Error while executing Quickstart Notebook

tardis_error_sim.py

from tardis import run_tardis
from tardis.io.atom_data.util import download_atom_data


# the data is automatically downloaded
download_atom_data('kurucz_cd23_chianti_H_He')
# OUTPUT
[tardis.io.atom_data.atom_web_download][INFO   ]  
Downloading atomic data from https://media.githubusercontent.com/media/tardis-sn/tardis-refdata/master/atom_data/kurucz_cd23_chianti_H_He.h5 to /home/dhruvs/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (atom_web_download.py:48)


!curl -O https://raw.githubusercontent.com/tardis-sn/tardis/master/docs/using/components/models/examples/tardis_example.yml


#TARDIS now uses the data in the data repo
sim = run_tardis('tardis_example.yml')
# OUTPUT 
[tardis.plasma.standard_plasmas][INFO   ]  Reading Atomic Data from kurucz_cd23_chianti_H_He.h5 (standard_plasmas.py:87)
[tardis.io.atom_data.util][INFO   ]  Atom Data kurucz_cd23_chianti_H_He.h5 not found in local path. Exists in TARDIS Data repo /home/dhruvs/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (util.py:33)
[tardis.io.atom_data.base][INFO   ]  Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (base.py:170)
[tardis.io.atom_data.base][INFO   ]  Non provided atomic data: synpp_refs, photoionization_data (base.py:176)
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-4-1a68e481065f> in <module>
      1 #TARDIS now uses the data in the data repo
----> 2 sim = run_tardis('tardis_example.yml')

~/Repositories/tardis/tardis/base.py in run_tardis(config, atom_data, packet_source, simulation_callbacks)
     36         tardis_config = Configuration.from_config_dict(config)
     37 
---> 38     simulation = Simulation.from_config(
     39         tardis_config, packet_source=packet_source, atom_data=atom_data
     40     )

~/Repositories/tardis/tardis/simulation/base.py in from_config(cls, config, packet_source, **kwargs)
    531             plasma = kwargs["plasma"]
    532         else:
--> 533             plasma = assemble_plasma(
    534                 config, model, atom_data=kwargs.get("atom_data", None)
    535             )

~/Repositories/tardis/tardis/plasma/standard_plasmas.py in assemble_plasma(config, model, atom_data)
    206     kwargs["helium_treatment"] = config.plasma.helium_treatment
    207 
--> 208     plasma = BasePlasma(
    209         plasma_properties=plasma_modules,
    210         property_kwargs=property_kwargs,

~/Repositories/tardis/tardis/io/util.py in __new__(cls, *args, **kwargs)
    197         instance = super(HDFWriterMixin, cls).__new__(cls)
    198         instance.optional_hdf_properties = []
--> 199         instance.__init__(*args, **kwargs)
    200         return instance
    201 

~/Repositories/tardis/tardis/plasma/base.py in __init__(self, plasma_properties, property_kwargs, **kwargs)
     28         self._build_graph()
     29         #        self.write_to_tex('Plasma_Graph')
---> 30         self.update(**kwargs)
     31 
     32     def __getattr__(self, item):

~/Repositories/tardis/tardis/plasma/base.py in update(self, **kwargs)
    182 
    183         for module_name in self._resolve_update_list(kwargs.keys()):
--> 184             self.plasma_properties_dict[module_name].update()
    185 
    186     def _update_module_type_str(self):

~/Repositories/tardis/tardis/plasma/properties/base.py in update(self)
    106         if len(self.outputs) == 1:
    107             setattr(
--> 108                 self, self.outputs[0], self.calculate(*self._get_input_values())
    109             )
    110         else:

~/Repositories/tardis/tardis/plasma/properties/ion_population.py in calculate(g_electron, beta_rad, partition_function, ionization_data)
     72             phis[start_id - i : end_id - i - 1] = current_phis
     73 
---> 74         broadcast_ionization_energy = ionization_data[
     75             partition_function.index
     76         ].dropna()

~/.local/lib/python3.8/site-packages/pandas/core/series.py in __getitem__(self, key)
    846             return self._get_values(key)
    847 
--> 848         return self._get_with(key)
    849 
    850     def _get_with(self, key):

~/.local/lib/python3.8/site-packages/pandas/core/series.py in _get_with(self, key)
    886 
    887         # handle the dup indexing case GH#4246
--> 888         return self.loc[key]
    889 
    890     def _get_values_tuple(self, key):

~/.local/lib/python3.8/site-packages/pandas/core/indexing.py in __getitem__(self, key)
    892 
    893             maybe_callable = com.apply_if_callable(key, self.obj)
--> 894             return self._getitem_axis(maybe_callable, axis=axis)
    895 
    896     def _is_scalar_access(self, key: Tuple):

~/.local/lib/python3.8/site-packages/pandas/core/indexing.py in _getitem_axis(self, key, axis)
   1110                     raise ValueError("Cannot index with multidimensional key")
   1111 
-> 1112                 return self._getitem_iterable(key, axis=axis)
   1113 
   1114             # nested tuple slicing

~/.local/lib/python3.8/site-packages/pandas/core/indexing.py in _getitem_iterable(self, key, axis)
   1050 
   1051         # A collection of keys
-> 1052         keyarr, indexer = self._get_listlike_indexer(key, axis, raise_missing=False)
   1053         return self.obj._reindex_with_indexers(
   1054             {axis: [keyarr, indexer]}, copy=True, allow_dups=True

~/.local/lib/python3.8/site-packages/pandas/core/indexing.py in _get_listlike_indexer(self, key, axis, raise_missing)
   1263             keyarr, indexer, new_indexer = ax._reindex_non_unique(keyarr)
   1264 
-> 1265         self._validate_read_indexer(keyarr, indexer, axis, raise_missing=raise_missing)
   1266         return keyarr, indexer
   1267 

~/.local/lib/python3.8/site-packages/pandas/core/indexing.py in _validate_read_indexer(self, key, indexer, axis, raise_missing)
   1318 
   1319             with option_context("display.max_seq_items", 10, "display.width", 80):
-> 1320                 raise KeyError(
   1321                     "Passing list-likes to .loc or [] with any missing labels "
   1322                     "is no longer supported. "

KeyError: "Passing list-likes to .loc or [] with any missing labels is no longer supported. The following labels were missing: MultiIndex([( 8, 0),\n            (12, 0),\n            (14, 0),\n            (16, 0),\n            (18, 0),\n            (20, 0)],\n           names=['atomic_number', 'ion_number']). See https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#deprecate-loc-reindex-listlike"

This is the complete error & traceback 🤔

Can you roll back to python v3.7 to see if you get the same issue?

Sure I will check it once :)

Yes, it was fixed with Python version 3.8 ... Thank you very much for the info @jamesgillanders 😄