[yt-dev] [yt_analysis/yt] h5py serialization (issue #539)

[Sam Skillman]

New issue 539: h5py serialization
https://bitbucket.org/yt_analysis/yt/issue/539/h5py-serialization

Sam Skillman:

It seems that with some version of h5py, we now run into these issues when using pf.h.save_object() with any type of data:

```
#!python

In [1]: pf.h.save_object(np.ones(10), 'ones')
/home/skillman/local/lib/python2.7/site-packages/h5py/_hl/dataset.py:94: RuntimeWarning: tp_compare didn't return -1 or -2 for exception
  dset_id.write(h5s.ALL, h5s.ALL, data)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/home/skillman/local/src/yt-hg/yt/mods.pyc in <module>()
----> 1 pf.h.save_object(np.ones(10), 'ones')

/home/skillman/local/src/yt-hg/yt/data_objects/hierarchy.pyc in save_object(self, obj, name)
    318         """
    319         s = cPickle.dumps(obj, protocol=-1)
--> 320         self.save_data(s, "/Objects", name, force = True)
    321 
    322     def load_object(self, name):

/home/skillman/local/src/yt-hg/yt/data_objects/hierarchy.pyc in _save_data(self, array, node, name, set_attr, force, passthrough)
    293         for q in node.split('/'):
    294             if q: myGroup = myGroup.require_group(q)
--> 295         arr = myGroup.create_dataset(name,data=array)
    296         if set_attr is not None:
    297             for i, j in set_attr.items(): arr.attrs[i] = j

/home/skillman/local/lib/python2.7/site-packages/h5py/_hl/group.pyc in create_dataset(self, name, shape, dtype, data, **kwds)
     69         """
     70 
---> 71         dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
     72         dset = dataset.Dataset(dsid)
     73         if name is not None:

/home/skillman/local/lib/python2.7/site-packages/h5py/_hl/dataset.pyc in make_new_dset(parent, shape, dtype, data, chunks, compression, shuffle, fletcher32, maxshape, compression_opts, fillvalue)
     92 
     93     if data is not None:
---> 94         dset_id.write(h5s.ALL, h5s.ALL, data)
     95 
     96     return dset_id

/home/skillman/local/lib/python2.7/site-packages/h5py/h5d.so in h5py.h5d.DatasetID.write (h5py/h5d.c:2866)()

/home/skillman/local/lib/python2.7/site-packages/h5py/_proxy.so in h5py._proxy.dset_rw (h5py/_proxy.c:1766)()

/home/skillman/local/lib/python2.7/site-packages/h5py/defs.so in h5py.defs.H5Tconvert (h5py/defs.c:18439)()

/home/skillman/local/lib/python2.7/site-packages/h5py/_errors.so in h5py._errors.set_exception (h5py/_errors.c:711)()

/home/skillman/local/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.str2vlen (h5py/_conv.c:3382)()

/home/skillman/local/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.generic_converter (h5py/_conv.c:1302)()

/home/skillman/local/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.conv_str2vlen (h5py/_conv.c:2158)()

ValueError: VLEN strings do not support embedded NULLs

In [2]: 
```

Responsible: samskillman
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