Merged latest pydata-master to resample branch

.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

@@ -60,8 +60,8 @@ script:
   - python --version
   - python -OO -c "import xarray"
   - if [[ "$CONDA_ENV" == "docs" ]]; then
-      conda install -c conda-forge --override-channels sphinx sphinx_rtd_theme sphinx-gallery numpydoc "gdal>2.2.4";
-      sphinx-build -n -j auto -b html -d _build/doctrees doc _build/html;
+      cd doc;
+      sphinx-build -n -j auto -b html -d _build/doctrees . _build/html;
     elif [[ "$CONDA_ENV" == "lint" ]]; then
       pycodestyle xarray ;
     elif [[ "$CONDA_ENV" == "py36-hypothesis" ]]; then

ci/requirements-py36.yml

@@ -26,8 +26,8 @@ dependencies:
   - pseudonetcdf>=3.0.1
   - eccodes
   - cdms2
-  # - pynio  # xref #2683
-  # - iris>=1.10    # xref #2683
+# - pynio  # xref #2683
+# - iris>=1.10  # xref #2683
   - pydap
   - lxml
   - pip:

doc/conf.py

@@ -13,9 +13,10 @@
 # serve to show the default.
 from __future__ import absolute_import, division, print_function
 
+from contextlib import suppress
 import datetime
-import importlib
 import os
+import subprocess
 import sys
 
 import xarray
@@ -24,29 +25,33 @@
 
 print("python exec:", sys.executable)
 print("sys.path:", sys.path)
-for name in ('numpy scipy pandas matplotlib dask IPython seaborn '
-             'cartopy netCDF4 rasterio zarr iris flake8 '
-             'sphinx_gallery cftime').split():
-    try:
-        module = importlib.import_module(name)
-        if name == 'matplotlib':
-            module.use('Agg')
-        fname = module.__file__.rstrip('__init__.py')
-        print("%s: %s, %s" % (name, module.__version__, fname))
-    except ImportError:
-        print("no %s" % name)
-        # neither rasterio nor cartopy should be hard requirements for
-        # the doc build.
-        if name == 'rasterio':
-            allowed_failures.update(['gallery/plot_rasterio_rgb.py',
-                                     'gallery/plot_rasterio.py'])
-        elif name == 'cartopy':
-            allowed_failures.update(['gallery/plot_cartopy_facetgrid.py',
-                                     'gallery/plot_rasterio_rgb.py',
-                                     'gallery/plot_rasterio.py'])
+
+if 'conda' in sys.executable:
+    print('conda environment:')
+    subprocess.run(['conda', 'list'])
+else:
+    print('pip environment:')
+    subprocess.run(['pip', 'list'])
 
 print("xarray: %s, %s" % (xarray.__version__, xarray.__file__))
 
+with suppress(ImportError):
+    import matplotlib
+    matplotlib.use('Agg')
+
+try:
+    import rasterio
+except ImportError:
+    allowed_failures.update(['gallery/plot_rasterio_rgb.py',
+                             'gallery/plot_rasterio.py'])
+
+try:
+    import cartopy
+except ImportError:
+    allowed_failures.update(['gallery/plot_cartopy_facetgrid.py',
+                             'gallery/plot_rasterio_rgb.py',
+                             'gallery/plot_rasterio.py'])
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.

doc/environment.yml

@@ -2,22 +2,25 @@ name: xarray-docs
 channels:
   - conda-forge
 dependencies:
-  - python=3.6
-  - numpy=1.14.5
+  - python=3.7
+  - numpy=1.16.0
   - pandas=0.23.3
-  - scipy=1.1.0
-  - matplotlib=2.2.2
+  - scipy=1.2.0
+  - matplotlib=3.0.2
   - seaborn=0.9.0
-  - dask=0.18.2
-  - ipython=6.4.0
-  - netCDF4=1.4.0
-  - cartopy=0.16.0
-  - rasterio=1.0.1
+  - dask=1.1.0
+  - ipython=7.2.0
+  - netCDF4=1.4.2
+  - cartopy=0.17.0
+  - rasterio=1.0.13
   - zarr=2.2.0
-  - iris=2.1.0
-  - flake8=3.5.0
+  - iris=2.2.0
+  - flake8=3.6.0
   - cftime=1.0.3.4
-  - bottleneck=1.2
-  - sphinx=1.7.6
+  - bottleneck=1.2.1
+  - sphinx=1.8.2
   - numpydoc=0.8.0
   - sphinx-gallery=0.2.0
+  - pillow=5.4.1
+  - sphinx_rtd_theme=0.4.2
+  - mock=2.0.0

doc/examples/multidimensional-coords.rst

@@ -78,9 +78,8 @@ grid, we can take advantage of xarray's ability to apply
     ax = plt.axes(projection=ccrs.PlateCarree());
     ds.Tair[0].plot.pcolormesh(ax=ax, transform=ccrs.PlateCarree(),
                                x='xc', y='yc', add_colorbar=False);
-    ax.coastlines();
     @savefig xarray_multidimensional_coords_12_0.png width=100%
-    plt.tight_layout();
+    ax.coastlines();
 
 Multidimensional Groupby
 ------------------------

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/pandas.rst

@@ -14,7 +14,7 @@ __ http://pandas.pydata.org/pandas-docs/stable/visualization.html
 __ http://stanford.edu/~mwaskom/software/seaborn/
 
 .. ipython:: python
-   :suppress:
+    :suppress:
 
     import numpy as np
     import pandas as pd
@@ -93,7 +93,6 @@ DataFrames:
 
     s = ds['foo'].to_series()
     s
-
     # or equivalently, with Series.to_xarray()
     xr.DataArray.from_series(s)
 
@@ -173,11 +172,10 @@ So you can represent a Panel, in two ways:
 Let's take a look:
 
 .. ipython:: python
-   :okwarning:
+    :okwarning:
 
     panel = pd.Panel(np.random.rand(2, 3, 4), items=list('ab'), major_axis=list('mno'),
                      minor_axis=pd.date_range(start='2000', periods=4, name='date'))
-
     panel
 
 As a DataArray:

doc/time-series.rst

@@ -15,7 +15,6 @@ core functionality.
     import numpy as np
     import pandas as pd
     import xarray as xr
-
     np.random.seed(123456)
 
 Creating datetime64 data
@@ -241,7 +240,6 @@ coordinate with dates from a no-leap calendar and a
 
    from itertools import product
    from cftime import DatetimeNoLeap
-
    dates = [DatetimeNoLeap(year, month, 1) for year, month in
             product(range(1, 3), range(1, 13))]
    da = xr.DataArray(np.arange(24), coords=[dates], dims=['time'], name='foo')

doc/whats-new.rst

@@ -13,9 +13,9 @@ What's New
     import xarray as xr
     np.random.seed(123456)
 
-.. _whats-new.0.11.3:
+.. _whats-new.0.12.0:
 
-v0.11.3 (unreleased)
+v0.12.0 (unreleased)
 --------------------
 
 Breaking changes
@@ -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.
@@ -45,18 +47,39 @@ Enhancements
   :py:class:`~xarray.CFTimeIndex` is now possible. (:issue:`2191`).
   By `Jwen Fai Low <https://github.com/jwenfai>`_ and
   `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
 ~~~~~~~~~
 
+- Silenced warnings that appear when using pandas 0.24.
+  By `Stephan Hoyer <https://github.com/shoyer>`_
 - Interpolating via resample now internally specifies ``bounds_error=False``
   as an argument to ``scipy.interpolate.interp1d``, allowing for interpolation
   from higher frequencies to lower frequencies.  Datapoints outside the bounds
   of the original time coordinate are now filled with NaN (:issue:`2197`). By
   `Spencer Clark <https://github.com/spencerkclark>`_.
+
+.. _whats-new.0.11.3:
+
+v0.11.3 (26 January 2019)
+-------------------------
+
+Bug fixes
+~~~~~~~~~
+
 - Saving files with times encoded with reference dates with timezones
   (e.g. '2000-01-01T00:00:00-05:00') no longer raises an error
   (:issue:`2649`).  By `Spencer Clark <https://github.com/spencerkclark>`_.
+- Fixed performance regression with ``open_mfdataset`` (:issue:`2662`).
+  By `Tom Nicholas <https://github.com/TomNicholas>`_.
+- Fixed supplying an explicit dimension in the ``concat_dim`` argument to
+  to ``open_mfdataset`` (:issue:`2647`).
+  By `Ben Root <https://github.com/WeatherGod>`_.
 
 .. _whats-new.0.11.2:
 

setup.py

@@ -15,8 +15,6 @@
     'Operating System :: OS Independent',
     'Intended Audience :: Science/Research',
     'Programming Language :: Python',
-    'Programming Language :: Python :: 2',
-    'Programming Language :: Python :: 2.7',
     'Programming Language :: Python :: 3',
     'Programming Language :: Python :: 3.5',
     'Programming Language :: Python :: 3.6',

xarray/__init__.py

@@ -1,7 +1,4 @@
 # flake8: noqa
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
 
 from ._version import get_versions
 __version__ = get_versions()['version']