search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/branch.rb

@@ -0,0 +1,104 @@
+module Git
+  class Branch < Path
+    
+    attr_accessor :full, :remote, :name
+    
+    def initialize(base, name)
+      @remote = nil
+      @full = name
+      @base = base
+      @gcommit = nil
+      @stashes = nil
+      
+      parts = name.split('/')
+      if parts[1]
+        @remote = Git::Remote.new(@base, parts[0])
+        @name = parts[1]
+      else
+        @name = parts[0]
+      end
+    end
+    
+    def gcommit
+      @gcommit ||= @base.gcommit(@full)
+      @gcommit
+    end
+    
+    def stashes
+      @stashes ||= Git::Stashes.new(@base)
+    end
+    
+    def checkout
+      check_if_create
+      @base.checkout(@full)
+    end
+    
+    def archive(file, opts = {})
+      @base.lib.archive(@full, file, opts)
+    end
+    
+    # g.branch('new_branch').in_branch do
+    #   # create new file
+    #   # do other stuff
+    #   return true # auto commits and switches back
+    # end
+    def in_branch (message = 'in branch work')
+      old_current = @base.lib.branch_current
+      checkout
+      if yield
+        @base.commit_all(message)
+      else
+        @base.reset_hard
+      end
+      @base.checkout(old_current)
+    end
+    
+    def create
+      check_if_create
+    end
+    
+    def delete
+      @base.lib.branch_delete(@name)
+    end
+    
+    def current
+      determine_current
+    end
+    
+    def merge(branch = nil, message = nil)
+      if branch
+        in_branch do 
+          @base.merge(branch, message)
+          false
+        end
+        # merge a branch into this one
+      else
+        # merge this branch into the current one
+        @base.merge(@name)
+      end
+    end
+    
+    def update_ref(commit)
+      @base.lib.update_ref(@full, commit)
+    end
+    
+    def to_a
+      [@full]
+    end
+    
+    def to_s
+      @full
+    end
+    
+    private 
+
+      def check_if_create
+        @base.lib.branch_new(@name) rescue nil
+      end
+      
+      def determine_current
+        @base.lib.branch_current == @name
+      end
+    
+  end
+end

data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/branches.rb

@@ -0,0 +1,48 @@
+module Git
+  
+  # object that holds all the available branches
+  class Branches
+    include Enumerable
+    
+    def initialize(base)
+      @branches = {}
+      
+      @base = base
+            
+      @base.lib.branches_all.each do |b|
+        @branches[b[0]] = Git::Branch.new(@base, b[0])
+      end
+    end
+
+    def local
+      self.select { |b| !b.remote }
+    end
+    
+    def remote
+      self.select { |b| b.remote }
+    end
+    
+    # array like methods
+
+    def size
+      @branches.size
+    end    
+    
+    def each(&block)
+      @branches.values.each(&block)
+    end
+    
+    def [](symbol)
+      @branches[symbol.to_s]
+    end
+    
+    def to_s
+      out = ''
+      @branches.each do |k, b|
+        out << (b.current ? '* ' : '  ') << b.to_s << "\n"
+      end
+      out
+    end
+    
+  end
+end

data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/diff.rb

@@ -0,0 +1,146 @@
+module Git
+  
+  # object that holds the last X commits on given branch
+  class Diff
+    include Enumerable
+    
+    def initialize(base, from = nil, to = nil)
+      @base = base
+      @from = from.to_s
+      @to = to.to_s
+
+      @path = nil
+      @full_diff = nil
+      @full_diff_files = nil
+      @stats = nil
+    end
+    attr_reader :from, :to
+    
+    def path(path)
+      @path = path
+      return self
+    end
+    
+    def size
+      cache_stats
+      @stats[:total][:files]
+    end
+    
+    def lines
+      cache_stats
+      @stats[:total][:lines]
+    end
+    
+    def deletions
+      cache_stats
+      @stats[:total][:deletions]
+    end
+    
+    def insertions
+      cache_stats
+      @stats[:total][:insertions]
+    end
+    
+    def stats
+      cache_stats
+      @stats
+    end
+    
+    # if file is provided and is writable, it will write the patch into the file
+    def patch(file = nil)
+      cache_full
+      @full_diff
+    end
+    alias_method :to_s, :patch
+    
+    # enumerable methods
+    
+    def [](key)
+      process_full
+      @full_diff_files.assoc(key)[1]
+    end
+    
+    def each(&block) # :yields: each Git::DiffFile in turn
+      process_full
+      @full_diff_files.map { |file| file[1] }.each(&block)
+    end
+    
+    class DiffFile
+      attr_accessor :patch, :path, :mode, :src, :dst, :type
+      @base = nil
+      
+      def initialize(base, hash)
+        @base = base
+        @patch = hash[:patch]
+        @path = hash[:path]
+        @mode = hash[:mode]
+        @src = hash[:src]
+        @dst = hash[:dst]
+        @type = hash[:type]
+        @binary = hash[:binary]
+      end
+
+      def binary?
+        !!@binary
+      end
+      
+      def blob(type = :dst)
+        if type == :src
+          @base.object(@src) if @src != '0000000'
+        else
+          @base.object(@dst) if @dst != '0000000'
+        end
+      end
+    end
+    
+    private
+    
+      def cache_full
+        unless @full_diff
+          @full_diff = @base.lib.diff_full(@from, @to, {:path_limiter => @path})
+        end
+      end
+      
+      def process_full
+        unless @full_diff_files
+          cache_full
+          @full_diff_files = process_full_diff
+        end
+      end
+      
+      def cache_stats
+        unless @stats
+          @stats = @base.lib.diff_stats(@from, @to, {:path_limiter => @path})
+        end
+      end
+      
+      # break up @diff_full
+      def process_full_diff
+        final = {}
+        current_file = nil
+        @full_diff.split("\n").each do |line|
+          if m = /diff --git a\/(.*?) b\/(.*?)/.match(line)
+            current_file = m[1]
+            final[current_file] = {:patch => line, :path => current_file, 
+                                    :mode => '', :src => '', :dst => '', :type => 'modified'}
+          else
+            if m = /index (.......)\.\.(.......)( ......)*/.match(line)
+              final[current_file][:src] = m[1]
+              final[current_file][:dst] = m[2]
+              final[current_file][:mode] = m[3].strip if m[3]
+            end
+            if m = /(.*?) file mode (......)/.match(line)
+              final[current_file][:type] = m[1]
+              final[current_file][:mode] = m[2]
+            end
+            if m = /^Binary files /.match(line)
+              final[current_file][:binary] = true
+            end
+            final[current_file][:patch] << "\n" + line 
+          end
+        end
+        final.map { |e| [e[0], DiffFile.new(@base, e[1])] }
+      end
+      
+  end
+end

data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/index.rb

@@ -0,0 +1,5 @@
+module Git
+  class Index < Git::Path
+    
+  end
+end

data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/lib.rb

@@ -0,0 +1,719 @@
+require 'tempfile'
+
+module Git
+  
+  class GitExecuteError < StandardError 
+  end
+  
+  class Lib
+      
+    def initialize(base = nil, logger = nil)
+      @git_dir = nil
+      @git_index_file = nil
+      @git_work_dir = nil
+      @path = nil
+      
+      if base.is_a?(Git::Base)
+        @git_dir = base.repo.path
+        @git_index_file = base.index.path if base.index
+        @git_work_dir = base.dir.path if base.dir
+      elsif base.is_a?(Hash)
+        @git_dir = base[:repository]
+        @git_index_file = base[:index] 
+        @git_work_dir = base[:working_directory]
+      end
+      @logger = logger
+    end
+    
+    def init
+      command('init')
+    end
+    
+    # tries to clone the given repo
+    #
+    # returns {:repository} (if bare)
+    #         {:working_directory} otherwise
+    #
+    # accepts options:
+    #  :remote:: name of remote (rather than 'origin')
+    #  :bare::   no working directory
+    #  :depth::  the number of commits back to pull
+    # 
+    # TODO - make this work with SSH password or auth_key
+    #
+    def clone(repository, name, opts = {})
+      @path = opts[:path] || '.'
+      clone_dir = opts[:path] ? File.join(@path, name) : name
+      
+      arr_opts = []
+      arr_opts << "--bare" if opts[:bare]
+      arr_opts << "-o" << opts[:remote] if opts[:remote]
+      arr_opts << "--depth" << opts[:depth].to_i if opts[:depth] && opts[:depth].to_i > 0
+
+      arr_opts << '--'
+      arr_opts << repository
+      arr_opts << clone_dir
+      
+      command('clone', arr_opts)
+      
+      opts[:bare] ? {:repository => clone_dir} : {:working_directory => clone_dir}
+    end
+    
+    
+    ## READ COMMANDS ##
+    
+    
+    def log_commits(opts = {})
+      arr_opts = ['--pretty=oneline']
+      arr_opts << "-#{opts[:count]}" if opts[:count]
+      arr_opts << "--since=#{opts[:since]}" if opts[:since].is_a? String
+      arr_opts << "--until=#{opts[:until]}" if opts[:until].is_a? String
+      arr_opts << "--grep=#{opts[:grep]}" if opts[:grep].is_a? String
+      arr_opts << "--author=#{opts[:author]}" if opts[:author].is_a? String
+      arr_opts << "#{opts[:between][0].to_s}..#{opts[:between][1].to_s}" if (opts[:between] && opts[:between].size == 2)
+      arr_opts << opts[:object] if opts[:object].is_a? String
+      arr_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
+
+      command_lines('log', arr_opts, true).map { |l| l.split.first }
+    end
+    
+    def full_log_commits(opts = {})
+      arr_opts = ['--pretty=raw']
+      arr_opts << "-#{opts[:count]}" if opts[:count]
+      arr_opts << "--skip=#{opts[:skip]}" if opts[:skip]
+      arr_opts << "--since=#{opts[:since]}" if opts[:since].is_a? String
+      arr_opts << "--until=#{opts[:until]}" if opts[:until].is_a? String
+      arr_opts << "--grep=#{opts[:grep]}" if opts[:grep].is_a? String
+      arr_opts << "--author=#{opts[:author]}" if opts[:author].is_a? String
+      arr_opts << "#{opts[:between][0].to_s}..#{opts[:between][1].to_s}" if (opts[:between] && opts[:between].size == 2)
+      arr_opts << opts[:object] if opts[:object].is_a? String
+      arr_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
+      
+      full_log = command_lines('log', arr_opts, true)
+      process_commit_data(full_log)
+    end
+    
+    def revparse(string)
+      return string if string =~ /[A-Fa-f0-9]{40}/  # passing in a sha - just no-op it
+      rev = ['head', 'remotes', 'tags'].map do |d|
+        File.join(@git_dir, 'refs', d, string)
+      end.find do |path|
+        File.file?(path)
+      end
+      return File.read(rev).chomp if rev
+      command('rev-parse', string)
+    end
+    
+    def namerev(string)
+      command('name-rev', string).split[1]
+    end
+    
+    def object_type(sha)
+      command('cat-file', ['-t', sha])
+    end
+    
+    def object_size(sha)
+      command('cat-file', ['-s', sha]).to_i
+    end
+    
+    # returns useful array of raw commit object data
+    def commit_data(sha)
+      sha = sha.to_s
+      cdata = command_lines('cat-file', ['commit', sha])
+      process_commit_data(cdata, sha, 0)
+    end
+    
+    def process_commit_data(data, sha = nil, indent = 4)
+      in_message = false
+            
+      if sha
+        hsh = {'sha' => sha, 'message' => '', 'parent' => []}
+      else
+        hsh_array = []        
+      end
+    
+      data.each do |line|
+        line = line.chomp
+        if line == ''
+          in_message = !in_message
+        elsif in_message
+          hsh['message'] << line[indent..-1] << "\n"
+        else
+          data = line.split
+          key = data.shift
+          value = data.join(' ')
+          if key == 'commit'
+            sha = value
+            hsh_array << hsh if hsh
+            hsh = {'sha' => sha, 'message' => '', 'parent' => []}
+          end
+          if key == 'parent'
+            hsh[key] << value
+          else
+            hsh[key] = value
+          end
+        end
+      end
+      
+      if hsh_array
+        hsh_array << hsh if hsh
+        hsh_array
+      else
+        hsh
+      end
+    end
+    
+    def object_contents(sha, &block)
+      command('cat-file', ['-p', sha], &block)
+    end
+
+    def ls_tree(sha)
+      data = {'blob' => {}, 'tree' => {}}
+      
+      command_lines('ls-tree', sha).each do |line|
+        (info, filenm) = line.split("\t")
+        (mode, type, sha) = info.split
+        data[type][filenm] = {:mode => mode, :sha => sha}
+      end
+      
+      data
+    end
+
+    def mv(file1, file2)
+      command_lines('mv', ['--', file1, file2])
+    end
+        
+    def full_tree(sha)
+      command_lines('ls-tree', ['-r', sha])
+    end
+            
+    def tree_depth(sha)
+      full_tree(sha).size
+    end
+
+    def change_head_branch(branch_name)
+      command('symbolic-ref', ['HEAD', "refs/heads/#{branch_name}"])
+    end
+    
+    def branches_all
+      arr = []
+      command_lines('branch', '-a').each do |b| 
+        current = (b[0, 2] == '* ')
+        arr << [b.gsub('* ', '').strip, current]
+      end
+      arr
+    end
+
+    def list_files(ref_dir)
+      dir = File.join(@git_dir, 'refs', ref_dir)
+      files = []
+      Dir.chdir(dir) { files = Dir.glob('**/*').select { |f| File.file?(f) } } rescue nil
+      files
+    end
+    
+    def branch_current
+      branches_all.select { |b| b[1] }.first[0] rescue nil
+    end
+
+
+    # returns hash
+    # [tree-ish] = [[line_no, match], [line_no, match2]]
+    # [tree-ish] = [[line_no, match], [line_no, match2]]
+    def grep(string, opts = {})
+      opts[:object] ||= 'HEAD'
+
+      grep_opts = ['-n']
+      grep_opts << '-i' if opts[:ignore_case]
+      grep_opts << '-v' if opts[:invert_match]
+      grep_opts << '-e'
+      grep_opts << string
+      grep_opts << opts[:object] if opts[:object].is_a?(String)
+      grep_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
+
+      hsh = {}
+      command_lines('grep', grep_opts).each do |line|
+        if m = /(.*)\:(\d+)\:(.*)/.match(line)        
+          hsh[m[1]] ||= []
+          hsh[m[1]] << [m[2].to_i, m[3]] 
+        end
+      end
+      hsh
+    end
+    
+    def diff_full(obj1 = 'HEAD', obj2 = nil, opts = {})
+      diff_opts = ['-p']
+      diff_opts << obj1
+      diff_opts << obj2 if obj2.is_a?(String)
+      diff_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
+
+      command('diff', diff_opts)
+    end
+    
+    def diff_stats(obj1 = 'HEAD', obj2 = nil, opts = {})
+      diff_opts = ['--numstat']
+      diff_opts << obj1
+      diff_opts << obj2 if obj2.is_a?(String)
+      diff_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
+
+      hsh = {:total => {:insertions => 0, :deletions => 0, :lines => 0, :files => 0}, :files => {}}
+      
+      command_lines('diff', diff_opts).each do |file|
+        (insertions, deletions, filename) = file.split("\t")
+        hsh[:total][:insertions] += insertions.to_i
+        hsh[:total][:deletions] += deletions.to_i
+        hsh[:total][:lines] = (hsh[:total][:deletions] + hsh[:total][:insertions])
+        hsh[:total][:files] += 1
+        hsh[:files][filename] = {:insertions => insertions.to_i, :deletions => deletions.to_i}
+      end
+            
+      hsh
+    end
+
+    # compares the index and the working directory
+    def diff_files
+      hsh = {}
+      command_lines('diff-files').each do |line|
+        (info, file) = line.split("\t")
+        (mode_src, mode_dest, sha_src, sha_dest, type) = info.split
+        hsh[file] = {:path => file, :mode_file => mode_src.to_s[1, 7], :mode_index => mode_dest, 
+                      :sha_file => sha_src, :sha_index => sha_dest, :type => type}
+      end
+      hsh
+    end
+    
+    # compares the index and the repository
+    def diff_index(treeish)
+      hsh = {}
+      command_lines('diff-index', treeish).each do |line|
+        (info, file) = line.split("\t")
+        (mode_src, mode_dest, sha_src, sha_dest, type) = info.split
+        hsh[file] = {:path => file, :mode_repo => mode_src.to_s[1, 7], :mode_index => mode_dest, 
+                      :sha_repo => sha_src, :sha_index => sha_dest, :type => type}
+      end
+      hsh
+    end
+            
+    def ls_files(location=nil)
+      hsh = {}
+      command_lines('ls-files', ['--stage', location]).each do |line|
+        (info, file) = line.split("\t")
+        (mode, sha, stage) = info.split
+        file = eval(file) if file =~ /^\".*\"$/ # This takes care of quoted strings returned from git
+        hsh[file] = {:path => file, :mode_index => mode, :sha_index => sha, :stage => stage}
+      end
+      hsh
+    end
+
+
+    def ignored_files
+      command_lines('ls-files', ['--others', '-i', '--exclude-standard'])
+    end
+
+
+    def config_remote(name)
+      hsh = {}
+      config_list.each do |key, value|
+        if /remote.#{name}/.match(key)
+          hsh[key.gsub("remote.#{name}.", '')] = value
+        end
+      end
+      hsh
+    end
+
+    def config_get(name)
+      do_get = lambda do
+        command('config', ['--get', name])
+      end
+
+      if @git_dir
+        Dir.chdir(@git_dir, &do_get)
+      else
+        build_list.call
+      end
+    end
+
+    def global_config_get(name)
+      command('config', ['--global', '--get', name], false)
+    end
+    
+    def config_list
+      build_list = lambda do |path|
+        parse_config_list command_lines('config', ['--list'])
+      end
+      
+      if @git_dir
+        Dir.chdir(@git_dir, &build_list)
+      else
+        build_list.call
+      end
+    end
+
+    def global_config_list
+      parse_config_list command_lines('config', ['--global', '--list'], false)
+    end
+    
+    def parse_config_list(lines)
+      hsh = {}
+      lines.each do |line|
+        (key, *values) = line.split('=')
+        hsh[key] = values.join('=')
+      end
+      hsh
+    end
+
+    def parse_config(file)
+      hsh = {}
+      parse_config_list command_lines('config', ['--list', '--file', file], false)
+      #hsh = {}
+      #file = File.expand_path(file)
+      #if File.file?(file)
+      #  current_section = nil
+      #  File.readlines(file).each do |line|
+      #    if m = /\[(\w+)\]/.match(line)
+      #      current_section = m[1]
+      #    elsif m = /\[(\w+?) "(.*?)"\]/.match(line)
+      #      current_section = "#{m[1]}.#{m[2]}"
+      #    elsif m = /(\w+?) = (.*)/.match(line)
+      #      key = "#{current_section}.#{m[1]}"
+      #      hsh[key] = m[2] 
+      #    end
+      #  end
+      #end
+      #hsh
+    end
+    
+    ## WRITE COMMANDS ##
+        
+    def config_set(name, value)
+      command('config', [name, value])
+    end
+
+    def global_config_set(name, value)
+      command('config', ['--global', name, value], false)
+    end
+          
+    def add(path = '.')
+      arr_opts = ['--']
+      if path.is_a?(Array)
+        arr_opts += path
+      else
+        arr_opts << path
+      end
+      command('add', arr_opts)
+    end
+    
+    def remove(path = '.', opts = {})
+      arr_opts = ['-f']  # overrides the up-to-date check by default
+      arr_opts << ['-r'] if opts[:recursive]
+      arr_opts << '--'
+      if path.is_a?(Array)
+        arr_opts += path
+      else
+        arr_opts << path
+      end
+
+      command('rm', arr_opts)
+    end
+
+    def commit(message, opts = {})
+      arr_opts = ['-m', message]
+      arr_opts << '-a' if opts[:add_all]
+      arr_opts << '--allow-empty' if opts[:allow_empty]
+      arr_opts << "--author" << opts[:author] if opts[:author]
+      command('commit', arr_opts)
+    end
+
+    def reset(commit, opts = {})
+      arr_opts = []
+      arr_opts << '--hard' if opts[:hard]
+      arr_opts << commit if commit
+      command('reset', arr_opts)
+    end
+    
+    def apply(patch_file)
+      arr_opts = []
+      arr_opts << '--' << patch_file if patch_file
+      command('apply', arr_opts)
+    end
+    
+    def apply_mail(patch_file)
+      arr_opts = []
+      arr_opts << '--' << patch_file if patch_file
+      command('am', arr_opts)
+    end
+    
+    def stashes_all
+      arr = []
+      filename = File.join(@git_dir, 'logs/refs/stash')
+      if File.exist?(filename)
+        File.open(filename).each_with_index { |line, i|
+          m = line.match(/:(.*)$/)
+          arr << [i, m[1].strip]
+        }
+      end
+      arr
+    end
+    
+    def stash_save(message)
+      output = command('stash save', ['--', message])
+      output =~ /HEAD is now at/
+    end
+
+    def stash_apply(id = nil)
+      if id
+        command('stash apply', [id])
+      else
+        command('stash apply')
+      end
+    end
+    
+    def stash_clear
+      command('stash clear')
+    end
+    
+    def stash_list
+      command('stash list')
+    end
+    
+    def branch_new(branch)
+      command('branch', branch)
+    end
+    
+    def branch_delete(branch)
+      command('branch', ['-D', branch])
+    end
+    
+    def checkout(branch, opts = {})
+      arr_opts = []
+      arr_opts << '-f' if opts[:force]
+      arr_opts << '-b' << opts[:new_branch] if opts[:new_branch]
+      arr_opts << branch
+      
+      command('checkout', arr_opts)
+    end
+
+    def checkout_file(version, file)
+      arr_opts = []
+      arr_opts << version
+      arr_opts << file
+      command('checkout', arr_opts)
+    end
+    
+    def merge(branch, message = nil)      
+      arr_opts = []
+      arr_opts << '-m' << message if message
+      arr_opts += [branch]
+      command('merge', arr_opts)
+    end
+
+    def unmerged
+      unmerged = []
+      command_lines('diff', ["--cached"]).each do |line|
+        unmerged << $1 if line =~ /^\* Unmerged path (.*)/
+      end
+      unmerged
+    end
+
+    def conflicts # :yields: file, your, their
+      self.unmerged.each do |f|
+        your = Tempfile.new("YOUR-#{File.basename(f)}").path
+        command('show', ":2:#{f}", true, "> #{escape your}") 
+
+        their = Tempfile.new("THEIR-#{File.basename(f)}").path
+        command('show', ":3:#{f}", true, "> #{escape their}") 
+        yield(f, your, their)
+      end
+    end
+
+    def remote_add(name, url, opts = {})
+      arr_opts = ['add']
+      arr_opts << '-f' if opts[:with_fetch]
+      arr_opts << '--'
+      arr_opts << name
+      arr_opts << url
+      
+      command('remote', arr_opts)
+    end
+    
+    # this is documented as such, but seems broken for some reason
+    # i'll try to get around it some other way later
+    def remote_remove(name)
+      command('remote', ['rm', '--', name])
+    end
+    
+    def remotes
+      command_lines('remote')
+    end
+
+    def tags
+      command_lines('tag')
+    end
+
+    def tag(tag)
+      command('tag', tag)
+    end
+
+    
+    def fetch(remote)
+      command('fetch', remote)
+    end
+    
+    def push(remote, branch = 'master', tags = false)
+      command('push', [remote, branch])
+      command('push', ['--tags', remote]) if tags
+    end
+    
+    def tag_sha(tag_name)
+      head = File.join(@git_dir, 'refs', 'tags', tag_name)
+      return File.read(head).chomp if File.exists?(head)
+      
+      command('show-ref',  ['--tags', '-s', tag_name])
+    end  
+    
+    def repack
+      command('repack', ['-a', '-d'])
+    end
+    
+    def gc
+      command('gc', ['--prune', '--aggressive', '--auto'])
+    end
+    
+    # reads a tree into the current index file
+    def read_tree(treeish, opts = {})
+      arr_opts = []
+      arr_opts << "--prefix=#{opts[:prefix]}" if opts[:prefix]
+      arr_opts += [treeish]
+      command('read-tree', arr_opts)
+    end
+    
+    def write_tree
+      command('write-tree')
+    end
+    
+    def commit_tree(tree, opts = {})
+      opts[:message] ||= "commit tree #{tree}"
+      t = Tempfile.new('commit-message')
+      t.write(opts[:message])
+      t.close
+      
+      arr_opts = []
+      arr_opts << tree
+      arr_opts << '-p' << opts[:parent] if opts[:parent]
+      arr_opts += [opts[:parents]].map { |p| ['-p', p] }.flatten if opts[:parents]
+      command('commit-tree', arr_opts, true, "< #{escape t.path}")
+    end
+    
+    def update_ref(branch, commit)
+      command('update-ref', [branch, commit])
+    end
+    
+    def checkout_index(opts = {})
+      arr_opts = []
+      arr_opts << "--prefix=#{opts[:prefix]}" if opts[:prefix]
+      arr_opts << "--force" if opts[:force]
+      arr_opts << "--all" if opts[:all]
+      arr_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
+
+      command('checkout-index', arr_opts)
+    end
+    
+    # creates an archive file
+    #
+    # options
+    #  :format  (zip, tar)
+    #  :prefix
+    #  :remote
+    #  :path
+    def archive(sha, file = nil, opts = {})
+      opts[:format] ||= 'zip'
+      
+      if opts[:format] == 'tgz'
+        opts[:format] = 'tar' 
+        opts[:add_gzip] = true
+      end
+      
+      file ||= Tempfile.new('archive').path
+      
+      arr_opts = []
+      arr_opts << "--format=#{opts[:format]}" if opts[:format]
+      arr_opts << "--prefix=#{opts[:prefix]}" if opts[:prefix]
+      arr_opts << "--remote=#{opts[:remote]}" if opts[:remote]
+      arr_opts << sha
+      arr_opts << '--' << opts[:path] if opts[:path]
+      command('archive', arr_opts, true, (opts[:add_gzip] ? '| gzip' : '') + " > #{escape file}")
+      return file
+    end
+
+    # returns the current version of git, as an Array of Fixnums.
+    def current_command_version
+      output = command('version', [], false)
+      version = output[/\d+\.\d+(\.\d+)+/]
+      version.split('.').collect {|i| i.to_i}
+    end
+
+    def required_command_version
+      [1, 6, 0, 0]
+    end
+
+    def meets_required_version?
+      current_version  = self.current_command_version
+      required_version = self.required_command_version
+
+      return current_version[0] >= required_version[0] && 
+             current_version[1] >= required_version[1] &&
+             (current_version[2] ? current_version[2] >= required_version[2] : true) &&
+             (current_version[3] ? current_version[3] >= required_version[3] : true)
+    end
+
+
+    private
+    
+    def command_lines(cmd, opts = [], chdir = true, redirect = '')
+      command(cmd, opts, chdir).split("\n")
+    end
+    
+    def command(cmd, opts = [], chdir = true, redirect = '', &block)
+      ENV['GIT_DIR'] = @git_dir
+      ENV['GIT_INDEX_FILE'] = @git_index_file
+      ENV['GIT_WORK_TREE'] = @git_work_dir
+      path = @git_work_dir || @git_dir || @path
+
+      opts = [opts].flatten.map {|s| escape(s) }.join(' ')
+      git_cmd = "git #{cmd} #{opts} #{redirect} 2>&1"
+
+      out = nil
+      if chdir && (Dir.getwd != path)
+        Dir.chdir(path) { out = run_command(git_cmd, &block) } 
+      else
+        out = run_command(git_cmd, &block)
+      end
+      
+      if @logger
+        @logger.info(git_cmd)
+        @logger.debug(out)
+      end
+            
+      if $?.exitstatus > 0
+        if $?.exitstatus == 1 && out == ''
+          return ''
+        end
+        raise Git::GitExecuteError.new(git_cmd + ':' + out.to_s) 
+      end
+      out
+    end
+    
+    def run_command(git_cmd, &block)
+      if block_given?
+        IO.popen(git_cmd, &block)
+      else
+        `#{git_cmd}`.chomp
+      end
+    end
+
+    def escape(s)
+      escaped = s.to_s.gsub('\'', '\'\\\'\'')
+      %Q{"#{escaped}"}
+    end
+
+  end
+end