Mon Mar 13 03:57:28 PST 2006

Author: kaben
Date: 2006-03-13 06:11:36 -0500 (Mon, 13 Mar 2006)
New Revision: 506

Added:
   trunk/consistencytests/
   trunk/consistencytests/CMakeLists.txt
   trunk/consistencytests/CMakeModules/
   trunk/consistencytests/CMakeModules/CVS/
   trunk/consistencytests/CMakeModules/CVS/Entries
   trunk/consistencytests/CMakeModules/CVS/Repository
   trunk/consistencytests/CMakeModules/CVS/Root
   trunk/consistencytests/CMakeModules/Templates/
   trunk/consistencytests/CMakeModules/Templates/CVS/
   trunk/consistencytests/CMakeModules/Templates/CVS/Entries
   trunk/consistencytests/CMakeModules/Templates/CVS/Repository
   trunk/consistencytests/CMakeModules/Templates/CVS/Root
   trunk/consistencytests/CMakeModules/Templates/check_tails.py.in
   trunk/consistencytests/CMakeModules/Templates/generate_tails.py.in
   trunk/consistencytests/CVS/
   trunk/consistencytests/CVS/Entries
   trunk/consistencytests/CVS/Repository
   trunk/consistencytests/CVS/Root
   trunk/consistencytests/Doc/
   trunk/consistencytests/Doc/CVS/
   trunk/consistencytests/Doc/CVS/Entries
   trunk/consistencytests/Doc/CVS/Repository
   trunk/consistencytests/Doc/CVS/Root
   trunk/consistencytests/Doc/html/
   trunk/consistencytests/Doc/html/CVS/
   trunk/consistencytests/Doc/html/CVS/Entries
   trunk/consistencytests/Doc/html/CVS/Repository
   trunk/consistencytests/Doc/html/CVS/Root
   trunk/consistencytests/Doc/html/ccmake.jpg
   trunk/consistencytests/Doc/html/index.html
   trunk/consistencytests/Doc/html/page01.html
   trunk/consistencytests/Doc/html/page02.html
   trunk/consistencytests/Doc/html/page03.html
   trunk/consistencytests/Doc/html/page04.html
   trunk/consistencytests/Doc/html/page06.html
   trunk/consistencytests/Doc/html/page07.html
   trunk/consistencytests/Support/
   trunk/consistencytests/Support/CVS/
   trunk/consistencytests/Support/CVS/Entries
   trunk/consistencytests/Support/CVS/Repository
   trunk/consistencytests/Support/CVS/Root
   trunk/consistencytests/Support/python/
   trunk/consistencytests/Support/python/CVS/
   trunk/consistencytests/Support/python/CVS/Entries
   trunk/consistencytests/Support/python/CVS/Repository
   trunk/consistencytests/Support/python/CVS/Root
   trunk/consistencytests/Support/python/avida_consistency_checks/
   trunk/consistencytests/Support/python/avida_consistency_checks/CVS/
   trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Entries
   trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Repository
   trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Root
   trunk/consistencytests/Support/python/avida_consistency_checks/TailChecker.py
   trunk/consistencytests/Support/python/avida_consistency_checks/TailChecker.pyc
   trunk/consistencytests/Support/python/avida_consistency_checks/TailGenerator.py
   trunk/consistencytests/Support/python/avida_consistency_checks/TailGenerator.pyc
   trunk/consistencytests/Support/python/avida_consistency_checks/__init__.py
   trunk/consistencytests/Support/python/avida_consistency_checks/__init__.pyc
   trunk/consistencytests/Tests/
   trunk/consistencytests/Tests/CMakeLists.txt
   trunk/consistencytests/Tests/CVS/
   trunk/consistencytests/Tests/CVS/Entries
   trunk/consistencytests/Tests/CVS/Repository
   trunk/consistencytests/Tests/CVS/Root
   trunk/consistencytests/Tests/Researchers/
   trunk/consistencytests/Tests/Researchers/CMakeLists.txt
   trunk/consistencytests/Tests/Researchers/CVS/
   trunk/consistencytests/Tests/Researchers/CVS/Entries
   trunk/consistencytests/Tests/Researchers/CVS/Repository
   trunk/consistencytests/Tests/Researchers/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/
   trunk/consistencytests/Tests/Researchers/dule/CMakeLists.txt
   trunk/consistencytests/Tests/Researchers/dule/CVS/
   trunk/consistencytests/Tests/Researchers/dule/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/detail_pop.100.expected_last_line
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/README
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Root
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/creature.final.asex
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/environment.cfg
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/events.cfg
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.asex
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.sex
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/organism.100.sex
   trunk/consistencytests/Tests/Researchers/dule/LocalSex/run_list.kaben
   trunk/consistencytests/Tests/Researchers/dule/modularity/
   trunk/consistencytests/Tests/Researchers/dule/modularity/CMakeLists.txt
   trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/
   trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Entries
   trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Repository
   trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Root
   trunk/consistencytests/Tests/Researchers/goingssh/
   trunk/consistencytests/Tests/Researchers/goingssh/CMakeLists.txt
   trunk/consistencytests/Tests/Researchers/goingssh/CVS/
   trunk/consistencytests/Tests/Researchers/goingssh/CVS/Entries
   trunk/consistencytests/Tests/Researchers/goingssh/CVS/Repository
   trunk/consistencytests/Tests/Researchers/goingssh/CVS/Root
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CMakeLists.txt
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Entries
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Repository
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Root
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Entries
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Repository
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Root
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/analyze.cfg
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/environment.cfg
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/events.cfg
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/genesis
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/inst_set.default
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/kazi.org
   trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/organism.default
   trunk/run_consistencytests
Log:

Attempting to restore consistency tests.



Added: trunk/consistencytests/CMakeLists.txt
===================================================================

--- trunk/consistencytests/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,36 @@
+SET(CMAKE_VERBOSE_MAKEFILE ON CACHE BOOL
+"If this value is on, makefiles will be generated without the .SILENT directive, and all commands will be echoed to the console during the make.  This is useful for debugging only."
+)
+
+PROJECT(AvidaConsistencyChecks)
+
+#SET(AvidaExePath "/Users/kaben/Projects/Software/Avida/branch.kaben/current--HEAD--cvs/build.cmake.dbg/bin/primitive")
+#SET(PythonExePath "/sw/bin/python")
+FIND_PROGRAM(_AvidaExePath
+  NAMES primitive
+  PATHS ${PROJECT_BINARY_DIR}
+  DOC "Where can the Avida executable 'primitive' be found ?"
+)
+IF(_AvidaExePath)
+  SET(AvidaExePath_FOUND TRUE)
+ENDIF(_AvidaExePath)
+
+FIND_PROGRAM(_PythonExePath
+  NAMES python python2.3
+  DOC "Where can the Python executable be found ?"
+)
+IF(_PythonExePath)
+  SET(PythonExePath_FOUND TRUE)
+ENDIF(_PythonExePath)
+
+OPTION(AVD_CONSISTENCY_TEST_PRIMITIVE "Enable consistency check test suites." OFF)
+VARIABLE_REQUIRES(AVD_CONSISTENCY_TEST_PRIMITIVE ChecksExes_FOUND AvidaExePath_FOUND PythonExePath_FOUND)
+
+IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+  ENABLE_TESTING()
+  #INCLUDE(${CMAKE_ROOT}/Modules/Dart.cmake)
+ENDIF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+
+SET(AvidaConsistencyChecksPythonSiteDir "${PROJECT_SOURCE_DIR}/Support/python")
+
+SUBDIRS(Tests)

Added: trunk/consistencytests/CMakeModules/CVS/Entries
===================================================================
--- trunk/consistencytests/CMakeModules/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+D/Templates////

Added: trunk/consistencytests/CMakeModules/CVS/Repository
===================================================================
--- trunk/consistencytests/CMakeModules/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/CMakeModules

Added: trunk/consistencytests/CMakeModules/CVS/Root
===================================================================
--- trunk/consistencytests/CMakeModules/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/CMakeModules/Templates/CVS/Entries
===================================================================
--- trunk/consistencytests/CMakeModules/Templates/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/Templates/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,3 @@
+/check_tails.py.in/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/generate_tails.py.in/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D

Added: trunk/consistencytests/CMakeModules/Templates/CVS/Repository
===================================================================
--- trunk/consistencytests/CMakeModules/Templates/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/Templates/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/CMakeModules/Templates

Added: trunk/consistencytests/CMakeModules/Templates/CVS/Root
===================================================================
--- trunk/consistencytests/CMakeModules/Templates/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/Templates/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/CMakeModules/Templates/check_tails.py.in
===================================================================
--- trunk/consistencytests/CMakeModules/Templates/check_tails.py.in	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/Templates/check_tails.py.in	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,34 @@
+
+import sys
+import site
+site.addsitedir('@AvidaConsistencyChecksPythonSiteDir@')
+from avida_consistency_checks import *
+
+avida_exe_path = '@_AvidaExePath@'
+seed_set = @SeedSet@
+run_subdir_path_base = '@RunSubdirPathBase@'
+output_file_name = '@OutputFileName@'
+expectation_file_path_base = '@ExpectationFilePathBase@'
+expectation_file_name = '@ExpectationFileName@'
+genesis_file = '@GenesisFile@'
+avida_args = '@AvidaArgs@'
+
+tail_checker = TailChecker(
+  seed_set,
+  run_subdir_path_base,
+  genesis_file,
+  output_file_name,
+  expectation_file_path_base,
+  expectation_file_name,
+  avida_exe_path,
+  avida_args
+)
+tail_checker.check_tails()
+
+for seed, lines in tail_checker.failures_dict.iteritems():
+  print 'Seed', seed, 'produced unexpected last line in file', output_file_name, ':'
+  print lines[0]
+  print 'Expected last line in file', expectation_file_name, ':'
+  print lines[1]
+
+sys.exit(len(tail_checker.failures_dict))

Added: trunk/consistencytests/CMakeModules/Templates/generate_tails.py.in
===================================================================
--- trunk/consistencytests/CMakeModules/Templates/generate_tails.py.in	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CMakeModules/Templates/generate_tails.py.in	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,30 @@
+
+import site
+import sys
+import site
+site.addsitedir('@AvidaConsistencyChecksPythonSiteDir@')
+from avida_consistency_checks import *
+
+avida_exe_path = '@_AvidaExePath@'
+seed_set = @SeedSet@
+run_subdir_path_base = '@RunSubdirPathBase@'
+output_file_name = '@OutputFileName@'
+# The line below causes expectation files to be saved in the same place
+# as the rest of Avida's output files (specifically this should avoid
+# overwritin existing expectation files saved in the source tree.
+expectation_file_path_base = '@RunSubdirPathBase@'
+expectation_file_name = '@ExpectationFileName@'
+genesis_file = '@GenesisFile@'
+avida_args = '@AvidaArgs@'
+
+tail_generator = TailGenerator(
+  seed_set,
+  run_subdir_path_base,
+  genesis_file,
+  output_file_name,
+  expectation_file_path_base,
+  expectation_file_name,
+  avida_exe_path,
+  avida_args
+)
+tail_generator.generate_tails()

Added: trunk/consistencytests/CVS/Entries
===================================================================
--- trunk/consistencytests/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,7 @@
+/.CMakeLists.txt.swp/1.1.1.1/Tue Sep  7 16:06:15 2004//
+/CMakeLists.txt/1.1.1.1/Tue Sep  7 16:06:15 2004//
+D/CMakeModules////
+D/Doc////
+D/Support////
+D/Tests////
+D/build////

Added: trunk/consistencytests/CVS/Repository
===================================================================
--- trunk/consistencytests/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests

Added: trunk/consistencytests/CVS/Root
===================================================================
--- trunk/consistencytests/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Doc/CVS/Entries
===================================================================
--- trunk/consistencytests/Doc/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+D/html////

Added: trunk/consistencytests/Doc/CVS/Repository
===================================================================
--- trunk/consistencytests/Doc/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Doc

Added: trunk/consistencytests/Doc/CVS/Root
===================================================================
--- trunk/consistencytests/Doc/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Doc/html/CVS/Entries
===================================================================
--- trunk/consistencytests/Doc/html/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,16 @@
+/.index.html.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.page01.html.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.page02.html.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.page03.html.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.page04.html.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.page06.html.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.page07.html.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/ccmake.jpg/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/index.html/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/page01.html/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/page02.html/1.2/Tue Sep  7 16:49:38 2004//
+/page03.html/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/page04.html/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/page06.html/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/page07.html/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D

Added: trunk/consistencytests/Doc/html/CVS/Repository
===================================================================
--- trunk/consistencytests/Doc/html/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Doc/html

Added: trunk/consistencytests/Doc/html/CVS/Root
===================================================================
--- trunk/consistencytests/Doc/html/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Doc/html/ccmake.jpg
===================================================================
(Binary files differ)


Property changes on: trunk/consistencytests/Doc/html/ccmake.jpg
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/consistencytests/Doc/html/index.html
===================================================================
--- trunk/consistencytests/Doc/html/index.html	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/index.html	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,31 @@
+<html>
+
+<head>
+<title>
+Avida consistency-checks project
+</title>
+</head>
+<body>
+<hr>
+The consistency-checks comprise short reproducible Avida runs. If any of
+their outcomes change, it should be on purpose. This collection of
+testsuites will be incorporated into our testing dashboard on toto, but
+will not be available to the public.
+<p>
+<a href="page01.html">Obtaining most recent version</a>
+<p>
+<a href="page02.html">Configuring the tests</a>
+<p>
+<a href="page03.html">Running the tests</a>
+<p>
+<a href="page04.html">Directory layout</a>
+<p>
+<a href="page06.html">Questions</a>
+<p>
+<a href="page07.html">ToDo</a>
+<p>
+Have fun -- Kaben Nanlohy
+</body>
+
+</html>
+

Added: trunk/consistencytests/Doc/html/page01.html
===================================================================
--- trunk/consistencytests/Doc/html/page01.html	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/page01.html	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,15 @@
+<html>
+
+<head>
+<title>
+Avida consistency-checks project : Obtaining most recent version
+</title>
+</head>
+<body>
+<hr>
+Will be available through cvs on a private msu server (which one ?).
+<p>
+</body>
+
+</html>
+

Added: trunk/consistencytests/Doc/html/page02.html
===================================================================
--- trunk/consistencytests/Doc/html/page02.html	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/page02.html	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,65 @@
+<html>
+
+<head>
+<title>
+Avida consistency-checks project : Configuring the tests
+</title>
+</head>
+<body>
+<hr>
+Obtaining cmake : see <a href="http://www.cmake.org">www.cmake.org</a>.
+<p>
+<hr>
+Documentation of cmake : see <a href="http://www.cmake.org/HTML/Documentation.html">www.cmake.org/HTML/Documentation.html</a>.
+<p>
+<hr>
+Running cmake (the concise way) :
+<code>
+$ pwd
+<p>
+/Users/kaben/Projects/Software/Avida/consistency-tests
+<p>
+$ ls
+<p>
+CMakeLists.txt  CMakeModules    Doc             Support         Tests
+<p>
+$ mkdir build
+<p>
+$ cd build
+<p>
+$ cmake -D_CONSISTENCY_TEST_PRIMITIVE:BOOL=ON ..
+</code>
+<p>
+<hr>
+Running cmake (the verbose way) :
+<p>
+<code>
+$ pwd
+<p>
+/Users/kaben/Projects/Software/Avida/consistency-tests
+<p>
+$ ls
+<p>
+CMakeLists.txt  CMakeModules    Doc             Support         Tests
+<p>
+$ mkdir build
+<p>
+$ cd build
+<p>
+$ ccmake ..
+</code>
+<p>
+<img src="ccmake.jpg">
+<p>
+Press 'h' for help; use up and down keys to navigate, 'return' to enter
+a field so you can change it; press 'c' to configure the makefiles, and
+'g' to generate the makefiles.
+<p>
+Fields which are marked with an asterisk represent changed and
+unsatisfied variable dependencies -- just keep pressing 'c' until the
+asterisks are all gone.
+</body>
+
+</html>
+
+

Added: trunk/consistencytests/Doc/html/page03.html
===================================================================
--- trunk/consistencytests/Doc/html/page03.html	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/page03.html	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,57 @@
+<html>
+
+<head>
+<title>
+Avida consistency-checks project : Running the tests
+</title>
+</head>
+<body>
+<hr>
+<code>
+$ pwd
+<p>
+/Users/kaben/Projects/Software/Avida/consistency-tests
+<p>
+$ ls
+<p>
+CMakeLists.txt  CMakeModules    Doc             Support         Tests
+<p>
+$ cd build
+<p>
+$ make test
+<p>
+Building tests test...
+<p>
+/sw/bin/ctest
+<p>
+Test project
+<p>
+Changing directory into
+<p>
+/Users/kaben/Projects/Software/Avida/consistency-tests/build/Tests/Researchers/dule/LocalSex
+<p>
+Testing GlobalAsex                        Passed
+<p>
+Changing directory into
+<p>
+/Users/kaben/Projects/Software/Avida/consistency-tests/build/Tests/Researchers/goingssh/Kazi
+<p>
+Testing GlobalAsex                     ***Failed
+<p>
+Testing GlobalAsex                     ***Failed
+<p>
+33% tests passed, 2 tests failed out of 3
+<p>
+The following tests FAILED:
+<p>
+        GlobalAsex
+<p>
+        GlobalAsex
+<p>
+make: *** [test] Error 2
+</code>
+<p>
+</body>
+
+</html>
+

Added: trunk/consistencytests/Doc/html/page04.html
===================================================================
--- trunk/consistencytests/Doc/html/page04.html	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/page04.html	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,27 @@
+<html>
+
+<head>
+<title>
+Avida consistency-checks project : Directory layout
+</title>
+</head>
+<body>
+<hr>
+<code>
+Tests:
+<p>
+Tests/Researchers:
+<p>
+brian/ charles/ dehua/ dule/ eliz/ gabe/ goingssh/ jeff/
+<p>
+Tests/Researchers/dule:
+<p>
+LocalSex/GlobalAsex_1??
+LocalSex/config
+</code>
+<p>
+</body>
+
+</html>
+
+

Added: trunk/consistencytests/Doc/html/page06.html
===================================================================
--- trunk/consistencytests/Doc/html/page06.html	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/page06.html	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,23 @@
+<html>
+
+<head>
+<title>
+Avida consistency-checks project : Questions
+</title>
+</head>
+<body>
+<hr>
+Will be available through cvs on an msu server (which one ?).
+<p>
+Some researchers have many projects archived, e.g., Dule has
+2_fold_cost, epistasis, error_correction, group_error, local_sex, mattr,
+modularity paco, sex, some_sex, spatial. Would researchers like test
+suites for each of their archived projects ?
+<p>
+Is this a good directory layout ?
+<p>
+</body>
+
+</html>
+
+

Added: trunk/consistencytests/Doc/html/page07.html
===================================================================
--- trunk/consistencytests/Doc/html/page07.html	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Doc/html/page07.html	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,31 @@
+<html>
+
+<head>
+<title>
+Avida consistency-checks project : ToDo
+</title>
+</head>
+<body>
+<hr>
+Figure out where to host cvs repository.
+<p>
+Test suites for Brian, Charles, Dehua, Eliz, Gabe... Who else ?
+<p>
+Can't obtain a final organism for Dule's GlobalSex suite.
+<p>
+The Kazi suite can't be run without using a specially compiled version
+of Avida. Need to know hot to build this version.
+<p>
+Connect to test-results server on toto.
+<p>
+Integrate with 'current' Avida project (i.e., autodetect presence of
+consistency-tests when they're dropped into the 'current' directory).
+<p>
+Add default cmake variables so that people can just type 'cmake ..'.
+<p>
+</body>
+
+</html>
+
+
+

Added: trunk/consistencytests/Support/CVS/Entries
===================================================================
--- trunk/consistencytests/Support/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+D/python////

Added: trunk/consistencytests/Support/CVS/Repository
===================================================================
--- trunk/consistencytests/Support/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Support

Added: trunk/consistencytests/Support/CVS/Root
===================================================================
--- trunk/consistencytests/Support/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Support/python/CVS/Entries
===================================================================
--- trunk/consistencytests/Support/python/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+D/avida_consistency_checks////

Added: trunk/consistencytests/Support/python/CVS/Repository
===================================================================
--- trunk/consistencytests/Support/python/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Support/python

Added: trunk/consistencytests/Support/python/CVS/Root
===================================================================
--- trunk/consistencytests/Support/python/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Entries
===================================================================
--- trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,7 @@
+/TailChecker.py/1.3/Thu Sep  9 19:45:27 2004//
+/TailChecker.pyc/1.3/Thu Sep  9 20:53:14 2004//
+/TailGenerator.py/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/TailGenerator.pyc/1.2/Thu Sep  9 17:51:28 2004//
+/__init__.py/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/__init__.pyc/1.2/Thu Sep  9 17:51:28 2004//
+D

Added: trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Repository
===================================================================
--- trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Support/python/avida_consistency_checks

Added: trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Root
===================================================================
--- trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/avida_consistency_checks/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Support/python/avida_consistency_checks/TailChecker.py
===================================================================
--- trunk/consistencytests/Support/python/avida_consistency_checks/TailChecker.py	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/avida_consistency_checks/TailChecker.py	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,88 @@
+"""
+Class that uses Avida and an Avida configuration to produce a set of
+last lines of Avida output files, and then compares them to a set of
+corresponding expected last lines that were generated by the companion
+class TailGenerator.
+"""
+
+import sys
+import os               
+import shutil
+
+class TailChecker:
+
+  def __init__(self,
+    seed_set,
+    run_subdir_path_base,
+    genesis_file_path,
+    output_file_name,
+    expectation_file_path_base,
+    expectation_file_name,
+    avida_exe_path,
+    avida_args
+  ):
+    self.seed_set = seed_set
+    self.run_subdir_path_base = run_subdir_path_base
+    self.genesis_file_path = genesis_file_path
+    self.output_file_name = output_file_name
+    self.expectation_file_path_base = expectation_file_path_base
+    self.expectation_file_name = expectation_file_name
+    self.avida_exe_path = avida_exe_path
+    self.avida_args = avida_args
+
+    self.failures_dict = {}
+
+  def _check_tail(self, seed):
+    run_subdir = self.run_subdir_path_base + str(seed)
+    expectation_file_path = self.expectation_file_path_base + str(seed) + '/' + self.expectation_file_name
+    avida_command = self.avida_exe_path + ' ' + self.avida_args % seed
+
+    old_cwd = os.getcwd()
+
+    print "from run_subdir " + run_subdir + " : using command : " + avida_command + " :"
+
+    try:
+      shutil.rmtree(run_subdir, True)
+    except OSError:
+      print "couldn't remove run-subdirectory " + run_subdir + "; continuing."
+
+    try:
+      os.makedirs(run_subdir)
+    except OSError:
+      print "failed to make run-subdirectory " + run_subdir + "; continuing."
+
+    shutil.copy(self.genesis_file_path, run_subdir)
+    os.chdir(run_subdir)
+    avida_output_fd = os.popen(avida_command)
+    line = avida_output_fd.readline()
+    while line != "":
+      print line,
+      line = avida_output_fd.readline()
+    avida_output_fd.close()
+
+    detail_fd = file(self.output_file_name,"rU") 
+    next_detail_line = detail_fd.readline()
+    while next_detail_line != "":
+      last_detail_line = next_detail_line
+      next_detail_line = detail_fd.readline()
+    detail_fd.close()
+
+    print "last line of output file \"" + self.output_file_name + "\" : "
+    print last_detail_line
+    
+    expected_last_line_fd = file(expectation_file_path, "rU")
+    expected_last_detail_line = expected_last_line_fd.readline()
+    expected_last_line_fd.close()
+
+    if last_detail_line != expected_last_detail_line:
+      print "last line of output file doesn't match expected last line."
+      self.failures_dict[seed] = (last_detail_line, expected_last_detail_line)
+    else:
+      print "last line of output file matches expected last line."
+
+    os.chdir(old_cwd)
+
+  def check_tails(self):
+    for seed in self.seed_set:
+      self._check_tail(seed)
+

Added: trunk/consistencytests/Support/python/avida_consistency_checks/TailChecker.pyc
===================================================================
(Binary files differ)


Property changes on: trunk/consistencytests/Support/python/avida_consistency_checks/TailChecker.pyc
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/consistencytests/Support/python/avida_consistency_checks/TailGenerator.py
===================================================================
--- trunk/consistencytests/Support/python/avida_consistency_checks/TailGenerator.py	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/avida_consistency_checks/TailGenerator.py	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,77 @@
+"""
+Class that uses Avida to generate a set of expected last lines of output
+files for a particular Avida configuration.
+
+The companion class TailChecker can subsequently use Avida with the same
+configuration to generate a set of actual last lines of corresponding
+output files, compare them to the expected last lines, and report the
+result.
+"""
+
+import sys
+import os               
+import shutil
+
+class TailGenerator:
+
+  def __init__(self,
+    seed_set,
+    run_subdir_path_base,
+    genesis_file_path,
+    output_file_name,
+    expectation_file_path_base,
+    expectation_file_name,
+    avida_exe_path,
+    avida_args
+  ):
+    self.seed_set = seed_set
+    self.run_subdir_path_base = run_subdir_path_base
+    self.genesis_file_path = genesis_file_path
+    self.output_file_name = output_file_name
+    self.expectation_file_path_base = expectation_file_path_base
+    self.expectation_file_name = expectation_file_name
+    self.avida_exe_path = avida_exe_path
+    self.avida_args = avida_args
+
+  def _generate_tail(self, seed):
+    run_subdir = self.run_subdir_path_base + str(seed)
+    expectation_file_path = self.expectation_file_path_base + str(seed) + '/' + self.expectation_file_name
+    avida_command = self.avida_exe_path + ' ' + self.avida_args % seed
+
+    old_cwd = os.getcwd()
+
+    print "from run_subdir " + run_subdir + " : using command : " + avida_command + " :"
+
+    shutil.rmtree(run_subdir, True)
+    try:
+      os.makedirs(run_subdir)
+    except OSError:
+      pass
+    shutil.copy(self.genesis_file_path, run_subdir)
+    os.chdir(run_subdir)
+    avida_output_fd = os.popen(avida_command)
+    line = avida_output_fd.readline()
+    while line != "":
+      print line,
+      line = avida_output_fd.readline()
+    avida_output_fd.close()
+
+    detail_fd = file(self.output_file_name,"rU") 
+    next_detail_line = detail_fd.readline()
+    while next_detail_line != "":
+      last_detail_line = next_detail_line
+      next_detail_line = detail_fd.readline()
+    detail_fd.close()
+
+    print "last line of output file \"" + self.output_file_name + "\" : "
+    print last_detail_line
+    
+    expected_last_line_fd = file(expectation_file_path, "wU")
+    expected_last_line_fd.write(last_detail_line)
+    expected_last_line_fd.close()
+
+    os.chdir(old_cwd)
+
+  def generate_tails(self):
+    for seed in self.seed_set:
+      self._generate_tail(seed)

Added: trunk/consistencytests/Support/python/avida_consistency_checks/TailGenerator.pyc
===================================================================
(Binary files differ)


Property changes on: trunk/consistencytests/Support/python/avida_consistency_checks/TailGenerator.pyc
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/consistencytests/Support/python/avida_consistency_checks/__init__.py
===================================================================
--- trunk/consistencytests/Support/python/avida_consistency_checks/__init__.py	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Support/python/avida_consistency_checks/__init__.py	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,13 @@
+"""
+avida_consistency_checks base package init. Contains classes to generate
+test data sets, and classes to verify test data sets.
+
+Public symbols :
+  * TailGenerator
+  * TailChecker
+"""
+
+__version__ = "0.1.1"
+
+from TailGenerator import TailGenerator
+from TailChecker import TailChecker

Added: trunk/consistencytests/Support/python/avida_consistency_checks/__init__.pyc
===================================================================
(Binary files differ)


Property changes on: trunk/consistencytests/Support/python/avida_consistency_checks/__init__.pyc
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/consistencytests/Tests/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+SUBDIRS(Researchers)

Added: trunk/consistencytests/Tests/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,3 @@
+/.CMakeLists.txt.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/CMakeLists.txt/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D/Researchers////

Added: trunk/consistencytests/Tests/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests

Added: trunk/consistencytests/Tests/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/Researchers/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,5 @@
+SUBDIRS(
+  dule
+  #goingssh
+)
+

Added: trunk/consistencytests/Tests/Researchers/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,5 @@
+/.CMakeLists.txt.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/CMakeLists.txt/1.2/Thu Sep  9 20:53:14 2004//
+/dule.tgz/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D/dule////
+D/goingssh////

Added: trunk/consistencytests/Tests/Researchers/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers

Added: trunk/consistencytests/Tests/Researchers/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+SUBDIRS(LocalSex)
+#SUBDIRS(LocalSex modularity)

Added: trunk/consistencytests/Tests/Researchers/dule/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,4 @@
+/.CMakeLists.txt.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/CMakeLists.txt/1.2/Thu Sep  9 20:53:14 2004//
+D/LocalSex////
+D/modularity////

Added: trunk/consistencytests/Tests/Researchers/dule/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule

Added: trunk/consistencytests/Tests/Researchers/dule/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,103 @@
+
+# Note :
+#
+# ${CMAKE_CURRENT_SOURCE_DIR} points to the current source directory,
+# i.e., .../Tests/Researchers/dule/LocalSex/.
+#
+# ${CMAKE_CURRENT_BINARY_DIR} points to the equivalent binary directory,
+# i.e., .../build/Tests/Researchers/dule/LocalSex/.
+#
+
+#
+# Avida configuration
+#
+SET(ConfigDir "${CMAKE_CURRENT_SOURCE_DIR}/config")
+SET(GenesisFile "${ConfigDir}/genesis")
+SET(InstSetFile "${ConfigDir}/inst_set.sex")
+SET(EventFile "${ConfigDir}/events.cfg")
+SET(EnvironmentFile "${ConfigDir}/environment.cfg")
+SET(StartCreatureFile "${ConfigDir}/organism.100.sex")
+SET(AvidaArgs "-seed %d -set INST_SET ${InstSetFile} -set EVENT_FILE ${EventFile} -set ENVIRONMENT_FILE ${EnvironmentFile} -set START_CREATURE ${StartCreatureFile} -set BIRTH_METHOD 4")
+
+#
+# Consistency checks configuration
+#
+
+# This is Python list of Avida random seeds.
+# E.g., "range(100,15)" is equivalent to the Python list "[100,101,102,103,104]".
+# I.e., SET(SeedSet "range(100,105)") is equivalent to SET(SeedSet "[100,101,102,103,104]").
+SET(SeedSet "range(100,110)")
+# Avida will be run in, and store output files in, ${CMAKE_CURRENT_BINARY_DIR}/Test_100, and so on.
+SET(RunSubdirPathBase "${CMAKE_CURRENT_BINARY_DIR}/GlobalSex_")
+# I've written ${ConfigDir}/events.cfg to stop Avida after 100 updates,
+# and to output a single detail-population file "detail_pop.100" per run,
+# i.e., ${CMAKE_CURRENT_SOURCE_DIR}/Test_100/detail_pop.100, and so on.
+SET(OutputFileName "detail_pop.100")
+# Similar to above, except that this tells the testing scripts where to find
+# expected last lines of detail_pop.100 files,
+# i.e., ${CMAKE_CURRENT_SOURCE_DIR}/Test_100/detail_pop.100.expected_last_line, and so on.
+SET(ExpectationFilePathBase "${CMAKE_CURRENT_SOURCE_DIR}/GlobalSex_")
+SET(ExpectationFileName "detail_pop.100.expected_last_line")
+
+#
+# This generates the Python script that performs consistency checks.
+# Several of the variables defined above make their ways into the script.
+# See CMake's documentaton of the CONFIGURE_FILE command for details.
+
+SET(CheckTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/check_tails.py.in") 
+SET(CheckTailsScript "${CMAKE_CURRENT_BINARY_DIR}/sex_check_tails.py") 
+CONFIGURE_FILE(${CheckTailsScriptTemplate} ${CheckTailsScript} IMMEDIATE)
+
+IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+  #ADD_TEST("Consistency-Check--GlobalSex" "${_PythonExePath}" "${CheckTailsScript}")
+ENDIF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+
+#
+# Generation of expected last lines of detail_pop.100 files.
+#
+# To trigger this script, use commands like the following :
+#   $ pushd ${CMAKE_CURRENT_BINARY_DIR} # i.e., cd .../build/Tests/Researchers/dule/LocalSex/
+#   $ tar cvfz Tests.tgz `find . -name detail_pop.100.expected_last_line`
+#   $ cd ${CMAKE_CURRENT_SOURCE_DIR}
+#   $ tar xvfz ${CMAKE_CURRENT_BINARY_DIR}/Tests.tgz
+#   $ popd
+#
+# I think it's safer to require that these steps be performed by hand in order
+# to reduce the chance of inadvertently clobbering existing consistency-check suites.
+#
+SET(GenerateTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/generate_tails.py.in") 
+SET(GenerateTailsScript "${CMAKE_CURRENT_BINARY_DIR}/sex_generate_tails.py") 
+CONFIGURE_FILE(${GenerateTailsScriptTemplate} ${GenerateTailsScript} IMMEDIATE)
+
+
+#
+# Reconfigure for GlobalAsex
+#
+
+SET(ConfigDir "${CMAKE_CURRENT_SOURCE_DIR}/config")
+SET(GenesisFile "${ConfigDir}/genesis")
+SET(InstSetFile "${ConfigDir}/inst_set.asex")
+SET(EventFile "${ConfigDir}/events.cfg")
+SET(EnvironmentFile "${ConfigDir}/environment.cfg")
+#SET(StartCreatureFile "${ConfigDir}/organism.100.asex")
+SET(StartCreatureFile "${ConfigDir}/creature.final.asex")
+SET(AvidaArgs "-seed %d -set INST_SET ${InstSetFile} -set EVENT_FILE ${EventFile} -set ENVIRONMENT_FILE ${EnvironmentFile} -set START_CREATURE ${StartCreatureFile} -set BIRTH_METHOD 4")
+
+SET(SeedSet "range(100,110)")
+SET(RunSubdirPathBase "${CMAKE_CURRENT_BINARY_DIR}/GlobalAsex_")
+SET(OutputFileName "detail_pop.100")
+SET(ExpectationFilePathBase "${CMAKE_CURRENT_SOURCE_DIR}/GlobalAsex_")
+SET(ExpectationFileName "detail_pop.100.expected_last_line")
+
+SET(CheckTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/check_tails.py.in") 
+SET(CheckTailsScript "${CMAKE_CURRENT_BINARY_DIR}/asex_check_tails.py") 
+CONFIGURE_FILE(${CheckTailsScriptTemplate} ${CheckTailsScript} IMMEDIATE)
+
+IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+  ADD_TEST("Consistency-Check--GlobalAsex" "${_PythonExePath}" "${CheckTailsScript}")
+ENDIF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+
+SET(GenerateTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/generate_tails.py.in") 
+SET(GenerateTailsScript "${CMAKE_CURRENT_BINARY_DIR}/asex_generate_tails.py") 
+CONFIGURE_FILE(${GenerateTailsScriptTemplate} ${GenerateTailsScript} IMMEDIATE)
+

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,15 @@
+/.CMakeLists.txt.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/CMakeLists.txt/1.2/Thu Sep  9 19:45:27 2004//
+/README/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/run_list.kaben/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D/GlobalAsex_100////
+D/GlobalAsex_101////
+D/GlobalAsex_102////
+D/GlobalAsex_103////
+D/GlobalAsex_104////
+D/GlobalAsex_105////
+D/GlobalAsex_106////
+D/GlobalAsex_107////
+D/GlobalAsex_108////
+D/GlobalAsex_109////
+D/config////

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:27 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_100/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+544 326 95 1 1 112 0 0 0 100 -1 2 cjfqplcagngdsancoasfqnqbyyqcqattcpqxbzbiuttycastttvabjrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:27 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_101/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+688 3 60 1 1 170 0 0 0 100 -1 2 jrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoabcjfqplcagngdsancosfqnqbyyqcqatktpqxbzbiuttycastttvabjrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:27 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_102/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+629 155 59 1 1 172 0 0 0 100 -1 2 jrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoabcjfqplcagngdsancoasfqnqbyyqcqactttpqxbzbiuttycastttvabjrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:27 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_103/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+706 56 1 1 1 111 0 0 0 100 -1 2 jrzavcwaujbiuzusgqipgpqpctfhcqcrpqcnadkazpctpbeadcqpbgcjoabcjfqplcagngdsancoasfqnqbyyqcqatttpqxbzbiuttycasttvab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:28 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_104/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+695 285 1 1 1 111 0 0 0 100 -1 2 jrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazptpbeadcqpbgcjoabcjfqplcagngdsancoasfqnqbyyqcqatttptxbzbiuttycastttvab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:28 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_105/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+195 1 2 1 2 111 0 0 0 89 -1 1 jrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoacjfqplcagngdsancoasfqnqbyyqcqxtttpqxbzbiuttycastttvab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:28 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_106/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+685 11 2 1 1 122 0 0 0 100 -1 3 jrzavkwaujbiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoabcjfqplcagngdsancoasfqnqbyyqcqatttpqxbzbiuttyastttvabjrzavcwkujb 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:28 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_107/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+383 229 1 1 1 222 0 0 0 100 -1 4 jrzavcwaujiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoabcjfqplcagngdsancoasfqnqbyyqcqatttpqxbzbiuttycastttvabjrzavcbaujiuzusgqipgpqpctfocqcrpqcnadkazpctpbeadcqpbgcjoabcjfqplcagngdsancoasfqnqbyyqcqatttpqxbzbiuttycastttvab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:28 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_108/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+313 103 1 1 2 112 0 0 0 87 -1 2 jrzavcwaujbiuzisgqipgpqpctfocqcrpqcnadkazpjtpbeadcqpbgcjoabcjgqplcagngdsancoasfqnqbyyqcqatttpqxbzbiuttycastttvab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/detail_pop.100.expected_last_line/1.2/Thu Sep  9 19:45:28 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/detail_pop.100.expected_last_line
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/detail_pop.100.expected_last_line	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/GlobalAsex_109/detail_pop.100.expected_last_line	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+572 37 1 1 1 113 0 0 0 100 -1 3 jrzavcwaujbiuzusgqipgpqpctfocqcrpqcnadkazpcvtpbeazcqpbgcjoabcjfqplcagngdsancoasfqnqbyyqcqatttpqxbzbiuytycastttvab 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/README
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/README	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/README	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,43 @@
+start date: 	6/7/04
+
+dir name: 	/home/dule/data/local_sex/LocalSex
+
+code used: 	/home/dule/avida-source/current-5-26-04
+
+duration: 	100,000 updates
+pop.size:	3600 organisms
+birth method:	0 (random local)
+
+death:		on
+		DEATH_METHOD 2 
+		# 2 = Die when inst executed = length * AGE_LIMIT (+ dev.)
+		AGE_LIMIT 20    # Modifies DEATH_METHOD
+
+ancestor: 	organism.100.sex 
+
+env file: 	environment.cfg
+lineages: 	on
+
+fixed length: 	no
+		CHILD_SIZE_RANGE 2.0   # Maximal differential between child and parent sizes.
+		MIN_COPIED_LINES 0.95    # Code fraction which must be copied before divide.
+		MIN_EXE_LINES    0.05    # Code fraction which must be executed before divide.
+
+mutations: 	INS_MUT_PROB    0.0005     # Insertion rate (per site, applied on divide).
+		DEL_MUT_PROB    0.0005     # Deletion rate (per site, applied on divide).
+		DIV_MUT_PROB    0.002      # Mutation rate (per site, applied on divide).
+
+run_list: 
+
+100..149 LocalSex ./primitive -s $seed 
+100..149 LocalAsex ./primitive -s $seed 
+
+comments: 
+
+Testing the effect of newly implemented local nature of sex, using local,
+random replacement as the birth method 
+
+All the parameters in these runs are the same as sex-nature-new-mut 
+(p. 150.1) other than the birth method. 
+
+Also added the same treatment with asexuals, and repeated the mass action sex/asex runs. 

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,8 @@
+/creature.final.asex/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/environment.cfg/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/events.cfg/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/genesis/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/inst_set.asex/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/inst_set.sex/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/organism.100.sex/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/LocalSex/config

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/creature.final.asex
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/creature.final.asex	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/creature.final.asex	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,143 @@
+# Filename........: creature.final
+# Update Output...: 100000
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: 99107
+# Genotype ID.....: 8095058
+# Parent Gen ID...: 8089738
+# Tree Depth......: 375
+# Parent Distance.: 1
+
+# Generation: 0
+# Merit...........:   2.2859e+08
+# Gestation Time..:          226
+# Fitness.........:  1.01146e+06
+# Errors..........:            4
+# Genome Size.....:          112
+# Copied Size.....:          112
+# Executed Size...:          109
+# Offspring.......:         SELF
+
+# not	1
+# nand	1
+# and	1
+# orn	1
+# or	1
+# andn	1
+# nor	1
+# xor	0
+# equ	1
+
+shift-r
+h-alloc
+set-flow
+nop-A
+mov-head
+nop-C
+jmp-head
+nop-A
+h-search
+shift-r
+nop-B
+swap
+h-search
+set-flow
+h-search
+div-asex
+push
+IO
+swap
+nand
+push
+nand
+IO
+nand
+nop-C
+h-copy
+pop
+sub
+nop-C
+IO
+nop-C
+h-alloc
+nand
+IO
+nop-C
+add
+nop-A
+if-n-equ
+shift-l
+nop-A
+set-flow
+nand
+nop-C
+h-copy
+nand
+nop-B
+if-less
+nop-A
+if-n-equ
+nop-C
+IO
+nand
+nop-B
+push
+nop-C
+shift-r
+sub
+nop-A
+nop-B
+nop-C
+shift-r
+pop
+IO
+nand
+inc
+nop-C
+nop-A
+push
+add
+push
+if-n-equ
+div-asex
+nop-A
+add
+nop-C
+sub
+nop-A
+div-asex
+pop
+IO
+add
+IO
+nop-B
+if-label
+if-label
+IO
+nop-C
+IO
+nop-A
+h-copy
+h-copy
+h-copy
+nand
+IO
+get-head
+nop-B
+set-flow
+nop-B
+swap
+h-search
+h-copy
+h-copy
+if-label
+nop-C
+nop-A
+div-asex
+h-copy
+h-copy
+h-copy
+mov-head
+nop-A
+nop-B

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/environment.cfg
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/environment.cfg	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/environment.cfg	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,23 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system.  From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see:  doc/environment.html
+# For other sample environments, see:  source/support/config/ 
+#
+##############################################################################
+
+REACTION  NOT  not   process:value=1.0:type=pow  requisite:max_count=1
+REACTION  NAND nand  process:value=1.0:type=pow  requisite:max_count=1
+REACTION  AND  and   process:value=2.0:type=pow  requisite:max_count=1
+REACTION  ORN  orn   process:value=2.0:type=pow  requisite:max_count=1
+REACTION  OR   or    process:value=3.0:type=pow  requisite:max_count=1
+REACTION  ANDN andn  process:value=3.0:type=pow  requisite:max_count=1
+REACTION  NOR  nor   process:value=4.0:type=pow  requisite:max_count=1
+REACTION  XOR  xor   process:value=4.0:type=pow  requisite:max_count=1
+REACTION  EQU  equ   process:value=5.0:type=pow  requisite:max_count=1

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/events.cfg
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/events.cfg	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/events.cfg	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,48 @@
+##############################################################################
+#
+# This is the setup file for the events system.  From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax:  [trigger]  [start:interval:stop]  [event] [arguments...]
+#
+# This file is currently setup to start off a population full of the 
+# starting organism specified in genesis, and then record key information
+# every 100 updates.
+#
+# For information on how to use this file, see:  doc/events.html
+# For other sample event configurations, see:  source/support/config/
+#
+##############################################################################
+#u 0     inject_all START_CREATURE       # Inject all the begining
+
+# u 10:10:end print_instruction_data
+
+# Print all of the standard data files...
+#u 0:100 print_dom                 # Save the most abundant genotypes
+#u 0:100:end print_average_data    # Save info about they average genotypes
+#u 0:100:end print_dominant_data   # Save info about most abundant genotypes
+#u 0:100:end print_stats_data      # Collect satistics about entire pop.
+#u 0:100:end print_count_data      # Count organisms, genotypes, species, etc.
+#u 0:100:end print_tasks_data      # Save organisms counts for each task.
+#u 0:100:end print_time_data       # Track time conversion (generations, etc.)
+#u 0:100:end print_resource_data   # Track resource abundance.
+#
+#u 100:100:end print_variance_data   # Variance on averages.
+#u 100:100:end print_error_data      # Std. Error on averages.
+
+# A few data files not printed by default
+# u 100:100:end print_totals_data     # Total counts over entire run.
+# u 100:100:end print_tasks_exe_data  # Num. times tasks have been executed.
+
+
+# Setup the exit time and full population data collection.
+#u 10000:10000 detail_pop           # Save current state of population.
+#u 50000:50000 dump_historic_pop    # Save ancestors of current population.
+
+#u 100000 print_dom creature.final
+
+u 100:100 detail_pop           # Save current state of population.
+u 100 exit                      # exit
+
+

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,173 @@
+#############################################################################
+# This file includes all the basic run-time defines for avida.
+# For more information, see doc/genesis.html
+#############################################################################
+
+VERSION_ID 1.99		# Do not change this value!
+
+### Architecture Variables ###
+MAX_UPDATES  -1         # Maximum updates to run simulation (-1 = no limit)
+MAX_GENERATIONS -1      # Maximum generations to run simulation (-1 = no limit)
+END_CONDITION_MODE 0	# End run when ...
+			# 0 = MAX_UPDATES _OR_ MAX_GENERATIONS is reached
+			# 1 = MAX_UPDATES _AND_ MAX_GENERATIONS is reached
+WORLD-X 60		# Width of the world in Avida mode.
+WORLD-Y 60		# Height of the world in Avida mode.
+MAX_CPU_THREADS 1	# Number of Threads CPU's can spawn
+RANDOM_SEED 0		# Random number seed. (0 for based on time)
+
+### Configuration Files ###
+DEFAULT_DIR ../work/              # Directory in which config files are found
+INST_SET inst_set.asex         # File containing instruction set
+EVENT_FILE events.cfg             # File containing list of events during run
+ANALYZE_FILE analyze.cfg          # File used for analysis mode
+ENVIRONMENT_FILE environment.cfg  # File that describes the environment
+START_CREATURE organism.100.asex   # Organism to seed the soup
+
+### Reproduction ###
+BIRTH_METHOD 0    # 0 = Replace random organism in neighborhood
+		  # 1 = Replace oldest organism in neighborhood
+		  # 2 = Replace largest Age/Merit in neighborhood
+		  # 3 = Place only in empty cells in neighborhood
+		  # 4 = Replace random from entire population (Mass Action)
+		  # 5 = Replace oldest in entire population (like Tierra)
+DEATH_METHOD 2    # 0 = Never die of old age.
+		  # 1 = Die when inst executed = AGE_LIMIT (with deviation)
+		  # 2 = Die when inst executed = length * AGE_LIMIT (+ dev.)
+AGE_LIMIT 20    # Modifies DEATH_METHOD
+AGE_DEVIATION 0   # Modified DEATH_METHOD
+ALLOC_METHOD 0    # 0 = Allocated space is set to default instruction.
+                  # 1 = Set to section of dead genome (Necrophilia)
+                  # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 1   # 0 = Divide leaves state of mother untouched.
+                  # 1 = Divide resets state of mother
+                  #     (after the divide, we have 2 children)
+
+GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
+                        #     increased on divide.
+			# 1 = Both the generation of the mother and child are
+			#     increased on divide (good with DIVIDE_METHOD 1).
+
+### Divide Restrictions ####
+CHILD_SIZE_RANGE 2.0	# Maximal differential between child and parent sizes.
+MIN_COPIED_LINES 0.95    # Code fraction which must be copied before divide.
+MIN_EXE_LINES    0.05    # Code fraction which must be executed before divide.
+REQUIRE_ALLOCATE   1    # Is a an allocate required before a divide? (0/1)
+REQUIRED_TASK -1  # Number of task required for successful divide.
+
+### Mutations ###
+
+# mutations that occur during execution..
+POINT_MUT_PROB  0.0     # Mutation rate (per-location per update)
+COPY_MUT_PROB   0.0     # Mutation rate (per copy).
+
+# mutations that occur on divide...
+INS_MUT_PROB    0.0005     # Insertion rate (per site, applied on divide).
+DEL_MUT_PROB    0.0005     # Deletion rate (per site, applied on divide).
+DIV_MUT_PROB    0.002      # Mutation rate (per site, applied on divide).
+DIVIDE_MUT_PROB 0.0     # Mutation rate (per divide).
+DIVIDE_INS_PROB 0.0     # Insertion rate (per divide).
+DIVIDE_DEL_PROB 0.0     # Deletion rate (per divide).
+PARENT_MUT_PROB 0.0     # Per-site, in parent, on divide
+
+# heads based mutations
+# READ_SHIFT_PROB   0.0
+# READ INS_PROB     0.0
+# READ_DEL_PROB     0.0
+# WRITE_SHIFT_PROB  0.0
+# WRITE_INS_PROB    0.0
+# WRITE_DEL_PROB    0.0
+
+MUT_RATE_SOURCE 0     # 0 = Organisms get mut rates from the environment
+		      # 1 =  ... from their parents
+MUT_RATE_INC 0.0      # Probability of mutation rates increasing... (at birth)
+MUT_RATE_DEC 0.0      # Probability of mutation rates decreasing... (at birth)
+MUT_CHANGE_FACTOR 1.0 # Factor by which mutation rates change (must be >= 1.0)
+
+MUT_RATE_FLOOR	   0.0	# Lowest possible mutation rate (for MUT_RATE_SOURCE=1)
+MUT_RATE_CEILING   1.0	# Highest possible mutation rate (for MUT_RATE_SOURCE=1)
+
+### Mutation reversions ###
+# these slow down avida a lot, and should be set to 0 normally.
+REVERT_FATAL       0.0  # Should any mutations be reverted on birth?
+REVERT_DETRIMENTAL 0.0  #   0.0 to 1.0; Probability of reversion.
+REVERT_NEUTRAL     0.0
+REVERT_BENEFICIAL  0.0
+
+STERILIZE_FATAL       0.0  # Should any mutations clear (kill) the organism?
+STERILIZE_DETRIMENTAL 0.0  #   0.0 to 1.0; Probability of reset.
+STERILIZE_NEUTRAL     0.0
+STERILIZE_BENEFICIAL  0.0
+
+FAIL_IMPLICIT     0	# Should copies that failed *not* due to mutations
+			# be eliminated?
+
+### Time Slicing ###
+AVE_TIME_SLICE 30
+SLICING_METHOD 2	# 0 = CONSTANT: all organisms get default...
+			# 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+			# 2 = INTEGRATED: Perfectly integrated deterministic.
+SIZE_MERIT_METHOD 4	# 0 = off (merit is independent of size)
+			# 1 = Merit proportional to copied size
+			# 2 = Merit prop. to executed size
+			# 3 = Merit prop. to full size
+			# 4 = Merit prop. to min of executed or copied size
+			# 5 = Merit prop. to sqrt of the minimum size
+TASK_MERIT_METHOD 1	# 0 = No task bonuses
+			# 1 = Bonus just equals the task bonus
+THREAD_SLICING_METHOD 0 # 0 = One thread executed per time slice.
+			# 1 = All threads executed each time slice.
+
+MAX_LABEL_EXE_SIZE 1	# Max nops marked as executed when labels are used
+MERIT_TIME 1            # 0 = Merit Calculated when task completed
+		        # 1 = Merit Calculated on Divide
+MAX_NUM_TASKS_REWARDED -1  # -1 = Unlimited
+
+### Genotype Info ###
+THRESHOLD 3		# Number of organisms in a genotype needed for it
+			#   to be considered viable.
+GENOTYPE_PRINT 0	# 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0	# Print out a genotype if it stays dominant for
+                        #   this many updates. (0 = off)
+SPECIES_THRESHOLD 2     # max failure count for organisms to be same species
+SPECIES_RECORDING 0	# 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0		# 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20    # Time allocated in test CPUs (multiple of length)
+TRACK_MAIN_LINEAGE 1    # Track primary lineage leading to final population?
+
+### Log Files ###
+LOG_CREATURES 0		# 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0		# 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0		# 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0		# 0/1 (off/on) toggle to print file.
+LOG_GENEOLOGY 0		# 0 = off, 1 = all, 2 = parents only.
+LOG_LANDSCAPE 0		# 0/1 (off/on) toggle to print file.
+
+LOG_LINEAGES 0          # 0/1 (off/on) to log advantageous mutations
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# See also LINEAGE_CREATION_METHOD.
+
+LINEAGE_CREATION_METHOD 0
+# Lineage creation options are.  Works only when LOG_LINEAGES is set to 1.
+#   0 = manual creation (on inject, use successive integers as lineage labels).
+#   1 = when a child's (potential) fitness is higher than that of its parent.
+#   2 = when a child's (potential) fitness is higher than max in population.
+#   3 = when a child's (potential) fitness is higher than max in dom. lineage
+#	*and* the child is in the dominant lineage, or (2)
+#   4 = when a child's (potential) fitness is higher than max in dom. lineage
+#	(and that of its own lineage)
+#   5 = same as child's (potential) fitness is higher than that of the
+#       currently dominant organism, and also than that of any organism
+#       currently in the same lineage.
+#   6 = when a child's (potential) fitness is higher than any organism
+#       currently in the same lineage.
+#   7 = when a child's (potential) fitness is higher than that of any
+#       organism in its line of descent
+
+### Debug ###
+DEBUG_LEVEL 2		# 0 = ERRORS ONLY, 1 = WARNINGS, 2 = COMMENTS
+
+### END ###
+
+

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.asex
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.asex	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.asex	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,52 @@
+nop-A      1   # a
+nop-B      1   # b
+nop-C      1   # c
+if-n-equ   1   # d
+if-less    1   # e
+pop        1   # f
+push       1   # g
+swap-stk   1   # h
+swap       1   # i 
+shift-r    1   # j
+shift-l    1   # k
+inc        1   # l
+dec        1   # m
+add        1   # n
+sub        1   # o
+nand       1   # p
+IO         1   # q   Puts current contents of register and gets new.
+h-alloc    1   # r   Allocate as much memory as organism can use.
+div-asex    1   # s   Cuts off everything between the read and write heads
+h-copy     1   # t   Combine h-read and h-write
+h-search   1   # u   Search for matching template, set flow head & return info
+               #   #   if no template, move flow-head here, set size&offset=0.
+mov-head   1   # v   Move ?IP? head to flow control.
+jmp-head   1   # w   Move ?IP? head by fixed amount in CX.  Set old pos in CX.
+get-head   1   # x   Get position of specified head in CX.
+if-label   1   # y
+set-flow   1   # z   Move flow-head to address in ?CX? 
+
+#adv-head   1
+#jump-f     1
+#jump-b     1
+#call       1
+#return     1
+#if-bit-1   1
+#get        1
+#put        1
+#h-read     1
+#h-write    1
+#set-head   1
+#search-f   1
+#search-b   1
+
+
+# Works on multiple nops:  pop  push  inc  dec  IO  adv-head 
+
+# What if we add a new head.  Search will return the location of something,
+# and put the new head there.  Then set-head will move another head to that
+# point.  In the case of the copy loop, it only needs to be set once and
+# this will speed up the code quite a bit!
+
+# Search with no template returns current position (abs line number) in
+# genome.

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.sex
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.sex	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/inst_set.sex	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,52 @@
+nop-A      1   # a
+nop-B      1   # b
+nop-C      1   # c
+if-n-equ   1   # d
+if-less    1   # e
+pop        1   # f
+push       1   # g
+swap-stk   1   # h
+swap       1   # i 
+shift-r    1   # j
+shift-l    1   # k
+inc        1   # l
+dec        1   # m
+add        1   # n
+sub        1   # o
+nand       1   # p
+IO         1   # q   Puts current contents of register and gets new.
+h-alloc    1   # r   Allocate as much memory as organism can use.
+div-sex    1   # s   Cuts off everything between the read and write heads
+h-copy     1   # t   Combine h-read and h-write
+h-search   1   # u   Search for matching template, set flow head & return info
+               #   #   if no template, move flow-head here, set size&offset=0.
+mov-head   1   # v   Move ?IP? head to flow control.
+jmp-head   1   # w   Move ?IP? head by fixed amount in CX.  Set old pos in CX.
+get-head   1   # x   Get position of specified head in CX.
+if-label   1   # y
+set-flow   1   # z   Move flow-head to address in ?CX? 
+
+#adv-head   1
+#jump-f     1
+#jump-b     1
+#call       1
+#return     1
+#if-bit-1   1
+#get        1
+#put        1
+#h-read     1
+#h-write    1
+#set-head   1
+#search-f   1
+#search-b   1
+
+
+# Works on multiple nops:  pop  push  inc  dec  IO  adv-head 
+
+# What if we add a new head.  Search will return the location of something,
+# and put the new head there.  Then set-head will move another head to that
+# point.  In the case of the copy loop, it only needs to be set once and
+# this will speed up the code quite a bit!
+
+# Search with no template returns current position (abs line number) in
+# genome.

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/organism.100.sex
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/organism.100.sex	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/organism.100.sex	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,100 @@
+h-alloc    # Allocate space for child
+h-search   # Locate the end of the organism
+nop-C      #
+nop-A      #
+mov-head   # Place write-head at beginning of offspring.
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+h-search   # Mark the beginning of the copy loop
+h-copy     # Do the copy
+if-label   # If we're done copying....
+nop-C      #
+nop-A      #
+div-sex   #    ...divide!
+mov-head   # Otherwise, loop back to the beginning of the copy loop.
+nop-A      # End label.
+nop-B      #

Added: trunk/consistencytests/Tests/Researchers/dule/LocalSex/run_list.kaben
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/run_list.kaben	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/run_list.kaben	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,32 @@
+set email dule at alife.org # User's e-mail address
+
+set freq_email job    # Frequency status is e-mailed to you.  Choices are:
+                        #   job -- when this job is completed (default)
+                        #   run -- when each run is completed
+                        #   crash -- when a run crashes
+                        #   never -- no e-mail is sent
+
+set priority 3          # Priority of the job.  Normally an integer between 1
+                        # (low priority) and 5 (high priority)  where 3 is the
+                        # default priority.
+
+set description sex local/global # Description of the job to run
+
+#set class_pref 4,3,2,1 # List in order of preference which class of computers
+                        # you wish to run your programs on.  Current classes:
+                        # class   GHz   MB Description
+                        #     1  0.50   64 Original Leviathan computers
+                        #     2  1.40  512 Original Alice computers
+                        #     3  2.40  512 Alice computers with newer CPUs
+                        #     4  2.80  512 Single CPU Intel computers
+                        #   201  0.50  128 Original Leviathan using both CPUs
+                        #   202  1.40 1024 Original Alice using both CPUs
+                        #   203  2.60 1024 New CPU Alice using both CPUs
+                        # Default = 4,3,2,1
+
+set max_cpus 50         # Maximum number of CPUs that this job can run on
+                        # default=20
+
+
+100..149 GlobalSex ./primitive -s $seed -set INST_SET inst_set.sex -set START_CREATURE organism.100.sex -set BIRTH_METHOD 4
+100..149 GlobalAsex ./primitive -s $seed -set INST_SET inst_set.asex -set START_CREATURE organism.100.asex -set BIRTH_METHOD 4

Added: trunk/consistencytests/Tests/Researchers/dule/modularity/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/modularity/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/modularity/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,103 @@
+
+# Note :
+#
+# ${CMAKE_CURRENT_SOURCE_DIR} points to the current source directory,
+# i.e., .../Tests/Researchers/dule/LocalSex/.
+#
+# ${CMAKE_CURRENT_BINARY_DIR} points to the equivalent binary directory,
+# i.e., .../build/Tests/Researchers/dule/LocalSex/.
+#
+
+#
+# Avida configuration
+#
+SET(ConfigDir "${CMAKE_CURRENT_SOURCE_DIR}/config")
+SET(GenesisFile "${ConfigDir}/genesis")
+SET(InstSetFile "${ConfigDir}/inst_set.sex")
+SET(EventFile "${ConfigDir}/events.cfg")
+SET(EnvironmentFile "${ConfigDir}/environment.cfg")
+SET(StartCreatureFile "${ConfigDir}/organism.100.sex")
+SET(AvidaArgs "-seed %d -set INST_SET ${InstSetFile} -set EVENT_FILE ${EventFile} -set ENVIRONMENT_FILE ${EnvironmentFile} -set START_CREATURE ${StartCreatureFile} -set BIRTH_METHOD 4")
+
+#
+# Consistency checks configuration
+#
+
+# This is Python list of Avida random seeds.
+# E.g., "range(100,15)" is equivalent to the Python list "[100,101,102,103,104]".
+# I.e., SET(SeedSet "range(100,105)") is equivalent to SET(SeedSet "[100,101,102,103,104]").
+SET(SeedSet "range(100,110)")
+# Avida will be run in, and store output files in, ${CMAKE_CURRENT_BINARY_DIR}/Test_100, and so on.
+SET(RunSubdirPathBase "${CMAKE_CURRENT_BINARY_DIR}/GlobalSex_")
+# I've written ${ConfigDir}/events.cfg to stop Avida after 100 updates,
+# and to output a single detail-population file "detail_pop.100" per run,
+# i.e., ${CMAKE_CURRENT_SOURCE_DIR}/Test_100/detail_pop.100, and so on.
+SET(OutputFileName "detail_pop.100")
+# Similar to above, except that this tells the testing scripts where to find
+# expected last lines of detail_pop.100 files,
+# i.e., ${CMAKE_CURRENT_SOURCE_DIR}/Test_100/detail_pop.100.expected_last_line, and so on.
+SET(ExpectationFilePathBase "${CMAKE_CURRENT_SOURCE_DIR}/GlobalSex_")
+SET(ExpectationFileName "detail_pop.100.expected_last_line")
+
+#
+# This generates the Python script that performs consistency checks.
+# Several of the variables defined above make their ways into the script.
+# See CMake's documentaton of the CONFIGURE_FILE command for details.
+
+SET(CheckTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/check_tails.py.in") 
+SET(CheckTailsScript "${CMAKE_CURRENT_BINARY_DIR}/sex_check_tails.py") 
+CONFIGURE_FILE(${CheckTailsScriptTemplate} ${CheckTailsScript} IMMEDIATE)
+
+IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+  #ADD_TEST("GlobalSex" "${_PythonExePath}" "${CheckTailsScript}")
+ENDIF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+
+#
+# Generation of expected last lines of detail_pop.100 files.
+#
+# To trigger this script, use commands like the following :
+#   $ pushd ${CMAKE_CURRENT_BINARY_DIR} # i.e., cd .../build/Tests/Researchers/dule/LocalSex/
+#   $ tar cvfz Tests.tgz `find . -name detail_pop.100.expected_last_line`
+#   $ cd ${CMAKE_CURRENT_SOURCE_DIR}
+#   $ tar xvfz ${CMAKE_CURRENT_BINARY_DIR}/Tests.tgz
+#   $ popd
+#
+# I think it's safer to require that these steps be performed by hand in order
+# to reduce the chance of inadvertently clobbering existing consistency-check suites.
+#
+SET(GenerateTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/generate_tails.py.in") 
+SET(GenerateTailsScript "${CMAKE_CURRENT_BINARY_DIR}/sex_generate_tails.py") 
+CONFIGURE_FILE(${GenerateTailsScriptTemplate} ${GenerateTailsScript} IMMEDIATE)
+
+
+#
+# Reconfigure for GlobalAsex
+#
+
+SET(ConfigDir "${CMAKE_CURRENT_SOURCE_DIR}/config")
+SET(GenesisFile "${ConfigDir}/genesis")
+SET(InstSetFile "${ConfigDir}/inst_set.asex")
+SET(EventFile "${ConfigDir}/events.cfg")
+SET(EnvironmentFile "${ConfigDir}/environment.cfg")
+#SET(StartCreatureFile "${ConfigDir}/organism.100.asex")
+SET(StartCreatureFile "${ConfigDir}/creature.final.asex")
+SET(AvidaArgs "-seed %d -set INST_SET ${InstSetFile} -set EVENT_FILE ${EventFile} -set ENVIRONMENT_FILE ${EnvironmentFile} -set START_CREATURE ${StartCreatureFile} -set BIRTH_METHOD 4")
+
+SET(SeedSet "range(100,110)")
+SET(RunSubdirPathBase "${CMAKE_CURRENT_BINARY_DIR}/GlobalAsex_")
+SET(OutputFileName "detail_pop.100")
+SET(ExpectationFilePathBase "${CMAKE_CURRENT_SOURCE_DIR}/GlobalAsex_")
+SET(ExpectationFileName "detail_pop.100.expected_last_line")
+
+SET(CheckTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/check_tails.py.in") 
+SET(CheckTailsScript "${CMAKE_CURRENT_BINARY_DIR}/asex_check_tails.py") 
+CONFIGURE_FILE(${CheckTailsScriptTemplate} ${CheckTailsScript} IMMEDIATE)
+
+IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+  ADD_TEST("GlobalAsex" "${_PythonExePath}" "${CheckTailsScript}")
+ENDIF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+
+SET(GenerateTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/generate_tails.py.in") 
+SET(GenerateTailsScript "${CMAKE_CURRENT_BINARY_DIR}/asex_generate_tails.py") 
+CONFIGURE_FILE(${GenerateTailsScriptTemplate} ${GenerateTailsScript} IMMEDIATE)
+

Added: trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,2 @@
+/CMakeLists.txt/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/dule/modularity

Added: trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/dule/modularity/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/goingssh/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+SUBDIRS(Kazi)

Added: trunk/consistencytests/Tests/Researchers/goingssh/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,3 @@
+/.CMakeLists.txt.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/CMakeLists.txt/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D/Kazi////

Added: trunk/consistencytests/Tests/Researchers/goingssh/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/goingssh

Added: trunk/consistencytests/Tests/Researchers/goingssh/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CMakeLists.txt	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CMakeLists.txt	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,47 @@
+SET(ConfigDir "${CMAKE_CURRENT_SOURCE_DIR}/testconfig")
+SET(GenesisFile "${ConfigDir}/genesis")
+SET(InstSetFile "${ConfigDir}/inst_set.default")
+SET(EventFile "${ConfigDir}/events.cfg")
+SET(EnvironmentFile "${ConfigDir}/environment.cfg")
+SET(StartCreatureFile "${ConfigDir}/kazi.org")
+SET(AvidaArgs "-seed %d -set INST_SET ${InstSetFile} -set EVENT_FILE ${EventFile} -set ENVIRONMENT_FILE ${EnvironmentFile} -set START_CREATURE ${StartCreatureFile}")
+
+SET(SeedSet "range(100,110)")
+SET(RunSubdirPathBase "${CMAKE_CURRENT_BINARY_DIR}/Kazi_")
+SET(OutputFileName "detail_pop.100")
+SET(ExpectationFilePathBase "${CMAKE_CURRENT_SOURCE_DIR}/Kazi_")
+SET(ExpectationFileName "detail_pop.100.expected_last_line")
+
+SET(CheckTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/check_tails.py.in") 
+SET(CheckTailsScript "${CMAKE_CURRENT_BINARY_DIR}/kazi_check_tails.py") 
+CONFIGURE_FILE(${CheckTailsScriptTemplate} ${CheckTailsScript} IMMEDIATE)
+
+IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+  ADD_TEST("GlobalAsex" "${_PythonExePath}" "${CheckTailsScript}")
+ENDIF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+
+SET(GenerateTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/generate_tails.py.in") 
+SET(GenerateTailsScript "${CMAKE_CURRENT_BINARY_DIR}/kazi_generate_tails.py") 
+CONFIGURE_FILE(${GenerateTailsScriptTemplate} ${GenerateTailsScript} IMMEDIATE)
+
+
+
+SET(SeedSet "range(100,110)")
+SET(RunSubdirPathBase "${CMAKE_CURRENT_BINARY_DIR}/GlobalAsex_")
+SET(OutputFileName "detail_pop.100")
+SET(ExpectationFilePathBase "${CMAKE_CURRENT_SOURCE_DIR}/GlobalAsex_")
+SET(ExpectationFileName "detail_pop.100.expected_last_line")
+
+SET(CheckTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/check_tails.py.in") 
+SET(CheckTailsScript "${CMAKE_CURRENT_BINARY_DIR}/asex_check_tails.py") 
+CONFIGURE_FILE(${CheckTailsScriptTemplate} ${CheckTailsScript} IMMEDIATE)
+
+IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+  ADD_TEST("GlobalAsex" "${_PythonExePath}" "${CheckTailsScript}")
+ENDIF(AVD_CONSISTENCY_TEST_PRIMITIVE)
+
+SET(GenerateTailsScriptTemplate "${PROJECT_SOURCE_DIR}/CMakeModules/Templates/generate_tails.py.in") 
+SET(GenerateTailsScript "${CMAKE_CURRENT_BINARY_DIR}/asex_generate_tails.py") 
+CONFIGURE_FILE(${GenerateTailsScriptTemplate} ${GenerateTailsScript} IMMEDIATE)
+
+

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,3 @@
+/.CMakeLists.txt.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/CMakeLists.txt/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D/testconfig////

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/goingssh/Kazi

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Entries
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Entries	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Entries	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,11 @@
+/.events.cfg.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.genesis.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/.kazi.org.swp/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/analyze.cfg/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/environment.cfg/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/events.cfg/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/genesis/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/inst_set.default/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/kazi.org/1.1.1.1/Tue Sep  7 16:06:17 2004//
+/organism.default/1.1.1.1/Tue Sep  7 16:06:17 2004//
+D

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Repository
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Repository	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Repository	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+consistencytests/Tests/Researchers/goingssh/Kazi/testconfig

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Root
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Root	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/CVS/Root	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1 @@
+/home/kaben/Projects/cvs-roots/avida

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/analyze.cfg
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/analyze.cfg	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/analyze.cfg	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,9 @@
+#############################################################################
+# This file is used to setup avida when it is in analysis-only mode (by
+# running "avida -a".  It allows variety of methods to load organisms
+# (specifying the type of each) and analyze them once loaded.
+#
+# See the documentation in doc/analyze_mode.html for usage, or the file
+# doc/analyze_samples.html for guidelines on writing programs.
+#
+#############################################################################

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/environment.cfg
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/environment.cfg	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/environment.cfg	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,23 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system.  From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see:  doc/environment.html
+# For other sample environments, see:  source/support/config/ 
+#
+##############################################################################
+
+REACTION  NOT  not   process:value=1.0:type=pow  requisite:max_count=1
+REACTION  NAND nand  process:value=1.0:type=pow  requisite:max_count=1
+REACTION  AND  and   process:value=2.0:type=pow  requisite:max_count=1
+REACTION  ORN  orn   process:value=2.0:type=pow  requisite:max_count=1
+REACTION  OR   or    process:value=3.0:type=pow  requisite:max_count=1
+REACTION  ANDN andn  process:value=3.0:type=pow  requisite:max_count=1
+REACTION  NOR  nor   process:value=4.0:type=pow  requisite:max_count=1
+REACTION  XOR  xor   process:value=4.0:type=pow  requisite:max_count=1
+REACTION  EQU  equ   process:value=5.0:type=pow  requisite:max_count=1

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/events.cfg
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/events.cfg	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/events.cfg	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,42 @@
+##############################################################################
+#
+# This is the setup file for the events system.  From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax:  [trigger]  [start:interval:stop]  [event] [arguments...]
+#
+# This file is currently setup to start off a population full of the 
+# starting organism specified in genesis, and then record key information
+# every 100 updates.
+#
+# For information on how to use this file, see:  doc/events.html
+# For other sample event configurations, see:  source/support/config/
+#
+##############################################################################
+
+u 0 inject_all kazi.org 100
+
+# Print all of the standard data files...
+#u 0:100 print_dom                 # Save the most abundant genotypes
+#u 0:100:end print_average_data    # Save info about they average genotypes
+#u 0:100:end print_dominant_data   # Save info about most abundant genotypes
+#u 0:100:end print_stats_data      # Collect satistics about entire pop.
+#u 0:100:end print_count_data      # Count organisms, genotypes, species, etc.
+#u 0:100:end print_tasks_data      # Save organisms counts for each task.
+#u 0:100:end print_time_data       # Track time conversion (generations, etc.)
+#u 0:100:end print_resource_data   # Track resource abundance.
+#
+## A few data files not printed by default
+## u 100:100:end print_error_data      # Std. Error on averages.
+## u 100:100:end print_variance_data   # Variance on averages.
+## u 100:100:end print_totals_data     # Total counts over entire run.
+#u 100:100:end print_tasks_exe_data  # Num. times tasks have been executed.
+#
+## Setup the exit time and full population data collection.
+#u 5000:5000 detail_pop           # Save current state of population.
+#u 5000:5000 dump_historic_pop    # Save ancestors of current population.
+#u 20000 exit                      # exit
+
+u 100:100 detail_pop           # Save current state of population.
+u 100 exit                      # exit

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/genesis
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/genesis	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/genesis	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,166 @@
+#############################################################################
+# This file includes all the basic run-time defines for avida.
+# For more information, see doc/genesis.html
+#############################################################################
+
+VERSION_ID 2.0b7		# Do not change this value!
+
+### Architecture Variables ###
+MAX_UPDATES  -1         # Maximum updates to run simulation (-1 = no limit)
+MAX_GENERATIONS -1      # Maximum generations to run simulation (-1 = no limit)
+END_CONDITION_MODE 0	# End run when ...
+			# 0 = MAX_UPDATES _OR_ MAX_GENERATIONS is reached
+			# 1 = MAX_UPDATES _AND_ MAX_GENERATIONS is reached
+WORLD-X 60		# Width of the world in Avida mode.
+WORLD-Y 60		# Height of the world in Avida mode.
+WORLD_GEOMETRY 2        # 1 = Bounded Grid
+                        # 2 = Torus (Default)
+RANDOM_SEED 0		# Random number seed. (0 for based on time)
+HARDWARE_TYPE 0		# 0 = Original CPUs
+			# 1 = New, Stack-based CPUs
+MAX_CPU_THREADS 1	# Number of Threads CPUs can spawn
+
+### Configuration Files ###
+DEFAULT_DIR ./              # Directory in which config files are found
+INST_SET inst_set.default         # File containing instruction set
+EVENT_FILE events.cfg             # File containing list of events during run
+ANALYZE_FILE analyze.cfg          # File used for analysis mode
+ENVIRONMENT_FILE environment.cfg  # File that describes the environment
+START_CREATURE organism.default   # Organism to seed the soup
+
+### Reproduction ###
+BIRTH_METHOD 0    # 0 = Replace random organism in neighborhood
+		  # 1 = Replace oldest organism in neighborhood
+		  # 2 = Replace largest Age/Merit in neighborhood
+		  # 3 = Place only in empty cells in neighborhood
+		  # 4 = Replace random from entire population (Mass Action)
+		  # 5 = Replace oldest in entire population (like Tierra)
+DEATH_METHOD 0    # 0 = Never die of old age.
+		  # 1 = Die when inst executed = AGE_LIMIT (with deviation)
+		  # 2 = Die when inst executed = length * AGE_LIMIT (+ dev.)
+AGE_LIMIT 5000    # Modifies DEATH_METHOD
+AGE_DEVIATION 0   # Modified DEATH_METHOD
+ALLOC_METHOD 0    # 0 = Allocated space is set to default instruction.
+                  # 1 = Set to section of dead genome (Necrophilia)
+                  # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 1   # 0 = Divide leaves state of mother untouched.
+                  # 1 = Divide resets state of mother
+                  #     (after the divide, we have 2 children)
+
+GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
+                        #     increased on divide.
+			# 1 = Both the generation of the mother and child are
+			#     increased on divide (good with DIVIDE_METHOD 1).
+
+### Divide Restrictions ####
+CHILD_SIZE_RANGE 1.0	# Maximal differential between child and parent sizes.
+MIN_COPIED_LINES 0.5    # Code fraction which must be copied before divide.
+MIN_EXE_LINES    0.5    # Code fraction which must be executed before divide.
+REQUIRE_ALLOCATE   1    # Is a an allocate required before a divide? (0/1)
+REQUIRED_TASK -1  # Number of task required for successful divide.
+
+### Mutations ###
+
+# mutations that occur during execution..
+POINT_MUT_PROB  0.0     # Mutation rate (per-location per update)
+COPY_MUT_PROB   0.002  # Mutation rate (per copy).
+
+# mutations that occur on divide...
+INS_MUT_PROB    0.0     # Insertion rate (per site, applied on divide).
+DEL_MUT_PROB    0.0     # Deletion rate (per site, applied on divide).
+DIV_MUT_PROB    0.0     # Mutation rate (per site, applied on divide).
+DIVIDE_MUT_PROB 0.0     # Mutation rate (per divide).
+DIVIDE_INS_PROB 0.0    # Insertion rate (per divide).
+DIVIDE_DEL_PROB 0.0    # Deletion rate (per divide).
+PARENT_MUT_PROB 0.0     # Per-site, in parent, on divide
+
+# heads based mutations
+# READ_SHIFT_PROB   0.0
+# READ INS_PROB     0.0
+# READ_DEL_PROB     0.0
+# WRITE_SHIFT_PROB  0.0
+# WRITE_INS_PROB    0.0
+# WRITE_DEL_PROB    0.0
+
+
+### Mutation reversions ###
+# these slow down avida a lot, and should be set to 0 normally.
+REVERT_FATAL       0.0  # Should any mutations be reverted on birth?
+REVERT_DETRIMENTAL 0.0  #   0.0 to 1.0; Probability of reversion.
+REVERT_NEUTRAL     0.0
+REVERT_BENEFICIAL  0.0
+
+STERILIZE_FATAL       0.0  # Should any mutations clear (kill) the organism?
+STERILIZE_DETRIMENTAL 0.0  #   0.0 to 1.0; Probability of reset.
+STERILIZE_NEUTRAL     0.0
+STERILIZE_BENEFICIAL  0.0
+
+FAIL_IMPLICIT     0	# Should copies that failed *not* due to mutations
+			# be eliminated?
+KAZI_DISTANCE	5	# HDT of any kaziing organism
+
+### Time Slicing ###
+AVE_TIME_SLICE 30
+SLICING_METHOD 2	# 0 = CONSTANT: all organisms get default...
+			# 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+			# 2 = INTEGRATED: Perfectly integrated deterministic.
+SIZE_MERIT_METHOD 4	# 0 = off (merit is independent of size)
+			# 1 = Merit proportional to copied size
+			# 2 = Merit prop. to executed size
+			# 3 = Merit prop. to full size
+			# 4 = Merit prop. to min of executed or copied size
+			# 5 = Merit prop. to sqrt of the minimum size
+TASK_MERIT_METHOD 1	# 0 = No task bonuses
+			# 1 = Bonus just equals the task bonus
+THREAD_SLICING_METHOD 0 # 0 = One thread executed per time slice.
+			# 1 = All threads executed each time slice.
+
+MAX_LABEL_EXE_SIZE 1	# Max nops marked as executed when labels are used
+MERIT_TIME 1            # 0 = Merit Calculated when task completed
+		        # 1 = Merit Calculated on Divide
+MAX_NUM_TASKS_REWARDED -1  # -1 = Unlimited
+
+### Genotype Info ###
+THRESHOLD 3		# Number of organisms in a genotype needed for it
+			#   to be considered viable.
+GENOTYPE_PRINT 0	# 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0	# Print out a genotype if it stays dominant for
+                        #   this many updates. (0 = off)
+SPECIES_THRESHOLD 2     # max failure count for organisms to be same species
+SPECIES_RECORDING 0	# 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0		# 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20    # Time allocated in test CPUs (multiple of length)
+TRACK_MAIN_LINEAGE 1    # Track primary lineage leading to final population?
+
+### Log Files ###
+LOG_CREATURES 0		# 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0		# 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0		# 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0		# 0/1 (off/on) toggle to print file.
+LOG_LANDSCAPE 0		# 0/1 (off/on) toggle to print file.
+
+LOG_LINEAGES 0          # 0/1 (off/on) to log advantageous mutations
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# See also LINEAGE_CREATION_METHOD.
+
+LINEAGE_CREATION_METHOD 0
+# Lineage creation options are.  Works only when LOG_LINEAGES is set to 1.
+#   0 = manual creation (on inject, use successive integers as lineage labels).
+#   1 = when a child's (potential) fitness is higher than that of its parent.
+#   2 = when a child's (potential) fitness is higher than max in population.
+#   3 = when a child's (potential) fitness is higher than max in dom. lineage
+#	*and* the child is in the dominant lineage, or (2)
+#   4 = when a child's (potential) fitness is higher than max in dom. lineage
+#	(and that of its own lineage)
+#   5 = same as child's (potential) fitness is higher than that of the
+#       currently dominant organism, and also than that of any organism
+#       currently in the same lineage.
+#   6 = when a child's (potential) fitness is higher than any organism
+#       currently in the same lineage.
+#   7 = when a child's (potential) fitness is higher than that of any
+#       organism in its line of descent
+
+### END ###
+
+

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/inst_set.default
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/inst_set.default	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/inst_set.default	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,54 @@
+nop-A      1   # a
+nop-B      1   # b
+nop-C      1   # c
+if-n-equ   1   # d
+if-less    1   # e
+pop        0   # f
+push       0   # g
+swap-stk   1   # h
+swap       1   # i 
+shift-r    1   # j
+shift-l    1   # k
+inc        1   # l
+dec        1   # m
+add        1   # n
+sub        1   # o
+nand       1   # p
+IO         1   # q   Puts current contents of register and gets new.
+h-alloc    1   # r   Allocate as much memory as organism can use.
+h-divide   1   # s   Cuts off everything between the read and write heads
+h-copy     1   # t   Combine h-read and h-write
+h-search   1   # u   Search for matching template, set flow head & return info
+               #   #   if no template, move flow-head here, set size&offset=0.
+mov-head   1   # v   Move ?IP? head to flow control.
+jmp-head   1   # w   Move ?IP? head by fixed amount in CX.  Set old pos in CX.
+get-head   1   # x   Get position of specified head in CX.
+if-label   1   # y
+set-flow   1   # z   Move flow-head to address in ?CX? 
+kazi 	   1    
+nop-X	   0
+
+#adv-head   1
+#jump-f     1
+#jump-b     1
+#call       1
+#return     1
+#if-bit-1   1
+#get        1
+#put        1
+#h-read     1
+#h-write    1
+#set-head   1
+#search-f   1
+#search-b   1
+
+
+# Works on multiple nops:  pop  push  inc  dec  IO  adv-head 
+
+# What if we add a new head.  Search will return the location of something,
+# and put the new head there.  Then set-head will move another head to that
+# point.  In the case of the copy loop, it only needs to be set once and
+# this will speed up the code quite a bit!
+
+# Search with no template returns current position (abs line number) in
+# genome.
\ No newline at end of file

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/kazi.org
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/kazi.org	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/kazi.org	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,101 @@
+h-alloc    # Allocate space for child
+h-search   # Locate the end of the organism
+nop-C      #
+nop-A      #
+mov-head   # Place write-head at beginning of offspring.
+nop-C      #
+nop-X	     #
+kazi	     #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+h-search   # Mark the beginning of the copy loop
+h-copy     # Do the copy
+if-label   # If we're done copying....
+nop-C      #
+nop-A      #
+h-divide   #    ...divide!
+mov-head   # Otherwise, loop back to the beginning of the copy loop.
+nop-A      # End label.
+nop-B      #
+

Added: trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/organism.default
===================================================================
--- trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/organism.default	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/consistencytests/Tests/Researchers/goingssh/Kazi/testconfig/organism.default	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,101 @@
+h-alloc    # Allocate space for child
+h-search   # Locate the end of the organism
+nop-C      #
+nop-A      #
+mov-head   # Place write-head at beginning of offspring.
+nop-C      #
+nop-C	     #
+nop-C	     #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-C      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+nop-X      #
+h-search   # Mark the beginning of the copy loop
+h-copy     # Do the copy
+if-label   # If we're done copying....
+nop-C      #
+nop-A      #
+h-divide   #    ...divide!
+mov-head   # Otherwise, loop back to the beginning of the copy loop.
+nop-A      # End label.
+nop-B      #
+

Added: trunk/run_consistencytests
===================================================================
--- trunk/run_consistencytests	2006-03-12 21:51:27 UTC (rev 505)
+++ trunk/run_consistencytests	2006-03-13 11:11:36 UTC (rev 506)
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+mkdir -p build
+cd build
+cmake \
+  -DAVD_CONSISTENCY_TEST_PRIMITIVE:BOOL=ON \
+  -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
+  ../
+make
+make install
+ctest -R Consistency
+


Property changes on: trunk/run_consistencytests
___________________________________________________________________
Name: svn:executable
   + *


