Merge remote-tracking branch 'upstream/main' into zarr-v3

.github/stale.yml

@@ -1,7 +1,7 @@
 # Configuration for probot-stale - https://github.com/probot/stale
 
 # Number of days of inactivity before an Issue or Pull Request becomes stale
-daysUntilStale: 700  # start with a large number and reduce shortly
+daysUntilStale: 600 # start with a large number and reduce shortly
 
 # Number of days of inactivity before an Issue or Pull Request with the stale label is closed.
 # Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale.
@@ -31,6 +31,9 @@ markComment: |
 
   If this issue remains relevant, please comment here or remove the `stale` label; otherwise it will be marked as closed automatically
 
+closeComment: |
+  The stalebot didn't hear anything for a while, so it closed this. Please reopen if this is still an issue.
+
 # Comment to post when removing the stale label.
 # unmarkComment: >
 #   Your comment here.
@@ -40,8 +43,7 @@ markComment: |
 #   Your comment here.
 
 # Limit the number of actions per hour, from 1-30. Default is 30
-limitPerRun: 1  # start with a small number
-
+limitPerRun: 2 # start with a small number
 
 # Limit to only `issues` or `pulls`
 # only: issues

.github/workflows/benchmarks.yml

@@ -67,7 +67,7 @@ jobs:
           cp benchmarks/README_CI.md benchmarks.log .asv/results/
         working-directory: ${{ env.ASV_DIR }}
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: always()
         with:
           name: asv-benchmark-results-${{ runner.os }}

.github/workflows/ci-additional.yaml

@@ -109,7 +109,7 @@ jobs:
              $PYTEST_EXTRA_FLAGS
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3.0.0
         with:
           file: ./coverage.xml
           flags: unittests,${{ matrix.env }}

.github/workflows/ci.yaml

@@ -98,13 +98,13 @@ jobs:
 
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: Test results for ${{ runner.os }}-${{ matrix.python-version }}
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3.0.0
         with:
           file: ./coverage.xml
           flags: unittests
@@ -118,7 +118,7 @@ jobs:
     if: github.repository == 'pydata/xarray'
     steps:
       - name: Upload
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: Event File
           path: ${{ github.event_path }}

.github/workflows/pypi-release.yaml

@@ -41,7 +41,7 @@ jobs:
           else
             echo "✅ Looks good"
           fi
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: releases
           path: dist
@@ -54,7 +54,7 @@ jobs:
         name: Install Python
         with:
           python-version: 3.8
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: releases
           path: dist
@@ -85,7 +85,7 @@ jobs:
     if: github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: releases
           path: dist

.github/workflows/upstream-dev-ci.yaml

@@ -92,7 +92,7 @@ jobs:
           && steps.status.outcome == 'failure'
           && github.event_name == 'schedule'
           && github.repository == 'pydata/xarray'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: output-${{ matrix.python-version }}-log
           path: output-${{ matrix.python-version }}-log
@@ -114,7 +114,7 @@ jobs:
       - uses: actions/setup-python@v3
         with:
           python-version: "3.x"
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           path: /tmp/workspace/logs
       - name: Move all log files into a single directory

doc/whats-new.rst

@@ -36,6 +36,9 @@ New Features
   elements which trigger summarization rather than full repr in (numpy) array
   detailed views of the html repr (:pull:`6400`).
   By `Benoît Bovy <https://github.com/benbovy>`_.
+- Allow passing chunks in **kwargs form to :py:meth:`Dataset.chunk`, :py:meth:`DataArray.chunk`, and
+  :py:meth:`Variable.chunk`. (:pull:`6471`)
+  By `Tom Nicholas <https://github.com/TomNicholas>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~

xarray/conventions.py

@@ -770,7 +770,7 @@ def _encode_coordinates(variables, attributes, non_dim_coord_names):
         # this will copy coordinates from encoding to attrs if "coordinates" in attrs
         # after the next line, "coordinates" is never in encoding
         # we get support for attrs["coordinates"] for free.
-        coords_str = pop_to(encoding, attrs, "coordinates")
+        coords_str = pop_to(encoding, attrs, "coordinates") or attrs.get("coordinates")
         if not coords_str and variable_coordinates[name]:
             coordinates_text = " ".join(
                 str(coord_name)

xarray/core/dataarray.py

@@ -1113,6 +1113,7 @@ def chunk(
         name_prefix: str = "xarray-",
         token: str = None,
         lock: bool = False,
+        **chunks_kwargs: Any,
     ) -> DataArray:
         """Coerce this array's data into a dask arrays with the given chunks.
 
@@ -1136,13 +1137,28 @@ def chunk(
         lock : optional
             Passed on to :py:func:`dask.array.from_array`, if the array is not
             already as dask array.
+        **chunks_kwargs : {dim: chunks, ...}, optional
+            The keyword arguments form of ``chunks``.
+            One of chunks or chunks_kwargs must be provided.
 
         Returns
         -------
         chunked : xarray.DataArray
         """
-        if isinstance(chunks, (tuple, list)):
+        if chunks is None:
+            warnings.warn(
+                "None value for 'chunks' is deprecated. "
+                "It will raise an error in the future. Use instead '{}'",
+                category=FutureWarning,
+            )
+            chunks = {}
+
+        if isinstance(chunks, (float, str, int)):
+            chunks = dict.fromkeys(self.dims, chunks)
+        elif isinstance(chunks, (tuple, list)):
             chunks = dict(zip(self.dims, chunks))
+        else:
+            chunks = either_dict_or_kwargs(chunks, chunks_kwargs, "chunk")
 
         ds = self._to_temp_dataset().chunk(
             chunks, name_prefix=name_prefix, token=token, lock=lock

xarray/core/dataset.py

@@ -2000,6 +2000,7 @@ def chunk(
         name_prefix: str = "xarray-",
         token: str = None,
         lock: bool = False,
+        **chunks_kwargs: Any,
     ) -> Dataset:
         """Coerce all arrays in this dataset into dask arrays with the given
         chunks.
@@ -2013,7 +2014,7 @@ def chunk(
 
         Parameters
         ----------
-        chunks : int, "auto" or mapping of hashable to int, optional
+        chunks : int, tuple of int, "auto" or mapping of hashable to int, optional
             Chunk sizes along each dimension, e.g., ``5``, ``"auto"``, or
             ``{"x": 5, "y": 5}``.
         name_prefix : str, optional
@@ -2023,6 +2024,9 @@ def chunk(
         lock : optional
             Passed on to :py:func:`dask.array.from_array`, if the array is not
             already as dask array.
+        **chunks_kwargs : {dim: chunks, ...}, optional
+            The keyword arguments form of ``chunks``.
+            One of chunks or chunks_kwargs must be provided
 
         Returns
         -------
@@ -2034,7 +2038,7 @@ def chunk(
         Dataset.chunksizes
         xarray.unify_chunks
         """
-        if chunks is None:
+        if chunks is None and chunks_kwargs is None:
             warnings.warn(
                 "None value for 'chunks' is deprecated. "
                 "It will raise an error in the future. Use instead '{}'",
@@ -2044,6 +2048,8 @@ def chunk(
 
         if isinstance(chunks, (Number, str, int)):
             chunks = dict.fromkeys(self.dims, chunks)
+        else:
+            chunks = either_dict_or_kwargs(chunks, chunks_kwargs, "chunk")
 
         bad_dims = chunks.keys() - self.dims.keys()
         if bad_dims:

xarray/core/utils.py

@@ -266,7 +266,7 @@ def either_dict_or_kwargs(
     kw_kwargs: Mapping[str, T],
     func_name: str,
 ) -> Mapping[Hashable, T]:
-    if pos_kwargs is None:
+    if pos_kwargs is None or pos_kwargs == {}:
         # Need an explicit cast to appease mypy due to invariance; see
         # https://github.com/python/mypy/issues/6228
         return cast(Mapping[Hashable, T], kw_kwargs)

xarray/core/variable.py

@@ -5,7 +5,7 @@
 import numbers
 import warnings
 from datetime import timedelta
-from typing import TYPE_CHECKING, Any, Hashable, Mapping, Sequence
+from typing import TYPE_CHECKING, Any, Hashable, Literal, Mapping, Sequence
 
 import numpy as np
 import pandas as pd
@@ -1012,7 +1012,19 @@ def chunksizes(self) -> Mapping[Any, tuple[int, ...]]:
 
     _array_counter = itertools.count()
 
-    def chunk(self, chunks={}, name=None, lock=False):
+    def chunk(
+        self,
+        chunks: (
+            int
+            | Literal["auto"]
+            | tuple[int, ...]
+            | tuple[tuple[int, ...], ...]
+            | Mapping[Any, None | int | tuple[int, ...]]
+        ) = {},
+        name: str = None,
+        lock: bool = False,
+        **chunks_kwargs: Any,
+    ) -> Variable:
         """Coerce this array's data into a dask array with the given chunks.
 
         If this variable is a non-dask array, it will be converted to dask
@@ -1034,6 +1046,9 @@ def chunk(self, chunks={}, name=None, lock=False):
         lock : optional
             Passed on to :py:func:`dask.array.from_array`, if the array is not
             already as dask array.
+        **chunks_kwargs : {dim: chunks, ...}, optional
+            The keyword arguments form of ``chunks``.
+            One of chunks or chunks_kwargs must be provided.
 
         Returns
         -------
@@ -1049,6 +1064,11 @@ def chunk(self, chunks={}, name=None, lock=False):
             )
             chunks = {}
 
+        if isinstance(chunks, (float, str, int, tuple, list)):
+            pass  # dask.array.from_array can handle these directly
+        else:
+            chunks = either_dict_or_kwargs(chunks, chunks_kwargs, "chunk")
+
         if utils.is_dict_like(chunks):
             chunks = {self.get_axis_num(dim): chunk for dim, chunk in chunks.items()}
 

xarray/tests/test_conventions.py

@@ -128,6 +128,25 @@ def test_multidimensional_coordinates(self) -> None:
         # Should not have any global coordinates.
         assert "coordinates" not in attrs
 
+    def test_var_with_coord_attr(self) -> None:
+        # regression test for GH6310
+        # don't overwrite user-defined "coordinates" attributes
+        orig = Dataset(
+            {"values": ("time", np.zeros(2), {"coordinates": "time lon lat"})},
+            coords={
+                "time": ("time", np.zeros(2)),
+                "lat": ("time", np.zeros(2)),
+                "lon": ("time", np.zeros(2)),
+            },
+        )
+        # Encode the coordinates, as they would be in a netCDF output file.
+        enc, attrs = conventions.encode_dataset_coordinates(orig)
+        # Make sure we have the right coordinates for each variable.
+        values_coords = enc["values"].attrs.get("coordinates", "")
+        assert set(values_coords.split()) == {"time", "lat", "lon"}
+        # Should not have any global coordinates.
+        assert "coordinates" not in attrs
+
     def test_do_not_overwrite_user_coordinates(self) -> None:
         orig = Dataset(
             coords={"x": [0, 1, 2], "y": ("x", [5, 6, 7]), "z": ("x", [8, 9, 10])},

xarray/tests/test_dataarray.py

@@ -804,6 +804,11 @@ def test_chunk(self):
         assert isinstance(blocked.data, da.Array)
         assert "testname_" in blocked.data.name
 
+        # test kwargs form of chunks
+        blocked = unblocked.chunk(dim_0=3, dim_1=3)
+        assert blocked.chunks == ((3,), (3, 1))
+        assert blocked.data.name != first_dask_name
+
     def test_isel(self):
         assert_identical(self.dv[0], self.dv.isel(x=0))
         assert_identical(self.dv, self.dv.isel(x=slice(None)))

xarray/tests/test_dataset.py

@@ -921,6 +921,9 @@ def test_chunk(self):
         expected_chunks = {"dim1": (8,), "dim2": (9,), "dim3": (10,)}
         assert reblocked.chunks == expected_chunks
 
+        # test kwargs form of chunks
+        assert data.chunk(**expected_chunks).chunks == expected_chunks
+
         def get_dask_names(ds):
             return {k: v.data.name for k, v in ds.items()}
 
@@ -947,7 +950,7 @@ def get_dask_names(ds):
         new_dask_names = get_dask_names(reblocked)
         assert reblocked.chunks == expected_chunks
         assert_identical(reblocked, data)
-        # recuhnking with same chunk sizes should not change names
+        # rechunking with same chunk sizes should not change names
         for k, v in new_dask_names.items():
             assert v == orig_dask_names[k]
 

xarray/tests/test_variable.py

@@ -2154,6 +2154,40 @@ def test_coarsen_keep_attrs(self, operation="mean"):
 class TestVariableWithDask(VariableSubclassobjects):
     cls = staticmethod(lambda *args: Variable(*args).chunk())
 
+    def test_chunk(self):
+        unblocked = Variable(["dim_0", "dim_1"], np.ones((3, 4)))
+        assert unblocked.chunks is None
+
+        blocked = unblocked.chunk()
+        assert blocked.chunks == ((3,), (4,))
+        first_dask_name = blocked.data.name
+
+        blocked = unblocked.chunk(chunks=((2, 1), (2, 2)))
+        assert blocked.chunks == ((2, 1), (2, 2))
+        assert blocked.data.name != first_dask_name
+
+        blocked = unblocked.chunk(chunks=(3, 3))
+        assert blocked.chunks == ((3,), (3, 1))
+        assert blocked.data.name != first_dask_name
+
+        # name doesn't change when rechunking by same amount
+        # this fails if ReprObject doesn't have __dask_tokenize__ defined
+        assert unblocked.chunk(2).data.name == unblocked.chunk(2).data.name
+
+        assert blocked.load().chunks is None
+
+        # Check that kwargs are passed
+        import dask.array as da
+
+        blocked = unblocked.chunk(name="testname_")
+        assert isinstance(blocked.data, da.Array)
+        assert "testname_" in blocked.data.name
+
+        # test kwargs form of chunks
+        blocked = unblocked.chunk(dim_0=3, dim_1=3)
+        assert blocked.chunks == ((3,), (3, 1))
+        assert blocked.data.name != first_dask_name
+
     @pytest.mark.xfail
     def test_0d_object_array_with_list(self):
         super().test_0d_object_array_with_list()