def test_save_backup(self):
"""Test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/121
Save backup of file before flushing changes.
"""
self.copy_file('scale.fits')
with ignore_warnings():
with fits.open(self.temp('scale.fits'),
mode='update',
save_backup=True) as hdul:
# Make some changes to the original file to force its header
# and data to be rewritten
hdul[0].header['TEST'] = 'TEST'
hdul[0].data[0] = 0
assert os.path.exists(self.temp('scale.fits.bak'))
with fits.open(self.data('scale.fits'),
do_not_scale_image_data=True) as hdul1:
with fits.open(self.temp('scale.fits.bak'),
do_not_scale_image_data=True) as hdul2:
assert hdul1[0].header == hdul2[0].header
assert (hdul1[0].data == hdul2[0].data).all()
with ignore_warnings():
with fits.open(self.temp('scale.fits'),
mode='update',
save_backup=True) as hdul:
# One more time to see if multiple backups are made
hdul[0].header['TEST2'] = 'TEST'
hdul[0].data[0] = 1
assert os.path.exists(self.temp('scale.fits.bak'))
assert os.path.exists(self.temp('scale.fits.bak.1'))
def test_save_backup(self):
"""Test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/121
Save backup of file before flushing changes.
"""
self.copy_file('scale.fits')
with ignore_warnings():
with fits.open(self.temp('scale.fits'), mode='update',
save_backup=True) as hdul:
# Make some changes to the original file to force its header
# and data to be rewritten
hdul[0].header['TEST'] = 'TEST'
hdul[0].data[0] = 0
assert os.path.exists(self.temp('scale.fits.bak'))
with fits.open(self.data('scale.fits'),
do_not_scale_image_data=True) as hdul1:
with fits.open(self.temp('scale.fits.bak'),
do_not_scale_image_data=True) as hdul2:
assert hdul1[0].header == hdul2[0].header
assert (hdul1[0].data == hdul2[0].data).all()
with ignore_warnings():
with fits.open(self.temp('scale.fits'), mode='update',
save_backup=True) as hdul:
# One more time to see if multiple backups are made
hdul[0].header['TEST2'] = 'TEST'
hdul[0].data[0] = 1
assert os.path.exists(self.temp('scale.fits.bak'))
assert os.path.exists(self.temp('scale.fits.bak.1'))
def test_uint_columns(self, utype):
"""Test basic functionality of tables with columns containing
pseudo-unsigned integers. See
https://github.com/astropy/astropy/pull/906
"""
bits = 8 * int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
bzero = self.utype_map[utype](2**(bits - 1))
one = self.utype_map[utype](1)
u0 = np.arange(bits + 1, dtype=self.utype_map[utype])
u = 2**u0 - one
if bits == 64:
u[63] = bzero - one
u[64] = u[63] + u[63] + one
uu = (u - bzero).view(self.itype_map[utype])
# Construct a table from explicit column
col = fits.Column(name=utype,
array=u,
format=self.format_map[utype],
bzero=bzero)
table = fits.BinTableHDU.from_columns([col])
assert (table.data[utype] == u).all()
# This used to be table.data.base, but now after adding a table to
# a BinTableHDU it gets stored as a view of the original table,
# even if the original was already a FITS_rec. So now we need
# table.data.base.base
assert (table.data.base.base[utype] == uu).all()
hdu0 = fits.PrimaryHDU()
hdulist = fits.HDUList([hdu0, table])
with ignore_warnings():
hdulist.writeto(self.temp('tempfile.fits'), overwrite=True)
# Test write of unsigned int
del hdulist
with fits.open(self.temp('tempfile.fits'), uint=True) as hdulist2:
hdudata = hdulist2[1].data
assert (hdudata[utype] == u).all()
assert (hdudata[utype].dtype == self.utype_map[utype])
assert (hdudata.base[utype] == uu).all()
# Construct recarray then write out that.
v = u.view(dtype=[(utype, self.utype_map[utype])])
with ignore_warnings():
fits.writeto(self.temp('tempfile2.fits'), v, overwrite=True)
with fits.open(self.temp('tempfile2.fits'), uint=True) as hdulist3:
hdudata3 = hdulist3[1].data
assert (
hdudata3.base[utype] == table.data.base.base[utype]).all()
assert (hdudata3[utype] == table.data[utype]).all()
assert (hdudata3[utype] == u).all()
def test_uint_columns(self, utype):
"""Test basic functionality of tables with columns containing
pseudo-unsigned integers. See
https://github.com/astropy/astropy/pull/906
"""
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
bzero = self.utype_map[utype](2**(bits-1))
one = self.utype_map[utype](1)
u0 = np.arange(bits+1, dtype=self.utype_map[utype])
u = 2**u0 - one
if bits == 64:
u[63] = bzero - one
u[64] = u[63] + u[63] + one
uu = (u - bzero).view(self.itype_map[utype])
# Construct a table from explicit column
col = fits.Column(name=utype, array=u,
format=self.format_map[utype], bzero=bzero)
table = fits.BinTableHDU.from_columns([col])
assert (table.data[utype] == u).all()
# This used to be table.data.base, but now after adding a table to
# a BinTableHDU it gets stored as a view of the original table,
# even if the original was already a FITS_rec. So now we need
# table.data.base.base
assert (table.data.base.base[utype] == uu).all()
hdu0 = fits.PrimaryHDU()
hdulist = fits.HDUList([hdu0, table])
with ignore_warnings():
hdulist.writeto(self.temp('tempfile.fits'), overwrite=True)
# Test write of unsigned int
del hdulist
with fits.open(self.temp('tempfile.fits'), uint=True) as hdulist2:
hdudata = hdulist2[1].data
assert (hdudata[utype] == u).all()
assert (hdudata[utype].dtype == self.utype_map[utype])
assert (hdudata.base[utype] == uu).all()
# Construct recarray then write out that.
v = u.view(dtype=[(utype, self.utype_map[utype])])
with ignore_warnings():
fits.writeto(self.temp('tempfile2.fits'), v, overwrite=True)
with fits.open(self.temp('tempfile2.fits'), uint=True) as hdulist3:
hdudata3 = hdulist3[1].data
assert (hdudata3.base[utype] ==
table.data.base.base[utype]).all()
assert (hdudata3[utype] == table.data[utype]).all()
assert (hdudata3[utype] == u).all()
def test_add_del_columns2(self):
hdulist = fits.open(self.data('tb.fits'))
table = hdulist[1]
assert table.data.dtype.names == ('c1', 'c2', 'c3', 'c4')
assert table.columns.names == ['c1', 'c2', 'c3', 'c4']
table.columns.del_col(str('c1'))
assert table.data.dtype.names == ('c2', 'c3', 'c4')
assert table.columns.names == ['c2', 'c3', 'c4']
table.columns.del_col(str('c3'))
assert table.data.dtype.names == ('c2', 'c4')
assert table.columns.names == ['c2', 'c4']
table.columns.add_col(fits.Column(str('foo'), str('3J')))
assert table.data.dtype.names == ('c2', 'c4', 'foo')
assert table.columns.names == ['c2', 'c4', 'foo']
hdulist.writeto(self.temp('test.fits'), overwrite=True)
with ignore_warnings():
# TODO: The warning raised by this test is actually indication of a
# bug and should *not* be ignored. But as it is a known issue we
# hide it for now. See
# https://github.com/spacetelescope/PyFITS/issues/44
with fits.open(self.temp('test.fits')) as hdulist:
table = hdulist[1]
assert table.data.dtype.names == ('c2', 'c4', 'foo')
assert table.columns.names == ['c2', 'c4', 'foo']
def test_uint(self, utype, compressed):
bits = 8 * int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(
np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(
np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale(f'int{bits:d}', '', bzero=2**(bits - 1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2**bits) - 3, (2**bits) - 2, (2**bits) - 1, 0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == f'uint{bits}'
assert (sec == d1[:1]).all()
def test_replace_mmap_data(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/25
Replacing the mmap'd data of one file with mmap'd data from a
different file should work.
"""
arr_a = np.arange(10)
arr_b = arr_a * 2
def test(mmap_a, mmap_b):
hdu_a = fits.PrimaryHDU(data=arr_a)
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.PrimaryHDU(data=arr_b)
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
with fits.open(self.temp('test_a.fits'), mode='update',
memmap=mmap_a) as hdul_a:
with fits.open(self.temp('test_b.fits'),
memmap=mmap_b) as hdul_b:
hdul_a[0].data = hdul_b[0].data
with fits.open(self.temp('test_a.fits')) as hdul_a:
assert np.all(hdul_a[0].data == arr_b)
with ignore_warnings():
test(True, True)
# Repeat the same test but this time don't mmap A
test(False, True)
# Finally, without mmaping B
test(True, False)
def test_replace_mmap_data(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/25
Replacing the mmap'd data of one file with mmap'd data from a
different file should work.
"""
arr_a = np.arange(10)
arr_b = arr_a * 2
def test(mmap_a, mmap_b):
hdu_a = fits.PrimaryHDU(data=arr_a)
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.PrimaryHDU(data=arr_b)
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
with fits.open(self.temp('test_a.fits'),
mode='update',
memmap=mmap_a) as hdul_a:
with fits.open(self.temp('test_b.fits'),
memmap=mmap_b) as hdul_b:
hdul_a[0].data = hdul_b[0].data
with fits.open(self.temp('test_a.fits')) as hdul_a:
assert np.all(hdul_a[0].data == arr_b)
with ignore_warnings():
test(True, True)
# Repeat the same test but this time don't mmap A
test(False, True)
# Finally, without mmaping B
test(True, False)
def test_add_del_columns2(self):
hdulist = fits.open(self.data('tb.fits'))
table = hdulist[1]
assert table.data.dtype.names == ('c1', 'c2', 'c3', 'c4')
assert table.columns.names == ['c1', 'c2', 'c3', 'c4']
table.columns.del_col('c1')
assert table.data.dtype.names == ('c2', 'c3', 'c4')
assert table.columns.names == ['c2', 'c3', 'c4']
table.columns.del_col('c3')
assert table.data.dtype.names == ('c2', 'c4')
assert table.columns.names == ['c2', 'c4']
table.columns.add_col(fits.Column('foo', '3J'))
assert table.data.dtype.names == ('c2', 'c4', 'foo')
assert table.columns.names == ['c2', 'c4', 'foo']
hdulist.writeto(self.temp('test.fits'), overwrite=True)
with ignore_warnings():
# TODO: The warning raised by this test is actually indication of a
# bug and should *not* be ignored. But as it is a known issue we
# hide it for now. See
# https://github.com/spacetelescope/PyFITS/issues/44
with fits.open(self.temp('test.fits')) as hdulist:
table = hdulist[1]
assert table.data.dtype.names == ('c2', 'c4', 'foo')
assert table.columns.names == ['c2', 'c4', 'foo']
def test_uint(self, utype, compressed):
bits = 8*int(utype[1])
if platform.architecture()[0] == '64bit' or bits != 64:
if compressed:
hdu = fits.CompImageHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 1
else:
hdu = fits.PrimaryHDU(np.array([-3, -2, -1, 0, 1, 2, 3], dtype=np.int64))
hdu_number = 0
hdu.scale('int{0:d}'.format(bits), '', bzero=2 ** (bits-1))
with ignore_warnings():
hdu.writeto(self.temp('tempfile.fits'), overwrite=True)
with fits.open(self.temp('tempfile.fits'), uint=True) as hdul:
assert hdul[hdu_number].data.dtype == self.utype_map[utype]
assert (hdul[hdu_number].data == np.array(
[(2 ** bits) - 3, (2 ** bits) - 2, (2 ** bits) - 1,
0, 1, 2, 3],
dtype=self.utype_map[utype])).all()
hdul.writeto(self.temp('tempfile1.fits'))
with fits.open(self.temp('tempfile1.fits'),
uint16=True) as hdul1:
d1 = hdul[hdu_number].data
d2 = hdul1[hdu_number].data
assert (d1 == d2).all()
if not compressed:
# TODO: Enable these lines if CompImageHDUs ever grow
# .section support
sec = hdul[hdu_number].section[:1]
assert sec.dtype.name == 'uint{}'.format(bits)
assert (sec == d1[:1]).all()
def test_open_zipped(self):
zip_file = self._make_zip_file()
with ignore_warnings():
with fits.open(zip_file) as fits_handle:
assert fits_handle._file.compression == 'zip'
assert len(fits_handle) == 5
with fits.open(zipfile.ZipFile(zip_file)) as fits_handle:
assert fits_handle._file.compression == 'zip'
assert len(fits_handle) == 5
def test_read_file_like_object(self):
"""Test reading a FITS file from a file-like object."""
filelike = io.BytesIO()
with open(self.data('test0.fits'), 'rb') as f:
filelike.write(f.read())
filelike.seek(0)
with ignore_warnings():
assert len(fits.open(filelike)) == 5
def test_read_file_like_object(self):
"""Test reading a FITS file from a file-like object."""
filelike = io.BytesIO()
with open(self.data('test0.fits'), 'rb') as f:
filelike.write(f.read())
filelike.seek(0)
with ignore_warnings():
assert len(fits.open(filelike)) == 5
def test_open_zipped(self):
zip_file = self._make_zip_file()
with ignore_warnings():
with fits.open(zip_file) as fits_handle:
assert fits_handle._file.compression == 'zip'
assert len(fits_handle) == 5
with fits.open(zipfile.ZipFile(zip_file)) as fits_handle:
assert fits_handle._file.compression == 'zip'
assert len(fits_handle) == 5
def test_open_bzipped(self):
bzip_file = self._make_bzip2_file()
with ignore_warnings():
with fits.open(bzip_file) as fits_handle:
assert fits_handle._file.compression == 'bzip2'
assert len(fits_handle) == 5
with fits.open(bz2.BZ2File(bzip_file)) as fits_handle:
assert fits_handle._file.compression == 'bzip2'
assert len(fits_handle) == 5
def test_open_bzipped(self):
bzip_file = self._make_bzip2_file()
with ignore_warnings():
with fits.open(bzip_file) as fits_handle:
assert fits_handle._file.compression == 'bzip2'
assert len(fits_handle) == 5
with fits.open(bz2.BZ2File(bzip_file)) as fits_handle:
assert fits_handle._file.compression == 'bzip2'
assert len(fits_handle) == 5
def __init__(self, filename='$GAMMA_CAT/docs/data/gammacat.fits.gz'):
filename = str(make_path(filename))
with ignore_warnings(): # ignore FITS units warnings
table = Table.read(filename, hdu=1)
self.filename = filename
source_name_key = 'common_name'
source_name_alias = ('other_names', 'gamma_names')
super(SourceCatalogGammaCat, self).__init__(
table=table,
source_name_key=source_name_key,
source_name_alias=source_name_alias,
)
def test_open_file_with_end_padding(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/106
Open files with end padding bytes.
"""
hdul = fits.open(self.data('test0.fits'),
do_not_scale_image_data=True)
info = hdul.info(output=False)
hdul.writeto(self.temp('temp.fits'))
with open(self.temp('temp.fits'), 'ab') as f:
f.seek(0, os.SEEK_END)
f.write(b'\0' * 2880)
with ignore_warnings():
assert info == fits.info(self.temp('temp.fits'), output=False,
do_not_scale_image_data=True)
def test_open_file_with_end_padding(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/106
Open files with end padding bytes.
"""
hdul = fits.open(self.data('test0.fits'), do_not_scale_image_data=True)
info = hdul.info(output=False)
hdul.writeto(self.temp('temp.fits'))
with open(self.temp('temp.fits'), 'ab') as f:
f.seek(0, os.SEEK_END)
f.write(b'\0' * 2880)
with ignore_warnings():
assert info == fits.info(self.temp('temp.fits'),
output=False,
do_not_scale_image_data=True)
def __init__(self, filename=None, hdu='HGPS_SOURCES'):
if not filename:
filename = Path(os.environ['HGPS_ANALYSIS']
) / 'data/catalogs/HGPS3/release/HGPS_v0.4.fits'
filename = str(make_path(filename))
with ignore_warnings(): # ignore FITS units warnings
table = Table.read(filename, hdu=hdu)
source_name_alias = ('Identified_Object', )
super(SourceCatalogHGPS, self).__init__(
table=table,
source_name_alias=source_name_alias,
)
self.components = Table.read(filename, hdu='HGPS_GAUSS_COMPONENTS')
self.associations = Table.read(filename, hdu='HGPS_ASSOCIATIONS')
self.identifications = Table.read(filename, hdu='HGPS_IDENTIFICATIONS')
def test_replace_mmap_data_2(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/25
Replacing the mmap'd data of one file with mmap'd data from a
different file should work. Like test_replace_mmap_data but with
table data instead of image data.
"""
arr_a = np.arange(10)
arr_b = arr_a * 2
def test(mmap_a, mmap_b):
col_a = fits.Column(name='a', format='J', array=arr_a)
col_b = fits.Column(name='b', format='J', array=arr_b)
hdu_a = fits.BinTableHDU.from_columns([col_a])
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.BinTableHDU.from_columns([col_b])
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
hdul_a = fits.open(self.temp('test_a.fits'),
mode='update',
memmap=mmap_a)
hdul_b = fits.open(self.temp('test_b.fits'), memmap=mmap_b)
hdul_a[1].data = hdul_b[1].data
hdul_a.close()
hdul_b.close()
hdul_a = fits.open(self.temp('test_a.fits'))
assert 'b' in hdul_a[1].columns.names
assert 'a' not in hdul_a[1].columns.names
assert np.all(hdul_a[1].data['b'] == arr_b)
with ignore_warnings():
test(True, True)
# Repeat the same test but this time don't mmap A
test(False, True)
# Finally, without mmaping B
test(True, False)
def __init__(self, filename='$GAMMA_CAT/docs/data/gammacat.fits.gz'):
filename = str(make_path(filename))
if 'GAMMA_CAT' not in os.environ:
msg = 'The gamma-cat repo is not available. '
msg += 'You have to set the GAMMA_CAT environment variable '
msg += 'to point to the location for it to be found.'
raise GammaCatNotFoundError(msg)
with ignore_warnings(): # ignore FITS units warnings
table = Table.read(filename, hdu=1)
self.filename = filename
source_name_key = 'common_name'
source_name_alias = ('other_names', 'gamma_names')
super(SourceCatalogGammaCat, self).__init__(
table=table,
source_name_key=source_name_key,
source_name_alias=source_name_alias,
)
def __init__(
self,
filename='$GAMMAPY_EXTRA/datasets/catalogs/fermi/gll_psch_v07.fit.gz'
):
filename = str(make_path(filename))
with ignore_warnings(): # ignore FITS units warnings
table = Table.read(filename, hdu='LAT_Point_Source_Catalog')
table_standardise(table)
source_name_key = 'Source_Name'
source_name_alias = ('ASSOC1', 'ASSOC2', 'ASSOC_TEV', 'ASSOC_GAM')
super(SourceCatalog1FHL, self).__init__(
table=table,
source_name_key=source_name_key,
source_name_alias=source_name_alias,
)
self.extended_sources_table = Table.read(filename,
hdu='ExtendedSources')
def test_replace_mmap_data_2(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/25
Replacing the mmap'd data of one file with mmap'd data from a
different file should work. Like test_replace_mmap_data but with
table data instead of image data.
"""
arr_a = np.arange(10)
arr_b = arr_a * 2
def test(mmap_a, mmap_b):
col_a = fits.Column(name='a', format='J', array=arr_a)
col_b = fits.Column(name='b', format='J', array=arr_b)
hdu_a = fits.BinTableHDU.from_columns([col_a])
hdu_a.writeto(self.temp('test_a.fits'), overwrite=True)
hdu_b = fits.BinTableHDU.from_columns([col_b])
hdu_b.writeto(self.temp('test_b.fits'), overwrite=True)
with fits.open(self.temp('test_a.fits'), mode='update',
memmap=mmap_a) as hdul_a:
with fits.open(self.temp('test_b.fits'),
memmap=mmap_b) as hdul_b:
hdul_a[1].data = hdul_b[1].data
with fits.open(self.temp('test_a.fits')) as hdul_a:
assert 'b' in hdul_a[1].columns.names
assert 'a' not in hdul_a[1].columns.names
assert np.all(hdul_a[1].data['b'] == arr_b)
with ignore_warnings():
test(True, True)
# Repeat the same test but this time don't mmap A
test(False, True)
# Finally, without mmaping B
test(True, False)
def __init__(
self,
filename='$GAMMAPY_EXTRA/datasets/catalogs/fermi/gll_psch_v08.fit.gz'
):
filename = str(make_path(filename))
with ignore_warnings(): # ignore FITS units warnings
table = Table.read(filename, hdu='2FHL Source Catalog')
table_standardise(table)
source_name_key = 'Source_Name'
source_name_alias = ('ASSOC', '3FGL_Name', '1FHL_Name', 'TeVCat_Name')
super(SourceCatalog2FHL, self).__init__(
table=table,
source_name_key=source_name_key,
source_name_alias=source_name_alias,
)
self.counts_image = SkyImage.read(filename, hdu='Count Map')
self.extended_sources_table = Table.read(filename,
hdu='Extended Sources')
self.rois = Table.read(filename, hdu='ROIs')
def pytest_report_header(config):
if not ASTROPY_INSTALLED:
return
# If the astropy display plugin is registered, we stop now and let it
# handle the header.
if ASTROPY_LT_40 and config.pluginmanager.hasplugin(
'astropy.tests.plugins.display'):
return
if not config.getoption("astropy_header") and not config.getini(
"astropy_header"):
return
astropy_header_packages_option = config.getoption(
"astropy_header_packages")
astropy_header_packages_ini = config.getini("astropy_header_packages")
if astropy_header_packages_option is not None:
if isinstance(astropy_header_packages_option, str):
astropy_header_packages_option = [
x.strip() for x in astropy_header_packages_option.split(',')
]
packages_to_display = OrderedDict([
(x, x) for x in astropy_header_packages_option
])
elif len(astropy_header_packages_ini) > 0:
if len(astropy_header_packages_ini) == 1:
astropy_header_packages_ini = [
x.strip() for x in astropy_header_packages_ini[0].split(',')
]
packages_to_display = OrderedDict([
(x, x) for x in astropy_header_packages_ini
])
else:
packages_to_display = PYTEST_HEADER_MODULES
try:
stdoutencoding = sys.stdout.encoding or 'ascii'
except AttributeError:
stdoutencoding = 'ascii'
args = config.args
# TESTED_VERSIONS can contain the affiliated package version, too
if len(TESTED_VERSIONS) > 1:
for pkg, version in TESTED_VERSIONS.items():
if pkg not in ['Astropy', 'astropy_helpers']:
s = "\nRunning tests with {} version {}.\n".format(
pkg, version)
else:
s = "\nRunning tests with Astropy version {}.\n".format(
TESTED_VERSIONS['Astropy'])
# Per https://github.com/astropy/astropy/pull/4204, strip the rootdir from
# each directory argument
if hasattr(config, 'rootdir'):
rootdir = str(config.rootdir)
if not rootdir.endswith(os.sep):
rootdir += os.sep
dirs = [
arg[len(rootdir):] if arg.startswith(rootdir) else arg
for arg in args
]
else:
dirs = args
s += "Running tests in {}.\n\n".format(" ".join(dirs))
s += "Date: {}\n\n".format(datetime.datetime.now().isoformat()[:19])
from platform import platform
plat = platform()
if isinstance(plat, bytes):
plat = plat.decode(stdoutencoding, 'replace')
s += "Platform: {plat}\n\n".format(plat=plat)
s += "Executable: {executable}\n\n".format(executable=sys.executable)
s += "Full Python Version: \n{version}\n\n".format(version=sys.version)
s += "encodings: sys: {}, locale: {}, filesystem: {}".format(
sys.getdefaultencoding(), locale.getpreferredencoding(),
sys.getfilesystemencoding())
s += '\n'
s += "byteorder: {byteorder}\n".format(byteorder=sys.byteorder)
s += "float info: dig: {0.dig}, mant_dig: {0.dig}\n\n".format(
sys.float_info)
s += "Package versions: \n"
for module_display, module_name in packages_to_display.items():
try:
with ignore_warnings(DeprecationWarning):
module = resolve_name(module_name)
except ImportError:
s += "{module_display}: not available\n".format(
module_display=module_display)
else:
try:
version = module.__version__
except AttributeError:
version = 'unknown (no __version__ attribute)'
s += "{module_display}: {version}\n".format(
module_display=module_display, version=version)
# Helpers version
if 'astropy_helpers' in TESTED_VERSIONS:
astropy_helpers_version = TESTED_VERSIONS['astropy_helpers']
else:
try:
from astropy.version import astropy_helpers_version
except ImportError:
astropy_helpers_version = None
if astropy_helpers_version:
s += "astropy-helpers: {astropy_helpers_version}\n".format(
astropy_helpers_version=astropy_helpers_version)
s += "\n"
special_opts = ["remote_data", "pep8"]
opts = []
for op in special_opts:
op_value = getattr(config.option, op, None)
if op_value:
if isinstance(op_value, str):
op = ': '.join((op, op_value))
opts.append(op)
if opts:
s += "Using Astropy options: {}.\n".format(", ".join(opts))
return s
def test_detect_bzipped(self):
"""Test detection of a bzip2 file when the extension is not .bz2."""
with ignore_warnings():
with fits.open(self._make_bzip2_file('test0.xx')) as fits_handle:
assert fits_handle._file.compression == 'bzip2'
assert len(fits_handle) == 5
def test_detect_gzipped(self):
"""Test detection of a gzip file when the extension is not .gz."""
with ignore_warnings():
with fits.open(self._make_gzip_file('test0.fz')) as fits_handle:
assert fits_handle._file.compression == 'gzip'
assert len(fits_handle) == 5
def test_detect_gzipped(self):
"""Test detection of a gzip file when the extension is not .gz."""
with ignore_warnings():
with fits.open(self._make_gzip_file('test0.fz')) as fits_handle:
assert fits_handle._file.compression == 'gzip'
assert len(fits_handle) == 5
def pytest_report_header(config):
try:
stdoutencoding = sys.stdout.encoding or 'ascii'
except AttributeError:
stdoutencoding = 'ascii'
args = config.args
# TESTED_VERSIONS can contain the affiliated package version, too
if len(TESTED_VERSIONS) > 1:
for pkg, version in TESTED_VERSIONS.items():
if pkg not in ['Astropy', 'astropy_helpers']:
s = "\nRunning tests with {0} version {1}.\n".format(
pkg, version)
else:
s = "\nRunning tests with Astropy version {0}.\n".format(
TESTED_VERSIONS['Astropy'])
# Per https://github.com/astropy/astropy/pull/4204, strip the rootdir from
# each directory argument
if hasattr(config, 'rootdir'):
rootdir = str(config.rootdir)
if not rootdir.endswith(os.sep):
rootdir += os.sep
dirs = [arg[len(rootdir):] if arg.startswith(rootdir) else arg
for arg in args]
else:
dirs = args
s += "Running tests in {0}.\n\n".format(" ".join(dirs))
s += "Date: {0}\n\n".format(datetime.datetime.now().isoformat()[:19])
from platform import platform
plat = platform()
if isinstance(plat, bytes):
plat = plat.decode(stdoutencoding, 'replace')
s += "Platform: {0}\n\n".format(plat)
s += "Executable: {0}\n\n".format(sys.executable)
s += "Full Python Version: \n{0}\n\n".format(sys.version)
s += "encodings: sys: {0}, locale: {1}, filesystem: {2}".format(
sys.getdefaultencoding(),
locale.getpreferredencoding(),
sys.getfilesystemencoding())
s += '\n'
s += "byteorder: {0}\n".format(sys.byteorder)
s += "float info: dig: {0.dig}, mant_dig: {0.dig}\n\n".format(
sys.float_info)
for module_display, module_name in PYTEST_HEADER_MODULES.items():
try:
with ignore_warnings(DeprecationWarning):
module = resolve_name(module_name)
except ImportError:
s += "{0}: not available\n".format(module_display)
else:
try:
version = module.__version__
except AttributeError:
version = 'unknown (no __version__ attribute)'
s += "{0}: {1}\n".format(module_display, version)
# Helpers version
if 'astropy_helpers' in TESTED_VERSIONS:
astropy_helpers_version = TESTED_VERSIONS['astropy_helpers']
else:
try:
from astropy.version import astropy_helpers_version
except ImportError:
astropy_helpers_version = None
if astropy_helpers_version:
s += "astropy_helpers: {0}\n".format(astropy_helpers_version)
special_opts = ["remote_data", "pep8"]
opts = []
for op in special_opts:
op_value = getattr(config.option, op, None)
if op_value:
if isinstance(op_value, str):
op = ': '.join((op, op_value))
opts.append(op)
if opts:
s += "Using Astropy options: {0}.\n".format(", ".join(opts))
return s
def test_detect_zipped(self):
"""Test detection of a zip file when the extension is not .zip."""
zf = self._make_zip_file(filename='test0.fz')
with ignore_warnings():
assert len(fits.open(zf)) == 5
def test_detect_bzipped(self):
"""Test detection of a bzip2 file when the extension is not .bz2."""
with ignore_warnings():
with fits.open(self._make_bzip2_file('test0.xx')) as fits_handle:
assert fits_handle._file.compression == 'bzip2'
assert len(fits_handle) == 5
def pytest_report_header(config):
try:
stdoutencoding = sys.stdout.encoding or 'ascii'
except AttributeError:
stdoutencoding = 'ascii'
args = config.args
# TESTED_VERSIONS can contain the affiliated package version, too
if len(TESTED_VERSIONS) > 1:
for pkg, version in TESTED_VERSIONS.items():
if pkg not in ['Astropy', 'astropy_helpers']:
s = "\nRunning tests with {0} version {1}.\n".format(
pkg, version)
else:
s = "\nRunning tests with Astropy version {0}.\n".format(
TESTED_VERSIONS['Astropy'])
# Per https://github.com/astropy/astropy/pull/4204, strip the rootdir from
# each directory argument
if hasattr(config, 'rootdir'):
rootdir = str(config.rootdir)
if not rootdir.endswith(os.sep):
rootdir += os.sep
dirs = [
arg[len(rootdir):] if arg.startswith(rootdir) else arg
for arg in args
]
else:
dirs = args
s += "Running tests in {0}.\n\n".format(" ".join(dirs))
s += "Date: {0}\n\n".format(datetime.datetime.now().isoformat()[:19])
from platform import platform
plat = platform()
if isinstance(plat, bytes):
plat = plat.decode(stdoutencoding, 'replace')
s += "Platform: {0}\n\n".format(plat)
s += "Executable: {0}\n\n".format(sys.executable)
s += "Full Python Version: \n{0}\n\n".format(sys.version)
s += "encodings: sys: {0}, locale: {1}, filesystem: {2}".format(
sys.getdefaultencoding(), locale.getpreferredencoding(),
sys.getfilesystemencoding())
s += '\n'
s += "byteorder: {0}\n".format(sys.byteorder)
s += "float info: dig: {0.dig}, mant_dig: {0.dig}\n\n".format(
sys.float_info)
for module_display, module_name in PYTEST_HEADER_MODULES.items():
try:
with ignore_warnings(DeprecationWarning):
module = resolve_name(module_name)
except ImportError:
s += "{0}: not available\n".format(module_display)
else:
try:
version = module.__version__
except AttributeError:
version = 'unknown (no __version__ attribute)'
s += "{0}: {1}\n".format(module_display, version)
# Helpers version
if 'astropy_helpers' in TESTED_VERSIONS:
astropy_helpers_version = TESTED_VERSIONS['astropy_helpers']
else:
try:
from astropy.version import astropy_helpers_version
except ImportError:
astropy_helpers_version = None
if astropy_helpers_version:
s += "astropy_helpers: {0}\n".format(astropy_helpers_version)
special_opts = ["remote_data", "pep8"]
opts = []
for op in special_opts:
op_value = getattr(config.option, op, None)
if op_value:
if isinstance(op_value, str):
op = ': '.join((op, op_value))
opts.append(op)
if opts:
s += "Using Astropy options: {0}.\n".format(", ".join(opts))
return s
def test_detect_zipped(self):
"""Test detection of a zip file when the extension is not .zip."""
zf = self._make_zip_file(filename='test0.fz')
with ignore_warnings():
assert len(fits.open(zf)) == 5
