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  • shoyer 8
  • joshburkart 3
  • ttung 2
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  • crusaderky 1
  • DerWeh 1
  • derhintze 1

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issue 1

  • Support non-string dimension/variable names · 18 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
979759002 https://github.com/pydata/xarray/issues/2292#issuecomment-979759002 https://api.github.com/repos/pydata/xarray/issues/2292 IC_kwDOAMm_X846Ze-a derhintze 25172489 2021-11-26T07:48:21Z 2021-11-26T07:52:42Z NONE

Would like to chime in that we use a similar approach as in the last comment of @DerWeh . But we extend this by overloading the __str__ method of the enum.Enum base class, and implement a Dimension base class to use for our enum dimensions:

``` class Dimension(str, enum.Enum): """Base class for all dimension enums

It is of type string because this is needed for xarray.
"""

def __str__(self):
    return type(self).__name__ + "." + self.name

```

Using this the xarray output is more consistent:

```

class CoordId(Dimension): ... LAT = 'lat' ... LON = 'lon' ... xr.DataArray( ... data=np.arange(3 * 2).reshape(3, 2), ... coords={CoordId.LAT: [1, 2, 3], CoordId.LON: [7, 8]}, ... dims=[CoordId.LAT, CoordId.LON], ... ) <xarray.DataArray (CoordId.LAT: 3, CoordId.LON: 2)> array([[0, 1], [2, 3], [4, 5]]) Coordinates: * CoordId.LAT (CoordId.LAT) int64 1 2 3 * CoordId.LON (CoordId.LON) int64 7 8 ```

We then have deserialization code, that re-creates enum members when reading NetCDF files with corresponding dimensions (and coordinates). Access to coordinates works with enum members as well as their string value.

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  Support non-string dimension/variable names 341643235
722565840 https://github.com/pydata/xarray/issues/2292#issuecomment-722565840 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDcyMjU2NTg0MA== DerWeh 22542812 2020-11-05T18:41:24Z 2020-11-05T18:41:24Z NONE

I just came along this question as I tried something similar to @joshburkart. Using a string-enum instead, the code works in principle:

```python import enum

import numpy as np import pandas as pd import xarray as xr

class CoordId(str, enum.Enum): LAT = 'lat' LON = 'lon'

pd.DataFrame({CoordId.LAT: [1,2,3]}).to_csv()

Returns: ',CoordId.LAT\n0,1\n1,2\n2,3\n'

xr.DataArray( data=np.arange(3 * 2).reshape(3, 2), coords={CoordId.LAT: [1, 2, 3], CoordId.LON: [7, 8]}, dims=[CoordId.LAT, CoordId.LON], )

output

<xarray.DataArray (lat: 3, lon: 2)>

array([[0, 1],

[2, 3],

[4, 5]])

Coordinates:

* lat (CoordId.LAT) int64 1 2 3

* lon (CoordId.LON) int64 7 8

```

We however got somewhat ambivalent results, that the dimensions are still enum elements dims = (<CoordId.LAT: 'lat'>, <CoordId.LON: 'lon'>), but the coordinate names are the strings. After writing and reading the DataArray, everything is a plain string, we can still access the elements using the enum elements, as they are equal to the strings.

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  Support non-string dimension/variable names 341643235
496435570 https://github.com/pydata/xarray/issues/2292#issuecomment-496435570 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQ5NjQzNTU3MA== crusaderky 6213168 2019-05-28T09:18:52Z 2019-05-28T09:18:52Z MEMBER

@shoyer the biggest problem I see with your suggestion is that, for DataArrays, you'd likewise need to write xarray.DataArray[str, np.ndarray], except that str in this case refers to the coords alone, which I think novice users may find confusing as they won't mentally associate a DataArray to a dict-like - even if you can write da[coord name].

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  Support non-string dimension/variable names 341643235
496064041 https://github.com/pydata/xarray/issues/2292#issuecomment-496064041 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQ5NjA2NDA0MQ== shoyer 1217238 2019-05-27T03:15:53Z 2019-05-27T03:15:53Z MEMBER

From a typing perspective, what if xarray.Dataset was a generic type? Then you could write something like xarray.Dataset[str, np.ndarray] to get a Dataset specialized to string keys and numpy arrays in the .data attribute of its constituent data.

I don't think we need to change the signature of xarray functions to support "hashable or sequence of hashable". It's OK if convenience features (like support for passing in only a single argument as a string) don't work in all cases. I agree that it would be a good idea to use a centralized helper function for this, though.

It is unfortunate that there doesn't seem to be a good way to distinguish between "string" and "non-string sequence of strings" in Python's typing system. But I don't know a good way to solve this problem. Certainly the folks who work on typing in Python are aware of this.

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  Support non-string dimension/variable names 341643235
490824656 https://github.com/pydata/xarray/issues/2292#issuecomment-490824656 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQ5MDgyNDY1Ng== gimperiale 47244312 2019-05-09T09:13:22Z 2019-05-09T09:13:22Z CONTRIBUTOR

A possible way out would be to open a PEP for "and" and "not" operators in the typing module. That way we could define a "variable-name-like" type and use it throughout the module:

xarray.utils: from typing import AllOf, Hashable, NoneOf VarName = AllOf[Hashable, NoneOf[None, tuple]] Elsewhere: from .utils import VarName def f(x: Union[VarName, Sequence[VarName], None]): if x is None: x = [DEFAULT] elif isinstance(x, VarName): x = [x] elif not isinstance(x, Sequence): raise TypeError('x: expected hashable or sequence of hashables)

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  Support non-string dimension/variable names 341643235
490821558 https://github.com/pydata/xarray/issues/2292#issuecomment-490821558 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQ5MDgyMTU1OA== gimperiale 47244312 2019-05-09T09:04:21Z 2019-05-09T09:05:48Z CONTRIBUTOR

There are problems with typing. I already mentioned them in #2929 but I'll summarize here.

The vast majority of xarray functions/methods allow for "string or sequence of strings, optional". When you move to "hashable or sequence of hashables, optional", however, you want to specifically avoid tuples, which are both Sequence and Hashable instances.

Most functions currently look like this: if isinstance(x, str): x = [x] elif x is None: x = [DEFAULT] for xi in x: ... After the change they would become: if x is None: x = [DEFAULT] elif isinstance(x, Hashable) and not isinstance(x, tuple): x = [x] for xi in x: ... Or: if x is None: x = [DEFAULT] elif isinstance(x, str) or not isinstance(x, Sequence): x = [x] for xi in x: ... Note how I moved the test for None above. This matters, because isinstance(None, Hashable) returns True. This is very error-prone and expensive to maintain, which will very easily cause beginner contributors to introduce bugs. Every test that currently runs three use cases, one for None, one for str and another for a sequence of str, will now be forced to be expanded to SIX test cases:

  1. str
  2. tuple (hashable sequence) of str
  3. list (non-hashable sequence) of str
  4. enum (non-str, non-sequence hashable)
  5. sequence of non-sortable hashables
  6. None

One way to mitigate it would be to have an helper function, which would be invoked everywhere around the codebase, and then religiously make sure that the helper function is always used. _no_default = [object()] def ensure_sequence(name: str, x: Union[Hashable, Sequence[Hashable]], default: Sequence[Hashable] = _no_default) -> Sequence[Hashable]: if x is None: if default is _no_default: raise ValueError(name + ' must be explicitly defined') return default if isinstance(x, Sequence) and not isinstance(x, str): return x if isinstance(x, Hashable): return [x] raise TypeError(name + ' must be a Hashable or Sequence of Hashable') You would still be forced to implement the test for non-sortable hashables, though.


A completely separate problem with typing is that I expect a huge amount of xarray users to just assume variable names and dims are always strings. They'll have things like for k, v in ds.data_vars: if k.startswith('foo'): ... or [dim for dim in da.dims if "foo" in dim] The above will fill the mypy output with errors as soon as xarray becomes integrated in mypy (#2929), and the user will have to go through a lot of explicitly forcing dims and variable names to str, even if in their project all dims and variables names are always str.


The final problem is that integers are Hashables, and there's a wealth of cases in xarray where there is special logic that dynamically treats ints as positional indices.

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  Support non-string dimension/variable names 341643235
410121888 https://github.com/pydata/xarray/issues/2292#issuecomment-410121888 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQxMDEyMTg4OA== shoyer 1217238 2018-08-03T02:04:33Z 2018-08-03T02:04:33Z MEMBER

I disagree that base classes aren't very pythonic.

I should have said that required base classes don't feel very Pythonic. I'm not opposed to base classes in principle, and I'm definitely sympathetic to a desire to use static typing. See also https://github.com/pydata/xarray/issues/1900 for related discussion.

One consideration is what the advantages are of using enums over "dummy enums" like: class A: X = 'X' Y = 'Y' Z = 'Z' (i.e., constants in a namespace)

You can still refer to these programmatically like A.X, but I guess the string repr is different. On the plus side, "dummy enums" will serialize/deserialize perfectly to strings (because they are indeed strings).

I don't love the sound of names that deserialize to different types than their inputs. That seems very error prone, even if you do your best to overload all the special methods like __eq__.

What does seems like potentially a better idea to me would be a library with dedicated loader functions that "destringify" names by turning them back into enum objects.

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  Support non-string dimension/variable names 341643235
410008899 https://github.com/pydata/xarray/issues/2292#issuecomment-410008899 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQxMDAwODg5OQ== ttung 280924 2018-08-02T17:38:52Z 2018-08-02T17:38:52Z CONTRIBUTOR

The problem with generic scalar types is that it wouldn't work after serialization and deserialization (which would presumably go to strings). My suggestion has the advantage of being able to create a __eq__ method in the base class that would match both the object itself or its string equivalent, so that one could use the scalar type even after ser/deser. I disagree that base classes aren't very pythonic.

However, I think (1)/(2) are both reasonable solution (in fact, they seem to be identical except for when you call str). It has its warts, as even a mutable sequence would pass muster. :)

If that's the direction you'd like to see the project go towards, I'd be happy to take a stab at it.

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  Support non-string dimension/variable names 341643235
409829431 https://github.com/pydata/xarray/issues/2292#issuecomment-409829431 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwOTgyOTQzMQ== shoyer 1217238 2018-08-02T07:12:17Z 2018-08-02T07:12:17Z MEMBER

Most of the places in the code where we do the isinstance(obj, string) checks are where we allow passing in a single string as a convenient shortcut to a list of names. So I'm not sure it's really essential to allow flexible types there.

That said, checking explicitly for strings wasn't take a careful API choice. I could see a case for replacing all these "as sequence" casts with something more generic, e.g., based on checking explicitly for more generic scalar types. Certainly enums should be scalars.

If possible, I would rather stick to duck typing for any requirements we put on names. Base classes don't feel terribly Pythonic.

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  Support non-string dimension/variable names 341643235
409822333 https://github.com/pydata/xarray/issues/2292#issuecomment-409822333 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwOTgyMjMzMw== ttung 280924 2018-08-02T06:38:32Z 2018-08-02T06:38:32Z CONTRIBUTOR

We're using xarray in a project that is encouraging use of python typing, and we too would like to use enums as data dimension names. How do you feel about using a base class that data dimension classes need to subclass?

Here's a really simple proof-of-concept (though not very thorough, as it would certainly fail serialization): https://github.com/ttung/xarray/commit/8e623ebebc8f5c1e5615e6d07a82451c0dbe763d

``` In [1]: import xarray as xr

In [2]: import numpy as np

In [5]: from enum import Enum

In [6]: class A(xr.core.dataarray.DimensionBase, Enum): ...: X = "abc" ...: Y = "def" ...: Z = "ghi" ...:

In [7]: a = xr.DataArray(np.random.randint(0, 255, size=(4, 3, 5)), dims=[A.X, A.Y, A.Z])

In [8]: a[A.X] Out[8]: <xarray.DataArray \<A.X: 'abc'> (A.X: 4)> array([0, 1, 2, 3]) Dimensions without coordinates: A.X

In [9]: a.max(A.X) Out[9]: <xarray.DataArray (A.Y: 3, A.Z: 5)> array([[254, 226, 181, 191, 233], [139, 195, 212, 167, 169], [191, 241, 199, 174, 208]]) Dimensions without coordinates: A.Y, A.Z

In [10]: ```

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  Support non-string dimension/variable names 341643235
406639686 https://github.com/pydata/xarray/issues/2292#issuecomment-406639686 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNjYzOTY4Ng== shoyer 1217238 2018-07-20T15:41:45Z 2018-07-20T15:41:45Z MEMBER

Oops, I was reading a little too quickly. I did indeed mean (1) above. The one thing I would emphasize is that we don't actually want to check for something like hasattr(dim, '__str__') if possible, but rather just call str(dim). (Though I guess Python's object type defines a default __str__ method, so pretty much everything will pass that test.)

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  Support non-string dimension/variable names 341643235
406371878 https://github.com/pydata/xarray/issues/2292#issuecomment-406371878 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNjM3MTg3OA== shoyer 1217238 2018-07-19T18:29:11Z 2018-07-20T15:39:10Z MEMBER

~~(2)~~ (1) seems like a pretty decent option to me. It's compatible with Python's duck-typing philosophy, and we don't really need string variable/dimension names for anything other than various serialization formats like netCDF. So the full requirement for names would be "Hashable, can be coerced with str() and not None" (we use None as a sentinel value to indicate the lack of a name in xarray).

CC @pydata/xarray in case anyone else has opinions.

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  Support non-string dimension/variable names 341643235
406617353 https://github.com/pydata/xarray/issues/2292#issuecomment-406617353 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNjYxNzM1Mw== joshburkart 3888181 2018-07-20T14:28:07Z 2018-07-20T14:28:07Z NONE

Just to clarify @shoyer, you said (2) sounds best to you, but your other comments (e.g. duck typing, requiring hashable) seem to describe (1)...? Slightly confused...

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  Support non-string dimension/variable names 341643235
406356945 https://github.com/pydata/xarray/issues/2292#issuecomment-406356945 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNjM1Njk0NQ== joshburkart 3888181 2018-07-19T17:37:34Z 2018-07-19T17:37:34Z NONE

Some options that come to mind:

  1. Allow any object with a __str__ method to be supplied as a variable/dimension label, but then delegate all internal sorting/printing/etc. logic to str(label).
  2. Just implicitly run str on everything a user tries to input as a label (both when creating an xarray object and when accessing fields from an existing object), so that only strings are used internally.
  3. Put this on the user, and only allow calling xarray objects/methods/etc. with labels already strings, as you suggested @shoyer.

I dunno. Whatever the maintainers think is best? (3) seems least complex on the xarray side, but (1) or (2) might be more convenient for users.

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  Support non-string dimension/variable names 341643235
406345790 https://github.com/pydata/xarray/issues/2292#issuecomment-406345790 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNjM0NTc5MA== shoyer 1217238 2018-07-19T16:58:41Z 2018-07-19T16:58:41Z MEMBER

Another choice would be to intentionally simplify xarray's data model and not allow anything other than strings for variable/dimension names.

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  Support non-string dimension/variable names 341643235
405396751 https://github.com/pydata/xarray/issues/2292#issuecomment-405396751 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNTM5Njc1MQ== shoyer 1217238 2018-07-16T22:07:18Z 2018-07-16T22:07:18Z MEMBER

It would be an improvement even to clearly document the requirements for dimension/variable names.

I suspect we don't actually need them to be sortable, though we do using sorting as part of the current repr() for some xarray objecs. This is mostly to ensure reproducible displays across multiple loads/runs of a file, but it's increasingly less relevant now than Python's dict is ordered by default (since Python 3.6).

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  Support non-string dimension/variable names 341643235
405380136 https://github.com/pydata/xarray/issues/2292#issuecomment-405380136 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNTM4MDEzNg== joshburkart 3888181 2018-07-16T20:59:13Z 2018-07-16T20:59:13Z NONE

Thanks @shoyer. I'll see if I can take a look in the near future...

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  Support non-string dimension/variable names 341643235
405371789 https://github.com/pydata/xarray/issues/2292#issuecomment-405371789 https://api.github.com/repos/pydata/xarray/issues/2292 MDEyOklzc3VlQ29tbWVudDQwNTM3MTc4OQ== shoyer 1217238 2018-07-16T20:30:16Z 2018-07-16T20:30:16Z MEMBER

Hi @joshburkart -- thanks for raising this concern.

I agree, it would be nice to support enums (really any hashable value) as dimension names. Our current checks for strings are somewhat inconsistent, e.g., you can actually use these in an xarray.Dataset if you use the fully explicit API for constructing a dataset: python ds = xr.Dataset( data_vars={'foo': ((CoordId.LAT, CoordId.LON), np.arange(3 * 2).reshape(3, 2))}, coords={CoordId.LAT: ((CoordId.LAT,), [1, 2, 3]), CoordId.LON: ((CoordId.LON,), [7, 8])}, )

But now if you try to print the dataset, you get an error about sorting: ```python-traceback


TypeError Traceback (most recent call last) /usr/local/lib/python3.6/dist-packages/IPython/core/formatters.py in call(self, obj) 697 type_pprinters=self.type_printers, 698 deferred_pprinters=self.deferred_printers) --> 699 printer.pretty(obj) 700 printer.flush() 701 return stream.getvalue()

/usr/local/lib/python3.6/dist-packages/IPython/lib/pretty.py in pretty(self, obj) 396 if callable(meth): 397 return meth(obj, self, cycle) --> 398 return _default_pprint(obj, self, cycle) 399 finally: 400 self.end_group()

/usr/local/lib/python3.6/dist-packages/IPython/lib/pretty.py in default_pprint(obj, p, cycle) 516 if _safe_getattr(klass, '__repr__', None) not in _baseclass_reprs: 517 # A user-provided repr. Find newlines and replace them with p.break() --> 518 _repr_pprint(obj, p, cycle) 519 return 520 p.begin_group(1, '<')

/usr/local/lib/python3.6/dist-packages/IPython/lib/pretty.py in repr_pprint(obj, p, cycle) 707 """A pprint that just redirects to the normal repr function.""" 708 # Find newlines and replace them with p.break() --> 709 output = repr(obj) 710 for idx,output_line in enumerate(output.splitlines()): 711 if idx:

/usr/local/lib/python3.6/dist-packages/xarray/core/formatting.py in repr(self) 62 63 def repr(self): ---> 64 return ensure_valid_repr(self.unicode()) 65 66

/usr/local/lib/python3.6/dist-packages/xarray/core/dataset.py in unicode(self) 1188 1189 def unicode(self): -> 1190 return formatting.dataset_repr(self) 1191 1192 def info(self, buf=None):

/usr/local/lib/python3.6/dist-packages/xarray/core/formatting.py in dataset_repr(ds) 415 416 dims_start = pretty_print(u'Dimensions:', col_width) --> 417 summary.append(u'%s(%s)' % (dims_start, dim_summary(ds))) 418 419 if ds.coords:

/usr/local/lib/python3.6/dist-packages/xarray/core/formatting.py in dim_summary(obj) 324 325 def dim_summary(obj): --> 326 elements = [u'%s: %s' % (k, v) for k, v in obj.sizes.items()] 327 return u', '.join(elements) 328

/usr/local/lib/python3.6/dist-packages/xarray/core/formatting.py in <listcomp>(.0) 324 325 def dim_summary(obj): --> 326 elements = [u'%s: %s' % (k, v) for k, v in obj.sizes.items()] 327 return u', '.join(elements) 328

/usr/lib/python3.6/_collections_abc.py in iter(self) 741 742 def iter(self): --> 743 for key in self._mapping: 744 yield (key, self._mapping[key]) 745

/usr/local/lib/python3.6/dist-packages/xarray/core/utils.py in iter(self) 311 312 def iter(self): --> 313 return iter(self.mapping) 314 315 def len(self):

/usr/local/lib/python3.6/dist-packages/xarray/core/utils.py in iter(self) 347 348 def iter(self): --> 349 return iter(sorted(self.mapping)) 350 351 def len(self):

TypeError: '<' not supported between instances of 'CoordId' and 'CoordId' ```

I would be open to PRs to improve the situation.

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  Support non-string dimension/variable names 341643235

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