feat: update openbabel to 3.1.1+dfsg-10

debian/changelog

@@ -1,14 +1,67 @@
-openbabel (3.1.1.1-deepin1) unstable; urgency=medium
+openbabel (3.1.1.1+dfsg-10deepin1) unstable; urgency=medium
 
-  * add missing lib ctime 
+  * fix changelog.
 
- -- ZhengJie-Niu <niuzj0@gmail.com>  Wed, 07 Dec 2022 07:36:26 +0000
+ -- LiChengGang <lichenggang@uniontech.com>  Thu, 01 Aug 2024 16:57:34 +0800
 
-openbabel (3.1.1+dfsg-6.1-deepin1) unstalbe; urgency=medium
+openbabel (3.1.1+dfsg-10) unstable; urgency=medium
 
-  * add missing lib ctime
+  [ Drew Parsons ]
+  * update Homepage to https://openbabel.org
+
+  [ Andrius Merkys ]
+  * Restore compatibility with libxml (Closes: #1073327)
+
+ -- Andrius Merkys <merkys@debian.org>  Mon, 01 Jul 2024 02:14:46 -0400
+
+openbabel (3.1.1+dfsg-9) unstable; urgency=medium
+
+  * Remove dh_missing call from override_dh_install to fix arch:all build.
+
+ -- Andrius Merkys <merkys@debian.org>  Thu, 01 Dec 2022 02:47:57 -0500
+
+openbabel (3.1.1+dfsg-8) unstable; urgency=medium
+
+  * Acknowledge NMUs.
+  * Fix debian/watch to watch GitHub tags.
+  * Transition to wxwidgets3.2 (Closes: #1019808)
+  * Simplify a path in debian/copyright.
+  * Bump debhelper from old 12 to 13.
+  * Set upstream metadata fields: Repository-Browse.
+  * Update standards version to 4.6.1, no changes needed.
+  * Remove Homepage from debian/upstream/metadata.
+
+ -- Andrius Merkys <merkys@debian.org>  Mon, 28 Nov 2022 10:26:44 -0500
+
+openbabel (3.1.1+dfsg-7.2) unstable; urgency=medium
+
+  * Non-maintainer upload
+  * tests: further tune which tests to run with latest results from ci.d.n
+
+ -- Paul Gevers <elbrus@debian.org>  Thu, 24 Nov 2022 13:15:37 +0100
+
+openbabel (3.1.1+dfsg-7.1) unstable; urgency=medium
+
+  * Non-maintainer upload
+
+  [ Matthias Klose ]
+  * 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
+    (Closes: #953630)
+  * Skip the testbindings.py and testsym.py tests on non amd64 architectures.
+
+  [ Paul Gevers ]
+  * Run all tests that don't timeout, but ignore specific failures on
+    specific architectures
+
+ -- Paul Gevers <elbrus@debian.org>  Sun, 20 Nov 2022 10:24:49 +0100
+
+openbabel (3.1.1+dfsg-7) unstable; urgency=medium
+
+  * Include <ctime> in obutil.h (Closes: #1016227)
 
- -- root <root@f34afac46ce7>  Wed, 07 Dec 2022 07:32:43 +0000
+ -- Andrius Merkys <merkys@debian.org>  Thu, 08 Sep 2022 08:29:09 -0400
 
 openbabel (3.1.1+dfsg-6) unstable; urgency=medium
 

debian/control

@@ -6,7 +6,7 @@ Uploaders: Michael Banck <mbanck@debian.org>,
            Daniel Leidert <dleidert@debian.org>,
            Andrius Merkys <merkys@debian.org>
 Build-Depends: cmake,
-               debhelper-compat (= 12),
+               debhelper-compat (= 13),
                dh-python,
                doxygen,
                ghostscript,
@@ -18,7 +18,7 @@ Build-Depends: cmake,
                libinchi-dev,
                libmaeparser-dev,
                libperl-dev,
-               libwxgtk3.0-gtk3-dev,
+               libwxgtk3.2-dev,
                libxml2-dev,
                pkg-config,
                python3-all,
@@ -30,9 +30,9 @@ Build-Depends: cmake,
                texlive-latex-base,
                texlive-latex-extra,
                zlib1g-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.6.1
 Rules-Requires-Root: no
-Homepage: http://openbabel.sourceforge.net
+Homepage: https://openbabel.org
 Vcs-Browser: https://salsa.debian.org/debichem-team/openbabel
 Vcs-Git: https://salsa.debian.org/debichem-team/openbabel.git
 

debian/copyright

@@ -180,7 +180,7 @@ Copyright: 2001-2008, Greg Landrum and Rational Discovery LLC
 License: BSD-3-Clause
 
 
-Files: ./data/SMARTS_InteLigand.txt
+Files: data/SMARTS_InteLigand.txt
 Copyright: 2005, Inte:Ligand Software-Entwicklungs und Consulting GmbH
 License: LGPL-3
 

debian/gbp.conf

@@ -0,0 +1,7 @@
+[DEFAULT]
+pristine-tar = false
+debian-branch = master
+verbose = true
+
+[buildpackage]
+overlay = true

debian/libchemistry-openbabel-perl.install

@@ -0,0 +1 @@
+usr/lib/*/perl5

debian/not-installed

@@ -0,0 +1,2 @@
+usr/bin/roundtrip
+usr/share/man/man1/roundtrip.1

debian/patches/7acf50c9d73f8016e15eb2a45ce74c8909152883.patch

@@ -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;
+     }

debian/patches/add-ctime.patch

@@ -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

debian/patches/series

@@ -2,4 +2,5 @@ remove_link_top.diff
 7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch
 2315.patch
 650b1f829ac47cc84877a330366ec9485da3ec99.patch
-missing-lib.patch
+add-ctime.patch
+7acf50c9d73f8016e15eb2a45ce74c8909152883.patch

debian/rules

@@ -34,14 +34,11 @@ override_dh_auto_build:
 	dh_auto_build
 	make -C $(CURDIR)/builddir docs
 
-override_dh_install:
-	dh_install -Nlibchemistry-openbabel-perl
-	dh_missing --list-missing -Nlibchemistry-openbabel-perl
-	mkdir -p $(CURDIR)/debian/tmp/$(PERL_ARCHLIB)
+override_dh_auto_install:
+	dh_auto_install
+	mkdir --parents $(CURDIR)/debian/tmp/$(PERL_ARCHLIB)
 	mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/auto debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/Chemistry \
-	  $(CURDIR)/debian/tmp/$(PERL_ARCHLIB)
-	dh_install -plibchemistry-openbabel-perl -Xperllocal.pod --autodest $(PERL_ARCHLIB)
-	dh_missing --list-missing -plibchemistry-openbabel-perl -Xperllocal.pod
+		$(CURDIR)/debian/tmp/$(PERL_ARCHLIB)
 
 override_dh_installexamples:
 	dh_installexamples -X.pyc
@@ -50,7 +47,7 @@ override_dh_installdocs:
 	dh_installdocs -X.js
 
 override_dh_compress:
-	dh_compress -Xusr/share/doc/libopenbabel-dev/html/ \
+	dh_compress -Xusr/share/doc/libopenbabel-dev/html \
 	            -Xusr/share/doc/python3-openbabel/examples
 
 override_dh_auto_test:

debian/salsa-ci.yml

@@ -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

debian/tests/python3

@@ -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

debian/upstream/metadata

@@ -1,6 +1,5 @@
 Bug-Database: https://github.com/openbabel/openbabel/issues
 Bug-Submit: https://github.com/openbabel/openbabel/issues/new
-Homepage: http://openbabel.org
 FAQ: http://openbabel.org/wiki/FAQ
 Reference:
  - Debian-Package: openbabel
@@ -23,3 +22,4 @@ Reference:
    URL: http://journal.chemistrycentral.com/content/2/1/5
    eprint: http://journal.chemistrycentral.com/content/pdf/1752-153X-2-5.pdf
    DOI: 10.1186/1752-153X-2-5
+Repository-Browse: https://github.com/openbabel/openbabel

debian/watch

@@ -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@