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ChangeLog.txt
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G E N E S I S
Summary of changes and revision history
***************************************
Last edited: $Date: Tue Nov 11 14:05:40 MST 2014 $
Each set of changes listed below is prefaced with the version number for
which the changes apply. For development releases, two version numbers
are listed on separate lines, the first being the development release
version and the second being the proposed public release version. The
proposed release is subject to discussion and change.
------------------------------------------
FINAL RELEASE 2.4
2014-November
------------------------------------------
- A new autoconf-based build system has been incorporated, so that a
simple "./configure" command will create the appropriate Makefile.
- Three new network connection commands, 'volumeconnect3', 'volumeweight3',
and 'volumedelay3', have been added and documented. These allow
distance-dependent connection probabilities and/or weights and the use
of periodic boundary conditions for network connectivity.
- Added HTML indexing to the 'genesis' directory and subdirectories.
README files have been replaced or supplemented with '.txt' or '.html' files.
- Several source code bug-fixes and changes to src/Makefile.dist were
made in order to solve compilation problems on newer OS versions.
------------------------------------------
BETA RELEASE 2.4 beta
2014-July
------------------------------------------
- addition of 'stdp_rules' object, documentation, and Scripts for implementing
spike timing dependent plasticity in networks of hsolved cells
- the chemesis library for modeling second messengers and calcium dynamics
has been added to GENESIS
- new tutorial Scripts were added for chemesis, gpython-tools,
purkinje, stdp_rules, VAnet2
------------------------------------------
FINAL RELEASE 2.3
2006-March
------------------------------------------
-Last-minute pgenesis doc updates.
-Makefile.dist changes to development targets srcdist and bindist and some
comment clarifications.
-Added Izhikevich simple spiking neuron model objects and demo scripts. Plain
text documentation is included under Doc only.
-Added float_format field for asc_file and res_ascfile objects.
-Update of the new purkinje cell tutorial to allow graphing of multiple data
streams.
-Documentation has been revised for BoG.txt, Changes.txt, asc_file.txt, and
Objects.txt, tabchannel.txt, README.cygwin.
-Some files were moved and Makefile.dist updated to facilitate creating src and
binary distributions with minimal impact on the existing directory hierarchy.
------------------------------------------
STABLE RELEASE CANDIDATE 2.3
2006-January
------------------------------------------
- Completely updated documentation! Including pgenesis and many of the
tutorials.
- Fixed some display issues in the squid tutorial and eliminated the restriction
on the number of steps which can be performed.
- Fixed crash of Xodus when resizing windows.
- Made Xodus dialogs behave correctly in the face of newer window managers
which may attempt to enforce "focus stealing prevention".
- Script parser should now operate correctly on scripts with Mac- and Windows/
DOS- like line endings.
- A new purkinje tutorial with a cell plugin framework, on-the-fly generation
of tabchannels, and the ability to select compartment names for ascii ouput
and current injection.
- Added channels and made some small changes to accomodate leechlib.
- Fixed small bug in Xodus display.
- Increased sizes of buffers for compartment names to accomodate cvapp
conversion from neurolucida files.
- Updated kinetikit example files to sync with kkit11.
- Additional makefile targets for binary distributions.
Intended for developers.
------------------------------------------
DEVELOPMENT RELEASE 2.3 (aka 2.3 beta)
All changes intended for 2.3 release
2005-August
------------------------------------------
- Incorporated patches for variable argument functions.
The old-style varargs.h usage is deprecated and has been replaced by
stdarg.h.
- Incorporated MacOSX patches submitted by Alfonso Delgado-Reyes,
Cengiz Gunay, and Werner Van Geit. Since OSX (and other OS's) may use
case-insensitive file systems, some directory name conflicts
were resolved under the Xodus tree.
- Incorporated Cygwin patches submitted by Sergio Daicz.
Cygwin installations had the same problems mentioned above with Xodus
directory names requiring the same solution. Other fixes included
changing the size of hash table to avoid overflow. This was fixed by
changing the hash table size to a prime number (10007), resulting in a
more evenly distributed hash.
- Incorporated bug fixes for the kinetics library.
- Removed references to PARSER in Makefiles since it is no longer used.
Since it's use was not well documented, it was tempting to define it
with the same path as YACC. This would cause problems on most compilers
since PARSER was used as an argument to '-D'.
- Removed [references to] extra fortran and C++ source code files.
The fortran and c++ code libraries are not used by GENESIS.
- Modified Makefiles to pass appropriate variables to SPRNG.
The SPRNG random number generation libraries should now compile on
all known architectures. Variables are now passed from the top-level
Makefile.
------------------------------------------
STABLE RELEASE 2.2.1
2005-June
------------------------------------------
* 2.2.1 development code relocated to sourceforge repository
- Changed AUTHORS permissions to 644 from 755
- Removed empty file VERSION_2.2.1
- Removed empty directory src/sprng/DOCS
- Added COPYRIGHT
- Added GLPLicense, GNU Lesser Public License
- Removed file src/diskio/interface/netcdf/netcdf-3.4/src/macros.make
since it is generated from macros.make.in
- Removed Doc/Manual.tar.Z. Now accessible from the sourceforge
project site. Updated Doc/README.manual to indicate relocation.
- Moved src/CHANGES to this file (ChangeLog).
------------------------------------------
DEVELOPMENT RELEASE 2.2.1 (aka 2.2.1 beta)
All changes intended for 2.2.1 release
------------------------------------------
* Bug fixes from January 2002:
- Changes to disk_out, asc_file, and res_ascfile. In GENESIS 2.2, these
three objects were changed to write data files in double precision
format (type double) instead of single (type float). Unfortunately, the
resulting files were incompatible with the disk_in and xsimplot objects
(which expect floats), and existing utilities that people have written
to read the output of disk_out. GENESIS 2.2.1 reverts to the single
precision format.
- Corrected a bug in the timetable object that can produce segmentation
faults.
- Corrected a bug in readcell (tools/new_parser.c). When readcell was
invoked twice, in order to create two different cells, Em in all the
compartments of the second cell was set to 0, instead of the value of
EREST_ACT that is specified in the cell parameter file. (This doesn't
happen if ELEAK is specifically set in the cell parameter file.)
- Added changes from Mike Vanier to allow the the supplementary plotting
program src/contrib/xplot (not the GENESIS xplot object) to compile with
the Sun C compiler, as well a with gcc.
- Although the use of "deleteall -force" is discouraged (it isn't always
guaranteed to reset all parameters to the same values as when genesis
was started), it is used in the Scripts/piriform simulation. Mike
Vanier fixed a bug in sim/sim_malloc.c that produced a segmentation
violation when this command was used. Some code cleanup was done in
sim/sim_event.c, while investigating a possible bug.
- Fixed some problems in executing the shell script "test_dir" in
Scripts/piriform.
- Fixed a corrupted data file "testfile" in
Scripts/examples/diskiolib/diskio.
* Bug fixes from August 2002 genesis-2.2.1-beta-20020812
- Fix to hines/hines_chip_init.c submitted by Hugo Cornelis.
Instantaneous tabchannel gates (i.e. those that use the instant field)
produced inaccurate results under hsolve chanmodes 2-5.
- Fix to readcell (tools/new_parser.c) by Hugo Cornelis for core dump with
difshell STOREINFLUX message.
- Fixes submitted by Mikael Lindqvist for concen/fura2.c (missing break in
PROCESS case, and incorrect MSGVALUE arguments for CONCEN message), and
for concen/concpool.c (typo in test for dia <= 0.0).
- Fix to sim/sim_dump.c, provided by Upi Bhalla. It fixes a segmentation
violation that happens with IRIX when kinetikit is used, but not under
Linux.
- Fix by Dave Beeman for an error in olf/olflib.g that caused the SUM
message for the table2D object to fail.
- Two new debugging commands gctrace (for tracing GENESIS commands) and
gftrace (for tracing script language functions) were contributed by Hugo
Cornelis. The changed files are ss/script.y, ss/parse.h, ss/parse.c,
ss/eval.c, ss/ss_func_ext.h, shell/shelllib.g, shell/shell_func_ext.h,
shell/shell_exec.c, and shell/shell_debug.c. Usage summary:
gctrace <level>
if <level> is 1, command tracing is enabled.
if <level> is 0, command tracing disabled.
gftrace <level>
if <level> is 1, function tracing is enabled.
if <level> is 0, function tracing disabled.
gftrace is particularly useful for finding out which script functions are
called from the script field of Xodus widgets without having to locate the
widget in the genesis hierarchy.
* Bug fixes from March 2003:
- Fixes from Mike Vanier for ss/script.y and convert/script.y to prevent
parse errors with recent versions of GNU bison (e.g. ver. 1.75).
- Fixes from Mike Vanier for ss/parse.h and convert/parse.h.
According to Mike: There was a type error involving the YYSTYPE
expression and some ifdef's which had the combined effect of making the
compiler think that YYSTYPE was an int even though it is defined here.
I think that giving an explicit type for YYSTYPE is the Wrong Thing to
do; you should always #define it since bison generates lines like
"#ifdef YYSTYPE". My fix was simple: I just added '#define YYSTYPE
YYSTYPE' after the typedef for YYSTYPE.
Yes, this actually works. Apparently, #define uses a separate namespace
or something than the C compiler itself, so the "typedef union"
statement above doesn't actually define YYSTYPE from the point of view
of the preprocessor. This is ugly, and I'm sure there is a better way
to do things, but it works.
- Changes provided by Malcom Tobias to allow IRIX 32 or 64 bit compilation
flags to be passed down from the main genesis/src/Makefile. Affects
Makefile.dist, sprng/SRC/Makefile, sprng/SRC/lcg64/Makefile, and
sprng/SRC/make.irix.
* Bug fixes from April and May 2003:
- Fix to hines/hines_init.c submitted by Hugo Cornelis. Fixes a bug
triggered under OS's that do not use gnu malloc, i.e. Mac OSX and
probably others, causing hsolve to give a 'bad access' violation.
- New version of kinetics library and Scripts/kinetikit (ver. 9) from
Upi Bhalla. This fixes a problem creating pool objects with gcc 3.2.
Scripts/kinetics/PARMS.g has been modified to set form sizes appropriate
for a 1024 x 768 display. Edit this file if you want larger forms for a
higher resolution display.
- Changes to Makefile.dist for IRIX 6.5 64-bit compile.
- Replaced C++ style "//-" comments with "/* ... */" for K&R compatiblility
in shell/shell_debug.c, shell_exec.c and ss/eval.c, parse.c.
- Included <errno.h> in convert/strsave.c and symtab.c, needed for gcc 3.2.
- Makefile.dist was modified so that the COPT define for the nxdefault target
contains "-DNO_X". This is needed by the file kinetics/text.c, which
normally has some dependence on the XODUS xtext widget.
- kinetics/file_info.c has been modified to disable the relatively obscure
commands dirlist and maxfileversion when compiling under Solaris. This is
because they make use of the functions scandir() and alphasort() that are
normally declared in /usr/include/dirent.h, except under Solaris.
----------------------------------------
DEVELOPMENT RELEASE 2.2.3 (aka 2.2 beta)
All changes intended for 2.2 release
----------------------------------------
* Addition of Michael Vanier's parameter search library and elimination
of Upi Bhalla's obsolete parameter search commands.
* Incorporation of numerous bug fixes and additions from Erik De
Schutter and Hugo Cornelis from their "Antwerp" version of GENESIS,
which is in turn based on GENESIS 2.1. The main changes are:
- Full support of symmetric compartments (also in hsolve).
- The comptmode field is not used anymore (but it's still there for
compatibility).
- Corrected some spine utilities in readcell. All the compartments in
a spine are now indexed; this was necessary because findsolvefield
could otherwise not find the synapse.
- Instantaneous gating of tab(2D)channels possible with the use of the
instant field. Erik also included updated scripts for the traub91
tutorial which demonstrate the use of the instant field (three shell
variables are pre-defined) and uses symmetric compts in hsolve mode.
These have been incorporated into the Scripts/traub91 scripts.
- Supports single diffusion shells in a compartment.
- New dev object: calculator (allows you to add, subtract etc using
messages, no tables needed).
- New concen object: hillpump (like mmpump but you can specify a
Hill coefficient).
- Added a TUBE shape for concpools and updated readcell.
- TABSAVE and TABREAD now write/read platform independent binary files.
- hsolve chanmode 5: like chanmode 4 but normalizes the currents and
conductances stored in hsolve->givals array (for display purposes
only).
- Updates to readcell in tools/new_parser.c.
* The automatic attempt to interpret unknown GENESIS commands as UNIX
shell commands inside {} is disabled by default unless the command is
the first on the command line. Executing shell commands elsewhere
requires using "sh"; e.g., "echo {pwd}" does not work but "echo {sh
pwd}" does. This removes a potentially dangerous effect if the user
mistypes a command such as "echo {rm * Ca}" instead of "echo {Rm *
Ca}".
* Incorporation of Steve Van Hooser's 1998 changes to tools/new_parser.c
to implement "double endpoint" mode in .p files and to extend
"*lambda_warn" support to allow MIN and MAX parameters.
* Full support for SPRNG 1.0, a library of fast random number
generators. The SPRNG library is designed to select from among the
provided RNGs at compile time. src/Makefile defaults to using the
Lagged Fibonacci Generator, which in testing proved to be fastest
while also having the longest random number sequence. The SPRNG
random number generator can be selected at run-time (using the new
command setrand) instead of the previous Numerical Recipes-based
random number generation function.
* Setrandfield has been moved into tools and its -exponential option now
works like planardelay's.
* Implementation of the facsynchan object by Michael Vanier.
* Complete reimplementation of xgif and ximage for displaying GIF
images. The new version does not suffer from problems on displays
having more than 8-bit depths. This fixes a problem with displaying
under Solaris 2.6 CDE, reported by Avrama Blackwell and others. The
symptom was that calls to xgif would generate "X Error of failed
request: BadValue".
* Incorporation of newest version of netCDF library (v. 3.4). (Changes
provided by Upi Bhalla.)
* Diskio support for FMT1 files by Venkat Jagadish. NOTE: the
associated changes in XODUS result in diskio being a required
component for a full genesis. NetCDF can still be excluded if
desired.
* Reimplementation of GENESIS 1 xsimplot by Venkat Jagadish.
* New XODUS object xfastplot plus various XODUS fixes from Upi Bhalla:
- Minor typecasting stuff in Xodus/widg to get a cleaner compile.
- Addition of the FastPlot widget, which is essentially an
oscilloscope widget: fast and economical.
- An XgEventStep routine in Initialize.c, which does a single
event rather than exhaust the pending X events. It can be safely
ignored, as it turned out to be too unweildy.
- Minor fix to xshape to correct buffer overruns.
- Commented out an irritating printf in the xtree. Lets Kinetikit
start out without warnings.
- Added callback to ximage to try to get it to respond to mouse
clicks. Not yet complete.
- Fix in xo_callb.c which protects against segvs in some situations.
Some stuff in hines, which may just be fixes applied on the CDROM
after I got my version. I don't remember doing much there.
- A significant fix in hines_child.c which replaces some huge
dynamic arrays with static ones. This enables it to run on alpha
Linux.
- Some awful hacks in the kinetics library, which make things go
about 2 to 4x as fast specially on newer CPUs by bypassing the usual
messaging. Should be completely transparent to the user, and I have
not had trouble with them for over a year. But you can decide.
- Added object substitution in sum_dump.c
* Fixes to xfastplot implementation to solve X Windows errors on systems
using non-Pseudocolor visuals by default.
* Incorporation of Dieter Jaeger's spike analysis library. David
Bilitch did the work; he noted the following: "I've integrated the
spike analysis library with devices. I've taken Dave Beeman's
suggestion and renamed doac and doxc to autocorr and crosscorr. I
also fetched Dieter's versions of freq_monitor and peristim and made
these the default. The old versions continue to be compiled in,
though they are not added as objects. There are a couple of variables
in the devlib.g startup which can toggle between the old and new
versions (requiring a recompile). I've also changed the class for
autocorr and crosscorr to device as Dieter suggested."
* Enhancements to src/device/timetable.c from Dieter Jaeger.
* New function "fileconnect" from Upi Bhalla, plus associated demo
scripts in Scripts/examples/fileconnect.
* Changes to the normalization of ACTIVATION messages to a synchan, to
make them behave the same with hsolve as without. Implementation and
mods to the Purkinje tutorial by Hugo Cornelis; fixes to the spinedemo
by Dave Beeman.
* Addition of new function, "countelementlist", by Hugo Cornelis. Using
a wildcard that expands a list like {argc} to more than 1000 elements
produced a core dump. The new function allows scripts to count
elements in a list and thereby be used to let scripts behave more
smartly with large lists.
* New actions OUT_OPEN and OUT_WRITE added to asc_file from Michael
Vanier.
* Hitting ^V now prints the current version string.
* Readcell now gives a different value for the axial resistance of a
spherical compartment in GENESIS 2.2 than it did in 2.1. Ra is chosen
as being that of an equivalent cylinder C with the same surface and
volume as the sphere S, where lenC = 3/2 diaS and diaC = 2/3 diaS.
Changes by Erik De Schutter.
* Large number of portability fixes to Makefiles and code for the
following: Solaris 2.6 and 2.7, Red Hat Linux 5.2 and 6.x, Debian
Linux, Mandrake Linux 7.0, SGI IRIX 6.5.3, 6.5.8 and 6.5.10, FreeBSD
4.1, and IBM AIX 4.2 and 4.3.
* The default compilation flags when using gcc now include -O2 and sets
__NO_MATH_INLINES.
* Fixes for outlib from Greg Hood.
* Fixes to src/ss/eval.c from Michael Vanier to improve the traceback
messages.
* Fixes from Greg Hood, Elliot Menschik and Chris Butson for compiling
GENESIS on the SGI Origin.
* Fixes to hsolve from Greg Hood for compiling with optimization under
Red Hat Linux and the Cray T3E.
* Fixes from Greg Hood for PGENESIS, including portability fixes for Red
Hat Linux and fixes to rvolumedelay and rvolumeweight.
* Fixes to src/ss/script.l to fix compilation under Solaris using Sun's
yacc.
* Fixes for tab2Dchannel bug discovered by Dave Beeman in Nov 1999 in
the pre-release DR 2.2.2. The bug symptom is that Upi Bhalla's mitral
cell simulation produced NaN values for the tab2Dchannel X gate.
* Fixes for src/oldconn/personal/expsum.c by Michael Vanier.
* Fixes to remarg from Michael Vanier.
* Fixes to randomize_value in newconn/delay.c from Michael Vanier.
* Fix src/startup/schedule.g to add an init action to PID.
* Fixes to newconn library delay2.c and weight2.c from David Beeman.
* Fixes from Hugo Cornelis to src/out/spike_history.c.
* Fixes from Hugo Cornelis to src/shell/shell_hash.c
* Fix to the version command: it now returns a string value to avoid
displaying a version number like 2.09999...
* Fix to pastechannel: it was using the full pathname of the source
channel when attempting to name the pasted channel in addmsg/sendmsg
message setup. Now uses just the pasted channel name.
* Fixes to synchan, hebbsynchan and facsynchan from Michael Vanier.
* Fix to pathname(), which now allows many more concurrent pathname
strings to be in use. The exact number is dependent on the pathname
lengths. Currently allows up to 1000 chars concurrently. This limit
is controlled by the PATHNAMES_BUF_LEN define, which may be overridden
by adding an appropriate define in the Makefile or suitable header
file.
* Fix from Dave Beeman for a numerical error in the calculation of beta
in TabToFile (src/olf/new_interp.c).
* Fix from Erik De Schutter to calculation of diffusion, involving
contact between shells. This affected a few files in src/concen,
hines/hines_conc_init.c, and files in Scripts/examples/spinedemo/.
* Fix by Dave Beeman to calculation error in tab2file in olf/new_interp.c.
* Fixes to script_out by Hugo Cornelis.
* Fix to hsolve by Hugo Cornelis that permits an hsolve DUPLICATE to be
performed from any working element if you use an absolute pathname as
the first call argument. The new syntax is
call hsolve1 DUPLICATE hsolve2 duplic_path
* Fixes to hsolve from Hugo Cornelis for a bug in which Vm is loaded too
late under some circumstances.
* Fix to provide tabcurrent elements created by readcell with the needed
VOLTAGE and CHANNEL messages.
* Fix by Hugo Cornelis for a bug in hines/hines_chip.c that caused hsolved
synchans to have inaccuracies in the calculated Gk for large time
steps.
* Fix by Hugo Cornelis for a bug in newconn/synchan.c that caused the Gk
calculated by synchans to lag behind the current simulation time by one
time step.
NOTE: These fixes have not been applied to the obsolete channelC2 and
channelC3 objects. Also, it should be noted that output objects (xplot,
asc_file, disk_out, etc.) report the time from the previous step. This
behavior has not been changed in GENESIS 2.2, because it may affect
simulations that do comparisons between values produced by asc_file,
disk_out, etc. with some existing files.
* Addition to tools/new_parser.c by Jose Manuel Ibarz del Olmo to prevent a
negative shell volume, in case someone should assign a value of thick >
dia/2 to a Ca_concen when using readcell.
* Fix to initialization in param/gen2spk.c by Lazarewicz Maciej.
* Fixes for AIX from Claus Weiland and Alex Kozlov.
* Fix to hines/hines_conc.c from Erik De Schutter for a bug that caused
numerical errors in simulations without buffers.
* Eliminination of old parallel library and -parallel option in
src/tools/cell_sheet.c.
* Numerous modification to top-level Makefile.dist & Makefile.<machine>,
including:
- Plain old "make" now does what "make all" previously did
- Eliminate warnings about "@echo: command not found"
- Fix "make install" to do a better job of installing into a
destination directory that is not the root of the GENESIS tree.
* Fix to startup/Usermake from Christo Panchev for compiling
nongraphical version of GENESIS.
* Introduction of src/contrib, which currently contains just one item,
Michael Vanier's version of xplot.
* Removal of src/olf/hh_tabchan.c and corresponding changes in olflib.g
and related Makefiles.
* Renaming of src/newconn/hebbsynchan3.c to newconn/hebbsynchan.c.
* Renaming of src/newconn/newconn.g to src/newconn/newconnlib.g.
* Renaming of src/newconn/synchan2.c to src/newconn/synchan.c.
* Removal of no longer used files src/newconn/synutils_test.g and
src/newconn/synutils2_test.g.
* Significant cleaning up of code throughout GENESIS to reduce or
eliminate various inconsistencies involving datatypes.
* Significant cleaning up of all code to reduce the number of
compilation warnings.
* Improvement of comments in src/Makefile and src/startup/Usermake about
the procedures for building GENESIS.
* Usermake file now allows for building nxgenesis, not just regular
graphical genesis.
* Enhancements to comments in src/Makefile.dist and src/README dealing
with some common problems involving alternate paths for some files or
libraries.
* Verification of Y2K compliance to satisfy Springer-Verlag.
----------------------------------------------
DEVELOPMENT RELEASE 2.1.4 (aka 2.1 prerelease)
All changes intended for 2.1 release
----------------------------------------------
- Version number and main copyright updated to reflect real release
- Added user supplied Makefile settings for compiling 64-bit under
IRIX 6.x
- Postscript graph compression changes from Randy Gobbel
- stdlib.h added to sys/header.h and to convert/ files for
malloc() definitions
- Suppress definition of uchar type in diskio on AIX machines
- Add define for MACHINE type to diskio CFLAGS
- Extraneous \ in printf control string in hines/h_init.c removed
- Bug in newconn/synchan2.c which applies hsolve related correction
to next pending event time when a new event is being merged in
even when hsolve is not used is fixed.
- Added SET action to randomspike to calculate realrate whenever
rate or abs_refract change.
- Changes to accomodate new glibc version of Linux libc
- Type mismatch fixes (non-Xodus only)
- sbrk() return type fix which prevented aix compiles from working
- Missing CopyString() for the return value in do_rand_comp() added
------------------------------------
DEVELOPMENT RELEASE 2.1.3
All changes intended for 2.1 release
------------------------------------
- hsolve has been changed to allow calling the SETUP action when
using the hsolve as root of cell convention even though the
working element is not the hsolve. (The code now temporarily
changes working element to the hsolve while scanning the hsolve
path.)
- bug in hines/hines.c calling write instead of fwrite fixed.
- findsolvefield and getsolvecompname now use G_getopt().
- a bug in which randomspike fails to output at the specified rate
for high spike rates (i.e. when rate approaches 1/abs_refract)
has been fixed.
- the kinetics library Makefile now has an install target
- the netcdf compile problem which appeared on Paragon, T3E,
Linux 1.2.1, Solaris and SGI have been fixed (the latter
three having been tested).
- the copyright message for netcdf now gives the correct path to
the full copyright file.
- added tabcurrent and hebbsynchan icons to xstartup.g
- the full DR 2.1.3 distribution also contains:
- updated Doc and Scripts directories
- the netcdf distribution included within the diskio library has
been pared down to include only what is needed.
------------------------------------
DEVELOPMENT RELEASE 2.1.2
All changes intended for 2.1 release
------------------------------------
- Main Makefile changes
- now includes kinetics and diskio
- oldconn, kinetics and diskio are in an optional libraries section
- liblist, nxliblist and minliblist are now generated from the
makefile
- Usermake changes
- Autogenerates liblist
- USERLIB now lists library names rather than library obj files
- USEROBJ now lists library object files
- kinetics, diskio, oldconn and Xodus as optional libraries
- libsh now ignores comment lines with # in column 1
- README and src/README updated for 2.1
- Bunch of bug fixes sent in from PSC
- Additional T3E mods
- Incorrectly called functions
- Uninitilized variables
- unallocated memory accesses
- hines/hh_update.c contains an inline function which sometimes fails
to compile properly. Added an INLINE macro which if set to nothing
(the default) will inhibit this inlining. Add -DINLINE=inline to
CFLAGS to enable the inlining.
- Bug preventing hsolve from calling the HPROCESS action is fixed.
- planarweight2 and planardelay2 added. These versions require
specification of both the source and destination elements and
improve the speed of setting the weights and delays.
- Bug in synchans which would sometimes prevent delivery of spikes
is fixed.
- Changed many comparisons in new_interp.c for setupalpha, et al for
== 0.0 to fabs(...) < SING_TINY. SING_TINY is 1e-6.
- A command callback mechanism was implemented to support calling
functions at exit. This was used to ensure diskio files are closed
at normal exit.
- Added icons in xstartup.g for new channel objects.
------------------------------------
DEVELOPMENT RELEASE 2.1.1
All changes intended for 2.1 release
------------------------------------
- Main Makefile changes to simplify building
- pgenesis patches from PSC
- T3E support
- new xview messages (you guys wanna write up some docs?)
- par_disk_out and par_asc_file
- -empty_ok option for setfield command
- code_sym now allows whitespace between indirection chars (i.e. '*')
in structure fields, etc.
- a bunch of bug fixes (thanks!)
- permanent fix for the getopt problem; -DGETOPT_PROBLEM is history
- ddsyn is back in olflib.g; inadvertantly removed by Antwerp update
- readfile no longer issues an error when reaching EOF allowing use of
eof command
- Update of ShowInterpol() calls in various places to include new
dimension argument
- nxliblist and minliblist are back
- other bug fixes
--------------------------------------------
DEVELOPMENT RELEASE 2.1
All changes are intended for the 2.1 release
--------------------------------------------
- compartments/segments now have start and end coordinates (GELEMENT)
- New ghk and concen libraries
- 2D tables and tabchannels
- tabchannel SCALE_GBAR message renamed to ADD_GBAR
- res_asc_file: asc_file object that only outputs if time or value
changes fall outside a given range
- spike_history: outputs spike times to file in ascii format
- normalize_weights field for synchan (flags to divide by nsynapes)
- planarweight2; more efficient version of planarweight
- hines code improvements + support for new objects and synchans
- readcell changes for new objects, GELEMENTs, hsolve as cell root
element
- nesting of form widgets for grouping widgets on a form
- lots of fixes for bugs including
- disk_in skipping initial data points from ascii files
- compile problems for IRIX 6.x and AIX 4.1.5
- core dumps when running tutorials back to back
- usage handling for xps
- clock change on xgraph is now passed on to xplots
- xgraph overlays were not compatible with 1.4 semantics
- synapse memory allocation problems
- spurious warning from check about bad clock settings
- path lookup problems referencing element index ranges (eg elm[1-5])
-------------------------
DEVELOPMENT RELEASE 2.0.1
-------------------------
- A bug in the MSGOUTLOOP macro which caused problems on DEC
Alphas has been fixed. (2.0.1)
- A bug in the XtVaSetValues() function causing problems on
DEC Alphas (and probably on other 64bit machines) has been
worked around by providing a fixed version of the Xt code
involved. The Xt problem appears to exist in all X11 versions
through X11R6. (2.0.1)
- A number of additional DEC Alpha related fixes in the
Xodus/Draw library. (2.0.1)
- XoGetPixelFromString() now handles pixes correctly. (2.0.1)
- Fix for xlabel freeing unallocated memory. (2.0.1)
- xforms can now be nested allowing for grouping of widgets
within a form using a nested form. (2.1)
- Added special handling of first message in loading messages
from a dump. (2.0.1)
- Dump files now use the new -continue option to loadtab to
allow continuation of loading long lists of table values. (2.1)
- The element path wildcard routines will now process white
space separated lists of path specifications and include all
elements matching each path. (Note that the commands still
take a single wildcard path argument and that the path list
must be passed in this single argument.) (2.1)
- A bug in special handling of the stdlib.h file for GNU gcc when
optimization is on caused the stdlib.h header to be skipped if
optimization was off. This header is included in all cases now.
(2.0.1)
- The loadtab command for loading tables from dump files has a
-continue option to work around script language limitations on
command line length. (2.1)
- The loadtab -xy option now takes an xdivs argument. (2.0.1)
- The loadtab -xy option now uses doubles to load data to preserve
double precision. (2.0.1)
- The setupalpha command now detects singularities and corrects
those that can be corrected. (2.1)
- Tables now use the simulation step time if the stepsize field is
zero. (2.1)
- xcell now handles cells with symcompartments correctly. (2.0.1)
- xplot now handles expansion of plots greater than 200 point
correctly. (2.0.1)
- The planar and volume weight and delay functions for synchans
now accept an optional destpath argument to restrict the set
of synchans affected by the command. (2.1)
- The protections for various newconn object fields have become
more restrictive. (2.1)
- References to hebbsynchan2 have been removed (2.0.1)
- Fixes for synchan/hebbsynchan MOD message and frequency normalization
bugs. (2.0.1)
-----------------------------------------------------------------------------
RELEASE 2.0
-----------------------------------------------------------------------------
This file contains information about changes introduced in updates
to GENESIS 2.0. For information on changes from GENESIS 1.4 to
GENESIS 2.0, please see the GENESIS Reference Manual.
------------------
BETA 2.0, PATCH 19
------------------
- Additional comments about SGIs in src/Makefile.dist
- Various changes in src/README regarding supported systems
and SGI issues.
- A bug in xview and xvar widgets affecting morphing of
shapes when the value range low and high values are
equal has been fixed.
- Xview update problems resulting in an incorrect initial
display are fixed. The problem likely affected display
during the simulation as well.
- The xtree ADDMSGARROW problem in calling the script_add
and script_drop scripts with incorrect arguments has been
fixed.
- The Usermake reference to the doc file describing how to
compile user libraries changed to refer to the new file name.
- Xdefaults.example has been changed to use the same resource
values found in the fallback resources within Xodus.
------------------
BETA 2.0, PATCH 18
------------------
- Copies of xshape objects no longer share the string field
values of the copied element. Additional code to close
memory leaks in xshape resulted in freeing the fields from
the copied element.
- xcell was writing past the end of two allocated arrays.
Now allocates the correct array sizes.
- xdialog and xlabel now have COPY actions which copy string
field values. Other widgets do not yet implement COPY actions,
but need to, since the internal Xt widget ends up being shared
between copies, but is destroyed if any one widget is deleted.
- NULL widget fields no longer set the corresponding Xt widget
resource to "nil".
------------------
BETA 2.0, PATCH 17
------------------
- The -coords option for x1shape objects ended up setting the
npts field to the number of coords in the first argument
following the -coords option name. This no longer happens.
- xview has been fixed so as not to change colors when the input
data is not changing.
- The hebsynchan object has been returned to the HebbSynchan
implementation, however, hebbsynchan2 is still removed.
------------------
BETA 2.0, PATCH 16
------------------
- xcell was not calculating the width of the soma resulting in
the soma not appearing on the display. xcell now calculates
the correct screen width.
- Additional xtree selection fixes from Upi Bhalla
- Code has been added to xvar and xview to avoid division
by zero if the low and high limit on input values are the
same. In these cases, the color defined by the low limit
shape is used.
- xpixflags is now the official name for the pixflags conversion
command. The old pixflags command name is retained for BC.
- The xpixflags command now uses the getopt() routines and its
usage message documents the negation operator as a tilde(~).
- A bug in xpixflags returning static storage after printing a
usage statement has been fixed to allocate the return value.
- Core leaks in setting of string fields in various widgets have
been patched.
- Added a -nox option to the genesis command line which results
in Xodus not being initialized. A related command, xgetstat,
has been added which returns 0 if Xodus is not properly init-
ialized.
- The xon command has been removed. The xinit command now maps
to a message indcating that xinit is no longer needed. (We
wouldn't want scripts accidently calling the X11 xinit command!)
- A problem with X1compat handling multiple arguments to the x1shape
-coords create command option has been fixed.
- convert now removes the xinit command when converting scripts.
- Changes from Erik DeSchutter to handle INJECT messages in hsolve
chanmode 0/1.
- The hebbsynchan object is now using the HebbSynchan2 implementation
and there is no longer a hebbsynchan2 object.