Use flake8 rather than pycodestyle (#3010)

* A few flake fixes

* isort

* bunch of flake8 errors fixed

* flake8 config

* pep8speaks config

* run flake8 in travis

* docs to flake8

* pep8speaks configs inherited from setup.cfg

* too much isort, skipped base __init__

* imports

* install flake8 in travis

* update 3.6 reqs

.pep8speaks.yml

@@ -1,16 +1,6 @@
-# File : .pep8speaks.yml
-
-# This should be kept in sync with the duplicate config in the [pycodestyle]
-# block of setup.cfg.
+# https://github.com/OrkoHunter/pep8speaks for more info
+# pep8speaks will use the flake8 configs in `setup.cfg`
 
 scanner:
-    diff_only: False  # If True, errors caused by only the patch are shown
-
-pycodestyle:
-    max-line-length: 79
-    ignore:  # Errors and warnings to ignore
-        - E402  # module level import not at top of file
-        - E731  # do not assign a lambda expression, use a def
-        - E741  # ambiguous variable name
-        - W503  # line break before binary operator
-        - W504  # line break after binary operator
+    diff_only: False
+    linter: flake8

.travis.yml

@@ -60,7 +60,7 @@ script:
       cd doc;
       sphinx-build -n -j auto -b html -d _build/doctrees . _build/html;
     elif [[ "$CONDA_ENV" == "lint" ]]; then
-      pycodestyle xarray ;
+      flake8 ;
     elif [[ "$CONDA_ENV" == "py36-hypothesis" ]]; then
       pytest properties ;
     else

asv_bench/benchmarks/__init__.py

@@ -1,6 +1,5 @@
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
+from __future__ import absolute_import, division, print_function
+
 import itertools
 
 import numpy as np

ci/requirements-py36.yml

@@ -14,7 +14,7 @@ dependencies:
   - pytest-cov
   - pytest-env
   - coveralls
-  - pycodestyle
+  - flake8
   - numpy>=1.12
   - pandas>=0.19
   - scipy

ci/requirements-py37.yml

@@ -15,7 +15,7 @@ dependencies:
   - pytest-cov
   - pytest-env
   - coveralls
-  - pycodestyle
+  - flake8
   - numpy>=1.12
   - pandas>=0.19
   - scipy

doc/conf.py

@@ -13,11 +13,11 @@
 # serve to show the default.
 from __future__ import absolute_import, division, print_function
 
-from contextlib import suppress
 import datetime
 import os
 import subprocess
 import sys
+from contextlib import suppress
 
 import xarray
 

doc/contributing.rst

@@ -351,20 +351,18 @@ the more common ``PEP8`` issues:
   - passing arguments should have spaces after commas, e.g. ``foo(arg1, arg2, kw1='bar')``
 
 :ref:`Continuous Integration <contributing.ci>` will run
-the `pycodestyle <http://pypi.python.org/pypi/pycodestyle>`_ tool
+the `flake8 <http://flake8.pycqa.org/en/latest/>`_ tool
 and report any stylistic errors in your code. Therefore, it is helpful before
-submitting code to run the check yourself::
+submitting code to run the check yourself:
 
-   pycodestyle xarray
+   flake8
 
 Other recommended but optional tools for checking code quality (not currently
 enforced in CI):
 
 - `mypy <http://mypy-lang.org/>`_ performs static type checking, which can
   make it easier to catch bugs. Please run ``mypy xarray`` if you annotate any
   code with `type hints <https://docs.python.org/3/library/typing.html>`_.
-- `flake8 <http://pypi.python.org/pypi/flake8>`_ includes a few more automated
-  checks than those enforced by pycodestyle.
 - `isort <https://github.com/timothycrosley/isort>`_ will highlight
   incorrectly sorted imports. ``isort -y`` will automatically fix them. See
   also `flake8-isort <https://github.com/gforcada/flake8-isort>`_.

doc/examples/_code/weather_data_setup.py

@@ -1,6 +1,6 @@
 import numpy as np
 import pandas as pd
-import seaborn as sns  # pandas aware plotting library
+import seaborn as sns  # noqa, pandas aware plotting library
 
 import xarray as xr
 

setup.cfg

@@ -11,9 +11,18 @@ env =
     UVCDAT_ANONYMOUS_LOG=no
 
 # This should be kept in sync with .pep8speaks.yml
-[pycodestyle]
+[flake8]
 max-line-length=79
-ignore=E402,E731,E741,W503,W504
+ignore=
+    E402
+    E731
+    E741
+    W503
+    W504
+    # Unused imports; TODO: Allow typing to work without triggering errors
+    F401
+exclude=
+    doc
 
 [isort]
 default_section=THIRDPARTY

xarray/__init__.py

@@ -1,3 +1,4 @@
+""" isort:skip_file """
 # flake8: noqa
 
 from ._version import get_versions

xarray/backends/__init__.py

@@ -3,16 +3,16 @@
 DataStores provide a uniform interface for saving and loading data in different
 formats. They should not be used directly, but rather through Dataset objects.
 """
-from .common import AbstractDataStore
-from .file_manager import FileManager, CachingFileManager, DummyFileManager
 from .cfgrib_ import CfGribDataStore
+from .common import AbstractDataStore
+from .file_manager import CachingFileManager, DummyFileManager, FileManager
+from .h5netcdf_ import H5NetCDFStore
 from .memory import InMemoryDataStore
 from .netCDF4_ import NetCDF4DataStore
+from .pseudonetcdf_ import PseudoNetCDFDataStore
 from .pydap_ import PydapDataStore
 from .pynio_ import NioDataStore
 from .scipy_ import ScipyDataStore
-from .h5netcdf_ import H5NetCDFStore
-from .pseudonetcdf_ import PseudoNetCDFDataStore
 from .zarr import ZarrStore
 
 __all__ = [

xarray/backends/file_manager.py

@@ -1,7 +1,7 @@
 import contextlib
 import threading
-from typing import Any, Dict
 import warnings
+from typing import Any, Dict
 
 from ..core import utils
 from ..core.options import OPTIONS

xarray/backends/locks.py

@@ -1,7 +1,7 @@
 import multiprocessing
 import threading
-from typing import Any, MutableMapping
 import weakref
+from typing import Any, MutableMapping
 
 try:
     from dask.utils import SerializableLock

xarray/backends/netCDF4_.py

@@ -174,7 +174,7 @@ def _force_native_endianness(var):
         # if endian exists, remove it from the encoding.
         var.encoding.pop('endian', None)
     # check to see if encoding has a value for endian its 'native'
-    if not var.encoding.get('endian', 'native') is 'native':
+    if not var.encoding.get('endian', 'native') == 'native':
         raise NotImplementedError("Attempt to write non-native endian type, "
                                   "this is not supported by the netCDF4 "
                                   "python library.")
@@ -237,6 +237,7 @@ def _extract_nc4_variable_encoding(variable, raise_on_invalid=False,
 
 class GroupWrapper:
     """Wrap netCDF4.Group objects so closing them closes the root group."""
+
     def __init__(self, value):
         self.value = value
 

xarray/coding/variables.py

@@ -1,7 +1,7 @@
 """Coders for individual Variable objects."""
-from typing import Any
 import warnings
 from functools import partial
+from typing import Any
 
 import numpy as np
 import pandas as pd

xarray/core/accessor_str.py

@@ -45,7 +45,6 @@
 
 from .computation import apply_ufunc
 
-
 _cpython_optimized_encoders = (
     "utf-8", "utf8", "latin-1", "latin1", "iso-8859-1", "mbcs", "ascii"
 )

xarray/core/alignment.py

@@ -8,7 +8,7 @@
 import numpy as np
 import pandas as pd
 
-from . import utils, dtypes
+from . import dtypes, utils
 from .indexing import get_indexer_nd
 from .utils import is_dict_like, is_full_slice
 from .variable import IndexVariable, Variable

xarray/core/combine.py

@@ -4,12 +4,12 @@
 
 import pandas as pd
 
-from . import utils, dtypes
+from . import dtypes, utils
 from .alignment import align
+from .computation import result_name
 from .merge import merge
 from .variable import IndexVariable, Variable, as_variable
 from .variable import concat as concat_vars
-from .computation import result_name
 
 
 def concat(objs, dim=None, data_vars='all', coords='different',

xarray/core/common.py

@@ -1,8 +1,9 @@
 from collections import OrderedDict
 from contextlib import suppress
 from textwrap import dedent
-from typing import (Any, Callable, Hashable, Iterable, Iterator, List, Mapping,
-                    MutableMapping, Optional, Tuple, TypeVar, Union)
+from typing import (
+    Any, Callable, Hashable, Iterable, Iterator, List, Mapping, MutableMapping,
+    Optional, Tuple, TypeVar, Union)
 
 import numpy as np
 import pandas as pd
@@ -13,7 +14,6 @@
 from .pycompat import dask_array_type
 from .utils import Frozen, ReprObject, SortedKeysDict, either_dict_or_kwargs
 
-
 # Used as a sentinel value to indicate a all dimensions
 ALL_DIMS = ReprObject('<all-dims>')
 

xarray/core/dataset.py

@@ -8,7 +8,7 @@
 from distutils.version import LooseVersion
 from numbers import Number
 from typing import (
-    Any, Callable, Dict, List, Optional, Set, Tuple, TypeVar, Union, Sequence)
+    Any, Callable, Dict, List, Optional, Sequence, Set, Tuple, TypeVar, Union)
 
 import numpy as np
 import pandas as pd
@@ -35,8 +35,7 @@
 from .pycompat import TYPE_CHECKING, dask_array_type
 from .utils import (
     Frozen, SortedKeysDict, _check_inplace, decode_numpy_dict_values,
-    either_dict_or_kwargs, ensure_us_time_resolution, hashable, is_dict_like,
-    maybe_wrap_array)
+    either_dict_or_kwargs, hashable, maybe_wrap_array)
 from .variable import IndexVariable, Variable, as_variable, broadcast_variables
 
 if TYPE_CHECKING:
@@ -4145,7 +4144,7 @@ def _integrate_one(self, coord, datetime_unit=None):
         from .variable import Variable
 
         if coord not in self.variables and coord not in self.dims:
-            raise ValueError('Coordinate {} does not exist.'.format(dim))
+            raise ValueError('Coordinate {} does not exist.'.format(coord))
 
         coord_var = self[coord].variable
         if coord_var.ndim != 1:

xarray/core/duck_array_ops.py

@@ -4,9 +4,9 @@
 accept or return xarray objects.
 """
 import contextlib
-from functools import partial
 import inspect
 import warnings
+from functools import partial
 
 import numpy as np
 import pandas as pd

xarray/core/missing.py

@@ -9,7 +9,7 @@
 from . import utils
 from .common import _contains_datetime_like_objects
 from .computation import apply_ufunc
-from .duck_array_ops import dask_array_type, datetime_to_numeric
+from .duck_array_ops import dask_array_type
 from .utils import OrderedSet, is_scalar
 from .variable import Variable, broadcast_variables
 

xarray/core/options.py

@@ -59,7 +59,7 @@ def _warn_on_setting_enable_cftimeindex(enable_cftimeindex):
 def _get_keep_attrs(default):
     global_choice = OPTIONS['keep_attrs']
 
-    if global_choice is 'default':
+    if global_choice == 'default':
         return default
     elif global_choice in [True, False]:
         return global_choice

xarray/core/resample_cftime.py

@@ -36,14 +36,16 @@
 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-from ..coding.cftimeindex import CFTimeIndex
-from ..coding.cftime_offsets import (cftime_range, normalize_date,
-                                     Day, MonthEnd, QuarterEnd, YearEnd,
-                                     CFTIME_TICKS, to_offset)
 import datetime
+
 import numpy as np
 import pandas as pd
 
+from ..coding.cftime_offsets import (
+    CFTIME_TICKS, Day, MonthEnd, QuarterEnd, YearEnd, cftime_range,
+    normalize_date, to_offset)
+from ..coding.cftimeindex import CFTimeIndex
+
 
 class CFTimeGrouper:
     """This is a simple container for the grouping parameters that implements a

xarray/core/rolling.py

@@ -7,8 +7,8 @@
 from . import dtypes, duck_array_ops, utils
 from .dask_array_ops import dask_rolling_wrapper
 from .ops import (
-    bn, has_bottleneck, inject_coarsen_methods,
-    inject_bottleneck_rolling_methods, inject_datasetrolling_methods)
+    bn, has_bottleneck, inject_bottleneck_rolling_methods,
+    inject_coarsen_methods, inject_datasetrolling_methods)
 from .pycompat import dask_array_type
 
 

xarray/core/utils.py

@@ -7,16 +7,16 @@
 import re
 import warnings
 from collections import OrderedDict
-from typing import (AbstractSet, Any, Callable, Container, Dict, Hashable,
-                    Iterable, Iterator, Optional, Sequence,
-                    Tuple, TypeVar, cast)
+from typing import (
+    AbstractSet, Any, Callable, Container, Dict, Hashable, Iterable, Iterator,
+    Mapping, MutableMapping, MutableSet, Optional, Sequence, Tuple, TypeVar,
+    cast)
 
 import numpy as np
 import pandas as pd
 
 from .pycompat import dask_array_type
 
-from typing import Mapping, MutableMapping, MutableSet
 try:  # Fix typed collections in Python 3.5.0~3.5.2
     from .pycompat import Mapping, MutableMapping, MutableSet  # noqa: F811
 except ImportError:

xarray/plot/__init__.py

@@ -1,7 +1,5 @@
-from .plot import (plot, line, step, contourf, contour,
-                   hist, imshow, pcolormesh)
-
 from .facetgrid import FacetGrid
+from .plot import contour, contourf, hist, imshow, line, pcolormesh, plot, step
 
 __all__ = [
     'plot',

xarray/plot/facetgrid.py

@@ -1,14 +1,13 @@
 import functools
 import itertools
 import warnings
-from inspect import getfullargspec
 
 import numpy as np
 
 from ..core.formatting import format_item
 from .utils import (
-    _infer_xy_labels, _process_cmap_cbar_kwargs,
-    import_matplotlib_pyplot, label_from_attrs)
+    _infer_xy_labels, _process_cmap_cbar_kwargs, import_matplotlib_pyplot,
+    label_from_attrs)
 
 # Overrides axes.labelsize, xtick.major.size, ytick.major.size
 # from mpl.rcParams
@@ -483,7 +482,7 @@ def map(self, func, *args, **kwargs):
                 # TODO: better way to verify that an artist is mappable?
                 # https://stackoverflow.com/questions/33023036/is-it-possible-to-detect-if-a-matplotlib-artist-is-a-mappable-suitable-for-use-w#33023522
                 if (maybe_mappable and
-                   hasattr(maybe_mappable, 'autoscale_None')):
+                        hasattr(maybe_mappable, 'autoscale_None')):
                     self._mappables.append(maybe_mappable)
 
         self._finalize_grid(*args[:2])