IndexError: Unlabeled multi-dimensional array cannot be used for indexing: samples

[alimanfoo]

This code run on colab:

sample_sets = ["AG1000G-MW"]
sample_query = "taxon = 'arabiensis'"
cyp6aap_region = "2R:28,480,000-28,510,000"
df_cyp6aap_cnv = ag3.gene_cnv_frequencies(
    region=cyp6aap_region,
    cohorts="admin2_year",
    sample_sets=sample_sets,
    sample_query=sample_query,
    sample_query_options=dict(engine="python"),
)
df_cyp6aap_cnv

...generates an exception:

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
[<ipython-input-13-c966e3aea42c>](https://localhost:8080/#) in <cell line: 0>()
      2 sample_query = "taxon = 'arabiensis'"
      3 cyp6aap_region = "2R:28,480,000-28,510,000"
----> 4 df_cyp6aap_cnv = ag3.gene_cnv_frequencies(
      5     region=cyp6aap_region,
      6     cohorts="admin2_year",

12 frames
[/usr/local/lib/python3.11/dist-packages/malariagen_data/util.py](https://localhost:8080/#) in check_types_wrapper(*args, **kwargs)
   1162                     error = TypeError(message)
   1163                     raise error from None
-> 1164         return f(*args, **kwargs)
   1165 
   1166     return check_types_wrapper

[/usr/local/lib/python3.11/dist-packages/malariagen_data/anoph/cnv_frq.py](https://localhost:8080/#) in gene_cnv_frequencies(***failed resolving arguments***)
    217         debug("access and concatenate data from regions")
    218         df = pd.concat(
--> 219             [
    220                 self._gene_cnv_frequencies(
    221                     region=r,

[/usr/local/lib/python3.11/dist-packages/malariagen_data/anoph/cnv_frq.py](https://localhost:8080/#) in <listcomp>(.0)
    218         df = pd.concat(
    219             [
--> 220                 self._gene_cnv_frequencies(
    221                     region=r,
    222                     cohorts=cohorts,

[/usr/local/lib/python3.11/dist-packages/malariagen_data/anoph/cnv_frq.py](https://localhost:8080/#) in _gene_cnv_frequencies(self, region, cohorts, sample_query, sample_query_options, min_cohort_size, sample_sets, drop_invariant, max_coverage_variance, include_counts, chunks, inline_array)
    263 
    264         debug("get gene copy number data")
--> 265         ds_cnv = self.gene_cnv(
    266             region=region,
    267             sample_sets=sample_sets,

[/usr/local/lib/python3.11/dist-packages/malariagen_data/util.py](https://localhost:8080/#) in check_types_wrapper(*args, **kwargs)
   1162                     error = TypeError(message)
   1163                     raise error from None
-> 1164         return f(*args, **kwargs)
   1165 
   1166     return check_types_wrapper

[/usr/local/lib/python3.11/dist-packages/malariagen_data/anoph/cnv_frq.py](https://localhost:8080/#) in gene_cnv(***failed resolving arguments***)
     61 
     62         ds = simple_xarray_concat(
---> 63             [
     64                 self._gene_cnv(
     65                     region=r,

[/usr/local/lib/python3.11/dist-packages/malariagen_data/anoph/cnv_frq.py](https://localhost:8080/#) in <listcomp>(.0)
     62         ds = simple_xarray_concat(
     63             [
---> 64                 self._gene_cnv(
     65                     region=r,
     66                     sample_sets=sample_sets,

[/usr/local/lib/python3.11/dist-packages/malariagen_data/anoph/cnv_frq.py](https://localhost:8080/#) in _gene_cnv(self, region, sample_sets, sample_query, sample_query_options, max_coverage_variance, chunks, inline_array)
    105 
    106         # Access HMM data.
--> 107         ds_hmm = self.cnv_hmm(
    108             region=cnv_region,
    109             sample_sets=sample_sets,

[/usr/local/lib/python3.11/dist-packages/malariagen_data/util.py](https://localhost:8080/#) in check_types_wrapper(*args, **kwargs)
   1162                     error = TypeError(message)
   1163                     raise error from None
-> 1164         return f(*args, **kwargs)
   1165 
   1166     return check_types_wrapper

[/usr/local/lib/python3.11/dist-packages/malariagen_data/anoph/cnv_data.py](https://localhost:8080/#) in cnv_hmm(***failed resolving arguments***)
    262                     raise ValueError(f"No samples found for query {sample_query!r}")
    263 
--> 264                 ds = ds.isel(samples=loc_query_samples)
    265 
    266             debug("handle coverage variance filter")

[/usr/local/lib/python3.11/dist-packages/xarray/core/dataset.py](https://localhost:8080/#) in isel(self, indexers, drop, missing_dims, **indexers_kwargs)
   3087         indexers = either_dict_or_kwargs(indexers, indexers_kwargs, "isel")
   3088         if any(is_fancy_indexer(idx) for idx in indexers.values()):
-> 3089             return self._isel_fancy(indexers, drop=drop, missing_dims=missing_dims)
   3090 
   3091         # Much faster algorithm for when all indexers are ints, slices, one-dimensional

[/usr/local/lib/python3.11/dist-packages/xarray/core/dataset.py](https://localhost:8080/#) in _isel_fancy(self, indexers, drop, missing_dims)
   3130         missing_dims: ErrorOptionsWithWarn = "raise",
   3131     ) -> Self:
-> 3132         valid_indexers = dict(self._validate_indexers(indexers, missing_dims))
   3133 
   3134         variables: dict[Hashable, Variable] = {}

[/usr/local/lib/python3.11/dist-packages/xarray/core/dataset.py](https://localhost:8080/#) in _validate_indexers(self, indexers, missing_dims)
   2910 
   2911                 if v.ndim > 1:
-> 2912                     raise IndexError(
   2913                         "Unlabeled multi-dimensional array cannot be "
   2914                         f"used for indexing: {k}"

IndexError: Unlabeled multi-dimensional array cannot be used for indexing: samples

Versions:

[ahernank]

I think this one might just be the == in the query (?)

[alimanfoo]

Thanks @ahernank, yep this all goes away if we use == in the query, thanks!