ttree_lex.py
3aea32f946b3lammps-icms

ttree_lex.py
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			# -- coding: iso-8859-1 --

			# Author: Andrew Jewett (jewett.aij at g mail)
			# http://www.chem.ucsb.edu/~sheagroup
			# License: 3-clause BSD License (See LICENSE.TXT)
			# Copyright (c) 2012, Regents of the University of California
			# All rights reserved.

			"""A lexical analyzer class for simple shell-like syntaxes.
			This version has been modified slightly to work better with unicode.
			It was forked from the version of shlex that ships with python 3.2.2.
			A few minor features and functions have been added. """

			# Module and documentation by Eric S. Raymond, 21 Dec 1998
			# Input stacking and error message cleanup added by ESR, March 2000
			# push_source() and pop_source() made explicit by ESR, January 2001.
			# Posix compliance, split(), string arguments, and
			# iterator interface by Gustavo Niemeyer, April 2003.
			# ("wordterminators" (unicode support) hack by Andrew Jewett September 2011)

			import os.path
			import sys
			from collections import deque
			import re, fnmatch
			import string
			#import gc


			try:
			from cStringIO import StringIO
			except ImportError:
			try:
			from StringIO import StringIO
			except ImportError:
			from io import StringIO

			__all__ = ["TtreeShlex",
			"split",
			"LineLex",
			"SplitQuotedString",
			"EscCharStrToChar",
			"SafelyEncodeString",
			"RemoveOuterQuotes",
			"MaxLenStr",
			"HasWildCard",
			#"IsRegex",
			"InputError",
			"ErrorLeader",
			"SrcLoc",
			"OSrcLoc",
			"TextBlock",
			"VarRef",
			"VarNPtr",
			"VarBinding",
			"SplitTemplate",
			"SplitTemplateMulti",
			"TableFromTemplate",
			"ExtractCatName",
			#"_TableFromTemplate",
			#"_DeleteLineFromTemplate",
			"DeleteLinesWithBadVars",
			"TemplateLexer"]




			class TtreeShlex(object):
			""" A lexical analyzer class for simple shell-like syntaxes.
			TtreeShlex is a backwards-compatible version of python's standard shlex
			module. It has the additional member: "self.wordterminators", which
			overrides the "self.wordchars" member. This enables better handling of
			unicode characters by allowing a much larger variety of characters to
			appear in words or tokens parsed by TtreeShlex.

			"""

			custom_path = None

			def __init__(self,
			instream=None,
			infile=None,
			custom_include_path=None,
			posix=False):
			if isinstance(instream, str):
			instream = StringIO(instream)
			if instream is not None:
			self.instream = instream
			self.infile = infile
			else:
			self.instream = sys.stdin
			self.infile = None
			self.posix = posix
			if posix:
			self.eof = None
			else:
			self.eof = ''
			self.commenters = '#'
			self.wordchars = ('abcdfeghijklmnopqrstuvwxyz'
			'ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_')
			if self.posix:
			self.wordchars += ('ßàáâãäåæçèéêëìíîïðñòóôõöøùúûüýþÿ'
			'ÀÁÂÃÄÅÆÇÈÉÊËÌÍÎÏÐÑÒÓÔÕÖØÙÚÛÜÝÞ')

			self.wordterminators = set([]) #WORDTERMINATORS
			self.prev_space_terminator = '' #WORDTERMINATORS
			self.whitespace = ' \t\r\f\n'
			self.whitespace_split = False
			self.quotes = '\'"'
			self.escape = '\\'
			self.escapedquotes = '"'
			self.state = ' '
			self.pushback = deque()
			self.lineno = 1
			self.debug = 0
			self.token = ''
			self.filestack = deque()
			# self.source_triggers
			# are tokens which allow the seamless insertion of other
			# files into the file being read.
			self.source_triggers=set(['source'])
			self.source_triggers_x=set([])
			#Note: self.source_triggers_x
			# This is a subset of self.source_triggers.
			# In this case file inclusion is exclusive.
			# In other words, if one of these tokens
			# is encountered, the file is only included
			# if it has not been included already.
			self.source_files_restricted = set([])
			self.include_path = []
			if TtreeShlex.custom_path:
			include_path_list = TtreeShlex.custom_path.split(':')
			self.include_path += [d for d in include_path_list if len(d)>0]
			if 'TTREE_PATH' in os.environ:
			include_path_list = os.environ['TTREE_PATH'].split(':')
			self.include_path += [d for d in include_path_list if len(d)>0]
			if self.debug:
			print('TtreeShlex: reading from %s, line %d' \
			% (self.instream, self.lineno))
			self.end_encountered = False


			@staticmethod #WORDTERMINATORS
			def _belongs_to(char, include_chars, exclude_chars): #WORDTERMINATORS
			if ((not exclude_chars) or (len(exclude_chars)==0)): #WORDTERMINATORS
			return char in include_chars #WORDTERMINATORS
			else: #WORDTERMINATORS
			return char not in exclude_chars #WORDTERMINATORS

			def push_raw_text(self, text):
			"""Push a block of text onto the stack popped by the ReadLine() method.
			(If multiple lines are present in the text, (which is determined by
			self.line_terminators), then the text is split into multiple lines
			and each one of them is pushed onto this stack individually.
			The "self.lineno" counter is also adjusted, depending on the number
			of newline characters in "line".
			Do not strip off the newline, or other line terminators
			at the end of the text block before using push_raw_text()!

			"""
			if self.debug >= 1:
			print("TtreeShlex: pushing token " + repr(text))
			for c in reversed(text): #WORDTERMINATORS
			self.pushback.appendleft(c) #WORDTERMINATORS
			if c == '\n': #WORDTERMINATORS
			self.lineno -= 1 #WORDTERMINATORS
			if len(text) > 0: #WORDTERMINATORS
			self.end_encountered = False #WORDTERMINATORS

			def push_token(self, text):
			"Push a token onto the stack popped by the get_token method"
			self.push_raw_text(text+self.prev_space_terminator)

			def push_source(self, newstream, newfile=None):
			"Push an input source onto the lexer's input source stack."
			if isinstance(newstream, str):
			newstream = StringIO(newstream)
			self.filestack.appendleft((self.infile, self.instream, self.lineno))
			self.infile = newfile
			self.instream = newstream
			self.lineno = 1
			if self.debug:
			if newfile is not None:
			print('TtreeShlex: pushing to file %s' % (self.infile,))
			else:
			print('TtreeShlex: pushing to stream %s' % (self.instream,))

			def pop_source(self):
			"Pop the input source stack."
			self.instream.close()
			(self.infile, self.instream, self.lineno) = self.filestack.popleft()
			if self.debug:
			print('TtreeShlex: popping to %s, line %d' \
			% (self.instream, self.lineno))
			self.state = ' '

			def get_token(self):
			"Get a token from the input stream (or from stack if it's nonempty)"
			#### #CHANGING: self.pushback is now a stack of characters, not tokens #WORDTERMINATORS
			#### if self.pushback: #WORDTERMINATORS
			#### tok = self.pushback.popleft() #WORDTERMINATORS
			#### if self.debug >= 1: #WORDTERMINATORS
			#### print("TtreeShlex: popping token " + repr(tok)) #WORDTERMINATORS
			#### return tok #WORDTERMINATORS
			#### No pushback. Get a token. #WORDTERMINATORS
			raw = self.read_token()
			# Handle inclusions
			if self.source_triggers is not None:
			while raw in self.source_triggers:
			fname=self.read_token()
			spec = self.sourcehook(fname)
			if spec:
			(newfile, newstream) = spec
			if ((raw not in self.source_triggers_x) or
			(newfile not in self.source_files_restricted)):
			self.push_source(newstream, newfile)
			if raw in self.source_triggers_x:
			self.source_files_restricted.add(newfile)
			else:
			if self.debug >= 0:
			sys.stderr.write('\ndebug warning: duplicate attempt to import file:\n \"'+newfile+'\"\n')
			raw = self.get_token()

			# Maybe we got EOF instead?
			while raw == self.eof:
			if not self.filestack:
			return self.eof
			else:
			self.pop_source()
			raw = self.get_token()
			# Neither inclusion nor EOF
			if self.debug >= 1:
			if raw != self.eof:
			print("TtreeShlex: token=" + repr(raw))
			else:
			print("TtreeShlex: token=EOF")

			if raw == self.eof: #WORDTERMINATORS
			self.end_encountered = True #WORDTERMINATORS

			return raw


			def read_char(self):
			if self.pushback: #WORDTERMINATORS
			nextchar = self.pushback.popleft() #WORDTERMINATORS
			assert((type(nextchar) is str) and (len(nextchar)==1)) #WORDTERMINATORS
			else: #WORDTERMINATORS
			nextchar = self.instream.read(1) #WORDTERMINATORS
			return nextchar


			def read_token(self):
			self.prev_space_terminator = '' #WORDTERMINATORS
			quoted = False
			escapedstate = ' '
			while True:
			#### self.pushback is now a stack of characters, not tokens #WORDTERMINATORS
			nextchar = self.read_char()
			if nextchar == '\n':
			self.lineno = self.lineno + 1
			if self.debug >= 3:
			print("TtreeShlex: in state", repr(self.state), \
			"I see character:", repr(nextchar))
			if self.state is None:
			self.token = '' # past end of file
			break
			elif self.state == ' ':
			if not nextchar:
			self.state = None # end of file
			break
			elif nextchar in self.whitespace:
			if self.debug >= 2:
			print("TtreeShlex: I see whitespace in whitespace state")
			if self.token or (self.posix and quoted):
			# Keep track of which whitespace
			# character terminated the token.
			self.prev_space_terminator = nextchar #WORDTERMINATORS
			break # emit current token
			else:
			continue
			elif nextchar in self.commenters:
			self.instream.readline()
			self.lineno = self.lineno + 1
			elif self.posix and nextchar in self.escape:
			escapedstate = 'a'
			self.state = nextchar
			elif TtreeShlex._belongs_to(nextchar, #WORDTERMINATORS
			self.wordchars, #WORDTERMINATORS
			self.wordterminators):#WORDTERMINATORS
			self.token = nextchar
			self.state = 'a'
			elif nextchar in self.quotes:
			if not self.posix:
			self.token = nextchar
			self.state = nextchar
			elif self.whitespace_split:
			self.token = nextchar
			self.state = 'a'
			else:
			self.token = nextchar
			if self.token or (self.posix and quoted):
			break # emit current token
			else:
			continue
			elif self.state in self.quotes:
			quoted = True
			if not nextchar: # end of file
			if self.debug >= 2:
			print("TtreeShlex: I see EOF in quotes state")
			# XXX what error should be raised here?
			raise ValueError("Error at or before "+self.error_leader()+"\n"
			" No closing quotation.")
			if nextchar == self.state:
			if not self.posix:
			self.token = self.token + nextchar
			self.state = ' '
			break
			else:
			self.state = 'a'
			elif self.posix and nextchar in self.escape and \
			self.state in self.escapedquotes:
			escapedstate = self.state
			self.state = nextchar
			else:
			self.token = self.token + nextchar
			elif self.state in self.escape:
			if not nextchar: # end of file
			if self.debug >= 2:
			print("TtreeShlex: I see EOF in escape state")
			# XXX what error should be raised here?
			raise ValueError("No escaped character")
			# In posix shells, only the quote itself or the escape
			# character may be escaped within quotes.
			if escapedstate in self.quotes and \
			nextchar != self.state and nextchar != escapedstate:
			self.token = self.token + self.state
			self.token = self.token + nextchar
			self.state = escapedstate
			elif self.state == 'a':
			if not nextchar:
			self.state = None # end of file
			break
			elif nextchar in self.whitespace:
			if self.debug >= 2:
			print("TtreeShlex: I see whitespace in word state")
			self.state = ' '
			if self.token or (self.posix and quoted):
			# Keep track of which whitespace
			# character terminated the token.
			self.prev_space_terminator = nextchar #WORDTERMINATORS
			break # emit current token
			else:
			continue
			elif nextchar in self.commenters:
			comment_contents = self.instream.readline()
			self.lineno = self.lineno + 1
			if self.posix:
			self.state = ' '
			if self.token or (self.posix and quoted):
			# Keep track of which character(s) terminated
			# the token (including whitespace and comments).
			self.prev_space_terminator = nextchar + comment_contents #WORDTERMINATORS
			break # emit current token
			else:
			continue
			elif self.posix and nextchar in self.quotes:
			self.state = nextchar
			elif self.posix and nextchar in self.escape:
			escapedstate = 'a'
			self.state = nextchar
			elif (TtreeShlex._belongs_to(nextchar, #WORDTERMINATORS
			self.wordchars, #WORDTERMINATORS
			self.wordterminators)#WORDTERMINATORS
			or (nextchar in self.quotes) #WORDTERMINATORS
			or (self.whitespace_split)): #WORDTERMINATORS
			self.token = self.token + nextchar
			else:
			self.pushback.appendleft(nextchar)
			if self.debug >= 2:
			print("TtreeShlex: I see punctuation in word state")
			self.state = ' '
			if self.token:
			break # emit current token
			else:
			continue
			result = self.token
			self.token = ''
			if self.posix and not quoted and result == '':
			result = None
			if self.debug > 1:
			if result:
			print("TtreeShlex: raw token=" + repr(result))
			else:
			print("TtreeShlex: raw token=EOF")
			return result

			def sourcehook(self, newfile):
			"Hook called on a filename to be sourced."
			newfile = RemoveOuterQuotes(newfile)
			# This implements cpp-like semantics for relative-path inclusion.
			if isinstance(self.infile, str) and not os.path.isabs(newfile):
			newfile_full = os.path.join(os.path.dirname(self.infile), newfile)
			try:
			f = open(newfile_full, "r")
			except IOError:
			# If not found,
			err = True
			# ...then check to see if the file is in one of the
			# directories in the self.include_path list.
			for d in self.include_path:
			newfile_full = os.path.join(d, newfile)
			try:
			f = open(newfile_full, "r")
			err = False
			break
			except IOError:
			err=True
			if err:
			raise InputError('Error at '+self.error_leader()+'\n'
			' unable to open file \"'+newfile+'\"\n'
			' for reading.\n')
			return (newfile, f)

			def error_leader(self, infile=None, lineno=None):
			"Emit a C-compiler-like, Emacs-friendly error-message leader."
			if infile is None:
			infile = self.infile
			if lineno is None:
			lineno = self.lineno
			return "\"%s\", line %d: " % (infile, lineno)

			def __iter__(self):
			return self

			def __next__(self):
			token = self.get_token()
			if token == self.eof:
			raise StopIteration
			return token

			def __bool__(self):
			return not self.end_encountered

			# For compatibility with python 2.x, I must also define:
			def __nonzero__(self):
			return self.__bool__()


			# The split() function was originally from shlex
			# It is included for backwards compatibility.
			def split(s, comments=False, posix=True):
			lex = TtreeShlex(s, posix=posix)
			lex.whitespace_split = True
			if not comments:
			lex.commenters = ''
			return list(lex)



			##################### NEW ADDITIONS (may be removed later) #################

			#"""
			# -- linelex.py --
			#linelex.py defines the LineLex class, which inherits from, and further
			#augments the capabilities of TtreeShlex by making it easier to parse
			#individual lines one at a time. (The original shlex's "source" inclusion
			#ability still works when reading entire lines, and lines are still counted.)
			#
			#"""

			#import sys


			class InputError(Exception):
			""" A generic exception object containing a string for error reporting.
			(Raising this exception implies that the caller has provided
			a faulty input file or argument.)

			"""

			def __init__(self, err_msg):
			self.err_msg = err_msg
			def __str__(self):
			return self.err_msg
			def __repr__(self):
			return str(self)


			def ErrorLeader(infile, lineno):
			return '\"'+infile+'\", line '+str(lineno)


			class SrcLoc(object):
			""" SrcLoc is essentially nothing more than a 2-tuple containing the name
			of a file (str) and a particular line number inside that file (an integer).

			"""
			def __init__(self, infile='', lineno=-1):
			self.infile = infile
			self.lineno = lineno




			def SplitQuotedString(string,
			quotes='\'\"',
			delimiters=' \t\r\f\n',
			escape='\\',
			comment_char='#'):
			tokens = []
			token = ''
			reading_token = True
			escaped_state = False
			quote_state = None
			for c in string:

			if (c in comment_char) and (not escaped_state) and (quote_state==None):
			tokens.append(token)
			return tokens

			elif (c in delimiters) and (not escaped_state) and (quote_state==None):
			if reading_token:
			tokens.append(token)
			token = ''
			reading_token = False

			elif c in escape:
			if escaped_state:
			token += c
			reading_token = True
			escaped_state = False
			else:
			escaped_state = True
			# and leave c (the '\' character) out of token
			elif (c in quotes) and (not escaped_state):
			if (quote_state != None):
			if (c == quote_state):
			quote_state = None
			else:
			quote_state = c
			token += c
			reading_token = True
			else:
			if (c == 'n') and (escaped_state == True):
			c = '\n'
			elif (c == 't') and (escaped_state == True):
			c = '\t'
			elif (c == 'r') and (escaped_state == True):
			c = '\r'
			elif (c == 'f') and (escaped_state == True):
			c = '\f'
			token += c
			reading_token = True
			escaped_state = False

			if len(string) > 0:
			tokens.append(token)
			return tokens


			def EscCharStrToChar(s_in, escape='\\'):
			"""
			EscCharStrToChar() replaces any escape sequences
			in a string with their 1-character equivalents.

			"""
			assert(len(escape) > 0)
			out_lstr = []
			escaped_state = False
			for c in s_in:
			if escaped_state:
			if (c == 'n'):
			out_lstr.append('\n')
			elif (c == 't'):
			out_lstr.append('\t')
			elif (c == 'r'):
			out_lstr.append('\r')
			elif (c == 'f'):
			out_lstr.append('\f')
			elif (c == '\''):
			out_lstr.append('\'')
			elif (c == '\"'):
			out_lstr.append('\"')
			elif c in escape:
			out_lstr.append(c)
			else:
			out_lstr.append(escape+c) # <- keep both characters
			escaped_state = False
			else:
			if c in escape:
			escaped_state = True
			else:
			out_lstr.append(c)

			return ''.join(out_lstr)



			def SafelyEncodeString(in_str,
			quotes='\'\"',
			delimiters=' \t\r\f\n',
			escape='\\',
			comment_char='#'):
			"""
			SafelyEncodeString(in_str) scans through the input string (in_str),
			and returns a new string in which probletic characters
			(like newlines, tabs, quotes, etc), are replaced by their two-character
			backslashed equivalents (like '\n', '\t', '\'', '\"', etc).
			The escape character is the backslash by default, but it too can be
			overridden to create custom escape sequences
			(but this does not effect the encoding for characters like '\n', '\t').

			"""
			assert(len(escape) > 0)
			out_lstr = []
			use_outer_quotes = False
			for c in in_str:
			if (c == '\n'):
			c = '\\n'
			elif (c == '\t'):
			c = '\\t'
			elif (c == '\r'):
			c = '\\r'
			elif (c == '\f'):
			c = '\\f'
			elif c in quotes:
			c = escape[0]+c
			elif c in escape:
			c = c+c
			elif c in delimiters:
			use_outer_quotes = True
			# hmm... that's all that comes to mind. Did I leave anything out?
			out_lstr.append(c)

			if use_outer_quotes:
			out_lstr = ['\"'] + out_lstr + ['\"']

			return ''.join(out_lstr)


			def RemoveOuterQuotes(text, quotes='\"\''):
			if ((len(text)>=2) and (text[0] in quotes) and (text[-1]==text[0])):
			return text[1:-1]
			else:
			return text



			def MaxLenStr(s1, s2):
			if len(s2) > len(s1):
			return s2
			else:
			return s1


			#def IsRegex(pat):
			# """
			# Check to see if string (pat) is bracketed by slashes.
			#
			# """
			# return (len(pat)>=2) and (pat[0]=='/') and (pat[-1] == '/')

			def HasWildCard(pat):
			"""
			Returns true if a string (pat) contains a '*' or '?' character.

			"""
			return (pat.find('*') != -1) or (pat.find('?') != -1)


			#def HasWildCard(pat):
			# """
			# Returns true if a string (pat) contains a non-backslash-protected
			# * or ? character.
			#
			# """
			# N=len(pat)
			# i=0
			# while i < N:
			# i = pat.find('*', i, N)
			# if i == -1:
			# break
			# elif (i==0) or (pat[i-1] != '\\'):
			# return True
			# i += 1
			# i=0
			# while i < N:
			# i = pat.find('?', i, N)
			# if i == -1:
			# break
			# elif (i==0) or (pat[i-1] != '\\'):
			# return True
			# i += 1
			# return False


			def MatchesPattern(s, pattern):
			if type(pattern) is str:
			#old code:
			#if ((len(s) > 1) and (s[0] == '/') and (s[-1] == '/'):
			# re_string = p[1:-1] # strip off the slashes '/' and '/'
			# if not re.search(re_string, s):
			# return False
			#new code:
			# uses precompiled regular expressions (See "pattern.search" below)
			if HasWildCard(pattern):
			if not fnmatch.fnmatchcase(s, pattern):
			return False
			elif s != pattern:
			return False
			else:
			#assert(type(p) is _sre.SRE_Match)
			# I assume pattern = re.compile(some_reg_expr)
			if not pattern.search(s):
			return False
			return True


			def MatchesAll(multi_string, pattern):
			assert(len(multi_string) == len(pattern))
			for i in range(0, len(pattern)):
			if not MatchesPattern(multi_string[i], pattern[i]):
			return False
			return True



			class LineLex(TtreeShlex):
			""" This class extends the TtreeShlex module (a slightly modified
			version of the python 3.2.2 version of shlex). LineLex has the
			ability to read one line at a time (in addition to one token at a time).
			(Many files and scripts must be parsed one line at a time instead of one
			token at a time. In these cases, the whitespace position also matters.)

			Arguably, this class might not be necessary.
			I could get rid of this class completely. That would be nice. To do that
			we would need to augment and generalize shlex's get_token() member function
			to make it read lines, not just tokens. Of course, you can always
			change the wordchars (or wordterminators). Even so, there are two other
			difficulties using the current version of shlex.get_token() to read lines:
			1) File inclusion happen whenever the beginning of a line/token matches one
			of the "source_triggers" (not the whole line as required by get_token()).
			2) Lines ending in a special character (by default the backslash character)
			continue on to the next line.
			This code seems to work on our test files, but I'm sure there are bugs.
			Andrew 2012-3-25

			"""
			def __init__(self,
			instream=None,
			infile=None,
			posix=False):
			TtreeShlex.__init__(self, instream, infile, posix)
			self.line_terminators = '\n'
			self.line_extend_chars = '\\'
			self.skip_comments_during_readline = True


			def _StripComments(self, line):
			if self.skip_comments_during_readline:
			for i in range(0, len(line)):
			if ((line[i] in self.commenters) and
			((i==0) or (line[i-1] not in self.escape))):
			return line[:i]
			return line



			def _ReadLine(self,
			recur_level=0):
			"""
			This function retrieves a block of text, halting at a
			terminal character. Escape sequences are respected.
			The self.lineno (newline counter) is also maintained.

			The main difference between Readline and get_token()
			is the way they handle the "self.source_triggers" member.
			Both Readline() and get_token() insert text from other files when they
			encounter a string in "self.source_triggers" in the text they read.
			However ReadLine() ONLY inserts text from other files if the token which
			matches with self.source_triggers appears at the beginning of the line.
			get_token() inserts text only if lex.source matches the entire token.

			comment-to-self:
			At some point, once I'm sure this code is working, I should replace
			shlex.get_token() with the code from ReadLine() which is more general.
			It would be nice to get rid of "class LineLex" entirely. ReadLine()
			is the only new feature that LineLex which was lacking in shlex.

			To do this I would need to add a couple optional arguments to
			"get_token()", allowing it to mimic ReadLine(), such as:
			"override_wordterms" argument (which we can pass a '\n'), and
			"token_extender" argument (like '\' for extending lines)

			"""
			first_token=''
			line = ''
			escaped_state = False
			found_space = False
			while True:
			nextchar = self.read_char()
			#sys.stderr.write('nextchar=\"'+nextchar+'\"\n')
			while nextchar == '':
			if not self.filestack:
			return self._StripComments(line), '', first_token, found_space
			else:
			self.pop_source()
			nextchar = self.read_char()
			if nextchar == '\n':
			self.lineno += 1

			if escaped_state:
			escaped_state = False
			else:
			if nextchar in self.escape:
			line += nextchar
			escaped_state = True
			else:
			escaped_state = False

			if not escaped_state:
			if (nextchar in self.whitespace):
			found_space = True
			while first_token in self.source_triggers:
			fname = RemoveOuterQuotes(self.get_token())
			if (fname == '') or (fname in self.source_triggers):
			raise InputError('Error: near '+self.error_leader()+'\n'
			' Nonsensical file inclusion request.\n')
			if self.debug >= 0:
			sys.stderr.write( (' ' * recur_level) +
			'reading file \"'+fname+'\"\n')
			spec = self.sourcehook(fname)
			if spec:
			(fname, subfile) = spec
			if ((first_token not in self.source_triggers_x) or
			(fname not in self.source_files_restricted)):
			self.push_source(subfile, fname)
			if first_token in self.source_triggers_x:
			self.source_files_restricted.add(fname)
			else:
			if self.debug >= 0:
			sys.stderr.write('\nWarning at '+self.error_leader()+':\n'
			' duplicate attempt to import file:\n \"'+fname+'\"\n')

			line, nextchar, first_token, found_space = \
			self._ReadLine(recur_level+1)


			if nextchar in self.line_terminators:
			line_nrw = line.rstrip(self.whitespace)
			#sys.stderr.write('line_nrw=\"'+line_nrw+'\"\n')
			if ((len(line_nrw) > 0) and
			(line_nrw[-1] in self.line_extend_chars) and
			((len(line_nrw) < 2) or (line_nrw[-2] not in self.escape))):
			line = line_nrw[:-1] #delete the line_extend character
			# from the end of that line and keep reading...
			else:
			return self._StripComments(line), nextchar, first_token, found_space
			else:
			line += nextchar
			if not found_space:
			first_token += nextchar



			def ReadLine(self, recur_level=0):
			line, nextchar, first_token, found_space = \
			self._ReadLine(recur_level)
			if nextchar == self.eof:
			self.end_encountered = True
			return line + nextchar


			@staticmethod
			def TextBlock2Lines(text, delimiters, keep_delim=True):
			""" This splits a string into a list of sub-strings split by delimiter
			characters. This function is different from the standard str.split()
			function: The string is split at every character which belongs to the
			"delimiters" argument (which can be a string or some other container).
			This character is included at the end of every substring. Example:
			TextBlock2Lines('\nabc\nde^fg\nhi j\n', '^\n')
			returns:
			['\n', 'abc\n', 'de^', 'fg\n', 'hi j\n']

			"""
			ls = []
			i = 0
			i_prev = 0
			while i < len(text):
			if text[i] in delimiters:
			if keep_delim:
			ls.append(text[i_prev:i+1])
			else:
			ls.append(text[i_prev:i])
			i_prev = i+1
			i += 1
			if (i_prev < len(text)):
			ls.append(text[i_prev:i+1])
			return ls

			def __iter__(self):
			return self

			def __next__(self):
			line = self.ReadLine()
			if line == self.eof:
			raise StopIteration
			return line


			class OSrcLoc(object):
			""" OSrcLoc is barely more than a 2-tuple containing the name of a file
			(a string) and a particular line number inside that file (an integer).
			These objects are passed around and stored in the nodes of
			every tree, so that if a syntax error or broken link in that node
			is discovered, an error message can be provided to the user.

			"order"
			Later on, during development, the "order" member was added. Why:
			If you want to know whether block of text comes before or after a
			different block of text, unfortunately you can not just compare the
			corresponding line numbers of the files they come from because the
			files may differ, and multiple short blocks of text may occupy the
			same line. Consequently, "OSrcLoc" also maintains an internal
			counter which keeps track of how many OSrcLoc() objects have been
			created so far. (This can be useful if the user requests that
			variables and commands be assigned in a non-standard order.)
			The "order" member is assigned to this counter.
			Most of the time, the "order" member can be ignored.

			"""

			count = 0

			def __init__(self, infile='', lineno=-1):
			self.infile = infile
			self.lineno = lineno
			OSrcLoc.count += 1
			self.order = OSrcLoc.count

			def __lt__(self, x):
			return self.order < x.order

			#def __repr__(self):
			# return repr((self.infile, self.lineno, self.order))



			class TextBlock(object):
			"""TextBlock is just a 3-tuple consisting of a string, and an OSrcLoc
			to help locate it in the original file from which it was read."""
			def __init__(self, text, srcloc): #srcloc_end):
			self.text = text
			if srcloc == None:
			self.srcloc = OSrcLoc()
			else:
			self.srcloc = srcloc
			#if srcloc_end == None:
			# self.srcloc_end = OSrcLoc()
			#else:
			# self.srcloc_end = srcloc_end

			def __repr__(self):
			return '\"'+self.text+'\"'



			class VarRef(object):
			"""VarRef stores variable names, and paths, and other attribute information,
			as well as a "OSrcLoc" to keep track of the file it was defined in."""
			def __init__(self,
			prefix = '', # '$' or '${'
			descr_str = '', # <- descriptor string: "cpath/category:lpath"
			suffix = '', # '}'
			srcloc = None,# location in file where defined
			binding = None,# a pointer to a tuple storing the value
			nptr = None):# <- see class VarNPtr

			self.prefix = prefix #Any text before the descriptor string goes here
			self.suffix = suffix #Any text after the descriptor string goes here
			self.descr_str = descr_str
			if srcloc == None: # <- Location in text file where variable appears
			self.srcloc = OSrcLoc()
			else:
			self.srcloc = srcloc

			self.binding = binding

			if nptr == None:
			self.nptr = VarNPtr()
			else:
			self.nptr = nptr

			def __lt__(self, x):
			return self.order < x.order

			#def __repr__(self):
			# return repr((self.prefix + self.descr_str + self.suffix, srcloc))


			class VarNPtr(object):
			"""
			Every time a variable appears in a template, it has has a "descritpor".
			For example, consider the variable
			"$atom:CA"
			This is a string which encodes 3 pieces of information.
			1) the category name: This is essentialy indicates the variable's type.
			(ie "atom", in the example above)
			2) the category node: Some TYPES have limited scope. Users can
			specify the root node of the portion of the tree
			in which this variable's type makes sense.
			If this node is the root node, then that category
			is relevant everywhere, and is not molecule or class
			specific. All variables have a category node, which
			is often not explicitly defined to by the user.
			It must be inferred/determined.)
			(Category node = the root "/", in the example above.)
			3) the leaf node: This is a node whose ".name" member matches the name
			of a variable. This node is created for this purpose
			and it's position in the tree is a reflection of
			that variable's intended scope.
			In a molecule this "name" might be the name
			of a type of atom, or an atom ID, or a bond type,
			which is found in a particular molecule.
			(Leaf node would be named "CA" in the example above.)

			The VarNPtr class is simply a 3-tuple which
			keeps these 3 pieces of data together.

			"""
			def __init__(self, cat_name='', cat_node=None, leaf_node=None):
			self.cat_name = cat_name
			self.cat_node = cat_node
			self.leaf_node = leaf_node

			#def __repr__(self):
			# return repr((self.cat_name, self.cat_node.name, self.leaf_node.name))


			class VarBinding(object):
			""" VarBinding is essentially a tuple consistng of (full_name, binding, refs):

			"self.full_name" is canonical name for this variable. This is a string
			which specifies full path leading to the category node (beginning with '/'),
			the category name (followed by a ':'),
			as well as the leaf node (including the path leading up to it from cat_node)
			This triplet identifies the variable uniquely.

			"self.value" is the data that the variable refers to (usually a string).

			"self.refs" stores a list of VarRefs which mention the same variable
			from the various places inside various templates in the tree.

			"""
			def __init__(self,
			full_name = '',
			nptr = None,
			value = None,
			refs = None,
			order = None,
			category = None):
			self.full_name = full_name
			self.nptr = nptr
			self.value = value
			self.refs = refs
			self.order = order
			self.category = category

			def __lt__(self, x):
			return self.order < x.order

			def __repr__(self):
			return repr((self.full_name, self.value, self.order))


			def ExtractCatName(descr_str):
			""" When applied to a VarRef's "descr_str" member,
			this function will extract the "catname" of it's corresponding
			"nptr" member. This can be useful for error reporting.
			(I use it to insure that the user is using the correct counter
			variable types at various locations in their input files.)

			"""

			ib = descr_str.find(':')
			if ib == -1:
			ib = len(descr_str)
			ia = descr_str.rfind('/')
			if ia == -1:
			ia = 0
			return descr_str[ia:ib]
			else:
			str_before_colon = descr_str[0:ib]
			ia = str_before_colon.rfind('/')
			if ia == -1:
			return str_before_colon
			else:
			return str_before_colon[ia+1:]



			def _DeleteLineFromTemplate(tmpl_list,
			i_entry, # index into tmpl_list
			newline_delimiter='\n'):
			""" Delete a single line from tmpl_list.
			tmpl_list is an alternating list of VarRefs and TextBlocks.
			To identify the line, the index corresponding to one of the
			entries in the tmpl_list is used. (Usually it is a VarRef)
			The text after the preceeding newline, and the text up to the next newline
			(starting from the beginning of the current entry, if a TextBlock)
			is deleted, including any VarRef (variables) located in between.

			It returns the index corresponding to the next
			entry in the list (after deletion).

			"""

			i_prev_newline = i_entry
			while i_prev_newline >= 0:
			entry = tmpl_list[i_prev_newline]
			if isinstance(entry, TextBlock):
			i_char_newline = entry.text.rfind(newline_delimiter)
			if i_char_newline != -1: # then newline found
			# Delete the text after this newline
			entry.text = entry.text[:i_char_newline+1]
			break
			i_prev_newline -= 1

			first_var = True
			#i_next_newline = i_entry
			i_next_newline = i_prev_newline+1
			while i_next_newline < len(tmpl_list):
			entry = tmpl_list[i_next_newline]
			if isinstance(entry, TextBlock):
			i_char_newline = entry.text.find(newline_delimiter)
			if i_char_newline != -1: # then newline found
			# Delete the text before this newline (including the newline)
			entry.text = entry.text[i_char_newline+1:]
			break
			# Invoke DeleteSelf() on the first variables on this line. This will
			# insure that it is deleted from the ttree_assignments.txt file.
			elif isinstance(entry, VarRef):
			if first_var:
			entry.nptr.leaf_node.DeleteSelf()
			first_var = False
			i_next_newline += 1

			del tmpl_list[i_prev_newline + 1 : i_next_newline]
			return i_prev_newline + 1



			def DeleteLinesWithBadVars(tmpl_list,
			delete_entire_template = False,
			newline_delimiter = '\n'):
			"""
			Loop through the entries in a template,
			an alternating list of TextBlocks and VarRefs (tmpl_list).
			If a VarRef points to a leaf_node which no longer exists
			(ie. no longer in the corresponding category's .bindings list).
			Then delete the line it came from from the template (tmpl_list).

			"""

			out_str_list = []
			i = 0
			while i < len(tmpl_list):
			entry = tmpl_list[i]
			if isinstance(entry, VarRef):
			var_ref = entry
			var_bindings = var_ref.nptr.cat_node.categories[var_ref.nptr.cat_name].bindings
			#if var_ref.nptr.leaf_node not in var_bindings:
			if var_ref.nptr.leaf_node.IsDeleted():
			if delete_entire_template:
			del tmpl_list[:]
			return 0
			else:
			i = _DeleteLineFromTemplate(tmpl_list,
			i,
			newline_delimiter)
			else:
			i += 1
			else:
			i += 1







			def SplitTemplate(ltmpl, delim, delete_blanks = False):
			"""
			Split a template "ltmpl" into a list of "tokens" (sub-templates)
			using a single delimiter string "delim".

			INPUT arguments:
			"ltmpl" should be an list of TextBlocks and VarRefs.
			"delim" should be a simple string (type str)
			"delete_blanks" should be a boolean True/False value.
			When true, successive occurrences of the delimiter
			should not create blank entries in the output list.

			OUTPUT:
			A list of tokens.
			Each "token" is either a TextBlock, a VarRef,
			or a (flat, 1-dimensional) list containing more than one of these objects.
			The number of "tokens" returned equals the number of times the delimiter
			is encountered in any of the TextBlocks in the "ltmpl" argument, plus one.
			(... Unless "delete_blanks" is set to True.
			Again, in that case, empty entries in this list are deleted.)

			"""
			assert(type(delim) is str)
			if not hasattr(ltmpl, '__len__'):
			ltmpl = [ltmpl]

			tokens_lltmpl = []
			token_ltmpl = []
			i = 0
			while i < len(ltmpl):
			entry = ltmpl[i]
			if isinstance(entry, TextBlock):
			#if hasattr(entry, 'text'):
			prev_src_loc = entry.srcloc

			tokens_str = entry.text.split(delim)

			lineno = entry.srcloc.lineno

			j = 0
			while j < len(tokens_str):
			token_str = tokens_str[j]

			delim_found = False
			if (j < len(tokens_str)-1):
			delim_found = True

			if token_str == '':
			if delete_blanks:
			if delim == '\n':
			lineno += 1
			if len(token_ltmpl) > 0:
			if len(token_ltmpl) == 1:
			tokens_lltmpl.append(token_ltmpl[0])
			else:
			tokens_lltmpl.append(token_ltmpl)
			del token_ltmpl
			token_ltmpl = []
			j += 1
			continue

			new_src_loc = OSrcLoc(prev_src_loc.infile, lineno)
			new_src_loc.order = prev_src_loc.order

			for c in token_str:
			# Reminder to self: c != delim (so c!='\n' if delim='\n')
			# (We keep track of '\n' characters in delimiters above.)
			if c == '\n':
			lineno +=1

			new_src_loc.lineno = lineno

			text_block = TextBlock(token_str,
			new_src_loc)

			prev_src_loc = new_src_loc

			if len(token_ltmpl) == 0:
			if delim_found:
			tokens_lltmpl.append(text_block)
			del token_ltmpl
			token_ltmpl = []
			else:
			token_ltmpl.append(text_block)
			else:
			if delim_found:
			if len(token_str) > 0:
			token_ltmpl.append(text_block)
			tokens_lltmpl.append(token_ltmpl)
			del token_ltmpl
			token_ltmpl = []
			else:
			assert(not delete_blanks)
			if (isinstance(token_ltmpl[-1], VarRef)
			and
			((j>0)
			or
			((j == len(tokens_str)-1) and
			(i == len(ltmpl)-1))
			)):
			# In that case, this empty token_str corresponds
			# to a delimiter which was located immediately
			# after the variable name,
			# AND
			# -there is more text to follow,
			# OR
			# -we are at the end of the template.
			token_ltmpl.append(text_block)
			if len(token_ltmpl) == 1:
			tokens_lltmpl.append(token_ltmpl[0])
			else:
			tokens_lltmpl.append(token_ltmpl)
			del token_ltmpl
			token_ltmpl = []
			else:
			token_ltmpl.append(text_block)

			if (delim_found and (delim == '\n')):
			lineno += 1

			j += 1

			elif isinstance(entry, VarRef):
			#elif hasattr(entry, 'descr_str'):
			lineno = entry.srcloc.lineno
			if ((len(token_ltmpl) == 1) and
			isinstance(token_ltmpl[0], TextBlock) and
			(len(token_ltmpl[0].text) == 0)):
			# special case: if the previous entry was "", then it means
			# the delimeter appeared at the end of the previous text block
			# leading up to this variable. It separates the variable from
			# the previous text block. It is not a text block of length 0.
			token_ltmpl[0] = entry
			else:
			token_ltmpl.append(entry)
			elif entry == None:
			token_ltmpl.append(entry)
			else:
			assert(False)

			i += 1

			# Append left over remains of the last token
			if len(token_ltmpl) == 1:
			tokens_lltmpl.append(token_ltmpl[0])
			elif len(token_ltmpl) > 1:
			tokens_lltmpl.append(token_ltmpl)
			del token_ltmpl

			return tokens_lltmpl






			def SplitTemplateMulti(ltmpl, delims, delete_blanks=False):
			"""
			Split a template "ltmpl" into a list of templates using a
			single one or more delimiter strings "delim_list".
			If multiple delimiter strings are provided, splitting
			begins using the first delimiter string in the list.
			Then each token in the resulting list of templates
			is split using the next delimiter string
			and so on until we run out of delimiter strings.

			"ltmpl" should be an list of TextBlocks and VarRefs.
			"delims" should be a simple string (type str) or a list of strings
			"delete_blanks" is either True or False
			If True, then any blank entries in the resulting list of
			tokens (sub-templates) will be deleted.

			"""

			if hasattr(delims, '__len__'): # then it hopefully is a list of strings
			delim_list = delims
			else:
			delim_list = [delims] # then it hopefully is a string

			tokens = [ltmpl]
			for delim in delim_list:
			assert(type(delim) is str)
			tokens_il = []
			for t in tokens:
			sub_tokens = SplitTemplate(t, delim, delete_blanks)
			for st in sub_tokens:
			if hasattr(st, '__len__'):
			if (len(st) > 0) or (not delete_blanks):
			tokens_il.append(st)
			else:
			tokens_il.append(st)
			tokens = tokens_il
			del tokens_il

			return tokens



			def _TableFromTemplate(d, ltmpl, delimiters, delete_blanks):
			"""
			See the docstring for the TableFromTemplate() function for an explanation.
			(This _TableFromTemplate() and SplitTemplate() are the workhorse functions
			for TableFromTemplate().)

			"""

			output = SplitTemplateMulti(ltmpl, delimiters[d], delete_blanks[d])

			if d > 0:
			i = 0
			while i < len(output):
			output[i] = _TableFromTemplate(d-1,
			output[i],
			delimiters,
			delete_blanks)
			# Delete empty LISTS?
			if (delete_blanks[d] and
			hasattr(output[i], '__len__') and
			(len(output[i]) == 0)):
			del output[i]
			else:
			i += 1

			return output


			def TableFromTemplate(ltmpl, delimiters, delete_blanks=True):
			"""
			This function can be used to split a template
			(a list containing TextBlocks and VarRefs) into a table
			into a multidimensional table, with an arbitrary number of dimensions.

			Arguments:

			ltmpl

			An alternating list of TextBlocks and VarRefs containing
			the contents of this text template.

			delimiters

			The user must supply a list or tuple of delimiters: one delimiter for
			each dimension in the table, with low-priority delimiters
			(such as spaces ' ') appearing first, and higher-priority delimiters
			(sich as newlines '\n') appearing later on in the list.
			This function will divide the entire "ltmpl" into an n-dimensional
			table. Initially the text is split into a list of text using the
			highest-priority delimiter. Then each entry in the resulting list is
			split into another list according to the next highest-priority delimiter.
			This continues until all of the delimiters are used up and an
			n-dimensional list-of-lists is remaining.

			delete_blanks

			The optional "delete_blanks" argument can be used to indicate whether
			or not to delete blank entries in the table (which occur as a result
			of placing two delimiters next to each other). It should be either
			None (default), or it should be an array of booleans matching the
			size of the "delimiters" argument. This allows the caller to customize
			the merge settings separately for each dimension (for example: to allow
			merging of whitespace within a line, without ignoring blank lines).


			---- Details: ----

			1) Multi-character delimiters ARE allowed (like '\n\n').

			2) If a delimiter in the "delimiters" argument is not a string
			but is a tuple (or a list) of strings, then the text is split according
			to any of the delimiters in that tuple/list (starting from the last entry).
			This way, users can use this feature to split text according to multiple
			different kinds of whitespace characters (such as ' ' and '\t'), for
			example, buy setting delimiters[0] = (' ','\t'). If, additionally,
			delete_blanks[0] == True, then this will cause this function to
			divide text in without regard to whitespace on a given line (for example).

			Detailed example:

			table2D = TableFromTmplList(ltmpl,
			delimiters = ((' ','\t'), '\n'),
			delete_blanks = (True, False))

			This divides text in a similar way that the "awk" program does by default,
			ie, by ignoring various kinds of whitespace between text fields, but NOT
			ignoring blank lines.

			3) Any text contained in variable-names is ignored.

			"""

			# Make a copy of ltmpl
			# (The workhorse function "_TableFromTemplate()" makes in-place changes to
			# its "ltmpl" argument. I don't want to modify "ltmpl", so I make a copy
			# of it before I invoke "_TableFromTemplate()" on it.)

			output = [ltmpl[i] for i in range(0, len(ltmpl))]

			d = len(delimiters) - 1
			output = _TableFromTemplate(d, output, delimiters, delete_blanks)
			return output










			class TemplateLexer(TtreeShlex):
			""" This class extends the standard python lexing module, shlex, adding a
			new member function (ReadTemplate()), which can read in a block of raw text,
			(halting at an (non-escaped) terminal character), and split the text into
			alternating blocks of text and variables. (As far as this lexer is
			concerned, "variables" are simply tokens preceeded by $ or @ characters,
			and surrounded by optional curly-brackets {}.)

			"""
			def __init__(self,
			instream=None,
			infile=None,
			posix=False):
			TtreeShlex.__init__(self, instream, infile, posix)
			self.var_delim = '$@' #characters which can begin a variable name
			self.var_open_paren = '{' #optional parenthesis surround a variable
			self.var_close_paren = '}' #optional parenthesis surround a variable
			self.newline = '\n'
			self.comment_skip_var = '#'

			# Which characters belong in words?
			#
			# We want to allow these characters:
			# ./$@&%^!*~`-_:;?<>[]()
			# to appear inside the tokens that TtreeShlex.get_token()
			# retrieves (TtreeShlex.get_token() is used to read class
			# names, and instance names, and variable names)
			#
			# settings.lex.wordchars+='./$@&%^!*~`-_+:;?<>[]' #Allow these chars
			#
			# Ommisions:
			# Note: I left out quotes, whitespace, comment chars ('#'), and escape
			# characters ('\\') because they are also dealt with separately.
			# Those characters should not overlap with settings.lex.wordchars.
			#
			# Enabling unicode support requires that we override this choice
			# by specifying "lex.wordterminators" instead of "wordchars".
			#
			# lex.wordterminators should be the (printable) set inverse of lex.wordchars
			# I'm not sure which ascii characters are NOT included in the string above
			# (We need to figure that out, and put them in settings.lex.wordterminators)
			# To figure that out, uncomment the 8 lines below:
			#
			#self.wordterminators=''
			#for i in range(0,256):
			# c = chr(i)
			# if c not in self.wordchars:
			# self.wordterminators += c
			#sys.stderr.write('-------- wordterminators = --------\n')
			#sys.stderr.write(self.wordterminators+'\n')
			#sys.stderr.write('-----------------------------------\n')
			#
			# Here is the result:
			self.wordterminators = '(),={\|}' + \
			self.whitespace + \
			self.quotes + \
			self.escape + \
			self.commenters
			# Note:
			# self.whitespace = ' \t\r\f\n'
			# self.quotes = '\'"'
			# self.escape = '\\'
			# self.commenters = '#'

			self.source_triggers=set(['include','import'])
			self.source_triggers_x=set(['import'])




			def GetSrcLoc(self):
			return OSrcLoc(self.infile, self.lineno)


			def ReadTemplate(self,
			simplify_output=False,
			terminators='}',
			other_esc_chars='{',
			keep_terminal_char = True):
			"""
			ReadTemplate() reads a block of text (between terminators)
			and divides it into variables (tokens following a '$' or '@' character)
			and raw text. This is similar to pythons string.Template(),
			however it reads from streams (files), not strings, and it allows use
			of more complicated variable names with multiple variable delimiters
			(eg '$' and '@').
			This readline()-like member function terminates when reaching a
			user-specified terminator character character (second argument),
			or when variable (eg: "$var"$ is encountered). The result is
			a list of variable-separated text-blocks (stored in the first
			argument). For example, the string:
			"string with $var1 and $var2 variables.}" contains:
			"string with ",
			$var1,
			" and ",
			$var2,
			" variables.}"
			This simplifies the final process of rendering
			(substituting text into) the text blocks later on.
			Output:
			This function returns a list of (alternating) blocks of
			text, and variable names. Each entry in the list is either:
			1) a text block:
			Raw text is copied from the source, verbatim, along with
			some additional data (filename and line numbers), to
			help retroactively identify where the text came from
			(in case a syntax error in the text is discovered later).
			In this case, the list entry is stored as a list
			The format (TextBlock) is similar to:
			[text_string, ((filenameA,lineBegin), (filenameB,lineEnd))],
			where the tuples, (filenameA,lineBegin) and (filenameB,lineEnd)
			denote the source file(s) from which the text was read, and
			line number at the beginning and ending of the text block.
			(This information is useful for generating helpful error
			messages. Note that the "TtreeShlex" class allows users to
			combine multiple files transparently into one stream using
			the "source" (or "sourcehook()") member. For this reason, it
			is possible, although unlikely, that the text-block
			we are reading could span multiple different files.)
			2) a variable (for example "$var" or "${var}"):
			In this case, the list entry is stored in the "VarRef" format
			which is essentialy shown below:
			[[var_prefix, var_nptr, var_suffix], (filename,lineno)]
			where var_prefix and var_suffix are strings containing brackets
			and other text enclosing the variable name (and may be empty).

			As an example, we consider a file named "datafile" which
			contains the text containing 2 text blocks and 1 variable:
			"some\n text\n before ${var}. Text after\n".
			ReadTemplate() will read this and return a list with 3 entries:
			[ ['some\n text\n before', (('datafile', 1), ('datafile', 3))],
			[['${', 'var', '}'], ('datafile', 3, 3)],
			['Text after\n', (('datafile', 3), ('datafile', 4))] ]

			Note that while parsing the text, self.lineno counter is
			incremented whenever a newline character is encountered.
			(Also: Unlike shlex.get_token(), this function does not
			delete commented text, or insert text from other files.)

			Exceptional Cases:
			Terminator characters are ignored if they are part of a variable
			reference. (For example, the '}' in "${var}", is used to denote a
			bracketed variable, and does not cause ReadTemplate() to stop reading)
			OR if they are part of a two-character escape sequence
			(for example, '}' in "\}" does not cause terminate parsing).
			In that case, the text is considered normal text. (However the
			'\' character is also stripped out. It is also stripped out if it
			preceeds any characters in "other_esc_chars", which is
			the second argument. Otherwise it is left in the text block.)

			"""
			#print(' ReadTemplate('+terminators+') invoked at '+self.error_leader())

			# The main loop of the parser reads only one variable at time.
			# The following variables keep track of where we are in the template.
			reading_var=False # Are we currently reading in the name of a variable?

			prev_char_delim=False #True iff we just read a var_delim character like '$'
			escaped_state=False #True iff we just read a (non-escaped) esc character '\'
			commented_state=False #True iff we are in a region of text where vars should be ignored
			var_paren_depth=0 # This is non-zero iff we are inside a
			# bracketed variable's name for example: "${var}"
			var_terminators = self.whitespace + self.newline + self.var_delim + '{}'

			tmpl_list = [] # List of alternating tuples of text_blocks and
			# variable names (see format comment above)
			# This list will be returned to the caller.

			#sys.stderr.write('report_progress='+str(report_progress))

			prev_filename = self.infile
			prev_lineno = self.lineno
			var_prefix = ''
			var_descr_plist = []
			var_suffix = ''
			text_block_plist = []

			done_reading = False

			while not done_reading:

			terminate_text = False
			terminate_var = False
			#delete_prior_escape = False

			nextchar = self.read_char()


			#print(' ReadTemplate() nextchar=\''+nextchar+'\' at '+self.error_leader()+' esc='+str(escaped_state)+', pvar='+str(prev_char_delim)+', paren='+str(var_paren_depth))



			# Count newlines:
			if nextchar in self.newline:
			commented_state = False
			self.lineno += 1

			elif ((nextchar in self.comment_skip_var) and
			(not escaped_state)):
			commented_state = True

			# Check for end-of-file:
			if nextchar == '':

			if escaped_state:
			raise InputError('Error: in '+self.error_leader()+'\n\n'
			'No escaped character.')
			if reading_var:
			terminate_var = True
			else:
			terminate_text = True

			done_reading = True


			# --- Now process the character: ---


			# What we do next depends on which "mode" we are in.
			# If we are reading a regular text block (reading_var == False),
			# then we keep appending characters onto the end of "text_block",
			# checking for terminal characters, or variable delimiters.
			# If we are reading a variable name (reading_var == True),
			# then we append characters to the end of "var_descr_plist[]",
			# checking for variable terminator characters, as well as
			# parenthesis (some variables are surrounded by parenthesis).

			elif reading_var:

			if nextchar in terminators:
			#sys.stdout.write(' ReadTemplate() readmode found terminator.\n')
			if escaped_state:
			# In this case, the '\' char was only to prevent terminating
			# string prematurely, so delete the '\' character.
			#delete_prior_escape = True
			if not (nextchar in self.var_close_paren):
			del var_descr_plist[-1]
			var_descr_plist.append(nextchar)

			elif not ((var_paren_depth>0) and (nextchar in self.var_close_paren)):
			terminate_var = True
			done_reading = True

			if nextchar in self.var_open_paren: # eg: nextchar == '{'
			#sys.stdout.write(' ReadTemplate() readmode found {.\n')
			if escaped_state:
			# In this case, the '\' char was only to prevent
			# interpreting '{' as a variable prefix
			#delete_prior_escape=True # so delete the '\' character
			del var_descr_plist[-1]
			var_descr_plist.append(nextchar)
			else:
			# "${var}" is a valid way to refer to a variable
			if prev_char_delim:
			var_prefix += nextchar
			var_paren_depth = 1
			# "${{var}}" is also a valid way to refer to a variable,
			# (although strange), but "$va{r}" is not.
			# Parenthesis (in bracketed variable names) must
			# immediately follow the '$' character (as in "${var}")
			elif var_paren_depth > 0:
			var_paren_depth += 1

			elif nextchar in self.var_close_paren:
			#sys.stdout.write(' ReadTemplate() readmode found }.\n')
			if escaped_state:
			# In this case, the '\' char was only to prevent
			# interpreting '}' as a variable suffix,
			#delete_prior_escape=True #so skip the '\' character
			if (nextchar not in terminators):
			del var_descr_plist[-1]
			var_descr_plist.append(nextchar)
			else:
			if var_paren_depth > 0:
			var_paren_depth -= 1
			if var_paren_depth == 0:
			var_suffix = nextchar
			terminate_var = True

			elif nextchar in var_terminators:
			#sys.stdout.write(' ReadTemplate() readmode found var_terminator \"'+nextchar+'\"\n')
			if (escaped_state or (var_paren_depth>0)):
			# In this case, the '\' char was only to prevent
			# interpreting nextchar as a variable terminator
			#delete_prior_escape = True # so skip the '\' character
			del var_descr_plist[-1]
			var_descr_plist.append(nextchar)
			else:
			terminate_var = True

			elif nextchar in self.var_delim: # such as '$'
			#sys.stdout.write(' ReadTemplate() readmode found var_delim.\n')
			if escaped_state:
			# In this case, the '\' char was only to prevent
			# interpreting '$' as a new variable name
			#delete_prior_escape = True # so skip the '\' character
			del var_descr_plist[-1]
			var_descr_plist.append(nextchar)
			else:
			prev_var_delim = True
			# Then we are processing a new variable name
			terminate_var = True
			else:
			var_descr_plist.append(nextchar)
			prev_char_delim = False


			else: # begin else clause for "if reading_var:"

			# Then we are reading a text_block

			if nextchar in terminators:
			if escaped_state:
			# In this case, the '\' char was only to prevent terminating
			# string prematurely, so delete the '\' character.
			#delete_prior_escape = True
			del text_block_plist[-1]
			text_block_plist.append(nextchar)
			elif commented_state:
			text_block_plist.append(nextchar)
			else:
			terminate_text = True
			done_reading = True

			elif nextchar in self.var_delim: # such as '$'
			if escaped_state:
			# In this case, the '\' char was only to prevent
			# interpreting '$' as a variable prefix.
			#delete_prior_escape=True #so delete the '\' character
			del text_block_plist[-1]
			text_block_plist.append(nextchar)
			elif commented_state:
			text_block_plist.append(nextchar)
			else:
			prev_char_delim = True
			reading_var = True
			var_paren_depth = 0
			terminate_text = True
			else:
			text_block_plist.append(nextchar)
			#TO DO: use "list_of_chars.join()" instead of '+='
			prev_char_delim = False # the previous character was not '$'


			# Now deal with "other_esc_chars"
			#if escaped_state and (nextchar in other_esc_chars):

			if escaped_state and (nextchar in other_esc_chars):
			if reading_var:
			#sys.stdout.write(' ReadTemplate: var_descr_str=\''+''.join(var_descr_plist)+'\'\n')
			assert(var_descr_plist[-2] in self.escape)
			del var_descr_plist[-2]
			else:
			#sys.stdout.write(' ReadTemplate: text_block=\''+''.join(text_block_plist)+'\'\n')
			assert(text_block_plist[-2] in self.escape)
			del text_block_plist[-2]


			if terminate_text:
			#sys.stdout.write('ReadTemplate() appending: ')
			#sys.stdout.write(text_block)

			#tmpl_list.append( [text_block,
			# ((prev_filename, prev_lineno),
			# (self.infile, self.lineno))] )

			if simplify_output:
			tmpl_list.append(''.join(text_block_plist))
			else:
			tmpl_list.append(TextBlock(''.join(text_block_plist),
			OSrcLoc(prev_filename, prev_lineno)))
			#, OSrcLoc(self.infile, self.lineno)))
			if not done_reading:
			# The character that ended the text block
			# was a variable delimiter (like '$'), in which case
			# we should put it (nextchar) in the variable's prefix.
			var_prefix = nextchar
			else:
			var_prefix = ''
			var_descr_plist = []
			var_suffix = ''
			prev_filename = self.infile
			prev_lineno = self.lineno
			del text_block_plist
			text_block_plist = []
			#gc.collect()


			elif terminate_var:
			# Print an error if we terminated in the middle of
			# an incomplete variable name:
			if prev_char_delim:
			raise InputError('Error: near '+self.error_leader()+'\n\n'
			'Null variable name.')
			if var_paren_depth > 0:
			raise InputError('Error: near '+self.error_leader()+'\n\n'
			'Incomplete bracketed variable name.')

			var_descr_str = ''.join(var_descr_plist)

			# Now check for variable format modifiers,
			# like python's ".rjust()" and ".ljust()".
			# If present, then put these in the variable suffix.
			if ((len(var_descr_plist)>0) and (var_descr_plist[-1]==')')):
			#i = len(var_descr_plist)-1
			#while i >= 0:
			# if var_descr_plist[i] == '(':
			# break
			# i -= 1
			i = var_descr_str.rfind('(')
			if (((i-6) >= 0) and
			((var_descr_str[i-6:i] == '.rjust') or
			(var_descr_str[i-6:i] == '.ljust'))):
			var_suffix =''.join(var_descr_plist[i-6:])+var_suffix
			#var_descr_plist = var_descr_plist[:i-6]
			var_descr_str = var_descr_str[:i-6]

			# Process any special characters in the variable name
			var_descr_str = EscCharStrToChar(var_descr_str)

			#tmpl_list.append( [[var_prefix, var_descr_str, var_suffix],
			# (self.infile, self.lineno)] )
			if simplify_output:
			tmpl_list.append(var_prefix + var_descr_str + var_suffix)
			else:
			tmpl_list.append( VarRef(var_prefix, var_descr_str, var_suffix,
			OSrcLoc(self.infile, self.lineno)) )

			#if report_progress:
			#sys.stderr.write(' parsed variable '+var_prefix+var_descr_str+var_suffix+'\n')

			#sys.stdout.write('ReadTemplate() appending: ')
			#print(var_prefix + var_descr_str + var_suffix)

			del var_descr_plist
			del var_descr_str

			prev_filename = self.infile
			prev_lineno = self.lineno
			var_prefix = ''
			var_descr_plist = []
			var_suffix = ''
			# Special case: Variable delimiters like '$'
			# terminate the reading of variables,
			# but they also signify that a new
			# variable is being read.
			if nextchar in self.var_delim:
			# Then we are processing a new variable name
			prev_var_delim = True
			reading_var = True
			var_paren_depth = 0
			var_prefix = nextchar

			elif nextchar in self.var_close_paren:
			del text_block_plist
			text_block_plist = []
			#gc.collect()
			prev_var_delim = False
			reading_var = False

			else:
			# Generally, we don't want to initialize the next text block
			# with the empty string. Consider that whatever character
			# caused us to stop reading the previous variable and append
			# it to the block of text that comes after.
			del text_block_plist
			text_block_plist = [nextchar]
			#gc.collect()
			prev_var_delim = False
			reading_var = False


			# If we reached the end of the template (and the user requests it),
			# then the terminal character can be included in the list
			# of text_blocks to be returned to the caller.
			if done_reading and keep_terminal_char:
			#sys.stdout.write('ReadTemplate() appending: \''+nextchar+'\'\n')
			# Here we create a new text block which contains only the
			# terminal character (nextchar).
			#tmpl_list.append( [nextchar,
			# ((self.infile, self.lineno),
			# (self.infile, self.lineno))] )
			if simplify_output:
			tmpl_list.append(nextchar)
			else:
			tmpl_list.append(TextBlock(nextchar,
			OSrcLoc(self.infile, self.lineno)))
			#, OSrcLoc(self.infile, self.lineno)))


			if escaped_state:
			escaped_state = False
			else:
			if nextchar in self.escape:
			escaped_state = True

			#print("* TMPL_LIST0 = *", tmpl_list)
			return tmpl_list # <- return value stored here




			def GetParenExpr(self, prepend_str='', left_paren='(', right_paren=')'):
			""" GetParenExpr() is useful for reading in strings
			with nested parenthesis and spaces.
			This function can read in the entire string:

			.trans(0, 10.0sin(30), 10.0cos(30))

			(Because I was too lazy to write this correctly...)
			Spaces are currently stripped out of the expression.
			(...unless surrounded by quotes) The string above becomes:

			".trans(0,10.0sin(30),10.0cos(30))"

			Sometimes the caller wants to prepend some text to the beginning
			of the expression (which may contain parenthesis). For this
			reason, an optional first argument ("prepend_str") can be
			provided. By default it is empty.

			"""
			orig_wordterm = self.wordterminators
			self.wordterminators = self.wordterminators.replace(left_paren,'').replace(right_paren,'')

			token = self.get_token()
			if ((token == '') or
			(token == self.eof)):
			return prepend_str


			expr_str = prepend_str + token

			#if (expr_str.find(left_paren) == -1):
			# raise InputError('Error near or before '+self.error_leader()+'\n'
			# 'Expected an open-paren (\"'+prepend_str+left_paren+'\") before this point.\n')
			# return expr_str

			paren_depth = expr_str.count(left_paren) - expr_str.count(right_paren)
			while ((len(expr_str) == 0) or (paren_depth > 0)):
			token = self.get_token()
			if ((type(token) is not str) or
			(token == '')):
			raise InputError('Error near or before '+self.error_leader()+'\n'
			'Invalid expression: \"'+expr_str+'\"')
			expr_str += token
			paren_depth = expr_str.count(left_paren) - expr_str.count(right_paren)
			if (paren_depth != 0):
			raise InputError('Error near or before '+self.error_leader()+'\n'
			'Invalid expression: \"'+expr_str+'\"')
			self.wordterminators = orig_wordterm
			return expr_str










			if __name__ == '__main__':
			if len(sys.argv) == 1:
			lexer = TtreeShlex()
			else:
			file = sys.argv[1]
			lexer = TtreeShlex(open(file), file)
			while 1:
			tt = lexer.get_token()
			if tt:
			print("Token: " + repr(tt))
			else:
			break

lammps/tools/moltemplate/src/ttree_lex.py3aea32f946b3lammps-icms

ttree_lex.pyView Options

lammps/tools/moltemplate/src/ttree_lex.py
3aea32f946b3lammps-icms

ttree_lex.py
View Options