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Source: openbabel

openbabel (3.1.1+dfsg-3ubuntu1) groovy; urgency=medium * Merge from Debian unstable. Remaining changes: - Make the autopkg tests more verbose, don't fail on the first failing test. - Re-enable the tests on arm64. - Skip the test/testroundtrip.py test on all architectures, times out on the buildds. - Skip the testbindings.py and testsym.py tests on non amd64 architectures. - debian/patches/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch: - upstream fix for test/testdistgeom.py test failure - Skip also test/testobconv_writers.py, they are new tests, fail on non-amd64 targets (precision issue) -- Gianfranco Costamagna <locutusofborg@debian.org> Sat, 13 Jun 2020 23:51:20 +0200

Modifications :
  1. Download patch debian/patches/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch

    --- 3.1.1+dfsg-3/debian/patches/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch 1970-01-01 00:00:00.000000000 +0000 +++ 3.1.1+dfsg-3ubuntu1/debian/patches/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch 2020-06-13 21:51:08.000000000 +0000 @@ -0,0 +1,42 @@ +## Description: add some description +## Origin/Author: add some origin or author +## Bug: bug URL +From 7de27f309db5f7ec026ef5c5235e5b33bf7d1a85 Mon Sep 17 00:00:00 2001 +From: John Bollinger <John.Bollinger@StJude.org> +Date: Thu, 14 May 2020 08:46:40 -0500 +Subject: [PATCH] Fix test failure with Python 3 + +When run with Python 3.6, test/testdistgeom.py fails with a SyntaxError +about a malformed character escape. This arises from a failure to escape +literal backslash characters in single-quoted SMILES strings (several +occurrences). Python 2 accepts this and does the right things with it, +but Python 3 rejects it. + +Fixes #2217 +--- + test/testdistgeom.py | 10 +++++----- + 1 file changed, 5 insertions(+), 5 deletions(-) + +diff --git a/test/testdistgeom.py b/test/testdistgeom.py +index 0fa5adb57..fc3a7515b 100644 +--- a/test/testdistgeom.py ++++ b/test/testdistgeom.py +@@ -42,13 +42,13 @@ def testSMItoSMI(self): + 'C1CC[C@H]2[C@@H](C1)CCCC2', # cis-decalin + 'C1CC[C@@H]2[C@@H](C1)CCCC2', # trans-decalin + '[C@H]1(NC[C@H]2[C@H]1N2)OC', +- 'Clc1cccc(Cl)c1\C=N\NC(=O)c1cccs1', +- 'O=C1NC(=S)S\C1=C/c1ccco1', ++ 'Clc1cccc(Cl)c1\\C=N\\NC(=O)c1cccs1', ++ 'O=C1NC(=S)S\\C1=C/c1ccco1', + 'S=C1NC(=O)/C(=C/c2ccco2)/S1', +- 'O=C1NC(=S)N\C1=C\c1ccncc1', ++ 'O=C1NC(=S)N\\C1=C\\c1ccncc1', + 'S=C1NC(=O)C(=C)N1', +- 'CC(=O)N\N=C\c1ccncc1', +- 'N/N=c/1\sc2c(n1C)cccc2', ++ 'CC(=O)N\\N=C\\c1ccncc1', ++ 'N/N=c/1\\sc2c(n1C)cccc2', + 'OCCN/C=C\\1/C(=NN(C1=O)c1ccccc1)C', + 'Cc1ccc(o1)/C=C/C=O', + # disabled to make test run faster:
  2. Download patch debian/tests/python3

    --- 3.1.1+dfsg-3/debian/tests/python3 2020-06-09 07:00:07.000000000 +0000 +++ 3.1.1+dfsg-3ubuntu1/debian/tests/python3 2020-06-13 21:51:08.000000000 +0000 @@ -1,10 +1,33 @@ #!/bin/bash -test "$(dpkg --print-architecture)" = arm64 && exit 77 +#test "$(dpkg --print-architecture)" = arm64 && exit 77 sed -i 's/"\.\."/"\/usr"/' test/testbabel.py +arch=$(dpkg --print-architecture) +fails= for TEST in test/test*.py do - python3 ${TEST} + case $TEST in + test/testroundtrip.py) + echo "Skipping ${TEST} ..." + continue;; + test/testbindings.py|test/testsym.py|test/testobconv_writers.py) + case "$arch" in arm64|armhf|ppc64el|s390x) + echo "Skipping ${TEST} on $arch ..." + continue;; + esac;; + esac + echo "Running ${TEST} ..." + if python3 ${TEST}; then + : + else + fails="$fails $TEST" + fi done + +if [ -n "$fails" ]; then + echo "Failing tests: $fails" + exit 1 +fi +exit 0
  3. Download patch debian/patches/series

    --- 3.1.1+dfsg-3/debian/patches/series 2020-06-09 07:00:07.000000000 +0000 +++ 3.1.1+dfsg-3ubuntu1/debian/patches/series 2020-06-13 21:51:08.000000000 +0000 @@ -1 +1,2 @@ remove_link_top.diff +7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch
  1. openbabel