lazar gem, version bumped to 0.9

6 files changed, 20 insertions, 64 deletions

diff --git a/VERSION b/VERSION
index c5d54ec..ac39a10 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.0.9
+0.9.0
diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
index 006e24c..a577baa 100644
--- a/ext/lazar/extconf.rb
+++ b/ext/lazar/extconf.rb
@@ -19,49 +19,9 @@ FileUtils.mkdir_p File.join(main_dir,"bin") # for Rserve binary
 rinstall = File.expand_path(File.join(File.dirname(__FILE__),"rinstall.R"))
 puts `Rscript --vanilla #{rinstall} #{r_dir}`
 
-# install OpenBabel
-
-openbabel_version = "2.3.2"
-
-openbabel_dir = File.join main_dir, "openbabel"
-src_dir = openbabel_dir 
-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"
-ruby_src_dir = File.join src_dir, "scripts", "ruby"
-
-begin
-  nr_processors = `getconf _NPROCESSORS_ONLN`.to_i # should be POSIX compatible
-rescue
-  nr_processors = 1
-end
-
-FileUtils.mkdir_p openbabel_dir
-Dir.chdir main_dir do
-  FileUtils.rm_rf src_dir
-  puts "Downloading OpenBabel sources"
-  system "git clone https://github.com/openbabel/openbabel.git"
-end
-
-FileUtils.mkdir_p build_dir
-FileUtils.mkdir_p install_dir
-Dir.chdir build_dir do
-  puts "Configuring OpenBabel"
-  cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUN_SWIG=ON -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}\"" 
-  system cmake
-end
-
-# local installation in gem directory
-Dir.chdir build_dir do
-  puts "Compiling OpenBabel sources."
-  system "make -j#{nr_processors}"
-  system "make install"
-  ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
+# create a fake Makefile
+File.open(File.join(File.dirname(__FILE__),"Makefile"),"w+") do |makefile|
+  makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
 end
 
 $makefile_created = true
diff --git a/ext/lazar/rinstall.R b/ext/lazar/rinstall.R
index 38e7377..4e4fac7 100644
--- a/ext/lazar/rinstall.R
+++ b/ext/lazar/rinstall.R
@@ -1,9 +1,8 @@
 libdir = commandArgs(trailingOnly=TRUE)[1]
-# chooseCRANmirror(ind=19); does not have any impact on selected server
-#args=paste0("--prefix=",libdir,"/..")
 #install.packages("Rserve",lib=libdir,configure.args=args)
-install.packages("gridExtra",lib=libdir);
-install.packages("ggplot2",lib=libdir);
-install.packages("pls",lib=libdir);
-install.packages("caret",lib=libdir);
-install.packages("doMC",lib=libdir);
+repo = "https://stat.ethz.ch/CRAN/"
+install.packages("gridExtra",lib=libdir,repos=repo);
+install.packages("ggplot2",lib=libdir,repos=repo);
+install.packages("pls",lib=libdir,repos=repo);
+install.packages("caret",lib=libdir,repos=repo);
+install.packages("doMC",lib=libdir,repos=repo);
diff --git a/lazar.gemspec b/lazar.gemspec
index fb443fe..a805edb 100644
--- a/lazar.gemspec
+++ b/lazar.gemspec
@@ -9,7 +9,7 @@ Gem::Specification.new do |s|
   s.homepage    = "http://github.com/opentox/lazar"
   s.summary     = %q{Lazar framework}
   s.description = %q{Libraries for lazy structure-activity relationships and read-across.}
-  s.license     = 'GPL-3'
+  s.license     = 'GPL-3.0'
 
   s.rubyforge_project = "lazar"
   s.files         = `git ls-files`.split("\n")
@@ -18,13 +18,11 @@ Gem::Specification.new do |s|
   s.require_paths = ["lib"]
 
   # specify any dependencies here; for example:
-  s.add_runtime_dependency "bundler"
-  s.add_runtime_dependency "rest-client"
-  s.add_runtime_dependency 'nokogiri'
-  s.add_runtime_dependency 'rserve-client'
-  #s.add_runtime_dependency 'celluloid'
-  s.add_runtime_dependency 'forkoff'
-  #s.add_runtime_dependency 'parallel'
-  s.add_runtime_dependency "mongoid", '~> 5.0beta'  
+  s.add_runtime_dependency 'bundler', '~> 1.11'
+  s.add_runtime_dependency 'rest-client', '~> 1.8'
+  s.add_runtime_dependency 'nokogiri', '~> 1.6'
+  s.add_runtime_dependency 'rserve-client', '~> 0.3'
+  s.add_runtime_dependency 'mongoid', '~> 5.0'
+  s.add_runtime_dependency 'openbabel', '~> 2.3', '>= 2.3.2.2'
 
 end
diff --git a/lib/lazar.rb b/lib/lazar.rb
index a0846e9..4b824dd 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -8,6 +8,7 @@ require 'mongoid'
 require 'rserve'
 require "nokogiri"
 require "base64"
+require 'openbabel'
 
 # Environment setup
 ENV["LAZAR_ENV"] ||= "production"
@@ -57,9 +58,6 @@ suppressPackageStartupMessages({
 })
 "
 
-# Require sub-Repositories
-require_relative '../openbabel/lib/openbabel'
-
 # OpenTox classes and includes
 CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules
 
diff --git a/test/setup.rb b/test/setup.rb
index dc577b3..be3140a 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -1,6 +1,7 @@
 ENV["LAZAR_ENV"] = "development"
 require 'minitest/autorun'
-require_relative '../lib/lazar.rb'
+#require_relative '../lib/lazar.rb'
+require 'lazar'
 include OpenTox
 TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 DATA_DIR ||= File.join(TEST_DIR,"data")