[Avida-cvs] [avida-svn] r691 - in development: . documentation documentation/content documentation/content/images

Thu May 18 08:50:35 PDT 2006

Author: brysonda
Date: 2006-05-18 11:50:35 -0400 (Thu, 18 May 2006)
New Revision: 691

Added:
   development/CHANGES
   development/documentation/content/images/
   development/documentation/content/images/AvidaLogo.gif
   development/documentation/notes/
Removed:
   development/AvidaLogo.gif
   development/DartConfig.cmake
   development/notes/
Modified:
   development/AUTHORS
   development/KNOWN_BUGS
Log:
Cleanup top level directory some. Moved notes into the documentation directory.  Added CHANGES file.  Updated AUTHORS file.

Modified: development/AUTHORS
===================================================================

--- development/AUTHORS	2006-05-18 12:42:26 UTC (rev 690)
+++ development/AUTHORS	2006-05-18 15:50:35 UTC (rev 691)
@@ -1,27 +1,79 @@
+The Avida Digital Life Platform
+--------------------------------------------------------------------------------
+
 This material was originally written and compiled by Charles Ofria from
-1993-2002 primarily at the California Institute of Technology and Michigan
-State University.
+1993-2002 primarily at the California Institute of Technology and Michigan State
+University.
 
-2005 - Present
-Starting with the 2.3 series, significant enhancements and features are being
-added, along vast portions of the code refactored.  David Michael Bryson,
-Charles Ofria, and Kaben Nanlohy are currently responsible for the changes.
+The following presents, in alphabetical order, a listing of many authors
+responsible for Avida's development.  A best effort has been made to include
+many of the contributors, however this list should in no way be interpreted as
+comprehensive.
 
-1999 - 2002
-The 2.0 release series contains many improvements over earlier releases.
-These improvements were written in 2000-2002 by Charles Ofria, Claus O. Wilke,
-and Kaben Nanlohy.
 
-1993 - 1998
-The core avida system was designed by Chris Adami, C. Titus Brown, and
-Charles Ofria in 1993-1998.  Portions of the design were supported by NSF
-grant #PHY91-15574, NSF grant #DEB-9981397, a Caltech divisional fellowship, 
-the 1993 Caltech SURF program, and the 1993 SUNY Stony Brook URECA program.
+Author  <email>
+  - Institution, Contributing Years
+--------------------------------------------------------------------------------
+Chris Adami
+  - California Institute of Technology 
 
-Portions of Avida have been implemented by: Charles Ofria, Claus O. Wilke,
-Kaben Nanlohy, Travis Collier, Dusan Misevic, Dennis Adler, and David Michael
-Bryson.
+Dennis Adler
+  - Microsoft
 
-This list is in no way comprehensive, many others have contributed various
-features.
+Brian Baer
+  - Michigan State University
 
+C. Titus Brown
+  - California Institute of Technology
+
+David Michael Bryson  <brysonda at msu.edu>
+  - Michigan State University, 2004 - present
+
+Jeff Clune
+  - Michigan State University
+
+Travis Collier
+  - California Institute of Technology
+
+Arthur Covert
+  - Michigan State University, 2004 - present
+
+Joshua Gerrish
+  - Michigan State University, 2005 - present
+
+Sherri Goings				
+  - Michigan State University
+
+Wei Huang
+  - Michigan State University, - 2005
+
+Dusan Misevic
+  - Michigan State University
+  - California Institute of Technology
+
+Kaben Nanlohy
+  - Michigan State University
+
+Charles Ofria
+  - Michigan State University, 1999 - present
+  - California Institute of Technology, 1993 - 1998
+
+Matthew Rupp
+  - Michigan State University
+
+Jason Stredwick
+  - Michigan State University, - 2006
+
+Claus O. Wilke
+  - California Institute of Technology
+
+Larry Wisne
+  - Stanford University
+
+
+Portions of the design were supported by NSF grant #PHY91-15574, NSF grant
+#DEB-9981397, a Caltech divisional fellowship, the 1993 Caltech SURF program,
+and the 1993 SUNY Stony Brook URECA program.
+
+
+Revised 2006-05-18 DMB

Deleted: development/AvidaLogo.gif
===================================================================
(Binary files differ)

Added: development/CHANGES
===================================================================
--- development/CHANGES	2006-05-18 12:42:26 UTC (rev 690)
+++ development/CHANGES	2006-05-18 15:50:35 UTC (rev 691)
@@ -0,0 +1,33 @@
+The Avida Digital Life Platform
+--------------------------------------------------------------------------------
+
+
+Avida 2.5 (change to 2.6 prior release)
+--------------------------------------------------------------------------------
+Important changes relative to previous Avida 2.x releases:
+
+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
+  the configuration file has not changed, save for two important exceptions. The
+  WORLD-X and WORLD-Y parameters have been changed to WORLD_X and WORLD_Y,
+  respectively.   Additionally, several new configuration options are available.
+
+Data output directory
+  All output data generated by Avida is now output within a subdirectory.  By
+  default this directory is called 'data', however it can be configured via
+  the configuration file parameter DATA_DIR.  The directory will created if it
+  does not exist at the start of Avida.  Note, however, if supplying a multi-
+  level path within DATA_DIR, only the last directory will be created.
+
+Multithreaded Analysis
+  Various analysis commands have been enhanced to make use of multiple threads.
+  Currently, the number of threads used is configured statically via the
+  configuration parameter MT_CONCURRENCY (defaults to 1).  On multiprocessor/
+  multicore systems, set this parameter up to the number of physical processors
+  available.
+
+  NOTE: Threads are currently unsupported under Win32.
+
+
+Revised 2006-05-18 DMB

Deleted: development/DartConfig.cmake
===================================================================
--- development/DartConfig.cmake	2006-05-18 12:42:26 UTC (rev 690)
+++ development/DartConfig.cmake	2006-05-18 15:50:35 UTC (rev 691)
@@ -1,27 +0,0 @@
-#
-# Dart server to submit results (used by client)
-#
-SET (DROP_METHOD "scp")
-SET (DROP_SITE "toto.mmg.msu.edu")
-SET (DROP_LOCATION "incoming")
-SET (DROP_SITE_USER "dummy")
-SET (TRIGGER_SITE "http://${DROP_SITE}/cgi-bin/dart--avida--current.pl")
-
-# Problem build email delivery variables
-SET (DELIVER_BROKEN_BUILD_EMAIL "Continuous")
-SET (EMAIL_FROM "avida.current.dashboard at stochastic.net")
-SET (DARTBOARD_BASE_URL "http://toto.mmg.msu.edu/avida-dashboards/current/build/Testing/HTML/TestingResults")
-SET (EMAIL_PROJECT_NAME "Avida 2.0")
-SET (BUILD_MONITORS "{.* avida.current.dashboard.monitors at stochastic.net}")
-SET (CVS_IDENT_TO_EMAIL "{kaben kaben.toto.mmg.msu.edu at kaben.stochastic.net} {brysonda brysonda.toto.mmg.msu.edu at kaben.stochastic.net} {jclune jclune.toto.mmg.msu.edu at kaben.stochastic.net} {dule123 dule123.toto.mmg.msu.edu at kaben.stochastic.net} {hagstrom hagstrom.toto.mmg.msu.edu at kaben.stochastic.net} {bdbaer bdbaer.toto.mmg.msu.edu at kaben.stochastic.net} {mercere99 mercere99.toto.mmg.msu.edu at kaben.stochastic.net} {covertar covertar.toto.mmg.msu.edu at kaben.stochastic.net} {ostrow24 ostrow24.toto.mmg.msu.edu at kaben.stochastic.net} {avidacrashdummy avidacrashdummy.toto.mmg.msu.edu at kaben.stochastic.net} {huangw10 huangw10.toto.mmg.msu.edu at kaben.stochastic.net} {goingssh goingssh.toto.mmg.msu.edu at kaben.stochastic.net} {wilke wilke.toto.mmg.msu.edu at kaben.stochastic.net} {stredwjm stredwjm.toto.mmg.msu.edu at kaben.stochastic.net}")
-SET (DELIVER_BROKEN_BUILD_EMAIL_WITH_CONFIGURE_FAILURES "1")
-SET (DELIVER_BROKEN_BUILD_EMAIL_WITH_BUILD_ERRORS "1")
-SET (DELIVER_BROKEN_BUILD_EMAIL_WITH_BUILD_WARNINGS "0")
-SET (DELIVER_BROKEN_BUILD_EMAIL_WITH_TEST_NOT_RUNS "1")
-SET (DELIVER_BROKEN_BUILD_EMAIL_WITH_TEST_FAILURES "1")
-
-CONFIGURE_FILE(
-  ${PROJECT_SOURCE_DIR}/AvidaLogo.gif 
-  ${PROJECT_BINARY_DIR}/Testing/HTML/TestingResults/Icons/Logo.gif
-  COPYONLY
-)

Modified: development/KNOWN_BUGS
===================================================================
--- development/KNOWN_BUGS	2006-05-18 12:42:26 UTC (rev 690)
+++ development/KNOWN_BUGS	2006-05-18 15:50:35 UTC (rev 691)
@@ -1,7 +1,7 @@
 This file is used to keep track of known "bugs" in avida that are not
 important enough to fix, but that we do want to keep track of.
 
--- Genesis File Related --
+-- Configuration File Related --
 * The PARENT_MUT_RATE setting will cause the parent's genome to mutate when
   it gives birth, but currently it is not treated like a second child, so
   the genotype will not be changed, and in general it cannot act with many

Copied: development/documentation/content/images/AvidaLogo.gif (from rev 690, development/AvidaLogo.gif)

Copied: development/documentation/notes (from rev 690, development/notes)


