Merge branch 'master' into refactor-plot-utils

* master:
  stale requires a label (pydata#2701)
  Update indexing.rst (pydata#2700)
  add line break to message posted (pydata#2698)
  Config for closing stale issues (pydata#2684)
  to_dict without data (pydata#2659)
  Update asv.conf.json (pydata#2693)
  try no rasterio in py36 env (pydata#2691)
  Detailed report for testing.assert_equal and testing.assert_identical (pydata#1507)
  Hotfix for pydata#2662 (pydata#2678)
  Update README.rst (pydata#2682)
  Fix test failures with numpy=1.16 (pydata#2675)

.github/stale.yml

@@ -0,0 +1,58 @@
+# Configuration for probot-stale - https://github.com/probot/stale
+
+# Number of days of inactivity before an Issue or Pull Request becomes stale
+daysUntilStale: 700  # start with a large number and reduce shortly
+
+# Number of days of inactivity before an Issue or Pull Request with the stale label is closed.
+# Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale.
+daysUntilClose: 30
+
+# Issues or Pull Requests with these labels will never be considered stale. Set to `[]` to disable
+exemptLabels:
+  - pinned
+  - security
+  - "[Status] Maybe Later"
+
+# Set to true to ignore issues in a project (defaults to false)
+exemptProjects: false
+
+# Set to true to ignore issues in a milestone (defaults to false)
+exemptMilestones: false
+
+# Set to true to ignore issues with an assignee (defaults to false)
+exemptAssignees: true
+
+# Label to use when marking as stale
+staleLabel: stale
+
+# Comment to post when marking as stale. Set to `false` to disable
+markComment: |
+  In order to maintain a list of currently relevant issues, we mark issues as stale after a period of inactivity
+  If this issue remains relevant, please comment here; otherwise it will be marked as closed automatically
+
+# Comment to post when removing the stale label.
+# unmarkComment: >
+#   Your comment here.
+
+# Comment to post when closing a stale Issue or Pull Request.
+# closeComment: >
+#   Your comment here.
+
+# Limit the number of actions per hour, from 1-30. Default is 30
+limitPerRun: 1  # start with a small number
+
+
+# Limit to only `issues` or `pulls`
+# only: issues
+
+# Optionally, specify configuration settings that are specific to just 'issues' or 'pulls':
+# pulls:
+#   daysUntilStale: 30
+#   markComment: >
+#     This pull request has been automatically marked as stale because it has not had
+#     recent activity. It will be closed if no further activity occurs. Thank you
+#     for your contributions.
+
+# issues:
+#   exemptLabels:
+#     - confirmed

.travis.yml

@@ -60,7 +60,7 @@ script:
   - python --version
   - python -OO -c "import xarray"
   - if [[ "$CONDA_ENV" == "docs" ]]; then
-      conda install -c conda-forge sphinx sphinx_rtd_theme sphinx-gallery numpydoc;
+      conda install -c conda-forge --override-channels sphinx sphinx_rtd_theme sphinx-gallery numpydoc "gdal>2.2.4";
       sphinx-build -n -j auto -b html -d _build/doctrees doc _build/html;
     elif [[ "$CONDA_ENV" == "lint" ]]; then
       pycodestyle xarray ;

README.rst

@@ -114,7 +114,7 @@ __ http://climate.com/
 License
 -------
 
-Copyright 2014-2018, xarray Developers
+Copyright 2014-2019, xarray Developers
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

asv_bench/asv.conf.json

@@ -40,7 +40,7 @@
 
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.
-    "pythons": ["2.7", "3.6"],
+    "pythons": ["3.6"],
 
     // The matrix of dependencies to test.  Each key is the name of a
     // package (in PyPI) and the values are version numbers.  An empty

ci/requirements-py36.yml

@@ -20,14 +20,14 @@ dependencies:
   - scipy
   - seaborn
   - toolz
-  - rasterio
+  # - rasterio  # xref #2683
   - bottleneck
   - zarr
   - pseudonetcdf>=3.0.1
   - eccodes
   - cdms2
-  - pynio
-  - iris>=1.10
+  # - pynio  # xref #2683
+  # - iris>=1.10    # xref #2683
   - pydap
   - lxml
   - pip:

doc/indexing.rst

@@ -371,7 +371,7 @@ Vectorized indexing also works with ``isel``, ``loc``, and ``sel``:
     ind = xr.DataArray([['a', 'b'], ['b', 'a']], dims=['a', 'b'])
     da.loc[:, ind]  # same as da.sel(y=ind)
 
-These methods may and also be applied to ``Dataset`` objects
+These methods may also be applied to ``Dataset`` objects
 
 .. ipython:: python
 

doc/io.rst

@@ -81,6 +81,16 @@ require external libraries and dicts can easily be pickled, or converted to
 json, or geojson. All the values are converted to lists, so dicts might
 be quite large.
 
+To export just the dataset schema, without the data itself, use the
+``data=False`` option:
+
+.. ipython:: python
+
+    ds.to_dict(data=False)
+
+This can be useful for generating indices of dataset contents to expose to
+search indices or other automated data discovery tools.
+
 .. _io.netcdf:
 
 netCDF
@@ -665,7 +675,7 @@ To read a consolidated store, pass the ``consolidated=True`` option to
 :py:func:`~xarray.open_zarr`::
 
     ds = xr.open_zarr('foo.zarr', consolidated=True)
-    
+
 Xarray can't perform consolidation on pre-existing zarr datasets. This should
 be done directly from zarr, as described in the
 `zarr docs <https://zarr.readthedocs.io/en/latest/tutorial.html#consolidating-metadata>`_.

doc/whats-new.rst

@@ -28,6 +28,8 @@ Breaking changes
 Enhancements
 ~~~~~~~~~~~~
 
+- Add ``data=False`` option to ``to_dict()`` methods. (:issue:`2656`)
+  By `Ryan Abernathey <https://github.com/rabernat>`_
 - :py:meth:`~xarray.DataArray.coarsen` and
   :py:meth:`~xarray.Dataset.coarsen` are newly added.
   See :ref:`comput.coarsen` for details.
@@ -36,6 +38,11 @@ Enhancements
 - Upsampling an array via interpolation with resample is now dask-compatible,
   as long as the array is not chunked along the resampling dimension.
   By `Spencer Clark <https://github.com/spencerkclark>`_.
+- :py:func:`xarray.testing.assert_equal` and
+  :py:func:`xarray.testing.assert_identical` now provide a more detailed
+  report showing what exactly differs between the two objects (dimensions /
+  coordinates / variables / attributes)  (:issue:`1507`).
+  By `Benoit Bovy <https://github.com/benbovy>`_.
 
 Bug fixes
 ~~~~~~~~~

xarray/core/combine.py

@@ -493,16 +493,21 @@ def _auto_combine_all_along_first_dim(combined_ids, dim, data_vars,
     return new_combined_ids
 
 
+def vars_as_keys(ds):
+    return tuple(sorted(ds))
+
+
 def _auto_combine_1d(datasets, concat_dim=_CONCAT_DIM_DEFAULT,
                      compat='no_conflicts',
                      data_vars='all', coords='different'):
     # This is just the old auto_combine function (which only worked along 1D)
     if concat_dim is not None:
         dim = None if concat_dim is _CONCAT_DIM_DEFAULT else concat_dim
-        grouped = itertools.groupby(datasets, key=lambda ds: tuple(sorted(ds)))
+        sorted_datasets = sorted(datasets, key=vars_as_keys)
+        grouped_by_vars = itertools.groupby(sorted_datasets, key=vars_as_keys)
         concatenated = [_auto_concat(list(ds_group), dim=dim,
                                      data_vars=data_vars, coords=coords)
-                        for id, ds_group in grouped]
+                        for id, ds_group in grouped_by_vars]
     else:
         concatenated = datasets
     merged = merge(concatenated, compat=compat)

xarray/core/dataarray.py

@@ -1760,7 +1760,7 @@ def to_netcdf(self, *args, **kwargs):
 
         return dataset.to_netcdf(*args, **kwargs)
 
-    def to_dict(self):
+    def to_dict(self, data=True):
         """
         Convert this xarray.DataArray into a dictionary following xarray
         naming conventions.
@@ -1769,22 +1769,20 @@ def to_dict(self):
         Useful for coverting to json. To avoid datetime incompatibility
         use decode_times=False kwarg in xarrray.open_dataset.
 
+        Parameters
+        ----------
+        data : bool, optional
+            Whether to include the actual data in the dictionary. When set to
+            False, returns just the schema.
+
         See also
         --------
         DataArray.from_dict
         """
-        d = {'coords': {}, 'attrs': decode_numpy_dict_values(self.attrs),
-             'dims': self.dims}
-
+        d = self.variable.to_dict(data=data)
+        d.update({'coords': {}, 'name': self.name})
         for k in self.coords:
-            data = ensure_us_time_resolution(self[k].values).tolist()
-            d['coords'].update({
-                k: {'data': data,
-                    'dims': self[k].dims,
-                    'attrs': decode_numpy_dict_values(self[k].attrs)}})
-
-        d.update({'data': ensure_us_time_resolution(self.values).tolist(),
-                  'name': self.name})
+            d['coords'][k] = self.coords[k].variable.to_dict(data=data)
         return d
 
     @classmethod

xarray/core/dataset.py

@@ -3221,7 +3221,7 @@ def to_dask_dataframe(self, dim_order=None, set_index=False):
 
         return df
 
-    def to_dict(self):
+    def to_dict(self, data=True):
         """
         Convert this dataset to a dictionary following xarray naming
         conventions.
@@ -3230,25 +3230,22 @@ def to_dict(self):
         Useful for coverting to json. To avoid datetime incompatibility
         use decode_times=False kwarg in xarrray.open_dataset.
 
+        Parameters
+        ----------
+        data : bool, optional
+            Whether to include the actual data in the dictionary. When set to
+            False, returns just the schema.
+
         See also
         --------
         Dataset.from_dict
         """
         d = {'coords': {}, 'attrs': decode_numpy_dict_values(self.attrs),
              'dims': dict(self.dims), 'data_vars': {}}
-
         for k in self.coords:
-            data = ensure_us_time_resolution(self[k].values).tolist()
-            d['coords'].update({
-                k: {'data': data,
-                    'dims': self[k].dims,
-                    'attrs': decode_numpy_dict_values(self[k].attrs)}})
+            d['coords'].update({k: self[k].variable.to_dict(data=data)})
         for k in self.data_vars:
-            data = ensure_us_time_resolution(self[k].values).tolist()
-            d['data_vars'].update({
-                k: {'data': data,
-                    'dims': self[k].dims,
-                    'attrs': decode_numpy_dict_values(self[k].attrs)}})
+            d['data_vars'].update({k: self[k].variable.to_dict(data=data)})
         return d
 
     @classmethod