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Re: R: R: [Pytables-users] Re: [ pytables-Patches-1192700 ] Multi-dimensional HDF5 attributes
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From: Antonio V. <val...@co...> - 2005-05-16 22:35:57
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Alle 13:33, domenica 15 maggio 2005, Francesc Altet ha scritto:
> Hola Antonio,
>
> On Sunday 15 May 2005 11:37, you wrote:
> > Hi Francesc,
> > I have uploaded the patch that implements what we discussed in the
> > previous posts on the patch section of the pytables project on
> > SourceForge (pytables-20050514-mdattr.patch - file format_version >=3D
> > 1.4).
> >
> > Some notes:
> >
> > - now all python objects are saved as cpickle strings and all numarra=
y
> > objects are saved as HDF5 numeric attributes. The only exceptions
> > are the numeric sys attributes (NROWS, EXTDIM, AUTOMATIC_INDEX,
> > REINDEX, DIRTY, NODE_TYPE_VERSION) that are still stored as scalar
> > HDF5 attributes and retrieved as python int.
> > This because I found that in some cases they are set from the C
> > extension code:
> > H5ARRAY.c H5ARRAYmake EXTDIM
> > H5TB.c H5TBdelete_record NROWS
> > H5TB.c H5TBmake_table NROWS
> > H5TB-opt.c H5TBOclose_append NROWS
> > In my opinion this is not so bad in that they are treated as specia=
l
> > attributes in any case.
>
> That's good. You had a small glitch converting NROWS to Python ints
> instead of longs (remember that PyTables supports objects with more
I'm sorry.
> than 2**31 rows). This has been corrected. If you would have run the
> tests in heavy mode you should have been warned about that.
I have run the the test in heavy mode today on the PC at work (not my lap=
top)
and got 3 errors for the snapshot-20060516
[...]
Reading an old version file node. ...=20
/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py:248:=20
UserWarning: problems loading leaf ``/test``: unsubscriptable object; it =
will=20
become an ``UnImplemented`` node
warnings.warn("""\
ERROR
Writing an old version file node. ... ERROR
Accessing attributes in an old version file node. ... ERROR
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
ERROR: Reading an old version file node.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/valentino/pyvm/src/pytables-20050516/test/test_filenode.py"=
,=20
line 909, in setUp
oldh5f =3D tables.openFile(self.oldh5fname)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
229, in openFile
return File(path, mode, title, new, trMap, rootUEP, isPTFile, filters=
)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
409, in __init__
self.root =3D self.__getRootGroup(rootUEP)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
460, in __getRootGroup
rootGroup =3D RootGroup(self, '/', rootUEP, new=3Dself._v_new)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 831, in __init__
self._g_openFile()
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 253, in _g_openFile
objleaf._g_putUnder(objgroup, name)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Leaf.py",=
line=20
222, in _g_putUnder
super(Leaf, self)._g_putUnder(parent, name)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Node.py",=
line=20
693, in _g_putUnder
parent._g_refNode(self, ptname, validate)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 323, in _g_refNode
raise NodeError(
NodeError: group ``/`` already has a child node named ``test``
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
ERROR: Writing an old version file node.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/valentino/pyvm/src/pytables-20050516/test/test_filenode.py"=
,=20
line 909, in setUp
oldh5f =3D tables.openFile(self.oldh5fname)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
229, in openFile
return File(path, mode, title, new, trMap, rootUEP, isPTFile, filters=
)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
409, in __init__
self.root =3D self.__getRootGroup(rootUEP)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
460, in __getRootGroup
rootGroup =3D RootGroup(self, '/', rootUEP, new=3Dself._v_new)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 831, in __init__
self._g_openFile()
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 253, in _g_openFile
objleaf._g_putUnder(objgroup, name)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Leaf.py",=
line=20
222, in _g_putUnder
super(Leaf, self)._g_putUnder(parent, name)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Node.py",=
line=20
693, in _g_putUnder
parent._g_refNode(self, ptname, validate)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 323, in _g_refNode
raise NodeError(
NodeError: group ``/`` already has a child node named ``test``
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
ERROR: Accessing attributes in an old version file node.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/valentino/pyvm/src/pytables-20050516/test/test_filenode.py"=
,=20
line 909, in setUp
oldh5f =3D tables.openFile(self.oldh5fname)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
229, in openFile
return File(path, mode, title, new, trMap, rootUEP, isPTFile, filters=
)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
409, in __init__
self.root =3D self.__getRootGroup(rootUEP)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/File.py",=
line=20
460, in __getRootGroup
rootGroup =3D RootGroup(self, '/', rootUEP, new=3Dself._v_new)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 831, in __init__
self._g_openFile()
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 253, in _g_openFile
objleaf._g_putUnder(objgroup, name)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Leaf.py",=
line=20
222, in _g_putUnder
super(Leaf, self)._g_putUnder(parent, name)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Node.py",=
line=20
693, in _g_putUnder
parent._g_refNode(self, ptname, validate)
File "/home/valentino/pyvm/lib/python2.4/site-packages/tables/Group.py"=
,=20
line 323, in _g_refNode
raise NodeError(
NodeError: group ``/`` already has a child node named ``test``
----------------------------------------------------------------------
Ran 2456 tests in 781.418s
FAILED (errors=3D3)
-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D=
-=3D
PyTables version: 1.1-alpha
Extension version: $Id: hdf5Extension.pyx 852 2005-05-15 11:31:50Z faltet=
$
HDF5 version: 1.6.4
numarray version: 1.3.1
Zlib version: 1.1.4
BZIP2 version: 1.0.2 (30-Dec-2001)
Python version: 2.4.1 (#1, May 4 2005, 11:47:31)
[GCC 3.2.2]
Platform: linux2-i686
Byte-ordering: little
-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D=
-=3D
Performing the complete test suite!
-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D=
-=3D
Skipping Numeric test suite
-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D=
-=3D
> > - I run the complete test suite an all tests are passed (see the
> > attached testlog.txt). Unfortunately now come out some warning
> > that I am unable to fix, I'm sorry :((
> > Warning: Encountered invalid numeric result(s) in greater_equal
> > Warning: Encountered invalid numeric result(s) in less_equal
> > Warning: Encountered invalid numeric result(s) in greater_equal
> > Warning: Encountered invalid numeric result(s) in less
> > Warning: Encountered invalid numeric result(s) in greater
> > Warning: Encountered invalid numeric result(s) in less_equal
> > Warning: Encountered invalid numeric result(s) in greater
> > Warning: Encountered invalid numeric result(s) in less
> > I only know that they come from the test_Numeric.py test suite.
>
> I'm not so sure that these warnings come from test_Numeric.py. I know
> that these warnings appears from time to time when running the tests,
> even before applying your patches. They seems unproblematic, though.
OK
[...]
> > Comments and suggestions are welcome.
>
> Very good work indeed. Many thanks in name of the PyTables community!
Thank you for pytables
> The changes has been uploaded into the SVN repository.
>
> Ciao,
>
> Francesc
ciao
--=20
Antonio Valentino
INNOVA - Consorzio per l'Informatica e la Telematica
via della Scienza - Zona Paip I
75100 Matera (MT) Italy
Tel.: +39 0835 309180
Fax: +39 0835 264705
Home Page: www.consorzio-innova.it
Email: val...@co...
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