# index.py
# Copyright (C) 2008, 2009 Michael Trier (mtrier@gmail.com) and contributors
#
# This module is part of GitPython and is released under
# the BSD License: http://www.opensource.org/licenses/bsd-license.php
"""Module containing Index implementation, allowing to perform all kinds of index
manipulations such as querying and merging."""
import tempfile
import os
import sys
import subprocess
import glob
from cStringIO import StringIO

from stat import (
					S_ISLNK,
					S_ISDIR,
					S_IFMT,
					S_IFDIR,
					S_IFLNK,
					S_IFREG
				)

from typ import (
					BaseIndexEntry, 
					IndexEntry, 
				)

from util import (
					TemporaryFileSwap,
					post_clear_cache, 
					default_index,
					git_working_dir
				)

import git.objects
import git.diff as diff

from git.exc import (
							GitCommandError,
							CheckoutError
						)

from git.objects import (
							Blob, 
							Tree, 
							Object, 
							Commit,
						)

from git.objects.util import Serializable

from git.util import (
							IndexFileSHA1Writer, 
							LazyMixin, 
							LockedFD, 
							join_path_native, 
							file_contents_ro,
						)

from fun import (
					entry_key,
					write_cache,
					read_cache,
					aggressive_tree_merge,
					write_tree_from_cache
				)

from gitdb.base import IStream
from gitdb.db import MemoryDB
from gitdb.util import to_bin_sha
from itertools import izip

__all__ = ( 'IndexFile', 'CheckoutError' )


class IndexFile(LazyMixin, diff.Diffable, Serializable):
	"""
	Implements an Index that can be manipulated using a native implementation in
	order to save git command function calls wherever possible.
	
	It provides custom merging facilities allowing to merge without actually changing
	your index or your working tree. This way you can perform own test-merges based
	on the index only without having to deal with the working copy. This is useful
	in case of partial working trees.

	``Entries``
	
	The index contains an entries dict whose keys are tuples of type IndexEntry
	to facilitate access.

	You may read the entries dict or manipulate it using IndexEntry instance, i.e.::
	
		index.entries[index.entry_key(index_entry_instance)] = index_entry_instance
	
	Make sure you use index.write() once you are done manipulating the index directly
	before operating on it using the git command"""
	__slots__ = ("repo", "version", "entries", "_extension_data", "_file_path")
	_VERSION = 2			# latest version we support
	S_IFGITLINK = 0160000	# a submodule

	def __init__(self, repo, file_path=None):
		"""Initialize this Index instance, optionally from the given ``file_path``.
		If no file_path is given, we will be created from the current index file.

		If a stream is not given, the stream will be initialized from the current
		repository's index on demand."""
		self.repo = repo
		self.version = self._VERSION
		self._extension_data = ''
		self._file_path = file_path or self._index_path()

	def _set_cache_(self, attr):
		if attr == "entries":
			# read the current index
			# try memory map for speed
			lfd = LockedFD(self._file_path)
			try:
				fd = lfd.open(write=False, stream=False)
			except OSError:
				lfd.rollback()
				# in new repositories, there may be no index, which means we are empty
				self.entries = dict()
				return
			# END exception handling

			stream = file_contents_ro(fd, stream=True, allow_mmap=True)
			
			try:
				self._deserialize(stream)
			finally:
				lfd.rollback()
				# The handles will be closed on desctruction
			# END read from default index on demand
		else:
			super(IndexFile, self)._set_cache_(attr)

	def _index_path(self):
		return join_path_native(self.repo.git_dir, "index")

	@property
	def path(self):
		""" :return: Path to the index file we are representing """
		return self._file_path

	def _delete_entries_cache(self):
		"""Safely clear the entries cache so it can be recreated"""
		try:
			del(self.entries)
		except AttributeError:
			# fails in python 2.6.5 with this exception
			pass
		# END exception handling

	#{ Serializable Interface 

	def _deserialize(self, stream):
		"""Initialize this instance with index values read from the given stream"""
		self.version, self.entries, self._extension_data, conten_sha = read_cache(stream)
		return self
		
	def _entries_sorted(self):
		""":return: list of entries, in a sorted fashion, first by path, then by stage"""
		entries_sorted = self.entries.values()
		entries_sorted.sort(key=lambda e: (e.path, e.stage))		# use path/stage as sort key
		return entries_sorted
		
	def _serialize(self, stream, ignore_tree_extension_data=False):
		entries = self._entries_sorted()
		write_cache(entries,
					stream,
					(ignore_tree_extension_data and None) or self._extension_data) 
		return self
		
		
	#} END serializable interface

	def write(self, file_path = None, ignore_tree_extension_data=False):
		"""Write the current state to our file path or to the given one

		:param file_path:
			If None, we will write to our stored file path from which we have
			been initialized. Otherwise we write to the given file path.
			Please note that this will change the file_path of this index to
			the one you gave.

		:param ignore_tree_extension_data:
			If True, the TREE type extension data read in the index will not
			be written to disk. Use this if you have altered the index and
			would like to use git-write-tree afterwards to create a tree
			representing your written changes.
			If this data is present in the written index, git-write-tree
			will instead write the stored/cached tree.
			Alternatively, use IndexFile.write_tree() to handle this case
			automatically

		:return: self"""
		# make sure we have our entries read before getting a write lock
		# else it would be done when streaming. This can happen 
		# if one doesn't change the index, but writes it right away
		self.entries
		lfd = LockedFD(file_path or self._file_path)
		stream = lfd.open(write=True, stream=True)
		
		self._serialize(stream, ignore_tree_extension_data)
		
		lfd.commit()

		# make sure we represent what we have written
		if file_path is not None:
			self._file_path = file_path

	@post_clear_cache
	@default_index
	def merge_tree(self, rhs, base=None):
		"""Merge the given rhs treeish into the current index, possibly taking
		a common base treeish into account.

		As opposed to the from_tree_ method, this allows you to use an already
		existing tree as the left side of the merge

		:param rhs:
			treeish reference pointing to the 'other' side of the merge.

		:param base:
			optional treeish reference pointing to the common base of 'rhs' and
			this index which equals lhs

		:return:
			self ( containing the merge and possibly unmerged entries in case of
			conflicts )

		:raise GitCommandError:
			If there is a merge conflict. The error will
			be raised at the first conflicting path. If you want to have proper
			merge resolution to be done by yourself, you have to commit the changed
			index ( or make a valid tree from it ) and retry with a three-way
			index.from_tree call. """
		# -i : ignore working tree status
		# --aggressive : handle more merge cases
		# -m : do an actual merge
		args = ["--aggressive", "-i", "-m"]
		if base is not None:
			args.append(base)
		args.append(rhs)

		self.repo.git.read_tree(args)
		return self

	@classmethod
	def new(cls, repo, *tree_sha):
		""" Merge the given treeish revisions into a new index which is returned.
		This method behaves like git-read-tree --aggressive when doing the merge.

		:param repo: The repository treeish are located in.

		:param tree_sha:
			20 byte or 40 byte tree sha or tree objects 

		:return:
			New IndexFile instance. Its path will be undefined. 
			If you intend to write such a merged Index, supply an alternate file_path 
			to its 'write' method."""
		base_entries = aggressive_tree_merge(repo.odb, [to_bin_sha(str(t)) for t in tree_sha])
		
		inst = cls(repo)
		# convert to entries dict
		entries = dict(izip(((e.path, e.stage) for e in base_entries), 
							(IndexEntry.from_base(e) for e in base_entries)))
		
		inst.entries = entries
		return inst


	@classmethod
	def from_tree(cls, repo, *treeish, **kwargs):
		"""Merge the given treeish revisions into a new index which is returned.
		The original index will remain unaltered

		:param repo:
			The repository treeish are located in.

		:param treeish:
			One, two or three Tree Objects, Commits or 40 byte hexshas. The result
			changes according to the amount of trees.
			If 1 Tree is given, it will just be read into a new index
			If 2 Trees are given, they will be merged into a new index using a
			 two way merge algorithm. Tree 1 is the 'current' tree, tree 2 is the 'other'
			 one. It behaves like a fast-forward.
			 If 3 Trees are given, a 3-way merge will be performed with the first tree
			 being the common ancestor of tree 2 and tree 3. Tree 2 is the 'current' tree,
			 tree 3 is the 'other' one

		:param kwargs:
			Additional arguments passed to git-read-tree

		:return:
			New IndexFile instance. It will point to a temporary index location which
			does not exist anymore. If you intend to write such a merged Index, supply
			an alternate file_path to its 'write' method.

		:note:
			In the three-way merge case, --aggressive will be specified to automatically
			resolve more cases in a commonly correct manner. Specify trivial=True as kwarg
			to override that.

			As the underlying git-read-tree command takes into account the current index,
			it will be temporarily moved out of the way to assure there are no unsuspected
			interferences."""
		if len(treeish) == 0 or len(treeish) > 3:
			raise ValueError("Please specify between 1 and 3 treeish, got %i" % len(treeish))

		arg_list = list()
		# ignore that working tree and index possibly are out of date
		if len(treeish)>1:
			# drop unmerged entries when reading our index and merging
			arg_list.append("--reset")
			# handle non-trivial cases the way a real merge does
			arg_list.append("--aggressive")
		# END merge handling

		# tmp file created in git home directory to be sure renaming
		# works - /tmp/ dirs could be on another device
		tmp_index = tempfile.mktemp('','',repo.git_dir)
		arg_list.append("--index-output=%s" % tmp_index)
		arg_list.extend(treeish)

		# move current index out of the way - otherwise the merge may fail
		# as it considers existing entries. moving it essentially clears the index.
		# Unfortunately there is no 'soft' way to do it.
		# The TemporaryFileSwap assure the original file get put back
		index_handler = TemporaryFileSwap(join_path_native(repo.git_dir, 'index'))
		try:
			repo.git.read_tree(*arg_list, **kwargs)
			index = cls(repo, tmp_index)
			index.entries		# force it to read the file as we will delete the temp-file
			del(index_handler)	# release as soon as possible
		finally:
			if os.path.exists(tmp_index):
				os.remove(tmp_index)
		# END index merge handling

		return index

	@classmethod
	def _stat_mode_to_index_mode(cls, mode):
		"""Convert the given mode from a stat call to the corresponding index mode
		and return it"""
		if S_ISLNK(mode):	# symlinks
			return S_IFLNK
		if S_ISDIR(mode) or S_IFMT(mode) == cls.S_IFGITLINK:	# submodules
			return cls.S_IFGITLINK
		return S_IFREG | 0644 | (mode & 0100) 		# blobs with or without executable bit

	# UTILITIES
	def _iter_expand_paths(self, paths):
		"""Expand the directories in list of paths to the corresponding paths accordingly,

		Note: git will add items multiple times even if a glob overlapped
		with manually specified paths or if paths where specified multiple
		times - we respect that and do not prune"""
		def raise_exc(e):
			raise e
		r = self.repo.working_tree_dir
		rs = r + '/'
		for path in paths:
			abs_path = path
			if not os.path.isabs(abs_path):
				abs_path = os.path.join(r, path)
			# END make absolute path

			# resolve globs if possible
			if '?' in path or '*' in path or '[' in path:
				for f in self._iter_expand_paths(glob.glob(abs_path)):
					yield f.replace(rs, '')
				continue
			# END glob handling
			try:
				for root, dirs, files in os.walk(abs_path, onerror=raise_exc):
					for rela_file in files:
						# add relative paths only
						yield os.path.join(root.replace(rs, ''), rela_file)
					# END for each file in subdir
				# END for each subdirectory
			except OSError:
				# was a file or something that could not be iterated
				yield path.replace(rs, '')
			# END path exception handling
		# END for each path

	def _write_path_to_stdin(self, proc, filepath, item, fmakeexc, fprogress, 
								read_from_stdout=True):
		"""Write path to proc.stdin and make sure it processes the item, including progress.

		:return: stdout string
		:param read_from_stdout: if True, proc.stdout will be read after the item
			was sent to stdin. In that case, it will return None
		:note: There is a bug in git-update-index that prevents it from sending
			reports just in time. This is why we have a version that tries to
			read stdout and one which doesn't. In fact, the stdout is not
			important as the piped-in files are processed anyway and just in time
		:note: Newlines are essential here, gits behaviour is somewhat inconsistent
			on this depending on the version, hence we try our best to deal with
			newlines carefully. Usually the last newline will not be sent, instead
			we will close stdin to break the pipe."""

		fprogress(filepath, False, item)
		rval = None
		try:
			proc.stdin.write("%s\n" % filepath)
		except IOError:
			# pipe broke, usually because some error happend
			raise fmakeexc()
		# END write exception handling
		proc.stdin.flush()
		if read_from_stdout:
			rval = proc.stdout.readline().strip()
		fprogress(filepath, True, item)
		return rval

	def iter_blobs(self, predicate = lambda t: True):
		"""
		:return: Iterator yielding tuples of Blob objects and stages, tuple(stage, Blob)

		:param predicate:
			Function(t) returning True if tuple(stage, Blob) should be yielded by the
			iterator. A default filter, the BlobFilter, allows you to yield blobs
			only if they match a given list of paths. """
		for entry in self.entries.itervalues():
			# TODO: is it necessary to convert the mode ? We did that when adding 
			# it to the index, right ?
			mode = self._stat_mode_to_index_mode(entry.mode)
			blob = Blob(self.repo, entry.binsha, mode, entry.path)
			blob.size = entry.size
			output = (entry.stage, blob)
			if predicate(output):
				yield output
		# END for each entry

	def unmerged_blobs(self):
		"""
		Returns
			Iterator yielding dict(path : list( tuple( stage, Blob, ...))), being
			a dictionary associating a path in the index with a list containing
			sorted stage/blob pairs

		Note:
			Blobs that have been removed in one side simply do not exist in the
			given stage. I.e. a file removed on the 'other' branch whose entries
			are at stage 3 will not have a stage 3 entry.
		"""
		is_unmerged_blob = lambda t: t[0] != 0
		path_map = dict()
		for stage, blob in self.iter_blobs(is_unmerged_blob):
			path_map.setdefault(blob.path, list()).append((stage, blob))
		# END for each unmerged blob
		for l in path_map.itervalues():
			l.sort()
		return path_map

	@classmethod
	def entry_key(cls, *entry):
		return entry_key(*entry)

	def resolve_blobs(self, iter_blobs):
		"""Resolve the blobs given in blob iterator. This will effectively remove the
		index entries of the respective path at all non-null stages and add the given
		blob as new stage null blob.

		For each path there may only be one blob, otherwise a ValueError will be raised
		claiming the path is already at stage 0.

		:raise ValueError: if one of the blobs already existed at stage 0
		:return: self

		:note:
			You will have to write the index manually once you are done, i.e.
			index.resolve_blobs(blobs).write()
		"""
		for blob in iter_blobs:
			stage_null_key = (blob.path, 0)
			if stage_null_key in self.entries:
				raise ValueError( "Path %r already exists at stage 0" % blob.path )
			# END assert blob is not stage 0 already

			# delete all possible stages
			for stage in (1, 2, 3):
				try:
					del( self.entries[(blob.path, stage)])
				except KeyError:
					pass
				# END ignore key errors
			# END for each possible stage

			self.entries[stage_null_key] = IndexEntry.from_blob(blob)
		# END for each blob

		return self

	def update(self):
		"""Reread the contents of our index file, discarding all cached information
		we might have.

		:note: This is a possibly dangerious operations as it will discard your changes
			to index.entries
		:return: self"""
		self._delete_entries_cache()
		# allows to lazily reread on demand
		return self

	def write_tree(self):
		"""Writes this index to a corresponding Tree object into the repository's
		object database and return it.
		
		:return: Tree object representing this index
		:note: The tree will be written even if one or more objects the tree refers to 
			does not yet exist in the object database. This could happen if you added
			Entries to the index directly.
		:raise ValueError: if there are no entries in the cache
		:raise UnmergedEntriesError: """
		# we obtain no lock as we just flush our contents to disk as tree
		# If we are a new index, the entries access will load our data accordingly
		mdb = MemoryDB()
		entries = self._entries_sorted()
		binsha, tree_items = write_tree_from_cache(entries, mdb, slice(0, len(entries)))
		
		# copy changed trees only
		mdb.stream_copy(mdb.sha_iter(), self.repo.odb)
		
		
		# note: additional deserialization could be saved if write_tree_from_cache
		# would return sorted tree entries
		root_tree = Tree(self.repo, binsha, path='')
		root_tree._cache = tree_items
		return root_tree
		
	def _process_diff_args(self, args):
		try:
			args.pop(args.index(self))
		except IndexError:
			pass
		# END remove self
		return args

	def _to_relative_path(self, path):
		""":return: Version of path relative to our git directory or raise ValueError
		if it is not within our git direcotory"""
		if not os.path.isabs(path):
			return path
		relative_path = path.replace(self.repo.working_tree_dir+os.sep, "")
		if relative_path == path:
			raise ValueError("Absolute path %r is not in git repository at %r" % (path,self.repo.working_tree_dir))
		return relative_path

	def _preprocess_add_items(self, items):
		""" Split the items into two lists of path strings and BaseEntries. """
		paths = list()
		entries = list()

		for item in items:
			if isinstance(item, basestring):
				paths.append(self._to_relative_path(item))
			elif isinstance(item, Blob):
				entries.append(BaseIndexEntry.from_blob(item))
			elif isinstance(item, BaseIndexEntry):
				entries.append(item)
			else:
				raise TypeError("Invalid Type: %r" % item)
		# END for each item
		return (paths, entries)

	@git_working_dir
	def add(self, items, force=True, fprogress=lambda *args: None, path_rewriter=None, 
				write=True):
		"""Add files from the working tree, specific blobs or BaseIndexEntries
		to the index. 

		:param items:
			Multiple types of items are supported, types can be mixed within one call.
			Different types imply a different handling. File paths may generally be
			relative or absolute.

			- path string
				strings denote a relative or absolute path into the repository pointing to
				an existing file, i.e. CHANGES, lib/myfile.ext, '/home/gitrepo/lib/myfile.ext'.

				Paths provided like this must exist. When added, they will be written
				into the object database.

				PathStrings may contain globs, such as 'lib/__init__*' or can be directories
				like 'lib', the latter ones will add all the files within the dirctory and
				subdirectories.

				This equals a straight git-add.

				They are added at stage 0

			- Blob object
				Blobs are added as they are assuming a valid mode is set.
				The file they refer to may or may not exist in the file system, but
				must be a path relative to our repository.

				If their sha is null ( 40*0 ), their path must exist in the file system
				relative to the git repository as an object will be created from 
				the data at the path.
				The handling now very much equals the way string paths are processed, except that
				the mode you have set will be kept. This allows you to create symlinks
				by settings the mode respectively and writing the target of the symlink
				directly into the file. This equals a default Linux-Symlink which
				is not dereferenced automatically, except that it can be created on
				filesystems not supporting it as well.

				Please note that globs or directories are not allowed in Blob objects.

				They are added at stage 0

			- BaseIndexEntry or type
				Handling equals the one of Blob objects, but the stage may be
				explicitly set. Please note that Index Entries require binary sha's.

		:param force:
			If True, otherwise ignored or excluded files will be
			added anyway.
			As opposed to the git-add command, we enable this flag by default
			as the API user usually wants the item to be added even though
			they might be excluded.

		:param fprogress:
			Function with signature f(path, done=False, item=item) called for each
			path to be added, one time once it is about to be added where done==False
			and once after it was added where done=True.
			item is set to the actual item we handle, either a Path or a BaseIndexEntry
			Please note that the processed path is not guaranteed to be present
			in the index already as the index is currently being processed.

		:param path_rewriter:
			Function with signature (string) func(BaseIndexEntry) function returning a path
			for each passed entry which is the path to be actually recorded for the
			object created from entry.path. This allows you to write an index which
			is not identical to the layout of the actual files on your hard-dist.
			If not None and ``items`` contain plain paths, these paths will be
			converted to Entries beforehand and passed to the path_rewriter.
			Please note that entry.path is relative to the git repository.

		:param write:
				If True, the index will be written once it was altered. Otherwise
				the changes only exist in memory and are not available to git commands.
		
		:return:
			List(BaseIndexEntries) representing the entries just actually added.

		:raise OSError:
			if a supplied Path did not exist. Please note that BaseIndexEntry
			Objects that do not have a null sha will be added even if their paths
			do not exist.
		"""
		# sort the entries into strings and Entries, Blobs are converted to entries
		# automatically
		# paths can be git-added, for everything else we use git-update-index
		entries_added = list()
		paths, entries = self._preprocess_add_items(items)

		if paths and path_rewriter:
			for path in paths:
				abspath = os.path.abspath(path)
				gitrelative_path = abspath[len(self.repo.working_tree_dir)+1:]
				blob = Blob(self.repo, Blob.NULL_BIN_SHA, 
							self._stat_mode_to_index_mode(os.stat(abspath).st_mode), 
							gitrelative_path)
				entries.append(BaseIndexEntry.from_blob(blob))
			# END for each path
			del(paths[:])
		# END rewrite paths


		def store_path(filepath):
			"""Store file at filepath in the database and return the base index entry"""
			st = os.lstat(filepath)		# handles non-symlinks as well
			stream = None
			if S_ISLNK(st.st_mode):
				stream = StringIO(os.readlink(filepath))
			else:
				stream = open(filepath, 'rb')
			# END handle stream
			fprogress(filepath, False, filepath)
			istream = self.repo.odb.store(IStream(Blob.type, st.st_size, stream))
			fprogress(filepath, True, filepath)
			return BaseIndexEntry((self._stat_mode_to_index_mode(st.st_mode), 
									istream.binsha, 0, filepath))
		# END utility method


		# HANDLE PATHS
		if paths:
			assert len(entries_added) == 0
			added_files = list()
			for filepath in self._iter_expand_paths(paths):
				entries_added.append(store_path(filepath))
			# END for each filepath
		# END path handling


		# HANDLE ENTRIES
		if entries:
			null_mode_entries = [ e for e in entries if e.mode == 0 ]
			if null_mode_entries:
				raise ValueError("At least one Entry has a null-mode - please use index.remove to remove files for clarity")
			# END null mode should be remove

			# HANLDE ENTRY OBJECT CREATION
			# create objects if required, otherwise go with the existing shas
			null_entries_indices = [ i for i,e in enumerate(entries) if e.binsha == Object.NULL_BIN_SHA ]
			if null_entries_indices:
				for ei in null_entries_indices:
					null_entry = entries[ei]
					new_entry = store_path(null_entry.path)
					
					# update null entry
					entries[ei] = BaseIndexEntry((null_entry.mode, new_entry.binsha, null_entry.stage, null_entry.path))
				# END for each entry index
			# END null_entry handling

			# REWRITE PATHS
			# If we have to rewrite the entries, do so now, after we have generated
			# all object sha's
			if path_rewriter:
				for i,e in enumerate(entries):
					entries[i] = BaseIndexEntry((e.mode, e.binsha, e.stage, path_rewriter(e)))
				# END for each entry
			# END handle path rewriting

			# just go through the remaining entries and provide progress info
			for i, entry in enumerate(entries):
				progress_sent = i in null_entries_indices
				if not progress_sent:
					fprogress(entry.path, False, entry)
					fprogress(entry.path, True, entry)
				# END handle progress
			# END for each enty
			entries_added.extend(entries)
		# END if there are base entries

		# FINALIZE
		# add the new entries to this instance
		for entry in entries_added:
			self.entries[(entry.path, 0)] = IndexEntry.from_base(entry)
			
		if write:
			self.write()
		# END handle write
		
		return entries_added

	def _items_to_rela_paths(self, items):
		"""Returns a list of repo-relative paths from the given items which
		may be absolute or relative paths, entries or blobs"""
		paths = list()
		for item in items:
			if isinstance(item, (BaseIndexEntry,Blob)):
				paths.append(self._to_relative_path(item.path))
			elif isinstance(item, basestring):
				paths.append(self._to_relative_path(item))
			else:
				raise TypeError("Invalid item type: %r" % item)
		# END for each item
		return paths

	@post_clear_cache
	@default_index
	def remove(self, items, working_tree=False, **kwargs):
		"""Remove the given items from the index and optionally from
		the working tree as well.

		:param items:
			Multiple types of items are supported which may be be freely mixed.

			- path string
				Remove the given path at all stages. If it is a directory, you must
				specify the r=True keyword argument to remove all file entries
				below it. If absolute paths are given, they will be converted
				to a path relative to the git repository directory containing
				the working tree

				The path string may include globs, such as *.c.

			- Blob object
				Only the path portion is used in this case.

			- BaseIndexEntry or compatible type
				The only relevant information here Yis the path. The stage is ignored.

		:param working_tree:
			If True, the entry will also be removed from the working tree, physically
			removing the respective file. This may fail if there are uncommited changes
			in it.

		:param kwargs:
			Additional keyword arguments to be passed to git-rm, such
			as 'r' to allow recurive removal of

		:return:
			List(path_string, ...) list of repository relative paths that have
			been removed effectively.
			This is interesting to know in case you have provided a directory or
			globs. Paths are relative to the repository. """
		args = list()
		if not working_tree:
			args.append("--cached")
		args.append("--")

		# preprocess paths
		paths = self._items_to_rela_paths(items)
		removed_paths = self.repo.git.rm(args, paths, **kwargs).splitlines()

		# process output to gain proper paths
		# rm 'path'
		return [ p[4:-1] for p in removed_paths ]

	@post_clear_cache
	@default_index
	def move(self, items, skip_errors=False, **kwargs):
		"""Rename/move the items, whereas the last item is considered the destination of
		the move operation. If the destination is a file, the first item ( of two )
		must be a file as well. If the destination is a directory, it may be preceeded
		by one or more directories or files.

		The working tree will be affected in non-bare repositories.

		:parma items:
			Multiple types of items are supported, please see the 'remove' method
			for reference.
		:param skip_errors:
			If True, errors such as ones resulting from missing source files will
			be skpped.
		:param kwargs:
			Additional arguments you would like to pass to git-mv, such as dry_run
			or force.

		:return:List(tuple(source_path_string, destination_path_string), ...)
			A list of pairs, containing the source file moved as well as its
			actual destination. Relative to the repository root.

		:raise ValueErorr: If only one item was given
			GitCommandError: If git could not handle your request"""
		args = list()
		if skip_errors:
			args.append('-k')

		paths = self._items_to_rela_paths(items)
		if len(paths) < 2:
			raise ValueError("Please provide at least one source and one destination of the move operation")

		was_dry_run = kwargs.pop('dry_run', kwargs.pop('n', None))
		kwargs['dry_run'] = True

		# first execute rename in dryrun so the command tells us what it actually does
		# ( for later output )
		out = list()
		mvlines = self.repo.git.mv(args, paths, **kwargs).splitlines()

		# parse result - first 0:n/2 lines are 'checking ', the remaining ones
		# are the 'renaming' ones which we parse
		for ln in xrange(len(mvlines)/2, len(mvlines)):
			tokens = mvlines[ln].split(' to ')
			assert len(tokens) == 2, "Too many tokens in %s" % mvlines[ln]

			# [0] = Renaming x
			# [1] = y
			out.append((tokens[0][9:], tokens[1]))
		# END for each line to parse

		# either prepare for the real run, or output the dry-run result
		if was_dry_run:
			return out
		# END handle dryrun


		# now apply the actual operation
		kwargs.pop('dry_run')
		self.repo.git.mv(args, paths, **kwargs)

		return out

	def commit(self, message, parent_commits=None, head=True):
		"""Commit the current default index file, creating a commit object.

		For more information on the arguments, see tree.commit.
		:note:
			If you have manually altered the .entries member of this instance,
			don't forget to write() your changes to disk beforehand.

		:return:
			Commit object representing the new commit"""
		tree = self.write_tree()
		return Commit.create_from_tree(self.repo, tree, message, parent_commits, head)

	@classmethod
	def _flush_stdin_and_wait(cls, proc, ignore_stdout = False):
		proc.stdin.flush()
		proc.stdin.close()
		stdout = ''
		if not ignore_stdout:
			stdout = proc.stdout.read()
		proc.stdout.close()
		proc.wait()
		return stdout

	@default_index
	def checkout(self, paths=None, force=False, fprogress=lambda *args: None, **kwargs):
		"""Checkout the given paths or all files from the version known to the index into
		the working tree.
		
		:note: Be sure you have written pending changes using the ``write`` method
			in case you have altered the enties dictionary directly

		:param paths:
			If None, all paths in the index will be checked out. Otherwise an iterable
			of relative or absolute paths or a single path pointing to files or directories
			in the index is expected.

		:param force:
			If True, existing files will be overwritten even if they contain local modifications.
			If False, these will trigger a CheckoutError.

		:param fprogress:
			see Index.add_ for signature and explanation.
			The provided progress information will contain None as path and item if no
			explicit paths are given. Otherwise progress information will be send
			prior and after a file has been checked out

		:param kwargs:
			Additional arguments to be pasesd to git-checkout-index

		:return:
			iterable yielding paths to files which have been checked out and are
			guaranteed to match the version stored in the index

		:raise CheckoutError:
			If at least one file failed to be checked out. This is a summary,
			hence it will checkout as many files as it can anyway.
			If one of files or directories do not exist in the index
			( as opposed to the	 original git command who ignores them ).
			Raise GitCommandError if error lines could not be parsed - this truly is
			an exceptional state"""
		args = ["--index"]
		if force:
			args.append("--force")

		def handle_stderr(proc, iter_checked_out_files):
			stderr = proc.stderr.read()
			if not stderr:
				return
			# line contents:
			# git-checkout-index: this already exists
			failed_files = list()
			failed_reasons = list()
			unknown_lines = list()
			endings = (' already exists', ' is not in the cache', ' does not exist at stage', ' is unmerged')
			for line in stderr.splitlines():
				if not line.startswith("git checkout-index: ") and not line.startswith("git-checkout-index: "):
					is_a_dir = " is a directory"
					unlink_issue = "unable to unlink old '"
					if line.endswith(is_a_dir):
						failed_files.append(line[:-len(is_a_dir)])
						failed_reasons.append(is_a_dir)
					elif line.startswith(unlink_issue):
						failed_files.append(line[len(unlink_issue):line.rfind("'")])
						failed_reasons.append(unlink_issue)
					else:
						unknown_lines.append(line)
					continue
				# END special lines parsing

				for e in endings:
					if line.endswith(e):
						failed_files.append(line[20:-len(e)])
						failed_reasons.append(e)
						break
					# END if ending matches
				# END for each possible ending
			# END for each line
			if unknown_lines:
				raise GitCommandError(("git-checkout-index", ), 128, stderr)
			if failed_files:
				valid_files = list(set(iter_checked_out_files) - set(failed_files))
				raise CheckoutError("Some files could not be checked out from the index due to local modifications", failed_files, valid_files, failed_reasons)
		# END stderr handler


		if paths is None:
			args.append("--all")
			kwargs['as_process'] = 1
			fprogress(None, False, None)
			proc = self.repo.git.checkout_index(*args, **kwargs)
			proc.wait()
			fprogress(None, True, None)
			rval_iter = ( e.path for e in self.entries.itervalues() )
			handle_stderr(proc, rval_iter)
			return rval_iter
		else:
			if isinstance(paths, basestring):
				paths = [paths]

			# make sure we have our entries loaded before we start checkout_index
			# which will hold a lock on it. We try to get the lock as well during 
			# our entries initialization
			self.entries
			
			args.append("--stdin")
			kwargs['as_process'] = True
			kwargs['istream'] = subprocess.PIPE
			proc = self.repo.git.checkout_index(args, **kwargs)
			make_exc = lambda : GitCommandError(("git-checkout-index",)+tuple(args), 128, proc.stderr.read())
			checked_out_files = list()

			for path in paths:
				path = self._to_relative_path(path)
				# if the item is not in the index, it could be a directory
				path_is_directory = False

				try:
					self.entries[(path, 0)]
				except KeyError:
					dir = path
					if not dir.endswith('/'):
						dir += '/'
					for entry in self.entries.itervalues():
						if entry.path.startswith(dir):
							p = entry.path
							self._write_path_to_stdin(proc, p, p, make_exc, 
														fprogress, read_from_stdout=False)
							checked_out_files.append(p)
							path_is_directory = True
						# END if entry is in directory
					# END for each entry
				# END path exception handlnig

				if not path_is_directory:
					self._write_path_to_stdin(proc, path, path, make_exc, 
												fprogress, read_from_stdout=False)
					checked_out_files.append(path)
				# END path is a file
			# END for each path
			self._flush_stdin_and_wait(proc, ignore_stdout=True)

			handle_stderr(proc, checked_out_files)
			return checked_out_files
		# END paths handling
		assert "Should not reach this point"

	@default_index
	def reset(self, commit='HEAD', working_tree=False, paths=None, head=False, **kwargs):
		"""Reset the index to reflect the tree at the given commit. This will not
		adjust our HEAD reference as opposed to HEAD.reset by default.

		:param commit:
			Revision, Reference or Commit specifying the commit we should represent.
			If you want to specify a tree only, use IndexFile.from_tree and overwrite
			the default index.

		:param working_tree:
			If True, the files in the working tree will reflect the changed index.
			If False, the working tree will not be touched
			Please note that changes to the working copy will be discarded without
			warning !

		:param head:
			If True, the head will be set to the given commit. This is False by default,
			but if True, this method behaves like HEAD.reset.

		:param kwargs:
			Additional keyword arguments passed to git-reset

		:return: self """
		# currently we have to use the git command to set the working copy.
		# Otherwise we can use our own one
		if working_tree:
			cur_head = self.repo.head
			prev_commit = cur_head.commit
			
			cur_head.reset(commit, index=True, working_tree=working_tree, paths=paths, **kwargs)
			
			# put the head back, possibly
			if not head:
				self.repo.head.commit = prev_commit
				
			self._delete_entries_cache()
		else:
			# what we actually want to do is to merge the tree into our existing
			# index, which is what git-read-tree does
			new_inst = type(self).from_tree(self.repo, commit)
			self.entries = new_inst.entries
			self.write()
			
			#new_inst = type(self).new(self.repo, self.repo.commit(commit).tree)
			#self.entries = new_inst.entries
			#self.write()
			# self.repo.git.update_index(ignore_missing=True, refresh=True, q=True)
			
			if head:
				self.repo.head.commit = self.repo.commit(commit)
		# END handle working tree

		return self

	@default_index
	def diff(self, other=diff.Diffable.Index, paths=None, create_patch=False, **kwargs):
		"""Diff this index against the working copy or a Tree or Commit object

		For a documentation of the parameters and return values, see
		Diffable.diff

		:note:
			Will only work with indices that represent the default git index as
			they have not been initialized with a stream.
		"""
		# index against index is always empty
		if other is self.Index:
			return diff.DiffIndex()

		# index against anything but None is a reverse diff with the respective
		# item. Handle existing -R flags properly. Transform strings to the object
		# so that we can call diff on it
		if isinstance(other, basestring):
			other = self.repo.rev_parse(other)
		# END object conversion

		if isinstance(other, Object):
			# invert the existing R flag
			cur_val = kwargs.get('R', False)
			kwargs['R'] = not cur_val
			return other.diff(self.Index, paths, create_patch, **kwargs)
		# END diff against other item handlin

		# if other is not None here, something is wrong
		if other is not None:
			raise ValueError( "other must be None, Diffable.Index, a Tree or Commit, was %r" % other )

		# diff against working copy - can be handled by superclass natively
		return super(IndexFile, self).diff(other, paths, create_patch, **kwargs)

