Andreas Tille pushed to branch master at Debian Med / python-cogent
Commits: e29c6cdb by Andreas Tille at 2018-06-05T21:53:43+02:00 Fix suite fails with latest matplotlib - - - - - 4 changed files: - debian/changelog - + debian/patches/numpy-doctests.patch - + debian/patches/numpy_xor.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -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 <[email protected]> Wed, 28 Mar 2018 19:03:41 +0200 + -- Andreas Tille <[email protected]> Tue, 05 Jun 2018 21:47:29 +0200 python-cogent (1.9-11) unstable; urgency=medium ===================================== debian/patches/numpy-doctests.patch ===================================== --- /dev/null +++ b/debian/patches/numpy-doctests.patch @@ -0,0 +1,26 @@ +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 <[email protected]> +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 ===================================== --- /dev/null +++ b/debian/patches/numpy_xor.patch @@ -0,0 +1,33 @@ +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 <[email protected]> +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 ===================================== --- a/debian/patches/series +++ b/debian/patches/series @@ -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 View it on GitLab: https://salsa.debian.org/med-team/python-cogent/commit/e29c6cdbf0f3cb2cf8f6a18a79359fdbb6b76d8a -- View it on GitLab: https://salsa.debian.org/med-team/python-cogent/commit/e29c6cdbf0f3cb2cf8f6a18a79359fdbb6b76d8a You're receiving this email because of your account on salsa.debian.org.
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