numpy boolean subtract, the `-` operator, is deprecated, use the bitwise_xor, the `^` operator, or the logical_xor function instead (Was: Bug#899205: python-cogent: Test suite fails with latest matplo
Control: tags -1 help Hi, I have reported the issue upstream but no response so far. While the error message contains some hint how to solve the issue I would like to backup this by some competent advise. == ERROR: test_consistent_gap_degen_handling (test_core.test_sequence.ModelSequenceTests) gap degen character should be treated consistently -- Traceback (most recent call last): File "/tmp/autopkgtest-lxc.5a99fnj6/downtmp/autopkgtest_tmp/tests/test_core/test_sequence.py", line 660, in test_consistent_gap_degen_handling self.assertEqual(dna.stripBadAndGaps(), raw_ungapped) File "/usr/lib/python2.7/dist-packages/cogent/core/sequence.py", line 1251, in stripBadAndGaps valid_indices -= self._data == i TypeError: numpy boolean subtract, the `-` operator, is deprecated, use the bitwise_xor, the `^` operator, or the logical_xor function instead. == I would be happy for some suggested patch how to solve this. The line in question is https://salsa.debian.org/med-team/python-cogent/blob/master/cogent/core/sequence.py Line 1251 If my feeling is not totally wrong the correct patch would be valid_indices -= (self._data == i) since the left value is rather an integer than boolean. What do you think? Kind regards Andreas. -- http://fam-tille.de
RFS: pcapy/0.11.3-1 [ITA]
Package: sponsorship-requests Severity: normal Dear mentors, I am looking for a sponsor for my package "pcapy" * Package name: pcapy Version : 0.11.3-1 Upstream Author : Core Security * URL : https://github.com/CoreSecurity/pcapy * License : Apache Software License Section : python It builds those binary packages: python-pcapy - Python interface to the libpcap packet capture library To access further information about this package, please visit the following URL: https://mentors.debian.net/package/pcapy Alternatively, one can download the package with dget using this command: dget -x https://mentors.debian.net/debian/pool/main/p/pcapy/pcapy_0.11.3-1.dsc More information about hello can be obtained from https://www.example.com. Changes since the last upload: [ Jakub Wilk ] * Use canonical URIs for Vcs-* fields. [ Ondřej Nový ] * Fixed VCS URL (https) * d/control: Set Vcs-* to salsa.debian.org * d/changelog: Remove trailing whitespaces * Remove debian/pycompat, it's not used by any modern Python helper [ Emmanuel Arias ] * new upstream version * update d/watch to download correctly the last upstream version * update d/control to add Maintainer the DPMT * update d/control to add me to Uploaders field (Closes: #895787) * update debhelper on d/contorl from 5.0.37.2 to 11 * update Standards-Version from 3.9.2 to 4.1.4 on d/control * add Testsuite: autopkgtest-pkg-python on d/control * update d/compat from 5 to 11 * add to copyright file the debian files copyright Regards, Emmanuel -- Arias Emmanuel https://www.linkedin.com/in/emmanuel-arias-437a6a8a http://eamanu.com
Re: Broken dbgsym packages for Python 3
On Tue, 5 Jun 2018, Andrey Rahmatullin wrote: Yes, I'm talking about the automatically generated -dbgsym packages that contain the /usr/lib/debug/.build-id/... files. Have you read Scott's email? Yes, but wouldn't they still be useful for symbolicating core dumps? Scott
Re: numpy boolean subtract, the `-` operator, is deprecated, use the bitwise_xor, the `^` operator, or the logical_xor function instead (Was: Bug#899205: python-cogent: Test suite fails with latest ma
On 05/06/2018 01:00, Andreas Tille wrote: > == > ERROR: test_consistent_gap_degen_handling > (test_core.test_sequence.ModelSequenceTests) > gap degen character should be treated consistently > -- > Traceback (most recent call last): > File > "/tmp/autopkgtest-lxc.5a99fnj6/downtmp/autopkgtest_tmp/tests/test_core/test_sequence.py", > line 660, in test_consistent_gap_degen_handling > self.assertEqual(dna.stripBadAndGaps(), raw_ungapped) > File "/usr/lib/python2.7/dist-packages/cogent/core/sequence.py", line 1251, > in stripBadAndGaps > valid_indices -= self._data == i > TypeError: numpy boolean subtract, the `-` operator, is deprecated, use the > bitwise_xor, the `^` operator, or the logical_xor function instead. > > == > > > I would be happy for some suggested patch how to solve this. The line > in question is > > > https://salsa.debian.org/med-team/python-cogent/blob/master/cogent/core/sequence.py > >Line 1251 > > If my feeling is not totally wrong the correct patch would be > >valid_indices -= (self._data == i) > > since the left value is rather an integer than boolean. > > What do you think? Without analyzing the code in the fine details, and assuming self._data is a numpy array or a subclass, I think the name of the variable is misleading. Looking at the whole function it seems to be a bool array. It should be easy to confirm this with pdb or simply inserting a print() statement in the right place. def stripBadAndGaps(self): """Returns copy of self with bad chars and gaps excised.""" 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 result = compress(valid_indices, self._data) return self.__class__(result, Info=self.Info) The fix should be to replace the subtraction with: valid_indices ^= self._data == i Cheers, Dan
Re: numpy boolean subtract, the `-` operator, is deprecated, use the bitwise_xor, the `^` operator, or the logical_xor function instead (Was: Bug#899205: python-cogent: Test suite fails with latest ma
Hi Andreas, > == > ERROR: test_consistent_gap_degen_handling > (test_core.test_sequence.ModelSequenceTests) gap degen character should be > treated consistently > -- > Traceback (most recent call last): > File > "/tmp/autopkgtest- lxc.5a99fnj6/downtmp/autopkgtest_tmp/tests/test_core/test_sequence.py", > line 660, in test_consistent_gap_degen_handling > self.assertEqual(dna.stripBadAndGaps(), raw_ungapped) > File "/usr/lib/python2.7/dist-packages/cogent/core/sequence.py", line > 1251, in stripBadAndGaps > valid_indices -= self._data == i > TypeError: numpy boolean subtract, the `-` operator, is deprecated, use > the bitwise_xor, the `^` operator, or the logical_xor function instead. > > == The error message basically describes the solution -- patch attached. Quite what the original meaning of "bool - bool" was supposed to be is hard to discern (and that is why numpy has deprecated it). You should get upstream to look at this carefully. Note that there is more than one test that fails like this. There also may be other places depending on how good their test coverage is. There are also failing doctests; a patch for them also attached, permitting the test to work with both old and new numpy. These two patches only get the package to compile though. Lintian will then tell you about other RC bugs that you need to fix prior to upload. regards Stuart -- Stuart Prescotthttp://www.nanonanonano.net/ stu...@nanonanonano.net Debian Developer http://www.debian.org/ stu...@debian.org GPG fingerprint90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7Description: 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 --- 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 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 --- 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",
Dask sourceless javascript passed by me.
Hi, I discovered a mistake I made with packaging dask. There's two static html files which embed some bokeh generated javascript plot code that's in dask 0.17.5 and I uploaded that to the Debian. There doesn't appear to be source to build the files. Bokeh is free software (BSD-3-Clause), but depends on a bunch of javascript libraries so isn't available in Debian. I should have repacked the archive to remove them, but I'm working on a -2 release, and there's no new upstream release yet for me to use as a base for repack. I was planning on patching the references to the .html files out and removing them in the debian/rules files. But is that enough? Diane signature.asc Description: This is a digitally signed message part
Re: Dask sourceless javascript passed by me.
On Wed, Jun 6, 2018 at 12:30 PM, Diane Trout wrote: > I was planning on patching the references to the .html files out and > removing them in the debian/rules files. > > But is that enough? That doesn't fix the orig.tar.gz. I would suggest talking to upstream about fixing this properly (no prebuilt files or embedded code copies in the VCS and tarballs). -- bye, pabs https://wiki.debian.org/PaulWise
Re: Dask sourceless javascript passed by me.
On June 6, 2018 4:42:44 AM UTC, Paul Wise wrote: >On Wed, Jun 6, 2018 at 12:30 PM, Diane Trout wrote: > >> I was planning on patching the references to the .html files out and >> removing them in the debian/rules files. >> >> But is that enough? > >That doesn't fix the orig.tar.gz. > >I would suggest talking to upstream about fixing this properly (no >prebuilt files or embedded code copies in the VCS and tarballs). And in the meantime repacking the existing tarball to remove the sourceless files. Scott K
