home / github

Menu
  • GraphQL API
  • Search all tables

issues

Table actions
  • GraphQL API for issues

2 rows where comments = 6, state_reason = "completed" and user = 35968931 sorted by updated_at descending

✎ View and edit SQL

This data as json, CSV (advanced)

Suggested facets: created_at (date), updated_at (date), closed_at (date)

type 1

  • issue 2

state 1

  • closed 2

repo 1

  • xarray 2
id node_id number title user state locked assignee milestone comments created_at updated_at ▲ closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
1020282789 I_kwDOAMm_X8480Eel 5843 Why are `da.chunks` and `ds.chunks` properties inconsistent? TomNicholas 35968931 closed 0     6 2021-10-07T17:21:01Z 2021-10-29T18:12:22Z 2021-10-29T18:12:22Z MEMBER      

Basically the title, but what I'm referring to is this:

```python In [2]: da = xr.DataArray([[0, 1], [2, 3]], name='foo').chunk(1)

In [3]: ds = da.to_dataset()

In [4]: da.chunks Out[4]: ((1, 1), (1, 1))

In [5]: ds.chunks Out[5]: Frozen({'dim_0': (1, 1), 'dim_1': (1, 1)}) ```

Why does DataArray.chunks return a tuple and Dataset.chunks return a frozen dictionary?

This seems a bit silly, for a few reasons:

1) it means that some perfectly reasonable code might fail unnecessarily if passed a DataArray instead of a Dataset or vice versa, such as

```python
def is_core_dim_chunked(obj, core_dim):
    return len(obj.chunks[core_dim]) > 1
```
which will work as intended for a dataset but raises a `TypeError` for a dataarray.

2) it breaks the pattern we use for .sizes, where

```python
In [14]: da.sizes
Out[14]: Frozen({'dim_0': 2, 'dim_1': 2})

In [15]: ds.sizes
Out[15]: Frozen({'dim_0': 2, 'dim_1': 2})
```

3) if you want the chunks as a tuple they are always accessible via da.data.chunks, which is a more sensible place to look to find the chunks without dimension names.

4) It's an undocumented difference, as the docstrings for ds.chunks and da.chunks both only say

`"""Block dimensions for this dataset’s data or None if it’s not a dask array."""`

which doesn't tell me anything about the return type, or warn me that the return types are different.

EDIT: In fact `DataArray.chunk` doesn't even appear to be listed on the API docs page at all.

In our codebase this difference is mostly washed out by us using ._to_temp_dataset() all the time, and also by the way that the .chunk() method accepts both the tuple and dict form, so both of these invariants hold (but in different ways):

ds == ds.chunk(ds.chunks) da == da.chunk(da.chunks)

I'm not sure whether making this consistent is worth the effort of a significant breaking change though :confused:

(Sort of related to https://github.com/pydata/xarray/issues/2103)

{
    "url": "https://api.github.com/repos/pydata/xarray/issues/5843/reactions",
    "total_count": 0,
    "+1": 0,
    "-1": 0,
    "laugh": 0,
    "hooray": 0,
    "confused": 0,
    "heart": 0,
    "rocket": 0,
    "eyes": 0
}
  completed xarray 13221727 issue
367763373 MDU6SXNzdWUzNjc3NjMzNzM= 2473 Recommended way to extend xarray Datasets using accessors? TomNicholas 35968931 closed 0     6 2018-10-08T12:19:21Z 2018-10-31T09:58:05Z 2018-10-31T09:58:05Z MEMBER      

Hi,

I'm now regularly using xarray (& dask) for organising and analysing the output of the simulation code I use (BOUT++) and it's very helpful, thank you!.

However my current approach is quite clunky at dealing the extra information and functionality that's specific to the simulation code I'm using, and I have questions about what the recommended way to extend the xarray Dataset class is. This seems like a general enough problem that I thought I would make an issue for it.

Desired

What I ideally want to do is extend the xarray.Dataset class to accommodate extra attributes and methods, while retaining as much xarray functionality as possible, but avoiding reimplementing any of the API. This might not be possible, but ideally I want to make a BoutDataset class which contains extra attributes to hold information about the run which doesn't naturally fit into the xarray data model, extra methods to perform analysis/plotting which only users of this code would require, but also be able to use xarray-specific methods and top-level functions:

```python bd = BoutDataset('/path/to/data')

ds = bd.data # access the wrapped xarray dataset extra_data = bd.extra_data # access the BOUT-specific data

bd.isel(time=-1) # use xarray dataset methods

bd2 = BoutDataset('/path/to/other/data') concatenated_bd = xr.concat([bd, bd2]) # apply top-level xarray functions to the data

bd.plot_tokamak() # methods implementing bout-specific functionality ```

Problems with my current approach

I have read the documentation about extending xarray, and the issue threads about subclassing Datasets (#706) and accessors (#1080), but I wanted to check that what I'm doing is the recommended approach.

Right now I'm trying to do something like

```python @xr.register_dataset_accessor('bout') class BoutDataset: def init(self, path): self.data = collect_data(path) # collect all my numerical data from output files self.extra_data = read_extra_data(path) # collect extra data about the simulation

def plot_tokamak():
    plot_in_bout_specific_way(self.data, self.extra_data)

```

which works in the sense that I can do

```python bd = BoutDataset('/path/to/data')

ds = bd.bout.data # access the wrapped xarray dataset extra_data = bd.bout.extra_data # access the BOUT-specific data bd.bout.plot_tokamak() # methods implementing bout-specific functionality ```

but not so well with

```python bd.isel(time=-1) # AttributeError: 'BoutDataset' object has no attribute 'isel' bd.bout.data.isel(time=-1) # have to do this instead, but this returns an xr.Dataset not a BoutDataset

concatenated_bd = xr.concat([bd1, bd2]) # TypeError: can only concatenate xarray Dataset and DataArray objects, got <class 'BoutDataset'> concatenated_ds = xr.concat([bd1.bout.data, bd2.bout.data]) # again have to do this instead, which again returns an xr.Dataset not a BoutDataset ```

If I have to reimplement the APl for methods like .isel() and top-level functions like concat(), then why should I not just subclass xr.Dataset?

There aren't very many top-level xarray functions so reimplementing them would be okay, but there are loads of Dataset methods. However I think I know how I want my BoutDataset class to behave when an xr.Dataset method is called on it: I want it to implement that method on the underlying dataset and return the full BoutDatset with extra data and attributes still attached.

Is it possible to do something like: "if calling an xr.Dataset method on an instance of BoutDataset, call the corresponding method on the wrapped dataset and return a BoutDataset that has the extra BOUT-specific data propagated through"?

Thanks in advance, apologies if this is either impossible or relatively trivial, I just thought other xarray users might have the same questions.

{
    "url": "https://api.github.com/repos/pydata/xarray/issues/2473/reactions",
    "total_count": 0,
    "+1": 0,
    "-1": 0,
    "laugh": 0,
    "hooray": 0,
    "confused": 0,
    "heart": 0,
    "rocket": 0,
    "eyes": 0
}
  completed xarray 13221727 issue

Advanced export

JSON shape: default, array, newline-delimited, object

CSV options:

CREATE TABLE [issues] (
   [id] INTEGER PRIMARY KEY,
   [node_id] TEXT,
   [number] INTEGER,
   [title] TEXT,
   [user] INTEGER REFERENCES [users]([id]),
   [state] TEXT,
   [locked] INTEGER,
   [assignee] INTEGER REFERENCES [users]([id]),
   [milestone] INTEGER REFERENCES [milestones]([id]),
   [comments] INTEGER,
   [created_at] TEXT,
   [updated_at] TEXT,
   [closed_at] TEXT,
   [author_association] TEXT,
   [active_lock_reason] TEXT,
   [draft] INTEGER,
   [pull_request] TEXT,
   [body] TEXT,
   [reactions] TEXT,
   [performed_via_github_app] TEXT,
   [state_reason] TEXT,
   [repo] INTEGER REFERENCES [repos]([id]),
   [type] TEXT
);
CREATE INDEX [idx_issues_repo]
    ON [issues] ([repo]);
CREATE INDEX [idx_issues_milestone]
    ON [issues] ([milestone]);
CREATE INDEX [idx_issues_assignee]
    ON [issues] ([assignee]);
CREATE INDEX [idx_issues_user]
    ON [issues] ([user]);
Powered by Datasette · Queries took 790.886ms · About: xarray-datasette