No module named plasma / BasePlasmaArray AttributeError

[jhmatthews]

I'm pretty sure this is just a documentation issue, but I thought I would flag anyway.

The documentation on readthedocs says to do the following to create a simple plasma:

>>> from tardis import atomic, plasma
>>> atom_data = atomic.AtomData.from_hdf5()
>>> my_plasma = plasma.BasePlasma({'Fe':0.5, 'Ni':0.5}, 10000, 1e-13, atom_data)
>>> print my_plasma.abundances
atomic_number abundance_fraction number_density
------------- ------------------ --------------
           28                0.5  513016973.936
           26                0.5  539183641.472

However, there I cannot import plasma (it does not exist):

>>> from tardis import plasma
ImportError                               Traceback (most recent call last)
<ipython-input-18-0dbefda4ca15> in <module>()
----> 1 from tardis import plasma

ImportError: cannot import name plasma

There is however, a module called plasma_array, containing the BasePlasmaArray class. I tried an analogous command:

>>>from tardis import plasma_array, atomic
>>> atom_data = atomic.AtomData.from_hdf5()
>>> my_plasma = plasma_array.BasePlasmaArray({'Fe':0.5, 'Ni':0.5}, 10000, 1e-13, atom_data)
AttributeError                            Traceback (most recent call last)
<ipython-input-24-a42101f19f8c> in <module>()
----> 1 my_plasma = plasma_array.BasePlasmaArray({'He':1.0}, 10000, 1e-13, atom_data)

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tardis/plasma_array.pyc in __init__(self, number_densities, atom_data, time_explosion, delta_treatment, nlte_config, ionization_mode, excitation_mode)
    141         self.nlte_config = nlte_config
    142         self.delta_treatment = delta_treatment
--> 143         self.electron_densities = self.number_densities.sum(axis=0)
    144 
    145         self.level_populations = pd.DataFrame(index=self.atom_data.levels.index, columns=number_densities.columns,

AttributeError: 'dict' object has no attribute 'sum'

This may be a separate issue, or perhaps the docs just need updating and I am running the wrong commands. Probably wants fixing regardless.

Also, please tell me if you'd rather I flagged issues like this somewhere else e.g. a user's group.

[jhmatthews]

System info:
OSX 10.8.2
Tardis 0.9.1
Cython 0.20
h5py 2.2.1
Numpy 1.8.0
Scipy 0.13.0
Astropy 0.3.1
Pandas 0.13.0

Also tested this on another Tardis user's machine here at Soton, same result.

[jhmatthews]

And this issue also applies to the documentation on Calculating zeta here

[ssim]

Thanks, James.
I think the problem is that the documentation is out of date - sorry.
@wkerzendorf - do you agree? If so can we just remove the offending documentation pages (unless you are able to update them)?

[ssim]

I think that this was resolved, so I'm closing this now.