Merge remote-tracking branch 'upstream/master'

.travis.yml

@@ -11,7 +11,6 @@ matrix:
   fast_finish: true
   include:
   - env: CONDA_ENV=py35-min
-  - env: CONDA_ENV=py35
   - env: CONDA_ENV=py36
   - env: CONDA_ENV=py37
   - env:

appveyor.yml

@@ -35,4 +35,4 @@ install:
 build: false
 
 test_script:
-  - "py.test xarray --verbose"
+  - "py.test xarray"

asv_bench/benchmarks/dataset_io.py

@@ -19,7 +19,7 @@
 os.environ['HDF5_USE_FILE_LOCKING'] = 'FALSE'
 
 
-class IOSingleNetCDF(object):
+class IOSingleNetCDF:
     """
     A few examples that benchmark reading/writing a single netCDF file with
     xarray
@@ -214,7 +214,7 @@ def time_load_dataset_scipy_with_time_chunks(self):
                             chunks=self.time_chunks).load()
 
 
-class IOMultipleNetCDF(object):
+class IOMultipleNetCDF:
     """
     A few examples that benchmark reading/writing multiple netCDF files with
     xarray
@@ -419,7 +419,7 @@ def create_delayed_write():
     return ds.to_netcdf('file.nc', engine='netcdf4', compute=False)
 
 
-class IOWriteNetCDFDask(object):
+class IOWriteNetCDFDask:
     timeout = 60
     repeat = 1
     number = 5
@@ -432,7 +432,7 @@ def time_write(self):
         self.write.compute()
 
 
-class IOWriteNetCDFDaskDistributed(object):
+class IOWriteNetCDFDaskDistributed:
     def setup(self):
         try:
             import distributed

asv_bench/benchmarks/indexing.py

@@ -58,7 +58,7 @@
 }
 
 
-class Base(object):
+class Base:
     def setup(self, key):
         self.ds = xr.Dataset(
             {'var1': (('x', 'y'), randn((nx, ny), frac_nan=0.1)),

asv_bench/benchmarks/interp.py

@@ -24,7 +24,7 @@
 new_y_long = np.linspace(0.1, 0.9, 1000)
 
 
-class Interpolation(object):
+class Interpolation:
     def setup(self, *args, **kwargs):
         self.ds = xr.Dataset(
             {'var1': (('x', 'y'), randn_xy),

asv_bench/benchmarks/reindexing.py

@@ -7,7 +7,7 @@
 from . import requires_dask
 
 
-class Reindex(object):
+class Reindex:
     def setup(self):
         data = np.random.RandomState(0).randn(1000, 100, 100)
         self.ds = xr.Dataset({'temperature': (('time', 'x', 'y'), data)},

asv_bench/benchmarks/rolling.py

@@ -19,7 +19,7 @@
 randn_long = randn((long_nx, ), frac_nan=0.1)
 
 
-class Rolling(object):
+class Rolling:
     def setup(self, *args, **kwargs):
         self.ds = xr.Dataset(
             {'var1': (('x', 'y'), randn_xy),

asv_bench/benchmarks/unstacking.py

@@ -7,7 +7,7 @@
 from . import requires_dask
 
 
-class Unstacking(object):
+class Unstacking:
     def setup(self):
         data = np.random.RandomState(0).randn(1, 1000, 500)
         self.ds = xr.DataArray(data).stack(flat_dim=['dim_1', 'dim_2'])

ci/requirements-py36-dask-dev.yml

@@ -13,8 +13,8 @@ dependencies:
   - pytest-env
   - coveralls
   - flake8
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz

ci/requirements-py36-hypothesis.yml

@@ -15,8 +15,8 @@ dependencies:
   - coveralls
   - hypothesis
   - flake8
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz

ci/requirements-py36-pandas-dev.yml

@@ -16,7 +16,7 @@ dependencies:
   - pytest-env
   - coveralls
   - flake8
-  - numpy
+  - numpy>=1.12
   - scipy
   - toolz
   - pip:

ci/requirements-py36-rasterio.yml

@@ -14,8 +14,8 @@ dependencies:
   - pytest-cov
   - pytest-env
   - coveralls
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz

ci/requirements-py36-windows.yml

@@ -12,11 +12,10 @@ dependencies:
   - netcdf4
   - pytest
   - pytest-env
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz
   - rasterio
   - zarr
-

ci/requirements-py36-zarr-dev.yml

@@ -12,8 +12,8 @@ dependencies:
   - pytest-env
   - coveralls
   - flake8
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz

ci/requirements-py36.yml

@@ -15,8 +15,8 @@ dependencies:
   - pytest-env
   - coveralls
   - pycodestyle
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz

ci/requirements-py37-windows.yml

@@ -13,8 +13,8 @@ dependencies:
   - netcdf4
   - pytest
   - pytest-env
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz

ci/requirements-py37.yml

@@ -16,8 +16,8 @@ dependencies:
   - pytest-env
   - coveralls
   - pycodestyle
-  - numpy
-  - pandas
+  - numpy>=1.12
+  - pandas>=0.19
   - scipy
   - seaborn
   - toolz

doc/contributing.rst

@@ -457,7 +457,7 @@ typically find tests wrapped in a class.
 
 .. code-block:: python
 
-    class TestReallyCoolFeature(object):
+    class TestReallyCoolFeature:
         ....
 
 Going forward, we are moving to a more *functional* style using the

doc/examples/_code/accessor_example.py

@@ -2,7 +2,7 @@
 
 
 @xr.register_dataset_accessor('geo')
-class GeoAccessor(object):
+class GeoAccessor:
     def __init__(self, xarray_obj):
         self._obj = xarray_obj
         self._center = None

doc/gallery/plot_rasterio.py

@@ -16,22 +16,16 @@
 original map projection (see :ref:`recipes.rasterio_rgb`).
 """
 
-import os
-import urllib.request
-
 import cartopy.crs as ccrs
 import matplotlib.pyplot as plt
 import numpy as np
 from rasterio.warp import transform
 
 import xarray as xr
 
-# Download the file from rasterio's repository
-url = 'https://github.com/mapbox/rasterio/raw/master/tests/data/RGB.byte.tif'
-urllib.request.urlretrieve(url, 'RGB.byte.tif')
-
 # Read the data
-da = xr.open_rasterio('RGB.byte.tif')
+url = 'https://github.com/mapbox/rasterio/raw/master/tests/data/RGB.byte.tif'
+da = xr.open_rasterio(url)
 
 # Compute the lon/lat coordinates with rasterio.warp.transform
 ny, nx = len(da['y']), len(da['x'])
@@ -54,6 +48,3 @@
                cmap='Greys_r', add_colorbar=False)
 ax.coastlines('10m', color='r')
 plt.show()
-
-# Delete the file
-os.remove('RGB.byte.tif')

doc/gallery/plot_rasterio_rgb.py

@@ -13,20 +13,14 @@
 transformation.
 """
 
-import os
-import urllib.request
-
 import cartopy.crs as ccrs
 import matplotlib.pyplot as plt
 
 import xarray as xr
 
-# Download the file from rasterio's repository
-url = 'https://github.com/mapbox/rasterio/raw/master/tests/data/RGB.byte.tif'
-urllib.request.urlretrieve(url, 'RGB.byte.tif')
-
 # Read the data
-da = xr.open_rasterio('RGB.byte.tif')
+url = 'https://github.com/mapbox/rasterio/raw/master/tests/data/RGB.byte.tif'
+da = xr.open_rasterio(url)
 
 # The data is in UTM projection. We have to set it manually until
 # https://github.com/SciTools/cartopy/issues/813 is implemented
@@ -37,6 +31,3 @@
 da.plot.imshow(ax=ax, rgb='band', transform=crs)
 ax.coastlines('10m', color='r')
 plt.show()
-
-# Delete the file
-os.remove('RGB.byte.tif')

doc/related-projects.rst

@@ -33,6 +33,7 @@ Geosciences
 - `xarray-simlab <https://xarray-simlab.readthedocs.io>`_: xarray extension for computer model simulations.
 - `xarray-topo <https://gitext.gfz-potsdam.de/sec55-public/xarray-topo>`_: xarray extension for topographic analysis and modelling.
 - `xbpch <https://github.com/darothen/xbpch>`_: xarray interface for bpch files.
+- `xclim <https://xclim.readthedocs.io/>`_: A library for calculating climate science indices with unit handling built from xarray and dask.
 - `xESMF <https://xesmf.readthedocs.io>`_: Universal Regridder for Geospatial Data.
 - `xgcm <https://xgcm.readthedocs.io/>`_: Extends the xarray data model to understand finite volume grid cells (common in General Circulation Models) and provides interpolation and difference operations for such grids.
 - `xmitgcm <http://xgcm.readthedocs.io/>`_: a python package for reading `MITgcm <http://mitgcm.org/>`_ binary MDS files into xarray data structures.

doc/whats-new.rst

@@ -21,17 +21,26 @@ v0.12.2 (unreleased)
 Enhancements
 ~~~~~~~~~~~~
 
+- Add ``fill_value`` argument for reindex, align, and merge operations
+  to enable custom fill values. (:issue:`2876`)
+  By `Zach Griffith <https://github.com/zdgriffith>`_.
 - Character arrays' character dimension name decoding and encoding handled by
   ``var.encoding['char_dim_name']`` (:issue:`2895`)
   By `James McCreight <https://github.com/jmccreight>`_.
-
+- Clean up Python 2 compatibility in code (:issue:`2950`)
+  By `Guido Imperiale <https://github.com/crusaderky>`_.
+
 Bug fixes
 ~~~~~~~~~
 
 - indexing with an empty list creates an object with zero-length axis (:issue:`2882`)
   By `Mayeul d'Avezac <https://github.com/mdavezac>`_.
 - Return correct count for scalar datetime64 arrays (:issue:`2770`)
   By `Dan Nowacki <https://github.com/dnowacki-usgs>`_.
+- Fix facetgrid colormap bug when ``extend=True``. (:issue:`2932`)
+  By `Deepak Cherian <https://github.com/dcherian`_.
+- A deep copy deep-copies the coords (:issue:`1463`)
+  By `Martin Pletcher <https://github.com/pletchm>`_.
 
 .. _whats-new.0.12.1:
 

xarray/backends/api.py

@@ -529,7 +529,7 @@ def open_dataarray(filename_or_obj, group=None, decode_cf=True,
     return data_array
 
 
-class _MultiFileCloser(object):
+class _MultiFileCloser:
     def __init__(self, file_objs):
         self.file_objs = file_objs
 

xarray/backends/common.py

@@ -154,7 +154,7 @@ def __exit__(self, exception_type, exception_value, traceback):
         self.close()
 
 
-class ArrayWriter(object):
+class ArrayWriter:
     def __init__(self, lock=None):
         self.sources = []
         self.targets = []

xarray/backends/file_manager.py

@@ -19,7 +19,7 @@
 _DEFAULT_MODE = utils.ReprObject('<unused>')
 
 
-class FileManager(object):
+class FileManager:
     """Manager for acquiring and closing a file object.
 
     Use FileManager subclasses (CachingFileManager in particular) on backend
@@ -237,7 +237,7 @@ def __repr__(self):
             type(self).__name__, self._opener, args_string, self._kwargs)
 
 
-class _RefCounter(object):
+class _RefCounter:
     """Class for keeping track of reference counts."""
     def __init__(self, counts):
         self._counts = counts

xarray/backends/locks.py

@@ -135,7 +135,7 @@ def acquire(lock, blocking=True):
         return lock.acquire(blocking)
 
 
-class CombinedLock(object):
+class CombinedLock:
     """A combination of multiple locks.
 
     Like a locked door, a CombinedLock is locked if any of its constituent
@@ -167,7 +167,7 @@ def __repr__(self):
         return "CombinedLock(%r)" % list(self.locks)
 
 
-class DummyLock(object):
+class DummyLock:
     """DummyLock provides the lock API without any actual locking."""
 
     def acquire(self, blocking=True):

xarray/backends/netCDF4_.py

@@ -228,7 +228,7 @@ def _extract_nc4_variable_encoding(variable, raise_on_invalid=False,
     return encoding
 
 
-class GroupWrapper(object):
+class GroupWrapper:
     """Wrap netCDF4.Group objects so closing them closes the root group."""
     def __init__(self, value):
         self.value = value