--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/utils/deoptparse.py	Mon Jan 16 07:03:36 2012 -0500
@@ -0,0 +1,258 @@
+#  Copyright (c) 2004 Gavin E. Crooks <gec@compbio.berkeley.edu>
+#
+#  This software is distributed under the MIT Open Source License.
+#  <http://www.opensource.org/licenses/mit-license.html>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a 
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+#  THE SOFTWARE.
+#
+
+"""Custom extensions to OptionParse for parsing command line options."""
+# FIXME: Docstring
+
+# TODO: Add profiling option
+
+# DeOptionParser : 
+# 
+#  http://docs.python.org/lib/module-optparse.html
+#
+# Random_options : 
+#   Set random generator and seed. Use options.random as
+#   source of random numbers
+# Copyright :
+#   print copyright information
+
+# Documentation :
+#   print extended document information
+#
+# Additional file_in and file_out types
+
+import sys
+from copy import copy
+from optparse import Option
+from optparse import OptionParser
+from optparse import IndentedHelpFormatter
+from optparse import OptionValueError
+import random
+
+
+
+def _copyright_callback(option, opt, value, parser):
+    if option or  opt or  value or parser: pass # Shut up lint checker
+    print parser.copyright
+    sys.exit()
+
+def _doc_callback(option, opt, value, parser):
+    if option or  opt or  value or parser: pass # Shut up lint checker
+    print parser.long_description
+    sys.exit()
+
+
+class DeHelpFormatter(IndentedHelpFormatter) :
+    def __init__ (self,
+                  indent_increment=2,
+                  max_help_position=32, 
+                  width=78,
+                  short_first=1):
+        IndentedHelpFormatter.__init__(
+            self, indent_increment, max_help_position,
+            width, short_first)
+
+    def format_option_strings (self, option):
+        """Return a comma-separated list of option strings & metavariables."""
+        if option.takes_value():
+            metavar = option.metavar or option.dest.upper()
+            short_opts = option._short_opts
+            long_opts = [lopt + " " + metavar for lopt in option._long_opts]
+        else:
+            short_opts = option._short_opts
+            long_opts = option._long_opts
+            
+        if not short_opts : short_opts = ["  ",]
+
+        if self.short_first:
+            opts = short_opts + long_opts
+        else:
+            opts = long_opts + short_opts
+
+        return " ".join(opts)
+
+
+
+def _check_file_in(option, opt, value):
+    if option or  opt or  value : pass # Shut up lint checker 
+    try:
+        return file(value, "r")
+    except IOError:
+        raise OptionValueError(
+            "option %s: cannot open file: %s" % (opt, value) )
+
+def _check_file_out(option, opt, value):
+    if option or  opt or  value : pass # Shut up lint checker 
+    try:
+        return file(value, "w+")
+    except IOError:
+        raise OptionValueError(
+            "option %s: cannot open file: %s" % (opt, value) )
+    
+def _check_boolean(option, opt, value) :
+    if option or  opt or  value : pass # Shut up lint checker 
+    v = value.lower()
+    choices = {'no': False, 'false':False, '0': False,
+            'yes': True, 'true': True, '1':True }   
+    try:
+        return choices[v]
+    except KeyError:
+        raise OptionValueError(
+            "option %s: invalid choice: '%s' " \
+            "(choose from 'yes' or 'no', 'true' or 'false')" %  (opt, value))
+
+def _check_dict(option, opt, value) :
+    if option or  opt or  value : pass # Shut up lint checker 
+    v = value.lower()
+    choices = option.choices
+    try:
+        return choices[v]
+    except KeyError:
+        raise OptionValueError(
+            "option %s: invalid choice: '%s' " \
+            "(choose from '%s')" %  (opt, value, "', '".join(choices)))
+ 
+
+                    
+class DeOption(Option):
+    TYPES = Option.TYPES + ("file_in","file_out", "boolean", "dict")
+    TYPE_CHECKER = copy(Option.TYPE_CHECKER)
+    TYPE_CHECKER["file_in"] = _check_file_in
+    TYPE_CHECKER["file_out"] = _check_file_out
+    TYPE_CHECKER["boolean"] = _check_boolean
+    TYPE_CHECKER["dict"] = _check_dict
+    choices = None
+
+    def _new_check_choice(self):
+        if self.type == "dict":
+            if self.choices is None:
+                raise OptionValueError(
+                    "must supply a dictionary of choices for type 'dict'")
+            elif not isinstance(self.choices, dict):
+                raise OptionValueError(
+                    "choices must be a dictinary ('%s' supplied)"
+                    % str(type(self.choices)).split("'")[1])
+            return
+        self._check_choice()
+ 
+    # Have to override _check_choices so that we can parse
+    # a dict through to check_dict
+    CHECK_METHODS = Option.CHECK_METHODS
+    CHECK_METHODS[2] = _new_check_choice
+    
+
+
+
+
+class DeOptionParser(OptionParser) :
+    def __init__(self,
+                usage=None,
+                option_list=None,
+                option_class=DeOption,
+                version=None,
+                conflict_handler="error",
+                description=None,
+                long_description = None,
+                formatter=DeHelpFormatter(),
+                add_help_option=True,
+                prog=None,
+                copyright=None,
+                add_verbose_options=True,
+                add_random_options=False
+                ):
+
+        OptionParser.__init__(self,
+                              usage,
+                              option_list,
+                              option_class,
+                              version,
+                              conflict_handler,
+                              description,
+                              formatter,
+                              add_help_option,
+                              prog )
+       
+        if long_description :
+            self.long_description = long_description
+            self.add_option("--doc",
+                            action="callback",
+                            callback=_doc_callback,
+                            help="Detailed documentation")
+    
+        if copyright :
+            self.copyright = copyright
+            self.add_option("--copyright",
+                            action="callback",
+                            callback=_copyright_callback,
+                            help="") 
+               
+        if add_verbose_options :
+            self.add_option("-q", "--quite",
+                action="store_false",
+                dest="verbose",
+                default=False,
+                help="Run quietly (default)")
+            
+            self.add_option("-v", "--verbose",
+                action="store_true",
+                dest="verbose",
+                default=False,
+                help="Verbose output (Not quite)")
+    
+        self.random_options = False
+        if add_random_options :
+            self.random_options = True
+            self.add_option("--seed",
+                action="store",
+                type = "int",
+                dest="random_seed",
+                help="Initial seed for pseudo-random number generator. (default: System time)",
+                metavar="INTEGER" )
+                            
+            self.add_option("--generator",
+                action="store",
+                dest="random_generator",
+                default="MersenneTwister",
+                help="Select MersenneTwister (default) or WichmannHill pseudo-random number generator", 
+                metavar="TYPE" )
+
+    def parse_args(self,args, values=None) :
+        (options, args) = OptionParser.parse_args(self, args, values)
+        
+        if self.random_options :
+            if options.random_generator is None or options.random_generator =="MersenneTwister" :
+                r = random.Random()
+            elif options.random_generator == "WichmannHill" :
+                r = random.WichmannHill()
+            else :
+                self.error("Acceptible generators are MersenneTwister (default) or WichmannHill")
+            if options.random_seed :
+                r.seed(options.random_seed)
+        
+            options.__dict__["random"] = r        
+                
+        
+        return (options, args)
+    
+    
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