Not obvious what packages need to be installed to run Cubed examples

[rbavery]

This error occurs in this example notebook: https://github.com/cubed-dev/cubed/blob/main/examples/pangeo-4-climatological-anomalies.ipynb

.mean doesn't take a method argument

Full Traceback:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[8], line 3
      1 # Note: we actually want skipna=True, but this isn't implemented in xarray yet
      2 # see https://github.com/pydata/xarray/issues/7243
----> 3 mean = ds.groupby("time.dayofyear").mean(method="map-reduce", skipna=False)
      4 mean

File ~/miniforge3/lib/python3.10/site-packages/xarray/core/_aggregations.py:2974, in DatasetGroupByAggregations.mean(self, dim, skipna, keep_attrs, **kwargs)
   2964     return self._flox_reduce(
   2965         func="mean",
   2966         dim=dim,
   (...)
   2971         **kwargs,
   2972     )
   2973 else:
-> 2974     return self._reduce_without_squeeze_warn(
   2975         duck_array_ops.mean,
   2976         dim=dim,
   2977         skipna=skipna,
   2978         numeric_only=True,
   2979         keep_attrs=keep_attrs,
   2980         **kwargs,
   2981     )

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py:1993](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py#line=1992), in DatasetGroupByBase._reduce_without_squeeze_warn(self, func, dim, axis, keep_attrs, keepdims, shortcut, **kwargs)
   1990     warnings.filterwarnings("ignore", message="The `squeeze` kwarg")
   1991     check_reduce_dims(dim, self.dims)
-> 1993 return self._map_maybe_warn(reduce_dataset, warn_squeeze=False)

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py:1839](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py#line=1838), in DatasetGroupByBase._map_maybe_warn(self, func, args, shortcut, warn_squeeze, **kwargs)
   1829 def _map_maybe_warn(
   1830     self,
   1831     func: Callable[..., Dataset],
   (...)
   1836 ) -> Dataset:
   1837     # ignore shortcut if set (for now)
   1838     applied = (func(ds, *args, **kwargs) for ds in self._iter_grouped(warn_squeeze))
-> 1839     return self._combine(applied)

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py:1859](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py#line=1858), in DatasetGroupByBase._combine(self, applied)
   1857 def _combine(self, applied):
   1858     """Recombine the applied objects like the original."""
-> 1859     applied_example, applied = peek_at(applied)
   1860     coord, dim, positions = self._infer_concat_args(applied_example)
   1861     combined = concat(applied, dim)

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/utils.py:205](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/utils.py#line=204), in peek_at(iterable)
    201 """Returns the first value from iterable, as well as a new iterator with
    202 the same content as the original iterable
    203 """
    204 gen = iter(iterable)
--> 205 peek = next(gen)
    206 return peek, itertools.chain([peek], gen)

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py:1838](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py#line=1837), in <genexpr>(.0)
   1829 def _map_maybe_warn(
   1830     self,
   1831     func: Callable[..., Dataset],
   (...)
   1836 ) -> Dataset:
   1837     # ignore shortcut if set (for now)
-> 1838     applied = (func(ds, *args, **kwargs) for ds in self._iter_grouped(warn_squeeze))
   1839     return self._combine(applied)

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py:1980](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/groupby.py#line=1979), in DatasetGroupByBase._reduce_without_squeeze_warn.<locals>.reduce_dataset(ds)
   1979 def reduce_dataset(ds: Dataset) -> Dataset:
-> 1980     return ds.reduce(
   1981         func=func,
   1982         dim=dim,
   1983         axis=axis,
   1984         keep_attrs=keep_attrs,
   1985         keepdims=keepdims,
   1986         **kwargs,
   1987     )

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/dataset.py:6942](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/dataset.py#line=6941), in Dataset.reduce(self, func, dim, keep_attrs, keepdims, numeric_only, **kwargs)
   6922         if (
   6923             # Some reduction functions (e.g. std, var) need to run on variables
   6924             # that don't have the reduce dims: PR5393
   (...)
   6935             # the former is often more efficient
   6936             # keep single-element dims as list, to support Hashables
   6937             reduce_maybe_single = (
   6938                 None
   6939                 if len(reduce_dims) == var.ndim and var.ndim != 1
   6940                 else reduce_dims
   6941             )
-> 6942             variables[name] = var.reduce(
   6943                 func,
   6944                 dim=reduce_maybe_single,
   6945                 keep_attrs=keep_attrs,
   6946                 keepdims=keepdims,
   6947                 **kwargs,
   6948             )
   6950 coord_names = {k for k in self.coords if k in variables}
   6951 indexes = {k: v for k, v in self._indexes.items() if k in variables}

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/variable.py:1662](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/variable.py#line=1661), in Variable.reduce(self, func, dim, axis, keep_attrs, keepdims, **kwargs)
   1655 keep_attrs_ = (
   1656     _get_keep_attrs(default=False) if keep_attrs is None else keep_attrs
   1657 )
   1659 # Noe that the call order for Variable.mean is
   1660 #    Variable.mean -> NamedArray.mean -> Variable.reduce
   1661 #    -> NamedArray.reduce
-> 1662 result = super().reduce(
   1663     func=func, dim=dim, axis=axis, keepdims=keepdims, **kwargs
   1664 )
   1666 # return Variable always to support IndexVariable
   1667 return Variable(
   1668     result.dims, result._data, attrs=result._attrs if keep_attrs_ else None
   1669 )

File [~/miniforge3/lib/python3.10/site-packages/xarray/namedarray/core.py:905](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/namedarray/core.py#line=904), in NamedArray.reduce(self, func, dim, axis, keepdims, **kwargs)
    901     if isinstance(axis, tuple) and len(axis) == 1:
    902         # unpack axis for the benefit of functions
    903         # like np.argmin which can't handle tuple arguments
    904         axis = axis[0]
--> 905     data = func(self.data, axis=axis, **kwargs)
    906 else:
    907     data = func(self.data, **kwargs)

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/duck_array_ops.py:704](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/duck_array_ops.py#line=703), in mean(array, axis, skipna, **kwargs)
    702     return _to_pytimedelta(mean_timedeltas, unit="us") + offset
    703 else:
--> 704     return _mean(array, axis=axis, skipna=skipna, **kwargs)

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/duck_array_ops.py:471](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/duck_array_ops.py#line=470), in _create_nan_agg_method.<locals>.f(values, axis, skipna, **kwargs)
    469     with warnings.catch_warnings():
    470         warnings.filterwarnings("ignore", "All-NaN slice encountered")
--> 471         return func(values, axis=axis, **kwargs)
    472 except AttributeError:
    473     if not is_duck_dask_array(values):

TypeError: mean() got an unexpected keyword argument 'method'

[rbavery]

fixed by installing flox. I'll push a PR to list at the top of the notebook packages that need to be installed

[rbavery]

new error at the last cell of that noteboook

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[13], line 1
----> 1 anomaly.to_zarr("anomaly.zarr", chunkmanager_store_kwargs=dict(callbacks=[RichProgressBar()]))

File [~/miniforge3/lib/python3.10/site-packages/xarray/core/dataset.py:2549](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/core/dataset.py#line=2548), in Dataset.to_zarr(self, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options, zarr_version, write_empty_chunks, chunkmanager_store_kwargs)
   2404 """Write dataset contents to a zarr group.
   2405 
   2406 Zarr chunks are determined in the following way:
   (...)
   2545     The I[/O](http://localhost:8888/O) user guide, with more details and examples.
   2546 """
   2547 from xarray.backends.api import to_zarr
-> 2549 return to_zarr(  # type: ignore[call-overload,misc]
   2550     self,
   2551     store=store,
   2552     chunk_store=chunk_store,
   2553     storage_options=storage_options,
   2554     mode=mode,
   2555     synchronizer=synchronizer,
   2556     group=group,
   2557     encoding=encoding,
   2558     compute=compute,
   2559     consolidated=consolidated,
   2560     append_dim=append_dim,
   2561     region=region,
   2562     safe_chunks=safe_chunks,
   2563     zarr_version=zarr_version,
   2564     write_empty_chunks=write_empty_chunks,
   2565     chunkmanager_store_kwargs=chunkmanager_store_kwargs,
   2566 )

File [~/miniforge3/lib/python3.10/site-packages/xarray/backends/api.py:1698](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/backends/api.py#line=1697), in to_zarr(dataset, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options, zarr_version, write_empty_chunks, chunkmanager_store_kwargs)
   1696 # TODO: figure out how to properly handle unlimited_dims
   1697 dump_to_store(dataset, zstore, writer, encoding=encoding)
-> 1698 writes = writer.sync(
   1699     compute=compute, chunkmanager_store_kwargs=chunkmanager_store_kwargs
   1700 )
   1702 if compute:
   1703     _finalize_store(writes, zstore)

File [~/miniforge3/lib/python3.10/site-packages/xarray/backends/common.py:258](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/backends/common.py#line=257), in ArrayWriter.sync(self, compute, chunkmanager_store_kwargs)
    256 def sync(self, compute=True, chunkmanager_store_kwargs=None):
    257     if self.sources:
--> 258         chunkmanager = get_chunked_array_type(*self.sources)
    260         # TODO: consider wrapping targets with dask.delayed, if this makes
    261         # for any discernible difference in performance, e.g.,
    262         # targets = [dask.delayed(t) for t in self.targets]
    264         if chunkmanager_store_kwargs is None:

File [~/miniforge3/lib/python3.10/site-packages/xarray/namedarray/parallelcompat.py:165](http://localhost:8888/~/miniforge3/lib/python3.10/site-packages/xarray/namedarray/parallelcompat.py#line=164), in get_chunked_array_type(*args)
    159 selected = [
    160     chunkmanager
    161     for chunkmanager in chunkmanagers.values()
    162     if chunkmanager.is_chunked_array(chunked_arr)
    163 ]
    164 if not selected:
--> 165     raise TypeError(
    166         f"Could not find a Chunk Manager which recognises type {type(chunked_arr)}"
    167     )
    168 elif len(selected) >= 2:
    169     raise TypeError(f"Multiple ChunkManagers recognise type {type(chunked_arr)}")

TypeError: Could not find a Chunk Manager which recognises type <class 'cubed.array_api.array_object.Array'>

[rbavery]

Here is where I specified what packages need to be installed and their purpose. once these are installed the notebook example runs without any changes.

https://github.com/cubed-dev/cubed/pull/501/files#diff-49aaa2819e35a856818ecec8c9fa7e1c79ad028d3f44bd749736353cfb51bac9R62

A to-do might be to explain in the docs site what packages Cubed integrates with and how. For example I hadn't heard of flox before but it seems like an important prerequisite to use Cubed for map reduce operations.

[rbavery]

addressed by #507