Compare commits

..

No commits in common. "rawhide" and "f32" have entirely different histories.
rawhide ... f32

15 changed files with 174 additions and 958 deletions

1
.gitignore vendored
View File

@ -8,4 +8,3 @@ openbabel-2.0.2.tar.gz
/openbabel-3a63a9849f8d9719c5989c43875d51be50c53019.tar.gz /openbabel-3a63a9849f8d9719c5989c43875d51be50c53019.tar.gz
/openbabel-2-4-0.tar.gz /openbabel-2-4-0.tar.gz
/openbabel-2-4-1.tar.gz /openbabel-2-4-1.tar.gz
/openbabel-openbabel-3-1-1.tar.gz

View File

@ -1,44 +0,0 @@
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

View File

@ -1,36 +0,0 @@
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

View File

@ -1,39 +0,0 @@
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:

View File

@ -1,34 +0,0 @@
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);

View File

@ -1,21 +1,21 @@
diff -up a/test/CMakeLists.txt.s390x b/test/CMakeLists.txt diff -up openbabel-openbabel-2-4-1/test/CMakeLists.txt.s390x openbabel-openbabel-2-4-1/test/CMakeLists.txt
--- a/test/CMakeLists.txt.s390x 2016-10-10 17:56:17.000000000 +0200 --- openbabel-openbabel-2-4-1/test/CMakeLists.txt.s390x 2016-10-10 17:56:17.000000000 +0200
+++ b/test/CMakeLists.txt 2019-01-27 19:32:21.568052461 +0100 +++ openbabel-openbabel-2-4-1/test/CMakeLists.txt 2019-01-27 19:32:21.568052461 +0100
@@ -74,7 +74,7 @@ @@ -62,7 +62,7 @@ set(origtests
) )
set (atom_parts 1 2 3 4) set (atom_parts 1 2 3 4)
set (ffmmff94_parts 1 2 3 4 5 6) set (ffmmff94_parts 1 2)
-set (math_parts 1 2 3 4) -set (math_parts 1 2 3 4)
+set (math_parts 1 2 3) +set (math_parts 1 2 3)
set (pdbreadfile_parts 1 2 3 4)
if(BUILD_SHARED) if(BUILD_SHARED)
@@ -250,8 +250,6 @@ if(LIBXML2_FOUND)
@@ -238,7 +238,7 @@ endif(NOT MINGW AND NOT CYGWIN)
if (PYTHON_BINDINGS)
include(UsePythonTest) include(UsePythonTest)
set(pybindtests set(pybindtests
bindings - bindings _pybel example)
- _pybel + bindings example)
- example foreach(pybindtest ${pybindtests})
obconv_writers SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES
cdjsonformat PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}"
pcjsonformat

View File

@ -1,16 +1,16 @@
diff -up a/test/CMakeLists.txt.tests b/test/CMakeLists.txt diff -up openbabel-openbabel-2-4-0/test/CMakeLists.txt.tests openbabel-openbabel-2-4-0/test/CMakeLists.txt
--- a/test/CMakeLists.txt.tests 2016-09-21 21:55:37.000000000 +0200 --- openbabel-openbabel-2-4-0/test/CMakeLists.txt.tests 2016-09-21 21:55:37.000000000 +0200
+++ b/test/CMakeLists.txt 2016-10-10 13:48:52.726803964 +0200 +++ openbabel-openbabel-2-4-0/test/CMakeLists.txt 2016-10-10 13:48:52.726803964 +0200
@@ -39,7 +39,7 @@ @@ -34,7 +34,7 @@ set (implicitH_parts 1)
set (isomorphism_parts 1 2 3 4 5 6 7 8 9) set (lssr_parts 1 2 3 4 5)
set (isomorphism_parts 1 2 3 4 5 6 7 8)
set (multicml_parts 1) set (multicml_parts 1)
set (periodic_parts 1 2 3 4) -set (regressions_parts 1 221 222 223 224)
-set (regressions_parts 1 221 222 223 224 225 226 227 228 240 241 242 1794 2111)
+set (regressions_parts 222 223 224) +set (regressions_parts 222 223 224)
set (rotor_parts 1 2 3 4) set (rotor_parts 1 2 3 4)
set (shuffle_parts 1 2 3 4 5) set (shuffle_parts 1 2 3 4 5)
set (smiles_parts 1 2 3) set (smiles_parts 1 2 3)
@@ -188,7 +188,7 @@ @@ -177,7 +177,7 @@ if(WITH_INCHI)
set_target_properties(test_inchiwrite PROPERTIES LINK_SEARCH_END_STATIC TRUE) set_target_properties(test_inchiwrite PROPERTIES LINK_SEARCH_END_STATIC TRUE)
endif() endif()
# files in test/inchi -- both .sdf and .txt # files in test/inchi -- both .sdf and .txt
@ -19,11 +19,11 @@ diff -up a/test/CMakeLists.txt.tests b/test/CMakeLists.txt
set(inchidata ${CMAKE_SOURCE_DIR}/test/inchi) set(inchidata ${CMAKE_SOURCE_DIR}/test/inchi)
foreach(test ${inchitests}) foreach(test ${inchitests})
add_test(inchi${test}_Test add_test(inchi${test}_Test
@@ -226,7 +226,7 @@ @@ -215,7 +215,7 @@ if(NOT MINGW AND NOT CYGWIN)
include(UsePythonTest) include(UsePythonTest)
if(PYTHON_EXECUTABLE) if(PYTHON_EXECUTABLE)
set(pytests set(pytests
- babel sym smartssym fastsearch distgeom unique kekule pdbformat RInChI) - babel sym smartssym fastsearch unique kekule pdbformat)
+ babel smartssym fastsearch unique kekule pdbformat) + babel smartssym fastsearch unique kekule pdbformat)
foreach(pytest ${pytests}) foreach(pytest ${pytests})
SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES

View File

@ -1,12 +1,11 @@
diff -up a/openbabel-3.pc.cmake.p b/openbabel-3.pc.cmake diff -up openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake.p openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake
--- a/openbabel-3.pc.cmake.p --- openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake.p 2016-10-10 17:56:17.000000000 +0200
+++ b/openbabel-3.pc.cmake +++ openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake 2019-01-27 10:47:00.905546971 +0100
@@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
prefix=@CMAKE_INSTALL_PREFIX@ prefix=@CMAKE_INSTALL_PREFIX@
exec_prefix=${prefix} exec_prefix=${prefix}
-libdir=${exec_prefix}/@LIB_INSTALL_DIR@ -libdir=${exec_prefix}/@LIB_INSTALL_DIR@
+libdir=${exec_prefix}/lib@LIB_SUFFIX@ +libdir=${exec_prefix}/lib@LIB_SUFFIX@
includedir=${prefix}/include includedir=${prefix}/include
pkgincludedir=${includedir}/openbabel@BABEL_MAJ_VER@ pkgincludedir=${includedir}/openbabel-2.0

View File

@ -1,502 +0,0 @@
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
that what they have is not the original version, so that the original
author's reputation will not be affected by problems that might be
introduced by others.
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
entire combination fits its criteria of freedom. The Lesser General
Public License permits more lax criteria for linking other code with
the library.
We call this license the "Lesser" General Public License because it
does Less to protect the user's freedom than the ordinary General
Public License. It also provides other free software developers Less
of an advantage over competing non-free programs. These disadvantages
are the reason we use the ordinary General Public License for many
libraries. However, the Lesser license provides advantages in certain
special circumstances.
For example, on rare occasions, there may be a special need to
encourage the widest possible use of a certain library, so that it becomes
a de-facto standard. To achieve this, non-free programs must be
allowed to use the library. A more frequent case is that a free
library does the same job as widely used non-free libraries. In this
case, there is little to gain by limiting the free library to free
software only, so we use the Lesser General Public License.
In other cases, permission to use a particular library in non-free
programs enables a greater number of people to use a large body of
free software. For example, permission to use the GNU C Library in
non-free programs enables many more people to use the whole GNU
operating system, as well as its variant, the GNU/Linux operating
system.
Although the Lesser General Public License is Less protective of the
users' freedom, it does ensure that the user of a program that is
linked with the Library has the freedom and the wherewithal to run
that program using a modified version of the Library.
The precise terms and conditions for copying, distribution and
modification follow. Pay close attention to the difference between a
"work based on the library" and a "work that uses the library". The
former contains code derived from the library, whereas the latter must
be combined with the library in order to run.
GNU LESSER GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any software library or other
program which contains a notice placed by the copyright holder or
other authorized party saying it may be distributed under the terms of
this Lesser General Public License (also called "this License").
Each licensee is addressed as "you".
A "library" means a collection of software functions and/or data
prepared so as to be conveniently linked with application programs
(which use some of those functions and data) to form executables.
The "Library", below, refers to any such software library or work
which has been distributed under these terms. A "work based on the
Library" means either the Library or any derivative work under
copyright law: that is to say, a work containing the Library or a
portion of it, either verbatim or with modifications and/or translated
straightforwardly into another language. (Hereinafter, translation is
included without limitation in the term "modification".)
"Source code" for a work means the preferred form of the work for
making modifications to it. For a library, complete source code means
all the source code for all modules it contains, plus any associated
interface definition files, plus the scripts used to control compilation
and installation of the library.
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running a program using the Library is not restricted, and output from
such a program is covered only if its contents constitute a work based
on the Library (independent of the use of the Library in a tool for
writing it). Whether that is true depends on what the Library does
and what the program that uses the Library does.
1. You may copy and distribute verbatim copies of the Library's
complete source code as you receive it, in any medium, provided that
you conspicuously and appropriately publish on each copy an
appropriate copyright notice and disclaimer of warranty; keep intact
all the notices that refer to this License and to the absence of any
warranty; and distribute a copy of this License along with the
Library.
You may charge a fee for the physical act of transferring a copy,
and you may at your option offer warranty protection in exchange for a
fee.
2. You may modify your copy or copies of the Library or any portion
of it, thus forming a work based on the Library, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) The modified work must itself be a software library.
b) You must cause the files modified to carry prominent notices
stating that you changed the files and the date of any change.
c) You must cause the whole of the work to be licensed at no
charge to all third parties under the terms of this License.
d) If a facility in the modified Library refers to a function or a
table of data to be supplied by an application program that uses
the facility, other than as an argument passed when the facility
is invoked, then you must make a good faith effort to ensure that,
in the event an application does not supply such function or
table, the facility still operates, and performs whatever part of
its purpose remains meaningful.
(For example, a function in a library to compute square roots has
a purpose that is entirely well-defined independent of the
application. Therefore, Subsection 2d requires that any
application-supplied function or table used by this function must
be optional: if the application does not supply it, the square
root function must still compute square roots.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Library,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Library, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote
it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Library.
In addition, mere aggregation of another work not based on the Library
with the Library (or with a work based on the Library) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may opt to apply the terms of the ordinary GNU General Public
License instead of this License to a given copy of the Library. To do
this, you must alter all the notices that refer to this License, so
that they refer to the ordinary GNU General Public License, version 2,
instead of to this License. (If a newer version than version 2 of the
ordinary GNU General Public License has appeared, then you can specify
that version instead if you wish.) Do not make any other change in
these notices.
Once this change is made in a given copy, it is irreversible for
that copy, so the ordinary GNU General Public License applies to all
subsequent copies and derivative works made from that copy.
This option is useful when you wish to copy part of the code of
the Library into a program that is not a library.
4. You may copy and distribute the Library (or a portion or
derivative of it, under Section 2) in object code or executable form
under the terms of Sections 1 and 2 above provided that you accompany
it with the complete corresponding machine-readable source code, which
must be distributed under the terms of Sections 1 and 2 above on a
medium customarily used for software interchange.
If distribution of object code is made by offering access to copy
from a designated place, then offering equivalent access to copy the
source code from the same place satisfies the requirement to
distribute the source code, even though third parties are not
compelled to copy the source along with the object code.
5. A program that contains no derivative of any portion of the
Library, but is designed to work with the Library by being compiled or
linked with it, is called a "work that uses the Library". Such a
work, in isolation, is not a derivative work of the Library, and
therefore falls outside the scope of this License.
However, linking a "work that uses the Library" with the Library
creates an executable that is a derivative of the Library (because it
contains portions of the Library), rather than a "work that uses the
library". The executable is therefore covered by this License.
Section 6 states terms for distribution of such executables.
When a "work that uses the Library" uses material from a header file
that is part of the Library, the object code for the work may be a
derivative work of the Library even though the source code is not.
Whether this is true is especially significant if the work can be
linked without the Library, or if the work is itself a library. The
threshold for this to be true is not precisely defined by law.
If such an object file uses only numerical parameters, data
structure layouts and accessors, and small macros and small inline
functions (ten lines or less in length), then the use of the object
file is unrestricted, regardless of whether it is legally a derivative
work. (Executables containing this object code plus portions of the
Library will still fall under Section 6.)
Otherwise, if the work is a derivative of the Library, you may
distribute the object code for the work under the terms of Section 6.
Any executables containing that work also fall under Section 6,
whether or not they are linked directly with the Library itself.
6. As an exception to the Sections above, you may also combine or
link a "work that uses the Library" with the Library to produce a
work containing portions of the Library, and distribute that work
under terms of your choice, provided that the terms permit
modification of the work for the customer's own use and reverse
engineering for debugging such modifications.
You must give prominent notice with each copy of the work that the
Library is used in it and that the Library and its use are covered by
this License. You must supply a copy of this License. If the work
during execution displays copyright notices, you must include the
copyright notice for the Library among them, as well as a reference
directing the user to the copy of this License. Also, you must do one
of these things:
a) Accompany the work with the complete corresponding
machine-readable source code for the Library including whatever
changes were used in the work (which must be distributed under
Sections 1 and 2 above); and, if the work is an executable linked
with the Library, with the complete machine-readable "work that
uses the Library", as object code and/or source code, so that the
user can modify the Library and then relink to produce a modified
executable containing the modified Library. (It is understood
that the user who changes the contents of definitions files in the
Library will not necessarily be able to recompile the application
to use the modified definitions.)
b) Use a suitable shared library mechanism for linking with the
Library. A suitable mechanism is one that (1) uses at run time a
copy of the library already present on the user's computer system,
rather than copying library functions into the executable, and (2)
will operate properly with a modified version of the library, if
the user installs one, as long as the modified version is
interface-compatible with the version that the work was made with.
c) Accompany the work with a written offer, valid for at
least three years, to give the same user the materials
specified in Subsection 6a, above, for a charge no more
than the cost of performing this distribution.
d) If distribution of the work is made by offering access to copy
from a designated place, offer equivalent access to copy the above
specified materials from the same place.
e) Verify that the user has already received a copy of these
materials or that you have already sent this user a copy.
For an executable, the required form of the "work that uses the
Library" must include any data and utility programs needed for
reproducing the executable from it. However, as a special exception,
the materials to be distributed need not include anything that is
normally distributed (in either source or binary form) with the major
components (compiler, kernel, and so on) of the operating system on
which the executable runs, unless that component itself accompanies
the executable.
It may happen that this requirement contradicts the license
restrictions of other proprietary libraries that do not normally
accompany the operating system. Such a contradiction means you cannot
use both them and the Library together in an executable that you
distribute.
7. You may place library facilities that are a work based on the
Library side-by-side in a single library together with other library
facilities not covered by this License, and distribute such a combined
library, provided that the separate distribution of the work based on
the Library and of the other library facilities is otherwise
permitted, and provided that you do these two things:
a) Accompany the combined library with a copy of the same work
based on the Library, uncombined with any other library
facilities. This must be distributed under the terms of the
Sections above.
b) Give prominent notice with the combined library of the fact
that part of it is a work based on the Library, and explaining
where to find the accompanying uncombined form of the same work.
8. You may not copy, modify, sublicense, link with, or distribute
the Library except as expressly provided under this License. Any
attempt otherwise to copy, modify, sublicense, link with, or
distribute the Library is void, and will automatically terminate your
rights under this License. However, parties who have received copies,
or rights, from you under this License will not have their licenses
terminated so long as such parties remain in full compliance.
9. You are not required to accept this License, since you have not
signed it. However, nothing else grants you permission to modify or
distribute the Library or its derivative works. These actions are
prohibited by law if you do not accept this License. Therefore, by
modifying or distributing the Library (or any work based on the
Library), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Library or works based on it.
10. Each time you redistribute the Library (or any work based on the
Library), the recipient automatically receives a license from the
original licensor to copy, distribute, link with or modify the Library
subject to these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties with
this License.
11. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Library at all. For example, if a patent
license would not permit royalty-free redistribution of the Library by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Library.
If any portion of this section is held invalid or unenforceable under any
particular circumstance, the balance of the section is intended to apply,
and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
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
original copyright holder who places the Library under this License may add
an explicit geographical distribution limitation excluding those countries,
so that distribution is permitted only in or among countries not thus
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.
Each version is given a distinguishing version number. If the Library
specifies a version number of this License which applies to it and
"any later version", you have the option of following the terms and
conditions either of that version or of any later version published by
the Free Software Foundation. If the Library does not specify a
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,
write to the author to ask for permission. For software which is
copyrighted by the Free Software Foundation, write to the Free
Software Foundation; we sometimes make exceptions for this. Our
decision will be guided by the two goals of preserving the free status
of all derivatives of our free software and of promoting the sharing
and reuse of software generally.
NO WARRANTY
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Libraries
If you develop a new library, and you want it to be of the greatest
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).
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!

View File

@ -0,0 +1,33 @@
diff -up openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp.nc openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp
--- openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp.nc 2016-02-16 23:47:25.000000000 +0100
+++ openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp 2016-02-18 19:01:40.509752461 +0100
@@ -218,7 +218,7 @@ bool PNGFormat::ReadMolecule(OBBase* pOb
_count=0;
_hasInputPngFile=true;
}
- const char pngheader[] = {-119,80,78,71,13,10,26,10,0};
+ const signed char pngheader[] = {-119,80,78,71,13,10,26,10,0};
char readbytes[9];
ifs.read(readbytes, 8);
diff -up openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp.nc openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp
--- openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp.nc 2016-02-16 23:47:25.000000000 +0100
+++ openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp 2016-02-18 23:22:23.786793588 +0100
@@ -472,7 +472,7 @@ bool YOBFormat::WriteMolecule(OBBase* pO
// bool hetatom;
char buffer[32],/*resname[4],*/atomname[5];
- char double1[8]={0,0,0,0,0,0,-16,0x3f};
+ const signed char double1[8]={0,0,0,0,0,0,-16,0x3f};
// char *str;
int i,j,/*m,q,*/pos;
int /*resno,chainNum,link,linktype,*/atoms,element,links/*,chain*/;
@@ -500,7 +500,7 @@ bool YOBFormat::WriteMolecule(OBBase* pO
mem_set(buffer,0,8);
for (i=0;i<4;i++)
{ for (j=0;j<4;j++)
- { if (i==j) ofs.write(double1,8);
+ { if (i==j) ofs.write(reinterpret_cast<const char*>(double1),8);
else ofs.write(buffer,8); } }
storeint32le(buffer,MOB_INFOEND);
storeint32le(&buffer[4],MOB_INFOENDSIZE);

View File

@ -1,30 +1,12 @@
diff -up a/CMakeLists.txt.plugindir b/CMakeLists.txt diff -up openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt.plugindir openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt
--- a/CMakeLists.txt.plugindir 2015-02-07 21:42:44.431479900 +0100 --- openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt.plugindir 2015-02-07 21:42:44.431479900 +0100
+++ b/CMakeLists.txt 2015-02-07 21:43:29.000429326 +0100 +++ openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt 2015-02-07 21:43:29.000429326 +0100
@@ -24,7 +24,7 @@ @@ -266,7 +266,7 @@ if(NOT MSVC)
# had too many 1.100.1 releases. :-) }
set(BABEL_MAJ_VER 3) " SCANDIR_NEEDS_CONST)
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(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}"
set(BABEL_LIBRARY openbabel) + set(OB_MODULE_PATH "${OB_PLUGIN_INSTALL_DIR}"
@@ -750,7 +750,7 @@ CACHE PATH "Set to system install for bindings only build")
"${openbabel_BINARY_DIR}/OpenBabel3ConfigVersion.cmake" @ONLY) add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"")
# Now to configure the installed config file.
-set(OB_CONFIG_DIR "${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@")

15
openbabel-python-dl.patch Normal file
View File

@ -0,0 +1,15 @@
diff -up openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3 openbabel-openbabel-2-4-1/scripts/CMakeLists.txt
--- openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3 2019-03-04 11:12:54.369464503 +0100
+++ openbabel-openbabel-2-4-1/scripts/CMakeLists.txt 2019-03-04 11:59:39.323264995 +0100
@@ -84,7 +84,10 @@ if (DO_PYTHON_BINDINGS)
COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py
COMMAND ${CMAKE_COMMAND} -E echo " import dl" >> ob.py
COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py
- COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py
+ COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py
+ COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py
+ COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py
+ COMMAND ${CMAKE_COMMAND} -E echo " import ctypes as dl" >> ob.py
COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py
COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py
COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py

32
openbabel-taberror.patch Normal file
View File

@ -0,0 +1,32 @@
diff -up openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror openbabel-openbabel-2-4-1/test/testpdbformat.py
--- openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror 2016-10-10 17:56:17.000000000 +0200
+++ openbabel-openbabel-2-4-1/test/testpdbformat.py 2019-03-04 11:09:24.786801658 +0100
@@ -24,12 +24,12 @@ class TestPDBFormat(BaseTest):
def testInsertionCodes(self):
"""
- Testing a PDB entry with insertion codes to distinguish residues
- upon conversion to FASTA.
+ Testing a PDB entry with insertion codes to distinguish residues
+ upon conversion to FASTA.
"""
self.canFindExecutable("babel")
- self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
+ self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
@@ -100,9 +100,9 @@ ATOM 473 HE1 TYR L 32 48.512
ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
"""
- output, error = run_exec(self.entryPDBwithInsertioncodes,
- "babel -ipdb -ofasta")
- self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
+ output, error = run_exec(self.entryPDBwithInsertioncodes,
+ "babel -ipdb -ofasta")
+ self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
if __name__ == "__main__":
testsuite = []

View File

@ -1,80 +1,54 @@
%global commit 3a63a9849f8d9719c5989c43875d51be50c53019
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%{!?perl_vendorarch:%global perl_vendorarch %(eval "`perl -V:installvendorarch`"; echo $installvendorarch)} %{!?perl_vendorarch:%global perl_vendorarch %(eval "`perl -V:installvendorarch`"; echo $installvendorarch)}
# we don't want to provide private Perl or Python extension libs # we don't want to provide private Perl or Python extension libs
%global __provides_exclude_from ^(%{perl_vendorarch}/auto|%{python3_sitearch})/.*\\.so$ %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 Name: openbabel
Version: 3.1.1 Version: 2.4.1
Release: 18%{?dist} Release: 28%{?dist}
Summary: Chemistry software file format converter Summary: Chemistry software file format converter
License: GPL-2.0-only License: GPLv2
URL: https://openbabel.org/ URL: https://openbabel.org/
Source0: https://github.com/openbabel/openbabel/archive/openbabel-openbabel-%(echo %{version} | tr '.' '-').tar.gz Source0: https://github.com/openbabel/openbabel/archive/openbabel-%(echo %{version} | tr '.' '-').tar.gz
Source1: obgui.desktop Source1: obgui.desktop
Source2: openbabel-inchi-license-lgpl-2.1.txt
# fix perl modules install path # fix perl modules install path
Patch0: %{name}-perl.patch Patch1: %{name}-perl.patch
# fix plugin directory location (#680292, patch by lg)
# fix openbabel version + cmake config files Patch4: openbabel-plugindir.patch
Patch1: %{name}-plugindir.patch
# fix SWIG_init even when not using swig (#772149) # fix SWIG_init even when not using swig (#772149)
Patch2: %{name}-noswig-rubymethod.patch Patch6: openbabel-noswig-rubymethod.patch
# On F-17, directory for C ruby files changed to use vendorarch directory # On F-17, directory for C ruby files changed to use vendorarch directory
Patch3: %{name}-ruby19-vendorarch.patch Patch7: openbabel-ruby19-vendorarch.patch
# temporarily disable some tests on: # temporarily disable some tests on:
# - ppc64 and s390(x) to unblock other builds (#1108103) # - ppc64 and s390(x) to unblock other builds (#1108103)
# - ARM (#1094491) # - ARM (#1094491)
# - aarch64 (#1094513) # - aarch64 (#1094513)
# Upstream bugs: https://sourceforge.net/p/openbabel/bugs/927/ https://sourceforge.net/p/openbabel/bugs/945/ # Upstream bugs: https://sourceforge.net/p/openbabel/bugs/927/ https://sourceforge.net/p/openbabel/bugs/945/
Patch4: %{name}-disable-tests.patch Patch8: openbabel-disable-tests.patch
Patch9: openbabel-narrowing-conversion.patch
# Fix path to libdir in .pc file # Fix path to libdir in .pc file
# https://bugzilla.redhat.com/show_bug.cgi?id=1669664 # https://bugzilla.redhat.com/show_bug.cgi?id=1669664
Patch5: %{name}-fix-libdir-in-pkgconfig.patch Patch10: openbabel-fix-libdir-in-pkgconfig.patch
# Math 4 test is failing on s390x only # Math 4 test is failing on s390x only
Patch6: %{name}-disable-tests-s390x.patch Patch11: openbabel-disable-tests-s390x.patch
# Fix inconsistent whitespace
Patch7: %{name}-3.1.1-fix_bug2223.patch Patch12: openbabel-taberror.patch
Patch8: %{name}-3.1.1-fix_bug2217.patch # Fix import of dl module in python3.7
Patch9: %{name}-3.1.1-bug2378.patch # https://github.com/openbabel/openbabel/pull/372
Patch10: %{name}-3.1.1-bug2493.patch Patch13: openbabel-python-dl.patch
BuildRequires: cmake
BuildRequires: make
%if 0%{?el7}
BuildRequires: boost169-devel
%else
BuildRequires: boost-devel
%endif
BuildRequires: swig
BuildRequires: cmake3
BuildRequires: dos2unix BuildRequires: dos2unix
BuildRequires: desktop-file-utils BuildRequires: desktop-file-utils
BuildRequires: eigen3-devel BuildRequires: eigen3-devel
BuildRequires: gcc-c++ BuildRequires: gcc-c++
%if 0%{?fedora}
BuildRequires: inchi-devel >= 1.0.3 BuildRequires: inchi-devel >= 1.0.3
BuildRequires: wxGTK-devel
%else
BuildRequires: wxGTK3-devel
%endif
BuildRequires: libxml2-devel BuildRequires: libxml2-devel
BuildRequires: swig
BuildRequires: wxGTK3-devel
BuildRequires: ImageMagick BuildRequires: ImageMagick
BuildRequires: rapidjson-devel
Requires: %{name}-libs%{?_isa} = %{version}-%{release}
%description %description
Open Babel is a free, open-source version of the Babel chemistry file Open Babel is a free, open-source version of the Babel chemistry file
@ -92,6 +66,7 @@ software.
%package devel %package devel
Summary: Development tools for programs which will use the Open Babel library Summary: Development tools for programs which will use the Open Babel library
Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: %{name}-libs%{?_isa} = %{version}-%{release}
Requires: pkgconfig
%description devel %description devel
The %{name}-devel package includes the header files and libraries The %{name}-devel package includes the header files and libraries
@ -106,7 +81,6 @@ This package contains additional documentation for Open Babel.
%package gui %package gui
Summary: Chemistry software file format converter - GUI version Summary: Chemistry software file format converter - GUI version
Requires: %{name}-libs%{?_isa} = %{version}-%{release}
%description gui %description gui
Open Babel is a free, open-source version of the Babel chemistry file Open Babel is a free, open-source version of the Babel chemistry file
@ -119,10 +93,6 @@ This package contains the graphical interface.
%package libs %package libs
Summary: Chemistry software file format converter - libraries 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 %description libs
Open Babel is a free, open-source version of the Babel chemistry file Open Babel is a free, open-source version of the Babel chemistry file
@ -136,6 +106,7 @@ file-translation code.
%package -n perl-%{name} %package -n perl-%{name}
Summary: Perl wrapper for the Open Babel library Summary: Perl wrapper for the Open Babel library
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: %{name}-libs%{?_isa} = %{version}-%{release}
BuildRequires: perl-devel BuildRequires: perl-devel
BuildRequires: perl-generators BuildRequires: perl-generators
@ -147,9 +118,8 @@ Perl wrapper for the Open Babel library.
Summary: Python wrapper for the Open Babel library Summary: Python wrapper for the Open Babel library
Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: %{name}-libs%{?_isa} = %{version}-%{release}
BuildRequires: python3-devel BuildRequires: python3-devel
BuildRequires: python3-setuptools
%{?python_provide:%python_provide python3-%{name}} %{?python_provide:%python_provide python3-%{name}}
Obsoletes: python2-%{name} < 0:%{version}-%{release} Obsoletes: python2-%{name} < 2.4.1-21
%description -n python3-%{name} %description -n python3-%{name}
Python3 wrapper for the Open Babel library. Python3 wrapper for the Open Babel library.
@ -165,28 +135,20 @@ Ruby wrapper for the Open Babel library.
%prep %prep
%setup -q -n %{name}-%{name}-%(echo %{version} | tr '.' '-') %setup -q -n %{name}-%{name}-%(echo %{version} | tr '.' '-')
%patch0 -p1 -b .perl_path %patch1 -p1 -b .perl_path
%patch1 -p1 -b .plugindir %patch4 -p1 -b .plugindir
%patch2 -p1 -b .noswig_ruby %patch6 -p1 -b .noswig_ruby
%patch3 -p1 -b .ruby_vendor %patch7 -p1 -b .ruby_vendor
%ifarch aarch64 %{arm} %{power64} s390x %ifarch aarch64 %{arm} %{power64} s390 s390x
%patch4 -p1 -b .tests %patch8 -p1 -b .tests
%endif %endif
%patch5 -p1 -b .s390x
%ifarch s390x %ifarch s390x
%patch6 -p1 -b .backup %patch11 -p1 -b .s390x
%endif %endif
%patch7 -p1 -b .backup %patch9 -p1 -b .nc
%patch8 -p1 -b .backup %patch10 -p1
%patch9 -p1 -b .backup %patch12 -p1 -b .taberr
%patch10 -p1 -b .backup %patch13 -p1 -b .py3dl
%if 0%{?fedora}
rm -rf src/formats/libinchi
%else
cp -p %{SOURCE2} ./inchi-license-lgpl-2.1.txt
%endif
# convert to Unix line endings # convert to Unix line endings
dos2unix -k \ dos2unix -k \
data/chemdrawcdx.h \ data/chemdrawcdx.h \
@ -207,94 +169,41 @@ done
popd popd
%build %build
mkdir -p %{_target_platform} %cmake \
%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 \ -DCMAKE_SKIP_RPATH:BOOL=ON \
-DBUILD_GUI:BOOL=ON \ -DBUILD_GUI:BOOL=ON \
-DPYTHON_BINDINGS:BOOL=ON \ -DPYTHON_BINDINGS:BOOL=ON \
-DPYTHON_EXECUTABLE=%{__python3} \ -DPYTHON_EXECUTABLE=%{__python3} \
-DPERL_BINDINGS:BOOL=ON \ -DPERL_BINDINGS:BOOL=ON \
-DRUBY_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 \ -DOPENBABEL_USE_SYSTEM_INCHI=true \
%endif
-DENABLE_VERSIONED_FORMATS=false \ -DENABLE_VERSIONED_FORMATS=false \
-DRUN_SWIG=true \ -DRUN_SWIG=true \
-DENABLE_TESTS:BOOL=ON \ -DENABLE_TESTS:BOOL=ON \
-DOPTIMIZE_NATIVE=OFF \ -DOPTIMIZE_NATIVE=OFF \
-DGLIBC_24_COMPATIBLE:BOOL=OFF \ .
%if 0%{?el7} make VERBOSE=1 %{?_smp_mflags}
-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
%make_build -C %{_target_platform}
%install %install
%make_install -C %{_target_platform} make VERBOSE=1 DESTDIR=%{buildroot} install
rm -f %{buildroot}%{_libdir}/cmake/openbabel2/*.cmake rm %{buildroot}%{_libdir}/cmake/openbabel2/*.cmake
desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE1} desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE1}
install -Dpm644 babel.png %{buildroot}%{_datadir}/pixmaps/babel.png install -Dpm644 babel.png %{buildroot}%{_datadir}/pixmaps/babel.png
# 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 %if 1
%check %check
%define _vpath_builddir %{_target_platform} # rm the built ruby bindings for testsuite to succeed (bug #1191173)
pushd %{_vpath_builddir} rm %{_lib}/openbabel.so
export CTEST_OUTPUT_ON_FAILURE=1 PYTHONPATH=%{buildroot}%{python3_sitearch}
# rm the built ruby bindings for testsuite to succeed (Red Hat bugzilla ticket #1191173) %make_build test
rm -f %{_lib}/openbabel.so
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 %endif
%if 0%{?el7}
%ldconfig_scriptlets libs %ldconfig_scriptlets libs
%endif
%files %files
%config(noreplace) %{_sysconfdir}/profile.d/openbabel3.sh %{_bindir}/babel
%config(noreplace) %{_sysconfdir}/profile.d/openbabel3.csh
%{_bindir}/ob* %{_bindir}/ob*
%{_bindir}/roundtrip %{_bindir}/roundtrip
%{_mandir}/man1/*.1* %{_mandir}/man1/*.1*
@ -302,15 +211,9 @@ ctest3 -j1 --force-new-ctest-process
%exclude %{_mandir}/man1/obgui.1* %exclude %{_mandir}/man1/obgui.1*
%files devel %files devel
%{_includedir}/%{name}3/ %{_includedir}/%{name}-2.0
%{_libdir}/libopenbabel.so %{_libdir}/libopenbabel.so
%{_libdir}/libopenbabel.so.7 %{_libdir}/pkgconfig/*.pc
%{_libdir}/pkgconfig/openbabel-3.pc
%{_libdir}/cmake/openbabel3/
%if 0%{?rhel}
%{_libdir}/libinchi.so
%{_includedir}/inchi/
%endif
%files doc %files doc
%doc doc/*.html doc/README* doc/dioxin.* %doc doc/*.html doc/README* doc/dioxin.*
@ -322,16 +225,9 @@ ctest3 -j1 --force-new-ctest-process
%{_mandir}/man1/obgui.1* %{_mandir}/man1/obgui.1*
%files libs %files libs
%license COPYING
%doc THANKS AUTHORS authors.txt README.md
%{_datadir}/%{name}/ %{_datadir}/%{name}/
%{_libdir}/%{name}3/ %{_libdir}/%{name}/
%{_libdir}/libopenbabel.so.7.0.0 %{_libdir}/libopenbabel.so.*
%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} %files -n perl-%{name}
%{perl_vendorarch}/Chemistry/OpenBabel.pm %{perl_vendorarch}/Chemistry/OpenBabel.pm
@ -339,100 +235,15 @@ ctest3 -j1 --force-new-ctest-process
%{perl_vendorarch}/*/Chemistry/OpenBabel/OpenBabel.so %{perl_vendorarch}/*/Chemistry/OpenBabel/OpenBabel.so
%files -n python3-%{name} %files -n python3-%{name}
%{python3_sitearch}/openbabel/ %{python3_sitearch}/_openbabel.so
%{python3_sitearch}/openbabel.py
%{python3_sitearch}/pybel.py
%{python3_sitearch}/__pycache__/*
%files -n ruby-%{name} %files -n ruby-%{name}
%{ruby_vendorarchdir}/openbabel.so %{ruby_vendorarchdir}/openbabel.so
%changelog %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 * Wed Jan 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-28
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild

View File

@ -1 +1 @@
SHA512 (openbabel-openbabel-3-1-1.tar.gz) = d46807e8f4e2f0f691e69943e5c5eda9c271271cfca6f66b6df136bbf384502fd3b65a4adf134a4e9e1f2452e1316c9515aa92292b73205b9eb4d7e4d7a85f18 c0e0aefeef0f9f2bb2c78109d65c30a5 openbabel-2-4-1.tar.gz