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Failure with tables version 3.0.0 (just released) #79

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rmcgibbo opened this issue Jun 5, 2013 · 1 comment
Closed

Failure with tables version 3.0.0 (just released) #79

rmcgibbo opened this issue Jun 5, 2013 · 1 comment

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@rmcgibbo
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rmcgibbo commented Jun 5, 2013

======================================================================
ERROR: MDTraj.test.test_hdf5.test_topology
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/rmcgibbo/local/mdtraj/MDTraj/test/test_hdf5.py", line 106, in test_topology
    f.topology = top
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/hdf5.py", line 73, in wrapper
    return f(*args, **kwargs)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/hdf5.py", line 258, in topology
    self._handle.createArray(where='/', name='topology', object=[str(json.dumps(topology_dict))])
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
TypeError: create_array() got an unexpected keyword argument 'object'

======================================================================
ERROR: Failure: TypeError (create_array() got an unexpected keyword argument 'object')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/nose/loader.py", line 253, in generate
    for test in g():
  File "/home/rmcgibbo/local/mdtraj/MDTraj/test/test_io.py", line 125, in test_groups
    f.createArray(where='/mygroup', name='myarray', object=x)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
TypeError: create_array() got an unexpected keyword argument 'object'

======================================================================
ERROR: Failure: TypeError (create_array() got an unexpected keyword argument 'object')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/nose/loader.py", line 253, in generate
    for test in g():
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/numpy/testing/decorators.py", line 153, in skipper_gen
    for x in f(*args, **kwargs):
  File "/home/rmcgibbo/local/mdtraj/MDTraj/test/test_reporter.py", line 67, in test_reporter
    simulation.step(100)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/simtk/openmm/app/simulation.py", line 127, in step
    reporter.report(self, state)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/reporters/hdf5reporter.py", line 172, in report
    self._initialize(simulation)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/reporters/hdf5reporter.py", line 126, in _initialize
    self._traj_file.topology = simulation.topology
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/hdf5.py", line 73, in wrapper
    return f(*args, **kwargs)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/hdf5.py", line 258, in topology
    self._handle.createArray(where='/', name='topology', object=[str(json.dumps(topology_dict))])
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
TypeError: create_array() got an unexpected keyword argument 'object'

======================================================================
ERROR: Failure: TypeError (create_array() got an unexpected keyword argument 'object')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/nose/loader.py", line 253, in generate
    for test in g():
  File "/home/rmcgibbo/local/mdtraj/MDTraj/test/test_trajectory.py", line 78, in test_box_load_save
    t.save(temp_fn)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/trajectory.py", line 1042, in save
    return saver(filename)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/trajectory.py", line 1057, in save_hdf
    f.topology = self.topology
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/hdf5.py", line 73, in wrapper
    return f(*args, **kwargs)
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/mdtraj-0.2-py2.7-linux-x86_64.egg/mdtraj/hdf5.py", line 258, in topology
    self._handle.createArray(where='/', name='topology', object=[str(json.dumps(topology_dict))])
  File "/home/rmcgibbo/envs/latest/lib/python2.7/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
TypeError: create_array() got an unexpected keyword argument 'object'
@rmcgibbo
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rmcgibbo commented Jun 5, 2013

fixed.

@rmcgibbo rmcgibbo closed this as completed Jun 5, 2013
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