Merge branch 'main' into grouper-public-api

Author: keewis

doc/whats-new.rst

@@ -24,7 +24,11 @@ New Features
 ~~~~~~~~~~~~
 - New "random" method for converting to and from 360_day calendars (:pull:`8603`).
   By `Pascal Bourgault <https://github.com/aulemahal>`_.
-
+- Xarray now makes a best attempt not to coerce :py:class:`pandas.api.extensions.ExtensionArray` to a numpy array
+  by supporting 1D `ExtensionArray` objects internally where possible.  Thus, `Dataset`s initialized with a `pd.Catgeorical`,
+  for example, will retain the object.  However, one cannot do operations that are not possible on the `ExtensionArray`
+  then, such as broadcasting.
+  By `Ilan Gold <https://github.com/ilan-gold>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
@@ -36,6 +40,12 @@ Bug fixes
 
 Internal Changes
 ~~~~~~~~~~~~~~~~
+- Migrates ``formatting_html`` functionality for `DataTree` into ``xarray/core`` (:pull: `8930`)
+  By `Eni Awowale <https://github.com/eni-awowale>`_, `Julia Signell <https://github.com/jsignell>`_
+  and `Tom Nicholas <https://github.com/TomNicholas>`_.
+- Migrates ``datatree_mapping`` functionality into ``xarray/core`` (:pull:`8948`)
+  By `Matt Savoie <https://github.com/flamingbear>`_ `Owen Littlejohns
+  <https://github.com/owenlittlejohns>` and `Tom Nicholas <https://github.com/TomNicholas>`_.
 
 
 .. _whats-new.2024.03.0:

properties/test_pandas_roundtrip.py

@@ -17,7 +17,9 @@
 from hypothesis import given  # isort:skip
 
 numeric_dtypes = st.one_of(
-    npst.unsigned_integer_dtypes(), npst.integer_dtypes(), npst.floating_dtypes()
+    npst.unsigned_integer_dtypes(endianness="="),
+    npst.integer_dtypes(endianness="="),
+    npst.floating_dtypes(endianness="="),
 )
 
 numeric_series = numeric_dtypes.flatmap(lambda dt: pdst.series(dtype=dt))

pyproject.toml

@@ -33,6 +33,7 @@ accel = ["scipy", "bottleneck", "numbagg", "flox", "opt_einsum"]
 complete = ["xarray[accel,io,parallel,viz,dev]"]
 dev = [
   "hypothesis",
+  "mypy",
   "pre-commit",
   "pytest",
   "pytest-cov",
@@ -86,8 +87,8 @@ exclude_lines = ["pragma: no cover", "if TYPE_CHECKING"]
 [tool.mypy]
 enable_error_code = "redundant-self"
 exclude = [
-	'xarray/util/generate_.*\.py',
-	'xarray/datatree_/.*\.py',
+  'xarray/util/generate_.*\.py',
+  'xarray/datatree_/.*\.py',
 ]
 files = "xarray"
 show_error_codes = true
@@ -98,8 +99,8 @@ warn_unused_ignores = true
 
 # Ignore mypy errors for modules imported from datatree_.
 [[tool.mypy.overrides]]
-module = "xarray.datatree_.*"
 ignore_errors = true
+module = "xarray.datatree_.*"
 
 # Much of the numerical computing stack doesn't have type annotations yet.
 [[tool.mypy.overrides]]
@@ -129,6 +130,7 @@ module = [
   "opt_einsum.*",
   "pandas.*",
   "pooch.*",
+  "pyarrow.*",
   "pydap.*",
   "pytest.*",
   "scipy.*",
@@ -255,6 +257,9 @@ target-version = "py39"
 # E402: module level import not at top of file
 # E501: line too long - let black worry about that
 # E731: do not assign a lambda expression, use a def
+extend-safe-fixes = [
+  "TID252", # absolute imports
+]
 ignore = [
   "E402",
   "E501",
@@ -268,9 +273,6 @@ select = [
   "I", # isort
   "UP", # Pyupgrade
 ]
-extend-safe-fixes = [
-  "TID252", # absolute imports
-]
 
 [tool.ruff.lint.per-file-ignores]
 # don't enforce absolute imports

xarray/core/dataset.py

@@ -24,6 +24,7 @@
 from typing import IO, TYPE_CHECKING, Any, Callable, Generic, Literal, cast, overload
 
 import numpy as np
+from pandas.api.types import is_extension_array_dtype
 
 # remove once numpy 2.0 is the oldest supported version
 try:
@@ -6853,10 +6854,13 @@ def reduce(
                 if (
                     # Some reduction functions (e.g. std, var) need to run on variables
                     # that don't have the reduce dims: PR5393
-                    not reduce_dims
-                    or not numeric_only
-                    or np.issubdtype(var.dtype, np.number)
-                    or (var.dtype == np.bool_)
+                    not is_extension_array_dtype(var.dtype)
+                    and (
+                        not reduce_dims
+                        or not numeric_only
+                        or np.issubdtype(var.dtype, np.number)
+                        or (var.dtype == np.bool_)
+                    )
                 ):
                     # prefer to aggregate over axis=None rather than
                     # axis=(0, 1) if they will be equivalent, because
@@ -7169,13 +7173,37 @@ def to_pandas(self) -> pd.Series | pd.DataFrame:
         )
 
     def _to_dataframe(self, ordered_dims: Mapping[Any, int]):
-        columns = [k for k in self.variables if k not in self.dims]
+        columns_in_order = [k for k in self.variables if k not in self.dims]
+        non_extension_array_columns = [
+            k
+            for k in columns_in_order
+            if not is_extension_array_dtype(self.variables[k].data)
+        ]
+        extension_array_columns = [
+            k
+            for k in columns_in_order
+            if is_extension_array_dtype(self.variables[k].data)
+        ]
         data = [
             self._variables[k].set_dims(ordered_dims).values.reshape(-1)
-            for k in columns
+            for k in non_extension_array_columns
         ]
         index = self.coords.to_index([*ordered_dims])
-        return pd.DataFrame(dict(zip(columns, data)), index=index)
+        broadcasted_df = pd.DataFrame(
+            dict(zip(non_extension_array_columns, data)), index=index
+        )
+        for extension_array_column in extension_array_columns:
+            extension_array = self.variables[extension_array_column].data.array
+            index = self[self.variables[extension_array_column].dims[0]].data
+            extension_array_df = pd.DataFrame(
+                {extension_array_column: extension_array},
+                index=self[self.variables[extension_array_column].dims[0]].data,
+            )
+            extension_array_df.index.name = self.variables[extension_array_column].dims[
+                0
+            ]
+            broadcasted_df = broadcasted_df.join(extension_array_df)
+        return broadcasted_df[columns_in_order]
 
     def to_dataframe(self, dim_order: Sequence[Hashable] | None = None) -> pd.DataFrame:
         """Convert this dataset into a pandas.DataFrame.
@@ -7322,11 +7350,13 @@ def from_dataframe(cls, dataframe: pd.DataFrame, sparse: bool = False) -> Self:
                 "cannot convert a DataFrame with a non-unique MultiIndex into xarray"
             )
 
-        # Cast to a NumPy array first, in case the Series is a pandas Extension
-        # array (which doesn't have a valid NumPy dtype)
-        # TODO: allow users to control how this casting happens, e.g., by
-        # forwarding arguments to pandas.Series.to_numpy?
-        arrays = [(k, np.asarray(v)) for k, v in dataframe.items()]
+        arrays = []
+        extension_arrays = []
+        for k, v in dataframe.items():
+            if not is_extension_array_dtype(v):
+                arrays.append((k, np.asarray(v)))
+            else:
+                extension_arrays.append((k, v))
 
         indexes: dict[Hashable, Index] = {}
         index_vars: dict[Hashable, Variable] = {}
@@ -7340,6 +7370,8 @@ def from_dataframe(cls, dataframe: pd.DataFrame, sparse: bool = False) -> Self:
                 xr_idx = PandasIndex(lev, dim)
                 indexes[dim] = xr_idx
                 index_vars.update(xr_idx.create_variables())
+            arrays += [(k, np.asarray(v)) for k, v in extension_arrays]
+            extension_arrays = []
         else:
             index_name = idx.name if idx.name is not None else "index"
             dims = (index_name,)
@@ -7353,7 +7385,9 @@ def from_dataframe(cls, dataframe: pd.DataFrame, sparse: bool = False) -> Self:
             obj._set_sparse_data_from_dataframe(idx, arrays, dims)
         else:
             obj._set_numpy_data_from_dataframe(idx, arrays, dims)
-        return obj
+        for name, extension_array in extension_arrays:
+            obj[name] = (dims, extension_array)
+        return obj[dataframe.columns] if len(dataframe.columns) else obj
 
     def to_dask_dataframe(
         self, dim_order: Sequence[Hashable] | None = None, set_index: bool = False

xarray/core/datatree.py

@@ -18,6 +18,14 @@
 from xarray.core.coordinates import DatasetCoordinates
 from xarray.core.dataarray import DataArray
 from xarray.core.dataset import Dataset, DataVariables
+from xarray.core.datatree_mapping import (
+    TreeIsomorphismError,
+    check_isomorphic,
+    map_over_subtree,
+)
+from xarray.core.formatting_html import (
+    datatree_repr as datatree_repr_html,
+)
 from xarray.core.indexes import Index, Indexes
 from xarray.core.merge import dataset_update_method
 from xarray.core.options import OPTIONS as XR_OPTS
@@ -33,14 +41,6 @@
 from xarray.core.variable import Variable
 from xarray.datatree_.datatree.common import TreeAttrAccessMixin
 from xarray.datatree_.datatree.formatting import datatree_repr
-from xarray.datatree_.datatree.formatting_html import (
-    datatree_repr as datatree_repr_html,
-)
-from xarray.datatree_.datatree.mapping import (
-    TreeIsomorphismError,
-    check_isomorphic,
-    map_over_subtree,
-)
 from xarray.datatree_.datatree.ops import (
     DataTreeArithmeticMixin,
     MappedDatasetMethodsMixin,

xarray/datatree_/datatree/mapping.py renamed to xarray/core/datatree_mapping.py

@@ -4,10 +4,9 @@
 import sys
 from itertools import repeat
 from textwrap import dedent
-from typing import TYPE_CHECKING, Callable, Tuple
+from typing import TYPE_CHECKING, Callable
 
 from xarray import DataArray, Dataset
-
 from xarray.core.iterators import LevelOrderIter
 from xarray.core.treenode import NodePath, TreeNode
 
@@ -84,14 +83,13 @@ def diff_treestructure(a: DataTree, b: DataTree, require_names_equal: bool) -> s
     for node_a, node_b in zip(LevelOrderIter(a), LevelOrderIter(b)):
         path_a, path_b = node_a.path, node_b.path
 
-        if require_names_equal:
-            if node_a.name != node_b.name:
-                diff = dedent(
-                    f"""\
+        if require_names_equal and node_a.name != node_b.name:
+            diff = dedent(
+                f"""\
                 Node '{path_a}' in the left object has name '{node_a.name}'
                 Node '{path_b}' in the right object has name '{node_b.name}'"""
-                )
-                return diff
+            )
+            return diff
 
         if len(node_a.children) != len(node_b.children):
             diff = dedent(
@@ -125,7 +123,7 @@ def map_over_subtree(func: Callable) -> Callable:
     func : callable
         Function to apply to datasets with signature:
 
-        `func(*args, **kwargs) -> Union[Dataset, Iterable[Dataset]]`.
+        `func(*args, **kwargs) -> Union[DataTree, Iterable[DataTree]]`.
 
         (i.e. func must accept at least one Dataset and return at least one Dataset.)
         Function will not be applied to any nodes without datasets.
@@ -154,7 +152,7 @@ def map_over_subtree(func: Callable) -> Callable:
     # TODO inspect function to work out immediately if the wrong number of arguments were passed for it?
 
     @functools.wraps(func)
-    def _map_over_subtree(*args, **kwargs) -> DataTree | Tuple[DataTree, ...]:
+    def _map_over_subtree(*args, **kwargs) -> DataTree | tuple[DataTree, ...]:
         """Internal function which maps func over every node in tree, returning a tree of the results."""
         from xarray.core.datatree import DataTree
 
@@ -259,19 +257,18 @@ def _map_over_subtree(*args, **kwargs) -> DataTree | Tuple[DataTree, ...]:
     return _map_over_subtree
 
 
-def _handle_errors_with_path_context(path):
+def _handle_errors_with_path_context(path: str):
     """Wraps given function so that if it fails it also raises path to node on which it failed."""
 
     def decorator(func):
         def wrapper(*args, **kwargs):
             try:
                 return func(*args, **kwargs)
             except Exception as e:
-                if sys.version_info >= (3, 11):
-                    # Add the context information to the error message
-                    e.add_note(
-                        f"Raised whilst mapping function over node with path {path}"
-                    )
+                # Add the context information to the error message
+                add_note(
+                    e, f"Raised whilst mapping function over node with path {path}"
+                )
                 raise
 
         return wrapper
@@ -287,7 +284,9 @@ def add_note(err: BaseException, msg: str) -> None:
         err.add_note(msg)
 
 
-def _check_single_set_return_values(path_to_node, obj):
+def _check_single_set_return_values(
+    path_to_node: str, obj: Dataset | DataArray | tuple[Dataset | DataArray]
+):
     """Check types returned from single evaluation of func, and return number of return values received from func."""
     if isinstance(obj, (Dataset, DataArray)):
         return 1

xarray/core/duck_array_ops.py

@@ -32,6 +32,7 @@
 from numpy import concatenate as _concatenate
 from numpy.lib.stride_tricks import sliding_window_view  # noqa
 from packaging.version import Version
+from pandas.api.types import is_extension_array_dtype
 
 from xarray.core import dask_array_ops, dtypes, nputils
 from xarray.core.options import OPTIONS
@@ -156,7 +157,7 @@ def isnull(data):
         return full_like(data, dtype=bool, fill_value=False)
     else:
         # at this point, array should have dtype=object
-        if isinstance(data, np.ndarray):
+        if isinstance(data, np.ndarray) or is_extension_array_dtype(data):
             return pandas_isnull(data)
         else:
             # Not reachable yet, but intended for use with other duck array
@@ -221,9 +222,19 @@ def asarray(data, xp=np):
 
 def as_shared_dtype(scalars_or_arrays, xp=np):
     """Cast a arrays to a shared dtype using xarray's type promotion rules."""
-    array_type_cupy = array_type("cupy")
-    if array_type_cupy and any(
-        isinstance(x, array_type_cupy) for x in scalars_or_arrays
+    if any(is_extension_array_dtype(x) for x in scalars_or_arrays):
+        extension_array_types = [
+            x.dtype for x in scalars_or_arrays if is_extension_array_dtype(x)
+        ]
+        if len(extension_array_types) == len(scalars_or_arrays) and all(
+            isinstance(x, type(extension_array_types[0])) for x in extension_array_types
+        ):
+            return scalars_or_arrays
+        raise ValueError(
+            f"Cannot cast arrays to shared type, found array types {[x.dtype for x in scalars_or_arrays]}"
+        )
+    elif array_type_cupy := array_type("cupy") and any(  # noqa: F841
+        isinstance(x, array_type_cupy) for x in scalars_or_arrays  # noqa: F821
     ):
         import cupy as cp