Merge branch 'main' into pydap4_scale

Author: Mikejmnez

doc/examples/multidimensional-coords.ipynb

@@ -126,7 +126,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In order to visualize the data on a conventional latitude-longitude grid, we can take advantage of xarray's ability to apply [cartopy](https://scitools.org.uk/cartopy/docs/latest/) map projections."
+    "In order to visualize the data on a conventional latitude-longitude grid, we can take advantage of xarray's ability to apply [cartopy](https://cartopy.readthedocs.io/stable/) map projections."
    ]
   },
   {

doc/get-help/faq.rst

@@ -169,7 +169,7 @@ different approaches to handling metadata: Iris strictly interprets
 integration with Cartopy_.
 
 .. _Iris: https://scitools-iris.readthedocs.io/en/stable/
-.. _Cartopy: https://scitools.org.uk/cartopy/docs/latest/
+.. _Cartopy: https://cartopy.readthedocs.io/stable/
 
 We think the design decisions we have made for xarray (namely, basing it on
 pandas) make it a faster and more flexible data analysis tool. That said, Iris

doc/getting-started-guide/installing.rst

@@ -57,7 +57,7 @@ For plotting
 ~~~~~~~~~~~~
 
 - `matplotlib <https://matplotlib.org>`__: required for :ref:`plotting`
-- `cartopy <https://scitools.org.uk/cartopy>`__: recommended for :ref:`plot-maps`
+- `cartopy <https://cartopy.readthedocs.io>`__: recommended for :ref:`plot-maps`
 - `seaborn <https://seaborn.pydata.org>`__: for better
   color palettes
 - `nc-time-axis <https://nc-time-axis.readthedocs.io>`__: for plotting

doc/user-guide/io.rst

@@ -1209,7 +1209,7 @@ Ncdata can also adjust file data within load and save operations, to fix data lo
 problems or provide exact save formatting without needing to modify files on disk.
 See for example : `ncdata usage examples`_
 
-.. _Iris: https://scitools.org.uk/iris
+.. _Iris: https://scitools-iris.readthedocs.io
 .. _Ncdata: https://ncdata.readthedocs.io/en/latest/index.html
 .. _ncdata usage examples: https://github.com/pp-mo/ncdata/tree/v0.1.2?tab=readme-ov-file#correct-a-miscoded-attribute-in-iris-input
 

doc/user-guide/plotting.rst

@@ -45,7 +45,7 @@ For more extensive plotting applications consider the following projects:
   dynamic plots (backed by ``Holoviews`` or ``Geoviews``) by adding a ``hvplot``
   accessor to DataArrays.
 
-- `Cartopy <https://scitools.org.uk/cartopy/docs/latest/>`_: Provides cartographic
+- `Cartopy <https://cartopy.readthedocs.io/stable/>`_: Provides cartographic
   tools.
 
 Imports

doc/user-guide/weather-climate.rst

@@ -54,7 +54,7 @@ CF-compliant coordinate variables
 
 .. _`MetPy`: https://unidata.github.io/MetPy/dev/index.html
 .. _`metpy documentation`:	https://unidata.github.io/MetPy/dev/tutorials/xarray_tutorial.html#coordinates
-.. _`Cartopy`: https://scitools.org.uk/cartopy/docs/latest/reference/crs.html
+.. _`Cartopy`: https://cartopy.readthedocs.io/stable/reference/crs.html
 
 .. _CFTimeIndex:
 

doc/whats-new.rst

@@ -6678,7 +6678,7 @@ Enhancements
 
 .. _Zarr: http://zarr.readthedocs.io/
 
-.. _Iris: http://scitools.org.uk/iris
+.. _Iris: http://scitools-iris.readthedocs.io
 
 .. _netcdftime: https://unidata.github.io/netcdftime
 

xarray/backends/api.py

@@ -304,7 +304,7 @@ def _protect_dataset_variables_inplace(dataset: Dataset, cache: bool) -> None:
 
 def _protect_datatree_variables_inplace(tree: DataTree, cache: bool) -> None:
     for node in tree.subtree:
-        _protect_dataset_variables_inplace(node, cache)
+        _protect_dataset_variables_inplace(node.dataset, cache)
 
 
 def _finalize_store(write, store):

xarray/core/datatree.py

@@ -439,7 +439,7 @@ def map(  # type: ignore[override]
 
 
 class DataTree(
-    NamedNode["DataTree"],
+    NamedNode,
     DataTreeAggregations,
     DataTreeOpsMixin,
     TreeAttrAccessMixin,
@@ -559,9 +559,12 @@ def _node_coord_variables_with_index(self) -> Mapping[Hashable, Variable]:
 
     @property
     def _coord_variables(self) -> ChainMap[Hashable, Variable]:
+        # ChainMap is incorrected typed in typeshed (only the first argument
+        # needs to be mutable)
+        # https://github.com/python/typeshed/issues/8430
         return ChainMap(
             self._node_coord_variables,
-            *(p._node_coord_variables_with_index for p in self.parents),
+            *(p._node_coord_variables_with_index for p in self.parents),  # type: ignore[arg-type]
         )
 
     @property
@@ -1340,7 +1343,7 @@ def equals(self, other: DataTree) -> bool:
         )
 
     def _inherited_coords_set(self) -> set[str]:
-        return set(self.parent.coords if self.parent else [])
+        return set(self.parent.coords if self.parent else [])  # type: ignore[arg-type]
 
     def identical(self, other: DataTree) -> bool:
         """
@@ -1563,9 +1566,33 @@ def match(self, pattern: str) -> DataTree:
         }
         return DataTree.from_dict(matching_nodes, name=self.name)
 
+    @overload
     def map_over_datasets(
         self,
-        func: Callable,
+        func: Callable[..., Dataset | None],
+        *args: Any,
+        kwargs: Mapping[str, Any] | None = None,
+    ) -> DataTree: ...
+
+    @overload
+    def map_over_datasets(
+        self,
+        func: Callable[..., tuple[Dataset | None, Dataset | None]],
+        *args: Any,
+        kwargs: Mapping[str, Any] | None = None,
+    ) -> tuple[DataTree, DataTree]: ...
+
+    @overload
+    def map_over_datasets(
+        self,
+        func: Callable[..., tuple[Dataset | None, ...]],
+        *args: Any,
+        kwargs: Mapping[str, Any] | None = None,
+    ) -> tuple[DataTree, ...]: ...
+
+    def map_over_datasets(
+        self,
+        func: Callable[..., Dataset | None | tuple[Dataset | None, ...]],
         *args: Any,
         kwargs: Mapping[str, Any] | None = None,
     ) -> DataTree | tuple[DataTree, ...]:
@@ -1600,8 +1627,7 @@ def map_over_datasets(
         map_over_datasets
         """
         # TODO this signature means that func has no way to know which node it is being called upon - change?
-        # TODO fix this typing error
-        return map_over_datasets(func, self, *args, kwargs=kwargs)
+        return map_over_datasets(func, self, *args, kwargs=kwargs)  # type: ignore[arg-type]
 
     @overload
     def pipe(
@@ -1695,7 +1721,7 @@ def groups(self):
 
     def _unary_op(self, f, *args, **kwargs) -> DataTree:
         # TODO do we need to any additional work to avoid duplication etc.? (Similar to aggregations)
-        return self.map_over_datasets(functools.partial(f, **kwargs), *args)  # type: ignore[return-value]
+        return self.map_over_datasets(functools.partial(f, **kwargs), *args)
 
     def _binary_op(self, other, f, reflexive=False, join=None) -> DataTree:
         from xarray.core.groupby import GroupBy
@@ -1911,7 +1937,7 @@ def to_zarr(
         )
 
     def _get_all_dims(self) -> set:
-        all_dims = set()
+        all_dims: set[Any] = set()
         for node in self.subtree:
             all_dims.update(node._node_dims)
         return all_dims

xarray/core/datatree_io.py

@@ -74,13 +74,13 @@ def _datatree_to_netcdf(
         at_root = node is dt
         ds = node.to_dataset(inherit=write_inherited_coords or at_root)
         group_path = None if at_root else "/" + node.relative_to(dt)
-        ds.to_netcdf(
+        ds.to_netcdf(  # type: ignore[misc]  # Not all union combinations were tried because there are too many unions
             target,
             group=group_path,
             mode=mode,
             encoding=encoding.get(node.path),
             unlimited_dims=unlimited_dims.get(node.path),
-            engine=engine,
+            engine=engine,  # type: ignore[arg-type]
             format=format,
             compute=compute,
             **kwargs,
@@ -134,7 +134,7 @@ def _datatree_to_zarr(
         at_root = node is dt
         ds = node.to_dataset(inherit=write_inherited_coords or at_root)
         group_path = None if at_root else "/" + node.relative_to(dt)
-        ds.to_zarr(
+        ds.to_zarr(  # type: ignore[call-overload]
             store,
             group=group_path,
             mode=mode,