Migrate datatree io.py and common.py into xarray/core (pydata#9011)

Author: owenlittlejohns

doc/whats-new.rst

@@ -17,7 +17,7 @@ What's New
 
 .. _whats-new.2024.05.1:
 
-v2024.05.1 (unreleased)
+v2024.06 (unreleased)
 -----------------------
 
 New Features
@@ -59,6 +59,10 @@ Documentation
 
 Internal Changes
 ~~~~~~~~~~~~~~~~
+- Migrates remainder of ``io.py`` to ``xarray/core/datatree_io.py`` and
+  ``TreeAttrAccessMixin`` into ``xarray/core/common.py`` (:pull: `9011`)
+  By `Owen Littlejohns <https://github.com/owenlittlejohns>`_ and
+  `Tom Nicholas <https://github.com/TomNicholas>`_.
 
 
 .. _whats-new.2024.05.0:
@@ -141,10 +145,9 @@ Internal Changes
   By `Owen Littlejohns <https://github.com/owenlittlejohns>`_, `Matt Savoie
   <https://github.com/flamingbear>`_ and `Tom Nicholas <https://github.com/TomNicholas>`_.
 - ``transpose``, ``set_dims``, ``stack`` & ``unstack`` now use a ``dim`` kwarg
-  rather than ``dims`` or ``dimensions``. This is the final change to unify
-  xarray functions to use ``dim``. Using the existing kwarg will raise a
-  warning.
-  By `Maximilian Roos <https://github.com/max-sixty>`_
+  rather than ``dims`` or ``dimensions``. This is the final change to make xarray methods
+  consistent with their use of ``dim``. Using the existing kwarg will raise a
+  warning. By `Maximilian Roos <https://github.com/max-sixty>`_
 
 .. _whats-new.2024.03.0:
 

xarray/backends/api.py

@@ -36,7 +36,7 @@
 from xarray.core.dataarray import DataArray
 from xarray.core.dataset import Dataset, _get_chunk, _maybe_chunk
 from xarray.core.indexes import Index
-from xarray.core.types import ZarrWriteModes
+from xarray.core.types import NetcdfWriteModes, ZarrWriteModes
 from xarray.core.utils import is_remote_uri
 from xarray.namedarray.daskmanager import DaskManager
 from xarray.namedarray.parallelcompat import guess_chunkmanager
@@ -1120,7 +1120,7 @@ def open_mfdataset(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: str | os.PathLike | None = None,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,
@@ -1138,7 +1138,7 @@ def to_netcdf(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: None = None,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,
@@ -1155,7 +1155,7 @@ def to_netcdf(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: str | os.PathLike,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,
@@ -1173,7 +1173,7 @@ def to_netcdf(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: str | os.PathLike,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,
@@ -1191,7 +1191,7 @@ def to_netcdf(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: str | os.PathLike,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,
@@ -1209,7 +1209,7 @@ def to_netcdf(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: str | os.PathLike,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,
@@ -1226,7 +1226,7 @@ def to_netcdf(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: str | os.PathLike | None,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,
@@ -1241,7 +1241,7 @@ def to_netcdf(
 def to_netcdf(
     dataset: Dataset,
     path_or_file: str | os.PathLike | None = None,
-    mode: Literal["w", "a"] = "w",
+    mode: NetcdfWriteModes = "w",
     format: T_NetcdfTypes | None = None,
     group: str | None = None,
     engine: T_NetcdfEngine | None = None,

xarray/core/common.py

@@ -347,6 +347,24 @@ def _ipython_key_completions_(self) -> list[str]:
         return list(items)
 
 
+class TreeAttrAccessMixin(AttrAccessMixin):
+    """Mixin class that allows getting keys with attribute access"""
+
+    # TODO: Ensure ipython tab completion can include both child datatrees and
+    # variables from Dataset objects on relevant nodes.
+
+    __slots__ = ()
+
+    def __init_subclass__(cls, **kwargs):
+        """This method overrides the check from ``AttrAccessMixin`` that ensures
+        ``__dict__`` is absent in a class, with ``__slots__`` used instead.
+        ``DataTree`` has some dynamically defined attributes in addition to those
+        defined in ``__slots__``. (GH9068)
+        """
+        if not hasattr(object.__new__(cls), "__dict__"):
+            pass
+
+
 def get_squeeze_dims(
     xarray_obj,
     dim: Hashable | Iterable[Hashable] | None = None,

xarray/core/dataarray.py

@@ -54,6 +54,7 @@
 from xarray.core.options import OPTIONS, _get_keep_attrs
 from xarray.core.types import (
     DaCompatible,
+    NetcdfWriteModes,
     T_DataArray,
     T_DataArrayOrSet,
     ZarrWriteModes,
@@ -3945,7 +3946,7 @@ def to_masked_array(self, copy: bool = True) -> np.ma.MaskedArray:
     def to_netcdf(
         self,
         path: None = None,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -3960,7 +3961,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -3976,7 +3977,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -3992,7 +3993,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -4005,7 +4006,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike | None = None,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,

xarray/core/dataset.py

@@ -88,6 +88,7 @@
 from xarray.core.missing import get_clean_interp_index
 from xarray.core.options import OPTIONS, _get_keep_attrs
 from xarray.core.types import (
+    NetcdfWriteModes,
     QuantileMethods,
     Self,
     T_ChunkDim,
@@ -2171,7 +2172,7 @@ def dump_to_store(self, store: AbstractDataStore, **kwargs) -> None:
     def to_netcdf(
         self,
         path: None = None,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -2186,7 +2187,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -2202,7 +2203,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -2218,7 +2219,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,
@@ -2231,7 +2232,7 @@ def to_netcdf(
     def to_netcdf(
         self,
         path: str | PathLike | None = None,
-        mode: Literal["w", "a"] = "w",
+        mode: NetcdfWriteModes = "w",
         format: T_NetcdfTypes | None = None,
         group: str | None = None,
         engine: T_NetcdfEngine | None = None,

xarray/core/datatree.py

@@ -9,12 +9,14 @@
     Any,
     Callable,
     Generic,
+    Literal,
     NoReturn,
     Union,
     overload,
 )
 
 from xarray.core import utils
+from xarray.core.common import TreeAttrAccessMixin
 from xarray.core.coordinates import DatasetCoordinates
 from xarray.core.dataarray import DataArray
 from xarray.core.dataset import Dataset, DataVariables
@@ -46,7 +48,6 @@
     maybe_wrap_array,
 )
 from xarray.core.variable import Variable
-from xarray.datatree_.datatree.common import TreeAttrAccessMixin
 
 try:
     from xarray.core.variable import calculate_dimensions
@@ -57,8 +58,9 @@
 if TYPE_CHECKING:
     import pandas as pd
 
+    from xarray.core.datatree_io import T_DataTreeNetcdfEngine, T_DataTreeNetcdfTypes
     from xarray.core.merge import CoercibleValue
-    from xarray.core.types import ErrorOptions
+    from xarray.core.types import ErrorOptions, NetcdfWriteModes, ZarrWriteModes
 
 # """
 # DEVELOPERS' NOTE
@@ -1475,7 +1477,16 @@ def groups(self):
         return tuple(node.path for node in self.subtree)
 
     def to_netcdf(
-        self, filepath, mode: str = "w", encoding=None, unlimited_dims=None, **kwargs
+        self,
+        filepath,
+        mode: NetcdfWriteModes = "w",
+        encoding=None,
+        unlimited_dims=None,
+        format: T_DataTreeNetcdfTypes | None = None,
+        engine: T_DataTreeNetcdfEngine | None = None,
+        group: str | None = None,
+        compute: bool = True,
+        **kwargs,
     ):
         """
         Write datatree contents to a netCDF file.
@@ -1499,26 +1510,47 @@ def to_netcdf(
             By default, no dimensions are treated as unlimited dimensions.
             Note that unlimited_dims may also be set via
             ``dataset.encoding["unlimited_dims"]``.
+        format : {"NETCDF4", }, optional
+            File format for the resulting netCDF file:
+
+            * NETCDF4: Data is stored in an HDF5 file, using netCDF4 API features.
+        engine : {"netcdf4", "h5netcdf"}, optional
+            Engine to use when writing netCDF files. If not provided, the
+            default engine is chosen based on available dependencies, with a
+            preference for "netcdf4" if writing to a file on disk.
+        group : str, optional
+            Path to the netCDF4 group in the given file to open as the root group
+            of the ``DataTree``. Currently, specifying a group is not supported.
+        compute : bool, default: True
+            If true compute immediately, otherwise return a
+            ``dask.delayed.Delayed`` object that can be computed later.
+            Currently, ``compute=False`` is not supported.
         kwargs :
             Addional keyword arguments to be passed to ``xarray.Dataset.to_netcdf``
         """
-        from xarray.datatree_.datatree.io import _datatree_to_netcdf
+        from xarray.core.datatree_io import _datatree_to_netcdf
 
         _datatree_to_netcdf(
             self,
             filepath,
             mode=mode,
             encoding=encoding,
             unlimited_dims=unlimited_dims,
+            format=format,
+            engine=engine,
+            group=group,
+            compute=compute,
             **kwargs,
         )
 
     def to_zarr(
         self,
         store,
-        mode: str = "w-",
+        mode: ZarrWriteModes = "w-",
         encoding=None,
         consolidated: bool = True,
+        group: str | None = None,
+        compute: Literal[True] = True,
         **kwargs,
     ):
         """
@@ -1541,17 +1573,26 @@ def to_zarr(
         consolidated : bool
             If True, apply zarr's `consolidate_metadata` function to the store
             after writing metadata for all groups.
+        group : str, optional
+            Group path. (a.k.a. `path` in zarr terminology.)
+        compute : bool, default: True
+            If true compute immediately, otherwise return a
+            ``dask.delayed.Delayed`` object that can be computed later. Metadata
+            is always updated eagerly. Currently, ``compute=False`` is not
+            supported.
         kwargs :
             Additional keyword arguments to be passed to ``xarray.Dataset.to_zarr``
         """
-        from xarray.datatree_.datatree.io import _datatree_to_zarr
+        from xarray.core.datatree_io import _datatree_to_zarr
 
         _datatree_to_zarr(
             self,
             store,
             mode=mode,
             encoding=encoding,
             consolidated=consolidated,
+            group=group,
+            compute=compute,
             **kwargs,
         )