[Avida-SVN] r3487 - in branches/tcmalloc-1.4: . Avida.xcodeproj source
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Wed Oct 14 20:19:23 PDT 2009
Author: brysonda
Date: 2009-10-14 23:19:23 -0400 (Wed, 14 Oct 2009)
New Revision: 3487
Removed:
branches/tcmalloc-1.4/source/LEVELS.txt
branches/tcmalloc-1.4/source/MAP.txt
branches/tcmalloc-1.4/source/bindings/
branches/tcmalloc-1.4/source/python/
branches/tcmalloc-1.4/source/testsuites/
Modified:
branches/tcmalloc-1.4/Avida.xcodeproj/project.pbxproj
branches/tcmalloc-1.4/CMakeLists.txt
Log:
Clean out quite a bit of cruft. At this point the core has drifted too far to easily fix up the current Avida-ED interface. We can always restore the code at a later date.
Modified: branches/tcmalloc-1.4/Avida.xcodeproj/project.pbxproj
===================================================================
--- branches/tcmalloc-1.4/Avida.xcodeproj/project.pbxproj 2009-10-15 03:08:46 UTC (rev 3486)
+++ branches/tcmalloc-1.4/Avida.xcodeproj/project.pbxproj 2009-10-15 03:19:23 UTC (rev 3487)
@@ -326,21 +326,21 @@
isa = PBXContainerItemProxy;
containerPortal = DCC30C4D0762532C008F7A48 /* Project object */;
proxyType = 1;
- remoteGlobalIDString = 7022469C107FC4F10079CD25 /* tcmalloc-1.4 */;
+ remoteGlobalIDString = 7022469C107FC4F10079CD25;
remoteInfo = "tcmalloc-1.4";
};
70C9D5C81086891B00472C46 /* PBXContainerItemProxy */ = {
isa = PBXContainerItemProxy;
containerPortal = DCC30C4D0762532C008F7A48 /* Project object */;
proxyType = 1;
- remoteGlobalIDString = 7022469C107FC4F10079CD25 /* tcmalloc-1.4 */;
+ remoteGlobalIDString = 7022469C107FC4F10079CD25;
remoteInfo = "tcmalloc-1.4";
};
70C9D5CB1086894A00472C46 /* PBXContainerItemProxy */ = {
isa = PBXContainerItemProxy;
containerPortal = DCC30C4D0762532C008F7A48 /* Project object */;
proxyType = 1;
- remoteGlobalIDString = 7022469C107FC4F10079CD25 /* tcmalloc-1.4 */;
+ remoteGlobalIDString = 7022469C107FC4F10079CD25;
remoteInfo = "tcmalloc-1.4";
};
/* End PBXContainerItemProxy section */
@@ -1000,7 +1000,6 @@
DCC315C2076253A5008F7A48 /* hist_map2.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = hist_map2.cc; sourceTree = "<group>"; };
DCC315C3076253A5008F7A48 /* Makefile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.make; path = Makefile; sourceTree = "<group>"; };
DCC315C4076253A5008F7A48 /* matlabify.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = matlabify.cc; sourceTree = "<group>"; };
- DCC315CD076253A5008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC315CE076253A5008F7A48 /* environment.rotate */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.rotate; sourceTree = "<group>"; };
DCC315D0076253A5008F7A48 /* task_event_gen.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.cc; sourceTree = "<group>"; };
DCC315D1076253A5008F7A48 /* task_event_gen.old.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.old.cc; sourceTree = "<group>"; };
@@ -1874,7 +1873,6 @@
DCC315C5076253A5008F7A48 /* task_events */ = {
isa = PBXGroup;
children = (
- DCC315CD076253A5008F7A48 /* CMakeLists.txt */,
DCC315CE076253A5008F7A48 /* environment.rotate */,
DCC315D0076253A5008F7A48 /* task_event_gen.cc */,
DCC315D1076253A5008F7A48 /* task_event_gen.old.cc */,
Modified: branches/tcmalloc-1.4/CMakeLists.txt
===================================================================
--- branches/tcmalloc-1.4/CMakeLists.txt 2009-10-15 03:08:46 UTC (rev 3486)
+++ branches/tcmalloc-1.4/CMakeLists.txt 2009-10-15 03:19:23 UTC (rev 3487)
@@ -603,65 +603,7 @@
INSTALL_TARGETS(/work unit-tests)
ENDIF(AVD_UNIT_TESTS)
-OPTION(AVD_TESTSUITES
- "Enable the testsuites executable. Running this target will test various low level functionality."
- OFF
-)
-IF(AVD_TESTSUITES)
- SET(TESTSUITES_DIR "${PROJECT_SOURCE_DIR}/../extras/source" CACHE PATH
- "The path to testsuite files."
- )
- IF(EXISTS ${TESTSUITES_DIR})
- SET(TESTSUITES_SOURCES
- ${TESTSUITES_DIR}/testsuites/nAGenotype.cpp
- ${TESTSUITES_DIR}/testsuites/nAnalyze.cpp
- ${TESTSUITES_DIR}/testsuites/nAnalyzeGenotype.cpp
- ${TESTSUITES_DIR}/testsuites/nAnalyzeTestFixture.cpp
- ${TESTSUITES_DIR}/testsuites/nChangeList.cpp
- ${TESTSUITES_DIR}/testsuites/nConsoleCatcher.cpp
- ${TESTSUITES_DIR}/testsuites/nDataEntry.cpp
- ${TESTSUITES_DIR}/testsuites/nDataFile.cpp
- ${TESTSUITES_DIR}/testsuites/nFile.cpp
- ${TESTSUITES_DIR}/testsuites/nFixedCoords.cpp
- ${TESTSUITES_DIR}/testsuites/nInitFile.cpp
- ${TESTSUITES_DIR}/testsuites/nMemTracker.cpp
- ${TESTSUITES_DIR}/testsuites/nRandom.cpp
- ${TESTSUITES_DIR}/testsuites/nString.cpp
- ${TESTSUITES_DIR}/testsuites/nStringList.cpp
- ${TESTSUITES_DIR}/testsuites/nTemplate.cpp
- ${TESTSUITES_DIR}/testsuites/nTestDriver.cpp
- ${TESTSUITES_DIR}/testsuites/nTestLib.cpp
- ${TESTSUITES_DIR}/testsuites/nTestSettings.cpp
- ${TESTSUITES_DIR}/testsuites/nTreeStats.cpp
- )
- SET(TESTSUITES_TOOL_SOURCES
- ${TESTSUITES_DIR}/tools/cAnalyzeTestFixture.cpp
- ${TESTSUITES_DIR}/tools/cConsoleCatcher.cpp
- ${TESTSUITES_DIR}/tools/cMemTracker.cpp
- ${TESTSUITES_DIR}/tools/cTestDriver.cpp
- ${TESTSUITES_DIR}/tools/cTestLib.cpp
- ${TESTSUITES_DIR}/tools/cTestSettings.cpp
- )
- SET(TESTSUITES_MAIN_SOURCES
- ${TESTSUITES_DIR}/targets/TestAvida/TestAvida.cpp
- )
- INCLUDE_DIRECTORIES(${TESTSUITES_DIR}/tools)
- ADD_EXECUTABLE(testsuites ${TESTSUITES_TOOL_SOURCES} ${TESTSUITES_SOURCES} ${TESTSUITES_MAIN_SOURCES})
- INSTALL_TARGETS(/work testsuites)
-
- SET(TESTSUITES_LIBS avidacore)
- IF(NOT MSVC)
- LIST(APPEND TESTSUITES_LIBS pthread)
- ENDIF(NOT MSVC)
- IF(AVD_ENABLE_TCMALLOC)
- LIST(APPEND TESTSUITES_LIBS tcmalloc)
- ENDIF(AVD_ENABLE_TCMALLOC)
- TARGET_LINK_LIBRARIES(testsuites ${TESTSUITES_LIBS})
-
- ENDIF(EXISTS ${TESTSUITES_DIR})
-ENDIF(AVD_TESTSUITES)
-
# Default Configuration Files
# - Installed into the work directory alongside selected targets
# ------------------------------------------------------------------------------
@@ -683,80 +625,3 @@
${CFG_FILES_DIR}/default-transsmt.org
)
INSTALL_FILES(/work FILES ${CFG_FILES})
-
-
-
-# Avida-ED Related
-# ------------------------------------------------------------------------------
-
-OPTION(AVD_GUI_PYQT
- "Enable the PyQt GUI interface. (EXPERIMENTAL)"
- OFF
-)
-IF(AVD_GUI_PYQT)
- SET(AVD_PY_BINDINGS ON CACHE BOOL "Avida Python Bindings MUST be built for the PyQt GUI." FORCE)
- FIND_PROGRAM(PYUIC pyuic DOC "Path to pyuic. Used to compile python files from .ui files.")
-ENDIF(AVD_GUI_PYQT)
-
-
-# Experimental Boost.Python interface to avida is disabled by default.
-OPTION(AVD_PY_BINDINGS
- "Enable Python interface to Avida. (EXPERIMENTAL)"
- OFF
-)
-IF(AVD_PY_BINDINGS)
- INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/avdFindPython.cmake)
- AVD_FIND_PYTHON(2.4 /Library/Frameworks)
- SET( BOOST_VERSION "1_32" CACHE STRING "Version of Boost Library to use")
- FIND_LIBRARY(
- BOOST_LIBRARY
- NAMES
- boost_python-${BOOST_VERSION}
- boost_python
- PATHS
- /usr/local/lib
- DOC "Path where the Boost Python Library can be found"
- )
- FIND_PATH(
- BOOST_INCLUDE_PATH
- boost/python/def.hpp
- /usr/local/include
- /usr/local/include/boost
- /usr/local/include/boost-${BOOST_VERSION}
- DOC "Path where the Boost Python header files can be found"
- )
- FIND_PROGRAM(
- GCCXML
- gccxml
- DOC "gccxml must be in the search path specified by your PATH environment variable in order for pyste to operate"
- )
- SET(UNIT_TESTS TRUE)
-
- ADD_SUBDIRECTORY(source/bindings)
- ADD_SUBDIRECTORY(source/python)
-ENDIF(AVD_PY_BINDINGS)
-
-
-# By default, compile all unit tests of primitive Avida classes. Tests
-# are run via 'make test' under unix.
-OPTION(AVD_CMAKE_UNIT_TESTS
- "Enable building primitive unit test suites."
- OFF
-)
-IF(AVD_CMAKE_UNIT_TESTS)
- SET(UNIT_TESTS TRUE)
- INCLUDE (${CMAKE_ROOT}/Modules/Dart.cmake)
- ADD_DEFINITIONS(-DENABLE_UNIT_TESTS)
- ADD_DEFINITIONS(-DUSE_tMemTrack=1)
- ENABLE_TESTING()
-ELSE(AVD_CMAKE_UNIT_TESTS)
- REMOVE_DEFINITIONS(-DENABLE_UNIT_TESTS)
- REMOVE_DEFINITIONS(-DUSE_tMemTrack=1)
-ENDIF(AVD_CMAKE_UNIT_TESTS)
-
-
-IF(BUILD_AvidaSupportLibs)
- IF(EXISTS source/third-party/AvidaSupportLibs/CMakeLists.txt)
- ADD_SUBDIRECTORY(source/third-party/AvidaSupportLibs)
- ENDIF(EXISTS source/third-party/AvidaSupportLibs/CMakeLists.txt)
-ENDIF(BUILD_AvidaSupportLibs)
Deleted: branches/tcmalloc-1.4/source/LEVELS.txt
===================================================================
--- branches/tcmalloc-1.4/source/LEVELS.txt 2009-10-15 03:08:46 UTC (rev 3486)
+++ branches/tcmalloc-1.4/source/LEVELS.txt 2009-10-15 03:19:23 UTC (rev 3487)
@@ -1,95 +0,0 @@
-Pure headers:
- defs.hh
- cpu_defs.hh
-
-A '*' indicates dependency is in the header, otherwise body is assumed.
-
---Component-- --Dependencies--
-LEVEL 0
-config [none]
-cpu_stats [none]
-cpu_stack [none]
-inst [none]
-label [none]
-mutations [none]
-pop_interface [none]
-reaction [none]
-reaction_result [none]
-resource [none]
-resource_count [none]
-tasks [none]
-
-LEVEL 1
-genome *inst
-inst_lib *inst
-stats config
-
-LEVEL 2
-environment *reaction *resource *tasks *inst_lib *mutations
- *reaction_result
-cpu_memory *genome
-genome_util genome
-hardware_base *inst inst_lib
-inst_util inst_lib genome
-
-LEVEL 3
-phenotype *environment config
-head *inst inst_lib hardware_base cpu_memory label
-
-LEVEL 4
-organism *mutations *pop_interface *cpu_stats *phenotype
- config inst_lib inst_util genome genome_util hardware_base
-
-LEVEL 5
-population_cell *mutations organism
-test_cpu config hardware_base inst_lib inst_util organism
- phenotype pop_interface resource_count tasks
-
-LEVEL 6
-fitness_matrix *stats *organism test_cpu config inst_lib
-genotype *genome config genome_util organism phenotype stats
- test_cpu
-hardware_cpu *cpu_memory *cpu_stack *label *head
- config inst_lib genome_util organism phenotype test_cpu
-
-LEVEL 7
-hardware_factory hardware_base hardware_cpu
-hardware_util inst_lib inst_util hardware_base hardware_cpu config
-lineage genotype stats
-species *genome stats genotype genome_util test_cpu
-test_util genome genotype inst_util organism phenotype stats
- hardware_base test_cpu
-
-LEVEL 8
-genebank species genotype config stats test_util
-landscape *genome *test_cpu cpu_memory stats inst_lib organism
- phenotype test_util
-
-LEVEL 9
-analyze *genome config species fitness_matrix inst_lib inst_util
- landscape phenotype genome_util test_cpu hardware_util
- test_util environment
-birth_chamber label genome organism genotype genebank
-lineage_control stats config lineage genome genome_util genebank
- genotype organism
-
-LEVEL 10
-population *resource_count *inst_lib *pop_interface *mutations config
- genebank genome_util genotype hardware_base
- hardware_factory hardware_util inst_util lineage
- lineage_control organism phenotype population_cell
- species stats tasks birth_chamber
-
-
-LEVEL 11
-analyze_util config genebank genome genome_util genotype inst_lib
- inst_util landscape organism phenotype population
- population_cell species stats test_cpu test_util
-callback_util avida config genotype organism population population_cell
- pop_interface hardware_base hardware_factory test_cpu
- birth_chamber
-
-LEVEL 12
-avida *stats environment genotype genebank analyze config
- species genome_util test_cpu callback_util population
- {events} {viewers}
Deleted: branches/tcmalloc-1.4/source/MAP.txt
===================================================================
--- branches/tcmalloc-1.4/source/MAP.txt 2009-10-15 03:08:46 UTC (rev 3486)
+++ branches/tcmalloc-1.4/source/MAP.txt 2009-10-15 03:19:23 UTC (rev 3487)
@@ -1,112 +0,0 @@
-These dependencies do not include built-in libraries, files from the
-tools directory in avida, or defs.hh. It is further assumed that a *.ii
-file has the corresponding *.hh as its first include, and likewise *.cc
-has both *.hh and *.ii. Files with nothing listed have no additional
-dependencies.
-
-There is a seperate tools MAP in the 'source/tools/' directory.
-
-DIRECTORY: source/main/
-
-analyze.hh : data_entry.hh genome.hh
-analyze.cc : config.hh species.hh fitness_matrix.hh
- inst_lib.hh landscape.hh phenotype.hh test_cpu.hh
-
-avida.hh :
-avida.cc : population.hh genotype.hh genebank.hh analyze.hh
- config.hh test_cpu.hh tasks.hh stats.hh
- species.hh
-
-config.hh :
-config.cc :
-
-fitness_matrix.hh : cpu.hh test_cpu.hh stats.hh
-fitness_matrix.cc : config.hh inst_lib.hh
-
-genebank.hh :
-genebank.cc : species.hh population.hh genotype.hh config.hh
- stats.hh test_cpu.hh
-
-genome.hh : inst.hh
-genome.cc :
-
-genome_util.hh :
-genome_util.cc : genome.hh
-
-genotype.hh : genome.hh
-genotype.cc : stats.hh config.hh test_cpu.hh
-
-inst.hh :
-inst.cc :
-
-inst_lib.hh : inst.hh
-inst_lib.cc : cpu.hh
-
-landscape.hh : test_cpu.hh
-landscape.cc : stats.hh inst_lib.hh
-
-lineage.hh :
-lineage.cc : stats.hh genotype.hh
-
-lineage_control.hh :
-lineage_control.cc : lineage.hh stats.hh config.hh genebank.hh
- landscape.hh genotype.hh cpu.hh
-
-phenotype.hh : tasks.hh
-phenotype.cc : config.hh cpu.hh
-
-population.hh : cpu.hh
-population.cc : avida.hh stats.hh genebank.hh inst_lib.hh
- species.hh genotype.hh landscape.hh tasks.hh
- config.hh environment.hh
- phenotype.hh lineage.hh lineage_control.hh
-
-species.hh : genome.hh
-species.cc : stats.hh genotype.hh test_cpu.hh
-
-stats.hh :
-stats.cc : config.hh genotype.hh lineage_control.hh
- lineage.hh test_cpu.hh
-
-task_buffer.hh :
-task_buffer.cc :
-
-tasks.hh : task_buffer.hh
-tasks.cc : stats.hh config.hh
-
-
-DIRECTORY: source/cpu/
-
-cpu.hh : cpu_defs.hh cpu_stats.hh cpu_memory.hh
- head.hh creature.hh hardware.hh
-cpu.cc : environment.hh phenotype.hh inst_lib.hh
- genotype.hh landscape.hh config.hh
- stats.hh genome.hh genome_util.hh
-
-cpu_memory.hh : genome.hh
-cpu_memory.cc :
-
-cpu_defs.hh :
-cpu_stats.hh :
-creature.hh :
-
-environment.hh : head.hh
-environment.cc : population.hh genebank.hh stats.hh genotype.hh
-
-hardware.hh : task_buffer.hh cpu_defs.hh label.hh
- head.hh cpu_memory.hh
-hardware.cc : config.hh phenotype.hh inst_lib.hh
-
-head.hh : inst.hh
-head.cc : environment.hh inst_lib.hh cpu.hh
-
-label.hh : cpu_defs.hh
-label.cc :
-
-test_cpu.hh : cpu.hh
-test_cpu.cc : hardware.hh genotype.hh config.hh
- phenotype.hh stats.hh inst_lib.hh
-
-
-DIRECTORY: source/viewers/
-
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