Merge remote-tracking branch 'upstream/master' into coarsen-reduce

* upstream/master: (22 commits)
  Added fill_value for unstack (pydata#3541)
  Add DatasetGroupBy.quantile (pydata#3527)
  ensure rename does not change index type (pydata#3532)
  Leave empty slot when not using accessors
  interpolate_na: Add max_gap support. (pydata#3302)
  units & deprecation merge (pydata#3530)
  Fix set_index when an existing dimension becomes a level (pydata#3520)
  add Variable._replace (pydata#3528)
  Tests for module-level functions with units (pydata#3493)
  Harmonize `FillValue` and `missing_value` during encoding and decoding steps (pydata#3502)
  FUNDING.yml (pydata#3523)
  Allow appending datetime & boolean variables to zarr stores (pydata#3504)
  warn if dim is passed to rolling operations. (pydata#3513)
  Deprecate allow_lazy (pydata#3435)
  Recursive tokenization (pydata#3515)
  format indexing.rst code with black (pydata#3511)
  add missing pint integration tests (pydata#3508)
  DOC: update bottleneck repo url (pydata#3507)
  add drop_sel, drop_vars, map to api.rst (pydata#3506)
  remove syntax warning (pydata#3505)
  ...

Author: dcherian

.github/FUNDING.yml

@@ -0,0 +1,2 @@
+github: numfocus
+custom: http://numfocus.org/donate-to-xarray

doc/api.rst

@@ -94,7 +94,7 @@ Dataset contents
    Dataset.rename_dims
    Dataset.swap_dims
    Dataset.expand_dims
-   Dataset.drop
+   Dataset.drop_vars
    Dataset.drop_dims
    Dataset.set_coords
    Dataset.reset_coords
@@ -118,6 +118,7 @@ Indexing
    Dataset.loc
    Dataset.isel
    Dataset.sel
+   Dataset.drop_sel
    Dataset.head
    Dataset.tail
    Dataset.thin
@@ -154,7 +155,7 @@ Computation
 .. autosummary::
    :toctree: generated/
 
-   Dataset.apply
+   Dataset.map
    Dataset.reduce
    Dataset.groupby
    Dataset.groupby_bins
@@ -263,7 +264,7 @@ DataArray contents
    DataArray.rename
    DataArray.swap_dims
    DataArray.expand_dims
-   DataArray.drop
+   DataArray.drop_vars
    DataArray.reset_coords
    DataArray.copy
 
@@ -283,6 +284,7 @@ Indexing
    DataArray.loc
    DataArray.isel
    DataArray.sel
+   DataArray.drop_sel
    DataArray.head
    DataArray.tail
    DataArray.thin
@@ -542,10 +544,10 @@ GroupBy objects
    :toctree: generated/
 
    core.groupby.DataArrayGroupBy
-   core.groupby.DataArrayGroupBy.apply
+   core.groupby.DataArrayGroupBy.map
    core.groupby.DataArrayGroupBy.reduce
    core.groupby.DatasetGroupBy
-   core.groupby.DatasetGroupBy.apply
+   core.groupby.DatasetGroupBy.map
    core.groupby.DatasetGroupBy.reduce
 
 Rolling objects
@@ -566,7 +568,7 @@ Resample objects
 ================
 
 Resample objects also implement the GroupBy interface
-(methods like ``apply()``, ``reduce()``, ``mean()``, ``sum()``, etc.).
+(methods like ``map()``, ``reduce()``, ``mean()``, ``sum()``, etc.).
 
 .. autosummary::
    :toctree: generated/

doc/computation.rst

@@ -95,6 +95,9 @@ for filling missing values via 1D interpolation.
 Note that xarray slightly diverges from the pandas ``interpolate`` syntax by
 providing the ``use_coordinate`` keyword which facilitates a clear specification
 of which values to use as the index in the interpolation.
+xarray also provides the ``max_gap`` keyword argument to limit the interpolation to
+data gaps of length ``max_gap`` or smaller. See :py:meth:`~xarray.DataArray.interpolate_na`
+for more.
 
 Aggregation
 ===========
@@ -183,7 +186,7 @@ a value when aggregating:
 
    Note that rolling window aggregations are faster and use less memory when bottleneck_ is installed. This only applies to numpy-backed xarray objects.
 
-.. _bottleneck: https://github.com/kwgoodman/bottleneck/
+.. _bottleneck: https://github.com/pydata/bottleneck/
 
 We can also manually iterate through ``Rolling`` objects:
 
@@ -462,13 +465,13 @@ Datasets support most of the same methods found on data arrays:
     abs(ds)
 
 Datasets also support NumPy ufuncs (requires NumPy v1.13 or newer), or
-alternatively you can use :py:meth:`~xarray.Dataset.apply` to apply a function
+alternatively you can use :py:meth:`~xarray.Dataset.map` to map a function
 to each variable in a dataset:
 
 .. ipython:: python
 
     np.sin(ds)
-    ds.apply(np.sin)
+    ds.map(np.sin)
 
 Datasets also use looping over variables for *broadcasting* in binary
 arithmetic. You can do arithmetic between any ``DataArray`` and a dataset:

doc/conf.py

@@ -340,9 +340,10 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
-    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
-    "iris": ("http://scitools.org.uk/iris/docs/latest/", None),
-    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
-    "numba": ("https://numba.pydata.org/numba-doc/latest/", None),
-    "matplotlib": ("https://matplotlib.org/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    "iris": ("https://scitools.org.uk/iris/docs/latest", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "numba": ("https://numba.pydata.org/numba-doc/latest", None),
+    "matplotlib": ("https://matplotlib.org", None),
 }

doc/dask.rst

@@ -292,7 +292,7 @@ For the best performance when using Dask's multi-threaded scheduler, wrap a
 function that already releases the global interpreter lock, which fortunately
 already includes most NumPy and Scipy functions. Here we show an example
 using NumPy operations and a fast function from
-`bottleneck <https://github.com/kwgoodman/bottleneck>`__, which
+`bottleneck <https://github.com/pydata/bottleneck>`__, which
 we use to calculate `Spearman's rank-correlation coefficient <https://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient>`__:
 
 .. code-block:: python

doc/groupby.rst

@@ -35,10 +35,11 @@ Let's create a simple example dataset:
 
 .. ipython:: python
 
-    ds = xr.Dataset({'foo': (('x', 'y'), np.random.rand(4, 3))},
-                    coords={'x': [10, 20, 30, 40],
-                            'letters': ('x', list('abba'))})
-    arr = ds['foo']
+    ds = xr.Dataset(
+        {"foo": (("x", "y"), np.random.rand(4, 3))},
+        coords={"x": [10, 20, 30, 40], "letters": ("x", list("abba"))},
+    )
+    arr = ds["foo"]
     ds
 
 If we groupby the name of a variable or coordinate in a dataset (we can also
@@ -93,15 +94,15 @@ Apply
 ~~~~~
 
 To apply a function to each group, you can use the flexible
-:py:meth:`~xarray.DatasetGroupBy.apply` method. The resulting objects are automatically
+:py:meth:`~xarray.DatasetGroupBy.map` method. The resulting objects are automatically
 concatenated back together along the group axis:
 
 .. ipython:: python
 
     def standardize(x):
         return (x - x.mean()) / x.std()
 
-    arr.groupby('letters').apply(standardize)
+    arr.groupby('letters').map(standardize)
 
 GroupBy objects also have a :py:meth:`~xarray.DatasetGroupBy.reduce` method and
 methods like :py:meth:`~xarray.DatasetGroupBy.mean` as shortcuts for applying an
@@ -202,7 +203,7 @@ __ http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#_two_dimen
         dims=['ny','nx'])
     da
     da.groupby('lon').sum(...)
-    da.groupby('lon').apply(lambda x: x - x.mean(), shortcut=False)
+    da.groupby('lon').map(lambda x: x - x.mean(), shortcut=False)
 
 Because multidimensional groups have the ability to generate a very large
 number of bins, coarse-binning via :py:meth:`~xarray.Dataset.groupby_bins`

doc/howdoi.rst

@@ -44,7 +44,7 @@ How do I ...
    * - convert a possibly irregularly sampled timeseries to a regularly sampled timeseries
      - :py:meth:`DataArray.resample`, :py:meth:`Dataset.resample` (see :ref:`resampling` for more)
    * - apply a function on all data variables in a Dataset
-     - :py:meth:`Dataset.apply`
+     - :py:meth:`Dataset.map`
    * - write xarray objects with complex values to a netCDF file
      - :py:func:`Dataset.to_netcdf`, :py:func:`DataArray.to_netcdf` specifying ``engine="h5netcdf", invalid_netcdf=True``
    * - make xarray objects look like other xarray objects