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Groups > linux.debian.maint.python > #10612 > unrolled thread
| Started by | Stuart Prescott <stuart@debian.org> |
|---|---|
| First post | 2018-06-05 17:30 +0200 |
| Last post | 2018-06-05 17:30 +0200 |
| Articles | 1 — 1 participant |
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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 matplotlib) Stuart Prescott <stuart@debian.org> - 2018-06-05 17:30 +0200
| From | Stuart Prescott <stuart@debian.org> |
|---|---|
| Date | 2018-06-05 17:30 +0200 |
| Subject | 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 matplotlib) |
| Message-ID | <vXm4h-7gs-3@gated-at.bofh.it> |
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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 Prescott http://www.nanonanonano.net/ stuart@nanonanonano.net Debian Developer http://www.debian.org/ stuart@debian.org GPG fingerprint 90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7
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