Comments (12)
Sorry about this - it is due to recent changes in the astropy master. Things have been in a state of flux with the upcoming 0.2 release, but once 0.2 is released, the core package will be a lot more stable. I'll see if there is a quick fix for this.
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Actually, I just noticed that this is an issue in Astropy itself.
@banados - can you update to the latest Astropy master to see if this fixes this error? You can either install the latest and greatest, or if you prefer installing from tar files, you can install the 0.2b2 beta from:
http://stsdas.stsci.edu/download/packages/index/astropy/index.html
Let us know if this fixes things!
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Hi Tom, so I updated to
In [16]: astropy.__version__
Out[16]: '0.3.dev3115'
(is that the version you meant?)
and now I get a different error:
table1 = vizier.vizquery(query)
ERROR: ValueError: masked should be one of True, False, None [astropy.table.table]
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-22-fddc0f7526fd> in <module>()
----> 1 table1 = vizier.vizquery(query)
/usr/local/lib/python2.7/dist-packages/astroquery/vizier/vizier.pyc in vizquery(query, server)
88 data = voTreeTable.array
89 # Add Table to the list
---> 90 tableList += [Table(data, names)]
91
92 # Merge the Table list
/home/eduardo/astropy/astropy/table/table.py in __init__(self, data, masked, names, dtypes, meta, copy)
760 # Set up a placeholder empty table
761 self._data = None
--> 762 self._set_masked(masked)
763 self.columns = TableColumns()
764 self.meta = OrderedDict() if meta is None else deepcopy(meta)
/home/eduardo/astropy/astropy/table/table.py in _set_masked(self, masked)
1232 self._masked = masked
1233 else:
-> 1234 raise ValueError("masked should be one of True, False, None")
1235 if self._masked:
1236 self._column_class = MaskedColumn
ValueError: masked should be one of True, False, None
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@banados - thanks for trying this! I'll look into it.
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@keflavich - the issue is this: Table(data, names)
- you should use the keyword names, i.e. Table(data=data, names=names)
because the second argument is now mask
. I'm going to be mostly offline in the next couple of days, so feel free to fix it (and make sure this doesn't need to be changd elsewhere).
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Thanks @astrofrog, I'll try to get this fixed.
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@astrofrog, @banados - this issue has been fixed in master since 1/10/2013 (commit 387d9ea, pr #43). @banados, can you check that you have the latest git version?
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So now I am sure I have the latest git version:
astropy.__version__
'0.3.dev3119'
When I do git log, the last change was on Date: Sun Feb 3 23:36:40 2013 -0800
Now, I get the same error I was getting at the beginning:
WARNING: W27: None:29:2: W27: COOSYS deprecated in VOTable 1.2 [astropy.io.vo.exceptions]
ERROR: AttributeError: 'module' object has no attribute 'get_data_fileobj' [astropy.io.vo.ucd]
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-6-fddc0f7526fd> in <module>()
----> 1 table1 = vizier.vizquery(query)
/usr/local/lib/python2.7/dist-packages/astroquery/vizier/vizier.pyc in vizquery(query, server)
75 http.request("POST", "/viz-bin/votable", body=body)
76 resp = http.getresponse()
---> 77 voTable = parse(cStringIO.StringIO(resp.read()), pedantic=False)
78
79 # Convert VOTABLE into a list of astropy Table.
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/table.pyc in parse(source, columns, invalid, pedantic, chunk_size, table_number, filename, _debug_python_based_parser)
106 _debug_python_based_parser=_debug_python_based_parser) as iterator:
107 return tree.VOTableFile(
--> 108 config=config, pos=(1, 1)).parse(iterator, config)
109
110
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in parse(self, iterator, config)
2879 if start:
2880 tag_mapping.get(tag, self._add_unknown_tag)(
-> 2881 iterator, tag, data, config, pos)
2882 elif tag == 'DESCRIPTION':
2883 if self.description is not None:
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in _add_resource(self, iterator, tag, data, config, pos)
2810 resource = Resource(config=config, pos=pos, **data)
2811 self.resources.append(resource)
-> 2812 resource.parse(self, iterator, config)
2813
2814 def _add_coosys(self, iterator, tag, data, config, pos):
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in parse(self, votable, iterator, config)
2664 if start:
2665 tag_mapping.get(tag, self._add_unknown_tag)(
-> 2666 iterator, tag, data, config, pos)
2667 elif tag == 'DESCRIPTION':
2668 if self.description is not None:
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in _add_table(self, iterator, tag, data, config, pos)
2621 table = Table(self._votable, config=config, pos=pos, **data)
2622 self.tables.append(table)
-> 2623 table.parse(iterator, config)
2624
2625 def _add_info(self, iterator, tag, data, config, pos):
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in parse(self, iterator, config)
2008
2009 tag_mapping.get(tag, self._add_unknown_tag)(
-> 2010 iterator, tag, data, config, pos)
2011 else:
2012 if tag == 'DESCRIPTION':
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in _add_field(self, iterator, tag, data, config, pos)
1937
1938 def _add_field(self, iterator, tag, data, config, pos):
-> 1939 field = Field(self._votable, config=config, pos=pos, **data)
1940 self.fields.append(field)
1941 field.parse(iterator, config)
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in __init__(self, votable, ID, name, datatype, arraysize, ucd, unit, width, precision, utype, ref, type, id, xtype, config, pos, **extra)
999 self.datatype = datatype
1000 self.arraysize = arraysize
-> 1001 self.ucd = ucd
1002 self.unit = unit
1003 self.width = width
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in ucd(self, ucd)
319 W28, W28, ('ucd', self._element_name, '1.2'),
320 self._config, self._pos)
--> 321 check_ucd(ucd, self._config, self._pos)
322 self._ucd = ucd
323
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/tree.pyc in check_ucd(ucd, config, pos)
209 check_controlled_vocabulary=config.get(
210 'version_1_2_or_later', False),
--> 211 has_colon=config.get('version_1_2_or_later', False))
212 except ValueError as e:
213 # This weird construction is for Python 3 compatibility
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/ucd.pyc in parse_ucd(ucd, check_controlled_vocabulary, has_colon)
101 global _ucd_singleton
102 if _ucd_singleton is None:
--> 103 _ucd_singleton = UCDWords()
104
105 if has_colon:
/usr/local/lib/python2.7/dist-packages/astropy/io/vo/ucd.pyc in __init__(self)
27 self._capitalization = {}
28
---> 29 with config.get_data_fileobj("data/ucd1p-words.txt") as fd:
30 for line in fd.readlines():
31 type, name, descr = [
AttributeError: 'module' object has no attribute 'get_data_fileobj'
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@banados - there's something strange with your installation - /usr/local/lib/python2.7/dist-packages/astropy/io/vo
does not exist in the latest Astropy. Could you try removing /usr/local/lib/python2.7/dist-packages/astropy
, then installing Astropy and trying again?
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ok... so it seems that the problem was that I checked that I had the latest git astropy version, but I didn't check the astroquery version.
Even after deleting the directory that @astrofrog suggested and installing astropy again I was getting the same error...
So I uninstalled astroquery, updated it to the last version and the error went away
Then, the astroquery version that crashes is:
astroquery.__version__
'0.0.dev189'
And the version that works without problems is
astroquery.__version__
'0.0.dev219
Thanks all for your help and sorry for not noticing this before!
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@banados - just to follow up on this - when you removed and reinstalled astropy, did you still get errors containing /usr/local/lib/python2.7/dist-packages/astropy/io/vo
? If so, there's still something weird because it should be /usr/local/lib/python2.7/dist-packages/astropy/io/votable
. Maybe you should try from a clean clone (there may be residual files in build
).
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When I removed and reinstalled astropy after deleting /usr/local/lib/python2.7/dist-packages/astropy/io/vo, I was getting the other error associated with the table:
ERROR: ValueError: masked should be one of True, False, None [astropy.table.table]
Actually I started from a clean one, I removed everything related with astropy and astroquery and installed them from scratch. And I confirm now that I have the correct directory instead:
/usr/local/lib/python2.7/dist-packages/astropy/io/votable/
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