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Description: Use xor rather than subtraction on booleans
Numpy no longer accepts the ambiguous construction of a-b when a and b are bools.
Normally, this can be replaced with XORs.
Author: Stuart Prescott <stuart@debian.org>
Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)
Origin: https://github.com/pycogent/pycogent/files/2072984/numpy_xor.patch
Bug-Debian: https://bugs.debian.org/899205
--- a/cogent/core/sequence.py
+++ b/cogent/core/sequence.py
@@ -1248,7 +1248,7 @@
gap_indices = map(self.Alphabet.index, self.MolType.Gaps)
valid_indices = self._data < len(self.Alphabet)
for i in gap_indices:
- valid_indices -= self._data == i
+ valid_indices ^= self._data == i
result = compress(valid_indices, self._data)
return self.__class__(result, Info=self.Info)
--- a/cogent/maths/distance_transform.py
+++ b/cogent/maths/distance_transform.py
@@ -670,9 +670,9 @@
return zeros((0,0),'d')
dists = zeros((numrows,numrows),'d')
for i in range(numrows):
- r1 = datamtx[i] # cache here
+ r1 = datamtx[i].astype(dists.dtype) # cache here
for j in range(i):
- dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j]))
+ dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j].astype(dists.dtype)))
return dists
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