openbsd/ports
1
0
Fork 0
mirror of https://github.com/openbsd/ports.git synced 2026-06-17 23:13:55 +02:00
Code Issues Packages Projects Releases Wiki Activity

Update to openbabel-3.2.0

Browse Source 
Changes:
https://github.com/openbabel/openbabel/releases/tag/openbabel-3-2-0
This commit is contained in:
bket
2026-05-27 14:50:32 +00:00
parent 4bf188169a
commit 20ff073932
15 changed files with 89 additions and 225 deletions
Download Patch File Download Diff File Expand all files Collapse all files
misc/openbabel/Makefile
+11 -17
View File
@@ -1,15 +1,17 @@
COMMENT= chemistry file translation program
V= 3.1.1
REVISION= 7
DISTNAME= openbabel-${V}
V= 3.2.0
DIST_TUPLE= github openbabel openbabel openbabel-${V:S/./-/g} . \
github schrodinger maeparser v1.3.3 maeparser \
github schrodinger coordgenlibs d20e735d96480385b2e257522288004038a08cc9 coordgen
PKGNAME= openbabel-${V}
CATEGORIES= misc
SHARED_LIBS += coordgen 0.0 \
inchi 0.0 \
maeparser 0.0 \
openbabel 6.1
SHARED_LIBS= coordgen 1.0 \
inchi 1.0 \
maeparser 1.0 \
openbabel 7.0
HOMEPAGE= https://openbabel.org
@@ -18,11 +20,8 @@ MAINTAINER= Bjorn Ketelaars <bket@openbsd.org>
# GPLv2
PERMIT_PACKAGE= Yes
WANTLIB+= ${COMPILER_LIBCXX} boost_iostreams-mt boost_regex-mt
WANTLIB+= c cairo m xml2 z boost_random-mt
SITES= https://github.com/openbabel/openbabel/releases/download/openbabel-${V:S/./-/g}/
EXTRACT_SUFX= -source.tar.bz2
WANTLIB= ${COMPILER_LIBCXX} boost_iostreams-mt boost_regex-mt \
c cairo m xml2 z boost_random-mt
COMPILER= base-clang ports-gcc
@@ -40,13 +39,8 @@ BUILD_DEPENDS= math/eigen3 \
CONFIGURE_ARGS= -DBUILD_GUI=OFF
MODCMAKE_POLICY_VERSION_OVERRIDE = Yes
SEPARATE_BUILD= No
SUBST_VARS= V
MODCMAKE_POLICY_VERSION_OVERRIDE = Yes
.include <bsd.port.mk>
misc/openbabel/distinfo
+6 -2
View File
@@ -1,2 +1,6 @@
SHA256 (openbabel-3.1.1-source.tar.bz2) = puyDgdWeoypLJByLH715mstSvpSrZM29clBvtOInDmg=
SIZE (openbabel-3.1.1-source.tar.bz2) = 27743669
SHA256 (openbabel-openbabel-openbabel-3-2-0.tar.gz) = mq358Bs9D/FdSfzSjX12uSMhjXC/EPmepMxGZgf0x+I=
SHA256 (schrodinger-coordgenlibs-d20e735d96480385b2e257522288004038a08cc9.tar.gz) = 6LT1srPdnSz3xr1uV+2ry1Nv8F1/i4lFYOSBd7AYKMk=
SHA256 (schrodinger-maeparser-v1.3.3.tar.gz) = eOdXGneepJUudS7O9Xxi+yZGOUfinvf0sxsRmI2Iygc=
SIZE (openbabel-openbabel-openbabel-3-2-0.tar.gz) = 37815471
SIZE (schrodinger-coordgenlibs-d20e735d96480385b2e257522288004038a08cc9.tar.gz) = 167157
SIZE (schrodinger-maeparser-v1.3.3.tar.gz) = 39896
misc/openbabel/patches/patch-CMakeLists_txt
+54 -19
View File
@@ -1,25 +1,60 @@
Revise for 3.1.1 release. Taken from
https://github.com/openbabel/openbabel/commit/650b1f829ac47cc84877a330366ec9485da3ec99
Index: CMakeLists.txt
--- CMakeLists.txt.orig
+++ CMakeLists.txt
@@ -10,9 +10,6 @@ set (CMAKE_CXX_STANDARD 11)
@@ -505,14 +505,14 @@ if(WITH_MAEPARSER)
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
- if(POLICY CMP0042)
- cmake_policy(SET CMP0042 OLD)
- endif()
endif()
set(MAEPARSER_VERSION "v1.3.3" CACHE STRING "Maeparser fallback version to download")
- set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}")
+ set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/maeparser")
option(MAEPARSER_BUILD_SHARED_LIBS "Build maeparser as a shared library" ${BUILD_SHARED})
# Do not build the test, as it will be put into the bin dir, where it won't be found by the test runner.
set(MAEPARSER_BUILD_TESTS OFF CACHE BOOL "Disable Maeparser tests")
- if(EXISTS "${MAEPARSER_DIR}/maeparser/CMakeLists.txt")
+ if(EXISTS "${MAEPARSER_DIR}/CMakeLists.txt")
message(STATUS "Building existing MaeParser '${MAEPARSER_VERSION}' source at ${MAEPARSER_DIR}.")
@@ -535,9 +535,9 @@ if(WITH_MAEPARSER)
endif()
- add_subdirectory("${MAEPARSER_DIR}/maeparser")
+ add_subdirectory("${MAEPARSER_DIR}")
- set(maeparser_INCLUDE_DIRS "${MAEPARSER_DIR}")
+ set(maeparser_INCLUDE_DIRS "${openbabel_SOURCE_DIR}")
set(maeparser_LIBRARIES maeparser)
message(STATUS "Maestro formats will be supported. Using MaeParser '${MAEPARSER_VERSION}' at ${MAEPARSER_DIR}")
@@ -565,13 +565,13 @@ if(WITH_COORDGEN)
# v3.0.2-10-gd20e735
set(COORDGEN_VERSION "d20e735d96480385b2e257522288004038a08cc9" CACHE STRING "Coordgen fallback version to download")
- set(COORDGEN_DIR "${openbabel_SOURCE_DIR}/external/coordgen-${COORDGEN_VERSION}")
+ set(COORDGEN_DIR "${openbabel_SOURCE_DIR}/coordgen")
# These won't work, since openbabel relocates them to the "bin" dir
set(COORDGEN_BUILD_TESTS OFF CACHE BOOL "Disable building Coordgen tests")
set(COORDGEN_BUILD_EXAMPLE OFF CACHE BOOL "Disable building Coordgen example")
- if(EXISTS "${COORDGEN_DIR}/coordgen/CMakeLists.txt")
+ if(EXISTS "${COORDGEN_DIR}/CMakeLists.txt")
message(STATUS "Building existing Coordgen '${COORDGEN_VERSION}' source at ${COORDGEN_DIR}.")
@@ -594,9 +594,9 @@ if(WITH_COORDGEN)
endif()
- add_subdirectory("${COORDGEN_DIR}/coordgen")
+ add_subdirectory("${COORDGEN_DIR}")
- set(coordgen_INCLUDE_DIRS "${COORDGEN_DIR}")
+ set(coordgen_INCLUDE_DIRS "${openbabel_SOURCE_DIR}")
set(coordgen_LIBRARIES coordgen)
include (CheckCXXCompilerFlag)
@@ -24,7 +21,7 @@ include (CheckCXXCompilerFlag)
# 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)
misc/openbabel/patches/patch-include_openbabel_inchiformat_h
-14
View File
@@ -1,14 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: include/openbabel/inchiformat.h
--- include/openbabel/inchiformat.h.orig
+++ include/openbabel/inchiformat.h
@@ -131,7 +131,6 @@ class InChIFormat : public OBMoleculeFormat (public)
// and "CH4" is less than "C2H6"
// and "CH4" is less than "ClH" (hydrogen chloride)
struct InchiLess
- : public std::binary_function<const std::string&, const std::string&, bool>
{
bool operator()(const std::string& s1, const std::string& s2) const
{
misc/openbabel/patches/patch-include_openbabel_plugin_h
-15
View File
@@ -1,15 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: include/openbabel/plugin.h
--- include/openbabel/plugin.h.orig
+++ include/openbabel/plugin.h
@@ -38,7 +38,7 @@ namespace OpenBabel
///@{
/// @brief Case insensitive string comparison for PluginMapType key.
-struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
+struct OBERROR CharPtrLess
{
bool operator()(const char* p1,const char* p2) const
{ return strcasecmp(p1,p2)<0; }
misc/openbabel/patches/patch-scripts_openbabel-R_i
-20
View File
@@ -1,20 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: scripts/openbabel-R.i
--- scripts/openbabel-R.i.orig
+++ scripts/openbabel-R.i
@@ -290,13 +290,6 @@ CAST_GENERICDATA_TO(VirtualBond)
%include <openbabel/chains.h>
%include <openbabel/typer.h>
-
-// To avoid warning in plugin.h about "Nothing known about std::binary_function"
-namespace std {
- template <T1, T2, T3>
- class binary_function {};
-}
-%template(dummy) std::binary_function <const char *, const char *, bool>;
%include <openbabel/plugin.h>
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
misc/openbabel/patches/patch-scripts_openbabel-csharp_i
-20
View File
@@ -1,20 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: scripts/openbabel-csharp.i
--- scripts/openbabel-csharp.i.orig
+++ scripts/openbabel-csharp.i
@@ -830,13 +830,6 @@ CAST_GENERICDATA_TO(VirtualBond);
%include <openbabel/chains.h>
%include <openbabel/typer.h>
-
-// To avoid warning in plugin.h about "Nothing known about std::binary_function"
-namespace std {
- template <T1, T2, T3>
- class binary_function {};
-}
-%template(dummy) std::binary_function <const char *, const char *, bool>;
%include <openbabel/plugin.h>
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
misc/openbabel/patches/patch-scripts_openbabel-java_i
-20
View File
@@ -1,20 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: scripts/openbabel-java.i
--- scripts/openbabel-java.i.orig
+++ scripts/openbabel-java.i
@@ -246,13 +246,6 @@ CAST_GENERICDATA_TO(VirtualBond)
%include <openbabel/chains.h>
%include <openbabel/typer.h>
-
-// To avoid warning in plugin.h about "Nothing known about std::binary_function"
-namespace std {
- template <T1, T2, T3>
- class binary_function {};
-}
-%template(dummy) std::binary_function <const char *, const char *, bool>;
%include <openbabel/plugin.h>
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
misc/openbabel/patches/patch-scripts_openbabel-perl_i
-20
View File
@@ -1,20 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: scripts/openbabel-perl.i
--- scripts/openbabel-perl.i.orig
+++ scripts/openbabel-perl.i
@@ -191,13 +191,6 @@ CAST_GENERICDATA_TO(VirtualBond)
%import <openbabel/chains.h>
%import <openbabel/typer.h>
-
-// To avoid warning in oberror.h about "Nothing known about std::binary_function"
-namespace std {
- template <T1, T2, T3>
- class binary_function {};
-}
-%template(Dummy) std::binary_function <const char *, const char *, bool>;
%include <openbabel/plugin.h>
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
misc/openbabel/patches/patch-scripts_openbabel-php_i
-20
View File
@@ -1,20 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: scripts/openbabel-php.i
--- scripts/openbabel-php.i.orig
+++ scripts/openbabel-php.i
@@ -223,13 +223,6 @@ CAST_GENERICDATA_TO(VirtualBond)
%include <openbabel/chains.h>
%include <openbabel/typer.h>
-
-// To avoid warning in plugin.h about "Nothing known about std::binary_function"
-namespace std {
- template <T1, T2, T3>
- class binary_function {};
-}
-%template(dummy) std::binary_function <const char *, const char *, bool>;
%include <openbabel/plugin.h>
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
misc/openbabel/patches/patch-scripts_openbabel-python_i
-20
View File
@@ -1,20 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: scripts/openbabel-python.i
--- scripts/openbabel-python.i.orig
+++ scripts/openbabel-python.i
@@ -266,13 +266,6 @@ CAST_GENERICDATA_TO(SquarePlanarStereo)
%include <openbabel/chains.h>
%include <openbabel/typer.h>
-
-// To avoid warning in plugin.h about "Nothing known about std::binary_function"
-namespace std {
- template <T1, T2, T3>
- class binary_function {};
-}
-%template(dummy) std::binary_function <const char *, const char *, bool>;
%include <openbabel/plugin.h>
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
misc/openbabel/patches/patch-scripts_openbabel-ruby_i
-20
View File
@@ -1,20 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: scripts/openbabel-ruby.i
--- scripts/openbabel-ruby.i.orig
+++ scripts/openbabel-ruby.i
@@ -212,13 +212,6 @@ CAST_GENERICDATA_TO(SquarePlanarStereo)
%import <openbabel/chains.h>
%import <openbabel/typer.h>
-
-// To avoid warning in oberror.h about "Nothing known about std::binary_function"
-namespace std {
- template <T1, T2, T3>
- class binary_function {};
-}
-%template(Dummy) std::binary_function <const char *, const char *, bool>;
%include <openbabel/plugin.h>
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
misc/openbabel/patches/patch-src_formats_libinchi_ichicano_c
+11
View File
@@ -0,0 +1,11 @@
Index: src/formats/libinchi/ichicano.c
--- src/formats/libinchi/ichicano.c.orig
+++ src/formats/libinchi/ichicano.c
@@ -43,7 +43,6 @@
#include <string.h>
#include <ctype.h>
#include <time.h>
-#include <sys/timeb.h>
#include <limits.h>
#include "mode.h"
misc/openbabel/patches/patch-src_ops_sort_cpp
-15
View File
@@ -1,15 +0,0 @@
Remove std::binary_function, which is removed in C++17. Taken from
https://github.com/openbabel/openbabel/pull/2464
Index: src/ops/sort.cpp
--- src/ops/sort.cpp.orig
+++ src/ops/sort.cpp
@@ -29,7 +29,7 @@ namespace OpenBabel
{
template<class T>
-struct Order : public std::binary_function<std::pair<OBBase*,T>, std::pair<OBBase*,T>, bool>
+struct Order
{
Order(OBDescriptor* pDesc, bool rev) : _pDesc(pDesc), _rev(rev){}
bool operator()(std::pair<OBBase*,T> p1, std::pair<OBBase*,T> p2) const
misc/openbabel/pkg/PLIST
+7 -3
View File
@@ -99,6 +99,7 @@ include/openbabel3/openbabel/kekulize.h
include/openbabel3/openbabel/kinetics.h
include/openbabel3/openbabel/lineend.h
include/openbabel3/openbabel/locale.h
include/openbabel3/openbabel/macrocycle.h
include/openbabel3/openbabel/math/
include/openbabel3/openbabel/math/align.h
include/openbabel3/openbabel/math/erf.h
@@ -130,7 +131,6 @@ include/openbabel3/openbabel/residue.h
include/openbabel3/openbabel/ring.h
include/openbabel3/openbabel/rotamer.h
include/openbabel3/openbabel/rotor.h
include/openbabel3/openbabel/shared_ptr.h
include/openbabel3/openbabel/spectrophore.h
include/openbabel3/openbabel/stereo/
include/openbabel3/openbabel/stereo/bindings.h
@@ -145,8 +145,10 @@ include/openbabel3/openbabel/text.h
include/openbabel3/openbabel/tokenst.h
include/openbabel3/openbabel/typer.h
include/openbabel3/openbabel/xml.h
lib/cmake/coordgen-config${MODCMAKE_BUILD_SUFFIX}
lib/cmake/coordgen-config.cmake
lib/cmake/coordgen/
lib/cmake/coordgen/coordgen-config${MODCMAKE_BUILD_SUFFIX}
lib/cmake/coordgen/coordgen-config-version.cmake
lib/cmake/coordgen/coordgen-config.cmake
lib/cmake/maeparser-config${MODCMAKE_BUILD_SUFFIX}
lib/cmake/maeparser-config.cmake
lib/cmake/openbabel3/
@@ -186,6 +188,7 @@ lib/openbabel/${V}/
@so lib/openbabel/${V}/chemdoodlejsonformat.so
@so lib/openbabel/${V}/chemdrawcdx.so
@so lib/openbabel/${V}/chemdrawct.so
@so lib/openbabel/${V}/chemicaljsonformat.so
@so lib/openbabel/${V}/chemkinformat.so
@so lib/openbabel/${V}/chemtoolformat.so
@so lib/openbabel/${V}/cifformat.so
@@ -222,6 +225,7 @@ lib/openbabel/${V}/
@so lib/openbabel/${V}/hinformat.so
@so lib/openbabel/${V}/inchiformat.so
@so lib/openbabel/${V}/jaguarformat.so
@so lib/openbabel/${V}/ketformat.so
@so lib/openbabel/${V}/lmpdatformat.so
@so lib/openbabel/${V}/lpmdformat.so
@so lib/openbabel/${V}/maeformat.so