[WIP] Changes required for python 3 compatibility

[jchodera]

Updating for python 3.x compatibility.

[jchodera]

Hm, I'm running into:

the length of the elements is 3
{'N_scalingFactor': 0.79, 'Cl_scalingFactor': 0.8, 'HN_radius': 1.3, 'Br_scalingFactor': 0.8, 'I_scalingFactor': 0.8, 'Br_radius': 1.5, 'F_scalingFactor': 0.88, 'O_scalingFactor': 0.85, 'P_scalingFactor': 0.86, 'H_radius': 1.2, 'S_radius': 1.8, 'S_scalingFactor': 0.96, 'C_radius': 1.7, 'F_radius': 1.5, 'Si_scalingFactor': 0.8, 'H_scalingFactor': 0.85, 'I_radius': 1.5, 'P_radius': 1.85, 'N_radius': 1.55, 'O_radius': 1.5, 'C_scalingFactor': 0.72, 'Si_radius': 2.1, 'HN_scalingFactor': 0.85, 'Cl_radius': 1.7}
Traceback (most recent call last):
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/kombu/serialization.py", line 50, in _reraise_errors
    yield
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/kombu/serialization.py", line 221, in dumps
    payload = encoder(data)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/kombu/utils/json.py", line 72, in dumps
    **dict(default_kwargs, **kwargs))
  File "/Users/choderaj/miniconda3/lib/python3.5/json/__init__.py", line 237, in dumps
    **kw).encode(obj)
  File "/Users/choderaj/miniconda3/lib/python3.5/json/encoder.py", line 198, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/Users/choderaj/miniconda3/lib/python3.5/json/encoder.py", line 256, in iterencode
    return _iterencode(o, 0)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/kombu/utils/json.py", line 62, in default
    return super(JSONEncoder, self).default(o)
  File "/Users/choderaj/miniconda3/lib/python3.5/json/encoder.py", line 179, in default
    raise TypeError(repr(o) + " is not JSON serializable")
TypeError: array(0.72) is not JSON serializable

[jchodera]

I made the change required for celery 4's update to JSON, but am now running into:

lski1962:gbff.choderalab choderaj$ python parameterize-using-database.py --types parameters/gbsa-amber-mbondi2.types --parameters parameters/gbsa-amber-mbondi2.parameters --database $FREESOLV_PATH/database.pickle --iterations 500 --mcmcout MCMC --verbose --mol2 datasets/FreeSolv/FreeSolv/tripos_mol2 --subset 10
the length of the elements is 0
the length of the elements is 0
the length of the elements is 0
the length of the elements is 0
the length of the elements is 0
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
the length of the elements is 3
{'Si_scalingFactor': 0.8, 'Cl_scalingFactor': 0.8, 'N_radius': 1.55, 'C_radius': 1.7, 'HN_radius': 1.3, 'I_radius': 1.5, 'Br_radius': 1.5, 'O_radius': 1.5, 'C_scalingFactor': 0.72, 'S_scalingFactor': 0.96, 'F_scalingFactor': 0.88, 'P_scalingFactor': 0.86, 'Cl_radius': 1.7, 'H_radius': 1.2, 'Br_scalingFactor': 0.8, 'I_scalingFactor': 0.8, 'P_radius': 1.85, 'HN_scalingFactor': 0.85, 'H_scalingFactor': 0.85, 'O_scalingFactor': 0.85, 'F_radius': 1.5, 'S_radius': 1.8, 'N_scalingFactor': 0.79, 'Si_radius': 2.1}
Traceback (most recent call last):
  File "parameterize-using-database.py", line 149, in <module>
    obcmodel = model.GBFFAllModels(database, parameters, energytasks.celery_hydration_energies_factory, ngbmodels=3)
  File "/Users/choderaj/github/choderalab/gbff/gbff.choderalab/model.py", line 255, in __init__
    super(GBFFAllModels, self).__init__(database, initial_parameters, parameter_types, hydration_energy_factory)
  File "/Users/choderaj/github/choderalab/gbff/gbff.choderalab/model.py", line 35, in __init__
    self.model = self._create_bayesian_gbmodel(solvated_system_database, initial_parameters)
  File "/Users/choderaj/github/choderalab/gbff/gbff.choderalab/model.py", line 88, in _create_bayesian_gbmodel
    gbffmodel_with_mols = self._add_parallel_gbffmodel(database, gbffmodel)
  File "/Users/choderaj/github/choderalab/gbff/gbff.choderalab/model.py", line 182, in _add_parallel_gbffmodel
    gbffmodel['dg_gbsa'] = pymc.Deterministic(eval=hydration_energy_function, doc='ComputedDeltaG', name='dg_gbsa', parents=self.parameter_model, dtype=float, trace=True, verbose=1)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/pymc/PyMCObjects.py", line 443, in __init__
    verbose=verbose)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/pymc/Node.py", line 214, in __init__
    Node.__init__(self, doc, name, parents, cache_depth, verbose=verbose)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/pymc/Node.py", line 129, in __init__
    self.parents = parents
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/pymc/Node.py", line 147, in _set_parents
    self.gen_lazy_function()
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/pymc/PyMCObjects.py", line 454, in gen_lazy_function
    self._value.force_compute()
  File "LazyFunction.pyx", line 257, in pymc.LazyFunction.LazyFunction.force_compute (pymc/LazyFunction.c:2409)
  File "/Users/choderaj/github/choderalab/gbff/gbff.choderalab/hydration_energies/energytasks.py", line 322, in hydration_energies
    return compute_hydration_energies_celery(database, parameters, platform_name='CPU')
  File "/Users/choderaj/github/choderalab/gbff/gbff.choderalab/hydration_energies/energytasks.py", line 316, in compute_hydration_energies_celery
    energies = [float(energy) for energy in energy_group.get()]
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/celery/result.py", line 630, in get
    on_message=on_message,
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/celery/result.py", line 744, in join_native
    raise value
KeyError: 'molecule'