Merge branch 'main' into groupby-save-codes-new

* main:
  absolufy-imports - No relative imports - PEP8 (pydata#7204)
  [skip-ci] whats-new for dev (pydata#7351)
  Whats-new: 2022.12.0 (pydata#7345)
  Fix assign_coords resetting all dimension coords to default index (pydata#7347)

Author: dcherian

.pre-commit-config.yaml

@@ -8,6 +8,11 @@ repos:
       - id: check-yaml
       - id: debug-statements
       - id: mixed-line-ending
+  - repo: https://github.com/MarcoGorelli/absolufy-imports
+    rev: v0.3.1
+    hooks:
+      - id: absolufy-imports
+        name: absolufy-imports
     # This wants to go before isort & flake8
   - repo: https://github.com/PyCQA/autoflake
     rev: "v2.0.0"

asv_bench/benchmarks/dataarray_missing.py

@@ -1,8 +1,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import parameterized, randn, requires_dask
+from asv_bench.benchmarks import parameterized, randn, requires_dask
 
 
 def make_bench_data(shape, frac_nan, chunks):

asv_bench/benchmarks/dataset_io.py

@@ -4,8 +4,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import _skip_slow, randint, randn, requires_dask
+from asv_bench.benchmarks import _skip_slow, randint, randn, requires_dask
 
 try:
     import dask

asv_bench/benchmarks/groupby.py

@@ -2,8 +2,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import _skip_slow, parameterized, requires_dask
+from asv_bench.benchmarks import _skip_slow, parameterized, requires_dask
 
 
 class GroupBy:

asv_bench/benchmarks/indexing.py

@@ -4,8 +4,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import parameterized, randint, randn, requires_dask
+from asv_bench.benchmarks import parameterized, randint, randn, requires_dask
 
 nx = 2000
 ny = 1000

asv_bench/benchmarks/interp.py

@@ -2,8 +2,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import parameterized, randn, requires_dask
+from asv_bench.benchmarks import parameterized, randn, requires_dask
 
 nx = 1500
 ny = 1000

asv_bench/benchmarks/pandas.py

@@ -2,8 +2,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import parameterized
+from asv_bench.benchmarks import parameterized
 
 
 class MultiIndexSeries:

asv_bench/benchmarks/polyfit.py

@@ -1,8 +1,7 @@
 import numpy as np
 
 import xarray as xr
-
-from . import parameterized, randn, requires_dask
+from asv_bench.benchmarks import parameterized, randn, requires_dask
 
 NDEGS = (2, 5, 20)
 NX = (10**2, 10**6)

asv_bench/benchmarks/reindexing.py

@@ -1,8 +1,7 @@
 import numpy as np
 
 import xarray as xr
-
-from . import requires_dask
+from asv_bench.benchmarks import requires_dask
 
 ntime = 500
 nx = 50

asv_bench/benchmarks/rolling.py

@@ -2,8 +2,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import parameterized, randn, requires_dask
+from asv_bench.benchmarks import parameterized, randn, requires_dask
 
 nx = 300
 long_nx = 30000

asv_bench/benchmarks/unstacking.py

@@ -2,8 +2,7 @@
 import pandas as pd
 
 import xarray as xr
-
-from . import requires_dask, requires_sparse
+from asv_bench.benchmarks import requires_dask, requires_sparse
 
 
 class Unstacking:

doc/whats-new.rst

@@ -14,11 +14,48 @@ What's New
 
     np.random.seed(123456)
 
-.. _whats-new.2022.11.1:
 
-v2022.11.1 (unreleased)
+.. _whats-new.2022.12.1:
+
+v2022.12.1 (unreleased)
+-----------------------
+
+New Features
+~~~~~~~~~~~~
+
+
+Breaking changes
+~~~~~~~~~~~~~~~~
+
+
+Deprecations
+~~~~~~~~~~~~
+
+
+Bug fixes
+~~~~~~~~~
+
+
+Documentation
+~~~~~~~~~~~~~
+
+
+Internal Changes
+~~~~~~~~~~~~~~~~
+- Add the pre-commit hook `absolufy-imports` to convert relative xarray imports to
+  absolute imports (:pull:`7204`).
+  By `Jimmy Westling <https://github.com/illviljan>`_.
+
+.. _whats-new.2022.12.0:
+
+v2022.12.0 (2022 Dec 2)
 -----------------------
 
+This release includes a number of bug fixes and experimental support for Zarr V3.
+Thanks to the 16 contributors to this release:
+Deepak Cherian, Francesco Zanetta, Gregory Lee, Illviljan, Joe Hamman, Justus Magin, Luke Conibear, Mark Harfouche, Mathias Hauser,
+Mick, Mike Taves, Sam Levang, Spencer Clark, Tom Nicholas, Wei Ji, templiert
+
 New Features
 ~~~~~~~~~~~~
 - Enable using `offset` and `origin` arguments in :py:meth:`DataArray.resample`
@@ -65,6 +102,8 @@ Bug fixes
   By `Michael Niklas <https://github.com/headtr1ck>`_.
 - Fix multiple reads on fsspec S3 files by resetting file pointer to 0 when reading file streams (:issue:`6813`, :pull:`7304`).
   By `David Hoese <https://github.com/djhoese>`_ and `Wei Ji Leong <https://github.com/weiji14>`_.
+- Fix :py:meth:`Dataset.assign_coords` resetting all dimension coordinates to default (pandas) index (:issue:`7346`, :pull:`7347`).
+  By `Benoît Bovy <https://github.com/benbovy>`_.
 
 Documentation
 ~~~~~~~~~~~~~
@@ -2601,7 +2640,7 @@ Breaking changes
   have removed the internal use of the ``OrderedDict`` in favor of Python's builtin
   ``dict`` object which is now ordered itself. This change will be most obvious when
   interacting with the ``attrs`` property on Dataset and DataArray objects.
-  (:issue:`3380`, :pull:`3389`).  HBy `Joeamman <https://github.com/jhamman>`_.
+  (:issue:`3380`, :pull:`3389`).  By `Joe Hamman <https://github.com/jhamman>`_.
 
 New functions/methods
 ~~~~~~~~~~~~~~~~~~~~~

xarray/__init__.py

@@ -1,22 +1,22 @@
-from . import testing, tutorial
-from .backends.api import (
+from xarray import testing, tutorial
+from xarray.backends.api import (
     load_dataarray,
     load_dataset,
     open_dataarray,
     open_dataset,
     open_mfdataset,
     save_mfdataset,
 )
-from .backends.rasterio_ import open_rasterio
-from .backends.zarr import open_zarr
-from .coding.cftime_offsets import cftime_range, date_range, date_range_like
-from .coding.cftimeindex import CFTimeIndex
-from .coding.frequencies import infer_freq
-from .conventions import SerializationWarning, decode_cf
-from .core.alignment import align, broadcast
-from .core.combine import combine_by_coords, combine_nested
-from .core.common import ALL_DIMS, full_like, ones_like, zeros_like
-from .core.computation import (
+from xarray.backends.rasterio_ import open_rasterio
+from xarray.backends.zarr import open_zarr
+from xarray.coding.cftime_offsets import cftime_range, date_range, date_range_like
+from xarray.coding.cftimeindex import CFTimeIndex
+from xarray.coding.frequencies import infer_freq
+from xarray.conventions import SerializationWarning, decode_cf
+from xarray.core.alignment import align, broadcast
+from xarray.core.combine import combine_by_coords, combine_nested
+from xarray.core.common import ALL_DIMS, full_like, ones_like, zeros_like
+from xarray.core.computation import (
     apply_ufunc,
     corr,
     cov,
@@ -26,15 +26,18 @@
     unify_chunks,
     where,
 )
-from .core.concat import concat
-from .core.dataarray import DataArray
-from .core.dataset import Dataset
-from .core.extensions import register_dataarray_accessor, register_dataset_accessor
-from .core.merge import Context, MergeError, merge
-from .core.options import get_options, set_options
-from .core.parallel import map_blocks
-from .core.variable import Coordinate, IndexVariable, Variable, as_variable
-from .util.print_versions import show_versions
+from xarray.core.concat import concat
+from xarray.core.dataarray import DataArray
+from xarray.core.dataset import Dataset
+from xarray.core.extensions import (
+    register_dataarray_accessor,
+    register_dataset_accessor,
+)
+from xarray.core.merge import Context, MergeError, merge
+from xarray.core.options import get_options, set_options
+from xarray.core.parallel import map_blocks
+from xarray.core.variable import Coordinate, IndexVariable, Variable, as_variable
+from xarray.util.print_versions import show_versions
 
 try:
     from importlib.metadata import version as _version

xarray/backends/__init__.py

@@ -3,19 +3,26 @@
 DataStores provide a uniform interface for saving and loading data in different
 formats. They should not be used directly, but rather through Dataset objects.
 """
-from .cfgrib_ import CfGribDataStore
-from .common import AbstractDataStore, BackendArray, BackendEntrypoint
-from .file_manager import CachingFileManager, DummyFileManager, FileManager
-from .h5netcdf_ import H5netcdfBackendEntrypoint, H5NetCDFStore
-from .memory import InMemoryDataStore
-from .netCDF4_ import NetCDF4BackendEntrypoint, NetCDF4DataStore
-from .plugins import list_engines
-from .pseudonetcdf_ import PseudoNetCDFBackendEntrypoint, PseudoNetCDFDataStore
-from .pydap_ import PydapBackendEntrypoint, PydapDataStore
-from .pynio_ import NioDataStore
-from .scipy_ import ScipyBackendEntrypoint, ScipyDataStore
-from .store import StoreBackendEntrypoint
-from .zarr import ZarrBackendEntrypoint, ZarrStore
+from xarray.backends.cfgrib_ import CfGribDataStore
+from xarray.backends.common import AbstractDataStore, BackendArray, BackendEntrypoint
+from xarray.backends.file_manager import (
+    CachingFileManager,
+    DummyFileManager,
+    FileManager,
+)
+from xarray.backends.h5netcdf_ import H5netcdfBackendEntrypoint, H5NetCDFStore
+from xarray.backends.memory import InMemoryDataStore
+from xarray.backends.netCDF4_ import NetCDF4BackendEntrypoint, NetCDF4DataStore
+from xarray.backends.plugins import list_engines
+from xarray.backends.pseudonetcdf_ import (
+    PseudoNetCDFBackendEntrypoint,
+    PseudoNetCDFDataStore,
+)
+from xarray.backends.pydap_ import PydapBackendEntrypoint, PydapDataStore
+from xarray.backends.pynio_ import NioDataStore
+from xarray.backends.scipy_ import ScipyBackendEntrypoint, ScipyDataStore
+from xarray.backends.store import StoreBackendEntrypoint
+from xarray.backends.zarr import ZarrBackendEntrypoint, ZarrStore
 
 __all__ = [
     "AbstractDataStore",

xarray/backends/api.py

@@ -25,20 +25,20 @@
 
 import numpy as np
 
-from .. import backends, conventions
-from ..core import indexing
-from ..core.combine import (
+from xarray import backends, conventions
+from xarray.backends import plugins
+from xarray.backends.common import AbstractDataStore, ArrayWriter, _normalize_path
+from xarray.backends.locks import _get_scheduler
+from xarray.core import indexing
+from xarray.core.combine import (
     _infer_concat_order_from_positions,
     _nested_combine,
     combine_by_coords,
 )
-from ..core.dataarray import DataArray
-from ..core.dataset import Dataset, _get_chunk, _maybe_chunk
-from ..core.indexes import Index
-from ..core.utils import is_remote_uri
-from . import plugins
-from .common import AbstractDataStore, ArrayWriter, _normalize_path
-from .locks import _get_scheduler
+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.utils import is_remote_uri
 
 if TYPE_CHECKING:
     try:
@@ -47,13 +47,13 @@
         Delayed = None  # type: ignore
     from io import BufferedIOBase
 
-    from ..core.types import (
+    from xarray.backends.common import BackendEntrypoint
+    from xarray.core.types import (
         CombineAttrsOptions,
         CompatOptions,
         JoinOptions,
         NestedSequence,
     )
-    from .common import BackendEntrypoint
 
     T_NetcdfEngine = Literal["netcdf4", "scipy", "h5netcdf"]
     T_Engine = Union[

xarray/backends/cfgrib_.py

@@ -5,18 +5,18 @@
 
 import numpy as np
 
-from ..core import indexing
-from ..core.utils import Frozen, FrozenDict, close_on_error, module_available
-from ..core.variable import Variable
-from .common import (
+from xarray.backends.common import (
     BACKEND_ENTRYPOINTS,
     AbstractDataStore,
     BackendArray,
     BackendEntrypoint,
     _normalize_path,
 )
-from .locks import SerializableLock, ensure_lock
-from .store import StoreBackendEntrypoint
+from xarray.backends.locks import SerializableLock, ensure_lock
+from xarray.backends.store import StoreBackendEntrypoint
+from xarray.core import indexing
+from xarray.core.utils import Frozen, FrozenDict, close_on_error, module_available
+from xarray.core.variable import Variable
 
 # FIXME: Add a dedicated lock, even if ecCodes is supposed to be thread-safe
 #   in most circumstances. See:

xarray/backends/common.py

@@ -8,10 +8,10 @@
 
 import numpy as np
 
-from ..conventions import cf_encoder
-from ..core import indexing
-from ..core.pycompat import is_duck_dask_array
-from ..core.utils import FrozenDict, NdimSizeLenMixin, is_remote_uri
+from xarray.conventions import cf_encoder
+from xarray.core import indexing
+from xarray.core.pycompat import is_duck_dask_array
+from xarray.core.utils import FrozenDict, NdimSizeLenMixin, is_remote_uri
 
 if TYPE_CHECKING:
     from io import BufferedIOBase

xarray/backends/file_manager.py

@@ -7,10 +7,10 @@
 import warnings
 from typing import Any, Hashable
 
-from ..core import utils
-from ..core.options import OPTIONS
-from .locks import acquire
-from .lru_cache import LRUCache
+from xarray.backends.locks import acquire
+from xarray.backends.lru_cache import LRUCache
+from xarray.core import utils
+from xarray.core.options import OPTIONS
 
 # Global cache for storing open files.
 FILE_CACHE: LRUCache[Any, io.IOBase] = LRUCache(