Problems with pandas slicing (again)

[ssim]

I'm seeing problems (again) when trying to use the macro atom mode - it complains:

/Users/stuartsim/Tardis/tardis/build/lib.macosx-10.10-x86_64-2.7/tardis/atomic.py:532: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
  'count_total'].values[:-1])))
/Users/stuartsim/Tardis/tardis/build/lib.macosx-10.10-x86_64-2.7/tardis/atomic.py:535: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
  self.macro_atom_references['references_idx'] = np.arange(len(self.macro_atom_references))
/Users/stuartsim/Tardis/tardis/build/lib.macosx-10.10-x86_64-2.7/tardis/atomic.py:537: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
  self.macro_atom_data['lines_idx'] = self.lines_index.ix[self.macro_atom_data['transition_line_id']].values
/Users/stuartsim/Tardis/tardis/build/lib.macosx-10.10-x86_64-2.7/tardis/atomic.py:553: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
  tmp_macro_destination_level_idx].values.astype(np.int64)

Here's the yml file I'm trying to use

tardis_config_version: v1.0

supernova:
    luminosity_requested: 9.44 log_lsun
    time_explosion: 13 day

atom_data: kurucz_cd23_chianti_H_He.h5

model:
    structure:
        type: specific

        velocity:
            start : 1.2e4 km/s
            stop : 20000 km/s
            num: 20

        density:
            type : power_law
            time_0: 2 day
            rho_0: 1e-11 g/cm^3
            v_0: 11000 km/s
            exponent: -7

    abundances:
        type: uniform
        C: 0.02
        O: 0.08
        Mg: 0.03
        Si: 0.52
        S: 0.25
        Ar: 0.04
        Ca: 0.03
        Fe: 0.01
        Co: 0.01
        Ni: 0.01

plasma:
    ionization: nebular
    excitation: dilute-lte
    radiative_rates_type: dilute-blackbody
    line_interaction_type: macroatom

montecarlo:
    seed: 23111963
    no_of_packets : 5.0e+4
    iterations: 10
    last_no_of_packets: 1.0e+5
    no_of_virtual_packets: 5

spectrum:
    start: 500 angstrom
    stop: 20000 angstrom
    num: 10000

This sounds like a similar sort of thing to what was in #105 #110 , which had been resolved (I thought). Can someone who knows about pandas @wkerzendorf @aoifeboyle have a look into this?

[aoifeboyle]

@ssim Yeah I've seen this before and it doesn't actually affect the running of the code but it is annoying. I haven't seen it with the current code though - has it just started happening? Leave it with me and I'll have a look.

[ssim]

Hi - yes, it just happened with me. I'm not 100% uptodate, perhaps - but I did update all my python packages and TARDIS last week so I think it's a "current" problem! :)

[wkerzendorf]

@ssim @aoifeboyle yes, I have to fix this. I've made the executive decision that pandas==0.16 is the new minimum version and it remains executive until someone bitterly complains.

[wkerzendorf]

and yes, I'll deal with it.

[ssim]

I have version 0.16.2 installed and get this error

[ssim]

Resolved by #403 #405

Closing.