openbabel-ruby 3.1.1.0 → 3.1.1.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: ee14805b357d1ac78aaf827fb3a5a0350c03dd0557db0786599e492cb78f7d78
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+  data.tar.gz: 677f07a3a433d11474db288b5a0da00c5b9623e9183cb8e32f20e28110bc6ca20990f2360e09aadb09ac93544978111ff93cd016153f32cc961f81d47f7d994d

data/Rakefile

@@ -1,5 +1,6 @@
 require "bundler/gem_tasks"
 require 'rake/testtask'
+require 'fileutils'
 
 Rake::TestTask.new do |t|
   t.libs << 'test'
@@ -7,3 +8,271 @@ end
 
 desc "Run tests"
 task :default => :test
+
+# =============================================================================
+# Native Gem Building Tasks
+# =============================================================================
+
+RUBY_VERSION_DIR = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
+GEM_ROOT = File.expand_path('..', __FILE__)
+NATIVE_DIR = File.join(GEM_ROOT, 'lib', 'openbabel', RUBY_VERSION_DIR)
+
+def find_installed_gem_dir
+  Gem::Specification.find_all_by_name('openbabel-ruby').each do |spec|
+    return spec.gem_dir if File.directory?(File.join(spec.gem_dir, 'openbabel'))
+  end
+  
+  Gem.path.each do |gem_path|
+    pattern = File.join(gem_path, 'gems', 'openbabel-ruby-*')
+    Dir[pattern].sort.reverse.each do |dir|
+      return dir if File.directory?(File.join(dir, 'openbabel'))
+    end
+  end
+  
+  nil
+rescue Gem::MissingSpecError
+  nil
+end
+
+def find_extension_path
+  gem_dir = find_installed_gem_dir
+  return nil unless gem_dir
+  
+  openbabel_lib = File.join(gem_dir, 'openbabel', 'lib')
+  
+  [
+    File.join(openbabel_lib, 'openbabel.so'),
+    File.join(openbabel_lib, 'openbabel.bundle')
+  ].each do |path|
+    return path if File.exist?(path)
+  end
+  
+  Dir[File.join(openbabel_lib, '**', 'openbabel.{so,bundle}')].first
+end
+
+def find_openbabel_libs
+  gem_dir = find_installed_gem_dir
+  return [] unless gem_dir
+  
+  lib_dir = File.join(gem_dir, 'openbabel', 'lib')
+  Dir[File.join(lib_dir, '*.so*')] + Dir[File.join(lib_dir, '*.dylib')]
+end
+
+def find_openbabel_data
+  gem_dir = find_installed_gem_dir
+  return nil unless gem_dir
+  
+  File.join(gem_dir, 'openbabel', 'share', 'openbabel')
+end
+
+def find_openbabel_plugins
+  gem_dir = find_installed_gem_dir
+  return nil unless gem_dir
+  
+  plugin_dir = Dir[File.join(gem_dir, 'openbabel', 'lib', 'openbabel', '*')].first
+  plugin_dir if plugin_dir && File.directory?(plugin_dir)
+end
+
+desc "Stage native binaries for packaging"
+task :stage_native do
+  puts "Staging native binaries for Ruby #{RUBY_VERSION_DIR}..."
+  
+  ext_path = find_extension_path
+  raise "Could not find openbabel extension. Run 'gem install openbabel-ruby' first." if ext_path.nil?
+  
+  FileUtils.mkdir_p(NATIVE_DIR)
+  
+  ext_name = File.basename(ext_path)
+  FileUtils.cp(ext_path, File.join(NATIVE_DIR, ext_name))
+  puts "  Copied #{ext_name}"
+  
+  find_openbabel_libs.each do |lib|
+    next if lib == ext_path
+    lib_name = File.basename(lib)
+    FileUtils.cp(lib, File.join(NATIVE_DIR, lib_name))
+    puts "  Copied #{lib_name}"
+  end
+  
+  plugin_dir = find_openbabel_plugins
+  if plugin_dir && File.directory?(plugin_dir)
+    target_plugin_dir = File.join(NATIVE_DIR, 'plugins')
+    FileUtils.cp_r(plugin_dir, target_plugin_dir)
+    puts "  Copied plugins directory"
+  end
+  
+  data_dir = find_openbabel_data
+  if data_dir && File.directory?(data_dir)
+    target_data_dir = File.join(NATIVE_DIR, 'data')
+    FileUtils.cp_r(data_dir, target_data_dir)
+    puts "  Copied data directory"
+  end
+  
+  puts "Staging complete: #{NATIVE_DIR}"
+end
+
+desc "Fix RPATH for Linux binaries"
+task :fix_rpath_linux do
+  puts "Fixing RPATH for Linux..."
+  
+  ext_path = find_extension_path
+  raise "Extension not found. Install the gem first: gem install openbabel-ruby" unless ext_path
+  
+  system("patchelf --set-rpath '$ORIGIN' #{ext_path}")
+  puts "  Fixed RPATH for #{File.basename(ext_path)}"
+  
+  find_openbabel_libs.each do |lib|
+    next unless lib.end_with?('.so') || lib.include?('.so.')
+    system("patchelf --set-rpath '$ORIGIN' #{lib}")
+    puts "  Fixed RPATH for #{File.basename(lib)}"
+  end
+end
+
+desc "Bundle system libraries for Linux"
+task :bundle_system_libs_linux do
+  puts "Bundling system libraries for Linux..."
+  
+  ext_path = find_extension_path
+  raise "Extension not found" unless ext_path
+  
+  lib_dir = File.dirname(ext_path)
+  libs_to_bundle = []
+  
+  ldd_output = `ldd #{ext_path} 2>/dev/null`
+  ldd_output.each_line do |line|
+    if line =~ /libopenbabel|libinchi|libcoordgen/
+      if line =~ /=> (.+\.so[^\s]*)/
+        lib_path = $1.strip
+        libs_to_bundle << lib_path if File.exist?(lib_path)
+      end
+    end
+  end
+  
+  libs_to_bundle.uniq.each do |lib|
+    target = File.join(lib_dir, File.basename(lib))
+    unless File.exist?(target)
+      FileUtils.cp(lib, target)
+      system("patchelf --set-rpath '$ORIGIN' #{target}")
+      puts "  Bundled #{File.basename(lib)}"
+    end
+  end
+end
+
+desc "Fix library paths for macOS binaries"
+task :fix_rpath_macos do
+  puts "Fixing library paths for macOS..."
+  
+  ext_path = find_extension_path
+  raise "Extension not found. Install the gem first: gem install openbabel-ruby" unless ext_path
+  
+  ext_name = File.basename(ext_path)
+  system("install_name_tool -id '@loader_path/#{ext_name}' #{ext_path}")
+  
+  otool_output = `otool -L #{ext_path}`
+  otool_output.each_line do |line|
+    next if line.include?(ext_name)
+    
+    if line =~ /^\s+(.+\.dylib)/
+      old_path = $1.split(' ').first
+      lib_name = File.basename(old_path)
+      
+      if old_path.start_with?('/') && !old_path.start_with?('/usr/lib', '/System')
+        system("install_name_tool -change '#{old_path}' '@loader_path/#{lib_name}' #{ext_path}")
+        puts "  Changed #{old_path} -> @loader_path/#{lib_name}"
+      end
+    end
+  end
+  
+  find_openbabel_libs.each do |lib|
+    next unless lib.end_with?('.dylib')
+    lib_name = File.basename(lib)
+    
+    system("install_name_tool -id '@loader_path/#{lib_name}' #{lib}")
+    
+    otool_output = `otool -L #{lib}`
+    otool_output.each_line do |line|
+      if line =~ /^\s+(.+\.dylib)/
+        old_path = $1.split(' ').first
+        dep_name = File.basename(old_path)
+        
+        if old_path.start_with?('/') && !old_path.start_with?('/usr/lib', '/System')
+          system("install_name_tool -change '#{old_path}' '@loader_path/#{dep_name}' #{lib}")
+        end
+      end
+    end
+  end
+end
+
+desc "Bundle system libraries for macOS"
+task :bundle_system_libs_macos do
+  puts "Bundling system libraries for macOS..."
+  
+  ext_path = find_extension_path
+  raise "Extension not found" unless ext_path
+  
+  lib_dir = File.dirname(ext_path)
+  libs_to_bundle = []
+  
+  otool_output = `otool -L #{ext_path}`
+  otool_output.each_line do |line|
+    if line =~ /^\s+(.+\.dylib)/
+      lib_path = $1.split(' ').first
+      if lib_path =~ /libopenbabel|libinchi|libcoordgen/ && File.exist?(lib_path)
+        libs_to_bundle << lib_path
+      end
+    end
+  end
+  
+  libs_to_bundle.uniq.each do |lib|
+    target = File.join(lib_dir, File.basename(lib))
+    unless File.exist?(target)
+      FileUtils.cp(lib, target)
+      lib_name = File.basename(lib)
+      system("install_name_tool -id '@loader_path/#{lib_name}' #{target}")
+      puts "  Bundled #{lib_name}"
+    end
+  end
+end
+
+desc "Build fat gem with precompiled binaries"
+task :build_fat_gem do
+  puts "Building fat gem..."
+  
+  staged_dirs = Dir[File.join(GEM_ROOT, 'lib', 'openbabel', '*.0')]
+  raise "No staged binaries found. Run stage_native first for each Ruby version." if staged_dirs.empty?
+  
+  puts "Found staged binaries for: #{staged_dirs.map { |d| File.basename(d) }.join(', ')}"
+  
+  ENV['OPENBABEL_PRECOMPILED'] = '1'
+  FileUtils.mkdir_p('pkg')
+  
+  platform = ENV['OPENBABEL_PLATFORM'] || begin
+    case RUBY_PLATFORM
+    when /darwin/
+      "#{`uname -m`.strip}-darwin"
+    when /linux/
+      arch = `uname -m`.strip
+      arch = 'aarch64' if arch == 'arm64'
+      "#{arch}-linux"
+    else
+      Gem::Platform.local.to_s
+    end
+  end
+  
+  puts "Building for platform: #{platform}"
+  ENV['OPENBABEL_PLATFORM'] = platform
+  
+  system("gem build openbabel.gemspec")
+  
+  Dir['openbabel-ruby-*.gem'].each do |gem_file|
+    FileUtils.mv(gem_file, 'pkg/')
+    puts "Built: pkg/#{gem_file}"
+  end
+end
+
+desc "Clean staged binaries"
+task :clean_staged do
+  Dir[File.join(GEM_ROOT, 'lib', 'openbabel', '*.0')].each do |dir|
+    FileUtils.rm_rf(dir)
+    puts "Removed #{dir}"
+  end
+end

data/ext/openbabel/extconf.rb

@@ -2,20 +2,18 @@ require 'fileutils'
 require 'rbconfig'
 require 'mkmf'
 
-main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
+main_dir = File.expand_path(File.join(File.dirname(__FILE__), '..', '..'))
+patches_dir = File.join(File.dirname(__FILE__), 'patches')
 
-# install OpenBabel
-
-openbabel_dir = File.join main_dir, "openbabel_src"
+openbabel_dir = File.join main_dir, 'openbabel_src'
 src_dir = openbabel_dir
-build_dir = File.join src_dir, "build"
-install_dir = File.join main_dir, "openbabel"
-install_lib_dir = File.join install_dir, "lib"
-ruby_src_dir = File.join src_dir, "scripts", "ruby"
+build_dir = File.join src_dir, 'build'
+install_dir = File.join main_dir, 'openbabel'
+install_lib_dir = File.join install_dir, 'lib'
 
 begin
-  nr_processors = `getconf _NPROCESSORS_ONLN`.to_i # should be POSIX compatible
-rescue
+  nr_processors = `getconf _NPROCESSORS_ONLN`.to_i
+rescue StandardError
   nr_processors = 1
 end
 
@@ -24,37 +22,47 @@ OPENBABEL_COMMIT = '889c350'
 FileUtils.mkdir_p openbabel_dir
 Dir.chdir main_dir do
   FileUtils.rm_rf src_dir
-  puts "Downloading OpenBabel sources"
+  puts 'Downloading OpenBabel sources'
   system "git clone https://github.com/openbabel/openbabel.git #{src_dir}"
   Dir.chdir(src_dir) do
     system "git checkout #{OPENBABEL_COMMIT}"
   end
 end
 
+puts 'Applying CMake 4.x compatibility patches...'
+FileUtils.cp(File.join(patches_dir, 'CMakeLists.txt'), File.join(src_dir, 'CMakeLists.txt'))
+FileUtils.cp(File.join(patches_dir, 'scripts', 'CMakeLists.txt'), File.join(src_dir, 'scripts', 'CMakeLists.txt'))
+
 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
+  puts 'Configuring OpenBabel'
+  cmake_args = [
+    "cmake #{src_dir}",
+    "-DCMAKE_INSTALL_PREFIX=#{install_dir}",
+    '-DBUILD_GUI=OFF',
+    '-DENABLE_TESTS=OFF',
+    '-DRUN_SWIG=ON',
+    '-DRUBY_BINDINGS=ON',
+    '-DCMAKE_CXX_STANDARD=14',
+    "-DCMAKE_INSTALL_RPATH:STRING=\"#{install_lib_dir}\"",
+    '-Wno-dev'
+  ].join(' ')
+
+  abort 'ERROR: CMake configuration failed' unless system(cmake_args)
 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))
+  puts 'Compiling OpenBabel sources.'
+  abort 'ERROR: OpenBabel compilation failed' unless system("make -j#{nr_processors}")
+  abort 'ERROR: OpenBabel installation failed' unless system('make install')
+  pc_file = Dir["#{install_dir}/**/openbabel*pc"].first
+  ENV['PKG_CONFIG_PATH'] = File.dirname(File.expand_path(pc_file)) if pc_file
 end
 
 FileUtils.remove_dir(openbabel_dir)
 
-# create a fake Makefile
-File.open(File.join(File.dirname(__FILE__),"Makefile"),"w+") do |makefile|
+File.open(File.join(File.dirname(__FILE__), 'Makefile'), 'w+') do |makefile|
   makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
 end