obj.dtype.names)
E TypeError: object of type 'NoneType' has no len()
astropy/io/fits/fitsrec.py:249: TypeError
___________________________________________________ TestChecksumFunctions.test_variable_length_table_data ___________________________________________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x2b5c64bef080>
def test_variable_length_table_data(self):
c1 = fits.Column(name='var', format='PJ()',
array=np.array([[45.0, 56], np.array([11, 12, 13])],
'O'))
c2 = fits.Column(name='xyz', format='2I', array=[[11, 3], [12, 4]])
tbhdu = fits.BinTableHDU.from_columns([c1, c2])
> tbhdu.writeto(self.temp('tmp.fits'), clobber=True, checksum=True)
astropy/io/fits/tests/test_checksum.py:189:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
astropy/io/fits/hdu/base.py:1754: in writeto
checksum=checksum)
astropy/io/fits/hdu/hdulist.py:680: in writeto
hdu._prewriteto(checksum=checksum)
astropy/io/fits/hdu/table.py:527: in _prewriteto
return super(_TableBaseHDU, self)._prewriteto(checksum, inplace)
astropy/io/fits/hdu/base.py:568: in _prewriteto
self._update_checksum(checksum)
astropy/io/fits/hdu/base.py:625: in _update_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1403: in add_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1353: in add_datasum
cs = self._calculate_datasum(blocking)
astropy/io/fits/hdu/table.py:834: in _calculate_datasum
return self._calculate_datasum_with_heap(blocking)
astropy/io/fits/hdu/table.py:804: in _calculate_datasum_with_heap
csum = self._compute_checksum(dout, blocking=blocking)
astropy/io/fits/hdu/base.py:1609: in _compute_checksum
sum32 = self._compute_hdu_checksum(data[i:i + length], sum32)
astropy/io/fits/fitsrec.py:486: in __getitem__
out = self.view(np.recarray).__getitem__(key).view(subtype)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("recarray has no attribute _nfields") raised in repr()] FITS_rec object at 0x2b5c64ac07b8>
obj = array([ 2, 0, 0, 0, 0, 0, 0, 0, 11, 0, 3, 0, 3, 0, 0, 0, 8,
0, 0, 0, 12, 0, 4, 0], dtype=uint8)
def __array_finalize__(self, obj):
if obj is None:
return
if isinstance(obj, FITS_rec):
self._converted = obj._converted
self._heapoffset = obj._heapoffset
self._heapsize = obj._heapsize
self._coldefs = obj._coldefs
self._nfields = obj._nfields
self._gap = obj._gap
self._uint = obj._uint
else:
# This will allow regular ndarrays with fields, rather than
# just other FITS_rec objects
> self._nfields = len(obj.dtype.names)
E TypeError: object of type 'NoneType' has no len()
astropy/io/fits/fitsrec.py:249: TypeError
__________________________________________________ TestChecksumFunctions.test_compressed_image_data_int16 ___________________________________________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x2b5c64940908>
def test_compressed_image_data_int16(self):
n = np.arange(100, dtype='int16')
hdu = fits.ImageHDU(n)
comp_hdu = fits.CompImageHDU(hdu.data, hdu.header)
> comp_hdu.writeto(self.temp('tmp.fits'), checksum=True)
astropy/io/fits/tests/test_checksum.py:246:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
astropy/io/fits/hdu/base.py:1754: in writeto
checksum=checksum)
astropy/io/fits/hdu/hdulist.py:680: in writeto
hdu._prewriteto(checksum=checksum)
astropy/io/fits/hdu/compressed.py:1844: in _prewriteto
inplace=inplace)
astropy/io/fits/hdu/table.py:527: in _prewriteto
return super(_TableBaseHDU, self)._prewriteto(checksum, inplace)
astropy/io/fits/hdu/base.py:568: in _prewriteto
self._update_checksum(checksum)
astropy/io/fits/hdu/base.py:625: in _update_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1403: in add_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1353: in add_datasum
cs = self._calculate_datasum(blocking)
astropy/io/fits/hdu/table.py:834: in _calculate_datasum
return self._calculate_datasum_with_heap(blocking)
astropy/io/fits/hdu/table.py:804: in _calculate_datasum_with_heap
csum = self._compute_checksum(dout, blocking=blocking)
astropy/io/fits/hdu/base.py:1609: in _compute_checksum
sum32 = self._compute_hdu_checksum(data[i:i + length], sum32)
astropy/io/fits/fitsrec.py:486: in __getitem__
out = self.view(np.recarray).__getitem__(key).view(subtype)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("recarray has no attribute _nfields") raised in repr()] FITS_rec object at 0x2b5c64a5e2e8>
obj = array([ 0, 0, 0, 42, 0, 0, 0, 0], dtype=uint8)
def __array_finalize__(self, obj):
if obj is None:
return
if isinstance(obj, FITS_rec):
self._converted = obj._converted
self._heapoffset = obj._heapoffset
self._heapsize = obj._heapsize
self._coldefs = obj._coldefs
self._nfields = obj._nfields
self._gap = obj._gap
self._uint = obj._uint
else:
# This will allow regular ndarrays with fields, rather than
# just other FITS_rec objects
> self._nfields = len(obj.dtype.names)
E TypeError: object of type 'NoneType' has no len()
astropy/io/fits/fitsrec.py:249: TypeError
_________________________________________________ TestChecksumFunctions.test_compressed_image_data_float32 __________________________________________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x2b5c64e736d8>
def test_compressed_image_data_float32(self):
n = np.arange(100, dtype='float32')
hdu = fits.ImageHDU(n)
comp_hdu = fits.CompImageHDU(hdu.data, hdu.header)
> comp_hdu.writeto(self.temp('tmp.fits'), checksum=True)
astropy/io/fits/tests/test_checksum.py:278:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
astropy/io/fits/hdu/base.py:1754: in writeto
checksum=checksum)
astropy/io/fits/hdu/hdulist.py:680: in writeto
hdu._prewriteto(checksum=checksum)
astropy/io/fits/hdu/compressed.py:1844: in _prewriteto
inplace=inplace)
astropy/io/fits/hdu/table.py:527: in _prewriteto
return super(_TableBaseHDU, self)._prewriteto(checksum, inplace)
astropy/io/fits/hdu/base.py:568: in _prewriteto
self._update_checksum(checksum)
astropy/io/fits/hdu/base.py:625: in _update_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1403: in add_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1353: in add_datasum
cs = self._calculate_datasum(blocking)
astropy/io/fits/hdu/table.py:834: in _calculate_datasum
return self._calculate_datasum_with_heap(blocking)
astropy/io/fits/hdu/table.py:804: in _calculate_datasum_with_heap
csum = self._compute_checksum(dout, blocking=blocking)
astropy/io/fits/hdu/base.py:1609: in _compute_checksum
sum32 = self._compute_hdu_checksum(data[i:i + length], sum32)
astropy/io/fits/fitsrec.py:486: in __getitem__
out = self.view(np.recarray).__getitem__(key).view(subtype)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("recarray has no attribute _nfields") raised in repr()] FITS_rec object at 0x2b5c640f1f28>
obj = array([ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 214, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0], dtype=uint8)
def __array_finalize__(self, obj):
if obj is None:
return
if isinstance(obj, FITS_rec):
self._converted = obj._converted
self._heapoffset = obj._heapoffset
self._heapsize = obj._heapsize
self._coldefs = obj._coldefs
self._nfields = obj._nfields
self._gap = obj._gap
self._uint = obj._uint
else:
# This will allow regular ndarrays with fields, rather than
# just other FITS_rec objects
> self._nfields = len(obj.dtype.names)
E TypeError: object of type 'NoneType' has no len()
astropy/io/fits/fitsrec.py:249: TypeError
________________________________________________ TestChecksumFunctions.test_open_update_mode_update_checksum ________________________________________________
self = <astropy.io.fits.tests.test_checksum.TestChecksumFunctions object at 0x2b5c648dff98>
def test_open_update_mode_update_checksum(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/148, part
2. This ensures that if a file contains a checksum, the checksum is
updated when changes are saved to the file, even if the file was opened
with the default of checksum=False.
An existing checksum and/or datasum are only stripped if the file is
opened with checksum='remove'.
"""
self.copy_file('checksum.fits')
with fits.open(self.temp('checksum.fits')) as hdul:
header = hdul[1].header.copy()
data = hdul[1].data.copy()
with fits.open(self.temp('checksum.fits'), mode='update') as hdul:
hdul[1].header['FOO'] = 'BAR'
> hdul[1].data[0]['TIME'] = 42
astropy/io/fits/tests/test_checksum.py:417:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
astropy/io/fits/hdu/hdulist.py:257: in __exit__
self.close()
astropy/io/fits/hdu/hdulist.py:710: in close
self.flush(output_verify=output_verify, verbose=verbose)
astropy/utils/decorators.py:522: in flush
**_get_function_args(wrapped))
astropy/io/fits/util.py:255: in wrapped
func(*args, **kwargs)
astropy/io/fits/hdu/hdulist.py:604: in flush
self._flush_update()
astropy/io/fits/hdu/hdulist.py:926: in _flush_update
hdu._prewriteto(checksum=hdu._output_checksum, inplace=True)
astropy/io/fits/hdu/table.py:527: in _prewriteto
return super(_TableBaseHDU, self)._prewriteto(checksum, inplace)
astropy/io/fits/hdu/base.py:568: in _prewriteto
self._update_checksum(checksum)
astropy/io/fits/hdu/base.py:625: in _update_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1403: in add_checksum
datasum_keyword=datasum_keyword)
astropy/io/fits/hdu/base.py:1353: in add_datasum
cs = self._calculate_datasum(blocking)
astropy/io/fits/hdu/table.py:834: in _calculate_datasum
return self._calculate_datasum_with_heap(blocking)
astropy/io/fits/hdu/table.py:804: in _calculate_datasum_with_heap
csum = self._compute_checksum(dout, blocking=blocking)
astropy/io/fits/hdu/base.py:1609: in _compute_checksum
sum32 = self._compute_hdu_checksum(data[i:i + length], sum32)
astropy/io/fits/fitsrec.py:486: in __getitem__
out = self.view(np.recarray).__getitem__(key).view(subtype)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("recarray has no attribute _nfields") raised in repr()] FITS_rec object at 0x2b5c6499f6d8>
obj = array([ 64, 69, 0, 0, 0, 0, 0, 0, 65, 188, 193, 210, 63,
167, 155, 86, 64, 134, 250, 252, 57,..., 82, 164, 64,
135, 8, 134, 83, 57, 130, 192, 65, 230, 182, 100, 63, 197,
252, 202], dtype=uint8)
def __array_finalize__(self, obj):
if obj is None:
return
if isinstance(obj, FITS_rec):
self._converted = obj._converted
self._heapoffset = obj._heapoffset
self._heapsize = obj._heapsize
self._coldefs = obj._coldefs
self._nfields = obj._nfields
self._gap = obj._gap
self._uint = obj._uint
else:
# This will allow regular ndarrays with fields, rather than
# just other FITS_rec objects
> self._nfields = len(obj.dtype.names)
E TypeError: object of type 'NoneType' has no len()
astropy/io/fits/fitsrec.py:249: TypeError
__________________________________________________________ TestSingleTable.test_read_from_fileobj ___________________________________________________________
self = <astropy.io.fits.tests.test_connect.TestSingleTable object at 0x2b5c64af6160>
tmpdir = local('/tmp/.private/justin/pytest-justin/pytest-2/test_read_from_fileobj0')
def test_read_from_fileobj(self, tmpdir):
filename = str(tmpdir.join('test_read_from_fileobj.fits'))
hdu = BinTableHDU(self.data)
hdu.writeto(filename)
with open(filename, 'rb') as f:
t = Table.read(f)
> assert equal_data(t, self.data)
E assert equal_data(<Table masked=False length=4>\n a b c \n int64 str128 float64 \n-------- ------ --...035316621e+185\n33554432 b 4.5\n 3 c 6.7\n 4 d 8.9, array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]))
E + where array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]) = <astropy.io.fits.tests.test_connect.TestSingleTable object at 0x2b5c64af6160>.data
astropy/io/fits/tests/test_connect.py:130: AssertionError
_________________________________________________________________ TestMultipleHDU.test_read _________________________________________________________________
self = <astropy.io.fits.tests.test_connect.TestMultipleHDU object at 0x2b5c64bf05c0>
tmpdir = local('/tmp/.private/justin/pytest-justin/pytest-2/test_read0')
def test_read(self, tmpdir):
filename = str(tmpdir.join('test_read.fits'))
self.hdus.writeto(filename)
with catch_warnings() as l:
t = Table.read(filename)
assert len(l) == 1
assert str(l[0].message).startswith(
'hdu= was not specified but multiple tables are present, reading in first available table (hdu=1)')
> assert equal_data(t, self.data1)
E assert equal_data(<Table masked=False length=4>\n a b c \n int64 str128 float64 \n-------- ------ --...035316621e+185\n33554432 b 4.5\n 3 c 6.7\n 4 d 8.9, array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]))
E + where array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]) = <astropy.io.fits.tests.test_connect.TestMultipleHDU object at 0x2b5c64bf05c0>.data1
astropy/io/fits/tests/test_connect.py:168: AssertionError
__________________________________________________________ TestMultipleHDU.test_read_with_hdu_1[1] __________________________________________________________
self = <astropy.io.fits.tests.test_connect.TestMultipleHDU object at 0x2b5c64dac400>
tmpdir = local('/tmp/.private/justin/pytest-justin/pytest-2/test_read_with_hdu_1_1_0'), hdu = 1
@pytest.mark.parametrize('hdu', [1, 'first'])
def test_read_with_hdu_1(self, tmpdir, hdu):
filename = str(tmpdir.join('test_read_with_hdu_1.fits'))
self.hdus.writeto(filename)
with catch_warnings() as l:
t = Table.read(filename, hdu=hdu)
assert len(l) == 0
> assert equal_data(t, self.data1)
E assert equal_data(<Table masked=False length=4>\n a b c \n int64 str128 float64 \n-------- ------ --...035316621e+185\n33554432 b 4.5\n 3 c 6.7\n 4 d 8.9, array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]))
E + where array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]) = <astropy.io.fits.tests.test_connect.TestMultipleHDU object at 0x2b5c64dac400>.data1
astropy/io/fits/tests/test_connect.py:184: AssertionError
________________________________________________________ TestMultipleHDU.test_read_with_hdu_1[first] ________________________________________________________
self = <astropy.io.fits.tests.test_connect.TestMultipleHDU object at 0x2b5c649dc390>
tmpdir = local('/tmp/.private/justin/pytest-justin/pytest-2/test_read_with_hdu_1_first_0'), hdu = 'first'
@pytest.mark.parametrize('hdu', [1, 'first'])
def test_read_with_hdu_1(self, tmpdir, hdu):
filename = str(tmpdir.join('test_read_with_hdu_1.fits'))
self.hdus.writeto(filename)
with catch_warnings() as l:
t = Table.read(filename, hdu=hdu)
assert len(l) == 0
> assert equal_data(t, self.data1)
E assert equal_data(<Table masked=False length=4>\n a b c \n int64 str128 float64 \n-------- ------ --...035316621e+185\n33554432 b 4.5\n 3 c 6.7\n 4 d 8.9, array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]))
E + where array([(1, 'a', 2.3), (2, 'b', 4.5), (3, 'c', 6.7), (4, 'd', 8.9)], \n dtype=[('a', '<i8'), ('b', '<U1'), ('c', '<f8')]) = <astropy.io.fits.tests.test_connect.TestMultipleHDU object at 0x2b5c649dc390>.data1
astropy/io/fits/tests/test_connect.py:184: AssertionError
=========================================================== 10 failed, 36 passed in 2.87 seconds ============================================================
Activity
mhvk commentedon Oct 19, 2015
@jlec - thanks for reporting this! It is actually a known issue (#3854), with, fortunately, a solution about ready to be merged (#4228). I'll close this therefore, but not without making a note in #4228 that really we should wrap this up... Please do keep raising issues if we find problems!