Commit e29c6cdb authored by Andreas Tille's avatar Andreas Tille
Browse files

Fix suite fails with latest matplotlib

parent 6e4a81fc

debian/changelog

+2 −1
Original line number Diff line number Diff line
@@ -7,8 +7,9 @@ python-cogent (1.9-12) UNRELEASED; urgency=medium 
  * debhelper 11

  * Point Vcs fields to salsa.debian.org

  * Standards-Version: 4.1.4

  * Fix suite fails with latest matplotlib



 -- Andreas Tille <tille@debian.org>  Wed, 28 Mar 2018 19:03:41 +0200

 -- Andreas Tille <tille@debian.org>  Tue, 05 Jun 2018 21:47:29 +0200



python-cogent (1.9-11) unstable; urgency=medium

debian/patches/numpy-doctests.patch

0 → 100644
+26 −0
Original line number Diff line number Diff line 
Description: Ensure doctests pass with different numpy versions

 The numpy output format changed with numpy 1.14 and this causes doctests to

 fail if raw numerical output is compared. See

 https://wiki.debian.org/ContinuousIntegration/TriagingTips/numpy-1.14-doctests

Author: Stuart Prescott <stuart@debian.org>

Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)

Origin: https://github.com/pycogent/pycogent/files/2072985/numpy-doctests.patch

Bug-Debian: https://bugs.debian.org/899205



--- a/tests/alltests.py

+++ b/tests/alltests.py

@@ -6,6 +6,14 @@

 import doctest, cogent.util.unit_test as unittest, sys, os

 from cogent.util.misc import app_path

 

+# Whitespace changes between numpy 1.13 and 1.14 will cause the doctests

+# to fail; when doctests are updated to 1.14 format, this can be removed.

+try:    # CRUFT

+    import numpy as np

+    np.set_printoptions(legacy='1.13')

+except TypeError:

+    pass

+

 __author__ = "Peter Maxwell and Gavin Huttley"

 __copyright__ = "Copyright 2007-2016, The Cogent Project"

 __credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",

debian/patches/numpy_xor.patch

0 → 100644
+33 −0
Original line number Diff line number Diff line 
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

debian/patches/series

+2 −0
Original line number Diff line number Diff line
@@ -9,3 +9,5 @@ skip_weak_tests.patch 
adapt_to_ncbi-data_201609.patch

ignore_numpy_test_issue.patch

usr_bin_ls.patch

numpy_xor.patch

numpy-doctests.patch