astropenguin/xarray-dataclasses

:zap: xarray data creation made easy by dataclass

xarray-dataclasses's Issues

Add methods module

Add methods module which provides helper methods for dataclasses.

Release v0.1.1

• Update version numbers written in:
  • pyproject.toml
  • xarray_dataclasses/__init__.py
  • tests/test_metadata.py

Update docstrings of class decorators

Fix missing default values for default DataArray and Dataset factories

This hotfix adds missing default values to the following factories and releases v0.5.1.

• dataarray.AsDataArray.__dataarray_factory__
• dataset.AsDataset.__dataset_factory__

Add options to dataarrayclass

Add deprecated module

Move codes that will be deprecated in v1.0.0 to the deprecated module.

Add methods to DataArray class

Update parser module

Add methods to DataArray class

Release v0.1.2

• Update version numbers written in:
  • pyproject.toml
  • xarray_dataclasses/__init__.py
  • tests/test_metadata.py

Release v0.4.0

Add factory fields for custom DataArray/Dataset creation

Add support of special fields (__dataarray_factory__, __dataset_factory__) for custom DataArray or Dataset creation.

class CustomDataset(xr.Dataset):
    __slots__ = ()


@dataclass
class Custom(DataArrayMixin):
    data: Data[tuple["x", "y"], float]
    __dataset_factory__ = CustomDataset


ds = asdataset(Custom(...)) # statically typed as CustomDataset
type(ds) # -> CustomDataset

Update README

• Add Zenodo budge
• Add Zenodo config
• Fix typos

Release v0.5.0

Remove verbose or unused internal functions

Do not use variables with ClassVar or InitVar types

Update field.infer_field_kind() so as not to assign values with ClassVar or InitVar types to xarray's attrs.

from dataclasses import ClassVar, InitVar
from xarray_dataclasses import Coord, Data, dataarrayclass


@dataarrayclass
class Image:
    data: Data[('x', 'y'), float]
    x: Coord['x', int] = 0
    y: Coord['y', int] = 0

    spam: str = "spam"  # -> a member of attrs
    ham: ClassVar[str] = "ham"  # -> not a member of attrs
    egg: InitVar[str] = "egg"  # -> not a member of attrs

Add bases module

Add bases module which provides DataArrayClass, a base class for dataclasses.

from xarray_dataclasses import DataArray, DataArrayClass


class Image(DataArrayClass):
    data: DataArray[("x", "y"), float]
    x: DataArray["x", int] = 0
    y: DataArray["y", int] = 0

Add typing module

Add typing module which provides a type for xarray.DataArray with fixed dims and dtype.

DataArray[("x", "y"), "f8"]

# DataArray[('x', 'y'), float64]

The type can be instantiated.

DataArray[("x", "y"), "f8"]([[0, 1], [2, 3]])

# <xarray.DataArray (x: 2, y: 2)>
# array([[0., 1.],
#        [2., 3.]])
# Dimensions without coordinates: x, y

Attributes on data array in dataset. (Feature)

Currently there seems to be no way to specify attributes for a DataArray in a Dataset. Indeed, even if they are passed to new() in a DataArray, they are discarded.

It would be nice to reuse DataArray specs to be able specify these:

from xarray_datasetclasses import dataarrayclass, datasetspce, Data, Attr, DataArray

@dataarrayclass
class FooSpec:
    data: Data['x', float]
    meta: Attr[int]

@datasetclass
class BarSpec:
    array: DataArray[FooSpec]

Does that look useful? Here DataArray is from xarray_datasetclasses ... if this name isn't good because of conflict with xarray, perhaps ... ArraySpec?

Add dataset module

Similar to dataarrayclass, introduce a class decorator datasetclass.
Here is an example code to express the dataset of xarray's docs.

from xarray_dataclasses.dataset import datasetclass
from xarray_dataclasses.typing import Coord, Data


@datasetclass
class Weather:
    # data variables
    temperature: Data[('x', 'y', 'time'), float]]
    precipitation: Data[('x', 'y', 'time'), float]]

    # dimensions
    x: Coord['x', int] = 0
    y: Coord['y', int] = 0
    time: Coord['time', 'datetime64[ns]'] = '2021-01-01'

    # coordinates
    lon: Coord[('x', 'y'), float] = 0.0
    lat: Coord[('x', 'y'), float] = 0.0
    reference_time: Coord[(), 'datetime64[ns]'] = '2021-01-01'

Add core module

Update bases module

Add Coord and Data types

Add Coord and Data types (subclass of typing.DataArray) to explicitly distinguish between data (data var) and coordinates. This is necessary to be done before adding @datasetclass (#24).

from xarray_dataclasses import Coord, Data, dataarrayclass


@dataarrayclass
class Image:
    data: Data[('x', 'y'), float]
    x: Coord['x', int] = 0
    y: Coord['y', int] = 0

Add field module

Update dataarray module

Fix wrong comment

Fix wrong comment at xarray_dataclasses/typing.py:L38.

• Before fix: # for Python 3.7 and 3.9
• After fix: # for Python 3.7 and 3.8

Add type hints for creating data/coord field from DataArray class

Update dev environment

• Update dev Python packages
• Update dev JavaScript packages
• Fix codes that cause type check errors

Update NumPy-like zeros, ones, ... to be compatible with sizes

Add development container

Add development container configs for VS Code Remote Containers.

Update docstrings

Update docstrings to be compatible with #65.

Add NumPy-like zeros, ones, ... to Dataset class

Release v0.6.0

Update mix-in classes

Update mix-in classes (AsDataArray, AsDataset) so that the annotations of .new() are dynamically updated.

Fix type hints

• Update Python codes to be compatible with the strict mode of Pyright
• Fix the version of Pyright

Update dataclass type

Use typing.ParamSpec in the dataclass type hint so that .new() can be statically typed.

Update typing module

Update xarray_dataclaases.typing.DataArray so that it accepts the same parameters as xarray.DataArray.

Release v0.3.0

Release v0.3.1

Release package that closes the following issues/PRs.

• #40 loosen Xarray dependency requirements

Refactor typing runtime functions

Update instance check of DataArray type

Update __instancecheck__ of typing.DataAarray so that the following tests are passed.

import numpy as np
from dataclasses import field
from xarray_dataclasses import DataArray


assert isinstance(0, DataArray['x', int])
assert isinstance(field(default=0), DataArray['x', int])
assert isinstance([0, 1, 2], DataArray['x', int])
assert isinstance(np.array([0, 1, 2]), DataArray['x', int])

Fix parsing dataclass under __future__.annotations enabled

The current (v0.4.0) dataclass parser (xarray_dataclasses.parse) does not work when the postponed evaluation of annotations (PEP 563) is enabled by importing from __future__ import annotations. This is because the parser gets type hints of dataclass fields from cls.__dataclass_fields__: Under such environments, field.type becomes string and loses runtime information.

This issue is for resolving the problem by using typing_extensions.get_type_hints(cls, include_extras=True) that ensures evaluated type hints made from strings.

Add Q&A section to README

Add type hints for creating data/coord field from DataArray class

Add new dataclass parser

Swap the order of dims and dtype in Coord[...] and Data[...]

Swap the order of dims and dtype s.t. Coord[dims, dtype] and Data[dims, dtype].
This is because their order in the printed format is (dims, dtype, value).

<xarray.DataArray (x: 3, y: 3)>
array([[0., 0., 0.],
       [0., 0., 0.],
       [0., 0., 0.]])
Coordinates:
  * x        (x) int64 0 0 0
  * y        (y) int64 0 0 0

Release v0.2.0

• Update docstrings of functions to be more detailed
• Update package version (0.1.2 → 0.2.0)
• Update README

Update typedarray function

Add advanced usage section to README

Rename module (parser → datamodel)