[Avida-cvs] [Avida2-svn] r138 - in trunk/source: bindings/Boost.Python cpu main python python/AvidaGui2 tools

[kaben at myxo.css.msu.edu]

Author: kaben
Date: 2005-04-13 05:32:08 -0400 (Wed, 13 Apr 2005)
New Revision: 138

Added:
   trunk/source/bindings/Boost.Python/cpu_defs-fixups.cc
   trunk/source/bindings/Boost.Python/cpu_defs-fixups.hh
   trunk/source/bindings/Boost.Python/cpu_defs.pyste
   trunk/source/bindings/Boost.Python/cpu_head-fixups.cc
   trunk/source/bindings/Boost.Python/cpu_head-fixups.hh
   trunk/source/bindings/Boost.Python/cpu_memory-fixups.cc
   trunk/source/bindings/Boost.Python/cpu_memory-fixups.hh
   trunk/source/bindings/Boost.Python/hardware_status_printer.pyste
   trunk/source/bindings/Boost.Python/hardware_tracer.pyste
   trunk/source/bindings/Boost.Python/hardware_tracer_4stack.pyste
   trunk/source/bindings/Boost.Python/hardware_tracer_cpu.pyste
   trunk/source/bindings/Boost.Python/hardware_tracer_test_cpu.pyste
   trunk/source/bindings/Boost.Python/py_hardware_tracer-fixups.cc
   trunk/source/bindings/Boost.Python/py_hardware_tracer.hh
   trunk/source/bindings/Boost.Python/py_hardware_tracer.pyste
   trunk/source/bindings/Boost.Python/resource_count-fixups.cc
   trunk/source/bindings/Boost.Python/resource_count-fixups.hh
   trunk/source/bindings/Boost.Python/tVector.pyste
   trunk/source/bindings/Boost.Python/tVector_instantiations.hh
   trunk/source/bindings/Boost.Python/test_cpu-fixups.cc
   trunk/source/bindings/Boost.Python/test_cpu-fixups.hh
   trunk/source/cpu/hardware_status_printer.cc
   trunk/source/cpu/hardware_status_printer.hh
   trunk/source/cpu/hardware_tracer.hh
   trunk/source/cpu/hardware_tracer_4stack.hh
   trunk/source/cpu/hardware_tracer_cpu.hh
   trunk/source/cpu/hardware_tracer_test_cpu.hh
   trunk/source/python/AvidaGui2/pyHardwareCPUTrace.py
Modified:
   trunk/source/bindings/Boost.Python/4stack_head.pyste
   trunk/source/bindings/Boost.Python/A.pyste
   trunk/source/bindings/Boost.Python/B.pyste
   trunk/source/bindings/Boost.Python/CMakeLists.txt
   trunk/source/bindings/Boost.Python/analyze.pyste
   trunk/source/bindings/Boost.Python/analyze_command.pyste
   trunk/source/bindings/Boost.Python/analyze_command_def.pyste
   trunk/source/bindings/Boost.Python/analyze_command_def_base.pyste
   trunk/source/bindings/Boost.Python/analyze_flow_command.pyste
   trunk/source/bindings/Boost.Python/analyze_flow_command_def.pyste
   trunk/source/bindings/Boost.Python/analyze_function.pyste
   trunk/source/bindings/Boost.Python/analyze_genotype.pyste
   trunk/source/bindings/Boost.Python/analyze_util.pyste
   trunk/source/bindings/Boost.Python/avida.pyste
   trunk/source/bindings/Boost.Python/avida_driver_analyze.pyste
   trunk/source/bindings/Boost.Python/avida_driver_base.pyste
   trunk/source/bindings/Boost.Python/avida_driver_population.pyste
   trunk/source/bindings/Boost.Python/avida_triggers.pyste
   trunk/source/bindings/Boost.Python/birth_chamber.pyste
   trunk/source/bindings/Boost.Python/block_struct.pyste
   trunk/source/bindings/Boost.Python/cCycleCheck.pyste
   trunk/source/bindings/Boost.Python/cID.pyste
   trunk/source/bindings/Boost.Python/cStringable.pyste
   trunk/source/bindings/Boost.Python/cTestCase.pyste
   trunk/source/bindings/Boost.Python/cTestProblem.pyste
   trunk/source/bindings/Boost.Python/cTestResult.pyste
   trunk/source/bindings/Boost.Python/cTextTestInterpreter.pyste
   trunk/source/bindings/Boost.Python/callback_util.pyste
   trunk/source/bindings/Boost.Python/code_label.pyste
   trunk/source/bindings/Boost.Python/config.pyste
   trunk/source/bindings/Boost.Python/const_schedule.pyste
   trunk/source/bindings/Boost.Python/count_tracker.pyste
   trunk/source/bindings/Boost.Python/cpu_head.pyste
   trunk/source/bindings/Boost.Python/cpu_memory.pyste
   trunk/source/bindings/Boost.Python/cpu_stack.pyste
   trunk/source/bindings/Boost.Python/cpu_stats.pyste
   trunk/source/bindings/Boost.Python/cpu_test_info.pyste
   trunk/source/bindings/Boost.Python/data_entry.pyste
   trunk/source/bindings/Boost.Python/data_file.pyste
   trunk/source/bindings/Boost.Python/data_file_manager.pyste
   trunk/source/bindings/Boost.Python/data_manager_base.pyste
   trunk/source/bindings/Boost.Python/double_sum.pyste
   trunk/source/bindings/Boost.Python/environment.pyste
   trunk/source/bindings/Boost.Python/event.pyste
   trunk/source/bindings/Boost.Python/event_factory.pyste
   trunk/source/bindings/Boost.Python/event_factory_manager.pyste
   trunk/source/bindings/Boost.Python/event_list.pyste
   trunk/source/bindings/Boost.Python/event_list_entry.pyste
   trunk/source/bindings/Boost.Python/event_list_iterator.pyste
   trunk/source/bindings/Boost.Python/event_triggers.pyste
   trunk/source/bindings/Boost.Python/file.pyste
   trunk/source/bindings/Boost.Python/fitness_matrix.pyste
   trunk/source/bindings/Boost.Python/fixed_block.pyste
   trunk/source/bindings/Boost.Python/fixed_coords.pyste
   trunk/source/bindings/Boost.Python/genebank.pyste
   trunk/source/bindings/Boost.Python/genesis.pyste
   trunk/source/bindings/Boost.Python/genome.pyste
   trunk/source/bindings/Boost.Python/genome_util.pyste
   trunk/source/bindings/Boost.Python/genotype.pyste
   trunk/source/bindings/Boost.Python/genotype_batch.pyste
   trunk/source/bindings/Boost.Python/genotype_birth_data.pyste
   trunk/source/bindings/Boost.Python/genotype_control.pyste
   trunk/source/bindings/Boost.Python/genotype_test_data.pyste
   trunk/source/bindings/Boost.Python/hardware_4stack.pyste
   trunk/source/bindings/Boost.Python/hardware_4stack_thread.pyste
   trunk/source/bindings/Boost.Python/hardware_base.pyste
   trunk/source/bindings/Boost.Python/hardware_cpu-fixups.cc
   trunk/source/bindings/Boost.Python/hardware_cpu.pyste
   trunk/source/bindings/Boost.Python/hardware_cpu_thread.pyste
   trunk/source/bindings/Boost.Python/hardware_factory.pyste
   trunk/source/bindings/Boost.Python/hardware_util.pyste
   trunk/source/bindings/Boost.Python/help_alias.pyste
   trunk/source/bindings/Boost.Python/help_entry.pyste
   trunk/source/bindings/Boost.Python/help_full_entry.pyste
   trunk/source/bindings/Boost.Python/help_manager.pyste
   trunk/source/bindings/Boost.Python/help_type.pyste
   trunk/source/bindings/Boost.Python/histogram.pyste
   trunk/source/bindings/Boost.Python/indexed_block_struct.pyste
   trunk/source/bindings/Boost.Python/init_file.pyste
   trunk/source/bindings/Boost.Python/inject_genebank.pyste
   trunk/source/bindings/Boost.Python/inject_genotype.pyste
   trunk/source/bindings/Boost.Python/inject_genotype_birth_data.pyste
   trunk/source/bindings/Boost.Python/inject_genotype_control.pyste
   trunk/source/bindings/Boost.Python/inject_genotype_element.pyste
   trunk/source/bindings/Boost.Python/inject_genotype_queue.pyste
   trunk/source/bindings/Boost.Python/inst_lib_base.pyste
   trunk/source/bindings/Boost.Python/inst_lib_cpu.pyste
   trunk/source/bindings/Boost.Python/inst_set.pyste
   trunk/source/bindings/Boost.Python/inst_util.pyste
   trunk/source/bindings/Boost.Python/instruction.pyste
   trunk/source/bindings/Boost.Python/int_sum.pyste
   trunk/source/bindings/Boost.Python/integrated_schedule.pyste
   trunk/source/bindings/Boost.Python/integrated_schedule_node.pyste
   trunk/source/bindings/Boost.Python/kaben_brainstorms.pyste
   trunk/source/bindings/Boost.Python/landscape.pyste
   trunk/source/bindings/Boost.Python/lineage.pyste
   trunk/source/bindings/Boost.Python/lineage_control.pyste
   trunk/source/bindings/Boost.Python/local_mutations.pyste
   trunk/source/bindings/Boost.Python/memory_flags.pyste
   trunk/source/bindings/Boost.Python/merit.pyste
   trunk/source/bindings/Boost.Python/mutation.pyste
   trunk/source/bindings/Boost.Python/mutation_lib.pyste
   trunk/source/bindings/Boost.Python/mutation_rates.pyste
   trunk/source/bindings/Boost.Python/mx_code_array.pyste
   trunk/source/bindings/Boost.Python/my_code_array_less_than.pyste
   trunk/source/bindings/Boost.Python/org_message.pyste
   trunk/source/bindings/Boost.Python/organism.pyste
   trunk/source/bindings/Boost.Python/phenotype.pyste
   trunk/source/bindings/Boost.Python/population.pyste
   trunk/source/bindings/Boost.Python/population_cell.pyste
   trunk/source/bindings/Boost.Python/population_event.pyste
   trunk/source/bindings/Boost.Python/population_event_factory.pyste
   trunk/source/bindings/Boost.Python/population_interface.pyste
   trunk/source/bindings/Boost.Python/prob_schedule.pyste
   trunk/source/bindings/Boost.Python/py_avida_driver-fixups.cc
   trunk/source/bindings/Boost.Python/py_avida_driver.pyste
   trunk/source/bindings/Boost.Python/random.pyste
   trunk/source/bindings/Boost.Python/reaction.pyste
   trunk/source/bindings/Boost.Python/reaction_lib.pyste
   trunk/source/bindings/Boost.Python/reaction_process.pyste
   trunk/source/bindings/Boost.Python/reaction_requisite.pyste
   trunk/source/bindings/Boost.Python/reaction_result.pyste
   trunk/source/bindings/Boost.Python/ref_block.pyste
   trunk/source/bindings/Boost.Python/resource.pyste
   trunk/source/bindings/Boost.Python/resource_count.pyste
   trunk/source/bindings/Boost.Python/resource_lib.pyste
   trunk/source/bindings/Boost.Python/running_average.pyste
   trunk/source/bindings/Boost.Python/scaled_block.pyste
   trunk/source/bindings/Boost.Python/schedule.pyste
   trunk/source/bindings/Boost.Python/spatial_count_elem.pyste
   trunk/source/bindings/Boost.Python/spatial_res_count.pyste
   trunk/source/bindings/Boost.Python/species.pyste
   trunk/source/bindings/Boost.Python/species_control.pyste
   trunk/source/bindings/Boost.Python/species_queue.pyste
   trunk/source/bindings/Boost.Python/stats.pyste
   trunk/source/bindings/Boost.Python/string.pyste
   trunk/source/bindings/Boost.Python/string_iterator.pyste
   trunk/source/bindings/Boost.Python/string_list.pyste
   trunk/source/bindings/Boost.Python/string_util.pyste
   trunk/source/bindings/Boost.Python/tArray.pyste
   trunk/source/bindings/Boost.Python/tBuffer.pyste
   trunk/source/bindings/Boost.Python/tDictionary.pyste
   trunk/source/bindings/Boost.Python/tList.pyste
   trunk/source/bindings/Boost.Python/tMatrix.pyste
   trunk/source/bindings/Boost.Python/task_entry.pyste
   trunk/source/bindings/Boost.Python/task_lib.pyste
   trunk/source/bindings/Boost.Python/test_cpu.pyste
   trunk/source/bindings/Boost.Python/test_util.pyste
   trunk/source/bindings/Boost.Python/tools.pyste
   trunk/source/bindings/Boost.Python/uint.pyste
   trunk/source/bindings/Boost.Python/weighted_index.pyste
   trunk/source/cpu/CMakeLists.txt
   trunk/source/cpu/cpu_test_info.cc
   trunk/source/cpu/cpu_test_info.hh
   trunk/source/cpu/hardware_4stack.cc
   trunk/source/cpu/hardware_4stack.hh
   trunk/source/cpu/hardware_base.cc
   trunk/source/cpu/hardware_base.hh
   trunk/source/cpu/hardware_cpu.cc
   trunk/source/cpu/hardware_cpu.hh
   trunk/source/cpu/hardware_factory.cc
   trunk/source/cpu/test_cpu.cc
   trunk/source/cpu/test_util.cc
   trunk/source/main/analyze.cc
   trunk/source/main/analyze_genotype.cc
   trunk/source/main/avida_driver_population.cc
   trunk/source/main/config.cc
   trunk/source/main/genotype.cc
   trunk/source/main/landscape.cc
   trunk/source/main/landscape.hh
   trunk/source/main/organism.cc
   trunk/source/main/population.cc
   trunk/source/python/AvidaEd-osx.py
   trunk/source/python/AvidaGui2/pyAnalyzeControlsView.ui
   trunk/source/python/AvidaGui2/pyOneOrg_ScopeView.ui
   trunk/source/python/AvidaGui2/pyOneOrganismView.ui
   trunk/source/python/AvidaGui2/pyOrganismScopeCtrl.py
   trunk/source/python/AvidaGui2/pyOrganismScopeView.py
   trunk/source/python/AvidaGui2/pyPetriCanvasView.py
   trunk/source/python/AvidaGui2/pyPetriDishCtrl.py
   trunk/source/python/AvidaGui2/pyPopulationCellItem.py
   trunk/source/python/AvidaGui2/pyTemporaryReloads.py
   trunk/source/python/CMakeLists.txt
   trunk/source/python/setup_osx.py.in
   trunk/source/tools/const_schedule.cc
   trunk/source/tools/integrated_schedule.cc
   trunk/source/tools/prob_schedule.cc
Log:
* Merged private branch developers/kaben-organism-scope changes -r127:137 into trunk.

Modified: trunk/source/bindings/Boost.Python/4stack_head.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/4stack_head.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/4stack_head.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,3 +12,5 @@
 set_policy(c4StackHead.FlagPointMut, return_internal_reference())
 set_policy(c4StackHead.FlagCopyMut, return_internal_reference())
 set_policy(c4StackHead.FlagBreakpoint, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/A.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/A.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/A.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
 A = Class("A", "A.hh")
 C = Class("C", "A.hh")
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/B.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/B.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/B.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
 Import("A.pyste")
 B = Class("B", "B.hh")
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/CMakeLists.txt
===================================================================
--- trunk/source/bindings/Boost.Python/CMakeLists.txt	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/CMakeLists.txt	2005-04-13 09:32:08 UTC (rev 138)
@@ -51,14 +51,12 @@
   # XXX : cScaledBlock is designed for use with raw pointers, and won't play well with Python. Hence, don't wrap it.
   #scaled_block::
 
-  # XXX skip for now. Boost is unhappy with references to bools.
-  #cpu_memory::${CMAKE_CURRENT_SOURCE_DIR}/genome.pyste:
   # XXX I can't figure out how it works.
   tArray::${CMAKE_CURRENT_SOURCE_DIR}/organism.pyste:${CMAKE_CURRENT_SOURCE_DIR}/merit.pyste:${CMAKE_CURRENT_SOURCE_DIR}/mutation.pyste:${CMAKE_CURRENT_SOURCE_DIR}/int_sum.pyste:
   # XXX Boost doesn't like that tMatrix returns refs to doubles.
   #tMatrix::
 
-  ###cpu_head::
+  cpu_head::
   ###4stack_head::${CMAKE_CURRENT_SOURCE_DIR}/cpu_head.pyste:
   ###event::
   ###population_event::${CMAKE_CURRENT_SOURCE_DIR}/event.pyste:
@@ -150,6 +148,8 @@
   fixed_block:: # XXX XXX
   fixed_coords:: # XXX XXX
   genome:: # XXX XXX
+  cpu_memory::${CMAKE_CURRENT_SOURCE_DIR}/genome.pyste:
+
   genome_util:: # XXX XXX
   genotype_test_data:: # XXX XXX
   histogram:: # XXX XXX
@@ -174,6 +174,7 @@
   avida_driver_population::${CMAKE_CURRENT_SOURCE_DIR}/avida_driver_base.pyste # XXX XXX XXX
   config:: # XXX XXX XXX
   count_tracker:: # XXX XXX XXX
+  cpu_defs::
   data_entry:: # XXX XXX XXX
   data_file:: # XXX XXX XXX
   data_file_manager:: # XXX XXX XXX
@@ -182,9 +183,15 @@
   file::${CMAKE_CURRENT_SOURCE_DIR}/file-fixups.hh # XXX XXX XXX
   init_file::${CMAKE_CURRENT_SOURCE_DIR}/file.pyste # XXX XXX XXX
   genesis::${CMAKE_CURRENT_SOURCE_DIR}/init_file.pyste:${CMAKE_CURRENT_SOURCE_DIR}/genesis-fixups.hh # XXX XXX XXX
-  hardware_base::${CPU_SRC_DIR}/hardware_base.hh # XXX XXX XXX
+  #hardware_base::${CPU_SRC_DIR}/hardware_base.hh # XXX XXX XXX
+  hardware_base::
   hardware_4stack::${CMAKE_CURRENT_SOURCE_DIR}/hardware_base.pyste # XXX XXX XXX
   hardware_cpu::${CMAKE_CURRENT_SOURCE_DIR}/hardware_base.pyste:${CMAKE_CURRENT_SOURCE_DIR}/hardware_cpu-fixups.hh # XXX XXX XXX
+  hardware_tracer::
+  hardware_tracer_cpu::
+  hardware_tracer_4stack::
+  hardware_tracer_test_cpu::
+  hardware_status_printer::
   hardware_util:: # XXX XXX XXX
   inst_lib_base:: # XXX XXX XXX
   inst_lib_cpu::${CMAKE_CURRENT_SOURCE_DIR}/inst_lib_base.pyste # XXX XXX XXX
@@ -192,6 +199,7 @@
   population:: # XXX XXX XXX
   population_interface:: # XXX XXX XXX
   py_avida_driver::${CMAKE_CURRENT_SOURCE_DIR}/avida_driver_population.pyste # XXX XXX XXX
+  py_hardware_tracer::
   reaction_lib:: # XXX XXX XXX
   resource_count:: # XXX XXX XXX
   resource_lib:: # XXX XXX XXX
@@ -201,13 +209,20 @@
   task_lib:: # XXX XXX XXX
   test_cpu:: # XXX XXX XXX
   tList::${CMAKE_CURRENT_SOURCE_DIR}/string.pyste # XXX XXX XXX
+  tVector::
 )
 SET(PyAvida_Extra_Cpp_Files
   AB.cc
+  cpu_defs-fixups.cc
+  cpu_head-fixups.cc
+  cpu_memory-fixups.cc
   file-fixups.cc
   genesis-fixups.cc
   hardware_cpu-fixups.cc
   py_avida_driver-fixups.cc
+  py_hardware_tracer-fixups.cc
+  resource_count-fixups.cc
+  test_cpu-fixups.cc
 )
 
 ADD_LIBRARY(PyAvidaRepairHacks SHARED ${PyAvida_Extra_Cpp_Files})

Modified: trunk/source/bindings/Boost.Python/analyze.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 Include("environment.hh")
 
 cAnalyze = Class("cAnalyze", "analyze.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_command.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_command.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_command.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 
 cAnalyzeCommand = Class("cAnalyzeCommand", "analyze_command.hh")
 set_policy(cAnalyzeCommand.GetCommandList, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_command_def.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_command_def.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_command_def.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,4 @@
 Import("analyze_command_def_base.pyste")
 cAnalyzeCommandDef = Class("cAnalyzeCommandDef", "analyze_command_def.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_command_def_base.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_command_def_base.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_command_def_base.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,3 +2,5 @@
 Include("analyze_command.hh")
 
 cAnalyzeCommandDefBase = Class("cAnalyzeCommandDefBase", "analyze_command_def_base.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_flow_command.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_flow_command.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_flow_command.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 
 cAnalyzeFlowCommand = Class("cAnalyzeFlowCommand", "analyze_flow_command.hh")
 set_policy(cAnalyzeFlowCommand.GetCommandList, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_flow_command_def.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_flow_command_def.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_flow_command_def.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,4 @@
 Import("analyze_command_def_base.pyste")
 cAnalyzeFlowCommandDef = Class("cAnalyzeFlowCommandDef", "analyze_flow_command_def.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_function.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_function.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_function.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 
 cAnalyzeFunction = Class("cAnalyzeFunction", "analyze_function.hh")
 set_policy(cAnalyzeFunction.GetCommandList, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_genotype.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_genotype.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_genotype.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 Include("inst_set.hh")
 
 cAnalyzeGenotype = Class("cAnalyzeGenotype", "analyze_genotype.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/analyze_util.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/analyze_util.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/analyze_util.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 Include("inst_set.hh")
 
 cAnalyzeUtil = Class("cAnalyzeUtil", "analyze_util.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/avida.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/avida.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/avida.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -9,3 +9,4 @@
 
 Function("SetupAvidaPython", "avida-fixups.hh")
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/avida_driver_analyze.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/avida_driver_analyze.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/avida_driver_analyze.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 Include("string.hh")
 
 cAvidaDriver_Analyze = Class("cAvidaDriver_Analyze", "avida_driver_analyze.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/avida_driver_base.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/avida_driver_base.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/avida_driver_base.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 """)
 
 cAvidaDriver_Base = Class("cAvidaDriver_Base", "avida_driver_base.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/avida_driver_population.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/avida_driver_population.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/avida_driver_population.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -6,3 +6,4 @@
 cAvidaDriver_Population = Class("cAvidaDriver_Population", "avida_driver_population.hh")
 set_policy(cAvidaDriver_Population.GetPopulation, return_internal_reference())
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/avida_triggers.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/avida_triggers.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/avida_triggers.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,6 @@
+
 Import("event_triggers.pyste")
+
 cAvidaTriggers = Class("cAvidaTriggers", "avida_triggers.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/birth_chamber.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/birth_chamber.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/birth_chamber.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Include("organism.hh")
 Include("genebank.hh")
 
@@ -2 +3,3 @@
 cBirthChamber = Class("cBirthChamber", "birth_chamber.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/block_struct.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/block_struct.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/block_struct.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cBlockStruct = Class("cBlockStruct", "block_struct.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cCycleCheck.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cCycleCheck.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cCycleCheck.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,3 +2,4 @@
 
 cCycleCheck = Class("cCycleCheck", "cCycleCheck.hh")
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cID.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cID.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cID.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,4 @@
+
 cID = Class("cID", "cID.hh")
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cStringable.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cStringable.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cStringable.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,4 @@
 
 cStringable = Class("cStringable", "cStringable.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cTestCase.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cTestCase.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cTestCase.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,4 +1,6 @@
+
 cTestCase = Class("cTestCase", "cTestCase.hh")
+
 # cTestCase recursively 'adopts' other cTestCase instances, i.e.,
 # removes responsibility from the user for deleting adopted instances.
 # This doesn't play well with python because python really wants to
@@ -6,9 +8,14 @@
 # shared-pointers removes responsibility for deleting the instances from
 # cTestCase, Python, and users' code. Deleting becomes responsibility of
 # the shared_ptr. shared_ptr saves the day.
+
 holder(cTestCase, lambda classname: "boost::shared_ptr<%s>" % classname)
+
 # adoptTestCase takes raw pointers. We don't want to let python use it.
 exclude(cTestCase.adoptTestCase)
+
 # pyAdoptTestCase takes shared_ptr instances. We want python to use
 # pyAdoptTestCase to make a cTestCase adopt another test case.:
 rename(cTestCase.pyAdoptTestCase, "adoptTestCase")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cTestProblem.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cTestProblem.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cTestProblem.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cTestProblem = Class("cTestProblem", "cTestProblem.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cTestResult.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cTestResult.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cTestResult.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -33,3 +33,5 @@
 set_policy(cTestResult.failures, return_value_policy(return_by_value))
 set_wrapper(cTestResult.errors, errors_wrapper)
 set_wrapper(cTestResult.failures, failures_wrapper)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cTextTestInterpreter.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cTextTestInterpreter.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cTextTestInterpreter.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cTextTestInterpreter = Class("cTextTestInterpreter", "cTextTestInterpreter.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/callback_util.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/callback_util.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/callback_util.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cCallbackUtil = Class("cCallbackUtil", "callback_util.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/code_label.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/code_label.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/code_label.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cCodeLabel = Class("cCodeLabel", "code_label.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/config.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/config.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/config.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -10,3 +10,5 @@
 set_policy(cConfig.GetStartCreature, return_value_policy(reference_existing_object))
 set_policy(cConfig.GetCloneFilename, return_value_policy(reference_existing_object))
 set_policy(cConfig.GetLoadPopFilename, return_value_policy(reference_existing_object))
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/const_schedule.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/const_schedule.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/const_schedule.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Import("schedule.pyste")
 
 Include("merit.hh")
@@ -3,2 +4,4 @@
 
 cConstSchedule = Class("cConstSchedule", "const_schedule.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/count_tracker.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/count_tracker.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/count_tracker.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,4 @@
 
 cCountTracker = Class("cCountTracker", "count_tracker.hh")
+
+# vim: set ft=python:

Copied: trunk/source/bindings/Boost.Python/cpu_defs-fixups.cc (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/cpu_defs-fixups.cc)

Copied: trunk/source/bindings/Boost.Python/cpu_defs-fixups.hh (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/cpu_defs-fixups.hh)

Copied: trunk/source/bindings/Boost.Python/cpu_defs.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/cpu_defs.pyste)

Copied: trunk/source/bindings/Boost.Python/cpu_head-fixups.cc (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/cpu_head-fixups.cc)

Copied: trunk/source/bindings/Boost.Python/cpu_head-fixups.hh (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/cpu_head-fixups.hh)

Modified: trunk/source/bindings/Boost.Python/cpu_head.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cpu_head.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cpu_head.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,12 +4,45 @@
 Include("hardware_base.hh")
 Include("code_label.hh")
 
-cCPUHead = Class("cCPUHead", "cpu_head.hh")
-set_policy(cCPUHead.FlagCopied, return_internal_reference())
-set_policy(cCPUHead.FlagMutated, return_internal_reference())
-set_policy(cCPUHead.FlagExecuted, return_internal_reference())
-set_policy(cCPUHead.FlagPointMut, return_internal_reference())
-set_policy(cCPUHead.FlagCopyMut, return_internal_reference())
+cCPUHead = Class("cCPUHead", "cpu_head-fixups.hh")
 set_policy(cCPUHead.GetCurHardware, return_internal_reference())
 set_policy(cCPUHead.GetMainHardware, return_internal_reference())
-set_policy(cCPUHead.FlagBreakpoint, return_internal_reference())
+
+exclude(cCPUHead.FlagCopied)
+exclude(cCPUHead.FlagMutated)
+exclude(cCPUHead.FlagExecuted)
+exclude(cCPUHead.FlagPointMut)
+exclude(cCPUHead.FlagCopyMut)
+exclude(cCPUHead.FlagBreakpoint)
+
+add_method(cCPUHead, "cCPUHead_GetFlagCopied")
+add_method(cCPUHead, "cCPUHead_GetFlagMutated")
+add_method(cCPUHead, "cCPUHead_GetFlagExecuted")
+add_method(cCPUHead, "cCPUHead_GetFlagPointMut")
+add_method(cCPUHead, "cCPUHead_GetFlagCopyMut")
+add_method(cCPUHead, "cCPUHead_GetFlagBreakpoint")
+
+add_method(cCPUHead, "cCPUHead_SetFlagCopied")
+add_method(cCPUHead, "cCPUHead_SetFlagMutated")
+add_method(cCPUHead, "cCPUHead_SetFlagExecuted")
+add_method(cCPUHead, "cCPUHead_SetFlagPointMut")
+add_method(cCPUHead, "cCPUHead_SetFlagCopyMut")
+add_method(cCPUHead, "cCPUHead_SetFlagBreakpoint")
+
+rename(cCPUHead.cCPUHead_GetFlagCopied, "GetFlagCopied");
+rename(cCPUHead.cCPUHead_GetFlagMutated, "GetFlagMutated");
+rename(cCPUHead.cCPUHead_GetFlagExecuted, "GetFlagExecuted");
+rename(cCPUHead.cCPUHead_GetFlagPointMut, "GetFlagPointMut");
+rename(cCPUHead.cCPUHead_GetFlagCopyMut, "GetFlagCopyMut");
+rename(cCPUHead.cCPUHead_GetFlagBreakpoint, "GetFlagBreakpoint");
+
+rename(cCPUHead.cCPUHead_SetFlagCopied, "SetFlagCopied");
+rename(cCPUHead.cCPUHead_SetFlagMutated, "SetFlagMutated");
+rename(cCPUHead.cCPUHead_SetFlagExecuted, "SetFlagExecuted");
+rename(cCPUHead.cCPUHead_SetFlagPointMut, "SetFlagPointMut");
+rename(cCPUHead.cCPUHead_SetFlagCopyMut, "SetFlagCopyMut");
+rename(cCPUHead.cCPUHead_SetFlagBreakpoint, "SetFlagBreakpoint");
+
+
+# vim: set ft=python:
+# vim: set ft=python:

Copied: trunk/source/bindings/Boost.Python/cpu_memory-fixups.cc (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/cpu_memory-fixups.cc)

Copied: trunk/source/bindings/Boost.Python/cpu_memory-fixups.hh (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/cpu_memory-fixups.hh)

Modified: trunk/source/bindings/Boost.Python/cpu_memory.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cpu_memory.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cpu_memory.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,10 +1,47 @@
+
 Import("genome.pyste")
 
-cCPUMemory = Class("cCPUMemory", "cpu_memory.hh")
-set_policy(cCPUMemory.FlagCopied, return_internal_reference())
-set_policy(cCPUMemory.FlagMutated, return_internal_reference())
-set_policy(cCPUMemory.FlagExecuted, return_internal_reference())
-set_policy(cCPUMemory.FlagPointMut, return_internal_reference())
-set_policy(cCPUMemory.FlagCopyMut, return_internal_reference())
-set_policy(cCPUMemory.FlagInjected, return_internal_reference())
-set_policy(cCPUMemory.FlagBreakpoint, return_internal_reference())
+cCPUMemory = Class("cCPUMemory", "cpu_memory-fixups.hh")
+
+exclude(cCPUMemory.FlagCopied)
+exclude(cCPUMemory.FlagMutated)
+exclude(cCPUMemory.FlagExecuted)
+exclude(cCPUMemory.FlagPointMut)
+exclude(cCPUMemory.FlagCopyMut)
+exclude(cCPUMemory.FlagInjected)
+exclude(cCPUMemory.FlagBreakpoint)
+
+add_method(cCPUMemory, "cCPUMemory_GetFlagCopied")
+add_method(cCPUMemory, "cCPUMemory_GetFlagMutated")
+add_method(cCPUMemory, "cCPUMemory_GetFlagExecuted")
+add_method(cCPUMemory, "cCPUMemory_GetFlagPointMut")
+add_method(cCPUMemory, "cCPUMemory_GetFlagCopyMut")
+add_method(cCPUMemory, "cCPUMemory_GetFlagInjected")
+add_method(cCPUMemory, "cCPUMemory_GetFlagBreakpoint")
+
+add_method(cCPUMemory, "cCPUMemory_SetFlagCopied")
+add_method(cCPUMemory, "cCPUMemory_SetFlagMutated")
+add_method(cCPUMemory, "cCPUMemory_SetFlagExecuted")
+add_method(cCPUMemory, "cCPUMemory_SetFlagPointMut")
+add_method(cCPUMemory, "cCPUMemory_SetFlagCopyMut")
+add_method(cCPUMemory, "cCPUMemory_SetFlagInjected")
+add_method(cCPUMemory, "cCPUMemory_SetFlagBreakpoint")
+
+rename(cCPUMemory.cCPUMemory_GetFlagCopied, "GetFlagCopied");
+rename(cCPUMemory.cCPUMemory_GetFlagMutated, "GetFlagMutated");
+rename(cCPUMemory.cCPUMemory_GetFlagExecuted, "GetFlagExecuted");
+rename(cCPUMemory.cCPUMemory_GetFlagPointMut, "GetFlagPointMut");
+rename(cCPUMemory.cCPUMemory_GetFlagCopyMut, "GetFlagCopyMut");
+rename(cCPUMemory.cCPUMemory_GetFlagInjected, "GetFlagInjected");
+rename(cCPUMemory.cCPUMemory_GetFlagBreakpoint, "GetFlagBreakpoint");
+
+rename(cCPUMemory.cCPUMemory_SetFlagCopied, "SetFlagCopied");
+rename(cCPUMemory.cCPUMemory_SetFlagMutated, "SetFlagMutated");
+rename(cCPUMemory.cCPUMemory_SetFlagExecuted, "SetFlagExecuted");
+rename(cCPUMemory.cCPUMemory_SetFlagPointMut, "SetFlagPointMut");
+rename(cCPUMemory.cCPUMemory_SetFlagCopyMut, "SetFlagCopyMut");
+rename(cCPUMemory.cCPUMemory_SetFlagInjected, "SetFlagInjected");
+rename(cCPUMemory.cCPUMemory_SetFlagBreakpoint, "SetFlagBreakpoint");
+
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cpu_stack.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cpu_stack.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cpu_stack.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cCPUStack = Class("cCPUStack", "cpu_stack.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cpu_stats.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cpu_stats.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cpu_stats.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 sCPUStats = Class("sCPUStats", "cpu_stats.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/cpu_test_info.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/cpu_test_info.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/cpu_test_info.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,8 +1,14 @@
 
+Include("hardware_tracer.hh")
 Include("organism.hh")
 
 cCPUTestInfo = Class("cCPUTestInfo", "cpu_test_info.hh")
 # returns std::ofstream &, i.e., not the Python Way.
-exclude(cCPUTestInfo.GetTraceFP)
+#exclude(cCPUTestInfo.GetTraceFP)
 set_policy(cCPUTestInfo.GetTestOrganism, return_internal_reference())
 set_policy(cCPUTestInfo.GetColonyOrganism, return_internal_reference())
+set_policy(cCPUTestInfo.GetColonyOrganism, return_internal_reference())
+# Another reason to use ref-counting... Dangerous return value policy in use:
+set_policy(cCPUTestInfo.GetTracer, return_value_policy(reference_existing_object))
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/data_entry.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/data_entry.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/data_entry.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 
 cDataEntry = Class("cDataEntry", "data_entry.hh")
 exclude(cDataEntry.operator['<<'])
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/data_file.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/data_file.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/data_file.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 
 cDataFile = Class("cDataFile", "data_file.hh")
 set_policy(cDataFile.GetOFStream, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/data_file_manager.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/data_file_manager.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/data_file_manager.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Include("data_file.hh")
 Include("string.hh")
 
@@ -4,3 +5,5 @@
 cDataFileManager = Class("cDataFileManager", "data_file_manager.hh")
 exclude(cDataFileManager.GetOFStream)
 set_policy(cDataFileManager.Get, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/data_manager_base.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/data_manager_base.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/data_manager_base.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 Include("data_file.hh")
 
 cDataManager_Base = Class("cDataManager_Base", "data_manager_base.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/double_sum.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/double_sum.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/double_sum.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,4 @@
 
 cDoubleSum = Class("cDoubleSum", "double_sum.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/environment.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/environment.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/environment.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -9,3 +9,5 @@
 set_policy(cEnvironment.GetTaskLib, return_internal_reference())
 set_policy(cEnvironment.GetInstSet, return_internal_reference())
 set_policy(cEnvironment.GetMutRates, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/event.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/event.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/event.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cEvent = Class("cEvent", "event.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/event_factory.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/event_factory.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/event_factory.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 
 cEventFactory = Class("cEventFactory", "event_factory.hh")
 set_policy(cEventFactory.ConstructEvent, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/event_factory_manager.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/event_factory_manager.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/event_factory_manager.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 
 cEventFactoryManager = Class("cEventFactoryManager", "event_factory_manager.hh")
 set_policy(cEventFactoryManager.ConstructEvent, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/event_list.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/event_list.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/event_list.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,6 @@
+
 Include("event_factory_manager.hh")
 
 cEventList = Class("cEventList", "event_list.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/event_list_entry.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/event_list_entry.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/event_list_entry.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 set_policy(cEventListEntry.GetEvent, return_internal_reference())
 set_policy(cEventListEntry.GetPrev, return_internal_reference())
 set_policy(cEventListEntry.GetNext, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/event_list_iterator.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/event_list_iterator.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/event_list_iterator.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cEventListIterator = Class("cEventListIterator", "event_list_iterator.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/event_triggers.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/event_triggers.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/event_triggers.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cEventTriggers = Class("cEventTriggers", "event_triggers.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/file.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/file.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/file.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 exclude(cFile.Open)
 add_method(cFile, "cFileOpenWrapper")
 rename(cFile.cFileOpenWrapper, "Open")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/fitness_matrix.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/fitness_matrix.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/fitness_matrix.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 Include("inst_set.hh")
 
 cFitnessMatrix = Class("cFitnessMatrix", "fitness_matrix.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/fixed_block.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/fixed_block.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/fixed_block.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cFixedBlock = Class("cFixedBlock", "fixed_block.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/fixed_coords.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/fixed_coords.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/fixed_coords.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cFixedCoords = Class("cFixedCoords", "fixed_coords.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genebank.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genebank.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genebank.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -14,3 +14,5 @@
 set_policy(cGenebank.GetGenotype, return_internal_reference())
 set_policy(cGenebank.NextGenotype, return_internal_reference())
 set_policy(cGenebank.ResetThread, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genesis.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genesis.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genesis.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 exclude(cGenesis.Open)
 add_method(cGenesis, "cGenesisOpenWrapper")
 rename(cGenesis.cGenesisOpenWrapper, "Open")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genome.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genome.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genome.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cGenome = Class("cGenome", "genome.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genome_util.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genome_util.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genome_util.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cGenomeUtil = Class("cGenomeUtil", "genome_util.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genotype.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genotype.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genotype.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,3 +12,5 @@
 set_policy(cGenotype.GetParentSpecies, return_internal_reference())
 set_policy(cGenotype.GetNext, return_internal_reference())
 set_policy(cGenotype.GetPrev, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genotype_batch.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genotype_batch.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genotype_batch.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,3 +2,5 @@
 cGenotypeBatch = Class("cGenotypeBatch", "genotype_batch.hh")
 set_policy(cGenotypeBatch.List, return_internal_reference())
 set_policy(cGenotypeBatch.Name, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genotype_birth_data.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genotype_birth_data.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genotype_birth_data.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Include("inst_set.hh")
 Include("species.hh")
 Include("genotype.hh")
@@ -3,2 +4,4 @@
 
 cGenotype_BirthData = Class("cGenotype_BirthData", "genotype_birth_data.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genotype_control.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genotype_control.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genotype_control.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,3 +12,5 @@
 set_policy(cGenotypeControl.ResetHistoric, return_internal_reference())
 set_policy(cGenotypeControl.Next, return_internal_reference())
 set_policy(cGenotypeControl.Prev, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/genotype_test_data.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/genotype_test_data.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/genotype_test_data.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,3 @@
 cGenotype_TestData = Class("cGenotype_TestData", "genotype_test_data.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/hardware_4stack.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_4stack.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_4stack.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -34,3 +34,5 @@
 cHardware4Stack.AdvanceIP returns a reference to a bool;
 rewrap by hand.
 """)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/hardware_4stack_thread.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_4stack_thread.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_4stack_thread.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Include("hardware_base.hh")
 Include("inject_genotype.hh")
 
@@ -2 +3,3 @@
 cHardware4Stack_Thread = Class("cHardware4Stack_Thread", "hardware_4stack_thread.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/hardware_base.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_base.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_base.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,6 +2,7 @@
 Include("code_label.hh")
 Include("cpu_memory.hh")
 Include("genome.hh")
+Include("hardware_tracer.hh")
 Include("inst_set.hh")
 Include("organism.hh")
 
@@ -9,3 +10,5 @@
 set_policy(cHardwareBase.GetOrganism, return_internal_reference())
 set_policy(cHardwareBase.GetMemory, return_internal_reference())
 exclude(cHardwareBase.ViewerLock)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/hardware_cpu-fixups.cc
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_cpu-fixups.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_cpu-fixups.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,6 +1,4 @@
-#ifndef HARDWARE_CPU_FIXUPS_HH
 #include "hardware_cpu-fixups.hh"
-#endif
 
 int cHardwareCPU_GetRegister(cHardwareCPU &hardware_cpu, int reg_id){
   return hardware_cpu.Register(reg_id);

Modified: trunk/source/bindings/Boost.Python/hardware_cpu.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_cpu.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_cpu.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Include("mutation.hh")
 Include("inst_lib_cpu.hh")
 Include("inst_set.hh")
@@ -21,16 +22,17 @@
 ### probably neither can Boost.Python -- with references to builtin
 ### types (I think). Possible solution is creating a
 ### cRegister class to wrap the int.
-#set_policy(cHardwareCPU.Register, return_value_policy(reference_existing_object))
 exclude(cHardwareCPU.Register)
 add_method(cHardwareCPU, "cHardwareCPU_GetRegister");
+add_method(cHardwareCPU, "cHardwareCPU_SetRegister");
 rename(cHardwareCPU.cHardwareCPU_GetRegister, "GetRegister");
-add_method(cHardwareCPU, "cHardwareCPU_SetRegister");
 rename(cHardwareCPU.cHardwareCPU_SetRegister, "SetRegister");
-class_code(cHardwareCPU, '.add_property("Register", &cHardwareCPU_GetRegister, &cHardwareCPU_SetRegister)');
+class_code(cHardwareCPU, '.add_property("m_register", &cHardwareCPU_GetRegister, &cHardwareCPU_SetRegister)');
 
 set_policy(cHardwareCPU.Memory, return_internal_reference())
 set_policy(cHardwareCPU.GetMemory, return_internal_reference())
 
 set_policy(cHardwareCPU.GetOrganism, return_internal_reference())
 exclude(cHardwareCPU.ViewerLock)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/hardware_cpu_thread.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_cpu_thread.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_cpu_thread.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,6 @@
+
 Include("hardware_base.hh")
 
 cHardwareCPU_Thread = Class("cHardwareCPU_Thread", "hardware_cpu_thread.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/hardware_factory.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_factory.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_factory.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 
 cHardwareFactory = Class("cHardwareFactory", "hardware_factory.hh")
 set_policy(cHardwareFactory.Create, return_internal_reference())
+
+# vim: set ft=python:

Copied: trunk/source/bindings/Boost.Python/hardware_status_printer.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/hardware_status_printer.pyste)

Copied: trunk/source/bindings/Boost.Python/hardware_tracer.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/hardware_tracer.pyste)

Copied: trunk/source/bindings/Boost.Python/hardware_tracer_4stack.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/hardware_tracer_4stack.pyste)

Copied: trunk/source/bindings/Boost.Python/hardware_tracer_cpu.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/hardware_tracer_cpu.pyste)

Copied: trunk/source/bindings/Boost.Python/hardware_tracer_test_cpu.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/hardware_tracer_test_cpu.pyste)

Modified: trunk/source/bindings/Boost.Python/hardware_util.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/hardware_util.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/hardware_util.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 
 cHardwareUtil = Class("cHardwareUtil", "hardware_util.hh")
 set_policy(cHardwareUtil.DefaultInstSet, return_value_policy(reference_existing_object))
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/help_alias.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/help_alias.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/help_alias.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -6,3 +6,5 @@
 
 cHelpAlias = Class("cHelpAlias", "help_alias.hh")
 set_policy(cHelpAlias.GetType, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/help_entry.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/help_entry.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/help_entry.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 
 cHelpEntry = Class("cHelpEntry", "help_entry.hh")
 set_policy(cHelpEntry.GetType, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/help_full_entry.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/help_full_entry.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/help_full_entry.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 
 cHelpFullEntry = Class("cHelpFullEntry", "help_full_entry.hh")
 set_policy(cHelpFullEntry.GetType, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/help_manager.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/help_manager.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/help_manager.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 
 cHelpManager = Class("cHelpManager", "help_manager.hh")
 set_policy(cHelpManager.FindEntry, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/help_type.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/help_type.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/help_type.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -8,3 +8,5 @@
 set_policy(cHelpType.AddEntry, return_internal_reference())
 set_policy(cHelpType.AddAlias, return_internal_reference())
 set_policy(cHelpType.FindEntry, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/histogram.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/histogram.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/histogram.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cHistogram = Class("cHistogram", "histogram.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/indexed_block_struct.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/indexed_block_struct.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/indexed_block_struct.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cIndexedBlockStruct = Class("cIndexedBlockStruct", "indexed_block_struct.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/init_file.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/init_file.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/init_file.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Import("file.pyste")
 
 cInitFile = Class("cInitFile", "init_file.hh")
@@ -2 +3,3 @@
 set_policy(cInitFile.GetFormat, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inject_genebank.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inject_genebank.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inject_genebank.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -11,3 +11,5 @@
 set_policy(cInjectGenebank.GetInjectGenotype, return_internal_reference())
 set_policy(cInjectGenebank.NextInjectGenotype, return_internal_reference())
 set_policy(cInjectGenebank.ResetThread, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inject_genotype.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inject_genotype.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inject_genotype.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 set_policy(cInjectGenotype.GetName, return_internal_reference())
 set_policy(cInjectGenotype.GetNext, return_internal_reference())
 set_policy(cInjectGenotype.GetPrev, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inject_genotype_birth_data.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inject_genotype_birth_data.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inject_genotype_birth_data.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,6 @@
+
 Include("inject_genotype.hh")
 
 cInjectGenotype_BirthData = Class("cInjectGenotype_BirthData", "inject_genotype_birth_data.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inject_genotype_control.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inject_genotype_control.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inject_genotype_control.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,3 +12,5 @@
 set_policy(cInjectGenotypeControl.ResetHistoric, return_internal_reference())
 set_policy(cInjectGenotypeControl.Next, return_internal_reference())
 set_policy(cInjectGenotypeControl.Prev, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inject_genotype_element.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inject_genotype_element.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inject_genotype_element.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 set_policy(cInjectGenotypeElement.GetInjectGenotype, return_internal_reference())
 set_policy(cInjectGenotypeElement.GetNext, return_internal_reference())
 set_policy(cInjectGenotypeElement.GetPrev, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inject_genotype_queue.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inject_genotype_queue.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inject_genotype_queue.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 
 cInjectGenotypeQueue = Class("cInjectGenotypeQueue", "inject_genotype_queue.hh")
 set_policy(cInjectGenotypeQueue.Find, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inst_lib_base.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inst_lib_base.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inst_lib_base.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -6,3 +6,5 @@
 set_policy(cInstLibBase.GetNopName, return_value_policy(reference_existing_object))
 set_policy(cInstLibBase.GetInstDefault, return_value_policy(reference_existing_object))
 set_policy(cInstLibBase.GetInstError, return_value_policy(reference_existing_object))
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inst_lib_cpu.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inst_lib_cpu.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inst_lib_cpu.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -9,3 +9,4 @@
 set_policy(cInstLibCPU.GetInstDefault, return_value_policy(reference_existing_object))
 set_policy(cInstLibCPU.GetInstError, return_value_policy(reference_existing_object))
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inst_set.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inst_set.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inst_set.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 
 cInstSet = Class("cInstSet", "inst_set.hh")
 set_policy(cInstSet.GetInstLib, return_value_policy(reference_existing_object))
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/inst_util.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/inst_util.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/inst_util.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 Include("inst_set.hh")
 
 cInstUtil = Class("cInstUtil", "inst_util.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/instruction.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/instruction.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/instruction.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cInstruction = Class("cInstruction", "instruction.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/int_sum.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/int_sum.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/int_sum.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cIntSum = Class("cIntSum", "int_sum.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/integrated_schedule.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/integrated_schedule.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/integrated_schedule.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Import("schedule.pyste")
 
 Include("merit.hh")
@@ -3,2 +4,4 @@
 
 cIntegratedSchedule = Class("cIntegratedSchedule", "integrated_schedule.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/integrated_schedule_node.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/integrated_schedule_node.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/integrated_schedule_node.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,3 +2,5 @@
 cIntegratedScheduleNode = Class("cIntegratedScheduleNode", "integrated_schedule_node.hh")
 set_policy(cIntegratedScheduleNode.GetNext, return_internal_reference())
 set_policy(cIntegratedScheduleNode.GetPrev, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/kaben_brainstorms.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/kaben_brainstorms.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/kaben_brainstorms.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -15,3 +15,5 @@
 ##endif
 #""")
 #Function("SetupAvida", "avida.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/landscape.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/landscape.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/landscape.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,8 @@
+
 Include("inst_set.hh")
 
+Include("fstream")
+
 cLandscape = Class("cLandscape", "landscape.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/lineage.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/lineage.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/lineage.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,6 @@
+
 Include("genotype.hh")
 
 cLineage = Class("cLineage", "lineage.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/lineage_control.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/lineage_control.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/lineage_control.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,3 +12,5 @@
 set_policy(cLineageControl.GetMaxFitnessLineage, return_internal_reference())
 set_policy(cLineageControl.GetBestLineage, return_internal_reference())
 set_policy(cLineageControl.GetDominantLineage, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/local_mutations.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/local_mutations.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/local_mutations.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,6 @@
+
 Include("mutation_lib.hh")
 
 cLocalMutations = Class("cLocalMutations", "local_mutations.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/memory_flags.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/memory_flags.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/memory_flags.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cMemoryFlags = Class("cMemoryFlags", "memory_flags.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/merit.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/merit.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/merit.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 exclude(cMerit.BinaryPrint)
 # operator is for ostreams; ditch it.
 exclude(cMerit.operator['<<'])
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/mutation.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/mutation.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/mutation.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cMutation = Class("cMutation", "mutation.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/mutation_lib.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/mutation_lib.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/mutation_lib.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 
 cMutationLib = Class("cMutationLib", "mutation_lib.hh")
 set_policy(cMutationLib.AddMutation, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/mutation_rates.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/mutation_rates.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/mutation_rates.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cMutationRates = Class("cMutationRates", "mutation_rates.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/mx_code_array.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/mx_code_array.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/mx_code_array.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Include("my_code_array_less_than.hh")
 Include("genome.hh")
 
@@ -2 +3,3 @@
 cMxCodeArray = Class("cMxCodeArray", "mx_code_array.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/my_code_array_less_than.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/my_code_array_less_than.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/my_code_array_less_than.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 MyCodeArrayLessThan = Class("MyCodeArrayLessThan", "my_code_array_less_than.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/org_message.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/org_message.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/org_message.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cOrgMessage = Class("cOrgMessage", "org_message.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/organism.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/organism.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/organism.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -26,3 +26,5 @@
 """)
 exclude(cOrganism.SaveState)
 exclude(cOrganism.LoadState)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/phenotype.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/phenotype.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/phenotype.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -32,3 +32,5 @@
 exclude(cPhenotype.CrossNum)
 exclude(cPhenotype.ChildFertile)
 exclude(cPhenotype.IsMultiThread)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/population.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/population.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/population.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -21,3 +21,5 @@
 cPopulation.GetEnvironment().
 """)
 set_policy(cPopulation.GetEnvironment, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/population_cell.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/population_cell.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/population_cell.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 set_policy(cPopulationCell.GetOrganism, return_internal_reference())
 set_policy(cPopulationCell.ConnectionList, return_internal_reference())
 set_policy(cPopulationCell.MutationRates, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/population_event.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/population_event.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/population_event.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,6 @@
+
 Import("event.pyste")
+
 cPopulationEvent = Class("cPopulationEvent", "population_event.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/population_event_factory.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/population_event_factory.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/population_event_factory.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -7,3 +7,5 @@
 
 cPopulationEventFactory = Class("cPopulationEventFactory", "population_event_factory.hh")
 set_policy(cPopulationEventFactory.ConstructEvent, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/population_interface.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/population_interface.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/population_interface.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -65,3 +65,5 @@
 exclude(cPopulationInterface.SetFun_UpdateMerit)
 
 Function("BuildTestPopInterface", "population_interface-fixups.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/prob_schedule.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/prob_schedule.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/prob_schedule.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Import("schedule.pyste")
 
 Include("merit.hh")
@@ -3,2 +4,4 @@
 
 cProbSchedule = Class("cProbSchedule", "prob_schedule.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/py_avida_driver-fixups.cc
===================================================================
--- trunk/source/bindings/Boost.Python/py_avida_driver-fixups.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/py_avida_driver-fixups.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,39 +1,20 @@
 
-#ifndef PY_AVIDA_DRIVER_HH
 #include "py_avida_driver.hh"
-#endif
 
-#ifndef GENEBANK_HH
 #include "main/genebank.hh"
-#endif
-#ifndef GENOTYPE_HH
 #include "main/genotype.hh"
-#endif
-#ifndef POPULATION_CELL_HH
 #include "main/population_cell.hh"
-#endif
-#ifndef HARDWARE_FACTORY_HH
 #include "cpu/hardware_factory.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "main/organism.hh"
-#endif  
-#ifndef HARDWARE_BASE_HH
 #include "cpu/hardware_base.hh"
-#endif
-#ifndef STRING_HH
 #include "tools/string.hh"
-#endif
-#ifndef CONFIG_HH
 #include "main/config.hh"
-#endif
-#ifndef POPULATION_HH
 #include "main/population.hh"
-#endif
 
 
 #include <iostream>
 
+
 bool pyAvidaDriver::preUpdate(const unsigned int){
   GetEvents();
   if(true == done_flag){ return false; }

Modified: trunk/source/bindings/Boost.Python/py_avida_driver.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/py_avida_driver.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/py_avida_driver.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,4 @@
 
 pyAvidaDriver = Class("pyAvidaDriver", "py_avida_driver.hh")
 
+# vim: set ft=python:

Copied: trunk/source/bindings/Boost.Python/py_hardware_tracer-fixups.cc (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/py_hardware_tracer-fixups.cc)

Copied: trunk/source/bindings/Boost.Python/py_hardware_tracer.hh (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/py_hardware_tracer.hh)

Copied: trunk/source/bindings/Boost.Python/py_hardware_tracer.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/py_hardware_tracer.pyste)

Modified: trunk/source/bindings/Boost.Python/random.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/random.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/random.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,3 +2,5 @@
 Include("tList.hh")
 
 cRandom = Class("cRandom", "random.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/reaction.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/reaction.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/reaction.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -7,3 +7,5 @@
 set_policy(cReaction.GetTask, return_internal_reference())
 set_policy(cReaction.AddProcess, return_internal_reference())
 set_policy(cReaction.AddRequisite, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/reaction_lib.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/reaction_lib.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/reaction_lib.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -6,3 +6,4 @@
 set_policy(cReactionLib.AddReaction, return_internal_reference())
 set_policy(cReactionLib.GetReaction, return_internal_reference())
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/reaction_process.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/reaction_process.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/reaction_process.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 set_policy(cReactionProcess.GetResource, return_internal_reference())
 set_policy(cReactionProcess.GetProduct, return_internal_reference())
 set_policy(cReactionProcess.GetDetect, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/reaction_requisite.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/reaction_requisite.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/reaction_requisite.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 Include("reaction.hh")
 
 cReactionRequisite = Class("cReactionRequisite", "reaction_requisite.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/reaction_result.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/reaction_result.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/reaction_result.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 cReactionResult = Class("cReactionResult", "reaction_result.hh")
 
 set_policy(cReactionResult.GetInstArray, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/ref_block.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/ref_block.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/ref_block.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cRefBlock = Class("cRefBlock", "ref_block.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/resource.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/resource.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/resource.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cResource = Class("cResource", "resource.hh")
+
+# vim: set ft=python:

Copied: trunk/source/bindings/Boost.Python/resource_count-fixups.cc (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/resource_count-fixups.cc)

Copied: trunk/source/bindings/Boost.Python/resource_count-fixups.hh (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/resource_count-fixups.hh)

Modified: trunk/source/bindings/Boost.Python/resource_count.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/resource_count.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/resource_count.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,5 +1,5 @@
 
-cResourceCount = Class("cResourceCount", "resource_count.hh")
+cResourceCount = Class("cResourceCount", "resource_count-fixups.hh")
 set_policy(cResourceCount.GetResources, return_internal_reference())
 set_policy(cResourceCount.GetCellResources, return_internal_reference())
 set_policy(cResourceCount.GetResourcesGeometry, return_internal_reference())
@@ -7,6 +7,9 @@
 
 exclude(cResourceCount.Setup)
 
+add_method(cResourceCount, "cResourceCount_SetTo");
+rename(cResourceCount.cResourceCount_SetTo, "SetTo");
+
 print("""
 FIXME for resource_count.pyste:
 Reenable cResourceCount.Setup(). This will take some work -- the c++
@@ -14,3 +17,4 @@
 system.
 """)
 
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/resource_lib.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/resource_lib.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/resource_lib.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,3 +5,5 @@
 cResourceLib = Class("cResourceLib", "resource_lib.hh")
 set_policy(cResourceLib.AddResource, return_internal_reference())
 set_policy(cResourceLib.GetResource, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/running_average.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/running_average.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/running_average.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cRunningAverage = Class("cRunningAverage", "running_average.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/scaled_block.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/scaled_block.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/scaled_block.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,5 @@
 
 cScaledBlock = Class("cScaledBlock", "scaled_block.hh")
 set_policy(cScaledBlock.GetData, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/schedule.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/schedule.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/schedule.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,6 @@
+
 Include("merit.hh")
 
 cSchedule = Class("cSchedule", "schedule.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/spatial_count_elem.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/spatial_count_elem.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/spatial_count_elem.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cSpatialCountElem = Class("cSpatialCountElem", "spatial_count_elem.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/spatial_res_count.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/spatial_res_count.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/spatial_res_count.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cSpatialResCount = Class("cSpatialResCount", "spatial_res_count.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/species.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/species.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/species.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -4,3 +4,5 @@
 cSpecies = Class("cSpecies", "species.hh")
 set_policy(cSpecies.GetNext, return_internal_reference())
 set_policy(cSpecies.GetPrev, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/species_control.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/species_control.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/species_control.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -9,3 +9,5 @@
 set_policy(cSpeciesControl.GetFirst, return_internal_reference())
 set_policy(cSpeciesControl.GetFirstInactive, return_internal_reference())
 set_policy(cSpeciesControl.GetFirstGarbage, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/species_queue.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/species_queue.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/species_queue.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 
 cSpeciesQueue = Class("cSpeciesQueue", "species_queue.hh")
 set_policy(cSpeciesQueue.GetFirst, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/stats.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/stats.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/stats.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -31,3 +31,5 @@
 set_policy(cStats.SumExeInst, return_internal_reference())
 set_policy(cStats.GetDataFileOFStream, return_internal_reference())
 set_policy(cStats.GetDataFile, return_internal_reference())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/string.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/string.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/string.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -19,3 +19,5 @@
 set_policy(cString.ClipEnd, return_self())
 set_policy(cString.ToLower, return_self())
 set_policy(cString.ToUpper, return_self())
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/string_iterator.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/string_iterator.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/string_iterator.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,6 @@
+
 Include("string_list.hh")
 
 cStringIterator = Class("cStringIterator", "string_iterator.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/string_list.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/string_list.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/string_list.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,3 +12,5 @@
     that I have't yet approached).
   - What to do about tList and memory-management issues?
 """)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/string_util.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/string_util.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/string_util.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,2 +1,4 @@
 
 cStringUtil = Class("cStringUtil", "string_util.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/tArray.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/tArray.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/tArray.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,6 +1,8 @@
-#  dir(specialized_type._DeclarationInfo__attributes) :
-#  {'__code__': ['.def("__len__", &tArray_int_len)', '.def("__getitem__", &tArray_int_getitem)', '.def("__setitem__", &tArray_int_setitem)'], 'exclude': False, 'include': 'tArray_instantiations.hh', 'name': 'tArray_int'} 
 
+
+# Functions providing python 'len()' and '[]' for class specializations
+# of tArray.
+
 def addClass__len__Wrapper(spec_str, spec_type):
   len_wrapper_name = "tArray_" + spec_str + "_len"
   class_code(spec_type, '.def("__len__", &' + len_wrapper_name + ')');
@@ -25,6 +27,11 @@
   tArray_class_T_setitem<>(array, i, item);
 }"""
 
+
+# Functions providing python '[]' for fundamental type specializations
+# of tArray. The 'len()' functionality provided for class types can be
+# reused here.
+
 def addFundamental__getitem__Wrapper(spec_str, spec_type):
   getitem_wrapper_name = "tArray_" + spec_str + "_getitem"
   class_code(spec_type, '.def("__getitem__", &' + getitem_wrapper_name + ')');
@@ -41,6 +48,9 @@
   tArray_class_T_setitem<>(array, i, item);
 }"""
 
+
+# Function to wrap class type specializations of tArray.
+
 def commonClassWrapperFactors(spec_str, spec_type):
   exclude(spec_type.ElementAt)
   decl_code_str = ""
@@ -49,6 +59,9 @@
   decl_code_str += addClass__setitem__Wrapper(spec_str, spec_type)
   return decl_code_str
 
+
+# Function to wrap fundamental type specializations of tArray.
+
 def commonFundamentalWrapperFactors(spec_str, spec_type):
   exclude(spec_type.ElementAt)
   decl_code_str = ""
@@ -69,6 +82,9 @@
 
 declaration_code_string = ""
 
+
+# Commands to specialize tArray for various types.
+
 pOrganism_str = "pOrganism"
 tArray_pOrganism = tArray(pOrganism_str)
 declaration_code_string += commonClassWrapperFactors(pOrganism_str, tArray_pOrganism)
@@ -94,59 +110,6 @@
 declaration_code_string += commonFundamentalWrapperFactors(int_str, tArray_int)
 
 
-
-
-#for specialization in class_specializers:
-#  specialized_type = tArray(specialization)
-#  exclude(specialized_type.ResizeClear)
-#  exclude(specialized_type.ElementAt)
-#  #
-#  len_wrapper_name = "tArray_" + specialization + "_len"
-#  getitem_wrapper_name = "tArray_" + specialization + "_getitem"
-#  setitem_wrapper_name = "tArray_" + specialization + "_setitem"
-#  #
-#  declaration_code_string += """
-#inline int """ + len_wrapper_name + "(tArray<" + specialization + """> &array) {
-#  return tArray_class_T_len<>(array);
-#}"""
-#  declaration_code_string += """
-#inline """ + specialization + " &" + getitem_wrapper_name + "(tArray<" + specialization + """> &array, int i) {
-#  return tArray_class_T_getitem<>(array, i);
-#}"""
-#  declaration_code_string += """
-#inline void """ + setitem_wrapper_name + "(tArray<" + specialization + "> &array, int i, " + specialization + """ &item) {
-#  tArray_class_T_setitem<>(array, i, item);
-#}"""
-#  #
-#  class_code(specialized_type, '.def("__len__", &' + len_wrapper_name + ')');
-#  class_code(specialized_type, '.def("__getitem__", &' + getitem_wrapper_name + ', return_internal_reference< 1 >())');
-#  class_code(specialized_type, '.def("__setitem__", &' + setitem_wrapper_name + ')');
-
-
-#for specialization in fundamental_specializers:
-#  specialized_type = tArray(specialization)
-#  exclude(specialized_type.ResizeClear)
-#  exclude(specialized_type.ElementAt)
-#  #
-#  len_wrapper_name = "tArray_" + specialization + "_len"
-#  getitem_wrapper_name = "tArray_" + specialization + "_getitem"
-#  setitem_wrapper_name = "tArray_" + specialization + "_setitem"
-#  #
-#  declaration_code_string += """
-#inline int """ + len_wrapper_name + "(tArray<" + specialization + """> &array) {
-#  return tArray_class_T_len<>(array);
-#}"""
-#  declaration_code_string += """
-#inline """ + specialization + " " + getitem_wrapper_name + "(tArray<" + specialization + """> &array, int i) {
-#  return tArray_fundamental_T_getitem<>(array, i);
-#}"""
-#  declaration_code_string += """
-#inline void """ + setitem_wrapper_name + "(tArray<" + specialization + "> &array, int i, " + specialization + """ item) {
-#  tArray_class_T_setitem<>(array, i, item);
-#}"""
-#  #
-#  class_code(specialized_type, '.def("__len__", &' + len_wrapper_name + ')');
-#  class_code(specialized_type, '.def("__getitem__", &' + getitem_wrapper_name + ')');
-#  class_code(specialized_type, '.def("__setitem__", &' + setitem_wrapper_name + ')');
-
 declaration_code(declaration_code_string)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/tBuffer.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/tBuffer.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/tBuffer.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -6,3 +6,5 @@
 
 for specialization in template_specializers:
   specialized_type = tBuffer(specialization)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/tDictionary.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/tDictionary.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/tDictionary.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -6,3 +6,5 @@
 
 for specialization in template_specializers:
   specialized_type = tDictionary(specialization)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/tList.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/tList.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/tList.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -55,3 +55,5 @@
   set_policy(const_list_iterator_type.Get , return_value_policy(reference_existing_object))
   set_policy(const_list_iterator_type.Next , return_value_policy(reference_existing_object))
   set_policy(const_list_iterator_type.Prev , return_value_policy(reference_existing_object))
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/tMatrix.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/tMatrix.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/tMatrix.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,3 +12,5 @@
   set_policy(specialized_type.ElementAt, return_internal_reference())
   set_policy(specialized_type.operator['()'], return_internal_reference())
   set_policy(specialized_type.operator['[]'], return_internal_reference())
+
+# vim: set ft=python:

Copied: trunk/source/bindings/Boost.Python/tVector.pyste (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/tVector.pyste)

Copied: trunk/source/bindings/Boost.Python/tVector_instantiations.hh (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/tVector_instantiations.hh)

Modified: trunk/source/bindings/Boost.Python/task_entry.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/task_entry.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/task_entry.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -3,3 +3,5 @@
 # GetTestFun returns a instance method pointer, doesn't play well with
 # Python.
 exclude(cTaskEntry.GetTestFun)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/task_lib.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/task_lib.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/task_lib.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,3 +2,5 @@
 
 cTaskLib = Class("cTaskLib", "task_lib.hh")
 set_policy(cTaskLib.AddTask, return_internal_reference())
+
+# vim: set ft=python:

Copied: trunk/source/bindings/Boost.Python/test_cpu-fixups.cc (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/test_cpu-fixups.cc)

Copied: trunk/source/bindings/Boost.Python/test_cpu-fixups.hh (from rev 137, branches/developers/kaben-organism-scope/source/bindings/Boost.Python/test_cpu-fixups.hh)

Modified: trunk/source/bindings/Boost.Python/test_cpu.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/test_cpu.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/test_cpu.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -6,26 +6,26 @@
 Include("population_interface.hh")
 Include("resource_count.hh")
 
-cTestCPU = Class("cTestCPU", "test_cpu.hh")
-print("""
-XXX in test_cpu.pyste: cTestCPU.GetInstSet needs autopointer to protect
-ownership.
-""")
+cTestCPU = Class("cTestCPU", "test_cpu-fixups.hh")
 set_policy(cTestCPU.GetInstSet, return_value_policy(reference_existing_object))
-print("""
-XXX in test_cpu.pyste: cTestCPU.GetEnvironment needs autopointer to protect
-ownership.
-""")
 set_policy(cTestCPU.GetEnvironment, return_value_policy(reference_existing_object))
-print("""
-XXX in test_cpu.pyste: cTestCPU.GetResources needs autopointer to protect
-ownership.
-""")
 set_policy(cTestCPU.GetResources, return_value_policy(reference_existing_object))
 set_policy(cTestCPU.GetResourceCount, return_value_policy(reference_existing_object))
+exclude(cTestCPU.UseResources)
+
+exclude(cTestCPU.UseResources)
+add_method(cTestCPU, "cTestCPU_GetUseResources");
+add_method(cTestCPU, "cTestCPU_SetUseResources");
+rename(cTestCPU.cTestCPU_GetUseResources, "GetUseResources");
+rename(cTestCPU.cTestCPU_SetUseResources, "SetUseResources");
+class_code(cTestCPU, '.add_property("UseResources", &cTestCPU_GetUseResources, &cTestCPU_SetUseResources)');
+
 print("""
-XXX in test_cpu.pyste: cTestCPU.UseResources temporarily disabled
-because it returns a reference to built-in type, which makes Pyste kinda
-cranky.
+XXX in test_cpu.pyste:
+- cTestCPU.GetInstSet needs autopointer to protect ownership.
+- cTestCPU.GetEnvironment needs autopointer to protect ownership.
+- cTestCPU.GetResources needs autopointer to protect ownership.
+- cTestCPU.GetResourceCount needs autopointer to protect ownership.
 """)
-exclude(cTestCPU.UseResources)
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/test_util.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/test_util.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/test_util.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,3 +1,4 @@
+
 Include("genome.hh")
 Include("inject_genotype.hh")
 Include("genotype.hh")
@@ -3,2 +4,4 @@
 
 cTestUtil = Class("cTestUtil", "test_util.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/tools.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/tools.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/tools.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,3 +2,5 @@
 Include("string.hh")
 
 cTools = Class("cTools", "tools.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/uint.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/uint.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/uint.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,3 @@
 cUInt = Class("cUInt", "uint.hh")
+
+# vim: set ft=python:

Modified: trunk/source/bindings/Boost.Python/weighted_index.pyste
===================================================================
--- trunk/source/bindings/Boost.Python/weighted_index.pyste	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/bindings/Boost.Python/weighted_index.pyste	2005-04-13 09:32:08 UTC (rev 138)
@@ -1 +1,4 @@
+
 cWeightedIndex = Class("cWeightedIndex", "weighted_index.hh")
+
+# vim: set ft=python:

Modified: trunk/source/cpu/CMakeLists.txt
===================================================================
--- trunk/source/cpu/CMakeLists.txt	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/CMakeLists.txt	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,6 +12,7 @@
   hardware_cpu_thread.cc
   hardware_factory.cc
   hardware_util.cc
+  hardware_status_printer.cc
   memory_flags.cc
   test_cpu.cc
   test_util.cc

Modified: trunk/source/cpu/cpu_test_info.cc
===================================================================
--- trunk/source/cpu/cpu_test_info.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/cpu_test_info.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,16 +5,11 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
 
-#ifndef ORGANISM_HH
+#include "hardware_status_printer.hh"
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
 
 #include <assert.h>
 
@@ -30,6 +25,7 @@
   , trace_task_order(false)
   , use_random_inputs(false)
   , org_array(max_tests)
+  , m_tracer(NULL)
 {
   org_array.SetAll(NULL);
   Clear();
@@ -60,11 +56,10 @@
 }
  
 
-void cCPUTestInfo::SetTraceExecution(const cString & filename)
+void cCPUTestInfo::SetTraceExecution(cHardwareTracer *tracer)
 {
-  trace_execution = true;
-  trace_fp.open(filename);
-  assert (trace_fp.good() == true); // Unable to open trace file.
+  trace_execution = (tracer)?(true):(false);
+  m_tracer = tracer;
 }
 
 

Modified: trunk/source/cpu/cpu_test_info.hh
===================================================================
--- trunk/source/cpu/cpu_test_info.hh	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/cpu_test_info.hh	2005-04-13 09:32:08 UTC (rev 138)
@@ -8,8 +8,6 @@
 #ifndef CPU_TEST_INFO_HH
 #define CPU_TEST_INFO_HH
 
-#include <fstream>
-
 #ifndef CPU_DEFS_HH
 #include "cpu_defs.hh"
 #endif
@@ -20,6 +18,7 @@
 #include "tArray.hh"
 #endif
 
+class cHardwareTracer;
 class cOrganism;
 class cString;
 
@@ -33,7 +32,7 @@
   bool trace_execution;       // Should we trace this CPU?
   bool trace_task_order;      // Should we keep track of ordering of tasks?
   bool use_random_inputs;     // Should we give the organism random inputs?
-  std::ofstream trace_fp;
+  cHardwareTracer *m_tracer;
 
   // Outputs...
   bool is_viable;         // Is this organism colony forming?
@@ -55,7 +54,7 @@
   void PrintThreads(bool _print=true) { print_threads = _print; }
   void TraceTaskOrder(bool _trace=true) { trace_task_order = _trace; }
   void UseRandomInputs(bool _rand=true) { use_random_inputs = _rand; }
-  void SetTraceExecution(const cString & filename="trace.dat");
+  void SetTraceExecution(cHardwareTracer *tracer = NULL);
 
   // Input Accessors
   int GetGenerationTests() const { return generation_tests; }
@@ -64,7 +63,7 @@
   bool GetTraceTaskOrder() const { return trace_task_order; }
   bool GetUseRandomInputs() const { return use_random_inputs; }
   bool GetTraceExecution() const { return trace_execution; }
-  std::ofstream & GetTraceFP() { return trace_fp; }
+  cHardwareTracer *GetTracer() { return m_tracer; }
 
 
   // Output Accessors

Modified: trunk/source/cpu/hardware_4stack.cc
===================================================================
--- trunk/source/cpu/hardware_4stack.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/hardware_4stack.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -7,52 +7,24 @@
 
 
 
-#ifndef HARDWARE_4STACK_HH
 #include "hardware_4stack.hh"
-#endif
 
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
-#ifndef FUNCTIONS_HH
 #include "functions.hh"
-#endif
-#ifndef GENOME_UTIL_HH
 #include "genome_util.hh"
-#endif
-#ifndef INST_LIB_BASE_HH
 #include "inst_lib_base.hh"
-#endif
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
-#ifndef MUTATION_HH
+#include "hardware_tracer.hh"
+#include "hardware_tracer_4stack.hh"
 #include "mutation.hh"
-#endif
-#ifndef MUTATION_LIB_HH
 #include "mutation_lib.hh"
-#endif
-#ifndef MUTATION_MACROS_HH
 #include "mutation_macros.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef RANDOM_HH
 #include "random.hh"
-#endif
-#ifndef STRING_UTIL_HH
 #include "string_util.hh"
-#endif
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
 
 #include <limits.h>
 
@@ -289,6 +261,29 @@
 }
 
 
+cHardware4Stack::cHardware4Stack(const cHardware4Stack &hardware_4stack)
+: cHardwareBase(hardware_4stack.organism, hardware_4stack.inst_set)
+, m_functions(hardware_4stack.m_functions)
+, memory_array(hardware_4stack.memory_array)
+, threads(hardware_4stack.threads)
+, thread_id_chart(hardware_4stack.thread_id_chart)
+, cur_thread(hardware_4stack.cur_thread)
+, mal_active(hardware_4stack.mal_active)
+, inst_cost(hardware_4stack.inst_cost)
+#ifdef INSTRUCTION_COSTS
+, inst_ft_cost(hardware_4stack.inst_ft_cost)
+, inst_remainder(hardware_4stack.inst_remainder)
+#endif
+{
+  for(int i = 0; i < NUM_GLOBAL_STACKS; i++){
+    global_stacks[i] = hardware_4stack.global_stacks[i];
+  }
+  for(int i = 0; i < sizeof(slice_array)/sizeof(float); i++){
+    slice_array[i] = hardware_4stack.slice_array[i];
+  }
+}
+
+
 cHardware4Stack::~cHardware4Stack()
 {
 }
@@ -386,9 +381,12 @@
 #endif
     
     // Print the status of this CPU at each step...
-    if (trace_fp != NULL) {
-      const cString & next_name = inst_set->GetName(IP().GetInst())();
-      organism->PrintStatus(*trace_fp, next_name);
+    if (m_tracer != NULL) {
+      if (cHardwareTracer_4Stack * tracer
+          = dynamic_cast<cHardwareTracer_4Stack *>(m_tracer)
+      ){
+        tracer->TraceHardware_4Stack(*this);
+      }
     }
     
     // Find the instruction to be executed
@@ -496,10 +494,12 @@
 
   // @CAO FIX PRINTING TO INDICATE THIS IS A BONUS
   // Print the status of this CPU at each step...
-  if (trace_fp != NULL) {
-    cString next_name = cStringUtil::Stringf("%s (bonus instruction)",
-					     inst_set->GetName(inst)());
-    organism->PrintStatus(*trace_fp, next_name);
+  if (m_tracer != NULL) {
+    if (cHardwareTracer_4Stack * tracer
+        = dynamic_cast<cHardwareTracer_4Stack *>(m_tracer)
+    ){
+      tracer->TraceHardware_4StackBonus(*this);
+    }
   }
     
   SingleProcess_ExecuteInst(inst);

Modified: trunk/source/cpu/hardware_4stack.hh
===================================================================
--- trunk/source/cpu/hardware_4stack.hh	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/hardware_4stack.hh	2005-04-13 09:32:08 UTC (rev 138)
@@ -109,6 +109,7 @@
 
 public:
   cHardware4Stack(cOrganism * in_organism, cInstSet * in_inst_set);
+  explicit cHardware4Stack(const cHardware4Stack &);
   ~cHardware4Stack();
   void Recycle(cOrganism * new_organism, cInstSet * in_inst_set);
   static cInstLibBase *GetInstLib();

Modified: trunk/source/cpu/hardware_base.cc
===================================================================
--- trunk/source/cpu/hardware_base.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/hardware_base.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,13 +5,9 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
 
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
 
 using namespace std;
 
@@ -21,7 +17,7 @@
   : organism(in_organism)
   , inst_set(in_inst_set)
   , viewer_lock(-1)
-  , trace_fp(NULL)
+  , m_tracer(NULL)
 {
   assert(inst_set->OK());
   assert(organism != NULL);

Modified: trunk/source/cpu/hardware_base.hh
===================================================================
--- trunk/source/cpu/hardware_base.hh	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/hardware_base.hh	2005-04-13 09:32:08 UTC (rev 138)
@@ -19,6 +19,7 @@
 class cCodeLabel;
 class cCPUMemory;
 class cGenome;
+class cHardwareTracer;
 class cInstruction; // aggregate
 class cInstSet;
 class cOrganism;
@@ -30,7 +31,7 @@
   int viewer_lock;            // Used if the viewer should only lock onto
                               //  one aspect of the hardware.
 
-  ostream * trace_fp;         // Set this if you want execution traced.
+  cHardwareTracer * m_tracer;         // Set this if you want execution traced.
 
   static int instance_count;
 public:
@@ -72,7 +73,7 @@
   virtual void SaveState(std::ostream & fp) = 0;
   virtual void LoadState(std::istream & fp) = 0;
 
-  void SetTrace(ostream * in_fp) { trace_fp = in_fp; }
+  void SetTrace(cHardwareTracer * tracer) { m_tracer = tracer; }
 
 
   // --------  Mutations (Must be Virtual)  --------

Modified: trunk/source/cpu/hardware_cpu.cc
===================================================================
--- trunk/source/cpu/hardware_cpu.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/hardware_cpu.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,52 +5,24 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef HARDWARE_CPU_HH
 #include "hardware_cpu.hh"
-#endif
 
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
-#ifndef FUNCTIONS_HH
 #include "functions.hh"
-#endif
-#ifndef GENOME_UTIL_HH
 #include "genome_util.hh"
-#endif
-#ifndef GENOTYPE_HH
 #include "genotype.hh"
-#endif
-#ifndef INST_LIB_CPU_HH
+#include "hardware_tracer.hh"
+#include "hardware_tracer_cpu.hh"
 #include "inst_lib_cpu.hh"
-#endif
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
-#ifndef MUTATION_HH
 #include "mutation.hh"
-#endif
-#ifndef MUTATION_LIB_HH
 #include "mutation_lib.hh"
-#endif
-#ifndef MUTATION_MACROS_HH
 #include "mutation_macros.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef STRING_UTIL_HH
 #include "string_util.hh"
-#endif
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
 
 #include <limits.h>
 #include <fstream>
@@ -410,6 +382,25 @@
 }
 
 
+cHardwareCPU::cHardwareCPU(const cHardwareCPU &hardware_cpu)
+: cHardwareBase(hardware_cpu.organism, hardware_cpu.inst_set)
+, m_functions(hardware_cpu.m_functions)
+, memory(hardware_cpu.memory)
+, global_stack(hardware_cpu.global_stack)
+, thread_time_used(hardware_cpu.thread_time_used)
+, threads(hardware_cpu.threads)
+, thread_id_chart(hardware_cpu.thread_id_chart)
+, cur_thread(hardware_cpu.cur_thread)
+, mal_active(hardware_cpu.mal_active)
+, advance_ip(hardware_cpu.advance_ip)
+#ifdef INSTRUCTION_COSTS
+, inst_cost(hardware_cpu.inst_cost)
+, inst_ft_cost(hardware_cpu.inst_ft_cost)
+#endif
+{
+}
+
+
 cHardwareCPU::~cHardwareCPU()
 {
 }
@@ -484,9 +475,12 @@
 #endif
     
     // Print the status of this CPU at each step...
-    if (trace_fp != NULL) {
-      const cString & next_name = inst_set->GetName(IP().GetInst())();
-      organism->PrintStatus(*trace_fp, next_name);
+    if (m_tracer != NULL) {
+      if (cHardwareTracer_CPU * tracer
+          = dynamic_cast<cHardwareTracer_CPU *>(m_tracer)
+      ){
+        tracer->TraceHardware_CPU(*this);
+      }
     }
     
     // Find the instruction to be executed
@@ -595,10 +589,12 @@
 
   // @CAO FIX PRINTING TO INDICATE THIS IS A BONUS
   // Print the status of this CPU at each step...
-  if (trace_fp != NULL) {
-    cString next_name = cStringUtil::Stringf("%s (bonus instruction)",
-					     inst_set->GetName(inst)());
-    organism->PrintStatus(*trace_fp, next_name);
+  if (m_tracer != NULL) {
+    if (cHardwareTracer_CPU * tracer
+        = dynamic_cast<cHardwareTracer_CPU *>(m_tracer)
+    ){
+      tracer->TraceHardware_CPUBonus(*this);
+    }
   }
     
   SingleProcess_ExecuteInst(inst);

Modified: trunk/source/cpu/hardware_cpu.hh
===================================================================
--- trunk/source/cpu/hardware_cpu.hh	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/hardware_cpu.hh	2005-04-13 09:32:08 UTC (rev 138)
@@ -105,6 +105,7 @@
 
 public:
   cHardwareCPU(cOrganism * in_organism, cInstSet * in_inst_set);
+  explicit cHardwareCPU(const cHardwareCPU &);
   ~cHardwareCPU();
   void Recycle(cOrganism * new_organism, cInstSet * in_inst_set);
   static cInstLibCPU *GetInstLib();

Modified: trunk/source/cpu/hardware_factory.cc
===================================================================
--- trunk/source/cpu/hardware_factory.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/hardware_factory.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,25 +5,13 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef HARDWARE_FACTORY_HH
 #include "hardware_factory.hh"
-#endif
 
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
-#ifndef HARDWARE_CPU_HH
 #include "hardware_cpu.hh"
-#endif
-#ifndef HARDWARE_4STACK_HH
 #include "hardware_4stack.hh"
-#endif
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
 
 using namespace std;
 

Copied: trunk/source/cpu/hardware_status_printer.cc (from rev 137, branches/developers/kaben-organism-scope/source/cpu/hardware_status_printer.cc)

Copied: trunk/source/cpu/hardware_status_printer.hh (from rev 137, branches/developers/kaben-organism-scope/source/cpu/hardware_status_printer.hh)

Copied: trunk/source/cpu/hardware_tracer.hh (from rev 137, branches/developers/kaben-organism-scope/source/cpu/hardware_tracer.hh)

Copied: trunk/source/cpu/hardware_tracer_4stack.hh (from rev 137, branches/developers/kaben-organism-scope/source/cpu/hardware_tracer_4stack.hh)

Copied: trunk/source/cpu/hardware_tracer_cpu.hh (from rev 137, branches/developers/kaben-organism-scope/source/cpu/hardware_tracer_cpu.hh)

Copied: trunk/source/cpu/hardware_tracer_test_cpu.hh (from rev 137, branches/developers/kaben-organism-scope/source/cpu/hardware_tracer_test_cpu.hh)

Modified: trunk/source/cpu/test_cpu.cc
===================================================================
--- trunk/source/cpu/test_cpu.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/test_cpu.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,61 +5,27 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
 
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef ENVIRONMENT_HH
 #include "environment.hh"
-#endif
-#ifndef FUNCTIONS_HH
 #include "functions.hh"
-#endif
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
-#ifndef INST_SET_HH
+#include "hardware_status_printer.hh"
 #include "inst_set.hh"
-#endif
-#ifndef INST_UTIL_HH
 #include "inst_util.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef POPULATION_INTERFACE_HH
 #include "population_interface.hh"
-#endif
-#ifndef RESOURCE_COUNT_HH
 #include "resource_count.hh"
-#endif
-#ifndef RESOURCE_LIB_HH
 #include "resource_lib.hh"
-#endif
-#ifndef RESOURCE_HH
 #include "resource.hh"
-#endif
-#ifndef STRING_UTIL_HH
 #include "string_util.hh"
-#endif
-#ifndef TMATRIX_HH
 #include "tMatrix.hh"
-#endif
 
 #include <iomanip>
 
-
-#include "population_interface.hh"
-
 using namespace std;
 
 
@@ -158,15 +124,15 @@
   cur_receive = 0;
 
   // Determine if we're tracing and what we need to print.
-  ostream * trace_fp =
-    test_info.GetTraceExecution() ? &(test_info.GetTraceFP()) : NULL;
+  cHardwareTracer * tracer =
+    test_info.GetTraceExecution() ? (test_info.GetTracer()) : NULL;
 
   int time_used = 0;
   while (time_used < time_allocated &&
 	 organism.GetHardware().GetMemory().GetSize() &&
 	 organism.GetPhenotype().GetNumDivides() == 0) {
     time_used++;
-    organism.GetHardware().SetTrace(trace_fp);
+    organism.GetHardware().SetTrace(tracer);
     organism.GetHardware().SingleProcess();
     organism.GetHardware().SetTrace(NULL);
     //resource_count.Update(1/cConfig::GetAveTimeslice());
@@ -174,19 +140,18 @@
   }
 
   // Print out some final info in trace...
-  if (trace_fp != NULL) {
-    if (time_used == time_allocated) {
-      *trace_fp << endl << "TIMEOUT: No offspring produced." << endl;
+  if (tracer != NULL) {
+    if (cHardwareTracer_TestCPU * tracer_test_cpu
+        = dynamic_cast<cHardwareTracer_TestCPU *>(tracer)
+    ){
+      tracer_test_cpu->TraceHardware_TestCPU(
+        time_used,
+        time_allocated,
+        organism.GetHardware().GetMemory().GetSize(),
+        organism.GetHardware().GetMemory().AsString(),
+        organism.ChildGenome().AsString()
+      );
     }
-    else if (organism.GetHardware().GetMemory().GetSize() == 0) {
-      *trace_fp << endl << "ORGANISM DEATH: No offspring produced." << endl;
-    }
-    else {
-      *trace_fp << endl << "Final Memory: "
-		<< organism.GetHardware().GetMemory().AsString() << endl
-		<< "Child Memory: " << organism.ChildGenome().AsString()
-		<< endl;
-    }
   }
 
   // For now, always return true.

Modified: trunk/source/cpu/test_util.cc
===================================================================
--- trunk/source/cpu/test_util.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/cpu/test_util.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,52 +5,28 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef TEST_UTIL_HH
 #include "test_util.hh"
-#endif
 
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
-#ifndef ENVIRONMENT_HH
 #include "environment.hh"
-#endif
-#ifndef GENOME_HH
 #include "genome.hh"
-#endif
-#ifndef GENOTYPE_HH
 #include "genotype.hh"
-#endif
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
-#ifndef INJECT_GENOTYPE_HH
 #include "inject_genotype.hh"
-#endif
-#ifndef INST_UTIL_HH
 #include "inst_util.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef STATS_HH
 #include "stats.hh"
-#endif
-#ifndef TASK_ENTRY_HH
 #include "task_entry.hh"
-#endif
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
 
 #include <fstream>
 #include <iomanip>
 
+
 using namespace std;
 
+
 void cTestUtil::PrintGenome(const cGenome & genome, cString filename,
 			    cGenotype * genotype, int update_out)
 {

Modified: trunk/source/main/analyze.cc
===================================================================
--- trunk/source/main/analyze.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/analyze.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -9,101 +9,40 @@
 #include <sstream>
 #include <string>
 
-#ifndef ANALYZE_HH
 #include "analyze.hh"
-#endif
 
-#ifndef ANALYZE_COMMAND_HH
 #include "analyze_command.hh"
-#endif
-#ifndef ANALYZE_COMMAND_DEF_HH
 #include "analyze_command_def.hh"
-#endif
-#ifndef ANALYZE_COMMAND_DEF_BASE_HH
 #include "analyze_command_def_base.hh"
-#endif
-#ifndef ANALYZE_FLOW_COMMAND_HH
 #include "analyze_flow_command.hh"
-#endif
-#ifndef ANALYZE_FLOW_COMMAND_DEF_HH
 #include "analyze_flow_command_def.hh"
-#endif
-#ifndef ANALYZE_FUNCTION_HH
 #include "analyze_function.hh"
-#endif
-#ifndef ANALYZE_GENOTYPE_HH
 #include "analyze_genotype.hh"
-#endif
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef DATA_FILE_HH
 #include "data_file.hh"
-#endif
-#ifndef ENVIRONMENT_HH
 #include "environment.hh"
-#endif
-#ifndef FITNESS_MATRIX_HH
 #include "fitness_matrix.hh"
-#endif
-#ifndef GENOME_UTIL_HH
 #include "genome_util.hh"
-#endif
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
-#ifndef HARDWARE_UTIL_HH
+#include "hardware_status_printer.hh"
 #include "hardware_util.hh"
-#endif
-#ifndef HELP_MANAGER_HH
 #include "help_manager.hh"
-#endif
-#ifndef INIT_FILE_HH
 #include "init_file.hh"
-#endif
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
-#ifndef INST_UTIL_HH
 #include "inst_util.hh"
-#endif
-#ifndef LANDSCAPE_HH
 #include "landscape.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef SPECIES_HH
 #include "species.hh"
-#endif
-#ifndef TARGDATAENTRY_HH
 #include "tArgDataEntry.hh"
-#endif
-#ifndef TASK_ENTRY_HH
 #include "task_entry.hh"
-#endif
-#ifndef TDATAENTRY_HH
 #include "tDataEntry.hh"
-#endif
-#ifndef TDATAENTRYCOMMAND_HH
 #include "tDataEntryCommand.hh"
-#endif
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
-#ifndef TEST_UTIL_HH
 #include "test_util.hh"
-#endif
-#ifndef RESOURCE_HH
 #include "resource.hh"
-#endif
 #ifdef WIN32
-# ifndef WIN32_MKDIR_HACK_HH
 #  include "win32_mkdir_hack.hh"
-# endif
 #endif
 
 extern "C" {
@@ -1215,14 +1154,21 @@
       break;
     }
 
+    // Build the hardware status printer for tracing.
+    ofstream trace_fp;
+    trace_fp.open(filename);
+    assert (trace_fp.good() == true); // Unable to open trace file.
+    cHardwareStatusPrinter trace_printer(trace_fp);
+
     // Build the test info for printing.
     cCPUTestInfo test_info;
     test_info.TestThreads();
-    test_info.SetTraceExecution(filename);
+    test_info.SetTraceExecution(&trace_printer);
 
     cTestCPU::TestGenome(test_info, genotype->GetGenome());
 
     if (verbose) cout << "  Tracing: " << filename << endl;
+    trace_fp.close();
   }
 
   if(useResources) {

Modified: trunk/source/main/analyze_genotype.cc
===================================================================
--- trunk/source/main/analyze_genotype.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/analyze_genotype.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,31 +5,15 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef ANALYZE_GENOTYPE_HH
 #include "analyze_genotype.hh"
-#endif
 
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
-#ifndef LANDSCAPE_HH
 #include "landscape.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
 
 using namespace std;
 

Modified: trunk/source/main/avida_driver_population.cc
===================================================================
--- trunk/source/main/avida_driver_population.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/avida_driver_population.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,61 +5,25 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef AVIDA_DRIVER_POPULATION_HH
 #include "avida_driver_population.hh"
-#endif
 
-#ifndef AVIDA_TRIGGERS_HH
 #include "avida_triggers.hh"
-#endif
-#ifndef CALLBACK_UTIL_HH
 #include "callback_util.hh"
-#endif
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef EVENT_FACTORY_MANAGER_HH
 #include "event_factory_manager.hh"
-#endif
-#ifndef EVENT_LIST_HH
 #include "event_list.hh"
-#endif
-#ifndef GENEBANK_HH
 #include "genebank.hh"
-#endif
-#ifndef GENOTYPE_HH
 #include "genotype.hh"
-#endif
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
-#ifndef HARDWARE_FACTORY_HH
 #include "hardware_factory.hh"
-#endif
-#ifndef INIT_FILE_HH
 #include "init_file.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef POPULATION_HH
 #include "population.hh"
-#endif
-#ifndef POPULATION_CELL_HH
 #include "population_cell.hh"
-#endif
-#ifndef POPULATION_EVENT_FACTORY_HH
 #include "population_event_factory.hh"
-#endif
-#ifndef POPULATION_INTERFACE_HH
 #include "population_interface.hh"
-#endif
-#ifndef STRING_HH
 #include "string.hh"
-#endif
-#ifndef TOOLS_HH
 #include "tools.hh"
-#endif
 
 #include <iostream>
 

Modified: trunk/source/main/config.cc
===================================================================
--- trunk/source/main/config.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/config.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,26 +5,14 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
 
-#ifndef DEFS_HH
 #include "defs.hh"
-#endif
-#ifndef GENESIS_HH
 #include "genesis.hh"
-#endif
-#ifndef TOOLS_HH
 #include "tools.hh"
-#endif
 
-#ifndef POPULATION_DESCR_HI
 #include "cPopulation_descr.hi" // declarations and definitions
-#endif
-#ifndef POPULATION_DESCR_CI
 #include "cPopulation_descr.ci" // for event documentation
-#endif
 
 using namespace std;
 

Modified: trunk/source/main/genotype.cc
===================================================================
--- trunk/source/main/genotype.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/genotype.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,34 +5,16 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef GENOTYPE_HH
 #include "genotype.hh"
-#endif
 
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
-#endif
-#ifndef GENOME_UTIL_HH
 #include "genome_util.hh"
-#endif
-#ifndef MERIT_HH
 #include "merit.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
-#ifndef TOOLS_HH
 #include "tools.hh"
-#endif
 
 using namespace std;
 

Modified: trunk/source/main/landscape.cc
===================================================================
--- trunk/source/main/landscape.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/landscape.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,37 +5,17 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef LANDSCAPE_HH
 #include "landscape.hh"
-#endif
 
-#ifndef CPU_MEMORY_HH
 #include "cpu_memory.hh"
-#endif
-#ifndef ENVIRONMENT_HH
 #include "environment.hh"
-#endif
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef STATS_HH
 #include "stats.hh"             // For GetUpdate in outputs...
-#endif
-#ifndef TEST_CPU_HH
 #include "test_cpu.hh"
-#endif
-#ifndef TEST_UTIL_HH
 #include "test_util.hh"
-#endif
-#ifndef TOOLS_HH
 #include "tools.hh"
-#endif
 
 using namespace std;
 

Modified: trunk/source/main/landscape.hh
===================================================================
--- trunk/source/main/landscape.hh	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/landscape.hh	2005-04-13 09:32:08 UTC (rev 138)
@@ -8,8 +8,6 @@
 #ifndef LANDSCAPE_HH
 #define LANDSCAPE_HH
 
-#include <iostream>
-
 #ifndef CPU_TEST_INFO_HH
 #include "cpu_test_info.hh"
 #endif

Modified: trunk/source/main/organism.cc
===================================================================
--- trunk/source/main/organism.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/organism.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,55 +5,23 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
 
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef CPU_DEFS_HH
 #include "cpu_defs.hh"
-#endif
-#ifndef ENVIRONMENT_HH
 #include "environment.hh"
-#endif
-#ifndef FUNCTIONS_HH
 #include "functions.hh"
-#endif
-#ifndef GENOME_HH
 #include "genome.hh"
-#endif
-#ifndef GENOME_UTIL_HH
 #include "genome_util.hh"
-#endif
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
-#ifndef INJECT_GENOTYPE_HH
 #include "inject_genotype.hh"
-#endif
-#ifndef INST_SET_HH
 #include "inst_set.hh"
-#endif
-#ifndef INST_UTIL_HH
 #include "inst_util.hh"
-#endif
-#ifndef ORG_MESSAGE_HH
 #include "org_message.hh"
-#endif
-#ifndef STRING_UTIL_HH
 #include "string_util.hh"
-#endif
-#ifndef TARRAY_HH
 #include "tArray.hh"
-#endif
-#ifndef TOOLS_HH
 #include "tools.hh"
-#endif
-#ifndef TLIST_HH
 #include "tList.hh"
-#endif
 
 #include <iomanip>
 

Modified: trunk/source/main/population.cc
===================================================================
--- trunk/source/main/population.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/main/population.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,92 +5,35 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef POPULATION_HH
 #include "population.hh"
-#endif
 
-
-#ifndef CONFIG_HH
 #include "config.hh"
-#endif
-#ifndef CONST_SCHEDULE_HH
 #include "const_schedule.hh"
-#endif
-#ifndef DATA_FILE_HH
 #include "data_file.hh"
-#endif
-#ifndef ENVIRONMENT_HH
 #include "environment.hh"
-#endif
-#ifndef FUNCTIONS_HH
 #include "functions.hh"
-#endif
-#ifndef GENEBANK_HH
 #include "genebank.hh"
-#endif
-#ifndef GENOME_UTIL_HH
 #include "genome_util.hh"
-#endif
-#ifndef GENOTYPE_HH
 #include "genotype.hh"
-#endif
-#ifndef HARDWARE_BASE_HH
 #include "hardware_base.hh"
-#endif
-#ifndef HARDWARE_FACTORY_HH
 #include "hardware_factory.hh"
-#endif
-#ifndef HARDWARE_4STACK_HH
 #include "hardware_4stack.hh"
-#endif
-#ifndef HARDWARE_UTIL_HH
 #include "hardware_util.hh"
-#endif
-#ifndef INIT_FILE_HH
 #include "init_file.hh"
-#endif
-#ifndef INJECT_GENEBANK_HH
 #include "inject_genebank.hh"
-#endif
-#ifndef INJECT_GENOTYPE_HH
 #include "inject_genotype.hh"
-#endif
-#ifndef INST_UTIL_HH
 #include "inst_util.hh"
-#endif
-#ifndef INTEGRATED_SCHEDULE_HH
 #include "integrated_schedule.hh"
-#endif
-#ifndef LINEAGE_HH
 #include "lineage.hh"
-#endif
-#ifndef LINEAGE_CONTROL_HH
 #include "lineage_control.hh"
-#endif
-#ifndef ORGANISM_HH
 #include "organism.hh"
-#endif
-#ifndef PHENOTYPE_HH
 #include "phenotype.hh"
-#endif
-#ifndef POPULATION_CELL_HH
 #include "population_cell.hh"
-#endif
-#ifndef PROB_SCHEDULE_HH
 #include "prob_schedule.hh"
-#endif
-#ifndef RESOURCE_HH
 #include "resource.hh"
-#endif
-#ifndef SPECIES_HH
 #include "species.hh"
-#endif
-#ifndef STATS_HH
 #include "stats.hh"
-#endif
-#ifndef TASK_ENTRY_HH
 #include "task_entry.hh"
-#endif
 
 #include <fstream>
 #include <vector>

Modified: trunk/source/python/AvidaEd-osx.py
===================================================================
--- trunk/source/python/AvidaEd-osx.py	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaEd-osx.py	2005-04-13 09:32:08 UTC (rev 138)
@@ -39,8 +39,8 @@
     edu_main_controller = AvidaGui2.pyEduMainCtrl.pyEduMainCtrl()
     edu_main_controller.construct()
     edu_main_controller.m_main_mdl.m_main_mdtr.m_main_controller_factory_mdtr.emit(
-    sys.exc_clear()
-    sys.exc_traceback = sys.last_traceback = None
+    #sys.exc_clear()
+    #sys.exc_traceback = sys.last_traceback = None
       qt.PYSIGNAL("newMainControllerSig"), ("pySessionCtrl",))
     return edu_main_controller
   

Modified: trunk/source/python/AvidaGui2/pyAnalyzeControlsView.ui
===================================================================
--- trunk/source/python/AvidaGui2/pyAnalyzeControlsView.ui	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyAnalyzeControlsView.ui	2005-04-13 09:32:08 UTC (rev 138)
@@ -8,14 +8,14 @@
         <rect>
             <x>0</x>
             <y>0</y>
-            <width>176</width>
-            <height>125</height>
+            <width>124</width>
+            <height>40</height>
         </rect>
     </property>
     <property name="caption">
         <string>pyAnalyzeControlsView</string>
     </property>
-    <vbox>
+    <hbox>
         <property name="name">
             <cstring>unnamed</cstring>
         </property>
@@ -25,291 +25,147 @@
         <property name="spacing">
             <number>0</number>
         </property>
-        <widget class="QSlider">
+        <spacer>
             <property name="name">
-                <cstring>slider1</cstring>
+                <cstring>spacer97_2</cstring>
             </property>
             <property name="orientation">
                 <enum>Horizontal</enum>
             </property>
-            <property name="tickmarks">
-                <enum>Below</enum>
+            <property name="sizeType">
+                <enum>Expanding</enum>
             </property>
-        </widget>
-        <widget class="QLayoutWidget">
+            <property name="sizeHint">
+                <size>
+                    <width>20</width>
+                    <height>20</height>
+                </size>
+            </property>
+        </spacer>
+        <widget class="QToolButton">
             <property name="name">
-                <cstring>layout136</cstring>
+                <cstring>toolButton23</cstring>
             </property>
-            <hbox>
-                <property name="name">
-                    <cstring>unnamed</cstring>
-                </property>
-                <widget class="QLabel">
-                    <property name="name">
-                        <cstring>textLabel7</cstring>
-                    </property>
-                    <property name="font">
-                        <font>
-                            <pointsize>10</pointsize>
-                        </font>
-                    </property>
-                    <property name="text">
-                        <string>slow</string>
-                    </property>
-                    <property name="alignment">
-                        <set>AlignVCenter|AlignLeft</set>
-                    </property>
-                </widget>
-                <widget class="QLabel">
-                    <property name="name">
-                        <cstring>textLabel7_2</cstring>
-                    </property>
-                    <property name="font">
-                        <font>
-                            <pointsize>10</pointsize>
-                        </font>
-                    </property>
-                    <property name="text">
-                        <string>fast</string>
-                    </property>
-                    <property name="alignment">
-                        <set>AlignVCenter|AlignRight</set>
-                    </property>
-                </widget>
-            </hbox>
+            <property name="text">
+                <string></string>
+            </property>
+            <property name="iconSet">
+                <iconset>image0</iconset>
+            </property>
         </widget>
-        <widget class="QLayoutWidget">
+        <widget class="QWidgetStack">
             <property name="name">
-                <cstring>layout141</cstring>
+                <cstring>widgetStack3</cstring>
             </property>
-            <hbox>
+            <widget class="QWidget">
                 <property name="name">
-                    <cstring>unnamed</cstring>
+                    <cstring>WStackPage</cstring>
                 </property>
-                <property name="margin">
+                <attribute name="id">
                     <number>0</number>
-                </property>
-                <property name="spacing">
-                    <number>0</number>
-                </property>
-                <widget class="QToolButton">
+                </attribute>
+                <vbox>
                     <property name="name">
-                        <cstring>toolButton23</cstring>
+                        <cstring>unnamed</cstring>
                     </property>
-                    <property name="text">
-                        <string></string>
+                    <property name="margin">
+                        <number>0</number>
                     </property>
-                    <property name="iconSet">
-                        <iconset>image0</iconset>
+                    <property name="spacing">
+                        <number>0</number>
                     </property>
-                </widget>
-                <widget class="QLayoutWidget">
-                    <property name="name">
-                        <cstring>layout140</cstring>
-                    </property>
-                    <vbox>
+                    <widget class="QToolButton">
                         <property name="name">
-                            <cstring>unnamed</cstring>
+                            <cstring>toolButton19</cstring>
                         </property>
-                        <property name="margin">
-                            <number>0</number>
+                        <property name="text">
+                            <string></string>
                         </property>
-                        <property name="spacing">
-                            <number>0</number>
+                        <property name="iconSet">
+                            <iconset>image1</iconset>
                         </property>
-                        <widget class="QLabel">
-                            <property name="name">
-                                <cstring>textLabel8</cstring>
-                            </property>
-                            <property name="font">
-                                <font>
-                                    <pointsize>10</pointsize>
-                                </font>
-                            </property>
-                            <property name="text">
-                                <string># of steps</string>
-                            </property>
-                            <property name="alignment">
-                                <set>AlignCenter</set>
-                            </property>
-                        </widget>
-                        <widget class="QLineEdit">
-                            <property name="name">
-                                <cstring>lineEdit1</cstring>
-                            </property>
-                            <property name="font">
-                                <font>
-                                    <pointsize>10</pointsize>
-                                </font>
-                            </property>
-                        </widget>
-                    </vbox>
-                </widget>
-                <widget class="QToolButton">
-                    <property name="name">
-                        <cstring>toolButton24</cstring>
-                    </property>
-                    <property name="text">
-                        <string></string>
-                    </property>
-                    <property name="iconSet">
-                        <iconset>image1</iconset>
-                    </property>
-                </widget>
-            </hbox>
-        </widget>
-        <widget class="QLayoutWidget">
-            <property name="name">
-                <cstring>layout137</cstring>
-            </property>
-            <hbox>
+                        <property name="usesBigPixmap">
+                            <bool>false</bool>
+                        </property>
+                    </widget>
+                </vbox>
+            </widget>
+            <widget class="QWidget">
                 <property name="name">
-                    <cstring>unnamed</cstring>
+                    <cstring>WStackPage</cstring>
                 </property>
-                <property name="margin">
-                    <number>0</number>
-                </property>
-                <property name="spacing">
-                    <number>0</number>
-                </property>
-                <spacer>
+                <attribute name="id">
+                    <number>1</number>
+                </attribute>
+                <vbox>
                     <property name="name">
-                        <cstring>spacer97_2</cstring>
+                        <cstring>unnamed</cstring>
                     </property>
-                    <property name="orientation">
-                        <enum>Horizontal</enum>
+                    <property name="margin">
+                        <number>0</number>
                     </property>
-                    <property name="sizeType">
-                        <enum>Expanding</enum>
+                    <property name="spacing">
+                        <number>0</number>
                     </property>
-                    <property name="sizeHint">
-                        <size>
-                            <width>10</width>
-                            <height>10</height>
-                        </size>
-                    </property>
-                </spacer>
-                <widget class="QWidgetStack">
-                    <property name="name">
-                        <cstring>widgetStack3</cstring>
-                    </property>
-                    <widget class="QWidget">
+                    <widget class="QToolButton">
                         <property name="name">
-                            <cstring>WStackPage</cstring>
+                            <cstring>toolButton20</cstring>
                         </property>
-                        <attribute name="id">
-                            <number>0</number>
-                        </attribute>
-                        <vbox>
-                            <property name="name">
-                                <cstring>unnamed</cstring>
-                            </property>
-                            <property name="margin">
-                                <number>0</number>
-                            </property>
-                            <property name="spacing">
-                                <number>0</number>
-                            </property>
-                            <widget class="QToolButton">
-                                <property name="name">
-                                    <cstring>toolButton19</cstring>
-                                </property>
-                                <property name="text">
-                                    <string></string>
-                                </property>
-                                <property name="iconSet">
-                                    <iconset>image2</iconset>
-                                </property>
-                                <property name="usesBigPixmap">
-                                    <bool>false</bool>
-                                </property>
-                            </widget>
-                        </vbox>
-                    </widget>
-                    <widget class="QWidget">
-                        <property name="name">
-                            <cstring>WStackPage</cstring>
+                        <property name="text">
+                            <string></string>
                         </property>
-                        <attribute name="id">
-                            <number>1</number>
-                        </attribute>
-                        <vbox>
-                            <property name="name">
-                                <cstring>unnamed</cstring>
-                            </property>
-                            <property name="margin">
-                                <number>0</number>
-                            </property>
-                            <property name="spacing">
-                                <number>0</number>
-                            </property>
-                            <widget class="QToolButton">
-                                <property name="name">
-                                    <cstring>toolButton20</cstring>
-                                </property>
-                                <property name="text">
-                                    <string></string>
-                                </property>
-                                <property name="iconSet">
-                                    <iconset>image3</iconset>
-                                </property>
-                                <property name="usesBigPixmap">
-                                    <bool>false</bool>
-                                </property>
-                            </widget>
-                        </vbox>
+                        <property name="iconSet">
+                            <iconset>image2</iconset>
+                        </property>
+                        <property name="usesBigPixmap">
+                            <bool>false</bool>
+                        </property>
                     </widget>
-                </widget>
-                <spacer>
-                    <property name="name">
-                        <cstring>spacer97</cstring>
-                    </property>
-                    <property name="orientation">
-                        <enum>Horizontal</enum>
-                    </property>
-                    <property name="sizeType">
-                        <enum>Expanding</enum>
-                    </property>
-                    <property name="sizeHint">
-                        <size>
-                            <width>10</width>
-                            <height>10</height>
-                        </size>
-                    </property>
-                </spacer>
-            </hbox>
+                </vbox>
+            </widget>
         </widget>
+        <widget class="QToolButton">
+            <property name="name">
+                <cstring>toolButton24</cstring>
+            </property>
+            <property name="text">
+                <string></string>
+            </property>
+            <property name="iconSet">
+                <iconset>image3</iconset>
+            </property>
+        </widget>
         <spacer>
             <property name="name">
-                <cstring>spacer99</cstring>
+                <cstring>spacer97</cstring>
             </property>
             <property name="orientation">
-                <enum>Vertical</enum>
+                <enum>Horizontal</enum>
             </property>
             <property name="sizeType">
                 <enum>Expanding</enum>
             </property>
             <property name="sizeHint">
                 <size>
-                    <width>10</width>
-                    <height>10</height>
+                    <width>20</width>
+                    <height>20</height>
                 </size>
             </property>
         </spacer>
-    </vbox>
+    </hbox>
 </widget>
 <images>
     <image name="image0">
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 <layoutdefaults spacing="6" margin="11"/>

Copied: trunk/source/python/AvidaGui2/pyHardwareCPUTrace.py (from rev 137, branches/developers/kaben-organism-scope/source/python/AvidaGui2/pyHardwareCPUTrace.py)

Modified: trunk/source/python/AvidaGui2/pyOneOrg_ScopeView.ui
===================================================================
--- trunk/source/python/AvidaGui2/pyOneOrg_ScopeView.ui	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyOneOrg_ScopeView.ui	2005-04-13 09:32:08 UTC (rev 138)
@@ -26,6 +26,14 @@
             <property name="name">
                 <cstring>m_organism_scope_ctrl</cstring>
             </property>
+            <property name="sizePolicy">
+                <sizepolicy>
+                    <hsizetype>5</hsizetype>
+                    <vsizetype>3</vsizetype>
+                    <horstretch>0</horstretch>
+                    <verstretch>0</verstretch>
+                </sizepolicy>
+            </property>
         </widget>
         <widget class="QSlider">
             <property name="name">
@@ -104,7 +112,7 @@
         </sizehint>
         <container>0</container>
         <sizepolicy>
-            <hordata>5</hordata>
+            <hordata>0</hordata>
             <verdata>0</verdata>
             <horstretch>0</horstretch>
             <verstretch>0</verstretch>
@@ -113,6 +121,8 @@
         <property type="0">3</property>
         <property type="1">pyAnalyzeControlsCtrl</property>
         <property type="3">-1</property>
+        <property type="1">pyAnalyzeControlsCtrl</property>
+        <property type="3">-1</property>
         <property type="pyAnalyzeControlsCtrl"></property>
         <property type="-1">1</property>
     </customwidget>

Modified: trunk/source/python/AvidaGui2/pyOneOrganismView.ui
===================================================================
--- trunk/source/python/AvidaGui2/pyOneOrganismView.ui	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyOneOrganismView.ui	2005-04-13 09:32:08 UTC (rev 138)
@@ -12,7 +12,7 @@
             <x>0</x>
             <y>0</y>
             <width>613</width>
-            <height>510</height>
+            <height>434</height>
         </rect>
     </property>
     <property name="caption">
@@ -151,54 +151,14 @@
                     <hsizetype>5</hsizetype>
                     <vsizetype>3</vsizetype>
                     <horstretch>0</horstretch>
-                    <verstretch>1</verstretch>
+                    <verstretch>0</verstretch>
                 </sizepolicy>
             </property>
         </widget>
-        <widget class="pyTimelineCtrl">
-            <property name="name">
-                <cstring>pyTimelineCtrl3</cstring>
-            </property>
-            <property name="sizePolicy">
-                <sizepolicy>
-                    <hsizetype>3</hsizetype>
-                    <vsizetype>3</vsizetype>
-                    <horstretch>0</horstretch>
-                    <verstretch>1</verstretch>
-                </sizepolicy>
-            </property>
-        </widget>
     </vbox>
 </widget>
 <customwidgets>
     <customwidget>
-        <class>pyTimelineCtrl</class>
-        <header location="global">1</header>
-        <sizehint>
-            <width>-1</width>
-            <height>0</height>
-        </sizehint>
-        <container>0</container>
-        <sizepolicy>
-            <hordata>0</hordata>
-            <verdata>0</verdata>
-            <horstretch>0</horstretch>
-            <verstretch>0</verstretch>
-        </sizepolicy>
-        <pixmap>image2</pixmap>
-        <property type="0">3</property>
-        <property type="1">pyTimelineCtrl</property>
-        <property type="3">-1</property>
-        <property type="1">pyTimelineCtrl</property>
-        <property type="3">-1</property>
-        <property type="1">pyTimelineCtrl</property>
-        <property type="4">-1</property>
-        <property type="1">pyTimelineCtrl</property>
-        <property type="4">-1</property>
-        <property type="pyTimelineCtrl"></property>
-        <property type="-1">1</property>
-    </customwidget>
-    <customwidget>
         <class>pyOneOrg_ScopeCtrl</class>
         <header location="local">1</header>
         <sizehint>
@@ -229,6 +189,5 @@
 <layoutdefaults spacing="6" margin="11"/>
 <includehints>
     <includehint>pyoneorg_scopectrl.h</includehint>
-    <includehint>pytimelinectrl.h</includehint>
 </includehints>
 </UI>

Modified: trunk/source/python/AvidaGui2/pyOrganismScopeCtrl.py
===================================================================
--- trunk/source/python/AvidaGui2/pyOrganismScopeCtrl.py	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyOrganismScopeCtrl.py	2005-04-13 09:32:08 UTC (rev 138)
@@ -2,8 +2,10 @@
 
 from pyOrganismScopeView import pyOrganismScopeView
 
-import AvidaCore
+from AvidaCore import cAnalyzeGenotype, cGenome, cInstruction, cInstUtil, cString
 
+from pyHardwareTracer import pyHardwareTracer
+
 from qt import *
 
 import os
@@ -33,148 +35,185 @@
     if(old_avida): del old_avida
 
   def setDebugOrganismFileSlot(self, organism_filename):
+    print "pyOrganismScopeCtrl.setDebugOrganismFileSlot"
     if self.m_avida:
-      # Analysis files.
-      genebank_dirname = self.m_session_mdl.m_tempdir
-      organism_file_basename = os.path.basename(str(organism_filename))
-      analyze_filename = '%s/organism_analyze.cfg' % self.m_session_mdl.m_tempdir
-      trace_filename = '%s/%s.trace' % (genebank_dirname, organism_file_basename)
-      genotype_filename = '%s/%s.gen' % (genebank_dirname, organism_file_basename)
+      inst_set = self.m_avida.m_environment.GetInstSet()
+      genome = cGenome(cInstUtil.LoadGenome(cString(organism_filename.ascii()), inst_set) )
+      analyze_genotype = cAnalyzeGenotype(genome, inst_set)
+      hardware_tracer = pyHardwareTracer()
+      hardware_tracer.traceAnalyzeGenotype(analyze_genotype, self.m_avida.m_environment, should_use_resources = False)
 
-      # Analysis results files.
-      is_viable_info_filename = '%s/is_viable.info' % self.m_session_mdl.m_tempdir
-      gestation_time_info_filename = '%s/gestation_time.info' % self.m_session_mdl.m_tempdir
-      fitness_info_filename = '%s/fitness.info' % self.m_session_mdl.m_tempdir
-      size_info_filename = '%s/size.info' % self.m_session_mdl.m_tempdir
-      genome_info_filename = '%s/genome.info' % self.m_session_mdl.m_tempdir
-      tasks_info_filename = '%s/tasks.info' % self.m_session_mdl.m_tempdir
-      ihead_info_filename = '%s/ihead.info' % self.m_session_mdl.m_tempdir
-      rhead_info_filename = '%s/rhead.info' % self.m_session_mdl.m_tempdir
-      whead_info_filename = '%s/whead.info' % self.m_session_mdl.m_tempdir
-      fhead_info_filename = '%s/fhead.info' % self.m_session_mdl.m_tempdir
+      for i in range(len(hardware_tracer.m_hardware_trace.m_genome_info)):
+        print "step %d:" % i,
+        print "  genome", hardware_tracer.m_hardware_trace.m_genome_info[i]
+        #print "  ihead", hardware_tracer.m_hardware_trace.m_ihead_info[i]
+        #print "  rhead", hardware_tracer.m_hardware_trace.m_rhead_info[i]
+        #print "  whead", hardware_tracer.m_hardware_trace.m_whead_info[i]
+        #print "  fhead", hardware_tracer.m_hardware_trace.m_fhead_info[i]
+        #print "  ax", hardware_tracer.m_hardware_trace.m_register_ax_info[i]
+        #print "  bx", hardware_tracer.m_hardware_trace.m_register_bx_info[i]
+        #print "  cx", hardware_tracer.m_hardware_trace.m_register_cx_info[i]
+        #print "  read_label", hardware_tracer.m_hardware_trace.m_read_label_info[i]
+        print "  last_copy", hardware_tracer.m_hardware_trace.m_last_copy_info[i]
 
-      # Create a temporary analyze file using organism file name.
-      analyze_file = open(analyze_filename, 'w')
-      analyze_file.write('LOAD_ORGANISM %s\n' % organism_filename)
-      analyze_file.write('RECALCULATE\n')
-      analyze_file.write('TRACE %s\n' % genebank_dirname)
-      analyze_file.write('PRINT %s\n' % genebank_dirname)
-      analyze_file.close()
+        #print "  tasks:"
+        #for j in range(hardware_tracer.m_hardware_trace.m_tasks_info[i].GetSize()):
+        #  print "    %d" % j, hardware_tracer.m_hardware_trace.m_tasks_info[i][j]
 
-      # Create an analyze object using the temporary analyze file and
-      # the environment of the current avida object.
-      AvidaCore.cConfig.SetAnalyzeFilename(AvidaCore.cString(analyze_filename))
-      avida_driver_analyze = AvidaCore.cAvidaDriver_Analyze(
-        False, self.m_avida.m_environment)
-      avida_driver_analyze.Run()
+      print "is_viable", hardware_tracer.m_hardware_trace.m_is_viable
+      print "gestation_time", hardware_tracer.m_hardware_trace.m_gestation_time
+      print "fitness", hardware_tracer.m_hardware_trace.m_fitness
+      print "size", hardware_tracer.m_hardware_trace.m_size
 
-      # Extract organism viability, gestation time, fitness, and size numbers.
-      os.system( 'cat ' + genotype_filename + ' | grep Is | grep Viable | cut -d\  -f4-20  > ' + is_viable_info_filename)
-      os.system( 'cat ' + genotype_filename + ' | grep Gestation | cut -d\  -f4-20  > ' + gestation_time_info_filename)
-      os.system( 'cat ' + genotype_filename + ' | grep Fitness | cut -d\  -f4-20  > ' + fitness_info_filename)
-      os.system( 'cat ' + genotype_filename + ' | grep Genome | cut -d\  -f4-20  > ' + size_info_filename)
-      # Extract genome info.
-      os.system( 'cat ' + trace_filename + ' | grep Mem | cut -d\  -f6 > ' + genome_info_filename)
-      # Extract the tasks done at each point in execution.
-      os.system( 'cat ' + trace_filename + ' | grep Task | cut -d\  -f9-17 > ' + tasks_info_filename)
-      # Extract the instruction pointer locations from the trace file.
-      os.system( 'cat ' + trace_filename + ' | grep IP | cut -d\  -f2 | cut -b4-7 > ' + ihead_info_filename)
-      # Extract the read/write/flow head info.
-      os.system( 'cat ' + trace_filename + ' | grep "R-Head" | cut -d\  -f3 | cut -d\: -f2 > ' + rhead_info_filename)
-      os.system( 'cat ' + trace_filename + ' | grep "W-Head" | cut -d\  -f4 | cut -d\: -f2 > ' + whead_info_filename)
-      os.system( 'cat ' + trace_filename + ' | grep "F-Head" | cut -d\  -f5 | cut -d\: -f2 > ' + fhead_info_filename)
 
-      # Load organism viability, gestation time, fitness, and size.
-      def load_info(info_filename):
-        info_file = file(info_filename, 'rU')
-        info = info_file.read()
-        info_file.close()
-        return info.strip()
-
-      ( is_viable_info_string,
-        gestation_time_info_string,
-        fitness_info_string,
-        size_info_string,
-      ) = [load_info(info_filename) for info_filename in (
-        is_viable_info_filename,
-        gestation_time_info_filename,
-        fitness_info_filename,
-        size_info_filename,)]
-      is_viable_info = bool(int(is_viable_info_string))
-      gestation_time_info = int(gestation_time_info_string)
-      fitness_info = float(fitness_info_string)
-      size_info = int(size_info_string)
-
-      # Load genome, tasks, and heads at each point in execution.
-      def load_info_lines(info_filename):
-        info_file = file(info_filename, 'rU')
-        info_lines = info_file.readlines()
-        info_file.close()
-        return [info_line.strip() for info_line in info_lines]
-
-      ( genome_info,
-        tasks_info_strings,
-        ihead_info_strings,
-        rhead_info_strings,
-        whead_info_strings,
-        fhead_info_strings,
-      ) = [load_info_lines(info_filename) for info_filename in (
-        genome_info_filename,
-        tasks_info_filename,
-        ihead_info_filename,
-        rhead_info_filename,
-        whead_info_filename,
-        fhead_info_filename,)]
-      tasks_info = [[bool(int(task)) for task in tasks] for tasks in [line.split() for line in tasks_info_strings]]
-      ihead_info = [int(line) for line in ihead_info_strings]
-      rhead_info = [int(line) for line in rhead_info_strings]
-      whead_info = [int(line) for line in whead_info_strings]
-      fhead_info = [int(line) for line in fhead_info_strings]
-
-      class pyMdl: pass
-      frames = pyMdl()
-      frames.m_is_viable = is_viable_info
-      frames.m_gestation_time = gestation_time_info
-      frames.m_fitness = fitness_info
-      frames.m_size = size_info
-      frames.m_genome_info = genome_info
-      frames.m_tasks_info = tasks_info
-      frames.m_ihead_info = ihead_info
-      frames.m_rhead_info = rhead_info
-      frames.m_whead_info = whead_info
-      frames.m_fhead_info = fhead_info
-
-      # Delete analyze files and analysis results files.
-      #for filename in (
-      #  analyze_filename,
-      #  trace_filename,
-      #  genotype_filename,
-      #  is_viable_info_filename,
-      #  gestation_time_info_filename,
-      #  fitness_info_filename,
-      #  size_info_filename,
-      #  genome_info_filename,
-      #  tasks_info_filename,
-      #  ihead_info_filename,
-      #  rhead_info_filename,
-      #  whead_info_filename,
-      #  fhead_info_filename,
-      #):
-      #  os.remove(filename)
-
       # Translate from string genome representation to actual command names.
       inst_names = {}
       inst_set = self.m_avida.m_environment.GetInstSet()
-      instruction = AvidaCore.cInstruction()
+      instruction = cInstruction()
       for id in range(inst_set.GetSize()):
         instruction.SetOp(id)
         inst_names[instruction.GetSymbol()] = str(inst_set.GetName(instruction))
 
       self.setInstNames(inst_names)
-      self.setFrames(frames)
+      self.setFrames(hardware_tracer.m_hardware_trace)
 
-      # load task info
-      #   determine points at which tasks appear, both in genome and
-      #   frame number
 
+      # Organism viability.
+
+      # Gestation time.
+
+      # Fitness.
+
+      # Genome frames.
+        # Position of last-used instruction. Before allocate, this is
+        # the position of the last instruction of the organism. After
+        # allocate, at each frame this is the position of the final
+        # copied instruction. Usually as each new instructions is copied
+        # it becomes the final copied instruction in the genome. I'm
+        # tracking this information because I want to animate addition
+        # of new instructions at the end of the genome as the organism
+        # copies itself.
+
+      # Task frames.
+
+      # Head positions at each frame.
+
       pass
+    #if self.m_avida:
+    #  # Analysis files.
+    #  genebank_dirname = self.m_session_mdl.m_tempdir
+    #  organism_file_basename = os.path.basename(str(organism_filename))
+    #  analyze_filename = '%s/organism_analyze.cfg' % self.m_session_mdl.m_tempdir
+    #  trace_filename = '%s/%s.trace' % (genebank_dirname, organism_file_basename)
+    #  genotype_filename = '%s/%s.gen' % (genebank_dirname, organism_file_basename)
+
+    #  # Analysis results files.
+    #  is_viable_info_filename = '%s/is_viable.info' % self.m_session_mdl.m_tempdir
+    #  gestation_time_info_filename = '%s/gestation_time.info' % self.m_session_mdl.m_tempdir
+    #  fitness_info_filename = '%s/fitness.info' % self.m_session_mdl.m_tempdir
+    #  size_info_filename = '%s/size.info' % self.m_session_mdl.m_tempdir
+    #  genome_info_filename = '%s/genome.info' % self.m_session_mdl.m_tempdir
+    #  tasks_info_filename = '%s/tasks.info' % self.m_session_mdl.m_tempdir
+    #  ihead_info_filename = '%s/ihead.info' % self.m_session_mdl.m_tempdir
+    #  rhead_info_filename = '%s/rhead.info' % self.m_session_mdl.m_tempdir
+    #  whead_info_filename = '%s/whead.info' % self.m_session_mdl.m_tempdir
+    #  fhead_info_filename = '%s/fhead.info' % self.m_session_mdl.m_tempdir
+
+    #  # Create a temporary analyze file using organism file name.
+    #  analyze_file = open(analyze_filename, 'w')
+    #  analyze_file.write('LOAD_ORGANISM %s\n' % organism_filename)
+    #  analyze_file.write('RECALCULATE\n')
+    #  analyze_file.write('TRACE %s\n' % genebank_dirname)
+    #  analyze_file.write('PRINT %s\n' % genebank_dirname)
+    #  analyze_file.close()
+
+    #  # Create an analyze object using the temporary analyze file and
+    #  # the environment of the current avida object.
+    #  AvidaCore.cConfig.SetAnalyzeFilename(AvidaCore.cString(analyze_filename))
+    #  avida_driver_analyze = AvidaCore.cAvidaDriver_Analyze(False, self.m_avida.m_environment)
+    #  avida_driver_analyze.Run()
+
+    #  # Extract organism viability, gestation time, fitness, and size numbers.
+    #  os.system( 'cat ' + genotype_filename + ' | grep Is | grep Viable | cut -d\  -f4-20  > ' + is_viable_info_filename)
+    #  os.system( 'cat ' + genotype_filename + ' | grep Gestation | cut -d\  -f4-20  > ' + gestation_time_info_filename)
+    #  os.system( 'cat ' + genotype_filename + ' | grep Fitness | cut -d\  -f4-20  > ' + fitness_info_filename)
+    #  os.system( 'cat ' + genotype_filename + ' | grep Genome | cut -d\  -f4-20  > ' + size_info_filename)
+    #  # Extract genome info.
+    #  os.system( 'cat ' + trace_filename + ' | grep Mem | cut -d\  -f6 > ' + genome_info_filename)
+    #  # Extract the tasks done at each point in execution.
+    #  os.system( 'cat ' + trace_filename + ' | grep Task | cut -d\  -f9-17 > ' + tasks_info_filename)
+    #  # Extract the instruction pointer locations from the trace file.
+    #  os.system( 'cat ' + trace_filename + ' | grep IP | cut -d\  -f2 | cut -b4-7 > ' + ihead_info_filename)
+    #  # Extract the read/write/flow head info.
+    #  os.system( 'cat ' + trace_filename + ' | grep "R-Head" | cut -d\  -f3 | cut -d\: -f2 > ' + rhead_info_filename)
+    #  os.system( 'cat ' + trace_filename + ' | grep "W-Head" | cut -d\  -f4 | cut -d\: -f2 > ' + whead_info_filename)
+    #  os.system( 'cat ' + trace_filename + ' | grep "F-Head" | cut -d\  -f5 | cut -d\: -f2 > ' + fhead_info_filename)
+
+    #  # Load organism viability, gestation time, fitness, and size.
+    #  def load_info(info_filename):
+    #    info_file = file(info_filename, 'rU')
+    #    info = info_file.read()
+    #    info_file.close()
+    #    return info.strip()
+
+    #  ( is_viable_info_string,
+    #    gestation_time_info_string,
+    #    fitness_info_string,
+    #    size_info_string,
+    #  ) = [load_info(info_filename) for info_filename in (
+    #    is_viable_info_filename,
+    #    gestation_time_info_filename,
+    #    fitness_info_filename,
+    #    size_info_filename,)]
+    #  is_viable_info = bool(int(is_viable_info_string))
+    #  gestation_time_info = int(gestation_time_info_string)
+    #  fitness_info = float(fitness_info_string)
+    #  size_info = int(size_info_string)
+
+    #  # Load genome, tasks, and heads at each point in execution.
+    #  def load_info_lines(info_filename):
+    #    info_file = file(info_filename, 'rU')
+    #    info_lines = info_file.readlines()
+    #    info_file.close()
+    #    return [info_line.strip() for info_line in info_lines]
+
+    #  ( genome_info,
+    #    tasks_info_strings,
+    #    ihead_info_strings,
+    #    rhead_info_strings,
+    #    whead_info_strings,
+    #    fhead_info_strings,
+    #  ) = [load_info_lines(info_filename) for info_filename in (
+    #    genome_info_filename,
+    #    tasks_info_filename,
+    #    ihead_info_filename,
+    #    rhead_info_filename,
+    #    whead_info_filename,
+    #    fhead_info_filename,)]
+    #  tasks_info = [[bool(int(task)) for task in tasks] for tasks in [line.split() for line in tasks_info_strings]]
+    #  ihead_info = [int(line) for line in ihead_info_strings]
+    #  rhead_info = [int(line) for line in rhead_info_strings]
+    #  whead_info = [int(line) for line in whead_info_strings]
+    #  fhead_info = [int(line) for line in fhead_info_strings]
+
+    #  # Delete analyze files and analysis results files.
+    #  #for filename in (
+    #  #  analyze_filename,
+    #  #  trace_filename,
+    #  #  genotype_filename,
+    #  #  is_viable_info_filename,
+    #  #  gestation_time_info_filename,
+    #  #  fitness_info_filename,
+    #  #  size_info_filename,
+    #  #  genome_info_filename,
+    #  #  tasks_info_filename,
+    #  #  ihead_info_filename,
+    #  #  rhead_info_filename,
+    #  #  whead_info_filename,
+    #  #  fhead_info_filename,
+    #  #):
+    #  #  os.remove(filename)
+
+    #  # load task info
+    #  #   determine points at which tasks appear, both in genome and
+    #  #   frame number

Modified: trunk/source/python/AvidaGui2/pyOrganismScopeView.py
===================================================================
--- trunk/source/python/AvidaGui2/pyOrganismScopeView.py	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyOrganismScopeView.py	2005-04-13 09:32:08 UTC (rev 138)
@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 
 
-from qt import *
-from qtcanvas import *
+from qt import PYSIGNAL, QFont, QFontMetrics, QScrollView, QWMatrix
+from qtcanvas import QCanvas, QCanvasView, QCanvasText
+import math
 
-
 class pyOrganismScopeView(QCanvasView):
   def __init__(self,parent = None,name = None,fl = 0):
     QCanvasView.__init__(self,parent,name,fl)
@@ -14,9 +14,23 @@
     self.setHScrollBarMode(QScrollView.AlwaysOff)
     self.m_canvas = QCanvas()
     self.setCanvas(self.m_canvas)
+
+    font = QFont(self.font())
+    font_metrics = QFontMetrics(font)
+    self.m_font_points_per_pixel = font.pointSizeFloat()/font_metrics.height()
+
+    self.m_organism_circle_margin = 10
+    self.m_font_oversize_factor = 1.2
+
+    self.m_visible_width = 0
+    self.m_visible_height = 0
+
     self.reset()
 
   def reset(self):
+    if hasattr(self, "m_instruction_items") and self.m_instruction_items is not None:
+      for instruction_item in self.m_instruction_items:
+        instruction_item.setCanvas(None)
     self.m_instruction_items = None
     self.m_task_items = None
     self.m_ihead_item = None
@@ -56,24 +70,49 @@
       if self.m_frames.m_genome_info is not None:
         self.m_max_genome_size = max([len(genome) for genome in self.m_frames.m_genome_info])
         self.m_instruction_items = [QCanvasText(self.m_canvas) for i in range(self.m_max_genome_size)]
+      self.emit(PYSIGNAL("gestationTimeChangedSig"),(self.m_frames.m_gestation_time,))
       self.updateCircle()
-      self.emit(PYSIGNAL("gestationTimeChangedSig"),(self.m_frames.m_gestation_time,))
       self.showFrame(0)
 
-  def resizeEvent(self, resize_event):
-    new_size = resize_event.size()
-    self.m_canvas.resize(new_size.width(), new_size.height())
-    QCanvasView.resizeEvent(self, resize_event)
+  def viewportResizeEvent(self, resize_event):
+    QCanvasView.viewportResizeEvent(self, resize_event)
+    # XXX Fragility: If the top-level Avida-ED window is allowed to change height, this is going to cause a painful slow-down
+    # whenever the window height changes.  But having chosen a fixed window height, we're okay for now.
+    #
+    # @kgn
+    if self.m_visible_height != resize_event.size().height() or self.m_visible_width != resize_event.size().width():
+      self.m_canvas.resize(resize_event.size().width(), resize_event.size().height())
+      self.m_visible_width = resize_event.size().width()
+      self.m_visible_height = resize_event.size().height()
+      self.updateCircle()
+      self.showFrame(self.m_current_frame_number)
 
   def updateCircle(self):
+    self.m_circle_center_x = self.m_visible_width / 2
+    self.m_circle_center_y = self.m_visible_height / 2
+    self.m_max_circle_radius = (self.m_visible_height / 2) - self.m_organism_circle_margin
     if self.m_instruction_items is not None:
-      x = 0
+      text_height = 2 * 3.14159 * self.m_max_circle_radius / self.m_max_genome_size
+      font = QFont(self.font())
+      font.setPointSizeFloat(self.m_font_oversize_factor * text_height * self.m_font_points_per_pixel)
       for instruction_item in self.m_instruction_items:
-        x += 5
-        instruction_item.setX(x)
-        instruction_item.setY(100)
-        instruction_item.setText('@')
-        instruction_item.hide()
+        instruction_item.setFont(font)
+      self.m_circles = []
+      for frame_no in range(self.m_frames.m_gestation_time):
+        organism_current_size = max(self.m_frames.m_last_copy_info[frame_no] + 1, self.m_frames.m_size)
+        circumference = text_height * organism_current_size
+        radius = circumference / (2 * 3.14159)
+        dt = 2 * 3.14159 / (organism_current_size + 1)
+        angle_offset = 3.14159 / 2
+        circle_pts = []
+        for i in range(organism_current_size):
+          theta = i * dt + angle_offset
+          c = math.cos(theta)
+          s = -math.sin(theta)
+          x = radius * c + self.m_circle_center_x
+          y = radius * s + self.m_circle_center_y
+          circle_pts.append((x,y))
+        self.m_circles.append(circle_pts)
 
   def showFrame(self, frame_number = 0):
     old_frame_number = self.m_current_frame_number
@@ -96,27 +135,39 @@
       self.m_current_frame_number = frame_number
       if self.m_frames.m_genome_info is not None:
         self.m_current_genome = self.m_frames.m_genome_info[frame_number]
+        circle_pts = self.m_circles[self.m_current_frame_number]
         if old_genome is None:
+          displayed_genome_size = max(self.m_frames.m_last_copy_info[self.m_current_frame_number], self.m_frames.m_size)
           # Update all instruction_items.
-          for i in range(len(self.m_current_genome)):
-            self.m_instruction_items[i].setText(self.m_current_genome[i])
-            self.m_instruction_items[i].show()
+          for i in range(displayed_genome_size):
+            instruction_item = self.m_instruction_items[i]
+            instruction_item.setX(circle_pts[i][0])
+            instruction_item.setY(circle_pts[i][1])
+            instruction_item.setText(self.m_current_genome[i])
+            instruction_item.show()
         else:
           # Update changed instruction_items.
-          old_length = len(old_genome)
-          new_length = len(self.m_current_genome)
+          old_length = max(self.m_frames.m_last_copy_info[old_frame_number] + 1, self.m_frames.m_size)
+          new_length = max(self.m_frames.m_last_copy_info[self.m_current_frame_number] + 1, self.m_frames.m_size)
           compare_max = min(old_length, new_length)
           range_end = max(old_length, new_length)
           for i in range(compare_max):
+            instruction_item = self.m_instruction_items[i]
+            instruction_item.setX(circle_pts[i][0])
+            instruction_item.setY(circle_pts[i][1])
             if old_genome[i] == self.m_current_genome[i]:
               pass
             else:
-              self.m_instruction_items[i].setText(self.m_current_genome[i])
+              #self.m_instruction_items[i].setText(self.m_current_genome[i])
+              instruction_item.setText(self.m_current_genome[i])
 
           if old_length < new_length:
             for i in range(compare_max, range_end):
-              self.m_instruction_items[i].setText(self.m_current_genome[i])
-              self.m_instruction_items[i].show()
+              instruction_item = self.m_instruction_items[i]
+              instruction_item.setX(circle_pts[i][0])
+              instruction_item.setY(circle_pts[i][1])
+              instruction_item.setText(self.m_current_genome[i])
+              instruction_item.show()
           else:
             for i in range(compare_max, range_end):
               self.m_instruction_items[i].hide()

Modified: trunk/source/python/AvidaGui2/pyPetriCanvasView.py
===================================================================
--- trunk/source/python/AvidaGui2/pyPetriCanvasView.py	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyPetriCanvasView.py	2005-04-13 09:32:08 UTC (rev 138)
@@ -8,8 +8,9 @@
   def contentsMousePressEvent(self,e): # QMouseEvent e
     if e.button() != Qt.LeftButton: return
     point = self.inverseWorldMatrix().map(e.pos())
-    ilist = self.canvas().collisions(point) #QCanvasItemList ilist
-    for item in ilist:
-      if item.rtti()==271828:
-        self.emit(PYSIGNAL("orgClickedOnSig"), (item.m_population_cell.GetID(),))
+    if self.canvas():
+      ilist = self.canvas().collisions(point) #QCanvasItemList ilist
+      for item in ilist:
+        if item.rtti()==271828:
+          self.emit(PYSIGNAL("orgClickedOnSig"), (item.m_population_cell.GetID(),))
 

Modified: trunk/source/python/AvidaGui2/pyPetriDishCtrl.py
===================================================================
--- trunk/source/python/AvidaGui2/pyPetriDishCtrl.py	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyPetriDishCtrl.py	2005-04-13 09:32:08 UTC (rev 138)
@@ -10,8 +10,8 @@
 from AvidaCore import cConfig
 
 from math import exp
-from qt import Qt, QWidget, QSize, QVBoxLayout, QLayout, QColor, QWMatrix, PYSIGNAL
-from qtcanvas import QCanvas
+from qt import PYSIGNAL, QBrush, QColor, QLayout, QPen, QSize, Qt, QVBoxLayout, QWidget, QWMatrix
+from qtcanvas import QCanvas, QCanvasRectangle
 from pyPetriCanvasView import pyPetriCanvasView
 from pyPopulationCellItem import pyPopulationCellItem
 #from pyPetriDishView import pyPetriDishView
@@ -39,6 +39,7 @@
     self.m_changed_cell_items = []
     self.m_indexer = None
     self.m_color_lookup_functor = None
+    self.m_background_rect = None
 
     self.connect( self.m_session_mdl.m_session_mdtr, PYSIGNAL("setAvidaSig"), self.setAvidaSlot)
     self.connect( self.m_canvas_view, PYSIGNAL("orgClickedOnSig"), self.m_session_mdl.m_session_mdtr, PYSIGNAL("orgClickedOnSig"))
@@ -62,7 +63,14 @@
 
     if self.m_canvas: del self.m_canvas
     self.m_canvas = QCanvas(self.m_map_cell_w * world_w, self.m_map_cell_h * world_h)
+    self.m_canvas.setBackgroundColor(Qt.darkGray)
     self.m_canvas_view.setCanvas(self.m_canvas)
+    if self.m_background_rect: del self.m_background_rect
+    self.m_background_rect = QCanvasRectangle(0, 0, self.m_map_cell_w * world_w, self.m_map_cell_h * world_h, self.m_canvas)
+    self.m_background_rect.setBrush(QBrush(Qt.black))
+    self.m_background_rect.setPen(QPen(Qt.black))
+    self.m_background_rect.show()
+    self.m_background_rect.setZ(0.0)
 
     if self.m_cell_info: del self.m_cell_info
     self.m_cell_info = [pyPopulationCellItem(

Modified: trunk/source/python/AvidaGui2/pyPopulationCellItem.py
===================================================================
--- trunk/source/python/AvidaGui2/pyPopulationCellItem.py	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyPopulationCellItem.py	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,6 +5,7 @@
 class pyPopulationCellItem(QCanvasRectangle):
 
   s_empty_color = QColor(Qt.black)
+  s_null_pen = QPen(Qt.NoPen)
 
   def rtti(self):
     return 271828
@@ -14,6 +15,8 @@
     self.m_population_cell = population_cell
     self.m_index = 0
     self.show()
+    self.setZ(1.0 + population_cell.GetID())
+    self.setPen(self.s_null_pen)
 
   def checkNormalizedIndexUsingFunctor(self, functor, min, range):
     index = 1.0
@@ -30,5 +33,4 @@
   def updateColorUsingFunctor(self, functor):
     color = (self.m_population_cell.IsOccupied() and functor) and functor(self.m_index) or self.s_empty_color
     self.setBrush(QBrush(color))
-    self.setPen(QPen(color))
 

Modified: trunk/source/python/AvidaGui2/pyTemporaryReloads.py
===================================================================
--- trunk/source/python/AvidaGui2/pyTemporaryReloads.py	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/AvidaGui2/pyTemporaryReloads.py	2005-04-13 09:32:08 UTC (rev 138)
@@ -54,6 +54,8 @@
   "AvidaGui2.pyGradientScaleCtrl",
   "AvidaGui2.pyGraphView",
   "AvidaGui2.pyGraphCtrl",
+  "AvidaGui2.pyHardwareCPUTrace",
+  "AvidaGui2.pyHardwareTracer",
   "AvidaGui2.pyInstructionSet",
   "AvidaGui2.pyLiveControlsView",
   "AvidaGui2.pyLiveControlsCtrl",

Modified: trunk/source/python/CMakeLists.txt
===================================================================
--- trunk/source/python/CMakeLists.txt	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/CMakeLists.txt	2005-04-13 09:32:08 UTC (rev 138)
@@ -21,21 +21,21 @@
 
   IF(UNIX)
     IF(APPLE)
-      CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/AvidaEd-osx.py ${CMAKE_CURRENT_BINARY_DIR}/AvidaEd.py COPYONLY)
+      CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/AvidaEd-osx.py ${CMAKE_CURRENT_BINARY_DIR}/Avida-ED.py COPYONLY)
       CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/setup_osx.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
 
       # CMake custom targets often produce strange and idiosyncratic
       # output in Makefiles, and this has become a real pain. I would
       # like a different build system again.
       # @kgn
-      ADD_CUSTOM_TARGET(BUILD_AvidaEd ALL DEPENDS ${EXECUTABLE_OUTPUT_PATH}/AvidaEd.app)
+      ADD_CUSTOM_TARGET(BUILD_AvidaEd ALL DEPENDS ${EXECUTABLE_OUTPUT_PATH}/Avida-ED.app)
       #ADD_CUSTOM_TARGET(
       #  ${CMAKE_CURRENT_BINARY_DIR}/build
       #  ALL
       #  DEPENDS ${EXECUTABLE_OUTPUT_PATH}/AvidaEd.app/Contents/MacOS/AvidaEd
       #)
       ADD_CUSTOM_COMMAND(
-        OUTPUT ${EXECUTABLE_OUTPUT_PATH}/AvidaEd.app
+        OUTPUT ${EXECUTABLE_OUTPUT_PATH}/Avida-ED.app
         COMMAND ${PYTHON_EXE}
         DEPENDS ${LIBRARY_OUTPUT_PATH}/libPyAvidaRepairHacks.dylib
         ARGS setup.py py2app

Modified: trunk/source/python/setup_osx.py.in
===================================================================
--- trunk/source/python/setup_osx.py.in	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/python/setup_osx.py.in	2005-04-13 09:32:08 UTC (rev 138)
@@ -47,6 +47,7 @@
       includes = ['iqt', 'qt', 'qwt', 'readline', 'unittest', 'IPython', 'AvidaGui2', 'AvidaCore'],
       packages = ['IPython', 'AvidaGui2'],
       dist_dir = '${EXECUTABLE_OUTPUT_PATH}',
+      strip = False,
     )
   ),
   data_files=[
@@ -70,3 +71,9 @@
   + svn_metadata_files,
 )
 
+print """
+FIXME:
+Remember to reenable symbol stripping by commenting-out the option "strip = False"
+at line 51 of source/python/setup_osx.py.in.
+ at kgn
+"""

Modified: trunk/source/tools/const_schedule.cc
===================================================================
--- trunk/source/tools/const_schedule.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/tools/const_schedule.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,14 +5,11 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef CONST_SCHEDULE_HH
 #include "const_schedule.hh"
-#endif
 
-#ifndef MERIT_HH
 #include "merit.hh"
-#endif
 
+
 ////////////////////
 //  cConstSchedule
 ////////////////////

Modified: trunk/source/tools/integrated_schedule.cc
===================================================================
--- trunk/source/tools/integrated_schedule.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/tools/integrated_schedule.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,20 +5,13 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef INTEGRATED_SCHEDULE_HH
 #include "integrated_schedule.hh"
-#endif
 
-#ifndef FUNCTIONS_HH
 #include "functions.hh"
-#endif
-#ifndef INTEGRATED_SCHEDULE_NODE_HH
 #include "integrated_schedule_node.hh"
-#endif
-#ifndef MERIT_HH
 #include "merit.hh"
-#endif
 
+
 /////////////////////////
 //  cIntegratedSchedule
 /////////////////////////

Modified: trunk/source/tools/prob_schedule.cc
===================================================================
--- trunk/source/tools/prob_schedule.cc	2005-04-13 00:32:18 UTC (rev 137)
+++ trunk/source/tools/prob_schedule.cc	2005-04-13 09:32:08 UTC (rev 138)
@@ -5,17 +5,12 @@
 // before continuing.  SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE.     //
 //////////////////////////////////////////////////////////////////////////////
 
-#ifndef PROB_SCHEDULE_HH
 #include "prob_schedule.hh"
-#endif
 
-#ifndef MERIT_HH
 #include "merit.hh"
-#endif
-#ifndef TOOLS_HH
 #include "tools.hh"
-#endif
 
+
 ///////////////////
 //  cProbSchedule
 ///////////////////