Passing tuples as coordinate values gives `ValueError` after sampling

[michaelosthege]

Description of your problem

This minimum example uses a tuple for coordinate values. Nothing fancy, right?

with pymc3.Model(coords={
    "city": ("Bonn", "Berlin")
}):
    pymc3.Normal("x", dims="city")
    pymc3.sample(return_inferencedata=True)

Kaboom 🧨 after sampling.

ValueError: dimensions ('city',) must have the same length as the number of data dimensions, ndim=0

Traceback

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-132-c3a70b936a71> in <module>
      3 }):
      4     pymc3.Normal("x", dims="city")
----> 5     pymc3.sample(return_inferencedata=True)

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\pymc3\sampling.py in sample(draws, step, init, n_init, start, trace, chain_idx, chains, cores, tune, progressbar, model, random_seed, discard_tuned_samples, compute_convergence_checks, callback, jitter_max_retries, return_inferencedata, idata_kwargs, mp_ctx, pickle_backend, **kwargs)
    652         if idata_kwargs:
    653             ikwargs.update(idata_kwargs)
--> 654         idata = pm.to_inference_data(trace, **ikwargs)
    655 
    656     if compute_convergence_checks:

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\pymc3\backends\arviz.py in to_inference_data(trace, prior, posterior_predictive, log_likelihood, coords, dims, model, save_warmup, density_dist_obs)
    636         return trace
    637 
--> 638     return InferenceDataConverter(
    639         trace=trace,
    640         prior=prior,

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\pymc3\backends\arviz.py in to_inference_data(self)
    567         """
    568         id_dict = {
--> 569             "posterior": self.posterior_to_xarray(),
    570             "sample_stats": self.sample_stats_to_xarray(),
    571             "log_likelihood": self.log_likelihood_to_xarray(),

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\arviz\data\base.py in wrapped(cls, *args, **kwargs)
     44                 if all([getattr(cls, prop_i) is None for prop_i in prop]):
     45                     return None
---> 46             return func(cls, *args, **kwargs)
     47 
     48         return wrapped

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\pymc3\backends\arviz.py in posterior_to_xarray(self)
    337                 )
    338         return (
--> 339             dict_to_dataset(
    340                 data,
    341                 library=pymc3,

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\pymc3\backends\arviz.py in dict_to_dataset(data, library, coords, dims, attrs, default_dims, skip_event_dims, index_origin)
    119     """
    120     if default_dims is None:
--> 121         return _dict_to_dataset(
    122             data,
    123             attrs=attrs,

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\arviz\data\base.py in dict_to_dataset(data, attrs, library, coords, dims, skip_event_dims)
    238     data_vars = {}
    239     for key, values in data.items():
--> 240         data_vars[key] = numpy_to_data_array(
    241             values, var_name=key, coords=coords, dims=dims.get(key), skip_event_dims=skip_event_dims
    242         )

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\arviz\data\base.py in numpy_to_data_array(ary, var_name, coords, dims, skip_event_dims)
    196 
    197     # filter coords based on the dims
--> 198     coords = {key: xr.IndexVariable((key,), data=coords[key]) for key in dims}
    199     return xr.DataArray(ary, coords=coords, dims=dims)
    200 

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\arviz\data\base.py in <dictcomp>(.0)
    196 
    197     # filter coords based on the dims
--> 198     coords = {key: xr.IndexVariable((key,), data=coords[key]) for key in dims}
    199     return xr.DataArray(ary, coords=coords, dims=dims)
    200 

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\xarray\core\variable.py in __init__(self, dims, data, attrs, encoding, fastpath)
   2532 
   2533     def __init__(self, dims, data, attrs=None, encoding=None, fastpath=False):
-> 2534         super().__init__(dims, data, attrs, encoding, fastpath)
   2535         if self.ndim != 1:
   2536             raise ValueError(f"{type(self).__name__} objects must be 1-dimensional")

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\xarray\core\variable.py in __init__(self, dims, data, attrs, encoding, fastpath)
    313         """
    314         self._data = as_compatible_data(data, fastpath=fastpath)
--> 315         self._dims = self._parse_dimensions(dims)
    316         self._attrs = None
    317         self._encoding = None

~\AppData\Local\Continuum\miniconda3\envs\CARenv\lib\site-packages\xarray\core\variable.py in _parse_dimensions(self, dims)
    572         dims = tuple(dims)
    573         if len(dims) != self.ndim:
--> 574             raise ValueError(
    575                 f"dimensions {dims} must have the same length as the "
    576                 f"number of data dimensions, ndim={self.ndim}"

ValueError: dimensions ('city',) must have the same length as the number of data dimensions, ndim=0

Versions and main components

• PyMC3 Version: main (not the latest though, but AFAIK there was no work done on the converter recently)

[OriolAbril]

I think I got the "culprit". coordinate values are taken as is by pymc and arviz and eventually passed as data argument to https://xarray.pydata.org/en/stable/generated/xarray.IndexVariable.html which does not seem to support tuples.

We can fix that in https://github.com/arviz-devs/arviz/blob/main/arviz/data/base.py#L249 by using np.asarray(coords[key]) for example but I'm not sure to which extent this is a design choice on xarray's part or an undesired side effect. I don't think I'll make a PR for the fix until after 2-3 weeks so feel free to take over.

I also realized that the workaround that needs to be removed (see #5042) is probably wrong and untested, so the quicker we get rid of it the better.