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Apply yapf to python files

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This commit is contained in:
Matt Weiden
2019-12-19 15:20:41 -08:00
parent 42a8d45bd7
commit cdca128a01
43 changed files with 1143 additions and 678 deletions
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server/app/util/matrix_proxy.py
+42 -29
View File
@@ -2,7 +2,6 @@ import abc
from itertools import zip_longest
from copy import copy
import numpy as np
"""
cellxgene deals with a variety of matrix data types, many of which do
not support a consistent API. This framework allows proxies to be created
@@ -18,6 +17,7 @@ class _ArrayProxyBase(abc.ABC):
Private base class for array or matrix proxy. This summarizes
the interface used by the rest of cellxgene.
"""
@property
@abc.abstractmethod
def dtype(self):
@@ -59,7 +59,6 @@ class MatrixProxy(_ArrayProxyBase):
This class primarily provides the factory method and related support.
All other functionality is delegated to subclasses.
"""
"""
Registry of types to proxy class, where values are:
* None: unsupported
@@ -128,21 +127,25 @@ class MatrixProxyView(MatrixProxy):
"""
2D matrix view to a 2D matrix
"""
def __init__(self, arg1, shape=None, index=(),
transposed=False, copy=False):
def __init__(self,
arg1,
shape=None,
index=(),
transposed=False,
copy=False):
if not copy:
m = arg1
super().__init__(m)
if shape is None:
shape = m.shape
assert(len(shape) == 2)
assert (len(shape) == 2)
index = tuple(
map(lambda s_i:
slice(0, s_i[0], 1) if s_i[1] is None else s_i[1],
zip_longest(shape, index))
)
map(
lambda s_i: slice(0, s_i[0], 1)
if s_i[1] is None else s_i[1], zip_longest(shape, index)))
self._shape = shape
self._index = index
@@ -234,21 +237,29 @@ class MatrixProxyView(MatrixProxy):
NOTE: these follow the numpy rules for dimensionality reduction
when an integer index is specified.
"""
def _getitem_intXint(self, row, col):
return self.m[row, col]
def _getitem_intXslice(self, row, col):
shape = (_slice_length(col, self.m.shape[1]), )
return self.__class__.create_array(self.m, shape=shape, index=(row, col))
shape = (_slice_length(col, self.m.shape[1]),)
return self.__class__.create_array(self.m,
shape=shape,
index=(row, col))
def _getitem_sliceXint(self, row, col):
shape = (_slice_length(row, self.m.shape[0]), )
return self.__class__.create_array(self.m, shape=shape, index=(row, col))
shape = (_slice_length(row, self.m.shape[0]),)
return self.__class__.create_array(self.m,
shape=shape,
index=(row, col))
def _getitem_sliceXslice(self, row, col):
shape = (_slice_length(row, self.m.shape[0]),
_slice_length(col, self.m.shape[1]))
return self.__class__(self.m, shape=shape, index=(row, col), transposed=self.transposed)
return self.__class__(self.m,
shape=shape,
index=(row, col),
transposed=self.transposed)
def toarray(self):
arr = self.m[self._index]
@@ -261,22 +272,24 @@ class ArrayProxyView(_ArrayProxyBase):
"""
1D array view to a 2D matrix
"""
def __init__(self, arg1, shape=None, index=None, copy=False):
super().__init__()
if not copy:
m = arg1
# one index MUST be an integer and the other MUST be a slice
assert(len(index) == 2)
assert(all(isinstance(idx, INT_TYPES + (slice, )) for idx in index))
assert(isinstance(index[0], INT_TYPES) != isinstance(index[1], INT_TYPES))
assert (len(index) == 2)
assert (all(isinstance(idx, INT_TYPES + (slice,)) for idx in index))
assert (isinstance(index[0], INT_TYPES) != isinstance(
index[1], INT_TYPES))
if shape is None:
if isinstance(index[0], INT_TYPES):
shape = (m.shape[0], )
shape = (m.shape[0],)
else:
shape = (m.shape[1], )
assert(len(shape) == 1)
shape = (m.shape[1],)
assert (len(shape) == 1)
self._shape = shape
self.m = m
@@ -336,7 +349,7 @@ class ArrayProxyView(_ArrayProxyBase):
elif isinstance(col, slice):
return self._getitem_intXslice(row, col)
elif isinstance(row, slice):
assert(isinstance(col, INT_TYPES))
assert (isinstance(col, INT_TYPES))
return self._getitem_sliceXint(row, col)
raise IndexError("unsupported column index types")
@@ -345,11 +358,11 @@ class ArrayProxyView(_ArrayProxyBase):
return self.m[row, col]
def _getitem_intXslice(self, row, col):
shape = (_slice_length(col, self.m.shape[1]), )
shape = (_slice_length(col, self.m.shape[1]),)
return self.__class__(self.m, shape=shape, index=(row, col))
def _getitem_sliceXint(self, row, col):
shape = (_slice_length(row, self.m.shape[0]), )
shape = (_slice_length(row, self.m.shape[0]),)
return self.__class__(self.m, shape=shape, index=(row, col))
def toarray(self):
@@ -358,7 +371,7 @@ class ArrayProxyView(_ArrayProxyBase):
def _unpack_index(index, shape):
if not isinstance(index, tuple):
index = (index, )
index = (index,)
if len(shape) < len(index):
raise IndexError("invalid index dimensionality - must be 2")
@@ -366,7 +379,7 @@ def _unpack_index(index, shape):
for shp, idx in zip_longest(shape, index):
idx = slice(None) if idx is None else idx
idx = _slice_defaults(idx, shp) if isinstance(idx, slice) else idx
unpacked += (idx, )
unpacked += (idx,)
return unpacked
@@ -376,7 +389,7 @@ def _slice_slice(outer, outer_len, inner, inner_len):
slice a slice - we take advantage of Python 3 range's support
for indexing.
"""
assert(outer_len >= inner_len)
assert (outer_len >= inner_len)
outer_rng = range(*outer.indices(outer_len))
rng = outer_rng[inner]
start, stop, step = rng.start, rng.stop, rng.step
@@ -387,8 +400,8 @@ def _slice_slice(outer, outer_len, inner, inner_len):
def _range_length(start, stop, step):
""" return length of range """
assert(step != 0)
assert(start is not None and stop is not None and step is not None)
assert (step != 0)
assert (start is not None and stop is not None and step is not None)
if step > 0 and start < stop:
return 1 + (stop - 1 - start) // step
elif step < 0 and start > stop:
@@ -404,7 +417,7 @@ def _slice_length(s, length):
def _slice_defaults(s, length):
""" apply slice defaulting conventions """
assert(length >= 0)
assert (length >= 0)
step = 1 if s.step is None else s.step