update for version 2.3.2, local installation fixed, workaround for plugin loading

5 files changed, 56 insertions, 31 deletions

diff --git a/README.md b/README.md
index c248ee2..b1b131e 100644
--- a/README.md
+++ b/README.md
@@ -2,17 +2,19 @@
 
 GEM for [OpenBabel](http://openbabel.sf.net), a chemical library by Geoff Hutchison and others.
 
-openbabel gem has been tested with ruby 1.9. It only compiles on POSIX systems and requires the following to be installed already:
+openbabel gem has been tested with ruby 1.9 and 2.0. It compiles only on POSIX systems and requires the following programs and libraries (details at http://openbabel.org/docs/2.3.0/Installation/install.html#compiling-open-babel):
 
-  * openbabel library
-  * cmake
+  * cmake 2.4.8 or later
   * curl
   * tar, sed, make (those should be present anyway)
+  * libxml2 (optional)
+  * zlib (optional)
+  * Eigen 2.0.3 or later (optional)
 
 ## Install
 gem install openbabel
 
-It downloads the sources, compiles OpenBabel (if not installed) and the ruby bindings and installs them.
+It downloads the sources, compiles and installs OpenBabel (if not installed system wide) and ruby bindings.
 If OpenBabel is not yet installed installation may last very long - please be patient.
 
 Check out [http://cs.maunz.de](http://cs.maunz.de) for more information.
diff --git a/ext/openbabel/extconf.rb b/ext/openbabel/extconf.rb
index ae9c3f2..e44ec5d 100644
--- a/ext/openbabel/extconf.rb
+++ b/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
diff --git a/lib/openbabel.rb b/lib/openbabel.rb
index 6f6e60a..97ac94f 100644
--- a/lib/openbabel.rb
+++ b/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
diff --git a/lib/openbabel/version.rb b/lib/openbabel/version.rb
index cfc1bd8..3a367cb 100644
--- a/lib/openbabel/version.rb
+++ b/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
diff --git a/openbabel.gemspec b/openbabel.gemspec
index ca6d11b..4c8b6d6 100644
--- a/openbabel.gemspec
+++ b/openbabel.gemspec
@@ -8,11 +8,12 @@ Gem::Specification.new do |s|
   s.authors = ["Andreas Maunz, Christoph Helma, Katsuhiko Nishimra"]
   s.date = %q{2012-04-03}
   s.description = %q{OpenBabel as a GEM}
-  s.email = %q{andreas@maunz.de}
-  s.homepage = %q{http://cs.maunz.de}
+  s.email = ["andreas@maunz.de","helma@in-silico.ch"]
+  s.homepage = %q{http://github.com/opentox/openbabel-gem}
   s.require_paths = ["lib"]
   s.rubygems_version = %q{1.6.2}
   s.summary = %q{OpenBabel!}
+  s.license = "GPL-3"
   s.test_files = ["test/test_openbabel.rb"]
 
   s.files = %w{Rakefile lib/openbabel.rb lib/openbabel/version.rb}