Merge branch 'master' of github.com:pydata/xarray into ufunc-vectorize-meta

* 'master' of github.com:pydata/xarray:
  Feature/align in dot (pydata#3699)
  ENH: enable `H5NetCDFStore` to work with already open h5netcdf.File a… (pydata#3618)
  One-off isort run (pydata#3705)
  hardcoded xarray.__all__ (pydata#3703)
  Bump mypy to v0.761 (pydata#3704)
  remove DataArray and Dataset constructor deprecations for 0.15  (pydata#3560)
  Tests for variables with units (pydata#3654)

Author: dcherian

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     hooks:
       - id: flake8
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.730  # Must match ci/requirements/*.yml
+    rev: v0.761  # Must match ci/requirements/*.yml
     hooks:
       - id: mypy
   # run these occasionally, ref discussion https://github.com/pydata/xarray/pull/3194

ci/requirements/py36-min-all-deps.yml

@@ -25,7 +25,7 @@ dependencies:
   - iris=2.2
   - lxml=4.4  # Optional dep of pydap
   - matplotlib=3.1
-  - mypy=0.730  # Must match .pre-commit-config.yaml
+  - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis=1.2
   - netcdf4=1.4
   - numba=0.44

ci/requirements/py36.yml

@@ -21,7 +21,7 @@ dependencies:
   - iris
   - lxml    # optional dep of pydap
   - matplotlib
-  - mypy=0.730  # Must match .pre-commit-config.yaml
+  - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis
   - netcdf4
   - numba

ci/requirements/py37-windows.yml

@@ -21,7 +21,7 @@ dependencies:
   - iris
   - lxml    # Optional dep of pydap
   - matplotlib
-  - mypy=0.730  # Must match .pre-commit-config.yaml
+  - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis
   - netcdf4
   - numba

ci/requirements/py37.yml

@@ -21,7 +21,7 @@ dependencies:
   - iris
   - lxml    # Optional dep of pydap
   - matplotlib
-  - mypy=0.730  # Must match .pre-commit-config.yaml
+  - mypy=0.761  # Must match .pre-commit-config.yaml
   - nc-time-axis
   - netcdf4
   - numba

doc/conf.py

@@ -25,7 +25,7 @@
 os.environ["PYTHONPATH"] = str(root)
 sys.path.insert(0, str(root))
 
-import xarray
+import xarray  # isort:skip
 
 allowed_failures = set()
 

doc/whats-new.rst

@@ -22,9 +22,23 @@ v0.15.0 (unreleased)
 Breaking changes
 ~~~~~~~~~~~~~~~~
 - Bumped minimum ``dask`` version to 2.2.
+- Remove ``compat`` and ``encoding`` kwargs from ``DataArray``, which
+  have been deprecated since 0.12. (:pull:`3650`). 
+  Instead, specify the encoding when writing to disk or set 
+  the ``encoding`` attribute directly.
+  By `Maximilian Roos <https://github.com/max-sixty>`_
+- :py:func:`xarray.dot`, :py:meth:`DataArray.dot`, and the ``@`` operator now
+  use ``align="inner"`` (except when ``xarray.set_options(arithmetic_join="exact")``;
+  :issue:`3694`) by `Mathias Hauser <https://github.com/mathause>`_.
+
 
 New Features
 ~~~~~~~~~~~~
+- Support using an existing, opened h5netcdf ``File`` with
+  :py:class:`~xarray.backends.H5NetCDFStore`. This permits creating an
+  :py:class:`~xarray.Dataset` from a h5netcdf ``File`` that has been opened
+  using other means (:issue:`3618`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 - Implement :py:func:`median` and :py:func:`nanmedian` for dask arrays. This works by rechunking
   to a single chunk along all reduction axes. (:issue:`2999`).
   By `Deepak Cherian <https://github.com/dcherian>`_.
@@ -86,6 +100,8 @@ Bug fixes
 - Fix a regression in :py:meth:`Dataset.drop`: allow passing any
   iterable when dropping variables (:issue:`3552`, :pull:`3693`)
   By `Justus Magin <https://github.com/keewis>`_.
+- Fixed errors emitted by ``mypy --strict`` in modules that import xarray.
+  (:issue:`3695`) by `Guido Imperiale <https://github.com/crusaderky>`_.
 
 Documentation
 ~~~~~~~~~~~~~

properties/test_pandas_roundtrip.py

@@ -1,20 +1,20 @@
 """
 Property-based tests for roundtripping between xarray and pandas objects.
 """
-import pytest
-
-pytest.importorskip("hypothesis")
-
 from functools import partial
-import hypothesis.extra.numpy as npst
-import hypothesis.extra.pandas as pdst
-import hypothesis.strategies as st
-from hypothesis import given
 
 import numpy as np
 import pandas as pd
+import pytest
+
 import xarray as xr
 
+pytest.importorskip("hypothesis")
+import hypothesis.extra.numpy as npst  # isort:skip
+import hypothesis.extra.pandas as pdst  # isort:skip
+import hypothesis.strategies as st  # isort:skip
+from hypothesis import given  # isort:skip
+
 numeric_dtypes = st.one_of(
     npst.unsigned_integer_dtypes(), npst.integer_dtypes(), npst.floating_dtypes()
 )

xarray/__init__.py

@@ -1,5 +1,4 @@
 """ isort:skip_file """
-# flake8: noqa
 
 from ._version import get_versions
 
@@ -42,3 +41,55 @@
 from . import testing
 
 from .core.common import ALL_DIMS
+
+# A hardcoded __all__ variable is necessary to appease
+# `mypy --strict` running in projects that import xarray.
+__all__ = (
+    # Sub-packages
+    "ufuncs",
+    "testing",
+    "tutorial",
+    # Top-level functions
+    "align",
+    "apply_ufunc",
+    "as_variable",
+    "auto_combine",
+    "broadcast",
+    "cftime_range",
+    "combine_by_coords",
+    "combine_nested",
+    "concat",
+    "decode_cf",
+    "dot",
+    "full_like",
+    "load_dataarray",
+    "load_dataset",
+    "map_blocks",
+    "merge",
+    "ones_like",
+    "open_dataarray",
+    "open_dataset",
+    "open_mfdataset",
+    "open_rasterio",
+    "open_zarr",
+    "register_dataarray_accessor",
+    "register_dataset_accessor",
+    "save_mfdataset",
+    "set_options",
+    "show_versions",
+    "where",
+    "zeros_like",
+    # Classes
+    "CFTimeIndex",
+    "Coordinate",
+    "DataArray",
+    "Dataset",
+    "IndexVariable",
+    "Variable",
+    # Exceptions
+    "MergeError",
+    "SerializationWarning",
+    # Constants
+    "__version__",
+    "ALL_DIMS",
+)

xarray/backends/api.py

@@ -503,7 +503,7 @@ def maybe_decode_store(store, lock=False):
         elif engine == "pydap":
             store = backends.PydapDataStore.open(filename_or_obj, **backend_kwargs)
         elif engine == "h5netcdf":
-            store = backends.H5NetCDFStore(
+            store = backends.H5NetCDFStore.open(
                 filename_or_obj, group=group, lock=lock, **backend_kwargs
             )
         elif engine == "pynio":
@@ -527,7 +527,7 @@ def maybe_decode_store(store, lock=False):
         if engine == "scipy":
             store = backends.ScipyDataStore(filename_or_obj, **backend_kwargs)
         elif engine == "h5netcdf":
-            store = backends.H5NetCDFStore(
+            store = backends.H5NetCDFStore.open(
                 filename_or_obj, group=group, lock=lock, **backend_kwargs
             )
 
@@ -981,7 +981,7 @@ def open_mfdataset(
 WRITEABLE_STORES: Dict[str, Callable] = {
     "netcdf4": backends.NetCDF4DataStore.open,
     "scipy": backends.ScipyDataStore,
-    "h5netcdf": backends.H5NetCDFStore,
+    "h5netcdf": backends.H5NetCDFStore.open,
 }