[arch-commits] Commit in openbabel/trunk (PKGBUILD system-maeparser.patch)

Antonio Rojas arojas at archlinux.org
Wed May 6 08:06:24 UTC 2020


    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 <arojas at archlinux.org>
 # 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
+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 <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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