[Avida-cvs] [avida-svn] r884 - in development: . documentation documentation/content documentation/glossary documentation/notes
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Tue Aug 22 14:44:30 PDT 2006
Author: brysonda
Date: 2006-08-22 17:39:09 -0400 (Tue, 22 Aug 2006)
New Revision: 884
Added:
development/documentation/analyze_mode.html
development/documentation/analyze_samples.html
development/documentation/code_c++_intro.html
development/documentation/code_death_birth.html
development/documentation/code_environment.html
development/documentation/code_events.html
development/documentation/code_genesis.html
development/documentation/code_genome.html
development/documentation/code_init_file.html
development/documentation/code_instruction.html
development/documentation/code_life_cycle.html
development/documentation/code_task.html
development/documentation/cpu2.gif
development/documentation/cpu_tour.html
development/documentation/cvs.html
development/documentation/devel.html
development/documentation/environment.html
development/documentation/events.html
development/documentation/genesis.html
development/documentation/glossary/
development/documentation/images/
development/documentation/index.html
development/documentation/inst_set.html
development/documentation/level_map.html
development/documentation/notes/third-party-osx.xml
development/documentation/notes/third-party-win32.xml
development/documentation/print_data.html
development/documentation/screen.html
development/documentation/structure.html
Removed:
development/documentation/Architecture.graffle
development/documentation/content/images/
development/documentation/content/using/
development/documentation/forrest/
development/documentation/glossary/CMakeLists.txt
development/documentation/xdocs/
development/forrest.properties
development/status.xml
Modified:
development/CHANGES
development/README
Log:
Reorganize documentation directory. Removed forrest and simplified structure so that the HTML files are at the top level. Updated README and CHANGES.
Modified: development/CHANGES
===================================================================
--- development/CHANGES 2006-08-22 20:57:42 UTC (rev 883)
+++ development/CHANGES 2006-08-22 21:39:09 UTC (rev 884)
@@ -2,10 +2,15 @@
--------------------------------------------------------------------------------
-Avida 2.5 (change to 2.6 prior release)
+Avida 2.6
--------------------------------------------------------------------------------
Important changes relative to previous Avida 2.x releases:
+Binary Executable Names
+ The names of the executables generated by build systems have changed. The
+ 'primitive' binary is now called 'avida'. The NCurses viewer is called
+ 'avida-viewer'.
+
Configuration File
Previous versions of avida used a file called 'genesis' to configure primary
avida settings. This file has been replaced with 'avida.cfg'. The format of
@@ -29,5 +34,19 @@
NOTE: Threads are currently unsupported under Win32.
+Events and Actions
+ Events have been updated and enhanced under a new actions framework. In this
+ process the capitalization and sequence of many events have changed name. In
+ Avida 2.6 many of the previous names (99% of them) have been simply
+ deprecated but should still function. These deprecated namings will be
+ removed in future a future release. For details about the new namings, see
+ the included documentation.
-Revised 2006-05-18 DMB
+Performance
+ A number of significant performance enhancements have been implemented within
+ this release. All platforms should enjoy speedier runs and analysis. In
+ addition to algorithmic improvements, a new high performance malloc library
+ is used on POSIX (unix/linux/mac) platforms.
+
+
+Revised 2006-08-22 DMB
Modified: development/README
===================================================================
--- development/README 2006-08-22 20:57:42 UTC (rev 883)
+++ development/README 2006-08-22 21:39:09 UTC (rev 884)
@@ -1,4 +1,4 @@
-Avida 2.3.x
+Avida 2.6
----------------------------------------------------------------------
Digital Evolution Laboratory at Michigan State University
@@ -14,8 +14,8 @@
OR
In Mac OS X, an Xcode project has been provided for building the
-'primitive' console only version of Avida, as well as the NCurses
-viewer. Xcode 2.1 or greater is required.
+console only version of Avida, as well as the NCurses viewer.
+Xcode 2.1 or greater is required.
GETTING STARTED
@@ -31,7 +31,11 @@
OR
-In Mac OS X's Xcode, click the 'Build' button on the project window.
+In Mac OS X's Xcode, select the appropriate build style for the CPU
+type within your Mac (G4, G5, or Intel). Click the 'Build' button on
+the project window. The compiled binary and starting config files
+will be copied (by default) into:
+${PROJECT_DIR}/build/Deployment-{selected processor type}/Avida.work
CMAKE CONFIGURATION OPTIONS
@@ -101,4 +105,4 @@
-Revised 2005-16-10 DMB
+Revised 2006-08-22 DMB
Deleted: development/documentation/Architecture.graffle
===================================================================
--- development/documentation/Architecture.graffle 2006-08-22 20:57:42 UTC (rev 883)
+++ development/documentation/Architecture.graffle 2006-08-22 21:39:09 UTC (rev 884)
@@ -1,3828 +0,0 @@
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- <dict>
- <key>ID</key>
- <integer>297</integer>
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- <dict>
- <key>Class</key>
- <string>LineGraphic</string>
- <key>Head</key>
- <dict>
- <key>ID</key>
- <integer>328</integer>
- </dict>
- <key>ID</key>
- <integer>330</integer>
- <key>Labels</key>
- <array>
- <dict>
- <key>Filled</key>
- <string>NO</string>
- <key>Label</key>
- <dict>
- <key>Align</key>
- <integer>0</integer>
- <key>Text</key>
- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
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- <key>LabelVisible</key>
- <string>YES</string>
- <key>Offset</key>
- <real>5.3333330154418945</real>
- <key>Position</key>
- <real>0.20000000298023224</real>
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- <dict>
- <key>Filled</key>
- <string>NO</string>
- <key>FixedWidth</key>
- <real>24.560211181640625</real>
- <key>Label</key>
- <dict>
- <key>Align</key>
- <integer>0</integer>
- <key>Text</key>
- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
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- <key>LabelVisible</key>
- <string>YES</string>
- <key>Offset</key>
- <real>2.6666669845581055</real>
- <key>Position</key>
- <real>0.89999997615814209</real>
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- <key>Points</key>
- <array>
- <string>{345.539, 161.222}</string>
- <string>{83.8427, 178.278}</string>
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- <key>Style</key>
- <dict>
- <key>stroke</key>
- <dict>
- <key>Cap</key>
- <integer>0</integer>
- <key>HeadArrow</key>
- <string>0</string>
- <key>Join</key>
- <integer>0</integer>
- <key>LineType</key>
- <integer>1</integer>
- <key>TailArrow</key>
- <string>0</string>
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- <key>Tail</key>
- <dict>
- <key>ID</key>
- <integer>297</integer>
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- <dict>
- <key>Bounds</key>
- <string>{{12.18, 207.312}, {75.8427, 35}}</string>
- <key>Class</key>
- <string>MultiTextGraphic</string>
- <key>FitText</key>
- <string>Vertical</string>
- <key>Flow</key>
- <string>Resize</string>
- <key>ID</key>
- <integer>329</integer>
- <key>ListOrientation</key>
- <string>Vertical</string>
- <key>Style</key>
- <dict>
- <key>fill</key>
- <dict>
- <key>GradientAngle</key>
- <real>304</real>
- <key>GradientCenter</key>
- <string>{-0.294118, -0.264706}</string>
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- </dict>
- <key>TextList</key>
- <array>
- <dict>
- <key>Align</key>
- <integer>0</integer>
- <key>Text</key>
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- <dict>
- <key>Align</key>
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- <dict>
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- <dict>
- <key>Bounds</key>
- <string>{{8, 163.25}, {75.8427, 35}}</string>
- <key>Class</key>
- <string>MultiTextGraphic</string>
- <key>FitText</key>
- <string>Vertical</string>
- <key>Flow</key>
- <string>Resize</string>
- <key>ID</key>
- <integer>328</integer>
- <key>ListOrientation</key>
- <string>Vertical</string>
- <key>Style</key>
- <dict>
- <key>fill</key>
- <dict>
- <key>GradientAngle</key>
- <real>304</real>
- <key>GradientCenter</key>
- <string>{-0.294118, -0.264706}</string>
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- <key>TextList</key>
- <array>
- <dict>
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- <integer>0</integer>
- <key>Text</key>
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- <dict>
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- <key>TextPlacement</key>
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- <dict>
- <key>Class</key>
- <string>LineGraphic</string>
- <key>Head</key>
- <dict>
- <key>ID</key>
- <integer>323</integer>
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- <key>ID</key>
- <integer>327</integer>
- <key>Labels</key>
- <array>
- <dict>
- <key>Filled</key>
- <string>NO</string>
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- <real>16</real>
- <key>Label</key>
- <dict>
- <key>Align</key>
- <integer>0</integer>
- <key>Text</key>
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- <key>LabelVisible</key>
- <string>YES</string>
- <key>Offset</key>
- <real>5.3333330154418945</real>
- <key>Position</key>
- <real>0.20000000298023224</real>
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- <dict>
- <key>Filled</key>
- <string>NO</string>
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- <real>24.560211181640625</real>
- <key>Label</key>
- <dict>
- <key>Align</key>
- <integer>0</integer>
- <key>Text</key>
- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
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- <key>LabelVisible</key>
- <string>YES</string>
- <key>Offset</key>
- <real>2.6666669845581055</real>
- <key>Position</key>
- <real>0.89999997615814209</real>
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- <key>Points</key>
- <array>
- <string>{437.46, 390.5}</string>
- <string>{437.46, 417.625}</string>
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- <key>Style</key>
- <dict>
- <key>stroke</key>
- <dict>
- <key>Cap</key>
- <integer>0</integer>
- <key>HeadArrow</key>
- <string>0</string>
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- <key>TailArrow</key>
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- <key>Tail</key>
- <dict>
- <key>ID</key>
- <integer>322</integer>
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- <dict>
- <key>Class</key>
- <string>LineGraphic</string>
- <key>Head</key>
- <dict>
- <key>ID</key>
- <integer>322</integer>
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- <key>ID</key>
- <integer>326</integer>
- <key>Labels</key>
- <array>
- <dict>
- <key>Filled</key>
- <string>NO</string>
- <key>Label</key>
- <dict>
- <key>Align</key>
- <integer>0</integer>
- <key>Text</key>
- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
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- <key>LabelVisible</key>
- <string>YES</string>
- <key>Offset</key>
- <real>5.3333330154418945</real>
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- <real>0.20000000298023224</real>
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- <dict>
- <key>Filled</key>
- <string>NO</string>
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- <dict>
- <key>Align</key>
- <integer>0</integer>
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- <key>LabelVisible</key>
- <string>YES</string>
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- <real>2.6666669845581055</real>
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- </array>
- <key>Points</key>
- <array>
- <string>{421.085, 311.25}</string>
- <string>{432.82, 355.5}</string>
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- <key>Style</key>
- <dict>
- <key>stroke</key>
- <dict>
- <key>Cap</key>
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- <key>TailArrow</key>
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- <key>Tail</key>
- <dict>
- <key>ID</key>
- <integer>318</integer>
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- <dict>
- <key>Class</key>
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- <dict>
- <key>ID</key>
- <integer>324</integer>
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- <key>ID</key>
- <integer>325</integer>
- <key>Labels</key>
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- <string>NO</string>
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- <dict>
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- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
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- <key>LabelVisible</key>
- <string>YES</string>
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- <dict>
- <key>Filled</key>
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- <key>LabelVisible</key>
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- <key>Points</key>
- <array>
- <string>{373.689, 176.25}</string>
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- <dict>
- <key>stroke</key>
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- <dict>
- <key>ID</key>
- <integer>297</integer>
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- <dict>
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- <string>{{270.157, 276.25}, {75.8427, 35}}</string>
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- <string>MultiTextGraphic</string>
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- <string>Vertical</string>
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- <string>Resize</string>
- <key>ID</key>
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- <key>ListOrientation</key>
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- <dict>
- <key>fill</key>
- <dict>
- <key>GradientAngle</key>
- <real>304</real>
- <key>GradientCenter</key>
- <string>{-0.294118, -0.264706}</string>
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- <string>{{399.539, 417.625}, {75.8427, 35}}</string>
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- <key>ID</key>
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- <dict>
- <key>fill</key>
- <dict>
- <key>GradientAngle</key>
- <real>304</real>
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- <string>{-0.294118, -0.264706}</string>
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- <key>ID</key>
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- <dict>
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- <key>LabelVisible</key>
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- <dict>
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- <integer>297</integer>
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- <string>{{356.911, 276.25}, {119.067, 35}}</string>
- <key>Class</key>
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- <string>Vertical</string>
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- <string>Resize</string>
- <key>ID</key>
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- <key>fill</key>
- <dict>
- <key>GradientAngle</key>
- <real>304</real>
- <key>GradientCenter</key>
- <string>{-0.294118, -0.264706}</string>
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- <key>fill</key>
- <dict>
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- <integer>299</integer>
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- <string>Vertical</string>
- <key>Flow</key>
- <string>Resize</string>
- <key>ID</key>
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- <key>ListOrientation</key>
- <string>Vertical</string>
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- <key>fill</key>
- <dict>
- <key>GradientAngle</key>
- <real>304</real>
- <key>GradientCenter</key>
- <string>{-0.294118, -0.264706}</string>
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- <key>ListOrientation</key>
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- <key>fill</key>
- <dict>
- <key>GradientAngle</key>
- <real>304</real>
- <key>GradientCenter</key>
- <string>{-0.294118, -0.264706}</string>
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- <key>ID</key>
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- <key>Label</key>
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- <key>LabelVisible</key>
- <string>YES</string>
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- <key>Points</key>
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- <string>{524.809, 284.375}</string>
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- <dict>
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- <dict>
- <key>ID</key>
- <integer>298</integer>
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- <key>ID</key>
- <integer>302</integer>
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- <key>ID</key>
- <integer>306</integer>
- <key>Labels</key>
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- <dict>
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- <string>NO</string>
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- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
-{\fonttbl\f0\fswiss\fcharset77 Helvetica-Bold;}
-{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\qc
-
-\f0\b\fs20 \cf0 cDataFileManager}</string>
- </dict>
- </dict>
- <dict>
- <key>Bounds</key>
- <string>{{343, 18.25}, {58, 23}}</string>
- <key>Class</key>
- <string>ShapedGraphic</string>
- <key>FontInfo</key>
- <dict>
- <key>Font</key>
- <string>Helvetica-Bold</string>
- <key>Size</key>
- <real>11</real>
- </dict>
- <key>ID</key>
- <integer>279</integer>
- <key>Magnets</key>
- <array>
- <string>{0, 1}</string>
- <string>{0, -1}</string>
- <string>{1, 0}</string>
- <string>{-1, 0}</string>
- </array>
- <key>Shape</key>
- <string>Rectangle</string>
- <key>Text</key>
- <dict>
- <key>Text</key>
- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
-{\fonttbl\f0\fswiss\fcharset77 Helvetica-Bold;}
-{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\qc
-
-\f0\b\fs20 \cf0 cWorld}</string>
- </dict>
- </dict>
- <dict>
- <key>Bounds</key>
- <string>{{22, 69}, {85, 23}}</string>
- <key>Class</key>
- <string>ShapedGraphic</string>
- <key>FontInfo</key>
- <dict>
- <key>Font</key>
- <string>Helvetica-Bold</string>
- <key>Size</key>
- <real>11</real>
- </dict>
- <key>ID</key>
- <integer>278</integer>
- <key>Magnets</key>
- <array>
- <string>{0, 1}</string>
- <string>{0, -1}</string>
- <string>{1, 0}</string>
- <string>{-1, 0}</string>
- </array>
- <key>Shape</key>
- <string>Rectangle</string>
- <key>Text</key>
- <dict>
- <key>Text</key>
- <string>{\rtf1\mac\ansicpg10000\cocoartf824\cocoasubrtf230
-{\fonttbl\f0\fswiss\fcharset77 Helvetica-Bold;}
-{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\qc
-
-\f0\b\fs20 \cf0 cEnvironment}</string>
- </dict>
- </dict>
- </array>
- <key>GridInfo</key>
- <dict>
- <key>ShowsGrid</key>
- <string>YES</string>
- </dict>
- <key>GuidesLocked</key>
- <string>NO</string>
- <key>GuidesVisible</key>
- <string>YES</string>
- <key>HPages</key>
- <integer>1</integer>
- <key>ImageCounter</key>
- <integer>1</integer>
- <key>IsPalette</key>
- <string>NO</string>
- <key>Layers</key>
- <array>
- <dict>
- <key>Lock</key>
- <string>NO</string>
- <key>Name</key>
- <string>Layer 1</string>
- <key>Print</key>
- <string>YES</string>
- <key>View</key>
- <string>YES</string>
- </dict>
- </array>
- <key>LayoutInfo</key>
- <dict>
- <key>ChildOrdering</key>
- <integer>2</integer>
- </dict>
- <key>LinksVisible</key>
- <string>NO</string>
- <key>MagnetsVisible</key>
- <string>NO</string>
- <key>ModificationDate</key>
- <string>2005-11-11 10:12:08 -0500</string>
- <key>Modifier</key>
- <string>David</string>
- <key>Orientation</key>
- <integer>1</integer>
- <key>PageBreaks</key>
- <string>YES</string>
- <key>PageSetup</key>
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Copied: development/documentation/analyze_mode.html (from rev 883, development/documentation/content/using/analyze_mode.html)
Copied: development/documentation/analyze_samples.html (from rev 883, development/documentation/content/using/analyze_samples.html)
Copied: development/documentation/code_c++_intro.html (from rev 883, development/documentation/content/using/code_c++_intro.html)
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Copied: development/documentation/code_environment.html (from rev 883, development/documentation/content/using/code_environment.html)
Copied: development/documentation/code_events.html (from rev 883, development/documentation/content/using/code_events.html)
Copied: development/documentation/code_genesis.html (from rev 883, development/documentation/content/using/code_genesis.html)
Copied: development/documentation/code_genome.html (from rev 883, development/documentation/content/using/code_genome.html)
Copied: development/documentation/code_init_file.html (from rev 883, development/documentation/content/using/code_init_file.html)
Copied: development/documentation/code_instruction.html (from rev 883, development/documentation/content/using/code_instruction.html)
Copied: development/documentation/code_life_cycle.html (from rev 883, development/documentation/content/using/code_life_cycle.html)
Copied: development/documentation/code_task.html (from rev 883, development/documentation/content/using/code_task.html)
Copied: development/documentation/cpu2.gif (from rev 883, development/documentation/content/using/cpu2.gif)
Copied: development/documentation/cpu_tour.html (from rev 883, development/documentation/content/using/cpu_tour.html)
Copied: development/documentation/cvs.html (from rev 883, development/documentation/content/using/cvs.html)
Copied: development/documentation/devel.html (from rev 883, development/documentation/content/using/devel.html)
Copied: development/documentation/environment.html (from rev 883, development/documentation/content/using/environment.html)
Copied: development/documentation/events.html (from rev 883, development/documentation/content/using/events.html)
Copied: development/documentation/genesis.html (from rev 883, development/documentation/content/using/genesis.html)
Copied: development/documentation/glossary (from rev 883, development/documentation/content/using/glossary)
Deleted: development/documentation/glossary/CMakeLists.txt
===================================================================
--- development/documentation/content/using/glossary/CMakeLists.txt 2006-08-22 20:57:42 UTC (rev 883)
+++ development/documentation/glossary/CMakeLists.txt 2006-08-22 21:39:09 UTC (rev 884)
@@ -1,2 +0,0 @@
-INSTALL_FILES(/doc_html/glossary .*[.]html)
-INSTALL_FILES(/doc_html/glossary .*[.]help)
Copied: development/documentation/images (from rev 883, development/documentation/content/images)
Copied: development/documentation/index.html (from rev 883, development/documentation/content/using/index.html)
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Copied: development/documentation/structure.html (from rev 883, development/documentation/content/using/structure.html)
Deleted: development/forrest.properties
===================================================================
--- development/forrest.properties 2006-08-22 20:57:42 UTC (rev 883)
+++ development/forrest.properties 2006-08-22 21:39:09 UTC (rev 884)
@@ -1,106 +0,0 @@
-# Copyright 2002-2004 The Apache Software Foundation
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-##############
-# Properties used by forrest.build.xml for building the website
-# These are the defaults, un-comment them if you need to change them.
-##############
-
-# Prints out a summary of Forrest settings for this project
-#forrest.echo=true
-
-# Project name (used to name .war file)
-#project.name=my-project
-
-# Specifies name of Forrest skin to use
-#project.skin=tigris
-#project.skin=pelt
-
-# comma separated list, file:// is supported
-#forrest.skins.descriptors=http://forrest.apache.org/skins/skins.xml,file:///c:/myskins/skins.xml
-
-##############
-# behavioural properties
-#project.menu-scheme=tab_attributes
-#project.menu-scheme=directories
-
-##############
-# layout properties
-
-# Properties that can be set to override the default locations
-#
-# Parent properties must be set. This usually means uncommenting
-# project.content-dir if any other property using it is uncommented
-
-#project.status=status.xml
-project.content-dir=documentation/forrest
-project.raw-content-dir=documentation/content
-#project.conf-dir=${project.content-dir}/conf
-#project.sitemap-dir=${project.content-dir}
-project.xdocs-dir=documentation/xdocs
-#project.resources-dir=${project.content-dir}/resources
-#project.stylesheets-dir=${project.resources-dir}/stylesheets
-#project.images-dir=${project.resources-dir}/images
-#project.schema-dir=${project.resources-dir}/schema
-#project.skins-dir=${project.content-dir}/skins
-#project.skinconf=${project.content-dir}/skinconf.xml
-#project.lib-dir=${project.content-dir}/lib
-#project.classes-dir=${project.content-dir}/classes
-#project.translations-dir=${project.content-dir}/translations
-project.build-dir=${project.home}/build
-project.site-dir=${project.build-dir}/documentation
-
-##############
-# validation properties
-
-# This set of properties determine if validation is performed
-# Values are inherited unless overridden.
-# e.g. if forrest.validate=false then all others are false unless set to true.
-#forrest.validate=true
-#forrest.validate.xdocs=${forrest.validate}
-#forrest.validate.skinconf=${forrest.validate}
-#forrest.validate.sitemap=${forrest.validate}
-#forrest.validate.stylesheets=${forrest.validate}
-#forrest.validate.skins=${forrest.validate}
-#forrest.validate.skins.stylesheets=${forrest.validate.skins}
-
-# *.failonerror=(true|false) - stop when an XML file is invalid
-#forrest.validate.failonerror=true
-
-# *.excludes=(pattern) - comma-separated list of path patterns to not validate
-# e.g.
-#forrest.validate.xdocs.excludes=samples/subdir/**, samples/faq.xml
-#forrest.validate.xdocs.excludes=
-
-
-##############
-# General Forrest properties
-
-# The URL to start crawling from
-#project.start-uri=linkmap.html
-# Set logging level for messages printed to the console
-# (DEBUG, INFO, WARN, ERROR, FATAL_ERROR)
-#project.debuglevel=ERROR
-# Max memory to allocate to Java
-#forrest.maxmemory=64m
-# Any other arguments to pass to the JVM. For example, to run on an X-less
-# server, set to -Djava.awt.headless=true
-#forrest.jvmargs=
-# The bugtracking URL - the issue number will be appended
-#project.bugtracking-url=http://issues.apache.org/bugzilla/show_bug.cgi?id=
-#project.bugtracking-url=http://issues.apache.org/jira/browse/
-# The issues list as rss
-#project.issues-rss-url=
-#I18n Property only works for the "forrest run" target.
-#project.i18n=true
Deleted: development/status.xml
===================================================================
--- development/status.xml 2006-08-22 20:57:42 UTC (rev 883)
+++ development/status.xml 2006-08-22 21:39:09 UTC (rev 884)
@@ -1,944 +0,0 @@
-<?xml version="1.0"?>
-<!--
- Copyright 2002-2004 The Apache Software Foundation
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<status>
-
- <developers>
- <person name="Brian Baer" email="baerb at msu.edu" id="BDB" />
- <person name="David Bryson" email="brysonda at msu.edu" id="DMB" />
- <person name="Jeff Clune" email="jclune at msu.edu" id="JMC" />
- <person name="Dusan Misevic" email="" id="DM" />
- <person name="Kaben Nanlohy" email="" id="KGN" />
- <person name="Charles Ofria" email="ofria at cse.msu.edu" id="CAO" />
- </developers>
-
- <changes>
- <!-- Some action types have associated images. By default, images are
- defined for 'add', 'fix', 'remove', 'update' and 'hack'. If you add
- src/documentation/resources/images/<foo>.jpg images, these will
- automatically be used for entries of type <foo>. -->
-
- <!-- Add new releases here -->
-
- <release version="2.3.0 (r76) date="28 March 2005">
- <action dev="CAO" type="fix" context="feature">
- Fixed the output of <code>print_genotypes</code> event. It was
- double-printing all historic genotypes with different formats (ick.)
- </action>
- <action dev="KGN" type="remove" context="AvidaED">
- Removed python files that are supposed to be autogenerated.
- </action>
- <action dev="KGN" type="remove" context="AvidaED">
- Removed obsolete python and pyuic files.
- </action>
- <action dev="KGN" type="update" context="AvidaED">
- Moved AvidaED python files into source/python
- </action>
- <action dev="KGN" type="add" context="AvidaED">
- Added scripts to build OS X application. AvidaED.app on OS X can be
- launched from command line for an interactive interpreter, or by
- double-clicking on its icon in the finder.
- </action>
- <action dev="KGN" type="fix" context="AvidaED">
- Fixed bad build rule prevent build of AvidaED/Mac.
- </action>
- <action dev="KGN" type="update" context="AvidaED">
- AvidaED no longer starts an Avida Session at launch time. Instead
- an Avida object can be created after launch time using the sequence
- of commands (without semi-colons):
- <code>avida = pyAvida(); avida.construct(genesis);</code>
- </action>
- <action dev="KGN" type="add" context="AvidaED">
- Added an AvidaED Xcode project for editing files.
- </action>
- <action dev="KGN" type="update" context="AvidaED">
- Added pyuic build target to AvidaED Xcode project. Organized python
- files into sensible groups.
- </action>
- <action dev="BDB" type="fix" context="AvidaED">
- Fixed layout problems with <code>OnePop_PetriDishView</code>.
- </action>
- <action dev="BDB" type="add" context="AvidaED">
- Added code to call routine to read freezer items.
- </action>
- <action dev="BDB" type="update" context="AvidaED">
- Set <code>pyPetriConfigureView</code> to capture start signal.
- </action>
- <action dev="BDB" type="add" context="AvidaED">
- Added code to write files into the freezer directory.
- </action>
- <action dev="BDB" type="add" context="AvidaED">
- Added code to read default Genesis file, change values that have been
- modified by user in the PetriConfiguration screen, and write a new
- Genesis file into the working directory. Also copies the event,
- environment and organism file to working directory.
- </action>
- <action dev="BDB" type="add" context="AvidaED">
- Added new reload commands for recently added classes.
- </action>
- <action dev="BDB" type="add" context="AvidaED">
- Added signal support for the start button. Activated the start button.
- </action>
- <action dev="BDB" type="add" context="AvidaED">
- Added signals to support freezing a populated petri dish. Added
- <code>extractPopulationSlot<code> to send all organisms in population
- to be frozen.
- </action>
- <action dev="CAO" type="add" context="core">
- Added in <code>sense</code> instruction into <code>hardware_cpu</code>
- </action>
- <action dev="KGN" type="fix" context="AvidaED">
- Population graphing works again.
- </action>
- <action dev="JMC" type="add" context="AvidaED">
- Added statistics code to support population information and actual
- graphing support.
- </action>
- <action dev="BDB" type="update" context="AvidaED">
- Changed the look of various AvidaED windows.
- </action>
- <action dev="BDB" type="add" context="AvidaED">
- Added a utility that will check all <code>.ui</code> files and find
- ones that are newer than their equivalent <code>*.py</code> files.
- The program will then offer the user the chance to create the
- <code>.py</code> file. User may need to change the command line
- to reflect the location of the <code>pyuic</code> program.
- </action>
- </release>
- <release version="2.2.2 (r27) date="24 February 2005">
- <action dev="KGN" type="add" context="documentation">
- Added build instructions for third-party development software
- on OS X.
- </action>
- <action dev="KGN" type="update" context="admin">
- Clean up pyuic auto-generated files incorrectly being managed
- under source control. Updated Xcode project accordingly.
- </action>
- <action dev="CAO" type="update" context="core">
- Incorporated speed ups posted by Dave MacLachlan on SourceForge
- and the DigitalEvolution mailing list.
- </action>
- <action dev="DMB" type="update" context="admin">
- Fixed Xcode project so that optimization settings are appropriately
- set according to build type. Added in additional optimizations
- suggested by Dave MacLachlan.
- </action>
- <action dev="KGN" type="update" context="python code">
- Fixed various pyste and build system components to handle various
- recent updates.
- </action>
- </release>
- <release version="2.2.1 (r15) date="16 February 2005">
- <action dev="BDB" type="fix" context="platform support">
- Allow code to compile on Linux with GCC version 3.4.
- </action>
- <action dev="DMB" type="fix" context="bug">
- Modified bonus instructions to save and restore the previous
- execution state of the organism. Without this step, organisms
- could be prematurely marked as 'not running'. When combined
- with death, the objects could therefore be deleted twice.
- This would lead to stochastic memory corruption and crashes.
- </action>
- </release>
- <release version="2.2 (r12)" date="14 February 2005">
- <action dev="DMB" type="add" context="admin">
- Initial Subversion Import
- </action>
- <action dev="DMB" type="add" context="admin">
- Added support for Forrest Documentation
- </action>
- <action dev="CAO" type="fix" context="bug">
- Repair offspring merit calculation.
- </action>
- <action dev="DM" type="fix" context="feature">
- Minor modification to RECOMBINE comman in the analyze mode.
- A for loop was doing one less iteration that it shoud have
- resulting in creation of 2 less recombinant genomes.
- </action>
- <action dev="DM" type="add" context="feature">
- Added another event, set_reaction_value_mult, that allows tou to multiply
- the reaction value, not just set it. Useful for changing environments setup.
- See documentation for more.
- </action>
- </release>
- <release version="2.1" date="8 January 2005">
- <action dev="KGN" type="update" context="build">
- Windows release of latest updates for Discover Magazine article.
- </action>
- </release>
- <release version="2.0 beta 7" date="October 2003">
- <action dev="CAO" type="add" context="feature">
- New CPU model, GUI components, and various research specific improvements.
- </action>
- <action dev="CAO" type="add" context="feature">
- Implemented proportional merit with sex...
- </action>
- <action dev="CAO" type="add" context="feature">
- Setup environment file with an extra command:
- <source>SET_ACTIVE [type] [name] [active=true]</source>
- <p>
- Type can currently only be "reaction" (but soon I'll also get resources
- working, and eventually mutations). Name is the name of the resource,
- and fitnally a true or false if you want that reaction turned on.
- </p>
- <p>
- THEN I also added a command to the analyze mode called "ENVIRONMENT"
- which will allow you to add extra commands to define the environment
- file on the fly. For example, the analyze command:
- </p>
- <source>ENVIRONMENT SET_ACTIVE reaction NOT false</source>
- <p>
- Will turn off rewards for not. They can be turned back on again
- trivially with:
- </p>
- <source>ENVIRONMENT SET_ACTIVE reaction NOT true</source>
- </action>
- <action dev="CAO" type="fix" context="bug">
- Made changes to arrays in analyze mode so that they use tArray and
- tMatrix to make them easier to use with variable sizes.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added new functions "AnalyzeComplexity" and "AnalyzePopComplexity"
- to analyze source code.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added in three new events to modify the topology of a population:
- <br/>sever_column : sever a full column of cells
- <br/>connect_cells : connect two cells together
- <br/>disconnect_cells : disconnect two cells from each other.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added some info about the new AVERAGE_MODULARITY analyze command to
- the documentation files.
- </action>
- <action dev="CAO" type="add" context="feature">
- After much tweaking, implemented a new analyze function, <code>AVERAGE_MODULARITY</code>.
- <br/>Usage:
- <source>AVERAGE_MODULARITY output_file task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8</source>
- </action>
- <action dev="CAO" type="add" context="feature">
- Fixed the formula used to calculate Standard Error in various
- statistics parameters.
- </action>
- </release>
- <release version="2.0 beta 6" date="September 2003">
- <action dev="CAO" type="fix" context="bug">
- Widened number display fields in CPU viewer so that data can be read
- correctly.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added buttons to select number format (binary, decimal, or
- hexadecimal) in Register, Inputs, and Stacks views of CPU viewer in
- GUI.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Minor bugfixes in 4-stack cpu parasite code.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added option to count phenotypes based on tasks completed.
- </action>
- </release>
- <release version="2.0 beta 5" date="August 2003">
- <action dev="CAO" type="fix" context="bug">
- Workaround for bug in Qt/Windows: setInsideSpacing can't be safely
- called, so removed those calls.
- </action>
- <action dev="CAO" type="add" context="feature">
- Addition of CPU stats to instruction viewer in GUI.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Organism inputs are no longer per-cell, but per-organism; resolved
- related problem of request of now nonexistent inputs.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Restored missing initializations of subclass of cPopulationInterface
- class in qt-viewer.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Added documentation for some existing events. Changed some
- formatting of events.html documentation so file looks better with
- Safari web browser.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Added missing files to visual studio project.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Restored compatibility with older versions of gcc.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added parasite tracking for 4-stack cpus, added events
- "print_dom_parasite" and "detail_parasite_pop", added default
- organsisms and settings for the 4-stack cpu.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added Bounded Grid/Torus (world topology) switch to population.
- Leaving torus as the default.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Fixed some problems in mutation mapping in analyze mode.
- </action>
- </release>
- <release version="2.0 beta 4" date="July 2003">
- <action dev="CAO" type="fix" context="bug">
- Text viewer Zoom Screen Mini-Map fixed; Modified Map screen now in
- color; Thread Map screen now shows number of threads used by each
- organism.
- </action>
- <action dev="CAO" type="add" context="feature">
- Completion of 4 Stack Hardware. Inject command and parasite
- abilities now implemented. Text Viewer environment view mode in
- progress.
- </action>
- <action dev="CAO" type="update" context="internal">
- Added integer version WriteBlockElement to file output routines.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Correction of minor logical error in reaction handling.
- </action>
- </release>
- <release version="2.0 beta 3" date="June 2003">
- <action dev="CAO" type="add" context="feature">
- Avida now runs and builds on Windows. Many minor changes were made for this,
- .pro files were added to be used with qmake, the way the configure script searches
- for the ncurses library was modified, pdcurses was incorporated instead of ncurses,
- trio was added to fix some string problems, and some very minor code changes were
- implemented to allow for some differences in the visual studio compiler.
- </action>
- <action dev="CAO" type="add" context="feature">
- new 4 stack hardware is implemented but not yet fully functional. It's compatible
- with primitive and ncurses modes, however will cause qt-viewer to crash if used.
- No functionality associated with the original hardware has been changed.
- </action>
- <action dev="CAO" type="fix" context="bug">
- set up constant time slicer to skip over empty cells, this had been throwing an assert
- error in debug mode.
- </action>
- <action dev="CAO" type="fix" context="bug">
- removed Visual Studio.net support files as they are out of date and no longer work properly.
- </action>
- </release>
- <release version="2.0 beta 2" date="May 2003">
- <action dev="CAO" type="add" context="feature">
- introduced new 4 Stack CPU model. Removed 3 registers in CPU and replaced with
- 4 stacks. Added 4th NOP which allows use of all 4 stacks. Also changed complement system
- for nops. Pairs are now as follows: A,C; B,D; C,A; D,B;
- </action>
- <action dev="CAO" type="fix" context="bug">
- newer C++ compilers want scoping on templates defined inside class definition, event
- if they are only used inside the class.
- </action>
- <action dev="CAO" type="fix" context="bug">
- fixed problem with incorrect copying of instruction libraries when one instruction set was
- initialized to another one.
- </action>
- <action dev="CAO" type="add" context="feature">
- set up Avida to pring out a genesis file if none exists.
- </action>
- <action dev="CAO" type="update" context="internal">
- working on setting up Avida to generate an instruction set file in none exists. Attached
- 60 character or less descriptions to each of the default instructions, and attached a flag to all
- instructions declaring they are default.
- </action>
- <action dev="CAO" type="update" context="internal">
- added default event files in C++ that are generated from perl so Avida can be compiled in Windows
- without running perl script by hand as long as no new events are created or modified.
- </action>
- <action dev="CAO" type="fix" context="bug">
- updated .pro files so don't have to change any properties in Visual Studio to compile
- </action>
- <action dev="CAO" type="fix" context="bug">
- The hardware factory has always been creating CPU's of type cHardwareCPU even if everything else
- was assuming cHardware4Stack. This all works properly now.
- </action>
- <action dev="CAO" type="update" context="internal">
- added pdcurses.h and curses.lib to Avida so one doesn't have to actually check out the whole
- pdcurses suite to run on Windows.
- </action>
- <action dev="CAO" type="update" context="internal">
- added third party suite "Public Domain Curses" for Win32 compatability.
- </action>
- <action dev="CAO" type="add" context="feature">
- added event print_genotype_map that prints a Matlab file of the genotype IDs to a default file
- "genotype_map.m"
- </action>
- <action dev="CAO" type="fix" context="bug">
- added empty directory aclocal to CVS so don't have to create it by hand every time build Avida
- from scratch
- </action>
- <action dev="CAO" type="update" context="internal">
- update .pri files for Windows builds
- </action>
- <action dev="CAO" type="add" context="feature">
- added Visual Studio.net support files for ncurses viewer, primitive mode, and qt-viewer.
- </action>
- <action dev="CAO" type="update" context="internal">
- cHardware4Stack now hooked into Avida and working properly
- </action>
- <action dev="CAO" type="update" context="internal">
- added new hardware type cHardware4Stack. Not hooked into rest of Avida yet...
- </action>
- <action dev="CAO" type="update" context="internal">
- re-engineered cFile class to work based off of arrays instead of linked lists. Each line is
- now stored as part of a structure which has other info associated with it, such as line numbers
- for better error reporting. Not being used yet, but available...
- </action>
- <action dev="CAO" type="update" context="internal">
- added HARDWARE_TYPE to genesis file and setup config to load it into Avida, it's not being used yet.
- </action>
- <action dev="CAO" type="update" context="internal">
- modified test_cup.cc to improve the default inputs in the test CPUs so they are more similar
- to those in the environment, and ideally give more accurate answers.
- Setup the default instruction set to be hooked in with a proper instruction library so that
- they can be used outside of a population (i.e. in analyze mode)
- </action>
- <action dev="CAO" type="fix" context="bug">
- fixed bug in testCPU
- </action>
- <action dev="CAO" type="update" context="internal">
- changed cInstLib to cInstSet and cInstSuperLib to cInstLib. Renamed inst_lib.{cc,hh} to
- inst_set.{cc,hh} and inst_superlib.hh to inst_lib.hh. Updated other files accordingly to
- reflect this change
- </action>
- <action dev="CAO" type="update" context="internal">
- included instruction which injects a parasite into it's own thread. Also changed count.dat
- so that info regarding parasites is appended to the end of the file. Removed previous parasite
- info which is now obsolete.
- </action>
- </release>
- <release version="2.0 beta 1" date="April 2003">
- <action dev="CAO" type="fix" context="bug">
- edited Makefile.am to reflect the fact that built event source file depends are build-tree relative
- but cpu source file depends are source-tree relative
- </action>
- <action dev="CAO" type="update" context="internal">
- removed unused sourcecode from beneath qt subdirectory
- </action>
- <action dev="CAO" type="update" context="internal">
- introduced cInstSuperLib to contain a complete library of available instructions corresponding to
- a given hardware class. cInstLib now indexes into arrays provided by cInstSuperLib
- </action>
- <action dev="CAO" type="fix" context="bug">
- mkdir() is not defined in win32 so added win32_mkdir_hack.hh to define it as a macro so can
- use in windows version
- </action>
- <action dev="CAO" type="fix" context="bug">
- modified namespaces, adding 'using namespace std' appropriately throughout Avida to allow
- compilation on Windows
- </action>
- <action dev="CAO" type="update" context="internal">
- set up qt builds to be performed using qmake on seperately maintained .pro files
- </action>
- <action dev="CAO" type="fix" context="bug">
- fixed error in new tasks, now cast int to double before taking log
- </action>
- <action dev="CAO" type="update" context="internal">
- added code to allow spatial resources
- </action>
- <action dev="CAO" type="update" context="internal">
- allow long lines in an input file to be split across multiple physical lines by use of
- a \ character at the end of the line as a continuation marker
- </action>
- <action dev="CAO" type="add" context="feature">
- added two routines to aid the printing of spatial resource data:
- writeblock - allows for the output of individual grid points
- writeraw - allows any line to be written anywhere in an output file
- </action>
- <action dev="CAO" type="add" context="feature">
- added event kill_rectangle which allows user to kill all organisms in a rectangle
- described by points (X1, Y1) and (X2, Y2).
- </action>
- <action dev="CAO" type="fix" context="bug">
- no longer crashes when population dies out.
- </action>
- <action dev="CAO" type="update" context="internal">
- added version of Max function with type double. added function Neighbor
- that works with population and spatial resource arrays to find the current neighboring
- cells (even at edge of matrix).
- </action>
- <action dev="CAO" type="fix" context="bug">
- fixed time slicer problem where drastic drop in maximum merit would slow down a run
- considerably. Added warning when analyze mode tries to load in a string sequence
- thats supposed to represent a genome, but maximum char goes beyond instruction set size.
- </action>
- <action dev="CAO" type="update" context="internal">
- previous runs can no longer be replicated even when a random seed used is known
- due to extensive reorganization of portions of code that handle divides.
- </action>
- <action dev="CAO" type="add" context="feature">
- initial implementation of sex. Now exists divide-sex and divide-asex commands,
- former facilitating recombination between two offspring by swapping a region of
- their code.
- </action>
- <action dev="CAO" type="fix" context="bug">
- fixed hardware getting incorrect info as to if it lived through birth process.
- </action>
- <action dev="CAO" type="fix" context="bug">
- removed mutation rate drifting options and old style crossovers.
- </action>
- <action dev="CAO" type="update" context="internal">
- assembled framework for sexual divides. Mostly involved pushing some of the
- final offspring creation to the population and out of the organism.
- </action>
- </release>
- <release version="2.0 beta 0" date="April 2003">
- <action dev="CAO" type="update" context="release">
- Avida has been almost entirely rewritten.
- </action>
- </release>
- <release version="1.6.1" date="2001">
- <action dev="CAO" type="fix" context="bug">
- Fixed a problem with CHILD_SIZE_RANGE in the genesis file -- it used to
- only compare the child size to the *new* parent size; now it will properly
- compare it to the original parent size (and make sure that the new parent
- size also falls into the same legal range)
- </action>
- <action dev="CAO" type="update" context="viewer">
- Added an Average Fitness output in the primitive viewer.
- </action>
- <action dev="CAO" type="update" context="viewer">
- Added a column 10 to the stats.dat output file that indicates the
- depth of the most recent coalescent genotype.
- </action>
- <action dev="CAO" type="update" context="internal">
- Removed "" dependency from assert; stay out of debug move by
- default -- only enter it when DEBUG is defined.
- </action>
- <action dev="CAO" type="update" context="internal">
- Rebuilt data_file.??, simplifying the internal structure and using a
- proper linked list. Also removed dependency on .
- </action>
- <action dev="CAO" type="update" context="internal">
- Removed dependencies in string.?? ; fixed some bugs in Compare()
- that didn't turn up before, but seem real. Often '\0' was being
- saught when a cString was being compared to a char *, when the cString
- data does not end in a \0 (a seperate size measure is kept)
- </action>
- <action dev="CAO" type="update" context="internal">
- Removed global memory object. It was used throughout the code, but
- most allocations did *not* make use of it. We should use some kind
- of solid memory tracking method, but this one was less than optimal.
- </action>
- <action dev="CAO" type="update" context="internal">
- In the viewer, shifted the maps from being normal arrays to using the
- tArray object; also kept them all local to maps (rather than being
- allocated in one place and freed in another like they were)
- </action>
- <action dev="CAO" type="update" context="internal">
- Shifted environment connection lists such that they are now part of
- the environment from the beginning and only initialize (not created)
- by the population. Plus some general cleanup and organization in them.
- </action>
- <action dev="CAO" type="update" context="internal">
- Moved all cList objectes over to the cleaner, templated tList. This
- allowed for some standardization in our current way of doing things,
- a cleaner interface (and simplification of some code). In the future
- we may want to move all of this over to the STL list template, but for
- the moment this was much easier.
- </action>
- <action dev="CAO" type="update" context="internal">
- Cut down on the number of includes from cTools.h; most of them are
- not required.
- </action>
- <action dev="CAO" type="update" context="internal">
- Converted all of the "TRUE" and "FALSE" occurances to "true" and "false"
- throughout the entire code. Changed int to bool in most appropriate
- cases.
- </action>
- <action dev="CAO" type="update" context="internal">
- Moved code_array.?? entirely over to assert from debug.
- </action>
- <action dev="CAO" type="remove" context="internal">
- Anihilated old geneology stuff.
- </action>
- <action dev="CAO" type="update" context="internal">
- Went through header files in source/main/ and removed all non-required
- includes.
- </action>
- <action dev="CAO" type="remove" context="feature">
- Removed the very old [5+ years] resources implementation.
- </action>
- <action dev="CAO" type="remove" context="feature">
- Removed everything to do with redcode.
- </action>
- <action dev="CAO" type="remove" context="feature">
- Removed Block time slicer.
- </action>
- <action dev="CAO" type="update" context="internal">
- Abstracted out the time slicer so it just keeps a collection of ints,
- each with their own merit, and a "GetNextID()" method which returns the
- int that goes next... Moved both slice and merit into the tools
- directory.
- </action>
- <action dev="CAO" type="update" context="internal">
- Adjusted the header files in the viewer so that the viewer takes
- virtually no time to compile in primitive mode.
- </action>
- <action dev="CAO" type="update" context="internal">
- Added BENCHMARK file to keep track of timings of avida as changes
- are made. Added MAP file to track #include's. Add tMemTrack for
- potential tracking.
- </action>
- <action dev="CAO" type="remove" context="internal">
- Removed files:
-<source>
-source/cpu/cpu.ii source/cpu/hardware.ii source/cpu/head.ii
-source/cpu/interface.cc source/cpu/interface.hh
-source/main/classes.hh source/main/geneology.cc
-source/main/geneology.hh source/tools/include.hh
-source/tools/lookup.cc source/tools/lookup.hh
-source/tools/memory.cc source/tools/memory.hh
-source/tools/memory.ii source/tools/memtrack.cc
-source/tools/memtrack.hh source/tools/struct.cc
-source/tools/struct.hh
-</source>
- </action>
- <action dev="CAO" type="update" context="internal">
- Moved functionality from inst_lib.hh into its code file...
- </action>
- <action dev="CAO" type="remove" context="internal">
- Removed cFlags object entirely; got rid of tools.ii.
- </action>
- <action dev="CAO" type="remove" context="internal">
- Removed debug.ii, random.ii, and string.ii
- </action>
- <action dev="CAO" type="update" context="internal">
- Created a string_util.?? component to hold higher level string methods.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created a seperate inst_args.?? component to contain instructions that
- can have arguments. Ideally this needs to be further compartmentalized
- in the futures.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created cGenome and cCPUMemory to replace cCodeArray; a *much* cleaner
- interface. They are in main/genome.?? and cpu/cpu_memory.??
- respectively. [This was a very serious, code-wide change!] cGenome
- is a fixed length, doesn't have flags associated with each
- instruction, and is used for most of the old occurances of cCodeArray.
- cCPUMemory is more similar to the original cCodeArray, but is derived
- from cGenome (henece functions that that cGenome can use either) and has
- many fewer methods that should add up to the same functionality.
- </action>
- <action dev="CAO" type="update" context="internal">
- Added main/genome_util.?? for static genome manipulation and
- comparison functions (like Hamming and Edit distances).
- </action>
- <action dev="CAO" type="remove" context="internal">
- Stripped out a lot of the redundent methods from cHardware. More of this
- should be done.
- </action>
- <action dev="CAO" type="update" context="internal">
- Moved tracking of stepping through organisms in the viewer over to
- population. Got rid of all of the AltInstructionSet nonsense that
- used to handle it. There are now two tight loops in DoUpdate() ; one
- of them is run if you're stepping, the other if your not, so there
- should be no speed loss.
- </action>
- <action dev="CAO" type="update" context="internal">
- Continued to stip down the interface to cHardware. Ideally we'll be
- able to shift instruction execution in there soon (from cBaseCPU) and
- rebuild cBaseCPU into cOrganism or somesuch.
- </action>
- <action dev="CAO" type="update" context="internal">
- Re-vamped cInstLib. Made cInstEntry a private object, and generally
- cleaned up the insides. Inst libs might take longer to load at
- startup now (insignificant since its done only once, and we're talking
- miliseconds), but the interface is *much* cleaner.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created seperate inst_util.?? component to handle interations between
- inst_lib and genomes (such as printing) and initializations of
- inst libraries.
- </action>
- <action dev="CAO" type="remove" context="feature">
- Got rid of arg-based instruction set and binary instruction set entirely.
- This had remarkably far-reaching effects.
- </action>
- <action dev="CAO" type="remove" context="feature">
- Removed curses.?? [Its old enough that we shouldn't need it anymore,
- and the interface was out of date.]
- </action>
- <action dev="CAO" type="update" context="internal">
- Created a tDictionary template that takes in strings with arbitrary
- data, and can lookup the data via the string. Uses a hast table keyed
- off of the string.
- </action>
- <action dev="CAO" type="add" context="feature">
- Avida will now warn you if you attempt to load an instruction in the
- inst library that doesn't exits. It used to just ignore it.
- </action>
- <action dev="CAO" type="update" context="internal">
- Merged cCreature into cBaseCPU. Removed creature.hh
- </action>
- <action dev="CAO" type="update" context="internal">
- Moved cCPUStack into its own component
- </action>
- <action dev="CAO" type="update" context="internal">
- Separated out hardware and cpu into logical elements. This is a huge
- change, and I'm not going into detail here about it.
- </action>
- <action dev="CAO" type="update" context="internal">
- Setup memory allocation method Necrophelia to work more correctly -- it
- now uses the older memory that was lingering in the hardware the organism
- is in.
- </action>
- <action dev="CAO" type="update" context="internal">
- Shifted cpu/cpu.?? to main/organism.?? and cleaned up dependencies.
- </action>
- <action dev="CAO" type="update" context="internal">
- In genesis, changed the name of the RESET_* configuration variables, to
- the more acurate STERILIZE_*
- </action>
- <action dev="CAO" type="fix" context="bug">
- Added #include <string.h> in cString.h and debug.hh -- it was crashing on
- calls to strlen() on some newer compilers.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Fixed templates in tDictionary; reuse of "T" as templated class crashed on
- some newer compilers.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Fixed make_events.pl -- it was creating statments in the form of
- (test_input == "") variable=default : variable=input_value;
- This is a problem since the variable should always be on the outside of
- such statements. Unfortunatly, that gives other errors, so I changed it
- to a proper if-else. New format is:
- if (test_input == "") variable=default; else variable=input_value;
- </action>
- <action dev="CAO" type="fix" context="bug">
- Fixed some const problems in events.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added genesis option "REQUIRED_TASK", which lets the user set the id
- of a mandatory task for a divide to be successful.
- </action>
- <action dev="CAO" type="update" context="internal">
- Removed the cAvidaMain events files. All events are now defined in
- events/cPopulation.events. I removed two events completely, the one to
- change the viewer and the one to print the event list. I think both
- are pretty unnecessary (and are in the way of cleaning up the code more).
- </action>
- <action dev="CAO" type="remove" context="feature">
- Removed LINEAR_MEMORY option...
- </action>
- <action dev="CAO" type="update" context="internal">
- Systematically shifted some includes to be more restrictive (in .cc
- rather than .hh)
- </action>
- <action dev="CAO" type="update" context="internal">
- Removed class cCPUInfo entirely; placed most components into cPhenotype,
- and the rest directly into cOrganism.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created hardware_util.?? to handle loading of hardware methods into
- instruction libraries.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created lineage_util.?? to remove lineage printing (and hence all
- knowledge of lineages) from stats.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created organism_util.?? to provide a location for functions that act
- on organisms but require the use of both genotype and genebank.
- </action>
- <action dev="CAO" type="update" context="internal">
- Lots of changes throughout viewer to get it up and running again with
- all the modifications from the rest of the code...
- </action>
- <action dev="CAO" type="add" context="feature">
- Added more descriptive faults in the zoom mode of the viewer; helpful in
- debugging organism operation.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Changed minimum executed and copied size so that at the minimum values,
- the organisms are legal, but not below (changed a '<=' to just a '<').
- This means that with a minimum copied size of 1.0, everything must be
- copied (as opposed to more than everything, which was causing this to
- break before.
- </action>
- <action dev="CAO" type="update" context="internal">
- Generally did a lot of prep work to get the organisms well seperated from
- the population... That'll be the next big step.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created a population_cell.?? component; populations have a collection
- of cells instead of organisms -- the cells contain the organisms that
- make up the population.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created a seperate mutations.?? component, with a cMutationRates class
- to keep track of mutation rates, and handle basic functions dealing with
- them. Each population cell has its own mutaiton rates, which get passed
- to any organism placed into that cell. All traces of mutations have
- been removed from environments.
- </action>
- <action dev="CAO" type="update" context="internal">
- Most of the system has been fully levelized -- all of the files in the
- tools/ main/ and cpu/ directories are set; only the viewer and events
- are left to be done, and they should be rather straigh-forward. Take
- a look at current/source/tools/MAP and current/source/LEVELS for more
- info.
- </action>
- <action dev="CAO" type="update" context="internal">
- Organisms are now unique entities for their entire existance; they used to
- be referred to as CPUs in the code, and would have new genomes regularly
- loaded into them. A population is now a collection of cells, each of
- which can be occupied with an organism or not. When an organism gives
- birth, it passes a fully constructed offspring organism to the population
- to be placed.
- </action>
- <action dev="CAO" type="update" context="internal">
- The population object itself has been entirely overhauled. Its streamlined
- to now have a minimal number of methods, including the key methods
- ActivateOrganism(), which is always called to place an organism in
- a population, and KillOrganism() which must be called to remove an
- organism. This allows central points for statistics to be done, though
- they haven't been moved there yet.
- </action>
- <action dev="CAO" type="update" context="internal">
- Hardware construction and destruction has been centralized in a hardware
- factory object; this will allow recycling of hardware objects for a
- speed increase, though this optimization still needs to be finished.
- </action>
- <action dev="CAO" type="update" context="internal">
- A number of utility classes have been created to more complex manipulation
- of objects that don't belong inside of them. This has made the
- relevent classes cleaner and easier to understand.
- </action>
- <action dev="CAO" type="add" context="feature">
- Added configure mode --enable-normal to compile without either debug or
- optimization. Much faster for testing!
- </action>
- <action dev="CAO" type="update" context="internal">
- Major re-engineering of cPhenotype -- the internals should be much
- cleaner now.
- </action>
- <action dev="CAO" type="update" context="internal">
- Created symbol_util.?? component in viewers to remove all of the symbol
- handling from population_cell.??
- </action>
- <action dev="CAO" type="fix" context="bug">
- Got TestCPUs working properly at last.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Got death working again.
- </action>
- <action dev="CAO" type="update" context="viewer">
- Tracing now provides registers in both decimal and hex formats. Also,
- merit is broken down into initial (either constant or proportional to
- length) and earned bonuses.
- </action>
- <action dev="CAO" type="update" context="internal">
- Removed a bunch of viewer related methods from cAvidaMain that were either
- unused or redundant.
- </action>
- <action dev="CAO" type="update" context="internal">
- Cleaned up even more header files (in particular test_cpus were being
- included in some components they didn't need to be in any more.)
- </action>
- <action dev="CAO" type="fix" context="bug">
- The GetTest[...] methods in genotype had had some problems when a
- genotype wasn't viable; these should be fixed now.
- </action>
- <action dev="CAO" type="update" context="viewer">
- Surpressed output of warning that data files are bring over-written.
- Ideally, we'll put this back in properly at some point, but at the
- moment, its messes with the viewer.
- </action>
- <action dev="CAO" type="update" context="viewer">
- Improved output methods, and in particular "species.dat" for speciation
- measurements.
- </action>
- <action dev="CAO" type="update" context="internal">
- Moved task_buffer.?? to the more generic template tBuffer.h and placed
- it in tools.
- </action>
- <action dev="CAO" type="add" context="feature">
- Removed all portions of current resource system throughout code
- (in preperation of setting up a new one).
- </action>
- <action dev="CAO" type="update" context="viewer">
- Renamed event_list to events.cfg
- </action>
- <action dev="CAO" type="update" context="internal">
- Changed all "special" assert commands to the default assert.
- </action>
- <action dev="CAO" type="update" context="internal">
- Moved inst_lib and mutation rates into environment.
- </action>
- <action dev="CAO" type="fix" context="bug">
- Repaired generation counting... it was always incrementing the generation
- of parent no matter what the genesis file said, and *then* it would
- increment the generation of the parent. Obviously this was a bug all
- around and its now fixed. I did, however, set the defaults to splitting
- and increasing the generation of both parent and child.
- </action>
- </release>
- <release version="1.6" date="29 September 2000">
- <action dev="CAO" type="add" context="feature">
- Many new features, see info for details.
- </action>
- </release>
- <release version="1.4" date="29 September 2000">
- <action dev="CAO" type="add" context="feature">
- Added events and other features.
- </action>
- </release>
- <release version="1.3.2" date="11 November 1999">
- <action dev="CAO" type="fix" context="bug">
- Fixed ncurses under RedHat Linux 6.x, as well as other bugs.
- </action>
- </release>
- <release version="1.3.1" date="7 September 1999">
- <action dev="CAO" type="fix" context="bug">
- Fixed ncurses under RedHat Linux 5.x.
- </action>
- </release>
- <release version="1.3" date="12 August 1999"/>
- <release version="1.0.1" date="7 May 1998"/>
- </changes>
-
- <todo>
- <actions priority="high">
- <action context="admin" dev="DMB">
- Setup consistency tests.
- </action>
- <action context="refactor" dev="DMB">
- New cHardware base class, separate from Hardware CPU
- </action>
- <action context="refactor" dev="DMB">
- shift analyze commands into their own objects
- </action>
- <action context="refactor" dev="DMB">
- merge analyze and events into 'actions'
- </action>
- </actions>
- <actions priority="low">
-
- </actions>
- <!-- Add todo items. @context is an arbitrary string. Eg:
- <actions priority="high">
- <action context="code" dev="SN">
- </action>
- </actions>
- <actions priority="medium">
- <action context="docs" dev="open">
- </action>
- </actions>
- -->
- </todo>
-
-</status>
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