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feat: update openbabel to 3.1.1+dfsg-10
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| [DEFAULT] | ||
| pristine-tar = false | ||
| debian-branch = master | ||
| verbose = true | ||
|
|
||
| [buildpackage] | ||
| overlay = true |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| usr/lib/*/perl5 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| usr/bin/roundtrip | ||
| usr/share/man/man1/roundtrip.1 |
28 changes: 28 additions & 0 deletions
28
debian/patches/7acf50c9d73f8016e15eb2a45ce74c8909152883.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| From 3601e081f9ff8ae670d50ed47294a0c4f4760321 Mon Sep 17 00:00:00 2001 | ||
| From: Andrius Merkys <andrius.merkys@gmail.com> | ||
| Date: Fri, 21 Jun 2024 14:23:31 +0300 | ||
| Subject: [PATCH] Restore compatibility with libxml2 2.12.7. | ||
|
|
||
| --- | ||
| src/formats/xml/xml.cpp | 3 +-- | ||
| 1 file changed, 1 insertion(+), 2 deletions(-) | ||
|
|
||
| diff --git a/src/formats/xml/xml.cpp b/src/formats/xml/xml.cpp | ||
| index 2042b0c298..6b4eb614c0 100644 | ||
| --- a/src/formats/xml/xml.cpp | ||
| +++ b/src/formats/xml/xml.cpp | ||
| @@ -242,13 +242,12 @@ namespace OpenBabel | ||
|
|
||
| if(result==-1) | ||
| { | ||
| - xmlError* perr = xmlGetLastError(); | ||
| + const xmlError* perr = xmlGetLastError(); | ||
| if(perr && perr->level!=XML_ERR_NONE) | ||
| { | ||
| obErrorLog.ThrowError("XML Parser " + GetInFilename(), | ||
| perr->message, obError); | ||
| } | ||
| - xmlResetError(perr); | ||
| GetInStream()->setstate(ios::eofbit); | ||
| return false; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Description: Add '#include <ctime>' as 'clock' is defined there (#1016227). | ||
| Author: Andrius Merkys <merkys@debian.org> | ||
| --- a/include/openbabel/obutil.h | ||
| +++ b/include/openbabel/obutil.h | ||
| @@ -37,6 +37,7 @@ | ||
| #endif | ||
|
|
||
| #include <math.h> | ||
| +#include <ctime> | ||
|
|
||
| #ifndef M_PI | ||
| #define M_PI 3.14159265358979323846 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| include: | ||
| - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml | ||
| - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,58 @@ | ||
| #!/bin/bash | ||
|
|
||
| test "$(dpkg --print-architecture)" = arm64 && exit 77 | ||
| set -e | ||
|
|
||
| sed -i 's/"\.\."/"\/usr"/' test/testbabel.py | ||
|
|
||
| arch=$(dpkg --print-architecture) | ||
| fails= | ||
| for TEST in test/test*.py | ||
| do | ||
| python3 ${TEST} | ||
| fail_on_failure=true | ||
| case $TEST in | ||
| test/testroundtrip.py) | ||
| # timesout? | ||
| echo "Skipping ${TEST} ..." | ||
| continue;; | ||
| test/testdistgeom.py) | ||
| case "$arch" in amd64|armel) | ||
| # timesout on ci.d.n worker13 | ||
| # takes very long on armel | ||
| echo "Skipping ${TEST} ..." | ||
| continue;; | ||
| esac;; | ||
| test/testbindings.py) | ||
| case "$arch" in | ||
| amd64) | ||
| true;; | ||
| *) | ||
| fail_on_failure=false;; | ||
| esac;; | ||
| test/testsym.py) | ||
| # on most/all non-amd64 architecture it fails | ||
| # if it finishes at all, it takes a very long time | ||
| # on worker13, the test takes 1000 times longer than on other amd64 hosts | ||
| echo "Skipping ${TEST} ..." | ||
| continue;; | ||
| test/testobconv_writers.py) | ||
| case "$arch" in arm64|i386|ppc64el|s390x) | ||
| fail_on_failure=false;; | ||
| esac;; | ||
| esac | ||
| echo "Running ${TEST} ..." | ||
| if python3 ${TEST}; then | ||
| : | ||
| else | ||
| if [ $fail_on_failure = "false" ] ; then | ||
| echo "Ignoring ${TEST} on $arch ..." | ||
| else | ||
| fails="$fails $TEST" | ||
| fi | ||
| fi | ||
| done | ||
|
|
||
| if [ -n "$fails" ]; then | ||
| echo "Failing tests: $fails" | ||
| exit 1 | ||
| fi | ||
| exit 0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| version=4 | ||
| opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//,repack,compression=xz" \ | ||
| https://github.com/openbabel/openbabel/releases \ | ||
| (?:.*?/)?openbabel-(\d[\d.]*)-source\.tar\.bz2 | ||
| opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*@ARCHIVE_EXT@)%@PACKAGE@-$1%,repacksuffix=+dfsg,dversionmangle=auto,uversionmangle=s/-/./g,repack,compression=xz" \ | ||
| https://github.com/openbabel/openbabel/tags \ | ||
| (?:.*?/)?openbabel-@ANY_VERSION@@ARCHIVE_EXT@ |