Merge branch 'master' into fix_sel_float

Author: HasanAhmadQ7

ci/requirements/py36-hypothesis.yml

@@ -22,6 +22,7 @@ dependencies:
   - seaborn
   - toolz
   - rasterio
+  - boto3
   - bottleneck
   - zarr
   - pydap

ci/requirements/py36.yml

@@ -22,12 +22,15 @@ dependencies:
   - seaborn
   - toolz
   - rasterio
+  - boto3
   - bottleneck
   - zarr
   - pseudonetcdf>=3.0.1
   - cfgrib>=0.9.2
   - cdms2
-  - pynio
+  # Disabled due to conflicting dependencies:
+  # https://github.com/pydata/xarray/issues/3154
+  # - pynio
   - iris>=1.10
   - pydap
   - lxml

ci/requirements/py37-windows.yml

@@ -22,4 +22,5 @@ dependencies:
   - seaborn
   - toolz
   - rasterio
+  - boto3
   - zarr

ci/requirements/py37.yml

@@ -23,6 +23,7 @@ dependencies:
   - seaborn
   - toolz
   - rasterio
+  - boto3
   - bottleneck
   - zarr
   - pseudonetcdf>=3.0.1

doc/conf.py

@@ -66,6 +66,7 @@
     'sphinx.ext.intersphinx',
     'sphinx.ext.extlinks',
     'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
     'numpydoc',
     'IPython.sphinxext.ipython_directive',
     'IPython.sphinxext.ipython_console_highlighting',
@@ -83,6 +84,10 @@
                        }
 
 autosummary_generate = True
+autodoc_typehints = 'none'
+
+napoleon_use_param = True
+napoleon_use_rtype = True   
 
 numpydoc_class_members_toctree = True
 numpydoc_show_class_members = False

doc/io.rst

@@ -609,8 +609,9 @@ store is already present at that path, an error will be raised, preventing it
 from being overwritten. To override this behavior and overwrite an existing
 store, add ``mode='w'`` when invoking ``to_zarr``.
 
-It is also possible to append to an existing store. For that, add ``mode='a'``
-and set ``append_dim`` to the name of the dimension along which to append.
+It is also possible to append to an existing store. For that, set
+``append_dim`` to the name of the dimension along which to append. ``mode``
+can be omitted as it will internally be set to ``'a'``.
 
 .. ipython:: python
    :suppress:
@@ -628,7 +629,7 @@ and set ``append_dim`` to the name of the dimension along which to append.
                      coords={'x': [10, 20, 30, 40],
                              'y': [1,2,3,4,5],
                              't': pd.date_range('2001-01-03', periods=2)})
-    ds2.to_zarr('path/to/directory.zarr', mode='a', append_dim='t')
+    ds2.to_zarr('path/to/directory.zarr', append_dim='t')
 
 To store variable length strings use ``dtype=object``.
 

doc/whats-new.rst

@@ -28,13 +28,28 @@ New functions/methods
   By `Deepak Cherian <https://github.com/dcherian>`_ and `David Mertz 
   <http://github.com/DavidMertz>`_.
 
+- The xarray package is now discoverably by mypy (although typing hints
+  coverage is not complete yet). mypy users can now remove from their setup.cfg
+  the lines::
+
+    [mypy-xarray]
+    ignore_missing_imports = True
+
+   By `Guido Imperiale <https://github.com/crusaderky>`_
+
 Enhancements
 ~~~~~~~~~~~~
 
+- In :py:meth:`~xarray.Dataset.to_zarr`, passing ``mode`` is not mandatory if
+  ``append_dim`` is set, as it will automatically be set to ``'a'`` internally.
+  By `David Brochart <https://github.com/davidbrochart>`_.
+
 Bug fixes
 ~~~~~~~~~
-
-- Improved error handling and documentation for `.expand_dims()` 
+- Fix regression introduced in v0.12.2 where ``copy(deep=True)`` would convert
+  unicode indices to dtype=object (:issue:`3094`).
+  By `Guido Imperiale <https://github.com/crusaderky>`_.
+- Improved error handling and documentation for `.expand_dims()`
   read-only view.
 - Fix tests for big-endian systems (:issue:`3125`).
   By `Graham Inggs <https://github.com/ginggs>`_.
@@ -44,6 +59,13 @@ Bug fixes
 - Fix KeyError that arises when using .sel method with float values
   different from coords float type (:issue:`3137`).
   By `Hasan Ahmad <https://github.com/HasanAhmadQ7>`_.
+- Fixed bug in ``combine_by_coords()`` causing a `ValueError` if the input had
+  an unused dimension with coordinates which were not monotonic (:issue:`3150`).
+  By `Tom Nicholas <http://github.com/TomNicholas>`_.
+- Fixed crash when applying ``distributed.Client.compute()`` to a DataArray
+  (:issue:`3171`). By `Guido Imperiale <https://github.com/crusaderky>`_.
+
+
 .. _whats-new.0.12.3:
 
 v0.12.3 (10 July 2019)
@@ -65,7 +87,6 @@ New functions/methods
   (:issue:`3026`).
   By `Julia Kent <https://github.com/jukent>`_.
 
-
 Enhancements
 ~~~~~~~~~~~~
 
@@ -85,6 +106,8 @@ Bug fixes
 - Fix HDF5 error that could arise when reading multiple groups from a file at
   once (:issue:`2954`).
   By `Stephan Hoyer <https://github.com/shoyer>`_.
+- Better error message when using groupby on an empty DataArray (:issue:`3037`).
+  By `Hasan Ahmad <https://github.com/HasanAhmadQ7>`_.
 
 .. _whats-new.0.12.2:
 

setup.py

@@ -104,4 +104,4 @@
       tests_require=TESTS_REQUIRE,
       url=URL,
       packages=find_packages(),
-      package_data={'xarray': ['tests/data/*']})
+      package_data={'xarray': ['py.typed', 'tests/data/*']})

xarray/backends/api.py

@@ -1102,7 +1102,7 @@ def _validate_append_dim_and_encoding(ds_to_append, store, append_dim,
                 )
 
 
-def to_zarr(dataset, store=None, mode='w-', synchronizer=None, group=None,
+def to_zarr(dataset, store=None, mode=None, synchronizer=None, group=None,
             encoding=None, compute=True, consolidated=False, append_dim=None):
     """This function creates an appropriate datastore for writing a dataset to
     a zarr ztore
@@ -1118,7 +1118,7 @@ def to_zarr(dataset, store=None, mode='w-', synchronizer=None, group=None,
     _validate_dataset_names(dataset)
     _validate_attrs(dataset)
 
-    if mode == "a":
+    if mode == 'a':
         _validate_datatypes_for_zarr_append(dataset)
         _validate_append_dim_and_encoding(dataset, store, append_dim,
                                           group=group,

xarray/core/alignment.py

@@ -3,7 +3,16 @@
 import warnings
 from collections import OrderedDict, defaultdict
 from contextlib import suppress
-from typing import Any, Mapping, Optional, Tuple
+from typing import (
+    Any,
+    Dict,
+    Hashable,
+    Mapping,
+    Optional,
+    Tuple,
+    Union,
+    TYPE_CHECKING,
+)
 
 import numpy as np
 import pandas as pd
@@ -13,6 +22,10 @@
 from .utils import is_dict_like, is_full_slice
 from .variable import IndexVariable, Variable
 
+if TYPE_CHECKING:
+    from .dataarray import DataArray
+    from .dataset import Dataset
+
 
 def _get_joiner(join):
     if join == 'outer':
@@ -169,8 +182,8 @@ def deep_align(objects, join='inner', copy=True, indexes=None,
 
     This function is not public API.
     """
-    from .dataarray import DataArray
-    from .dataset import Dataset
+    from .dataarray import DataArray  # noqa: F811
+    from .dataset import Dataset  # noqa: F811
 
     if indexes is None:
         indexes = {}
@@ -222,7 +235,10 @@ def is_alignable(obj):
     return out
 
 
-def reindex_like_indexers(target, other):
+def reindex_like_indexers(
+    target: Union['DataArray', 'Dataset'],
+    other: Union['DataArray', 'Dataset'],
+) -> Dict[Hashable, pd.Index]:
     """Extract indexers to align target with other.
 
     Not public API.
@@ -236,7 +252,8 @@ def reindex_like_indexers(target, other):
 
     Returns
     -------
-    Dict[Any, pandas.Index] providing indexes for reindex keyword arguments.
+    Dict[Hashable, pandas.Index] providing indexes for reindex keyword
+    arguments.
 
     Raises
     ------
@@ -310,7 +327,7 @@ def reindex_variables(
     new_indexes : OrderedDict
         Dict of indexes associated with the reindexed variables.
     """
-    from .dataarray import DataArray
+    from .dataarray import DataArray  # noqa: F811
 
     # create variables for the new dataset
     reindexed = OrderedDict()  # type: OrderedDict[Any, Variable]
@@ -407,8 +424,8 @@ def _get_broadcast_dims_map_common_coords(args, exclude):
 
 def _broadcast_helper(arg, exclude, dims_map, common_coords):
 
-    from .dataarray import DataArray
-    from .dataset import Dataset
+    from .dataarray import DataArray  # noqa: F811
+    from .dataset import Dataset  # noqa: F811
 
     def _set_dims(var):
         # Add excluded dims to a copy of dims_map

xarray/core/combine.py

@@ -501,14 +501,13 @@ def combine_by_coords(datasets, compat='no_conflicts', data_vars='all',
                                    fill_value=fill_value)
 
         # Check the overall coordinates are monotonically increasing
-        for dim in concatenated.dims:
-            if dim in concatenated:
-                indexes = concatenated.indexes.get(dim)
-                if not (indexes.is_monotonic_increasing
-                        or indexes.is_monotonic_decreasing):
-                    raise ValueError("Resulting object does not have monotonic"
-                                     " global indexes along dimension {}"
-                                     .format(dim))
+        for dim in concat_dims:
+            indexes = concatenated.indexes.get(dim)
+            if not (indexes.is_monotonic_increasing
+                    or indexes.is_monotonic_decreasing):
+                raise ValueError("Resulting object does not have monotonic"
+                                 " global indexes along dimension {}"
+                                 .format(dim))
         concatenated_grouped_by_data_vars.append(concatenated)
 
     return merge(concatenated_grouped_by_data_vars, compat=compat,

xarray/core/common.py

@@ -3,7 +3,7 @@
 from textwrap import dedent
 from typing import (
     Any, Callable, Hashable, Iterable, Iterator, List, Mapping, MutableMapping,
-    Optional, Tuple, TypeVar, Union)
+    Tuple, TypeVar, Union)
 
 import numpy as np
 import pandas as pd
@@ -101,7 +101,7 @@ def __int__(self: Any) -> int:
     def __complex__(self: Any) -> complex:
         return complex(self.values)
 
-    def __array__(self: Any, dtype: Optional[DTypeLike] = None) -> np.ndarray:
+    def __array__(self: Any, dtype: DTypeLike = None) -> np.ndarray:
         return np.asarray(self.values, dtype=dtype)
 
     def __repr__(self) -> str:
@@ -448,7 +448,7 @@ def pipe(self, func: Union[Callable[..., T], Tuple[Callable[..., T], str]],
             return func(self, *args, **kwargs)
 
     def groupby(self, group, squeeze: bool = True,
-                restore_coord_dims: Optional[bool] = None):
+                restore_coord_dims: bool = None):
         """Returns a GroupBy object for performing grouped operations.
 
         Parameters
@@ -501,7 +501,7 @@ def groupby(self, group, squeeze: bool = True,
     def groupby_bins(self, group, bins, right: bool = True, labels=None,
                      precision: int = 3, include_lowest: bool = False,
                      squeeze: bool = True,
-                     restore_coord_dims: Optional[bool] = None):
+                     restore_coord_dims: bool = None):
         """Returns a GroupBy object for performing grouped operations.
 
         Rather than using all unique values of `group`, the values are discretized
@@ -557,8 +557,8 @@ def groupby_bins(self, group, bins, right: bool = True, labels=None,
                                              'include_lowest':
                                                  include_lowest})
 
-    def rolling(self, dim: Optional[Mapping[Hashable, int]] = None,
-                min_periods: Optional[int] = None, center: bool = False,
+    def rolling(self, dim: Mapping[Hashable, int] = None,
+                min_periods: int = None, center: bool = False,
                 **window_kwargs: int):
         """
         Rolling window object.
@@ -621,7 +621,7 @@ def rolling(self, dim: Optional[Mapping[Hashable, int]] = None,
 
     def rolling_exp(
         self,
-        window: Optional[Mapping[Hashable, int]] = None,
+        window: Mapping[Hashable, int] = None,
         window_type: str = 'span',
         **window_kwargs
     ):
@@ -658,7 +658,7 @@ def rolling_exp(
 
         return self._rolling_exp_cls(self, window, window_type)
 
-    def coarsen(self, dim: Optional[Mapping[Hashable, int]] = None,
+    def coarsen(self, dim: Mapping[Hashable, int] = None,
                 boundary: str = 'exact',
                 side: Union[str, Mapping[Hashable, str]] = 'left',
                 coord_func: str = 'mean',
@@ -721,11 +721,11 @@ def coarsen(self, dim: Optional[Mapping[Hashable, int]] = None,
             self, dim, boundary=boundary, side=side,
             coord_func=coord_func)
 
-    def resample(self, indexer: Optional[Mapping[Hashable, str]] = None,
-                 skipna=None, closed: Optional[str] = None,
-                 label: Optional[str] = None,
-                 base: int = 0, keep_attrs: Optional[bool] = None,
-                 loffset=None, restore_coord_dims: Optional[bool] = None,
+    def resample(self, indexer: Mapping[Hashable, str] = None,
+                 skipna=None, closed: str = None,
+                 label: str = None,
+                 base: int = 0, keep_attrs: bool = None,
+                 loffset=None, restore_coord_dims: bool = None,
                  **indexer_kwargs: str):
         """Returns a Resample object for performing resampling operations.
 
@@ -1003,7 +1003,7 @@ def __getitem__(self, value):
         raise NotImplementedError
 
 
-def full_like(other, fill_value, dtype: Optional[DTypeLike] = None):
+def full_like(other, fill_value, dtype: DTypeLike = None):
     """Return a new object with the same shape and type as a given object.
 
     Parameters
@@ -1044,7 +1044,7 @@ def full_like(other, fill_value, dtype: Optional[DTypeLike] = None):
 
 
 def _full_like_variable(other, fill_value,
-                        dtype: Optional[DTypeLike] = None):
+                        dtype: DTypeLike = None):
     """Inner function of full_like, where other must be a variable
     """
     from .variable import Variable
@@ -1061,13 +1061,13 @@ def _full_like_variable(other, fill_value,
     return Variable(dims=other.dims, data=data, attrs=other.attrs)
 
 
-def zeros_like(other, dtype: Optional[DTypeLike] = None):
+def zeros_like(other, dtype: DTypeLike = None):
     """Shorthand for full_like(other, 0, dtype)
     """
     return full_like(other, 0, dtype)
 
 
-def ones_like(other, dtype: Optional[DTypeLike] = None):
+def ones_like(other, dtype: DTypeLike = None):
     """Shorthand for full_like(other, 1, dtype)
     """
     return full_like(other, 1, dtype)