Merge branch 'main' into conditionally-disable-bottleneck

Author: keewis

.github/workflows/ci-additional.yaml

@@ -103,7 +103,7 @@ jobs:
              $PYTEST_EXTRA_FLAGS
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2.0.2
         with:
           file: ./coverage.xml
           flags: unittests,${{ matrix.env }}

.github/workflows/ci.yaml

@@ -100,7 +100,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2.0.2
         with:
           file: ./coverage.xml
           flags: unittests

.pre-commit-config.yaml

@@ -43,6 +43,7 @@ repos:
             types-pytz,
             # Dependencies that are typed
             numpy,
+            typing-extensions==3.10.0.0,
           ]
   # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
   # - repo: https://github.com/asottile/pyupgrade

doc/api-hidden.rst

@@ -54,7 +54,6 @@
    core.rolling.DatasetCoarsen.var
    core.rolling.DatasetCoarsen.boundary
    core.rolling.DatasetCoarsen.coord_func
-   core.rolling.DatasetCoarsen.keep_attrs
    core.rolling.DatasetCoarsen.obj
    core.rolling.DatasetCoarsen.side
    core.rolling.DatasetCoarsen.trim_excess
@@ -120,7 +119,6 @@
    core.rolling.DatasetRolling.var
    core.rolling.DatasetRolling.center
    core.rolling.DatasetRolling.dim
-   core.rolling.DatasetRolling.keep_attrs
    core.rolling.DatasetRolling.min_periods
    core.rolling.DatasetRolling.obj
    core.rolling.DatasetRolling.rollings
@@ -199,7 +197,6 @@
    core.rolling.DataArrayCoarsen.var
    core.rolling.DataArrayCoarsen.boundary
    core.rolling.DataArrayCoarsen.coord_func
-   core.rolling.DataArrayCoarsen.keep_attrs
    core.rolling.DataArrayCoarsen.obj
    core.rolling.DataArrayCoarsen.side
    core.rolling.DataArrayCoarsen.trim_excess
@@ -263,7 +260,6 @@
    core.rolling.DataArrayRolling.var
    core.rolling.DataArrayRolling.center
    core.rolling.DataArrayRolling.dim
-   core.rolling.DataArrayRolling.keep_attrs
    core.rolling.DataArrayRolling.min_periods
    core.rolling.DataArrayRolling.obj
    core.rolling.DataArrayRolling.window

doc/api.rst

@@ -24,7 +24,6 @@ Top-level functions
    combine_by_coords
    combine_nested
    where
-   set_options
    infer_freq
    full_like
    zeros_like
@@ -686,6 +685,7 @@ Dataset methods
    open_zarr
    Dataset.to_netcdf
    Dataset.to_pandas
+   Dataset.as_numpy
    Dataset.to_zarr
    save_mfdataset
    Dataset.to_array
@@ -716,6 +716,8 @@ DataArray methods
    DataArray.to_pandas
    DataArray.to_series
    DataArray.to_dataframe
+   DataArray.to_numpy
+   DataArray.as_numpy
    DataArray.to_index
    DataArray.to_masked_array
    DataArray.to_cdms2

doc/getting-started-guide/installing.rst

@@ -8,7 +8,6 @@ Required dependencies
 
 - Python (3.7 or later)
 - setuptools (40.4 or later)
-- typing-extensions (3.10 or later)
 - `numpy <http://www.numpy.org/>`__ (1.17 or later)
 - `pandas <http://pandas.pydata.org/>`__ (1.0 or later)
 

doc/whats-new.rst

@@ -14,11 +14,56 @@ What's New
 
     np.random.seed(123456)
 
-.. _whats-new.0.18.3:
 
-v0.18.3 (unreleased)
+.. _whats-new.0.19.1:
+
+v0.19.1 (unreleased)
 ---------------------
 
+New Features
+~~~~~~~~~~~~
+- Add a option to disable the use of ``bottleneck`` (:pull:`5560`)
+  By `Justus Magin <https://github.com/keewis>`_.
+- Added ``**kwargs`` argument to :py:meth:`open_rasterio` to access overviews (:issue:`3269`).
+  By `Pushkar Kopparla <https://github.com/pkopparla>`_.
+
+
+Breaking changes
+~~~~~~~~~~~~~~~~
+
+
+Deprecations
+~~~~~~~~~~~~
+
+
+Bug fixes
+~~~~~~~~~
+
+
+Documentation
+~~~~~~~~~~~~~
+
+
+Internal Changes
+~~~~~~~~~~~~~~~~
+
+.. _whats-new.0.19.0:
+
+v0.19.0 (23 July 2021)
+----------------------
+
+This release brings improvements to plotting of categorical data, the ability to specify how attributes
+are combined in xarray operations, a new high-level :py:func:`unify_chunks` function, as well as various
+deprecations, bug fixes, and minor improvements.
+
+
+Many thanks to the 29 contributors to this release!:
+
+Andrew Williams, Augustus, Aureliana Barghini, Benoit Bovy, crusaderky, Deepak Cherian, ellesmith88,
+Elliott Sales de Andrade, Giacomo Caria, github-actions[bot], Illviljan, Joeperdefloep, joooeey, Julia Kent,
+Julius Busecke, keewis, Mathias Hauser, Matthias Göbel, Mattia Almansi, Maximilian Roos, Peter Andreas Entschev,
+Ray Bell, Sander, Santiago Soler, Sebastian, Spencer Clark, Stephan Hoyer, Thomas Hirtz, Thomas Nicholas.
+
 New Features
 ~~~~~~~~~~~~
 - Allow passing argument ``missing_dims`` to :py:meth:`Variable.transpose` and :py:meth:`Dataset.transpose`
@@ -56,8 +101,10 @@ New Features
 - Allow removal of the coordinate attribute ``coordinates`` on variables by setting ``.attrs['coordinates']= None``
   (:issue:`5510`).
   By `Elle Smith <https://github.com/ellesmith88>`_.
-- Add a option to disable the use of ``bottleneck`` (:pull:`5560`)
-  By `Justus Magin <https://github.com/keewis>`_.
+- Added :py:meth:`DataArray.to_numpy`, :py:meth:`DataArray.as_numpy`, and :py:meth:`Dataset.as_numpy`. (:pull:`5568`).
+  By `Tom Nicholas <https://github.com/TomNicholas>`_.
+- Units in plot labels are now automatically inferred from wrapped :py:meth:`pint.Quantity` arrays. (:pull:`5561`).
+  By `Tom Nicholas <https://github.com/TomNicholas>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
@@ -75,6 +122,10 @@ Breaking changes
 Deprecations
 ~~~~~~~~~~~~
 
+- Removed the deprecated ``dim`` kwarg to :py:func:`DataArray.integrate` (:pull:`5630`)
+- Removed the deprecated ``keep_attrs`` kwarg to :py:func:`DataArray.rolling` (:pull:`5630`)
+- Removed the deprecated ``keep_attrs`` kwarg to :py:func:`DataArray.coarsen` (:pull:`5630`)
+- Completed deprecation of passing an ``xarray.DataArray`` to :py:func:`Variable` - will now raise a ``TypeError`` (:pull:`5630`)
 
 Bug fixes
 ~~~~~~~~~
@@ -99,10 +150,6 @@ Bug fixes
   By `Augustus Ijams <https://github.com/aijams>`_.
 
 
-Documentation
-~~~~~~~~~~~~~
-
-
 Internal Changes
 ~~~~~~~~~~~~~~~~
 - Run CI on the first & last python versions supported only; currently 3.7 & 3.9.
@@ -111,7 +158,6 @@ Internal Changes
 - Publish test results & timings on each PR.
   (:pull:`5537`)
   By `Maximilian Roos <https://github.com/max-sixty>`_.
-
 - Explicit indexes refactor: add a ``xarray.Index.query()`` method in which
   one may eventually provide a custom implementation of label-based data
   selection (not ready yet for public use). Also refactor the internal,
@@ -156,13 +202,6 @@ New Features
 - Raise more informative error when decoding time variables with invalid reference dates.
   (:issue:`5199`, :pull:`5288`). By `Giacomo Caria <https://github.com/gcaria>`_.
 
-Breaking changes
-~~~~~~~~~~~~~~~~
-
-
-Deprecations
-~~~~~~~~~~~~
-
 
 Bug fixes
 ~~~~~~~~~

setup.cfg

@@ -67,6 +67,7 @@ classifiers =
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
     Topic :: Scientific/Engineering
 
 [options]
@@ -78,7 +79,6 @@ install_requires =
     numpy >= 1.17
     pandas >= 1.0
     setuptools >= 40.4  # For pkg_resources
-    typing-extensions >= 3.10  # Backported type hints
 
 [options.extras_require]
 io =

xarray/backends/rasterio_.py

@@ -162,7 +162,14 @@ def default(s):
     return parsed_meta
 
 
-def open_rasterio(filename, parse_coordinates=None, chunks=None, cache=None, lock=None):
+def open_rasterio(
+    filename,
+    parse_coordinates=None,
+    chunks=None,
+    cache=None,
+    lock=None,
+    **kwargs,
+):
     """Open a file with rasterio (experimental).
 
     This should work with any file that rasterio can open (most often:
@@ -272,7 +279,13 @@ def open_rasterio(filename, parse_coordinates=None, chunks=None, cache=None, loc
     if lock is None:
         lock = RASTERIO_LOCK
 
-    manager = CachingFileManager(rasterio.open, filename, lock=lock, mode="r")
+    manager = CachingFileManager(
+        rasterio.open,
+        filename,
+        lock=lock,
+        mode="r",
+        kwargs=kwargs,
+    )
     riods = manager.acquire()
     if vrt_params is not None:
         riods = WarpedVRT(riods, **vrt_params)

xarray/core/combine.py

@@ -635,7 +635,7 @@ def _combine_single_variable_hypercube(
     return concatenated
 
 
-# TODO remove empty list default param after version 0.19, see PR4696
+# TODO remove empty list default param after version 0.21, see PR4696
 def combine_by_coords(
     data_objects=[],
     compat="no_conflicts",
@@ -849,11 +849,11 @@ def combine_by_coords(
         precipitation  (y, x) float64 0.4376 0.8918 0.9637 ... 0.5684 0.01879 0.6176
     """
 
-    # TODO remove after version 0.19, see PR4696
+    # TODO remove after version 0.21, see PR4696
     if datasets is not None:
         warnings.warn(
             "The datasets argument has been renamed to `data_objects`."
-            " In future passing a value for datasets will raise an error."
+            " From 0.21 on passing a value for datasets will raise an error."
         )
         data_objects = datasets