openbabel 2.3.1.9 → 2.3.2.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: cddb2ede193a07ad6d35d1c99ae5a544ec81883b
+  data.tar.gz: a9dbe5168fe13176b055ebad6599708db272ad85
+SHA512:
+  metadata.gz: b0670741fd4c602e1258fbd5014da664541b9ea37f773d35665ec9da67f89555a70c3493ef5f1d6d1e2e5ef1726afa198ddd185212d0e6fc0e421c7e1586016f
+  data.tar.gz: 732079f24513e2b06226243e807b7ecc51d1a73e4cd41fa37a4315d32f4d6606cc518866591d6d7677c4c2d0fd6ecafdfe6fd819f4b10ee48e12107f77b7ce63

data/ext/openbabel/extconf.rb

@@ -1,48 +1,68 @@
 require 'fileutils'
-require 'tmpdir'
 require 'mkmf'
+require 'rbconfig'
 $:.unshift File.expand_path('../../../lib', __FILE__)
 require 'openbabel/version'
 
 ob_num_ver = OpenBabel::VERSION
 ob_ver     = "openbabel-"+ob_num_ver
 
-RUBY=File.join(RbConfig::CONFIG['bindir'],
-               RbConfig::CONFIG['ruby_install_name'])
+RUBY=File.join(RbConfig::CONFIG['bindir'], RbConfig::CONFIG['ruby_install_name'])
 
-main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..","..","src"))
-lib_dir = File.expand_path(File.join(File.dirname(__FILE__),"..","..","src"))
-Dir.mkdir main_dir
-ob_main_dir = File.join(main_dir,ob_ver)
-ob_bindings_dir = File.join(ob_main_dir,"scripts","ruby")
+main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
+src_dir = File.join main_dir, ob_ver
+build_dir = File.join main_dir, "build"
+install_dir = main_dir 
+install_lib_dir = File.join install_dir, "lib"
+lib_dir = File.join main_dir, "lib", "openbabel"
+ruby_src_dir = File.join src_dir, "scripts", "ruby"
+
+begin
+  nr_processors = `grep processor /proc/cpuinfo | wc -l` # speed up compilation, Linux only
+rescue
+  nr_processors = 1
+end
 
 begin
   Dir.chdir main_dir do
-    FileUtils.rm_rf ob_main_dir
+    FileUtils.rm_rf src_dir
     puts "Downloading OpenBabel sources"
     system "curl -L -d use_mirror=netcologne 'http://downloads.sourceforge.net/project/openbabel/openbabel/#{ob_num_ver}/openbabel-#{ob_num_ver}.tar.gz' | tar xz"
+    system "sed -i -e 's/-Wl,-flat_namespace//;s/-flat_namespace//' #{File.join ruby_src_dir, "extconf.rb"}" # remove unrecognized compiler option
+    system "sed -i -e 's/Init_OpenBabel/Init_openbabel/g' #{File.join ruby_src_dir,"*cpp"}" # fix swig bindings
   end
-  Dir.chdir ob_main_dir do
+  FileUtils.mkdir_p build_dir
+  FileUtils.mkdir_p install_dir
+  Dir.chdir build_dir do
     puts "Configuring OpenBabel"
-    system "cmake #{ob_main_dir} -DCMAKE_INSTALL_PREFIX=#{lib_dir}"
-    openbabel_libs = have_library('openbabel')
-    unless openbabel_libs
+    cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUBY_BINDINGS=ON"
+    # set rpath for local installations
+    # http://www.cmake.org/Wiki/CMake_RPATH_handling
+    # http://vtk.1045678.n5.nabble.com/How-to-force-cmake-not-to-remove-install-rpath-td5721193.html
+    cmake += " -DCMAKE_INSTALL_RPATH:STRING=\"#{install_lib_dir}\"" unless have_library('openbabel')
+    system cmake
+  end
+  unless have_library('openbabel')
+    # local installation in gem directory
+    Dir.chdir build_dir do
       puts "OpenBabel not installed. Compiling sources."
-      system "make"
+      system "make -j#{nr_processors}"
       system "make install"
+      ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
     end
   end
-  Dir.chdir ob_bindings_dir do
-    puts "Compiling and instaling OpenBabel Ruby bindings."
-    system "sed -i -e 's/Init_OpenBabel/Init_openbabel/g' *cpp"
+  # compile ruby bindings
+  puts "Compiling and installing OpenBabel Ruby bindings."
+  Dir.chdir ruby_src_dir do
+    # fix rpath
+    system "sed -i 's|with_ldflags.*$|with_ldflags(\"#\$LDFLAGS -dynamic -Wl,-rpath,#{install_lib_dir}\") do|' #{File.join(ruby_src_dir,'extconf.rb')}" unless have_library('openbabel')
     # get include and lib from pkg-config
     ob_include=`pkg-config openbabel-2.0 --cflags-only-I`.sub(/\s+/,'').sub(/-I/,'')
     ob_lib=`pkg-config openbabel-2.0 --libs-only-L`.sub(/\s+/,'').sub(/-L/,'')
     system "#{RUBY} extconf.rb --with-openbabel-include=#{ob_include} --with-openbabel-lib=#{ob_lib}"
-    system "sed -i -e 's/-Wl,-flat_namespace//;s/-flat_namespace//' Makefile"
-    system "make"
+    system "make -j#{nr_processors}"
   end
-  FileUtils.cp(ob_bindings_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
+  FileUtils.cp(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
 	File.open('Makefile', 'w') do |makefile|
 		makefile.write <<"EOF"
 .PHONY: openbabel.#{RbConfig::CONFIG["DLEXT"]}
@@ -51,10 +71,10 @@ openbabel.#{RbConfig::CONFIG["DLEXT"]}:
 
 .PHONY: install
 install:
-	mkdir -p ../../lib/openbabel
-	mv openbabel.#{RbConfig::CONFIG["DLEXT"]} ../../lib/openbabel
+	mkdir -p #{lib_dir}
+	mv openbabel.#{RbConfig::CONFIG["DLEXT"]} #{lib_dir}
 EOF
 	end
 ensure
-  FileUtils.remove_entry_secure main_dir
+  FileUtils.remove_entry_secure src_dir, build_dir
 end

data/lib/openbabel.rb

@@ -1,2 +1,4 @@
 require 'openbabel/openbabel'
 require 'openbabel/version'
+# http://sourceforge.net/mailarchive/message.php?msg_id=31065700
+OpenBabel::OBConversion.new # required to load plugins

data/lib/openbabel/version.rb

@@ -1,4 +1,4 @@
 module OpenBabel
-  VERSION = '2.3.1'
-  GEMVERSION = VERSION + '.9'
+  VERSION = '2.3.2'
+  GEMVERSION = VERSION + '.0'
 end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: openbabel
 version: !ruby/object:Gem::Version
-  version: 2.3.1.9
-  prerelease: 
+  version: 2.3.2.0
 platform: ruby
 authors:
 - Andreas Maunz, Christoph Helma, Katsuhiko Nishimra
@@ -12,7 +11,9 @@ cert_chain: []
 date: 2012-04-03 00:00:00.000000000 Z
 dependencies: []
 description: OpenBabel as a GEM
-email: andreas@maunz.de
+email:
+- andreas@maunz.de
+- helma@in-silico.ch
 executables: []
 extensions:
 - ext/openbabel/extconf.rb
@@ -23,29 +24,29 @@ files:
 - lib/openbabel/version.rb
 - test/test_openbabel.rb
 - ext/openbabel/extconf.rb
-homepage: http://cs.maunz.de
-licenses: []
+homepage: http://github.com/opentox/openbabel-gem
+licenses:
+- GPL-3
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 2.0.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: OpenBabel!
 test_files:
 - test/test_openbabel.rb