Switch to SPDX license identifier

Signed-off-by: Fedora Release Engineering <releng@fedoraproject.org>

.cvsignore

@@ -1 +0,0 @@
-openbabel-2.2.3.tar.gz

.gitignore

@@ -0,0 +1,11 @@
+openbabel-2.0.2.tar.gz
+/openbabel-2.3.0b2-20100803-r3942.tar.gz
+/openbabel-2.3.0.tar.gz
+/openbabel-2.3.1.tar.gz
+/openbabel-2.3.2.tar.gz
+/openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d.tar.gz
+/openbabel-a345105b28173eb7da14ecd1e5beebe94140c6d7.tar.gz
+/openbabel-3a63a9849f8d9719c5989c43875d51be50c53019.tar.gz
+/openbabel-2-4-0.tar.gz
+/openbabel-2-4-1.tar.gz
+/openbabel-openbabel-3-1-1.tar.gz

Makefile

@@ -1,21 +0,0 @@
-# Makefile for source rpm: openbabel
-# $Id$
-NAME := openbabel
-SPECFILE = $(firstword $(wildcard *.spec))
-
-define find-makefile-common
-for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$d/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done
-endef
-
-MAKEFILE_COMMON := $(shell $(find-makefile-common))
-
-ifeq ($(MAKEFILE_COMMON),)
-# attept a checkout
-define checkout-makefile-common
-test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2
-endef
-
-MAKEFILE_COMMON := $(shell $(checkout-makefile-common))
-endif
-
-include $(MAKEFILE_COMMON)

obgui.desktop

@@ -0,0 +1,11 @@
+[Desktop Entry]
+Name=OpenBabel
+GenericName=Molecule Format Converter
+Comment=Convert between many known molecule data formats
+Exec=obgui
+Icon=babel
+Terminal=false
+Type=Application
+StartupNotify=true
+Categories=Education;Science;Chemistry;Physics;Biology;
+

openbabel-3.1.1-bug2378.patch

@@ -0,0 +1,44 @@
+From 4ba2fec17b786afebadfae800a015704ad533843 Mon Sep 17 00:00:00 2001
+From: dkoes <dkoes@pitt.edu>
+Date: Mon, 7 Jun 2021 11:04:25 -0400
+Subject: [PATCH] Resolve ImportError with make test
+
+This change will build _openbabel.so in scripts/python/openbabel instead
+of the default build/lib.  This is necessary because openbabel.py tries
+to import _openbabel like this:
+
+if __package__ or "." in __name__:
+    from . import _openbabel
+else:
+    import _openbabel
+
+This results in a circular import error when running make test (the
+first branch of the if is triggered).  This code appears to be generated by
+SWIG with no obvious way to change it to catch the ImportError and call
+import _openbabel instead.  Note the PYTHONPATH is set to include
+build/lib, but it doesn't matter because SWIG is forcing the import to
+happen in scripts/python/openbabel.
+
+I'm not sure why this hasn't been a problem in the past, perhaps there's
+been a change in SWIG.  This is with SWIG 4.0.1 and cmake 3.18.6.
+
+I think the best solution is to move all the files that are being built
+in /scripts to the build directory rather than polluting the src tree
+with them, but this would require changing all the bindings and I'm not
+up for building and testing every binding.
+---
+ scripts/CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
+index b715a546dd..56821641fe 100644
+--- a/scripts/CMakeLists.txt
++++ b/scripts/CMakeLists.txt
+@@ -106,6 +106,7 @@ if (DO_PYTHON_BINDINGS)
+         set_target_properties(bindings_python PROPERTIES
+             OUTPUT_NAME _openbabel
+             PREFIX ""
++            LIBRARY_OUTPUT_DIRECTORY "${openbabel_SOURCE_DIR}/scripts/python/openbabel/"
+             SUFFIX .so )
+         execute_process(
+           COMMAND

openbabel-3.1.1-bug2493.patch

@@ -0,0 +1,36 @@
+From c0570bfeb2d7e0a6a6de1f257cf28e7f3cac8739 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 12 Jun 2022 11:23:59 +0100
+Subject: [PATCH] CMake: fix time check typo (fixes build failure w/ GCC 12)
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Without this fixed check, we get a build failure with GCC 12:
+```
+/var/tmp/portage/sci-chemistry/openbabel-3.1.1_p20210225/work/openbabel-08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/include/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope; did you mean ‘clock_t’?
+   65 |       start= clock();
+      |              ^~~~~
+      |              clock_t
+```
+
+Bug: https://bugs.gentoo.org/851510
+---
+ src/config.h.cmake | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/config.h.cmake b/src/config.h.cmake
+index 1c59c67699..26e5dde94f 100644
+--- a/src/config.h.cmake
++++ b/src/config.h.cmake
+@@ -182,8 +182,8 @@
+ #define OB_MODULE_PATH "@OB_MODULE_PATH@"
+ 
+ #ifndef TIME_WITH_SYS_TIME
+-  #ifdef HAVE_SYS_TIME
+-    #ifdef HAVE_TIME
++  #ifdef HAVE_SYS_TIME_H
++    #ifdef HAVE_TIME_H
+       #define TIME_WITH_SYS_TIME 1
+     #else
+       #define TIME_WITH_SYS_TIME 0

openbabel-3.1.1-fix_bug2217.patch

@@ -0,0 +1,39 @@
+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 0fa5adb576..fc3a7515b9 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:

openbabel-3.1.1-fix_bug2223.patch

@@ -0,0 +1,34 @@
+From b75c392b75b3494d9dae15176f38facf7e61db17 Mon Sep 17 00:00:00 2001
+From: John Bollinger <John.Bollinger@StJude.org>
+Date: Fri, 15 May 2020 11:30:27 -0500
+Subject: [PATCH] Fix UB in UFF parameter parsing
+
+When evaluating atom coordination number, method
+OBForceFieldUFF::ParseParamFile() assumed that it may access a third character
+of the atom type string, but in fact that produces undefined behavior if the
+string is only one character long. A one-character atom type occurs in
+practice with the default parameter file (for deuterium).
+
+This change addresses the issue by verifying that the second character of
+each atom type string is not a C string terminator as a precondition for
+accessing the third. If the second is a string terminator then the same
+default behavior is provided as if the type were two characters long.
+
+Fixes #2223
+---
+ src/forcefields/forcefielduff.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/forcefields/forcefielduff.cpp b/src/forcefields/forcefielduff.cpp
+index 9bff879c9c..2e98e0e804 100644
+--- a/src/forcefields/forcefielduff.cpp
++++ b/src/forcefields/forcefielduff.cpp
+@@ -1647,7 +1647,7 @@ namespace OpenBabel {
+         parameter.b = 0; // used for tracking number of angles in 5-coordinate
+         parameter.c = 0;
+ 
+-        char coord = vs[1][2]; // 3rd character of atom type
++        char coord = vs[1][1] ? vs[1][2] : '\0'; // 3rd character of atom type, if any
+         switch (coord) {
+         case '1': // linear
+           parameter._ipar.push_back(1);

openbabel-disable-tests-s390x.patch

@@ -0,0 +1,21 @@
+diff -up a/test/CMakeLists.txt.s390x b/test/CMakeLists.txt
+--- a/test/CMakeLists.txt.s390x	2016-10-10 17:56:17.000000000 +0200
++++ b/test/CMakeLists.txt	2019-01-27 19:32:21.568052461 +0100
+@@ -74,7 +74,7 @@
+     )
+ set (atom_parts 1 2 3 4)
+ set (ffmmff94_parts 1 2 3 4 5 6)
+-set (math_parts 1 2 3 4)
++set (math_parts 1 2 3)
+ set (pdbreadfile_parts 1 2 3 4)
+ 
+ if(BUILD_SHARED)
+@@ -250,8 +250,6 @@
+   include(UsePythonTest)
+   set(pybindtests
+       bindings
+-      _pybel
+-      example 
+       obconv_writers
+       cdjsonformat
+       pcjsonformat

openbabel-disable-tests.patch

@@ -0,0 +1,30 @@
+diff -up a/test/CMakeLists.txt.tests b/test/CMakeLists.txt
+--- a/test/CMakeLists.txt.tests	2016-09-21 21:55:37.000000000 +0200
++++ b/test/CMakeLists.txt	2016-10-10 13:48:52.726803964 +0200
+@@ -39,7 +39,7 @@
+ set (isomorphism_parts 1 2 3 4 5 6 7 8 9)
+ set (multicml_parts 1)
+ set (periodic_parts 1 2 3 4)
+-set (regressions_parts 1 221 222 223 224 225 226 227 228 240 241 242 1794 2111)
++set (regressions_parts 222 223 224)
+ set (rotor_parts 1 2 3 4)
+ set (shuffle_parts 1 2 3 4 5)
+ set (smiles_parts 1 2 3)
+@@ -188,7 +188,7 @@
+     set_target_properties(test_inchiwrite PROPERTIES LINK_SEARCH_END_STATIC TRUE)
+   endif()
+   # files in test/inchi -- both .sdf and .txt
+-  set(inchitests Samples.sdf SamplesTechMan.sdf Steffen_PubChem.smi)
++  set(inchitests Samples.sdf SamplesTechMan.sdf)
+   set(inchidata ${CMAKE_SOURCE_DIR}/test/inchi)
+   foreach(test ${inchitests})
+     add_test(inchi${test}_Test
+@@ -226,7 +226,7 @@
+   include(UsePythonTest)
+   if(PYTHON_EXECUTABLE)
+     set(pytests
+-        babel sym smartssym fastsearch distgeom unique kekule pdbformat RInChI)
++        babel smartssym fastsearch unique kekule pdbformat)
+     foreach(pytest ${pytests})
+     SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES
+       PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}"

openbabel-fix-libdir-in-pkgconfig.patch

@@ -0,0 +1,12 @@
+diff -up a/openbabel-3.pc.cmake.p b/openbabel-3.pc.cmake
+--- a/openbabel-3.pc.cmake.p
++++ b/openbabel-3.pc.cmake
+@@ -1,6 +1,6 @@
+ prefix=@CMAKE_INSTALL_PREFIX@
+ exec_prefix=${prefix}
+-libdir=${exec_prefix}/@LIB_INSTALL_DIR@
++libdir=${exec_prefix}/lib@LIB_SUFFIX@
+ includedir=${prefix}/include
+ pkgincludedir=${includedir}/openbabel@BABEL_MAJ_VER@
+ 
+ 

openbabel-inchi-license-lgpl-2.1.txt

@@ -0,0 +1,502 @@
+                  GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL.  It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+  This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it.  You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+  When we speak of free software, we are referring to freedom of use,
+not price.  Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+  To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights.  These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+  For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you.  You must make sure that they, too, receive or can get the source
+code.  If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it.  And you must show them these terms so they know their rights.
+
+  We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+  To protect each distributor, we want to make it very clear that
+there is no warranty for the free library.  Also, if the library is
+modified by someone else and passed on, the recipients should know
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+
+  Finally, software patents pose a constant threat to the existence of
+any free program.  We wish to make sure that a company cannot
+effectively restrict the users of a free program by obtaining a
+restrictive license from a patent holder.  Therefore, we insist that
+any patent license obtained for a version of the library must be
+consistent with the full freedom of use specified in this license.
+
+  Most GNU software, including some libraries, is covered by the
+ordinary GNU General Public License.  This license, the GNU Lesser
+General Public License, applies to certain designated libraries, and
+is quite different from the ordinary General Public License.  We use
+this license for certain libraries in order to permit linking those
+libraries into non-free programs.
+
+  When a program is linked with a library, whether statically or using
+a shared library, the combination of the two is legally speaking a
+combined work, a derivative of the original library.  The ordinary
+General Public License therefore permits such linking only if the
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+Public License permits more lax criteria for linking other code with
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+
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+
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+
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+infringement or for any other reason (not limited to patent issues),
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+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  12. If the distribution and/or use of the Library is restricted in
+certain countries either by patents or by copyrighted interfaces, the
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+excluded.  In such case, this License incorporates the limitation as if
+written in the body of this License.
+
+  13. The Free Software Foundation may publish revised and/or new
+versions of the Lesser General Public License from time to time.
+Such new versions will be similar in spirit to the present version,
+but may differ in detail to address new problems or concerns.
+
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+conditions either of that version or of any later version published by
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+license version number, you may choose any version ever published by
+the Free Software Foundation.
+
+  14. If you wish to incorporate parts of the Library into other free
+programs whose distribution conditions are incompatible with these,
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+DAMAGES.
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+
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+
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+possible use to the public, we recommend making it free software that
+everyone can redistribute and change.  You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
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+  To apply these terms, attach the following notices to the library.  It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the library's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This library is free software; you can redistribute it and/or
+    modify it under the terms of the GNU Lesser General Public
+    License as published by the Free Software Foundation; either
+    version 2.1 of the License, or (at your option) any later version.
+
+    This library is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public
+    License along with this library; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the
+  library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+  <signature of Ty Coon>, 1 April 1990
+  Ty Coon, President of Vice
+
+That's all there is to it!

openbabel-inchi.patch

@@ -1,65 +0,0 @@
-diff -up openbabel-2.2.3/configure.in.inchi openbabel-2.2.3/configure.in
---- openbabel-2.2.3/configure.in.inchi	2009-07-29 03:05:04.000000000 +0200
-+++ openbabel-2.2.3/configure.in	2009-09-14 01:14:49.000000000 +0200
-@@ -239,8 +239,11 @@ AC_SUBST(LIBDL)
- AM_PATH_XML2(2.6.5)
- AM_CONDITIONAL(BUILD_XML, test x"$XML_LIBS" != "x")
- 
-+AC_CHECK_LIB(stdinchi, GetStdINCHI, LIBSTDINCHI="-lstdinchi", LIBSTDINCHI="")
- AC_CHECK_LIB(inchi, GetINCHI, LIBINCHI="-linchi", LIBINCHI="")
--AM_CONDITIONAL(BUILD_INCHI, test x"$LIBINCHI" = "x" -o "$inchi" = "yes")
-+AM_CONDITIONAL(HAVE_INCHI, test x"$LIBINCHI" != "x" -o x"$LIBSTDINCHI" != "x" -o "$inchi" = "yes")
-+AM_CONDITIONAL(HAVE_STDINCHI, test x"$LIBSTDINCHI" != "x")
-+AM_CONDITIONAL(BUILD_INCHI, test "$inchi" = "yes")
- 
- AC_CHECK_LIB(z, inflateEnd, [zlib_cv_libz=yes], [zlib_cv_libz=no])
- AC_CHECK_HEADER(zlib.h, [zlib_cv_zlib_h=yes], [zlib_cv_zlib_h=no])
-diff -up openbabel-2.2.3/src/formats/Makefile.am.inchi openbabel-2.2.3/src/formats/Makefile.am
---- openbabel-2.2.3/src/formats/Makefile.am.inchi	2009-07-09 15:05:02.000000000 +0200
-+++ openbabel-2.2.3/src/formats/Makefile.am	2009-09-14 01:15:55.000000000 +0200
-@@ -39,11 +39,17 @@ endif
- 
- if !BUILD_SHARED
- noinst_LTLIBRARIES = libformats.la
-+if HAVE_INCHI
- if BUILD_INCHI
- libformats_la_LIBADD = inchi102/libinchi.la
- else
-+if HAVE_STDINCHI
-+libformats_la_LIBADD = -lstdinchi
-+else
- libformats_la_LIBADD = -linchi
- endif
-+endif
-+endif
- libformats_la_SOURCES = \
- 	APIInterface.cpp MCDLformat.cpp \
- 	CSRformat.cpp PQSformat.cpp alchemyformat.cpp \
-@@ -124,7 +130,7 @@ if HAVE_SHARED_POINTER
- formats_LTLIBRARIES += chemdrawcdxformat.la chemkinformat.la \
-                           rxnformat.la rsmiformat.la
- endif
--if BUILD_INCHI
-+if HAVE_INCHI
- formats_LTLIBRARIES += inchiformat.la
- endif
- if BUILD_ZLIB
-@@ -261,12 +267,18 @@ hinformat_la_SOURCES = hinformat.cpp 
- hinformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la 
- 
- inchiformat_la_SOURCES = inchiformat.cpp  getinchi.cpp
-+if HAVE_INCHI
- if BUILD_INCHI
- inchiformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la inchi102/libinchi.la
- else
- inchiformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la
-+if HAVE_STDINCHI
-+inchiformat_la_LIBADD = -lstdinchi
-+else
- inchiformat_la_LIBADD = -linchi
- endif
-+endif
-+endif
- 
- jaguarformat_la_SOURCES = jaguarformat.cpp 
- jaguarformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la 

openbabel-noswig-rubymethod.patch

@@ -0,0 +1,20 @@
+diff -up openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt.noswig_ruby openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt
+--- openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt.noswig_ruby	2015-02-07 21:45:57.930604455 +0100
++++ openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt	2015-02-07 21:48:41.744097913 +0100
+@@ -374,10 +374,15 @@ if (DO_RUBY_BINDINGS)
+       set(WORKAROUND_CMAKE260_BUG "s/rb_define_module(\"Openbabel\")/rb_define_module(\"OpenBabel\")/")
+       add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp
+           COMMAND ${SWIG_EXECUTABLE} -ruby -c++ -small -O -templatereduce -naturalvar -autorename -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.txt ${openbabel_SOURCE_DIR}/scripts/openbabel-ruby.i
+-          COMMAND sed -e '${WORKAROUND_CMAKE_260_BUG}' -e's/void Init_OpenBabel/void Init_openbabel/' <${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.txt >${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp
++          COMMAND sed -e '${WORKAROUND_CMAKE260_BUG}' -e's/void Init_OpenBabel/void Init_openbabel/' <${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.txt >${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp
+           COMMAND ${CMAKE_COMMAND} -E remove ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.txt
+           MAIN_DEPENDENCY openbabel-ruby.i
+       )
++    else (RUN_SWIG)
++        # Fix openbabel-ruby.cpp also in this case 
++      execute_process(
++          COMMAND sed -i -e s/void\ Init_OpenBabel/void\ Init_openbabel/ ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp
++      )
+     endif (RUN_SWIG)
+ 
+     include_directories(

openbabel-perl.patch

@@ -0,0 +1,29 @@
+diff -up openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt.rpm openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt
+--- openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt.rpm	2015-02-04 20:04:57.000000000 +0100
++++ openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt	2015-02-07 23:38:54.649356914 +0100
+@@ -336,12 +336,23 @@ if (DO_PERL_BINDINGS)
+     if(NOT BINDINGS_ONLY)
+       add_dependencies(bindings_perl openbabel)
+     endif()
++    execute_process(
++      COMMAND
++        ${PERL_EXECUTABLE} -V:installvendorarch
++      OUTPUT_VARIABLE
++        PERL_INSTALL_DIR_OUTPUT
++      RESULT_VARIABLE
++        PERL_INSTALL_DIR_RESULT
++      )
++    if (NOT PERL_INSTALL_DIR_RESULT)
++      string(REGEX REPLACE "installvendorarch='([^']+)'.*" "\\1" PERL_INSTALL_DIR ${PERL_INSTALL_DIR_OUTPUT})
++    endif (NOT PERL_INSTALL_DIR_RESULT)
+ 
+     install(TARGETS bindings_perl
+-            LIBRARY DESTINATION ${LIB_INSTALL_DIR}/auto/Chemistry/OpenBabel/
++            LIBRARY DESTINATION ${PERL_INSTALL_DIR}/auto/Chemistry/OpenBabel/
+             COMPONENT bindings_perl)
+     install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm
+-            DESTINATION ${LIB_INSTALL_DIR}/Chemistry/
++            DESTINATION ${PERL_INSTALL_DIR}/Chemistry/
+             COMPONENT bindings_perl)
+ 
+ endif (DO_PERL_BINDINGS)

openbabel-plugindir.patch

@@ -0,0 +1,30 @@
+diff -up a/CMakeLists.txt.plugindir b/CMakeLists.txt
+--- a/CMakeLists.txt.plugindir	2015-02-07 21:42:44.431479900 +0100
++++ b/CMakeLists.txt	2015-02-07 21:43:29.000429326 +0100
+@@ -24,7 +24,7 @@
+ # had too many 1.100.1 releases. :-)
+ set(BABEL_MAJ_VER   3)
+ set(BABEL_MIN_VER   1)
+-set(BABEL_PATCH_VER 0)
++set(BABEL_PATCH_VER 1)
+ 
+ # This should be phased out in preference for just using the target name
+ set(BABEL_LIBRARY openbabel)
+@@ -750,7 +750,7 @@
+   "${openbabel_BINARY_DIR}/OpenBabel3ConfigVersion.cmake" @ONLY)
+ 
+ # Now to configure the installed config file.
+-set(OB_CONFIG_DIR "${LIB_INSTALL_DIR}/cmake/openbabel3")
++set(OB_CONFIG_DIR "lib${LIB_SUFFIX}/cmake/openbabel3")
+ set(OpenBabel3_INCLUDE_DIRS "\${OpenBabel3_INSTALL_PREFIX}/${OB_INCLUDE_DIRS}")
+ set(OpenBabel3_LIBRARIES "$<TARGET_FILE:openbabel>")
+ 
+--- a/OpenBabel3Config.cmake.orig.in	2020-05-08 17:38:02.000000000 +0200
++++ b/OpenBabel3Config.cmake.in	2022-09-29 21:36:17.995630395 +0200
+@@ -1,5 +1,5 @@
+ # The OpenBabel3 config file. To get the targets include the exports file.
+-get_filename_component(OpenBabel3_INSTALL_PREFIX "${OpenBabel3_DIR}@REL_REF@"
++get_filename_component(OpenBabel3_INSTALL_PREFIX "/usr"
+   ABSOLUTE)
+ 
+ set(OpenBabel3_VERSION_MAJOR   "@BABEL_MAJ_VER@")

openbabel-rpm.patch

@@ -1,15 +0,0 @@
-diff -up openbabel-2.2.1b3-20090215-r2890/scripts/Makefile.am.r openbabel-2.2.1b3-20090215-r2890/scripts/Makefile.am
-diff -up openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL.r openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL
---- openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL.r	2008-12-01 18:41:42.000000000 +0100
-+++ openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL	2009-03-01 10:43:01.000000000 +0100
-@@ -3,8 +3,8 @@ use ExtUtils::MakeMaker;
- use lib 'inc';
- use Devel::CheckLib;
- 
--check_lib_or_exit( lib => 'openbabel' , libpath =>
--@ENV{"LD_LIBRARY_PATH"});
-+#check_lib_or_exit( lib => 'openbabel' , libpath =>
-+#@ENV{"LD_LIBRARY_PATH"});
- 
- $CC = 'g++';
- $srcdir = '../../src';

openbabel-ruby19-vendorarch.patch

@@ -0,0 +1,12 @@
+diff -up openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt.ruby_vendor openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt
+--- openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt.ruby_vendor	2015-02-04 20:04:57.000000000 +0100
++++ openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/scripts/CMakeLists.txt	2015-02-07 23:38:54.649356914 +0100
+@@ -400,7 +416,7 @@ if (DO_RUBY_BINDINGS)
+     endif()
+ 
+     install(TARGETS bindings_ruby
+-            LIBRARY DESTINATION ${LIB_INSTALL_DIR}
++            LIBRARY DESTINATION ${LIB_INSTALL_DIR}/ruby/vendor_ruby
+             COMPONENT bindings_ruby)
+ 
+ endif (DO_RUBY_BINDINGS)

openbabel.spec

@@ -1,35 +1,80 @@
-%define perl_vendorarch %(eval "`perl -V:installvendorarch`"; echo $installvendorarch)
-%define perl_archlib %(eval "`perl -V:archlib`"; echo $archlib)
-%{!?python_sitelib: %define python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
-%{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
-%define ruby_sitearch %(ruby -rrbconfig -e 'puts Config::CONFIG["sitearchdir"]')
+%{!?perl_vendorarch:%global perl_vendorarch %(eval "`perl -V:installvendorarch`"; echo $installvendorarch)}
 
-%define beta_ver %{nil}
-%define beta_str %{nil}
+# we don't want to provide private Perl or Python extension libs
+%global __provides_exclude_from ^(%{perl_vendorarch}/auto|%{python3_sitearch})/.*\\.so$
+
+# Avoid LTO flags in these architectures:
+# eigen3/Eigen/src/Core/arch/AltiVec/MatrixProduct.h:1199:26:
+# error: inlining failed in call to 'always_inline' 'Eigen::internal::bload<Eigen::internal::blas_data_mapper<double, long, 0, 0, 1>, double __vector(2), long, 2l, 0, 
+%if 0%{?rhel}
+%ifarch %{power64}
+%define _lto_cflags %{nil}
+%endif
+%endif
 
 Name: openbabel
-Version: 2.2.3
-Release: 4%{beta_ver}%{?dist}
+Version: 3.1.1
+Release: 18%{?dist}
 Summary: Chemistry software file format converter
-License: GPLv2
-Group: Applications/File
-URL: http://openbabel.org/
-Source: http://downloads.sourceforge.net/sourceforge/openbabel/%{name}-%{version}%{beta_str}.tar.gz
-Patch1: %{name}-rpm.patch
-Patch3: %{name}-inchi.patch
-BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
-BuildRequires: inchi-devel >= 1.0.3
-BuildRequires: libtool
-BuildRequires: libxml2-devel
-BuildRequires: perl(ExtUtils::MakeMaker)
-BuildRequires: python
-BuildRequires: python-devel
-BuildRequires: ruby
-BuildRequires: ruby-devel
+License: GPL-2.0-only
+URL: https://openbabel.org/
+Source0: https://github.com/openbabel/openbabel/archive/openbabel-openbabel-%(echo %{version} | tr '.' '-').tar.gz
+Source1: obgui.desktop
+Source2: openbabel-inchi-license-lgpl-2.1.txt
+
+# fix perl modules install path
+Patch0: %{name}-perl.patch
+
+# fix openbabel version + cmake config files
+Patch1: %{name}-plugindir.patch
+
+# fix SWIG_init even when not using swig (#772149)
+Patch2: %{name}-noswig-rubymethod.patch
+
+# On F-17, directory for C ruby files changed to use vendorarch directory
+Patch3: %{name}-ruby19-vendorarch.patch
+
+# temporarily disable some tests on:
+# - ppc64 and s390(x) to unblock other builds (#1108103)
+# - ARM (#1094491)
+# - aarch64 (#1094513)
+# Upstream bugs: https://sourceforge.net/p/openbabel/bugs/927/ https://sourceforge.net/p/openbabel/bugs/945/
+Patch4: %{name}-disable-tests.patch
+
+# Fix path to libdir in .pc file
+# https://bugzilla.redhat.com/show_bug.cgi?id=1669664
+Patch5: %{name}-fix-libdir-in-pkgconfig.patch
+
+# Math 4 test is failing on s390x only
+Patch6: %{name}-disable-tests-s390x.patch
+
+Patch7: %{name}-3.1.1-fix_bug2223.patch
+Patch8: %{name}-3.1.1-fix_bug2217.patch
+Patch9: %{name}-3.1.1-bug2378.patch
+Patch10: %{name}-3.1.1-bug2493.patch
+
+BuildRequires: make
+%if 0%{?el7}
+BuildRequires: boost169-devel
+%else
+BuildRequires: boost-devel
+%endif
 BuildRequires: swig
-#TODO: enable when GUI is functional
-#BuildRequires: wxGTK-devel
-BuildRequires: zlib-devel
+BuildRequires: cmake3
+BuildRequires: dos2unix
+BuildRequires: desktop-file-utils
+BuildRequires: eigen3-devel
+BuildRequires: gcc-c++
+%if 0%{?fedora}
+BuildRequires: inchi-devel >= 1.0.3
+BuildRequires: wxGTK-devel
+%else
+BuildRequires: wxGTK3-devel
+%endif
+BuildRequires: libxml2-devel
+BuildRequires: ImageMagick
+BuildRequires: rapidjson-devel
+Requires:      %{name}-libs%{?_isa} = %{version}-%{release}
 
 %description
 Open Babel is a free, open-source version of the Babel chemistry file
@@ -38,149 +83,586 @@ Babel left off, as a cross-platform program and library designed to
 interconvert between many file formats used in molecular modeling,
 computational chemistry, and many related areas.
 
-Open Babel includes two components, a command-line utility and a C++
-library. The command-line utility is intended to be used as a replacement
-for the original babel program, to translate between various chemical file
-formats. The C++ library includes all of the file-translation code as well
-as a wide variety of utilities to foster development of other open source
-scientific software. 
+This package contains the command-line utility, which is intended to
+be used as a replacement for the original babel program, to translate
+between various chemical file formats as well as a wide variety of
+utilities to foster development of other open source scientific
+software.
 
 %package devel
 Summary: Development tools for programs which will use the Open Babel library
-Group: Development/Libraries
-Requires: %{name} = %{version}-%{release}
-Requires: pkgconfig
+Requires: %{name}-libs%{?_isa} = %{version}-%{release}
 
 %description devel
 The %{name}-devel package includes the header files and libraries
 necessary for developing programs using the Open Babel library.
 
-If you are going to develop programs which will use this library
-you should install %{name}-devel.  You'll also need to have the
-%{name} package installed.
+%package doc
+Summary: Additional documentation for the Open Babel library
+BuildArch: noarch
+
+%description doc
+This package contains additional documentation for Open Babel.
+
+%package gui
+Summary: Chemistry software file format converter - GUI version
+Requires: %{name}-libs%{?_isa} = %{version}-%{release}
+
+%description gui
+Open Babel is a free, open-source version of the Babel chemistry file
+translation program. Open Babel is a project designed to pick up where
+Babel left off, as a cross-platform program and library designed to
+interconvert between many file formats used in molecular modeling,
+computational chemistry, and many related areas.
+
+This package contains the graphical interface.
+
+%package libs
+Summary: Chemistry software file format converter - libraries
+%if 0%{?rhel}
+License: GPL-2.0-only AND LGPL-2.1-or-later
+Provides: bundled(libinchi) = 1.0.4
+%endif
+
+%description libs
+Open Babel is a free, open-source version of the Babel chemistry file
+translation program. Open Babel is a project designed to pick up where
+Babel left off, as a cross-platform program and library designed to
+interconvert between many file formats used in molecular modeling,
+computational chemistry, and many related areas.
+
+This package contains the C++ library, which includes all of the
+file-translation code.
 
 %package -n perl-%{name}
-Group: System Environment/Libraries
 Summary: Perl wrapper for the Open Babel library
-Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
-Obsoletes: %{name}-perl < 2.2.0
-Provides: %{name}-perl = %{version}-%{release}
+Requires: %{name}-libs%{?_isa} = %{version}-%{release}
+BuildRequires: perl-devel
+BuildRequires: perl-generators
 
 %description -n perl-%{name}
 Perl wrapper for the Open Babel library.
 
-%package -n python-%{name}
-Group: System Environment/Libraries
+%package -n python3-%{name}
 Summary: Python wrapper for the Open Babel library
-Obsoletes: %{name}-python < 2.2.0
-Provides: %{name}-python = %{version}-%{release}
+Requires: %{name}-libs%{?_isa} = %{version}-%{release}
+BuildRequires: python3-devel
+BuildRequires: python3-setuptools
+%{?python_provide:%python_provide python3-%{name}}
+Obsoletes: python2-%{name} < 0:%{version}-%{release}
 
-%description -n python-%{name}
-Python wrapper for the Open Babel library.
+%description -n python3-%{name}
+Python3 wrapper for the Open Babel library.
 
 %package -n ruby-%{name}
 Summary: Ruby wrapper for the Open Babel library
-Group: Development/Libraries
-Requires: ruby(abi) = 1.8
-Requires: %{name} = %{version}-%{release}
+Requires: ruby(release)
+Requires: %{name}-libs%{?_isa} = %{version}-%{release}
+BuildRequires: ruby-devel
 
 %description -n ruby-%{name}
 Ruby wrapper for the Open Babel library.
 
 %prep
-%setup -q -n %{name}-%{version}%{beta_str}
-%patch1 -p1 -b .r
-%patch3 -p1 -b .inchi
-chmod 644 src/formats/mmcifformat.cpp
+%setup -q -n %{name}-%{name}-%(echo %{version} | tr '.' '-')
+%patch0 -p1 -b .perl_path
+%patch1 -p1 -b .plugindir
+%patch2 -p1 -b .noswig_ruby
+%patch3 -p1 -b .ruby_vendor
+%ifarch aarch64 %{arm} %{power64} s390x
+%patch4 -p1 -b .tests
+%endif
+%patch5 -p1 -b .s390x
+%ifarch s390x
+%patch6 -p1 -b .backup
+%endif
+%patch7 -p1 -b .backup
+%patch8 -p1 -b .backup
+%patch9 -p1 -b .backup
+%patch10 -p1 -b .backup
+
+%if 0%{?fedora}
+rm -rf src/formats/libinchi
+%else
+cp -p %{SOURCE2} ./inchi-license-lgpl-2.1.txt
+%endif
+
+# convert to Unix line endings
+dos2unix -k \
+  data/chemdrawcdx.h \
+  include/openbabel/{tautomer.h,math/align.h} \
+  src/math/align.cpp \
+  test/testsmartssym.py \
+
+convert src/GUI/babel.xpm -transparent white babel.png
+
+# Remove duplicate html files
+pushd doc
+for man in *.1; do
+ html=`basename $man .1`.html
+ if [ -f $html ]; then
+   rm $html
+ fi
+done
+popd
 
 %build
-autoreconf --force --install
-%configure --enable-shared=yes --enable-static=no --disable-inchi --enable-maintainer-mode
-%{__make} %{?_smp_mflags}
+mkdir -p %{_target_platform}
+%if 0%{?fedora} || 0%{?eln}
+# RHBZ #1996330
+%ifarch %{power64}
+export CXXFLAGS="%{optflags} -DEIGEN_ALTIVEC_DISABLE_MMA"
+%endif
+%endif
+%cmake3 -B %{_target_platform} \
+ -Wno-dev \
+ -DCMAKE_SKIP_RPATH:BOOL=ON \
+ -DBUILD_GUI:BOOL=ON \
+ -DPYTHON_BINDINGS:BOOL=ON \
+ -DPYTHON_EXECUTABLE=%{__python3} \
+ -DPERL_BINDINGS:BOOL=ON \
+ -DRUBY_BINDINGS:BOOL=ON \
+ -DWITH_MAEPARSER:BOOL=OFF \
+ -DWITH_COORDGEN:BOOL=OFF \
+ -DOB_PLUGIN_INSTALL_DIR:PATH=%{_lib}/openbabel3 \
+%if 0%{?rhel}
+ -DOPENBABEL_USE_SYSTEM_INCHI=false \
+%else
+ -DOPENBABEL_USE_SYSTEM_INCHI=true \
+%endif
+ -DENABLE_VERSIONED_FORMATS=false \
+ -DRUN_SWIG=true \
+ -DENABLE_TESTS:BOOL=ON \
+ -DOPTIMIZE_NATIVE=OFF \
+ -DGLIBC_24_COMPATIBLE:BOOL=OFF \
+%if 0%{?el7}
+ -DBoost_FILESYSTEM_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_filesystem.so \
+ -DBoost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_serialization.so \
+ -DBoost_SYSTEM_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_system.so \
+ -DBoost_INCLUDE_DIR:PATH=%{_includedir}/boost169 \
+ -DBoost_LIBRARY_DIR_RELEASE:PATH=%{_libdir}/boost169
+%endif
 
-pushd scripts/perl
-perl Makefile.PL INSTALLDIRS="vendor"
-%{__make} %{?_smp_mflags} OPTIMIZE="$RPM_OPT_FLAGS"
-popd
-
-pushd scripts/python
-python setup.py build
-popd
-
-pushd scripts/ruby
-ruby extconf.rb --with-openbabel-include=../../include --with-openbabel-lib=../../src/.libs
-%{__make} %{?_smp_mflags}
-popd
+%make_build -C %{_target_platform}
 
 %install
-%{__rm} -rf $RPM_BUILD_ROOT
+%make_install -C %{_target_platform}
 
-%{__make} install DESTDIR=$RPM_BUILD_ROOT
+rm -f %{buildroot}%{_libdir}/cmake/openbabel2/*.cmake
 
-%{__rm} $RPM_BUILD_ROOT%{_libdir}{,/%{name}/%{version}%{beta_ver}}/*.la
+desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE1}
+install -Dpm644 babel.png %{buildroot}%{_datadir}/pixmaps/babel.png
 
-pushd scripts/perl
-%{__make} install DESTDIR=$RPM_BUILD_ROOT
-popd
-%{__rm} -f $RPM_BUILD_ROOT%{perl_archlib}/perllocal.pod
-%{__rm} -f $RPM_BUILD_ROOT%{perl_vendorarch}/*/Chemistry/OpenBabel/{.packlist,OpenBabel.bs}
-chmod 755 $RPM_BUILD_ROOT%{perl_vendorarch}/*/Chemistry/OpenBabel/OpenBabel.so
-
-pushd scripts/python
-%{__python} setup.py install --skip-build --root $RPM_BUILD_ROOT
-%{__python} setup.py install -O1 --skip-build --root $RPM_BUILD_ROOT
-popd
-chmod 755 $RPM_BUILD_ROOT%{python_sitearch}/_openbabel.so
-
-pushd scripts/ruby
-%{__make} install DESTDIR=$RPM_BUILD_ROOT
-popd
-
-%clean
-%{__rm} -rf $RPM_BUILD_ROOT
+# Create profile files
+mkdir -p %{buildroot}%{_sysconfdir}/profile.d
+cat > %{buildroot}%{_sysconfdir}/profile.d/openbabel3.sh <<EOF
+BABEL_LIBDIR=%{_libdir}/%{name}3
+export BABEL_LIBDIR
+BABEL_DATADIR=%{_datadir}/%{name}
+export BABEL_DATADIR
+EOF
+cat > %{buildroot}%{_sysconfdir}/profile.d/openbabel3.csh <<EOF
+setenv BABEL_LIBDIR %{_libdir}/%{name}3
+setenv BABEL_DATADIR %{_datadir}/%{name}
+EOF
 
+%if 1
 %check
-%{__make} check
+%define _vpath_builddir %{_target_platform}
+pushd %{_vpath_builddir}
 
-%post -p /sbin/ldconfig
+# rm the built ruby bindings for testsuite to succeed (Red Hat bugzilla ticket #1191173)
+rm -f %{_lib}/openbabel.so
 
-%postun -p /sbin/ldconfig
+export CTEST_OUTPUT_ON_FAILURE=1
+export PYTHONPATH=%{buildroot}%{python3_sitearch}
+%if 0%{?el7}
+ctest3 -j1 --force-new-ctest-process -E 'test_cifspacegroup_1|test_cifspacegroup_2'
+%else
+# See https://github.com/openbabel/openbabel/issues/2138
+%ifarch aarch64 %{arm} %{power64} s390x
+ctest3 -j1 --force-new-ctest-process -E 'pybindtest_bindings|pybindtest_obconv_writers'
+%else
+ctest3 -j1 --force-new-ctest-process
+%endif
+%endif
+%endif
+
+%if 0%{?el7}
+%ldconfig_scriptlets libs
+%endif
 
 %files
-%defattr(-,root,root,-)
-%doc AUTHORS COPYING ChangeLog README THANKS
-%doc doc/*.html
-%doc doc/README* doc/babel*.inc doc/dioxin.*
-%{_bindir}/*
-%{_mandir}/man1/*
-%{_datadir}/%{name}
-%{_libdir}/libopenbabel.so.*
-%{_libdir}/%{name}
+%config(noreplace) %{_sysconfdir}/profile.d/openbabel3.sh
+%config(noreplace) %{_sysconfdir}/profile.d/openbabel3.csh
+%{_bindir}/ob*
+%{_bindir}/roundtrip
+%{_mandir}/man1/*.1*
+%exclude %{_bindir}/obgui
+%exclude %{_mandir}/man1/obgui.1*
 
 %files devel
-%defattr(-,root,root,-)
-%{_includedir}/%{name}-2.0
+%{_includedir}/%{name}3/
 %{_libdir}/libopenbabel.so
-%{_libdir}/pkgconfig/*.pc
+%{_libdir}/libopenbabel.so.7
+%{_libdir}/pkgconfig/openbabel-3.pc
+%{_libdir}/cmake/openbabel3/
+%if 0%{?rhel}
+%{_libdir}/libinchi.so
+%{_includedir}/inchi/
+%endif
+
+%files doc
+%doc doc/*.html doc/README* doc/dioxin.*
+
+%files gui
+%{_bindir}/obgui
+%{_datadir}/applications/obgui.desktop
+%{_datadir}/pixmaps/babel.png
+%{_mandir}/man1/obgui.1*
+
+%files libs
+%license COPYING
+%doc THANKS AUTHORS authors.txt README.md
+%{_datadir}/%{name}/
+%{_libdir}/%{name}3/
+%{_libdir}/libopenbabel.so.7.0.0
+%if 0%{?rhel}
+%license inchi-license-lgpl-2.1.txt
+%{_libdir}/libinchi.so.0.4.1
+%{_libdir}/libinchi.so.0
+%endif
 
 %files -n perl-%{name}
-%defattr(-,root,root,-)
 %{perl_vendorarch}/Chemistry/OpenBabel.pm
 %dir %{perl_vendorarch}/*/Chemistry/OpenBabel
 %{perl_vendorarch}/*/Chemistry/OpenBabel/OpenBabel.so
 
-%files -n python-%{name}
-%defattr(-,root,root,-)
-%{python_sitearch}/_openbabel.so
-%{python_sitearch}/openbabel.py*
-%{python_sitearch}/pybel.py*
-%{python_sitearch}/openbabel*.egg-info
+%files -n python3-%{name}
+%{python3_sitearch}/openbabel/
 
 %files -n ruby-%{name}
-%defattr(-, root, root, -)
-%{ruby_sitearch}/openbabel.so
+%{ruby_vendorarchdir}/openbabel.so
 
 %changelog
+* Wed Feb 08 2023 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-18
+- Fix config files (rhbz#2168290)
+
+* Thu Jan 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.1-17
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
+
+* Wed Jan 04 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 3.1.1-16
+- Rebuild for https://fedoraproject.org/wiki/Changes/Ruby_3.2
+
+* Thu Sep 29 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-15
+- Fix openbabel version in CMakeLists.txt
+- Fix rhbz#2130870
+
+* Tue Sep 27 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-14
+- Fix EPEL builds
+
+* Tue Sep 27 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-13
+- New rebuild
+
+* Sun Aug 07 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-12
+- Add profile file openbabel3.sh (rhbz#2112710)
+
+* Thu Aug 04 2022 Scott Talbert <swt@techie.net> - 3.1.1-11
+- Rebuild with wxWidgets 3.2
+
+* Fri Jul 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.1-10
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
+
+* Fri Jul 08 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-9
+- Patched for rhbz#2105259
+
+* Mon Jun 13 2022 Python Maint <python-maint@redhat.com> - 3.1.1-8
+- Rebuilt for Python 3.11
+
+* Mon May 30 2022 Jitka Plesnikova <jplesnik@redhat.com> - 3.1.1-7
+- Perl 5.36 rebuild
+
+* Thu Jan 27 2022 Vít Ondruch <vondruch@redhat.com> - 3.1.1-6
+- Rebuilt for https://fedoraproject.org/wiki/Changes/Ruby_3.1
+
+* Thu Jan 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.1-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Sun Dec 12 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-4
+- Use bundled inchi on EPEL
+
+* Sat Nov 06 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-3
+- Fix CMake config file
+
+* Wed Sep 22 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-2
+- Fix patches order
+
+- Release 3.1.1
+
+* Thu Sep 02 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-1
+* Wed Sep 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-39
+- Install license file and some release documentation
+
+* Mon Aug 30 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-38
+- Use CMake3 in EPEL7
+
+* Thu Jul 22 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-37
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 2.4.1-36
+- Rebuilt for Python 3.10
+
+* Fri May 21 2021 Jitka Plesnikova <jplesnik@redhat.com> - 2.4.1-35
+- Perl 5.34 rebuild
+
+* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-34
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
+* Wed Jan 06 2021 Mamoru TASAKA <mtasaka@fedoraproject.org> - 2.4.1-33
+- F-34: rebuild against ruby 3.0
+
+* Thu Jul 30 2020 Rex Dieter <rdieter@fedoraproject.org> - 2.4.1-32
+- adjust for new %%cmake macros (#1859850)
+
+* Tue Jul 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-31
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Mon Jun 22 2020 Jitka Plesnikova <jplesnik@redhat.com> - 2.4.1-30
+- Perl 5.32 rebuild
+
+* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 2.4.1-29
+- Rebuilt for Python 3.9
+
+* Wed Jan 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-28
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
+
+* Sun Jan 19 2020 Mamoru TASAKA <mtasaka@fedoraproject.org> - 2.4.1-27
+- F-32: rebuild against ruby27
+
+* Thu Oct 03 2019 Miro Hrončok <mhroncok@redhat.com> - 2.4.1-26
+- Rebuilt for Python 3.8.0rc1 (#1748018)
+
+* Mon Aug 19 2019 Miro Hrončok <mhroncok@redhat.com> - 2.4.1-25
+- Rebuilt for Python 3.8
+
+* Thu Jul 25 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-24
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
+
+* Tue Jun 18 2019 Petr Pisar <ppisar@redhat.com> - 2.4.1-23
+- Obsolete by name only (bug #1685183)
+
+* Thu May 30 2019 Jitka Plesnikova <jplesnik@redhat.com> - 2.4.1-22
+- Perl 5.30 rebuild
+
+* Fri Mar 01 2019 Dominik Mierzejewski <rpm@greysector.net> - 2.4.1-21
+- drop python2 subpackage (#1648558)
+- fix running the testsuite with python3
+- fix line endings for some source files
+
+* Fri Feb 01 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-20
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
+
+* Mon Jan 28 2019 Mamoru TASAKA <mtasaka@fedoraproject.org> - 2.4.1-19
+- F-30: rebuild again against ruby26
+
+* Sun Jan 27 2019 Dominik Mierzejewski <rpm@greysector.net> - 2.4.1-18
+- Fix path to libdir in .pc (#1669664)
+- Use https for URL:
+- Exclude obgui from the main openbabel package
+- Disable failing test on s390x/F29+
+
+* Mon Jan 21 2019 Mamoru TASAKA <mtasaka@fedoraproject.org> - 2.4.1-17
+- F-30: rebuild against ruby26
+
+* Wed Nov 07 2018 Scott Talbert <swt@techie.net> - 2.4.1-16
+- Rebuild with wxWidgets 3.0
+- Exclude obgui from the main openbabel package
+
+* Fri Jul 13 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-15
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
+
+* Tue Jul 03 2018 Petr Pisar <ppisar@redhat.com> - 2.4.1-14
+- Perl 5.28 rebuild
+
+* Wed Jun 27 2018 Jitka Plesnikova <jplesnik@redhat.com> - 2.4.1-13
+- Perl 5.28 rebuild
+
+* Tue Jun 19 2018 Miro Hrončok <mhroncok@redhat.com> - 2.4.1-12
+- Rebuilt for Python 3.7
+
+* Thu Feb 08 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-11
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
+
+* Sat Jan 20 2018 Björn Esser <besser82@fedoraproject.org> - 2.4.1-10
+- Rebuilt for switch to libxcrypt
+
+* Fri Jan 05 2018 Mamoru TASAKA <mtasaka@fedoraproject.org> - 2.4.1-9
+- F-28: rebuild for ruby25
+
+* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-8
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
+
+* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-7
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
+
+* Sun Jun 04 2017 Jitka Plesnikova <jplesnik@redhat.com> - 2.4.1-6
+- Perl 5.26 rebuild
+
+* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
+
+* Thu Jan 12 2017 Vít Ondruch <vondruch@redhat.com> - 2.4.1-4
+- Rebuilt for https://fedoraproject.org/wiki/Changes/Ruby_2.4
+
+* Wed Dec 28 2016 Rich Mattes <richmattes@gmail.com> - 2.4.1-3
+- Rebuild for eigen3-3.3.1
+
+* Mon Dec 19 2016 Miro Hrončok <mhroncok@redhat.com> - 2.4.1-2
+- Rebuild for Python 3.6
+
+* Tue Oct 11 2016 Dominik Mierzejewski <rpm@greysector.net> - 2.4.1-1
+- update to 2.4.1
+
+* Tue Jul 19 2016 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.90-0.11.20160216git3a63a98
+- https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages
+
+* Sat May 14 2016 Jitka Plesnikova <jplesnik@redhat.com> - 2.3.90-0.10.20160216git3a63a98
+- Perl 5.24 rebuild
+
+* Thu Feb 18 2016 Dominik Mierzejewski <rpm@greysector.net> - 2.3.90-0.9.20160216git3a63a984
+- drop redundant BuildRoot and defattr
+- fix macro usage
+- update to current Git master HEAD
+- fix narrowing conversion compilation error
+- add python3 subpackage (#1285258)
+
+* Thu Feb 04 2016 Fedora Release Engineering <releng@fedoraproject.org> - 2.3.90-0.8.20150402gita345105
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
+
+* Tue Jan 12 2016 Vít Ondruch <vondruch@redhat.com> - 2.3.90-0.7.20150402gita345105
+- Rebuilt for https://fedoraproject.org/wiki/Changes/Ruby_2.3
+
+* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.90-0.6.20150402gita345105
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
+
+* Wed Jun 03 2015 Jitka Plesnikova <jplesnik@redhat.com> - 2.3.90-0.5.20150402gita345105
+- Perl 5.22 rebuild
+
+* Thu Apr 16 2015 Dominik Mierzejewski <rpm@greysector.net> - 2.3.90-0.4.20150402gita345105
+- updated to current Git master HEAD
+- dropped obsolete patches
+
+* Wed Mar 25 2015 Rex Dieter <rdieter@fedoraproject.org> 2.3.90-0.3.20150204git
+- rebuild (gcc5)
+
+* Thu Feb 12 2015 Dominik Mierzejewski <rpm@greysector.net> 2.3.90-0.2.20150204git75414ad
+- restore disttag, which got accidentally removed during last rebase
+
+* Sat Feb 07 2015 Dominik Mierzejewski <rpm@greysector.net> 2.3.90-0.1.20150204git75414ad
+- update to current Git master HEAD
+- drop obsolete patches
+- rebase remaining patches
+- drop zlib-devel from BR (required by libxml2-devel)
+- add gcc-c++ to BR
+- fix building bindings with swig-3.x
+- drop old Obsoletes: and Provides:
+- rm the built ruby bindings for testsuite to succeed (bug #1191173)
+
+* Tue Jan 27 2015 Marcin Juszkiewicz <mjuszkiewicz@redhat.com> - 2.3.2-11
+- Unify patches which disable tests on ppc64, s390(x), arm and enable
+  result also for aarch64. rhbugs: #1108103 #1094491 #1094513
+
+* Fri Jan 16 2015 Mamoru TASAKA <mtasaka@fedoraproject.org> - 2.3.2-10
+- Rebuild for https://fedoraproject.org/wiki/Changes/Ruby_2.2
+- Remove deprecated Config:: usage
+
+* Thu Nov 13 2014 Dan Horák <dan[at]danny.cz> - 2.3.2-9
+- disable some tests also on s390(x)
+
+* Wed Oct 15 2014 Karsten Hopp <karsten@redhat.com> 2.3.2-8
+- disable some tests on ppc64 to unblock other builds (#1108103)
+
+* Wed Aug 27 2014 Jitka Plesnikova <jplesnik@redhat.com> - 2.3.2-7
+- Perl 5.20 rebuild
+
+* Sun Aug 17 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.2-6
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
+
+* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.2-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
+
+* Sun Apr 27 2014 Dominik Mierzejewski <rpm@greysector.net> 2.3.2-4
+- fix and enable testsuite
+- drop ancient Obsoletes: (rhbz#1002135)
+- drop ruby < 2.0 conditional Requires:
+- temporarily disable two tests failing on ARM (rhbz#1094491)
+
+* Fri Apr 25 2014 Vít Ondruch <vondruch@redhat.com> - 2.3.2-3
+- Rebuilt for https://fedoraproject.org/wiki/Changes/Ruby_2.1
+
+* Sat Aug 03 2013 Petr Pisar <ppisar@redhat.com> - 2.3.2-2
+- Perl 5.18 rebuild
+
+* Thu Jul 18 2013 Susi Lehtola <jussilehtola@fedoraproject.org> - 2.3.2-1
+- Turned off versioned formats.
+- Filter out private provides.
+- Update to 2.3.2.
+
+* Wed Jul 17 2013 Petr Pisar <ppisar@redhat.com> - 2.3.1-9
+- Perl 5.18 rebuild
+
+* Fri Mar 22 2013 Vít Ondruch <vondruch@redhat.com> - 2.3.1-8
+- Rebuild for https://fedoraproject.org/wiki/Features/Ruby_2.0.0
+
+* Thu Feb 14 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.1-7
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
+
+* Fri Jul 20 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.1-6
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
+
+* Fri Jun 08 2012 Petr Pisar <ppisar@redhat.com> - 2.3.1-5
+- Perl 5.16 rebuild
+
+* Fri Apr  6 2012 Mamoru Tasaka <mtasaka@fedoraproject.org> - 2.3.1-4
+- Fix several issues related to ruby modules
+ - Fix build with gcc47 (on Linux)
+ - Fix SWIG_init even when not using swig (#772149)
+ - Use vendorarchdir instead of sitearch on F-17+
+ - Fix ruby(abi) requirement
+
+* Tue Feb 28 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.1-3
+- Rebuilt for c++ ABI breakage
+
+* Fri Jan 13 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.1-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
+
+* Fri Oct 21 2011 Dominik Mierzejewski <rpm@greysector.net> 2.3.1-1
+- update to 2.3.1
+- drop obsolete patches (merged upstream)
+- add desktop file for the GUI
+
+* Mon Jun 20 2011 Marcela Mašláňová <mmaslano@redhat.com> - 2.3.0-5
+- Perl mass rebuild
+
+* Thu Jun 09 2011 Marcela Mašláňová <mmaslano@redhat.com> - 2.3.0-4
+- Perl 5.14 mass rebuild
+
+* Tue Mar 22 2011 Kevin Kofler <Kevin@tigcc.ticalc.org> 2.3.0-3
+- fix plugin directory location (#680292, patch by lg)
+- show forcefields list in obenergy output (#680292, patch by lg)
+
+* Tue Feb 08 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.3.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
+
+* Sun Nov 21 2010 Dominik Mierzejewski <rpm@greysector.net> 2.3.0-1
+- build system switched to cmake
+- enabled GUI
+- enabled Eigen2
+- updated to 2.3.0 final
+- patched to fix various build issues
+- split libs and GUI into separate subpackages
+- fixed rpmlint warnings about strange file permissions
+
 * Wed Jul 21 2010 David Malcolm <dmalcolm@redhat.com> - 2.2.3-4
 - Rebuilt for https://fedoraproject.org/wiki/Features/Python_2.7/MassRebuild
 

sources

@@ -1 +1 @@
-7ea8845c54d6d3a9be378c78088af804  openbabel-2.2.3.tar.gz
+SHA512 (openbabel-openbabel-3-1-1.tar.gz) = d46807e8f4e2f0f691e69943e5c5eda9c271271cfca6f66b6df136bbf384502fd3b65a4adf134a4e9e1f2452e1316c9515aa92292b73205b9eb4d7e4d7a85f18