Examples fail with a syntax error

[Anonymous]

I am brand new user of Pyke (but very experienced in UNIX, C, C++, Java, Objective-C, Python, etc).  I want to use Pyke as the foundation of my PhD thesis work in cancer genomics.

Pyke installed cleanly on my Mac OS X running python 2.6.  But all of the examples give a syntax error parsing the krb file. See the example below.   Am I doing something wrong or is there a problem in https://sourceforge.net/projects/pyke/files/pyke/1.1.1/    ?

Thanks,
Ted
http://soe.ucsc.edu/~ted/

for example in family_relations

$ python
Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)
on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import driver
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "driver.py", line 49, in <module>
    engine = knowledge_engine.engine(__file__)
  File "/Library/Python/2.6/site-packages/pyke/knowledge_engine.py", line 105, in __init__
    target_package.compile(self)
  File "/Library/Python/2.6/site-packages/pyke/target_pkg.py", line 259, in compile
    source_filename))
  File "/Library/Python/2.6/site-packages/pyke/target_pkg.py", line 240, in do_by_ext
    return getattr(self, "%s_%s" % (prefix, ext))(filename, *args)
  File "/Library/Python/2.6/site-packages/pyke/target_pkg.py", line 269, in compile_krb
    self.directory, source_filename)
  File "/Library/Python/2.6/site-packages/pyke/krb_compiler/__init__.py", line 114, in compile_krb
    ast = krbparser.parse(krbparser, filename)
  File "/Library/Python/2.6/site-packages/pyke/krb_compiler/krbparser.py", line 599, in parse
    debug=debug)
  File "/Library/Python/2.6/site-packages/pyke/krb_compiler/ply/yacc.py", line 263, in parse
    return self.parseopt(input,lexer,debug,tracking,tokenfunc)
  File "/Library/Python/2.6/site-packages/pyke/krb_compiler/ply/yacc.py", line 792, in parseopt
    tok = self.errorfunc(errtoken)
  File "/Library/Python/2.6/site-packages/pyke/krb_compiler/krbparser.py", line 548, in p_error
    raise SyntaxError("invalid syntax", scanner.syntaxerror_params())
  File "/Users/tedgoldstein/Downloads/pyke/pyke-1.1.1/examples/family_relations/bc_example.krb", line 208
    return (prefix + (x,), prefix + (y,))
                                           ^
SyntaxError: invalid syntax
>>>
>>>

$ cat bc_example.krb
# $Id: bc_example.krb 2bb500de1268 2008-09-24 mtnyogi $
#
# Copyright © 2007-2008 Bruce Frederiksen
#
# 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.

father_son
    use child_parent($child, $father, father, son)
    when
family.son_of($child, $father, $mother)

mother_son
    use child_parent($child, $mother, mother, son)
    when
family.son_of($child, $father, $mother)

father_daughter
    use child_parent($child, $father, father, daughter)
    when
family.daughter_of($child, $father, $mother)

mother_daughter
    use child_parent($child, $mother, mother, daughter)
    when
family.daughter_of($child, $father, $mother)

# Establish sibling relationships:
brothers
    use siblings($brother1, $brother2, brother, brother)
    when
family.son_of($brother1, $father, $mother)
family.son_of($brother2, $father, $mother)
check $brother1 != $brother2

sisters
    use siblings($sister1, $sister2, sister, sister)
    when
family.daughter_of($sister1, $father, $mother)
family.daughter_of($sister2, $father, $mother)
check $sister1 != $sister2

brother_sister
    use siblings($sister, $brother, brother, sister)
    when
family.daughter_of($sister, $father, $mother)
family.son_of($brother, $father, $mother)

sister_brother
    use siblings($brother, $sister, sister, brother)
    when
family.son_of($brother, $father, $mother)
family.daughter_of($sister, $father, $mother)

as_au_brother_uncle
    use as_au(brother, uncle)

as_au_sister_aunt
    use as_au(sister, aunt)

as_nn_son_nephew
    use as_nn(son, nephew)

as_nn_daughter_niece
    use as_nn(daughter, niece)

niece_or_nephew_and_aunt_or_uncle
    use nn_au($nn, $au, $greats, $au_type, $nn_type)
    when
child_parent($nn, $parent, $depth, $_, $child_type)
siblings($parent, $au, $sibling_type, $_)
as_au($sibling_type, $au_type)
as_nn($child_type, $nn_type)
        $greats = ('great',) * len($depth)

# Note that these child_parent have an extra argument to handle
# ('grand',), ('great', 'grand'), etc.
parent_and_child
    use child_parent($child, $parent, (), $parent_type, $child_type)
    when
child_parent($child, $parent, $parent_type, $child_type)

grand_parent_and_child
    # Note that a comma is not required (but is allowed) for singleton
    # tuples in .krb files; in this case, "(grand)".
    use child_parent($child, $grand_parent, (grand), $parent_type, $child_type)
    when
child_parent($child, $parent, $_, $child_type)
child_parent($parent, $grand_parent, $parent_type, $_)

great_grand_parent_and_child
    use child_parent($child, $grand_parent, (great, $a, *$b),
                     $parent_type, $child_type)
    when
child_parent($child, $grand_child, $_, $child_type)
        # We use "($a, *$b)" in the next premise so that it won't match ().
child_parent($grand_child, $grand_parent, ($a, *$b), $parent_type, $_)

first_cousins
    use cousins($cousin1, $cousin2, 1)
    when
child_parent($cousin1, $sibling1, $_, $_)
siblings($sibling1, $sibling2, $_, $_)
child_parent($cousin2, $sibling2, $_, $_)

nth_cousins
    use cousins($next_cousin1, $next_cousin2, $next_n)
    when
child_parent($next_cousin1, $cousin1, $_, $_)
cousins($cousin1, $cousin2, $n)
child_parent($next_cousin2, $cousin2, $_, $_)
$next_n = $n + 1

how_related_child_parent
    use how_related($person1, $person2, $relationship)
    when
child_parent($person1, $person2, $prefix, $p2_type, $p1_type)
$relationship = add_prefix($prefix, $p1_type, $p2_type)

how_related_parent_child
    use how_related($person1, $person2, $relationship)
    when
        # Note that for how_related(Fixed_name, $variable) that this
        # subgoal is run "in reverse":
        #     child_parent($variable, Fixed_name, …)
        # This is very inefficient the way the following rules were written:
        #         grand_parent_and_child
        #     and great_grand_parent_and_child
        # It is left as an exercise for the reader to determine how to improve
        # these rules.  Here's a way to check whether a pattern variable is
        # bound (only 'variable_name' changes with different variables).  This
        # only checks the top-level binding.  It does not check whether
        # subordinate variables in tuples are bound:
        #     check context.is_bound(contexts.variable('variable_name'))
child_parent($person2, $person1, $prefix, $p1_type, $p2_type)
$relationship = add_prefix($prefix, $p1_type, $p2_type)

how_related_siblings
    use how_related($person1, $person2, ($p1_type, $p2_type))
    when
siblings($person1, $person2, $p2_type, $p1_type)

how_related_nn_au
    use how_related($person1, $person2, $relationship)
    when
nn_au($person1, $person2, $prefix, $p2_type, $p1_type)
$relationship = add_prefix($prefix, $p1_type, $p2_type)

how_related_au_nn
    use how_related($person1, $person2, $relationship)
    when
        # Here is another case where how_related(Fixed_name, $variable) is
        # very inefficient because of the way the
        # great_niece_or_nephew_and_aunt_or_uncle rule is written.
nn_au($person2, $person1, $prefix, $p1_type, $p2_type)
$relationship = add_prefix($prefix, $p1_type, $p2_type)

how_related_cousins
    use how_related($cousin1, $cousin2, ($nth, cousins))
    when
cousins($cousin1, $cousin2, $n)
        $nth = nth($n)

how_related_removed_cousins
    use how_related($removed_cousin1, $cousin2, ($nth, cousins, $r1, removed))
    when
        child_parent($removed_cousin1, $cousin1, $grand, $_, $_)
cousins($cousin1, $cousin2, $n)
        $nth = nth($n)
        $r1 = len($grand) + 1

how_related_cousins_removed
    use how_related($cousin1, $removed_cousin2, ($nth, cousins, $r1, removed))
    when
cousins($cousin1, $cousin2, $n)
        child_parent($removed_cousin2, $cousin2, $grand, $_, $_)
        $nth = nth($n)
        $r1 = len($grand) + 1

bc_extras
    def nth(n):
        if n % 10 not in (1, 2, 3) or 10 < n % 100 < 20: return "%dth" % n
        if n % 10 == 1: return "%dst" % n
        if n % 10 == 2: return "%dnd" % n
        if n % 10 == 3: return "%drd" % n

    def add_prefix(prefix, x, y):
        if not prefix: return (x, y)
return (prefix + (x,), prefix + (y,))

[Bruce Frederiksen]

Sounds like you have two versions of Pyke.  You have the examples from version 1.1.1 (the latest version).  Try:

$ python
>>> import pyke
>>> pyke.version

To see what version you have installed in /Library/Python/2.6/site-packages.