File: ChangeLog

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polyxmass-doc 0.9.0-1
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2006-06-28  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.9.0 with a new section about the import of raw text
	files.

2006-01-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.8 with all the modifications about the Find/Replace functionality...

2005-10-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Done the modification that provides the right Free Software
	Foundation address in all the relevant files. Copied the new
	version of file COPYING in the source tree.

2005-09-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.7

2005-09-01  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am: Put back the sgml source file for the man
	page. This is to comply with the Debian Free Software Guidelines.

2005-08-31  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* whole_project: reworked a number of files in order to make the
	LaTeX source files compatible with an almost automatic translation
	to HTML using tex4ht. This is so that it gets easy to make an HTML
	version of the documentation for publication on the polyxmass.org
	site.
	
	* debian/copyright: removed the full URL to the source package.


2005-07-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.6

	* Makefile.am: removed the polyxmass-doc.7 target, because the
	docbook-to-man utility is not present on all distributions. Thus,
	the man page is distributed as is.

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