massxpert (2.0.3-1) unstable; urgency=low

  * debian/control: Rename binary package from massxpert-bin to massxpert
    and remove Section: science field (inherits from the source package);
  
  * debian/control: Move all the Build-Depends-Indep dependencies
    (texlive-latex-recommended,qtexlive-fonts-recommended) to
    Build-Depends dependencies (Closes: #528086) to work around the
    builders bug. For more details, see bugs:
  
    - Bug #528086: massxpert_2.0.0-1(mips/unstable): FTBFS:
    missing build dependency
    
    - Bug #521918: pbuilder --build --binary-arch invokes 'build' target. 
  
  * debian/control: Remove no more required Build-Depends-Indep
    latex-related cm-super-minimal package (thanks to removing
    dependencies in the UseLATEX.cmake file;
  
  * debian/control: Add Vcs-Git and Vcs-Browser fields;
  
  * debian/control: Set Uploaders to Filippo Rusconi
    <rusconi-debian@laposte.net>;
  
  * debian/control: Set Maintainer to The Debichem Group
    <debichem-devel@lists.alioth.debian.org>;
  
  * debian/rules: Remove old unused variables;
  
  * debian/rules: Fully separated the arch/indep targets which build and
    install stuff in different directories;
  
  * debian/rules: .PHONY targets are now individually specified (so as not
    to forget them when targets change);
  
  * debian/control: remove unrequired Build-Depends-Indep packages;

  * debian/watch: added file;
    
  * debian/control: massxpert-bin to massxpert renaming:
    Conflict/Replace massxpert-bin
	
  * New upstream release (worked a lot with Lionel Elie Mamane):
    
    - gui/massxpert_fr.ts: updated the french translation;
    
    - usermanual/front-matter.tex & usermanual/massxpert.tex: remove user
    manual dependency on LaTeX package "textcomp", so as not to embed
    Type3 fonts in the PDF file. Replaced (C) with \copyright. Small
    typographical fixes.
    
    - usermanual/UseLATEX.cmake: remove other non-essential software
    requirements to reduce dependencies;
    
 -- Filippo Rusconi <rusconi-debian@laposte.net>  Wed, 10 Jun 2009 14:33:04 +0200

massxpert (2.0.2-1) UNRELEASED; urgency=low

  * New upstream release (worked a lot with Lionel Elie Mamane):
    
    - usermanual/CMakeLists.txt: remove the "-Werror" flag as almost any
    LaTeX compilation produces warnings;
    
    - gui/application.cpp: set sensible values for the default decimal
    places to use to display numerical data on the first program run;
    
    - usermanual/UseLATEX.cmake: update Copyright notice to reflect the
    fact that the file was modified by me;
    - lib/configSettings.cpp: remove unncessary configuration settings
    feedback messages, other improvements;
  
    - gui/main.cpp: remove unnecessary feedback for the loading of
    translation files;
  
    - Added 'Close' button to aboutDlg dialog window.
    
 -- Filippo Rusconi <rusconi-debian@laposte.net>  Fri, 15 May 2009 18:00:22 +0200

massxpert (2.0.1-1) UNRELEASED; urgency=low
  
  * New upstream release: bug fix release and other improvements.
  
    - Clean source tree;
    
    - lib/configSettings.cpp: fix typo (thanks Lionel Mamane);
    
    - Modify usermanual build process to use UseLATEX.cmake;
    
    - Fix bug due to not taking into account the locale while making
    textual mass lists starting from oligomer items in treeviews.
    
    - Fix locale-specific input/output inconsistencies;
    
    - Improved the simulations' result export as text;
    
    - usermanual/UseLATEX.cmake: removed the requirement of
    /usr/bin/convert from ImageMagick as we do not need it: using pdflatex
    and only png-format graphics files;

 -- Filippo Rusconi <rusconi-debian@laposte.net>  Wed, 15 Apr 2009 21:17:17 +0200

massxpert (2.0.0-1) unstable; urgency=low
  
  * Standards version is 3.8.1.

  * Bumped debian/compat to 7.
  
  * Entirely reworked debian/rules, which now has build-arch and
    build-indep fully separated targets totally fitting the Build-Depends
    and Build-Depends-Indep fields of debian/control.
  
  * New upstream release:
  
    - Fixed bug in XpertDef due to not verifying upon removal of a
    modification if it is used by a cross-linker. Crashes. Report by Ron
    Bakus (UCSD domain edu).

    - Fixed bug with storing polymer sequences and polymer chemistry
    definitions with crippled XML;
  
    - Added configurability to the number of decimal places used to
    display values for pH/pKa, atoms/isotopes, oligomers, polymers;
  
    - Fixed regression with un-cross-linking;
  
    - Fixed bug with calculation of right-end fragment boundaries;
  
    - Big work within the XpertMiner module;
  
    - Huge internal work with the ionization paradigm in particular within
    the fragmentation framework.

  * Fixes with the debian/* so that the source package now build three
    packages: massxpert-bin, massxpert-data, massxpert-doc.
  
  * A bunch of improvements in the Debian packaging thanks to Lionel
    Mamane mentoring (parallel support in rules and others).

  * Sponsored upload done by Lionel Elie Mamane <lmamane@debian.org>

 -- Filippo Rusconi <rusconi-debian@laposte.net>  Tue, 31 Mar 2009 23:06:14 +0200

massxpert (1.7.8-1) unstable; urgency=low

  * New upstream release:
  
    - Implemented multi-cleavages;
  
    - Updated the User Manual

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Tue, 08 Jul 2008 13:09:31 +0200

massxpert (1.7.7-1) unstable; urgency=low

  * New upstream release:
  
    - Implemented multi-region selections;

    - Updated the User Manual.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Fri, 04 Jul 2008 13:35:35 +0200

massxpert (1.7.6-1) unstable; urgency=low

  * New upstream release:
  
    - Moved the project to GNU GPL version 3;
  
    - Fixes for GUI bugs;
  
    - Fixes with the localization of double values in the GUI;
  
    - First implementation of the mzLab (still experimental feature);
  
    - Classes rework with better handling of ionization throughout the whole project;
  
    - Code cleanup, better handling of constness in the whole project;
  
    - Updated the User Manual.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Wed, 28 May 2008 15:18:37 +0200

massxpert (1.7.5-1) unstable; urgency=low

  * New upstream release:
  
    - Code cleanup throughout the code redesign of some classes and addition
    of Ion class;
  
    - Implemented namespace massXpert throughout the project;
  
    - Update of the french translation;
  
    - Bug fixes;

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Thu, 24 Apr 2008 21:12:56 +0200

massxpert (1.7.4-1) unstable; urgency=low

  * New upstream release:
  
    - Implemented new means to define fragmentation specifications that
    involve the decomposition of the fragmented monomer's side chain;
  
    - Fixed memory leak and bugs;
  
    - Updated the french translation and the user manual.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Wed, 02 Apr 2008 22:59:50 +0200

massxpert (1.7.3-1) unstable; urgency=low

  * Upstream release with main new feature: the filtering implemented for
    the previous version was extended also for the fragmentation and mass
    searching oligomer data;
  
  * Improved the use of the filtering feature thanks to modifications in
    the graphical user interface;
  
  * Implemented check that a cross-link name cannot be used already as a
    modification name (and vice versa);
  
  * Fixes to regressions that crept in during last version developments
    and code cleanup;
  
  * Update of the documentation;

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun, 30 Mar 2008 17:34:27 +0200

massxpert (1.7.2-1) unstable; urgency=low

  * Upstream release with main new figure: the oligomer data from a
    polymer sequence cleavage might be filtered live and in-place using a
    sortingProxy treeview (powerful feature of the Qt library);
  
  * User manual update;
  
  * Minor bugfixes.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Tue, 25 Mar 2008 22:11:17 +0100

massxpert (1.7.1-1) unstable; urgency=low

  * Upstream release with main new feature: intra-molecular cross-links.
  
  * Bug fixes and small improvements here and there.

  * Modified dh_shlibs line to exclude the plugins from the scan, as these
    are private libraries with no SONAME.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Tue, 18 Mar 2008 22:24:36 +0100

massxpert (1.7.0-1) unstable; urgency=low

  * Upstream bug-fix release. 
  
  * Fixed crash caused by elemental compositions calculations using
    manually-defined polymer sequence modifications (thanks to as
    calculations session with Fatima Boutimah in my lab);
  
  * Modified the polymer sequence file format so as to be able to save
    polymer sequence modifications with a fully qualified <mdf> (see
    polChemDef format) element. This allows storing the modifications with
    full qualification (and not only name) even when the modification is
    manually-defined.
  
  * Added man massxpert-doc.7 page documenting the User manual.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Thu, 21 Feb 2008 14:28:55 +0100

massxpert (1.6.9-1) unstable; urgency=low

  * Upstream release with more flexible monomer modification procedure
    (big inner code changes not visible by the user).
  
  * Update the documentation.
  
  * Extended copyright to 2008.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Fri, 15 Feb 2008 10:48:49 +0100

massxpert (1.6.8-1) unstable; urgency=low

  * Upstream release with some small modifications in the debian packaging
    (massxpert.1 man page an massxpert.desktop are installed differently
    so that these files might also be used when generating rpm packages);

  * The user manual now installs properly in /usr/share/doc/massxpert-doc
    and not /usr/share/doc/massxpert, as was the case before. Also, the
    user manual was updated so as to reflect the new polymer chemistry
    definition GUI design.

  * Removed the lintian override file, as I finally found why two of the
    three plugins would make lintian complain about
    shlib-with-non-pic-code.

  * Fully rewritten the polymer chemistry definition graphical interface.

  * Some bug fixes here and there.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Tue, 18 Dec 2007 11:39:06 +0100

massxpert (1.6.7-1) unstable; urgency=low

  * Upstream release with the following modifications:
  
  * CMake'ization of the source tree.
  
  * Fixed bug with calculation net charges with any given pH.
  
  * Standards-Version: 3.7.2

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun, 09 Dec 2007 18:40:55 +0100

massxpert (1.6.6-1) unstable; urgency=low

  * Upstream release with the following modifications: 
  
  * Update the french translation and the user manual to reflect the 
    new features of the cleavage- and fragmentation-base oligomer
    generation.
  
  * The oligomers from cleavage and fragmentation might now be calculated
    as multi-charged oligomers
  
  * Implemented the fragmentation stuff in new class MxpFragmenter and
    removed the corresponding code from the fragmentation dialog
    class. Also, made the same use of QList<MxpOligomerList *> * instead
    of two nested QList objects as previously performed with the cleavage
    code in the fragmentation code.
    
  * Implemented ionization level ranges for oligomers, starting with the
    cleavage application bits
  * Reimplemented the gui polymer sequence cleaving stuff to use the
    modified MxpCleaver object
  * Reimplemented the cleaver object to use the new oligomer list object
  
  * Implemented and added to library 'list of oligomers' new class:
    MxpOligomerList derived from QList<MxpOligomer *>

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun, 23 Sep 2007 14:26:47 +0200

massxpert (1.6.5-1) unstable; urgency=low

  * Upstream release with the following modifications: 
  
  * Added possibiliy to restrict monomer modifications to given
    monomers. If the user tries to modify a monomer with a modification
    that is not supported for it, the modification does not occur and the
    user gets a message. Implemented a mechanism by which these monomer
    modification limitations can be overridden.
  
  * Fixed bug with parsing atom symbols with more than 2 characters.
  
  * Added fake atoms so as to to allow defining formulas with precise
    masses.
  
  * Fixed bug with creation of default monomer modification vignette and
    setting it to the hash with a bad key. That would lead to bad
    reference counting and crashes upon unmodification of more than one
    modified monomer.
  
  * Better feedback messages to the sequence editor window's statusBar
    while doing initial sequence drawing.
  
  * Updated french translation.
  
  * Reverted to version 2 of the GPL as the Qt libraries are not using the
    'version 2 or any later version' wording.

 -- Filippo Rusconi <massxpert-maintainer@polyxmass.org>  Sun, 19 Aug 2007 16:51:09 +0200

massxpert (1.6.4-1) unstable; urgency=low

  * Upstream release with the following modifications:
  
  * Translated the application into french. Took advantage of the
  translation work to uniformize the messages and the labels on the UI
  widgets.

  * Bug fixes with modifications declared in some polymer chemisty
  definitions but not available as graphics files or not registered in
  the modification_dictionary.

  * Added default modification vignette, so that when a modification
  is defined without assigning a corresponding vignette the program
  does not crash.

  * Switch to 4.3.0 for MS-Windows also.

  * Minor bugfixes

 -- Filippo Rusconi <massxpert-maintainer@polyxmass.org>  Tue, 24 Jul 2007 22:06:00 +0200

massxpert (1.6.3-1) unstable; urgency=low

  * New upstream release.
  
  * Fixed glitches in some fields of the debian/control file.	

  * Fixed problems with the modification vignettes and declarations of
    modifications in the modification_dictionary of some polymer
    chemistry definition.

  * Many improvements in the user manual. 
  
  * Improved handling of polymer sequence modifications. 
  
  * Improvements the GUI and in the calculator recorder output. 

  * Added possibility to modify a polymer sequence arbitrarily by
  entering a chemical formula and not by choosing a modification in
  the polymer chemistry definition. 

  * Switch to 4.3.0 as the Qt dependency, which showed some glitches
  in the handling of the sequence editor graphics view that were
  fixed.

 -- Filippo Rusconi <massxpert-maintainer@polyxmass.org>  Thu, 19 Jul 2007 14:55:47 +0200

massxpert (1.6.1-1) unstable; urgency=low

  * Added new feature to the XpertEdit module: a mass list
  laboratory. Updated the documentation.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun,  1 Jul 2007 18:49:17 +0200

massxpert (1.6.0-rc2-1) unstable; urgency=low

  * Initial release.

 -- Filippo Rusconi <massxpert-maintainer@massxpert.org>  Sun,  1 Jul 2007 18:49:17 +0200

