html_url,issue_url,id,node_id,user,created_at,updated_at,author_association,body,reactions,performed_via_github_app,issue
https://github.com/pydata/xarray/issues/3959#issuecomment-612978261,https://api.github.com/repos/pydata/xarray/issues/3959,612978261,MDEyOklzc3VlQ29tbWVudDYxMjk3ODI2MQ==,6130352,2020-04-13T16:36:32Z,2020-04-13T16:36:32Z,NONE,"Thanks again @keewis!  I moved the static typing discussion to https://github.com/pydata/xarray/issues/3967.

This is closed out now as far as I'm concerned.","{""total_count"": 1, ""+1"": 1, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,597475005
https://github.com/pydata/xarray/issues/3959#issuecomment-612513722,https://api.github.com/repos/pydata/xarray/issues/3959,612513722,MDEyOklzc3VlQ29tbWVudDYxMjUxMzcyMg==,6130352,2020-04-11T21:07:07Z,2020-04-11T21:39:42Z,NONE,"Thanks @keewis!  I like those ideas so I experimented a bit and found a few things.

> you could emulate the availability of the accessors by checking your variables in the constructor of the accessor using
> ... now that we have a ""type"" registry, we could also have one accessor, and pass a kind parameter to your analyze function:

Is there any reason not to put the name of the type into ```attrs``` and just switch on that rather than the keys in ```data_vars```?  Forcing unique data_vars keys across the different dataset types isn't a big deal, but I thought a single type name or something of the like in ```attrs``` would be simpler.

> If someone actually gets this to work, we might be able to provide a xarray.typing module to allow something like (but depending on the amount of code needed, this could also fit in the Cookbook docs section)

I would love to try to use something like that.  I couldn't get it to work either when trying to have a TypedDict that represents entire datasets, so I tried creating them for ```data_vars``` and ```coords``` separately.  I think https://github.com/python/mypy/issues/4976 is particularly problematic in either case though.  The gist of that issue is that covariance for TypeDict types doesn't really exist (i.e. ```TypedDict -> Mapping``` is ok but not ```TypedDict -> Mapping[Hashable, Any]```) and contravariance definitely isn't supported (at least not with Dict or Mapping).   Some examples I played around with:

```python
MyDict = TypedDict('MyDict', {'x': str})
v1: MyDict = MyDict(x='x')

# This is fine
v2: Mapping = v1

# But this doesn't work:
v2: Mapping[Hashable, Any] = v1 # A notable examples since it's used in xr.Dataset
# error: Incompatible types in assignment (expression has type ""MyDict"", variable has type ""Mapping[Hashable, Any]"")

# And neither do any of these:
v2: dict = v1
# error: Incompatible types in assignment (expression has type ""MyDict"", variable has type ""Dict[Any, Any]"")
v2: Mapping[str, str] = v1
# error: Incompatible types in assignment (expression has type ""MyDict"", variable has type ""Mapping[str, str]"")
```

Going the other direction isn't possible at all (i.e. from ```Mapping -> TypeDict```) since TypedDict acts like a subtype of Mapping.  I think that's a big issue downstream if xr.Dataset requires ```Mapping``` types for data_vars and coords since you could never do something like this:

```python
ds = xr.Dataset(data_vars=MyTypedDict(data=...))
# Now assume a user wants to use data_vars/coords with type safety:
data_vars: MyTypedDict = ds.data_vars # This doesn't work 
```

Generics seem like a decent solution to all these problems, but it would obviously involve a lot of type annotation changes:

```python
# Ideally, xarray.typing would help specify more specific constraints, 
# but this works with what exists today:
GenotypeDataVars = TypedDict('GenotypeDataVars', {'data': DataArray, 'mask': DataArray})
GenotypeCoords = TypedDict('GenotypeCoords', {'variant': DataArray, 'sample': DataArray})

D = TypeVar('D', bound=Mapping)
C = TypeVar('C', bound=Mapping)

# Assume xr.Dataset was written something like this instead:
class Dataset(Generic[D, C]):
    
    def __init__(self, data_vars: D, coords: C):
        self.data_vars = data_vars
        self.coords = coords
        
ds1: Dataset[GenotypeDataVars, GenotypeCoords] = Dataset(
    GenotypeDataVars(data=xr.DataArray(), mask=xr.DataArray()), 
    GenotypeCoords(variant=xr.DataArray(), sample=xr.DataArray())
)

# Types should then be preserved even if xarray is constantly redefining 
# new instances in internal functions:
ds2: Dataset[GenotypeDataVars, GenotypeCoords] = type(ds1)(ds1.data_vars, ds1.coords) # This is OK
```

Anyways, my takeaways from everything on the thread so far are:

- Using accessors and some kind of runtime type analysis will cover what was in the scope of my original post, but it will prohibit any kind of static type safety.
- I imagine supporting type safety on the structure of arrays, coordinates, and attributes in Xarray would be far easier than supporting polymorphism for Dataset/DataArray so I'm curious if that has been discussed much.  Do you think it's worth opening a separate issue to continue a conversation that builds on your idea @keewis ?
  ","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,597475005
https://github.com/pydata/xarray/issues/3959#issuecomment-612050871,https://api.github.com/repos/pydata/xarray/issues/3959,612050871,MDEyOklzc3VlQ29tbWVudDYxMjA1MDg3MQ==,6130352,2020-04-10T14:23:20Z,2020-04-10T14:24:35Z,NONE,"Thanks @keewis, that would work though I think it leads to an awkward result if I'm understanding correctly.  Here's what I'm imagining:

```python
from genetics import api

# These are different types of data structures I originally wanted to model as classes
ds1 = api.create_genotype_call_dataset(...) 
ds2 = api.create_genotype_probability_dataset(...)
ds3 = api.create_haplotype_call_dataset(...)
# ds1, ds2, and ds3 are now just xr.Dataset instances

# For each of these different types of datasets I have separate accessors 
# that expose dataset-type-specific analytical methods:

@xr.register_dataset_accessor(""genotype_calls"")
class GenotypeCallAccessor:
    def __init__(self, ds):
        self.ds = ds

    @property
    def analyze(self):
        # Do something you can only do with genotype call data, not probabilities or 
        # haplotype data or CNV data or any other domain-specific kind of info
        pass

@xr.register_dataset_accessor(""genotype_probabilities"")
class GenotypeProbabilityAccessor: ??? # This also has some ""analyze"" method

@xr.register_dataset_accessor(""haplotype_calls"")
class HaplotypeCallAccessor: ??? # This also has some ""analyze"" method

#  ***** Now, how do I prevent this? *****
ds1.haplotype_calls.analyze()
# ds1 is really genotype call data so it shouldn't be possible to do a haplotype analysis on it
```

Is there a way to make accessors available on an xr.Dataset based on some conditions about the dataset itself?  That still seems like a bad solution, but I think it would help me here.  

I was trying to think of some way to use static structural subtyping but I don't see how that could ever work with accessors given that 1) they're attached at runtime and 2) all accessors are available on ALL Dataset instances, regardless of whether or not I know only certain things should be possible based on their content.

If accessors are the only way Xarray plans to facilitate extension, has anyone managed to enable static type analysis on their extensions?  In my case, I'd be happy to have any kind of safety whether its static or monkey-patched in at runtime, but I'm curious if making static analysis impossible was a part of the discussion in deciding on accessors.

","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,597475005
https://github.com/pydata/xarray/issues/3959#issuecomment-611973587,https://api.github.com/repos/pydata/xarray/issues/3959,611973587,MDEyOklzc3VlQ29tbWVudDYxMTk3MzU4Nw==,6130352,2020-04-10T10:20:37Z,2020-04-10T10:22:16Z,NONE,"> would it be too unclear for them to hang off each HaploAccessor.specific_method()?

That works for documenting the methods but I'm more concerned with documenting how to build the Dataset in the first place.  Specifically, this would mean describing how to construct several arrays relating to genotype calls, phasing information, variant call quality scores, individual pedigree info, blah blah etc. and all these domain-specific things can have some pretty nuanced relationships so I think describing how to create a sensible Dataset with them will be a big part of the learning curve for users.  I want to essentially override the constructor docs for Dataset and make it more specific to our use cases.  I can't see a good way to do that with accessors since the dataset would already need to have been created.

> Checking dtype and dimensions shouldn't be expensive though, or is it more than that?

It is, or at least I'd like not to preclude the checks from doing things like checking min/max values and asserting conditions along axes (i.e. sums to 1).

> If you have other questions about dtypes in xarray then please feel free to raise another issue about that.

Will do.","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,597475005
https://github.com/pydata/xarray/issues/3959#issuecomment-611950517,https://api.github.com/repos/pydata/xarray/issues/3959,611950517,MDEyOklzc3VlQ29tbWVudDYxMTk1MDUxNw==,6130352,2020-04-10T09:08:06Z,2020-04-10T09:08:06Z,NONE,"Thanks @TomNicholas, some thoughts on your points:

> xarray internally uses methods like self._construct_dataarray(dims, values, coords, attrs) to construct return values

I'm ok with the subtype being lost after running some methods.  I saw that so I'm assuming all functions that do anything with the data structures take and return Xarray objects alone.


> You could make custom accessors which perform checks on the input arrays when they get used?

Accessors could work but the issues I see with them are:

1. What's a natural way for a user to access documentation on how to build a compliant dataset?  A docstring on a constructor is great -- is there a way to do something like that with accessors?  The docs could hang off of the ```check_*``` type methods, but that seems very awkward.
2. Is there a way to avoid running ```check_*``` methods multiple times?  I think those checks could be expensive and If Xarray often builds new instances as return values, this will be an issue: 

```python
ds.haplo.do_custom_analysis_1()

# Do something with coords/indexes that causes a new Dataset to be created
# e.g. ds.reset_index ultimately hits https://github.com/pydata/xarray/blob/1eedc5c146d9e6ebd46ab2cc8b271e51b3a25959/xarray/core/dataset.py#L882
# which creates a new Dataset
ds = ds.reset_index()

# The `check_conforms_to_haplo_requirements` function will run again even though
# I would know it's not necessary at this point:
ds.haplo.do_custom_analysis_2()
```

> would something akin to pandas' ExtensionDtype solve your problem?

Ah  I can see how the title on the issue is misleading, but I don't actually have a need for dtypes beyond what's already available.  Well, we do actually have that problem in trying to find some way to represent 2-bit integers with sub-byte data types but I wasn't trying to get into that on this thread.  I'll make the title better.","{""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,597475005