[arch-commits] Commit in openbabel/repos/extra-x86_64 (3 files)
Antonio Rojas
arojas at archlinux.org
Fri Nov 29 13:54:23 UTC 2019
Date: Friday, November 29, 2019 @ 13:54:23
Author: arojas
Revision: 369910
archrelease: copy trunk to extra-x86_64
Added:
openbabel/repos/extra-x86_64/PKGBUILD
(from rev 369909, openbabel/trunk/PKGBUILD)
openbabel/repos/extra-x86_64/system-maeparser.patch
(from rev 369909, openbabel/trunk/system-maeparser.patch)
Deleted:
openbabel/repos/extra-x86_64/PKGBUILD
------------------------+
PKGBUILD | 98 ++++++++--------
system-maeparser.patch | 280 +++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 332 insertions(+), 46 deletions(-)
Deleted: PKGBUILD
===================================================================
--- PKGBUILD 2019-11-29 13:53:59 UTC (rev 369909)
+++ PKGBUILD 2019-11-29 13:54:23 UTC (rev 369910)
@@ -1,46 +0,0 @@
-# Maintainer: Andrea Scarpino <andrea at archlinux.org>
-# Contributor: Damir Perisa <damir.perisa at bluewin.ch>
-
-pkgbase=openbabel
-pkgname=(openbabel python-openbabel)
-pkgver=3.0.0
-pkgrel=2
-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' 'wxgtk' 'boost' 'python' 'swig')
-source=("https://github.com/openbabel/openbabel/releases/download/openbabel-${pkgver//./-}/openbabel-$pkgver-source.tar.bz2")
-sha256sums=('aad58ef8deaea9f58faeecb333f87bb18e0bdf4854e3a3b188a814a8c4517259')
-
-prepare() {
- mkdir -p build
-}
-
-build() {
- cd build
- cmake ../openbabel-$pkgver \
- -DCMAKE_INSTALL_PREFIX=/usr \
- -DwxWidgets_CONFIG_EXECUTABLE=/usr/bin/wx-config \
- -DRUN_SWIG=ON \
- -DPYTHON_BINDINGS=ON
- make
-
- # To split python bindings
- sed -i '/scripts.cmake_install.cmake/d' cmake_install.cmake
-}
-
-package_openbabel() {
- depends=('libxml2' 'libsm')
- optdepends=('wxgtk: GUI interface')
-
- cd build
- make DESTDIR="$pkgdir" install
-}
-
-package_python-openbabel() {
- depends=('python' 'openbabel')
-
- cd build/scripts
- make DESTDIR="$pkgdir" install
-}
Copied: openbabel/repos/extra-x86_64/PKGBUILD (from rev 369909, openbabel/trunk/PKGBUILD)
===================================================================
--- PKGBUILD (rev 0)
+++ PKGBUILD 2019-11-29 13:54:23 UTC (rev 369910)
@@ -0,0 +1,52 @@
+# Maintainer:
+# Contributor: Andrea Scarpino <andrea at archlinux.org>
+# Contributor: Damir Perisa <damir.perisa at bluewin.ch>
+
+pkgbase=openbabel
+pkgname=(openbabel python-openbabel)
+pkgver=3.0.0
+pkgrel=3
+pkgdesc="A library designed to interconvert between many file formats used in molecular modeling and computational chemistry"
+arch=('x86_64')
+url="https://openbabel.org/wiki/Main_Page"
+license=('GPL')
+makedepends=('cmake' 'eigen' 'wxgtk3' 'boost' 'python' 'swig' 'maeparser' 'rapidjson')
+source=("https://github.com/openbabel/openbabel/releases/download/openbabel-${pkgver//./-}/openbabel-$pkgver-source.tar.bz2"
+ system-maeparser.patch::"https://github.com/openbabel/openbabel/commit/8500f8a9.patch")
+sha256sums=('aad58ef8deaea9f58faeecb333f87bb18e0bdf4854e3a3b188a814a8c4517259'
+ '14d2b019dfb3e4d6d1b8a529e5da8c2ec84b1e599b9ae74913f8548542d0ab4b')
+
+prepare() {
+ mkdir -p build
+
+ cd $pkgbase-$pkgver
+ patch -p1 -i ../system-maeparser.patch # Unbundle maeparser
+}
+
+build() {
+ cd build
+ cmake ../openbabel-$pkgver \
+ -DCMAKE_INSTALL_PREFIX=/usr \
+ -DwxWidgets_CONFIG_EXECUTABLE=/usr/bin/wx-config-gtk3 \
+ -DRUN_SWIG=ON \
+ -DPYTHON_BINDINGS=ON
+ make
+
+ # To split python bindings
+ sed -i '/scripts.cmake_install.cmake/d' cmake_install.cmake
+}
+
+package_openbabel() {
+ depends=('libxml2' 'libsm')
+ optdepends=('wxgtk3: GUI interface' 'maeparser: maestro format support')
+
+ cd build
+ make DESTDIR="$pkgdir" install
+}
+
+package_python-openbabel() {
+ depends=('python' 'openbabel')
+
+ cd build/scripts
+ make DESTDIR="$pkgdir" install
+}
Copied: openbabel/repos/extra-x86_64/system-maeparser.patch (from rev 369909, openbabel/trunk/system-maeparser.patch)
===================================================================
--- system-maeparser.patch (rev 0)
+++ system-maeparser.patch 2019-11-29 13:54:23 UTC (rev 369910)
@@ -0,0 +1,280 @@
+From e259b6737787d2545f45b63c90f0f27a40e0179f Mon Sep 17 00:00:00 2001
+From: Ricardo R-S <rodriguez at schrodinger.com>
+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 <rodriguez at schrodinger.com>
+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 <rodriguez at schrodinger.com>
+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 <rodriguez at schrodinger.com>
+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 ${Boost_LIBRARIES} )
+ find_package(Threads REQUIRED)
+ if(THREADS_HAVE_PTHREAD_ARG)
+
+From 9d79d1358cfce4cf977629ffb638fbf659fc6573 Mon Sep 17 00:00:00 2001
+From: Ricardo R-S <rodriguez at schrodinger.com>
+Date: Mon, 11 Nov 2019 10:17:41 -0500
+Subject: [PATCH 6/7] set fixed versions; handle github dirs
+
+---
+ CMakeLists.txt | 17 +++++++++++------
+ 1 file changed, 11 insertions(+), 6 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 26edc9433..60a59576a 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -498,7 +498,7 @@ if(WITH_MAEPARSER)
+
+ else()
+
+- set(MAEPARSER_VERSION "master")
++ set(MAEPARSER_VERSION "v1.2.2" CACHE STRING "Maeparser fallback version to download")
+
+ set(MAEPARSER_DIR "${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 <rodriguez at schrodinger.com>
+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")
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