Date: Wednesday, May 6, 2020 @ 08:06:23 Author: arojas Revision: 382371
Update to 3.1.0 Modified: openbabel/trunk/PKGBUILD Deleted: openbabel/trunk/system-maeparser.patch ------------------------+ PKGBUILD | 17 +- system-maeparser.patch | 280 ----------------------------------------------- 2 files changed, 6 insertions(+), 291 deletions(-) Modified: PKGBUILD =================================================================== --- PKGBUILD 2020-05-06 07:50:19 UTC (rev 382370) +++ PKGBUILD 2020-05-06 08:06:23 UTC (rev 382371) @@ -1,26 +1,21 @@ -# Maintainer: +# Maintainer: Antonio Rojas <[email protected]> # Contributor: Andrea Scarpino <[email protected]> # Contributor: Damir Perisa <[email protected]> pkgbase=openbabel pkgname=(openbabel python-openbabel) -pkgver=3.0.0 -pkgrel=3 +pkgver=3.1.0 +pkgrel=1 pkgdesc="A library designed to interconvert between many file formats used in molecular modeling and computational chemistry" arch=('x86_64') url="https://openbabel.org/wiki/Main_Page"; license=('GPL') -makedepends=('cmake' 'eigen' 'wxgtk3' 'boost' 'python' 'swig' 'maeparser' 'rapidjson') -source=("https://github.com/openbabel/openbabel/releases/download/openbabel-${pkgver//./-}/openbabel-$pkgver-source.tar.bz2"; - system-maeparser.patch::"https://github.com/openbabel/openbabel/commit/8500f8a9.patch";) -sha256sums=('aad58ef8deaea9f58faeecb333f87bb18e0bdf4854e3a3b188a814a8c4517259' - '14d2b019dfb3e4d6d1b8a529e5da8c2ec84b1e599b9ae74913f8548542d0ab4b') +makedepends=('cmake' 'eigen' 'wxgtk3' 'boost' 'python' 'swig' 'maeparser' 'rapidjson' 'coordgen') +source=("https://github.com/openbabel/openbabel/releases/download/openbabel-${pkgver//./-}/openbabel-$pkgver-source.tar.bz2";) +sha256sums=('53ff96d53a190097d9a0d5243be2b7c97a6a844129a303e93cbe6e3aaf1723f9') prepare() { mkdir -p build - - cd $pkgbase-$pkgver - patch -p1 -i ../system-maeparser.patch # Unbundle maeparser } build() { Deleted: system-maeparser.patch =================================================================== --- system-maeparser.patch 2020-05-06 07:50:19 UTC (rev 382370) +++ system-maeparser.patch 2020-05-06 08:06:23 UTC (rev 382371) @@ -1,280 +0,0 @@ -From e259b6737787d2545f45b63c90f0f27a40e0179f Mon Sep 17 00:00:00 2001 -From: Ricardo R-S <[email protected]> -Date: Wed, 16 Oct 2019 15:57:46 -0400 -Subject: [PATCH 1/7] add Find modules for maeparser and coordgen - ---- - cmake/modules/Findcoordgen.cmake | 46 +++++++++++++++++++++++++++++++ - cmake/modules/Findmaeparser.cmake | 32 +++++++++++++++++++++ - 2 files changed, 78 insertions(+) - create mode 100644 cmake/modules/Findcoordgen.cmake - create mode 100644 cmake/modules/Findmaeparser.cmake - -diff --git a/cmake/modules/Findmaeparser.cmake b/cmake/modules/Findmaeparser.cmake -new file mode 100644 -index 000000000..920b3ec8e ---- /dev/null -+++ b/cmake/modules/Findmaeparser.cmake -@@ -0,0 +1,32 @@ -+# Try to find Schrodinger's MAEParser libraries. -+# -+# Different version handling is not yet supported -+# -+# Once found, this will find and define the following variables: -+# -+# maeparser_INCLUDE_DIRS - maeparser's includes directory -+# maeparser_LIBRARIES - maeparser's shared libraries -+# -+# -+ -+include(FindPackageHandleStandardArgs) -+ -+find_path(maeparser_INCLUDE_DIRS -+ NAMES "maeparser/Reader.hpp" -+ HINTS ${maeparser_DIR} -+ PATH_SUFFIXES "include" -+ DOC "include path for maeparser" -+) -+message(STATUS "maeparser include dir set as '${maeparser_INCLUDE_DIRS}'") -+ -+find_library(maeparser_LIBRARIES -+ NAMES maeparser -+ HINTS ${maeparser_DIR} -+ PATH_SUFFIXES "lib" -+ DOC "libraries for maeparser" -+) -+message(STATUS "maeparser libraries set as '${maeparser_LIBRARIES}'") -+ -+find_package_handle_standard_args(maeparser FOUND_VAR maeparser_FOUND -+ REQUIRED_VARS maeparser_INCLUDE_DIRS -+ maeparser_LIBRARIES) - -From c4c6ef37d91c8b27e0b8af9f2e4772332caa7cf1 Mon Sep 17 00:00:00 2001 -From: Ricardo R-S <[email protected]> -Date: Wed, 16 Oct 2019 15:59:18 -0400 -Subject: [PATCH 2/7] update CMakelists - ---- - CMakeLists.txt | 124 ++++++++++++++++++++++++++++++++++++++++++------- - 1 file changed, 108 insertions(+), 16 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index e8396dd17..26edc9433 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -482,33 +482,65 @@ find_package(Boost) - if(Boost_FOUND AND BUILD_SHARED) - include_directories(${Boost_INCLUDE_DIRS} ${Boost_INCLUDE_DIR}) - option(WITH_MAEPARSER "Build Maestro support" ON) - else() - option(WITH_MAEPARSER "Build Maestro support" OFF) - endif() - -- - if(WITH_MAEPARSER) -- set (CMAKE_CXX_STANDARD 11) -- -- set(MAEPARSER_VERSION 1.1) -- if(NOT EXISTS "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}") -- file(DOWNLOAD "https://github.com/schrodinger/maeparser/archive/v${MAEPARSER_VERSION}.tar.gz"; -- "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}.tar.gz" STATUS status) -- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf -- ${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}.tar.gz -- WORKING_DIRECTORY ${openbabel_SOURCE_DIR}/external) -- message(STATUS "Downloaded MaeParser to ${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}.") -+ -+ find_package(maeparser MODULE QUIET) -+ -+ if (maeparser_FOUND) -+ -+ message(STATUS "Maestro formats will be supported. Using MaeParser libraries at ${maeparser_LIBRARIES}.") -+ -+ else() -+ -+ set(MAEPARSER_VERSION "master") -+ -+ set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}") -+ -+ # Do not build the test, as it will be put into the bin dir, where it won't be found by the test runner. -+ set(MAEPARSER_BUILD_TESTS OFF CACHE BOOL "Disable Maeparser tests") -+ -+ if(EXISTS "${MAEPARSER_DIR}/maeparser/CMakeLists.txt") -+ -+ message(STATUS "Building existing MaeParser '${MAEPARSER_VERSION}' source at ${MAEPARSER_DIR}.") -+ -+ else() -+ -+ file(DOWNLOAD "https://github.com/schrodinger/maeparser/archive/${MAEPARSER_VERSION}.tar.gz"; -+ "${MAEPARSER_DIR}/maeparser-${MAEPARSER_VERSION}.tar.gz") -+ -+ execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf "maeparser-${MAEPARSER_VERSION}.tar.gz" -+ WORKING_DIRECTORY "${MAEPARSER_DIR}") -+ -+ file(RENAME "${MAEPARSER_DIR}/maeparser-${MAEPARSER_VERSION}" "${MAEPARSER_DIR}/maeparser") -+ -+ if(EXISTS "${MAEPARSER_DIR}/maeparser/CMakeLists.txt") -+ message(STATUS "Downloaded MaeParser '${MAEPARSER_VERSION}' to ${MAEPARSER_DIR}.") -+ else() -+ message(FATAL_ERROR "Failed getting or unpacking Maeparser '${MAEPARSER_VERSION}'.") -+ endif() -+ -+ endif() -+ -+ add_subdirectory("${MAEPARSER_DIR}/maeparser") -+ -+ set(maeparser_INCLUDE_DIRS "${MAEPARSER_DIR}") -+ set(maeparser_LIBRARIES maeparser) -+ -+ message(STATUS "Maestro formats will be supported. Using MaeParser '${MAEPARSER_VERSION}' at ${MAEPARSER_DIR}") -+ - endif() -- set(MAEPARSER_DIR ${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}) -- add_subdirectory(${MAEPARSER_DIR}) -- include_directories(${MAEPARSER_DIR}) -- set(libs ${libs} maeparser) - -- message(STATUS "Maestro formats will be supported. Using MaeParser ${MAEPARSER_VERSION} at ${MAEPARSER_INCLUDE_DIRS}") -+ include_directories(${maeparser_INCLUDE_DIRS}) -+ set(libs ${libs} ${maeparser_LIBRARIES}) -+ - else() - message(STATUS "Maestro formats will NOT be supported. Please install Boost to enable Maestro formats.") - endif() - - option(WITH_JSON "Build JSON support" ON) - option(OPENBABEL_USE_SYSTEM_RAPIDJSON "Use the system rapidjson if available." ON) - if(WITH_JSON) - -From 3809081838b673a9ab45f3e6061dc1a525eba4f3 Mon Sep 17 00:00:00 2001 -From: Ricardo R-S <[email protected]> -Date: Wed, 16 Oct 2019 15:58:13 -0400 -Subject: [PATCH 3/7] update maeparser include paths to use the same as coorden - ---- - src/formats/maeformat.cpp | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/src/formats/maeformat.cpp b/src/formats/maeformat.cpp -index 795f8d746..9efb2560f 100644 ---- a/src/formats/maeformat.cpp -+++ b/src/formats/maeformat.cpp -@@ -29,9 +29,9 @@ GNU General Public License for more details. - #include <iostream> - #include <map> - --#include <MaeConstants.hpp> --#include <Reader.hpp> --#include <Writer.hpp> -+#include <maeparser/MaeConstants.hpp> -+#include <maeparser/Reader.hpp> -+#include <maeparser/Writer.hpp> - - using namespace std; - using namespace schrodinger::mae; - -From 9e093701df695a9d0983298eac3e255e255aba56 Mon Sep 17 00:00:00 2001 -From: Ricardo R-S <[email protected]> -Date: Mon, 21 Oct 2019 08:29:20 -0400 -Subject: [PATCH 5/7] only use boost threads if not static build - ---- - src/CMakeLists.txt | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index 7c83ca355..de81c33f2 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -3,7 +3,7 @@ set(SOVERSION 6) - set(LIBRARY_VERSION 6.0.0) - - --find_package(Boost 1.45.0 COMPONENTS system) -+find_package(Boost 1.45.0 COMPONENTS system) - - - -@@ -248,8 +248,8 @@ add_library(openbabel ${BUILD_TYPE} - ) - - target_link_libraries(openbabel ${libs}) --if(Boost_FOUND) -- include_directories(${Boost_INCLUDE_DIRS}) -+if(Boost_FOUND AND (BUILD_SHARED OR BUILD_MIXED)) -+ include_directories(${Boost_INCLUDE_DIRS}) - target_link_libraries(openbabel ${Boost_LIBRARIES} ) - find_package(Threads REQUIRED) - if(THREADS_HAVE_PTHREAD_ARG) - -From 9d79d1358cfce4cf977629ffb638fbf659fc6573 Mon Sep 17 00:00:00 2001 -From: Ricardo R-S <[email protected]> -Date: Mon, 11 Nov 2019 10:17:41 -0500 -Subject: [PATCH 6/7] set fixed versions; handle github dirs - ---- - CMakeLists.txt | 17 +++++++++++------ - 1 file changed, 11 insertions(+), 6 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 26edc9433..60a59576a 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -498,7 +498,7 @@ if(WITH_MAEPARSER) - - else() - -- set(MAEPARSER_VERSION "master") -+ set(MAEPARSER_VERSION "v1.2.2" CACHE STRING "Maeparser fallback version to download") - - set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}") - -@@ -517,9 +517,13 @@ if(WITH_MAEPARSER) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf "maeparser-${MAEPARSER_VERSION}.tar.gz" - WORKING_DIRECTORY "${MAEPARSER_DIR}") - -- file(RENAME "${MAEPARSER_DIR}/maeparser-${MAEPARSER_VERSION}" "${MAEPARSER_DIR}/maeparser") -+ message(STATUS "${MAEPARSER_DIR}") - -- if(EXISTS "${MAEPARSER_DIR}/maeparser/CMakeLists.txt") -+ find_path(MAEPARSER_UNPACK_DIR "CMakeLists.txt" PATH "${MAEPARSER_DIR}/*" NO_DEFAULT_PATH) -+ message(STATUS ${MAEPARSER_UNPACK_DIR}) -+ -+ if(MAEPARSER_UNPACK_DIR) -+ file(RENAME "${MAEPARSER_UNPACK_DIR}" "${MAEPARSER_DIR}/maeparser") - message(STATUS "Downloaded MaeParser '${MAEPARSER_VERSION}' to ${MAEPARSER_DIR}.") - else() - message(FATAL_ERROR "Failed getting or unpacking Maeparser '${MAEPARSER_VERSION}'.") - -From a97306e9a32ee210701ae20d3073dd1d384dd68d Mon Sep 17 00:00:00 2001 -From: Ricardo R-S <[email protected]> -Date: Tue, 12 Nov 2019 14:30:58 -0500 -Subject: [PATCH 7/7] restore master as fallback; remove leftover debug msgs - ---- - CMakeLists.txt | 7 ++----- - 1 file changed, 2 insertions(+), 5 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 60a59576a..7d74d5ad4 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -498,7 +498,7 @@ if(WITH_MAEPARSER) - - else() - -- set(MAEPARSER_VERSION "v1.2.2" CACHE STRING "Maeparser fallback version to download") -+ set(MAEPARSER_VERSION "master" CACHE STRING "Maeparser fallback version to download") - - set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}") - -@@ -517,10 +517,7 @@ if(WITH_MAEPARSER) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf "maeparser-${MAEPARSER_VERSION}.tar.gz" - WORKING_DIRECTORY "${MAEPARSER_DIR}") - -- message(STATUS "${MAEPARSER_DIR}") -- - find_path(MAEPARSER_UNPACK_DIR "CMakeLists.txt" PATH "${MAEPARSER_DIR}/*" NO_DEFAULT_PATH) -- message(STATUS ${MAEPARSER_UNPACK_DIR}) - - if(MAEPARSER_UNPACK_DIR) - file(RENAME "${MAEPARSER_UNPACK_DIR}" "${MAEPARSER_DIR}/maeparser")
