From 76d30230f589026d7019ddbfa8ae0a511e171e27 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 31 Mar 2016 10:04:42 +0200 Subject: lazar gem, version bumped to 0.9 --- VERSION | 2 +- ext/lazar/extconf.rb | 46 +++------------------------------------------- ext/lazar/rinstall.R | 13 ++++++------- lazar.gemspec | 16 +++++++--------- lib/lazar.rb | 4 +--- test/setup.rb | 3 ++- 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") -- cgit v1.2.3