From c26112cbe94689da20688b4924c9025a995310ae Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sat, 15 Aug 2015 14:57:16 +0200
Subject: openbabel and fminer installation added

---
 ext/lazar/extconf.rb | 41 ++++++++++++++++++++++-------------------
 java/.gitignore      |  2 --
 2 files changed, 22 insertions(+), 21 deletions(-)
 delete mode 100644 java/.gitignore

diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
index 738a85b..c37b40b 100644
--- a/ext/lazar/extconf.rb
+++ b/ext/lazar/extconf.rb
@@ -1,17 +1,16 @@
 require 'fileutils'
+require 'rbconfig'
+
 main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
 
 # install OpenBabel
 
-require 'mkmf'
-require 'rbconfig'
-require 'openbabel/version'
 
-openbabel_version = 2.3.2
+openbabel_version = "2.3.2"
 
 openbabel_dir = File.join main_dir, "openbabel"
-src_dir = File.join openbabel_dir, "openbabel-#{openbabel_version}"
-build_dir = File.join openbabel_dir, "build"
+src_dir = openbabel_dir #File.join openbabel_dir, "openbabel-#{openbabel_version}"
+build_dir = File.join src_dir, "build"
 install_dir = openbabel_dir 
 install_lib_dir = File.join install_dir, "lib"
 lib_dir = File.join openbabel_dir, "lib", "openbabel"
@@ -23,14 +22,12 @@ rescue
   nr_processors = 1
 end
 
-Dir.chdir openbabel_dir do
+#FileUtils.mkdir_p openbabel_dir
+=begin
+Dir.chdir main_dir do
   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
-  system "sed  -i -e 's/Config::CONFIG/RbConfig::CONFIG/' #{File.join src_dir, "scripts", "CMakeLists.txt" }" # fix Ruby Config
-  system "sed  -i -e 's/Config::CONFIG/RbConfig::CONFIG/' #{File.join ruby_src_dir, "extconf.rb" }" # fix Ruby Config
+  system "git clone https://github.com/openbabel/openbabel.git"
 end
 FileUtils.mkdir_p build_dir
 FileUtils.mkdir_p install_dir
@@ -51,11 +48,13 @@ Dir.chdir build_dir do
   system "make install"
   ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
 end
+=end
 
 # 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/,'')
+ob_include= File.expand_path "../../openbabel/include/openbabel-2.0"
+ob_lib= File.expand_path "../../openbabel/lib"
 
+=begin
 # compile ruby bindings
 puts "Compiling and installing OpenBabel Ruby bindings."
 Dir.chdir ruby_src_dir do
@@ -64,10 +63,11 @@ Dir.chdir ruby_src_dir do
   system "#{RbConfig.ruby} extconf.rb --with-openbabel-include=#{ob_include} --with-openbabel-lib=#{ob_lib}"
   system "make -j#{nr_processors}"
 end
-FileUtils.cp(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
-FileUtils.mkdir_p lib_dir
-FileUtils.mv "openbabel.#{RbConfig::CONFIG["DLEXT"]}" lib_dir
-FileUtils.remove_entry_secure src_dir, build_dir
+#FileUtils.cp(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
+#FileUtils.mkdir_p lib_dir
+#FileUtils.mv "openbabel.#{RbConfig::CONFIG["DLEXT"]}", lib_dir
+#FileUtils.remove_entry_secure src_dir, build_dir
+=end
 
 # install fminer
 fminer_dir = File.join main_dir, "libfminer"
@@ -78,11 +78,14 @@ system "git clone git://github.com/amaunz/fminer2.git #{fminer_dir}"
   system "sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ #{ob_include},g' Makefile" 
   system "sed -i 's,^LDFLAGS_OB.*,LDFLAGS_OB\ =\ #{ob_lib},g' Makefile"
   system "sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ #{RbConfig::CONFIG['rubyhdrdir']},g' Makefile" 
+  # TODO fix in fminer Makefile
+  system "sed -i 's,-g, -g -I #{RbConfig::CONFIG['rubyhdrdir']} -I #{RbConfig::CONFIG['rubyarchhdrdir']} -I,' Makefile" # fix include path (CH)
+  system "sed -i '74s/$(CC)/$(CC) -L/' Makefile" # fix library path (CH)
   system "make ruby"
 end
 
 # install last-utils
 FileUtils.cd main_dir
-"git clone git://github.com/amaunz/last-utils.git"
+system "git clone git://github.com/amaunz/last-utils.git"
 
 # install R packagemain_dir
diff --git a/java/.gitignore b/java/.gitignore
deleted file mode 100644
index 533ae63..0000000
--- a/java/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-bak
-docs
-- 
cgit v1.2.3