2005-03-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.5 with modifications related to packaging the
	material in such a way that the pdf file can be compiled, and so
	that the pdf file itself is not shipped. This release is
	concomitant with the release of Debian packages.

	* autogen.sh : changed the file so that all the autotools-related
	files are updated neatly.

2005-03-08  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* autogen.sh (CFLAGS): added -O2 for the optimization.  Added
	--add-missing --force-missing for the automake call, so that the
	last system-wide files are always used.

2005-02-16  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman/Makefile.am (EXTRA_DIST): removed polyxmass.pdf from the
	distributed material, as it should be compiled.
	(clean): added *.pdf as pdf files should be removed since they
	should be compiled from scratch.

2005-02-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman/installation-overview.tex (section*{Installation On A
	\OSname{Mac~OS~X} System With \software{Fink}}): modified the
	paragraph on Fink installation according to a text provided by Dr
	Mark Tracy.

2004-12-07  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.3 with a new section about the electrical
	charge/isoelectric point calculations and detailed documentation
	of the acidobasic.xml file format.

2004-02-13  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman: transformed the pdf files in userman/figures/vector
	into png files, so that no font availability problems would be
	encountered when reading the polyxmass.pdf file.

2004-02-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in: modified the CONFDIR main configuration variable
	to now hold the "${packageprefix}/share/polyxmass.d" string. That
	will be the new location of the whole GNU polyxmass configuration
	files. This change was elicited by the making of Debian packages.

2004-01-26  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am (polyxmassdata_mandir): corrected wrong location of
	the installed man page from $(prefix)/man/man1 to
	$(prefix)/share/man/man1.

2004-01-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* added a new man page to the package. Note that this man page is
	now fully part of GNU polyxmassdata, and not of the Debian
	GNU/Linux package. It is being prepared in an sgml form and then
	converted to man with the command 'docbook-to-man
	polyxmassdata.sgml > polyxmassdata.man' in the file autogen.sh.

	* The user manual pdf file now is installed in
	$(prefix)/share/doc/$(PACKAGE)/pdf/, while all the texfiles and
	all the figures required to prepare that document are located in
	$(prefix)/share/doc/$(PACKAGE)/userman. This is to comply with the
	Debian GNU/Linux policy for the documentation material.

2004-01-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.4 

	* all GNUification of the polyxmassdata package. Modifications in
	some of the polymer sequence examples to show the annotation
	feature.

2004-01-19  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* all the polseqs/*.pxm files have been changed so that what was
	before a <prop> element with <name>COMMENT</name> have become a
	<prop> element that is actually a note of name COMMENT. That is
	because we have dropped support for the "COMMENT"-named prop
	object in libpxmchem/pxmchem-polymer.c file and in the
	pxmchem-plugin.c. See these files to check the differences.

2004-01-04  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polseqs/protein-sample.pxm: added a default attribute to the
	<data> element (type), so that the PxmNote objects can be stored
	easily as text data, still knowing what kind of data they were in
	the first place (str=string, int=integer, flt=float,
	dbl=double). Default is "str". This should be compatible with
	earlier sequences.
	

2003-11-14  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.3

	* Added a note example in the protein-sample.pxm file so that
	users can check that annotation new feature.
	
	* Improved the documentation so that it now better reflects new
	features in the polyxedit module (annotation features).

2003-10-28  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.2

	* Modifications in view of new release. Mainly, modifications in
	the documentation.

2003-09-30  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman/basics-polchem.tex (subsubsection*{Nucleic Acid
	Fragmentation}): corrected an error in the doc, where the z
	fragments' mass calculation was badly defined.
	(paragraph{\emph{y} fragment series} The calculation is
	mathematically): corrected an error in the doc, where the y
	fragments' mass calculation was badly defined.

2003-08-05  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.1

	* user_manual: bunch of bug fixes. Changed the polyxcalc chapter
	to reflect changes in the way polyxcalc understands the
	chempad.conf chemical pad configuration files.

2003-08-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* protein/chempad.conf: removed the chempad_rows$3 exactly for the
	same reason as described below.

	* chempad.conf: removed the chempad_rows$3 line, now polyxcalc can
	layout the chemical pad using only either a chempad_rows$x
	specification or a chempad_columns$x specification.

2003-07-29  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* user_manual: removed all the files that were remaining from the
	old doc version. These files did not make it into the new version
	of the doc. Changed the userman/Makefile.am file accordingly.

2003-07-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.6.0
	
	* user_manual: big progress in the user manual. Changes include
	adding a full chapter about polyxmassdata with a detailed
	description of the way the polyxmass computer framework can cope
	with an arbitrary number of different polymer chemistries.
	
	* configure.in: changed AC_INIT([polyxmassdata], 0.6.0... to
	AC_INIT(polyxmassdata, 0.6.0...

2003-07-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* all.package : the polyxmass' software suite configuration
	directory where the modules' config files are stored is now
	$(prefix)/etc/polyxmass.d, instead of hard coded
	/etc/polyxmass.d. This way people who do not administer their *nix
	machines can still install the software and use it fully. Thanks
	to Mark Tracy for pointing this bug to me. That's a big step that
	requires that all the modules in the polyxmass software suite be
	updated accordingly. Hence the big leap to 0.6.0.

2003-07-17  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.5.1 

	* userman: almost all the documentation about polyxdef and
	polyxcalc. Still need to complete the polyxedit chapter, add a
	chapter on the configuration of the filesystem hierarchy...

2003-06-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman: added the userman directory where the polyxmass userman
	files are stored so that they can be recompiled by the user.

2003-05-xx  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.5.0

