Bear

File Release Notes and Changelog

Release Name: 0.9.4

Notes:
This is mostly a bugfix release, addressing specifically problems building on
 Darwin / Mac OS X.  The overall portability of the code and build system 
have been improved somewhat--see the Change Log for details.  The source 
distribution for version 0.9.4 has been compiled successfully without 
changes on Debian GNU/Linux, Fedora Core 3, Ubuntu GNU/Linux, Solaris 
9, Mac OS X 10.2, and FreeBSD 4.8.

A couple of new features have been added to this release, most notably the 
LSODE differential equation solver is now supported as long as a FORTRAN 
compiler is available at build time.  As it is experimental, inclusion of LSODE 
is not the default, but can be enabled by passing '--enable-lsode' to the 
configure script.

A convenience feature was also added that tries to resolve name conflicts 
when, for example, a script attempts to save data to a HDF5 file using a 
dataset name that already exists.  Instead of allowing the operation to fail 
(and perhaps discarding results from a long calculation), a new name is 
created by appending a number to the existing name.

Full details on changes in this release are available in the Change Log.

Changes:
2005-06-06  David Dumas  <daviddumas@gmail.com>

	* configure.in: Made '--disable-lsode' the default behavior at
	configure time.  This fixes build problems on some platforms,
	notably Solaris with the Sun Workshop compiler.  Will investigate
	and perhaps re-enable by default for future release.

2005-06-04  David Dumas  <daviddumas@gmail.com>

	* bear-ref: Added description of the slope parameter for the
	linear module, which has been around for some time but which was
	not previously documented.

	* bear-ref: Documented LSODE method addition and relprecision
	parameters for bers and bers2 modules.  Minor changes to
	exposition in several parts.

2005-05-29  David Dumas  <daviddumas@gmail.com>

	* bear: changed prototype for h5disc_typeconv so that 'nelmts' is
	either hsize_t or size_t depending upon the HDF5 library version
	(<= 1.6.2 and >= 1.6.3, respectively).  Cleaned up other instances
	of hsize_t so that size_t is used wherever possible.

	* configure.in: check for the specific version of the HDF5 library
	by applying the preprocessor to the header file 'hdf5.h'; define
	H5_CONV_NELMTS_T to be the correct type for the 'nelmts' parameter
	to HDF5 type conversion functions, which changed between 1.6.2 and
	1.6.3 releases.

2005-05-28  David Dumas  <daviddumas@gmail.com>

	* bear: added 'compatibility' parameter to the discreteness and
	holonomy modules; if nonzero, HDF5 output will be written in a
	form readable by versions of HDF5 older than 1.6.0 (which don't
	understand shuffling).

2005-05-27  David Dumas  <daviddumas@gmail.com>

	* configure.in: added options to disable internal compression and
	shuffling of HDF5 files, even if these features are
	available. (Command-line options '--without-hdf5-new' and
	'--without-hdf5-deflate').

	* bear: wrapped use of HDF5 1.6 functions in conditionals to allow
	bear to compile with earlier versions (1.4 confirmed).  This
	amounts to disabling the shuffle output filter.

	* configure.in: added explicit checks for H5Pset_shuffle and
	H5Pall_filters_avail functions in HDF5 library, as these were only
	added in release 1.6.0.

	* bear: schwarz solver is now aware that the LSODE solver may or
	may not be available, and acts accordingly.  If not available,
	the 'lsode' solver type is treated as unknown.

	* configure.in: added '--disable-lsode' to remove all dependence
	on a FORTRAN compiler, and modified checks for F77 to be nonfatal
	when they fail.

2005-05-25  David Dumas  <daviddumas@gmail.com>

	* configure.in: check for strerror in configure; fixes bug where
	on a system with no error.h but with strerror (e.g. Mac OS X),
	build would fail on redefinition of strerror and type conflicts
	for related constants.

	* libreplace: error.h wrapped in #ifdef so that no prototypes are
	defined unless configure determined a replacement error function
	to be necessary.

	* makefiles: replace '-lg2c' hack with portable autoconf
	substitution of $(FLIBS) to build an executable from both C and
	FORTRAN object files.

	* configure.in: check for working F77 compiler and the necessary
	libraries to link FORTRAN code into a C program; fail if not found

	* clsode: replaced inclusion of obsolete 'malloc.h' with
	'stdlib.h'
	

2005-05-05  David Dumas  <daviddumas@gmail.com>

	* bear: h5pathspec.c: fixed bug where an internal path beginning
	with '/' would lead to attempt to open a group with garbage as its
	name.  Thus both "/path/file.h5:/group/dataset" as well as
	"/path/file.h5:group/dataset" are now acceptable.  (The former
	caused an error up to now.)

	* bear: h5io_util.h: changed maximum depth of hdf5 internal path
	to 8, since I noticed that some of my own files have depth up to 6.

2005-05-02  David Dumas  <daviddumas@gmail.com>

	* bear: Portability enhancements: early glibc used macros for some
	string functions, breaking the IFNDEF prototyping in several
	files.  Necessary to build on Debian 2.2 (potato).

	* bear: added prototypes for some string functions missed in
	previous modifications to allow for missing "string.h".
	
2005-04-028  David Dumas  <daviddumas@gmail.com>

	* bear: h5discreteness and h5holonomy now do name-conflict
	resolution so that data isn't lost if an attempt is made to write
	to an existing dataset.  

2005-04-20  David Dumas  <daviddumas@gmail.com>

	* bear: added LSODE differential equation driver, separating Heun
	solver into 'heun_gsl' and 'heun_lsode'; LSODE is built from
	fortran sources as a static library and linked in using a simple C
	wrapper from libwayne.


2005-04-13  David Dumas  <daviddumas@gmail.com>

	* bear: added 'piecewise_linear_alt' contour driver which breaks
	one of the segments into two halves joined at the point closest to
	the singularities of phi().  This may allow smart ODE integrators
	to better judge the necessary step size, i.e. they catch a thin
	but tall "spike" in phi() that might otherwise go unnoticed.
	
	* bear: modified piecewise linear contour driver so that the
	segment passing closest to the singularities is first.

	* bear: big cleanup in the PL contour driver making use of changes
	to contour API.
	
2005-04-05  David Dumas  <daviddumas@gmail.com>

	* bear: cleaned up contour driver API so that a contour is now
	a sequence of segments, and the driver must present a single
	contour function that takes a time value and segment index.  This
	replaces the old method where a separate function pointer was
	needed for each segment.

2005-03-24  David Dumas  <daviddumas@gmail.com>

	* bear: added anosov module for computing unstable manifolds of
	pseudo-anosov mapping classes.

	* bear: added pluggable integration contour API and new contour
	drivers "piecewise_linear", "ellipse", and "spline_ellipse".  The
	latter is a rewrite of the integration contour system used in
	previous versions.

	* bear: added bers2 module which computes holonomy via interpolation
	from a sparse grid, yielding a speed improvement when the holonomy
	does not vary too quickly

	* bear: updated test suite

	* bear: print more detailed information during computations, and
	add a linebreak ('\n') after each status update for more dependable
	output buffer flushing and easier reading of log files.
	
2004-05-07  David Dumas  <daviddumas@gmail.com>

	* bear: major rewrite of the I/O and scripting code.  HDF5 is now
	the main file format, and the extension language Lua is
	incorporated for input scripting.  There is now an interactive
	mode, which is invoked by default if STDIN is a tty and no input
	file is specified.

	* bear: dependence on "expat" removed; XML parsing is no longer
	necessary.

	* bear: the "dyadic iteration" experimental options have been
	removed for now, as they are difficult to interface with the new
	Lua scripting frontend.  They were primarily created to facilitate
	the development of an interactive Bers slice drawing program,
	which must now be redesigned.
	
	* bear: errors and debugging messages are now reported using the
	functions from GNU "error.h".  This file is replaced with a
	version packaged with bear in case it is not found on the host by
	the configure script.

	* bear: probably more changes than I can think of right now.
	Version 0.9.0 shares little more than core mathematical code with
	previous versions.
	
2003-11-02  David Dumas  <daviddumas@gmail.com>

	* bear: time differences are now computed using POSIXly correct
	difftime(), rather than a type cast; times will now be reportly
	correctly on systems where time_t is not a scalar (if there are
	any such systems).

	* bear: sign of the third element of each markov triple is now
	chosen correctly; note that the discreteness algorithm does not
	depend upon this sign.

	* bear: verbose output mode now displays statistics on the use of
	adaptive precision modification

	* bear: added new adaptive precision modification algorithm, and
	associated options "--delta", "--adapt", "--adapt-divisor",
	"--adapt-persist".

	* bear: verbose output mode now displays ETA

	* bear: minor rearrangement of Heun diffeq and contour calculation functions yielding i386 speed enhancement.

	* bear: added self-test suite to Makefiles to catch common
	discrepancy-causing issues like IEEE rounding and "unsafe"
	floating-point optimization.

	* bear: added first draft of texinfo documentation


2003-10-24  David Dumas  <daviddumas@gmail.com>

	* bear: added linear slice capability (option "--linear")
	
	* bear: added a new Jorgensen stability parameter J, where the
	Jorgensen test now checks |x| < J.  Default value of 0.999 seems
	to improve accuracy near the limit of the differential equation
	integration code.

	* bear: obsoleted the "trace_tiny" parameter, and made several
	speed-related improvements to the Bowditch algorithm.

	* bear: modified the formula for the Bowditch function H(x) -- the
	new function should be sufficient for discreteness testing, even
	at small scales.

2003-10-11  David Dumas  <daviddumas@gmail.com>

	* bear: rewrote integration contour setup code -- should now work
	correctly for any lambda such that there exists an ellipse
	containing 0 and lambda but not 1, and an ellipse containing 1 and
	lambda but not 0.  (Previous code cut out for lambda within ball
	of radius approx 0.14 about 0 or 1.)
	
	* bear: implemented trace_tiny functionality, removed dependence
	on qsort function.

	* bear: fixed computation_time functionality, so that computation
	times longer than 38 minutes ( = POSIX clock() wraparound time )
	are reported correctly.  Time resolution is now 1 second.

2003-09-25  David Dumas  <daviddumas@gmail.com>

	* bear: restored computation_time functionality.

	* bear: added xdf_name option and changed handling of existing
	output files; the newly created arrays are always the next
	siblings of the input array, if any, or are inserted at the
	beginning otherwise.

	* bear: completely rewrote the xdf input/output routines; bear now
	makes only a single pass through its input and output files, which
	is much faster than the previous "parse-to-memeory" system.
	REMOVED dependence on Scew.

2003-09-22  David Dumas  <daviddumas@gmail.com>

	* bear: added stubs for future "--trace-tiny" and "--trace-huge"
	option functionality

	* bear: added "--maxdepth" option to control max depth of the
	discreteness tree search


2003-09-18  David Dumas  <daviddumas@gmail.com>

	* claw: ripped out the old perl script and rewrote claw as a C
	program; the result is much faster but slightly less tolerant of
	XDF different than that produced by bear.

	* bear: added "--precision" option to control precision of the ODE
	solver.

2003-09-16  David Dumas  <daviddumas@gmail.com>

	* claw.pl: added XDF api to the list of external dependencies in
	README; added corresponding checks to configure.in.

2003-09-08  David Dumas  <daviddumas@gmail.com>

	* bear: initial version.