texzip 0.1.8 → 0.1.9

data/lib/texzip/Project.rb

@@ -8,522 +8,520 @@ class TeXzip::Error < Exception; end
 
 class TeXzip::Project < HighLine
 
-	PACKAGE_EXTENSIONS = %w(.sty .cls)
-	IMAGE_EXTENSIONS = %w(.png .jpg .pdf .eps .pstex)
-	TEXIMAGE_EXTENSIONS = %w(.pspdftex .pdf_t .pstex_t)
-
-	class Quit < Exception; end
-
-	attr_accessor :overwrite_all
-
-	class FilePath
-		def initialize(root_dir, file)
-			@root_dir = Pathname.new(root_dir).expand_path
-			@file = Pathname.new(file)
-			@file = @root_dir.join(file).expand_path.relative_path_from(@root_dir)
-			@out_file = @file
-		end
-
-		def set_output_directory dir
-			@out_dir = Pathname.new(dir).expand_path
-		end
-
-		def set_plain_output_directory dir
-			set_output_directory dir
-			@out_file = @file.basename
-		end
-
-		def file
-			@file
-		end
-
-		def out_file= file
-			@out_file = Pathname.new(file)
-		end
-
-		def output_path
-			@out_dir.join(@out_file).expand_path
-		end
-
-		def path
-			@root_dir.join(@file).expand_path
-		end
-
-		def extname
-			@file.extname
-		end
-
-		def hash
-			path.to_s.hash
-		end
-
-		def eql?(file_path)
-			path.to_s.eql? file_path.path.to_s
-		end
-	end
-
-	def initialize( master_file )
-		super()
-		@tex_master_file = Pathname.new(master_file).expand_path
-
-		# All possible include-paths for TeX
-		@tex_dirs = [@tex_master_file.dirname]
-		@tex_dirs.concat((ENV["TEXINPUTS"] || "").split(':').map{|d| Pathname.new(d)})
-		@tex_dirs.map! &:expand_path
-		@tex_dirs.uniq!
-
-		@overwrite_all = false
-
-		parse_files
-	end
-
-	def parse_files
-		# The hash of all files, including the whole text.
-		@tex_files = {}
-		@image_files = Set.new
-		@bib_files = Set.new
-		@cites = Set.new
-
-		# Read all files recursively
-		unparsed_files = [@tex_master_file]
-		until unparsed_files.empty?
-			fname = unparsed_files.pop
-			file = find_file( fname )
-			if file.nil? then
-				if PACKAGE_EXTENSIONS.include? File.extname(fname)
-					next
-				else
-					raise TeXzip::Error, "Can't find file: #{fname}"
-				end
-			end
-
-			unless @tex_files.has_key? file
-				included_files = parse_file file
-				unparsed_files.concat included_files
-			end
-		end
-
-		unless @bib_files.empty?
-			@bib = BibTeX::Bibliography.new
-			@bib_files.each do |bib_file|
-				bib = BibTeX.open(bib_file.path)
-				bib.replace_strings
-				@bib.add(bib.data)
-			end
-		else
-			@bib = nil
-		end
-	end
-
-	# Returns the master-file's path.
-	def master_file
-		@tex_master_file
-	end
-
-	# Returns a list of included tex and sty files.
-	# @return [Array<Pathname>] Included tex files.
-	def tex_files
-		@tex_files.keys
-	end
-
-	# Returns a list of included image-files.
-	# @return [Array<Pathname>] Included image files.
-	def image_files
-		@image_files.to_a
-	end
-
-	# Returns a list of included BibTeX-files.
-	# @return [Array<Pathname>] Included BibTeX files.
-	def bib_files
-		@bib_files.to_a
-	end
-
-	# Returns a list of citations.
-	# @return [Array<String>] Citations.
-	def cites
-		@cites.to_a
-	end
-
-	# Returns the full path for a certain file.
-	#
-	# The file is searched in the current directory as well as all
-	# directories given by the environment variable +TEXINPUTS+
-	#
-	# @param [String] file The (relative) path of the file.
-	# @param [Array<String>] extensions The (possible) file extensions.
-	# @return [Pathname,nil] The path to the file if exist.
-	def find_file( file, extensions = [] )
-		extensions.unshift "" # the empty extension
-		extensions.uniq!
-
-		@tex_dirs.each do |d|
-			extensions.each do |ext|
-				file_path = d.join(file + ext).expand_path
-				if File.file? file_path
-					return FilePath.new(d, file + ext)
-				end
-			end
-		end
-		return nil
-	end
-
-	# Returns the full paths for all variants of a certain file.
-	#
-	# The files are searched in the current directory as well as all
-	# directories given by the environment variable +TEXINPUTS+
-	#
-	# @param [String] file The base file-name.
-	# @param [Array<String>] extensions The possible file-extensions.
-	# @return [Array<Pathname>] All found files.
-	def find_files( file, extensions )
-		extensions.uniq!
-
-		files = []
-
-		extensions.each do |ext|
-			@tex_dirs.each do |d|
-				file_path = d.join(file + ext).expand_path
-				if file_path.file?
-					files << FilePath.new(d, file + ext)
-					break
-				end
-			end
-		end
-
-		files
-	end
-
-	# Load and parse a single tex-file.
-	#
-	# The file is parsed for commands including images, BibTeX-files
-	# and citations. The command along with the command's argument is
-	# passed to the block. The block is assumed to return a list of
-	# further tex-files to be parsed.
-	#
-	# @param [Pathname,String] file_name The name of the TeX-file to parse
-	# @return [Array<String>] A list of included TeX-files.
-	def parse_file file_name, &block
-		text = nil
-		File.open(file_name.path, "rb") do |f|
-			text = f.read
-		end
-		@tex_files[file_name] = text
-
-		block = method(:handle_command) unless block
-
-		included_files = []
-		text_without_comments = ""
-		text.each_line do |line|
-			comment_match = line.match /(?:\\)*%/
-			if comment_match and (comment_match.end(0) - comment_match.begin(0)).odd?
-				line = line[0...comment_match.end(0)]
-			end
-			text_without_comments.concat line
-		end
-
-		text_without_comments.scan(/\\(documentclass|usepackage|include|input|includegraphics|bibliography|cite)(?:\[[^\]]+\])?\{([^}]+)\}/) do |cmd, arg|
-			new_files = block.call cmd, arg
-			included_files.concat new_files if new_files
-		end
-		included_files
-	end
-
-	# Handles parsed commands.
-	def handle_command command, argument
-		case command
-		when "includegraphics"
-			add_image argument
-		when  "bibliography"
-			argument.split(',').uniq.each{|f| add_bib f.strip}
-		when "usepackage"
-			return [argument + ".sty"]
-		when "documentclass"
-			return [argument + ".cls"]
-		when "cite"
-			@cites.merge argument.split(',').map(&:strip)
-		else
-			ext = File.extname(argument)
-			if TEXIMAGE_EXTENSIONS.include?(ext)
-				file = find_file(argument)
-				unless file
-					puts "WARNING: Can't find tex-image file #{argument}"
-					return nil
-				end
-				dir = File.dirname(argument)
-				parse_file file do |command, arg|
-					if command == "includegraphics"
-						add_image File.join(dir, arg)
-					else
-						raise TeXzip::Error, "Unexpected command '\\#{command}' in tex-image file: \\#{argument}"
-					end
-					nil
-				end
-			elsif ext != ".tex"
-				argument += ".tex"
-			end
-			return [argument]
-		end
-		return nil
-	end
-
-	# Adds an image to the list of included images.
-	# @param [String] image_file_name The path of the image-file
-	def add_image image_file_name
-		ext = File.extname(image_file_name)
-		if ext == ""
-			image_files = find_files( image_file_name, IMAGE_EXTENSIONS )
-		else
-			image_files = [find_file( image_file_name )].compact
-		end
-
-		if image_files.empty?
-			puts "WARNING: Can't find included image #{image_file_name}"
-		else
-			@image_files.merge image_files
-		end
-	end
-
-	# Adds a BibTeX-file to the list of included BibTeX-files.
-	# @param [String] image_file_name The path of the BibTeX-file.
-	def add_bib bib_file_name
-		bib_file = find_file( bib_file_name, [".bib"] )
-
-		if bib_file.nil?
-			puts "WARNING: Can't find included BibTeX file #{bib_file_name}"
-		else
-			@bib_files.add bib_file
-		end
-	end
-
-	def modify_files outdir, image_dir, plain_img, bibtex_file
-		@output_directory = Pathname.new(outdir).expand_path
-		@output_image_directory = @output_directory.join(Pathname.new(image_dir)).expand_path
-		@output_bibtex = @output_directory.join(Pathname.new(bibtex_file)).expand_path
-		@modified_files = {}
-
-		plain_img_files = Hash.new{|h,k| h[k] = []}
-
-		@tex_files.each_key do |file|
-			if TEXIMAGE_EXTENSIONS.include? file.extname
-				if plain_img
-					file.set_plain_output_directory @output_image_directory
-					plain_img_files[file.file.to_s] << file
-				else
-					file.set_output_directory @output_image_directory
-				end
-			else
-				file.set_output_directory @output_directory
-			end
-		end
-		@tex_files.each_pair do |file, text|
-			@modified_files[file] = update_file file, text, plain_img
-		end
-
-		@image_files.each do |file|
-			if plain_img
-				file.set_plain_output_directory @output_image_directory
-				plain_img_files[file.file.to_s] << file
-			else
-				file.set_output_directory @output_image_directory
-			end
-		end
-
-		# maybe rename some files
-		plain_img_files.each_pair do |fname, files|
-			ext = File.extname(fname)
-			next if files.size <= 1
-			# TODO: not supported when updating references
-			raise "Multiple images with the same name but different directories"
-			cnt = 2
-			files.each do |file|
-				loop do
-					new_fname = fname.basename.sub_ext("#{cnt}#{ext}")
-					if plain_img_files.include?(new_fname.to_s)
-						cnt += 1
-					else
-						file.out_file = new_fname
-						break
-					end
-				end
-			end
-		end
-
-		filter_bibtex
-	end
-
-	def update_file tex_file, text, plain
-		ext = tex_file.path.extname
-
-		new_text = ""
-		text.each_line do |line|
-			comment_match = line.match /(?:\\)*%/
-			if comment_match and (comment_match.end(0) - comment_match.begin(0)).odd?
-				comment = line[comment_match.end(0) .. -1]
-				line = line[0...comment_match.end(0)]
-			else
-				comment = ""
-			end
-			new_line = line.gsub(/(\\(include|input|includegraphics|bibliography)(?:\[[^\]]+\])?)\{([^}]+)\}/) { |m|
-				start = $1
-				cmd = $2
-				file = $3
-				if cmd == "includegraphics"
-					if TEXIMAGE_EXTENSIONS.include? ext
-						file = File.join(tex_file.file.dirname, file)
-					end
-					new_file = @output_image_directory.join(Pathname.new(file)).relative_path_from(@output_directory)
-					# TODO: this does not support multiple files with same name
-					new_file = @output_image_directory.join(new_file.basename).relative_path_from(@output_directory) if plain
-				elsif cmd == "bibliography"
-					new_file = @output_bibtex.basename.to_s.gsub(/\.bib$/, '')
-				else
-					if TEXIMAGE_EXTENSIONS.include? File.extname(file)
-						new_file = @output_image_directory.join(Pathname.new(file)).relative_path_from(@output_directory)
-						# TODO: this does not support multiple files with same name
-						new_file = @output_image_directory.join(new_file.basename).relative_path_from(@output_directory) if plain
-					else
-						new_file = @output_directory.join(Pathname.new(file)).relative_path_from(@output_directory)
-					end
-				end
-				"#{start}{#{new_file}}"
-			}
-			new_text.concat new_line
-			new_text.concat comment
-		end
-
-		return new_text
-	end
-
-	def filter_bibtex
-		if @bib
-			cites = @cites.to_a.map{|c| c.to_s}
-			seen_cites = cites.to_set
-			until cites.empty?
-				cite = cites.pop
-				entries = @bib[cite]
-				if entries.nil?
-					puts "WARNING: Can't find BibTeX-entry #{cite}"
-				else
-					entries = [entries] unless entries.kind_of? Array
-					entries.each do |entry|
-						crossref = entry["crossref"]
-						if crossref
-							crossref.split(',').map(&:strip).each do |ref|
-								ref = ref.to_s
-								cites << ref if seen_cites.add? ref
-							end
-						end
-					end
-				end
-			end
-
-			@bib = BibTeX::Bibliography.new.add(@bib.data.select{|entry| seen_cites.include? entry.key.to_s})
-		end
-	end
-
-	def write_files( force = false )
-		cwd = Pathname.getwd.expand_path
-		write_data do |path, data|
-			puts "Write file #{path.relative_path_from(cwd)}"
-			FileUtils.mkdir_p path.dirname unless path.dirname.exist?
-			if data.kind_of? Pathname
-				FileUtils.copy data, path
-			else
-				File.open(path, "wb") do |f|
-					f.write data
-				end
-			end
-		end
-	end
-
-	def write_archive( archive_file, force = false )
-		require 'ffi-libarchive'
-
-		archive_file = Pathname.new(archive_file).expand_path
-		return unless ask_overwrite(archive_file)
-
-		compression = case File.basename(archive_file.to_s)
-		              when /\.tgz$/, /\.tar\.gz$/
-			              :gzip
-		              when /\.tbz2$/, /\.tar\.bz2$/
-			              :bzip2
-		              when /\.txz$/, /\.tar\.xz$/
-			              :xz
-		              when /\.tlzma$/, /\.tar\.lzma$/
-			              :lzma
-		              when /\.tZ$/, /\.tar\.Z$/
-			              :Z
-		              when /\.tar$/
-			              :none
-		              else
-			              raise TeXzip::Error, "Can't derive archive-type from file name #{archive_file}"
-		              end
-
-		puts "Write archive #{archive_file.relative_path_from(Pathname.getwd)}"
-		Archive.write_open_filename archive_file.to_s, compression, :tar do |ar|
-			write_data true do |path, data|
-				ar.add_entry do |e|
-					e.pathname = path.relative_path_from(@output_directory).to_s
-					if data.kind_of? Pathname
-						e.copy_stat(data.to_s)
-						File.open(data, "rb", &:read)
-					else
-						e.mode = 0644
-						e.atime = Time.now
-						e.mtime = Time.now
-						e.filetype = :file
-						data
-					end
-				end
-			end
-		end
-	end
-
-	def write_data( force = false, &block )
-		raise ArgumentError, "Block required" unless block
-
-		overwrite_all = force
-		commands = []
-
-		@modified_files.each_pair do |file, text|
-			if force or ask_overwrite(file.output_path)
-				commands << [file.output_path, text]
-			end
-		end
-
-		@image_files.each do |file|
-			if force or ask_overwrite(file.output_path)
-				commands << [file.output_path, file.path]
-			end
-		end
-
-		if @bib and (force or ask_overwrite(@output_bibtex))
-			commands << [@output_bibtex, @bib.to_s]
-		end
-
-		commands.each do |path, data|
-			block.call path, data
-		end
-	end
-
-	def ask_overwrite file
-		if !@overwrite_all and File.exist?(file)
-			ask("File #{file.relative_path_from(Pathname.getwd)} exists. Overwrite? [Ynaq]") do |q|
-				q.character = true
-				q.validate = /[ynaq\r ]/
-				q.case = :down
-				q.overwrite = false
-				q.answer_type = lambda{ |c|
-					case c
-					when "q"; raise Quit
-					when "y"; true
-					when "n"; false
-					when "a"; @overwrite_all = true; true
-					end
-				}
-			end
-		else
-			true
-		end
-	end
+  PACKAGE_EXTENSIONS = %w(.sty .cls).freeze
+  IMAGE_EXTENSIONS = %w(.png .jpg .pdf .eps .pstex).freeze
+  TEXIMAGE_EXTENSIONS = %w(.pspdftex .pdf_t .pstex_t).freeze
+
+  class Quit < Exception; end
+
+  attr_accessor :overwrite_all
+
+  class FilePath
+    def initialize(root_dir, file)
+      @root_dir = Pathname.new(root_dir).expand_path
+      @file = Pathname.new(file)
+      @file = @root_dir.join(file).expand_path.relative_path_from(@root_dir)
+      @out_file = @file
+    end
+
+    def set_output_directory(dir)
+      @out_dir = Pathname.new(dir).expand_path
+    end
+
+    def set_plain_output_directory(dir)
+      set_output_directory dir
+      @out_file = @file.basename
+    end
+
+    def file
+      @file
+    end
+
+    def out_file=(file)
+      @out_file = Pathname.new(file)
+    end
+
+    def output_path
+      @out_dir.join(@out_file).expand_path
+    end
+
+    def path
+      @root_dir.join(@file).expand_path
+    end
+
+    def extname
+      @file.extname
+    end
+
+    def hash
+      path.to_s.hash
+    end
+
+    def eql?(other)
+      path.to_s.eql? other.path.to_s
+    end
+  end
+
+  def initialize(master_file)
+    super()
+    @tex_master_file = Pathname.new(master_file).expand_path
+
+    # All possible include-paths for TeX
+    @tex_dirs = [@tex_master_file.dirname]
+    @tex_dirs.concat((ENV['TEXINPUTS'] || '').split(':').map {|d| Pathname.new(d)})
+    @tex_dirs.map!(&:expand_path)
+    @tex_dirs.uniq!
+
+    @overwrite_all = false
+
+    parse_files
+  end
+
+  def parse_files
+    # The hash of all files, including the whole text.
+    @tex_files = {}
+    @image_files = Set.new
+    @bib_files = Set.new
+    @cites = Set.new
+
+    # Read all files recursively
+    unparsed_files = [@tex_master_file]
+    until unparsed_files.empty?
+      fname = unparsed_files.pop
+      file = find_file(fname)
+      if file.nil? then
+        if PACKAGE_EXTENSIONS.include?(File.extname(fname))
+          next
+        else
+          raise TeXzip::Error, "Can't find file: #{fname}"
+        end
+      end
+
+      unless @tex_files.has_key?(file)
+        included_files = parse_file file
+        unparsed_files.concat included_files
+      end
+    end
+
+    if !@bib_files.empty?
+      @bib = nil
+    else
+      @bib = BibTeX::Bibliography.new
+      @bib_files.each do |bib_file|
+        bib = BibTeX.open(bib_file.path)
+        bib.replace_strings
+        @bib.add(bib.data)
+      end
+    end
+  end
+
+  # Returns the master-file's path.
+  def master_file
+    @tex_master_file
+  end
+
+  # Returns a list of included tex and sty files.
+  # @return [Array<Pathname>] Included tex files.
+  def tex_files
+    @tex_files.keys
+  end
+
+  # Returns a list of included image-files.
+  # @return [Array<Pathname>] Included image files.
+  def image_files
+    @image_files.to_a
+  end
+
+  # Returns a list of included BibTeX-files.
+  # @return [Array<Pathname>] Included BibTeX files.
+  def bib_files
+    @bib_files.to_a
+  end
+
+  # Returns a list of citations.
+  # @return [Array<String>] Citations.
+  def cites
+    @cites.to_a
+  end
+
+  # Returns the full path for a certain file.
+  #
+  # The file is searched in the current directory as well as all
+  # directories given by the environment variable +TEXINPUTS+
+  #
+  # @param [String] file The (relative) path of the file.
+  # @param [Array<String>] extensions The (possible) file extensions.
+  # @return [Pathname,nil] The path to the file if exist.
+  def find_file(file, extensions = [])
+    extensions.unshift '' # the empty extension
+    extensions.uniq!
+
+    @tex_dirs.each do |d|
+      extensions.each do |ext|
+        file_path = d.join(file + ext).expand_path
+        return FilePath.new(d, file + ext) if File.file?(file_path)
+      end
+    end
+    nil
+  end
+
+  # Returns the full paths for all variants of a certain file.
+  #
+  # The files are searched in the current directory as well as all
+  # directories given by the environment variable +TEXINPUTS+
+  #
+  # @param [String] file The base file-name.
+  # @param [Array<String>] extensions The possible file-extensions.
+  # @return [Array<Pathname>] All found files.
+  def find_files(file, extensions)
+    extensions.uniq!
+
+    files = []
+
+    extensions.each do |ext|
+      @tex_dirs.each do |d|
+        file_path = d.join(file + ext).expand_path
+        if file_path.file?
+          files << FilePath.new(d, file + ext)
+          break
+        end
+      end
+    end
+
+    files
+  end
+
+  # Load and parse a single tex-file.
+  #
+  # The file is parsed for commands including images, BibTeX-files
+  # and citations. The command along with the command's argument is
+  # passed to the block. The block is assumed to return a list of
+  # further tex-files to be parsed.
+  #
+  # @param [Pathname,String] file_name The name of the TeX-file to parse
+  # @return [Array<String>] A list of included TeX-files.
+  def parse_file(file_name, &block)
+    text = nil
+    File.open(file_name.path, 'rb') do |f|
+      text = f.read
+    end
+    @tex_files[file_name] = text
+
+    block = method(:handle_command) unless block
+
+    included_files = []
+    text_without_comments = ''
+    text.each_line do |line|
+      comment_match = line.match(/(?:\\)*%/)
+      if comment_match && (comment_match.end(0) - comment_match.begin(0)).odd?
+        line = line[0...comment_match.end(0)]
+      end
+      text_without_comments.concat line
+    end
+
+    text_without_comments.scan(/\\(documentclass|usepackage|include|input|includegraphics|bibliography|cite)(?:\[[^\]]+\])?\{([^}]+)\}/) do |cmd, arg|
+      new_files = block.call(cmd, arg)
+      included_files.concat(new_files) if new_files
+    end
+    included_files
+  end
+
+  # Handles parsed commands.
+  def handle_command(command, argument)
+    case command
+    when 'includegraphics'
+      add_image argument
+    when 'bibliography'
+      argument.split(',').uniq.each {|f| add_bib f.strip}
+    when 'usepackage'
+      return [argument + '.sty']
+    when 'documentclass'
+      return [argument + '.cls']
+    when 'cite'
+      @cites.merge argument.split(',').map(&:strip)
+    else
+      ext = File.extname(argument)
+      if TEXIMAGE_EXTENSIONS.include?(ext)
+        file = find_file(argument)
+        unless file
+          puts "WARNING: Can't find tex-image file #{argument}"
+          return nil
+        end
+        dir = File.dirname(argument)
+        parse_file file do |command, arg|
+          if command == 'includegraphics'
+            add_image File.join(dir, arg)
+          else
+            raise TeXzip::Error, "Unexpected command '\\#{command}' in tex-image file: \\#{argument}"
+          end
+          nil
+        end
+      elsif ext != '.tex'
+        argument += '.tex'
+      end
+      return [argument]
+    end
+    nil
+  end
+
+  # Adds an image to the list of included images.
+  # @param [String] image_file_name The path of the image-file
+  def add_image(image_file_name)
+    ext = File.extname(image_file_name)
+    image_files = if ext == ''
+                    find_files(image_file_name, IMAGE_EXTENSIONS)
+                  else
+                    [find_file(image_file_name)].compact
+                  end
+
+    if image_files.empty?
+      puts "WARNING: Can't find included image #{image_file_name}"
+    else
+      @image_files.merge image_files
+    end
+  end
+
+  # Adds a BibTeX-file to the list of included BibTeX-files.
+  # @param [String] image_file_name The path of the BibTeX-file.
+  def add_bib(bib_file_name)
+    bib_file = find_file(bib_file_name, ['.bib'])
+
+    if bib_file.nil?
+      puts "WARNING: Can't find included BibTeX file #{bib_file_name}"
+    else
+      @bib_files.add bib_file
+    end
+  end
+
+  def modify_files(outdir, image_dir, plain_img, bibtex_file)
+    @output_directory = Pathname.new(outdir).expand_path
+    @output_image_directory = @output_directory.join(Pathname.new(image_dir)).expand_path
+    @output_bibtex = @output_directory.join(Pathname.new(bibtex_file)).expand_path
+    @modified_files = {}
+
+    plain_img_files = Hash.new {|h,k| h[k] = []}
+
+    @tex_files.each_key do |file|
+      if TEXIMAGE_EXTENSIONS.include? file.extname
+        if plain_img
+          file.set_plain_output_directory @output_image_directory
+          plain_img_files[file.file.to_s] << file
+        else
+          file.set_output_directory @output_image_directory
+        end
+      else
+        file.set_output_directory @output_directory
+      end
+    end
+    @tex_files.each_pair do |file, text|
+      @modified_files[file] = update_file file, text, plain_img
+    end
+
+    @image_files.each do |file|
+      if plain_img
+        file.set_plain_output_directory @output_image_directory
+        plain_img_files[file.file.to_s] << file
+      else
+        file.set_output_directory @output_image_directory
+      end
+    end
+
+    # maybe rename some files
+    plain_img_files.each_pair do |fname, files|
+      ext = File.extname(fname)
+      next if files.size <= 1
+      # TODO: not supported when updating references
+      raise 'Multiple images with the same name but different directories'
+      cnt = 2
+      files.each do |file|
+        loop do
+          new_fname = fname.basename.sub_ext("#{cnt}#{ext}")
+          if plain_img_files.include?(new_fname.to_s)
+            cnt += 1
+          else
+            file.out_file = new_fname
+            break
+          end
+        end
+      end
+    end
+
+    filter_bibtex
+  end
+
+  def update_file(tex_file, text, plain)
+    ext = tex_file.path.extname
+
+    new_text = ''
+    text.each_line do |line|
+      comment_match = line.match(/(?:\\)*%/)
+      if comment_match && (comment_match.end(0) - comment_match.begin(0)).odd?
+        comment = line[comment_match.end(0)..-1]
+        line = line[0...comment_match.end(0)]
+      else
+        comment = ''
+      end
+      new_line = line.gsub(/(\\(include|input|includegraphics|bibliography)(?:\[[^\]]+\])?)\{([^}]+)\}/) do |m|
+        start = $1
+        cmd = $2
+        file = $3
+        if cmd == 'includegraphics'
+          if TEXIMAGE_EXTENSIONS.include? ext
+            file = File.join(tex_file.file.dirname, file)
+          end
+          new_file = @output_image_directory.join(Pathname.new(file)).relative_path_from(@output_directory)
+          # TODO: this does not support multiple files with same name
+          new_file = @output_image_directory.join(new_file.basename).relative_path_from(@output_directory) if plain
+        elsif cmd == 'bibliography'
+          new_file = @output_bibtex.basename.to_s.gsub(/\.bib$/, '')
+        elsif TEXIMAGE_EXTENSIONS.include?(File.extname(file))
+          new_file = @output_image_directory.join(Pathname.new(file)).relative_path_from(@output_directory)
+          # TODO: this does not support multiple files with same name
+          new_file = @output_image_directory.join(new_file.basename).relative_path_from(@output_directory) if plain
+        else
+          new_file = @output_directory.join(Pathname.new(file)).relative_path_from(@output_directory)
+        end
+        "#{start}{#{new_file}}"
+      end
+      new_text.concat new_line
+      new_text.concat comment
+    end
+
+    new_text
+  end
+
+  def filter_bibtex
+    if @bib
+      cites = @cites.to_a.map(&:to_s)
+      seen_cites = cites.to_set
+      until cites.empty?
+        cite = cites.pop
+        entries = @bib[cite]
+        if entries.nil?
+          puts "WARNING: Can't find BibTeX-entry #{cite}"
+        else
+          entries = [entries] unless entries.is_a?(Array)
+          entries.each do |entry|
+            crossref = entry['crossref']
+            if crossref
+              crossref.split(',').map(&:strip).each do |ref|
+                ref = ref.to_s
+                cites << ref if seen_cites.add? ref
+              end
+            end
+          end
+        end
+      end
+
+      @bib = BibTeX::Bibliography.new.add(@bib.data.select {|entry| seen_cites.include? entry.key.to_s})
+    end
+  end
+
+  def write_files(force = false)
+    cwd = Pathname.getwd.expand_path
+    write_data do |path, data|
+      puts "Write file #{path.relative_path_from(cwd)}"
+      FileUtils.mkdir_p path.dirname unless path.dirname.exist?
+      if data.is_a? Pathname
+        FileUtils.copy data, path
+      else
+        File.open(path, 'wb') do |f|
+          f.write data
+        end
+      end
+    end
+  end
+
+  def write_archive(archive_file, force = false)
+    require 'ffi-libarchive'
+
+    archive_file = Pathname.new(archive_file).expand_path
+    return unless ask_overwrite(archive_file)
+
+    compression = case File.basename(archive_file.to_s)
+                  when /\.tgz$/, /\.tar\.gz$/
+                    :gzip
+                  when /\.tbz2$/, /\.tar\.bz2$/
+                    :bzip2
+                  when /\.txz$/, /\.tar\.xz$/
+                    :xz
+                  when /\.tlzma$/, /\.tar\.lzma$/
+                    :lzma
+                  when /\.tZ$/, /\.tar\.Z$/
+                    :Z
+                  when /\.tar$/
+                    :none
+                  else
+                    raise TeXzip::Error, "Can't derive archive-type from file name #{archive_file}"
+                  end
+
+    puts "Write archive #{archive_file.relative_path_from(Pathname.getwd)}"
+    Archive.write_open_filename archive_file.to_s, compression, :tar do |ar|
+      write_data true do |path, data|
+        ar.add_entry do |e|
+          e.pathname = path.relative_path_from(@output_directory).to_s
+          if data.is_a? Pathname
+            e.copy_stat(data.to_s)
+            File.open(data, 'rb', &:read)
+          else
+            e.mode = 0644
+            e.atime = Time.now
+            e.mtime = Time.now
+            e.filetype = :file
+            data
+          end
+        end
+      end
+    end
+  end
+
+  def write_data(force = false)
+    raise ArgumentError, 'Block required' unless block_given?
+
+    overwrite_all = force
+    commands = []
+
+    @modified_files.each_pair do |file, text|
+      if force || ask_overwrite(file.output_path)
+        commands << [file.output_path, text]
+      end
+    end
+
+    @image_files.each do |file|
+      if force || ask_overwrite(file.output_path)
+        commands << [file.output_path, file.path]
+      end
+    end
+
+    if @bib && (force || ask_overwrite(@output_bibtex))
+      commands << [@output_bibtex, @bib.to_s]
+    end
+
+    commands.each do |path, data|
+      yield(path, data)
+    end
+  end
+
+  def ask_overwrite(file)
+    if !@overwrite_all && File.exist?(file)
+      ask("File #{file.relative_path_from(Pathname.getwd)} exists. Overwrite? [Ynaq]") do |q|
+        q.character = true
+        q.validate = /[ynaq\r ]/
+        q.case = :down
+        q.overwrite = false
+        q.answer_type = lambda do |c|
+          case c
+          when 'q' then raise Quit
+          when 'y' then true
+          when 'n' then false
+          when 'a' then
+            @overwrite_all = true
+            true
+          end
+        end
+      end
+    else
+      true
+    end
+  end
 end