Hi James,
I just submitted a pull request about this; a patch is attached to this
e-mail. To apply the patch, cd to $RDBASE and issue the following command:
patch -p0 < patch20150713.txt
Best,
p.
On 13/07/2015 15:16, James Davidson wrote:
Dear All,
I have just built revision 5775 on Windows, and the pyGraphMolWrap
test fails. The relevant bit of the verbose output is below:
78: ERROR: testGithub498 (__main__.TestCase)
78: ----------------------------------------------------------------------
78: Traceback (most recent call last):
78: File "C:/RDKit/Code/GraphMol/Wrap/rough_test.py", line 3033, in
testGithub498
78: outf = gzip.open(tempfile.mktemp(),'wt+')
78: File "C:\Anaconda\lib\gzip.py", line 34, in open
78: return GzipFile(filename, mode, compresslevel)
78: File "C:\Anaconda\lib\gzip.py", line 94, in __init__
78: fileobj = self.myfileobj = __builtin__.open(filename, mode or
'rb')
78: ValueError: Invalid mode ('wt+b')
This seems to be due to a difference in python/gzip behaviour on
Windows vs. eg Linux:
*On Ubuntu (Anaconda python):*
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
In [3]:
*On Windows (again Anaconda python):*
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6bee12287576> in <module>()
----> 1 outf = gzip.open(tempfile.mktemp(), 'wt+')
C:\Anaconda\lib\gzip.pyc in open(filename, mode, compresslevel)
32
33 """
---> 34 return GzipFile(filename, mode, compresslevel)
35
36 class GzipFile(io.BufferedIOBase):
C:\Anaconda\lib\gzip.pyc in __init__(self, filename, mode,
compresslevel, fileobj, mtime)
92 mode += 'b'
93 if fileobj is None:
---> 94 fileobj = self.myfileobj =
__builtin__.open(filename, mode or 'rb')
95 if filename is None:
96 # Issue #13781: os.fdopen() creates a fileobj with
a bogus name
ValueError: Invalid mode ('wt+b')
In [3]:
Is this an easy one to fix?
Kind regards
James
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*** Code/GraphMol/Wrap/rough_test.new.py Mon Jul 13 23:19:32 2015
--- Code/GraphMol/Wrap/rough_test.orig.py Mon Jul 13 23:18:35 2015
***************
*** 3030,3040 ****
def testGithub498(self):
import gzip,tempfile
! if (sys.version_info < (3, 0)):
! mode = 'w+'
! else:
! mode = 'wt+'
! outf = gzip.open(tempfile.mktemp(), mode)
m = Chem.MolFromSmiles('C')
w = Chem.SDWriter(outf)
w.write(m)
--- 3030,3036 ----
def testGithub498(self):
import gzip,tempfile
! outf = gzip.open(tempfile.mktemp(), 'wt+')
m = Chem.MolFromSmiles('C')
w = Chem.SDWriter(outf)
w.write(m)
------------------------------------------------------------------------------
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GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
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