source: Promot/trunk/promot/VERSIONS.txt

/*******************************************************************************
 *   ProMoT
 *  ---------------------------------------------------------------------------
 *   Copyright (c) 1997-2012 ProMoT Development Team
 *   Max Planck Institute Magdeburg, Germany
 *   http://www.mpi-magdeburg.mpg.de/projects/promot
 *   
 *   This is free software; you can redistribute it and/or modify it
 *   under the terms of the GNU General Public License as published
 *   by the Free Software Foundation; either version 2 of the License, or
 *   any later version.
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 *   OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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 *   along with this library; if not, write to the Free Software Foundation,
 *   Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 * 
 *  ---------------------------------------------------------------------------
 *   $Id$
 ******************************************************************************/

-------------------------------------------------------------------
 0.4.0
-------------------------------------------------------------------
- Initial revision of ProMoT version 0.4.0
- ProMoT ported to CVS

- Object-oriented language definition of MDL
- New version of FrameTalk (weak, strong parts, link-from)

-------------------------------------------------------------------
 0.4.1
-------------------------------------------------------------------
- `Component' renamed to `module'

-------------------------------------------------------------------
 0.4.2
-------------------------------------------------------------------
- mexpr.lisp: CG parser extended to slot paths
- In mexprs. variables are no longer represented as objects, but as
  instances of slot-path.
- promot-link introduced.
  The command option `:links' is no longer mapped to FDL.
  promot-link is rather used as strong parts.
  This led to major changes in the generation of link equations.

-------------------------------------------------------------------
 0.4.3
-------------------------------------------------------------------
- mdl.lisp: bug fixed when generating weak parts for mexprs in indices
- format-mexpr.lisp: now also generates LaTeX code
- First steps to implement module arrays

-------------------------------------------------------------------
 0.4.4
-------------------------------------------------------------------
- First version of implementing terminal arrays:
  This implementation is not based on FDL slot arrays.
  It does not allow the splitting of terminal arrays into single 
  terminals, which is a must!

- Fixed bug in sort-dependency-p (model.lisp).
- The call to sort-dependency-p was not symmetric.

-------------------------------------------------------------------
 0.4.5
-------------------------------------------------------------------
- Removed sort-dependency-p.
  - Sorting variables according to their dependencies with LISP `sort'
    was buggy.
  - Reason: If a>b and b>c, it cannot be concluded that a>c!
  - Now: 1) the dependency lists of all variables are agglomerated
         2) the total dependency graph is traversed by depth-first search
         3) the nodes that are traversed last are printed first
    + additional alphabetic sorting of `all-direct-variables' in
      `dependency-list' (roots-mixins.lisp)
  
-------------------------------------------------------------------
 0.4.6
-------------------------------------------------------------------
- Coupling, propagation of vector terminals now running for
  - Two-phases, three-phases in kb/test-arrays.mdl
- For this: model-name determination completely revised
  - path-indices-* methods introduced
- Module arrays now running, at least for all modules in `test-arrays.mdl'
- Terminal arrays now running, at least for all modules in `test-arrays.mdl'
- Complete revision of 
  - roots-mixins.lisp: path-indices-*
  - model.lisp: model-direct-identity-equations
- Lots of other changes, bug fixes, I can't remember

-------------------------------------------------------------------
 0.4.7
-------------------------------------------------------------------
- Output of variables with :report attribute 
  Now uses :x-scope, :y-scope, :z-scope in define-process-values

-------------------------------------------------------------------
 0.5.0
-------------------------------------------------------------------
- src/graphics/*:
  First new version of Model Editor that runs with FDL
- src/kernel/cg.lisp:
  Better formatting of CG file
- images/Makefile created
- kb/test-suite created for testing new ProMoT versions
- Lots of bug fixes

-------------------------------------------------------------------
 0.5.1, 1998-06-04
-------------------------------------------------------------------
- src/kernel/format-mexpr.lisp:
  Bug fixed when formatting :cond
- src/kernel/roots-mixins.lisp:
  Real and integer parameters are no longer indexed within indexed
  modules

-------------------------------------------------------------------
 0.5.2, 1998-06-16
-------------------------------------------------------------------
- src/kernel/cg.lisp:
  format-cg-commands improved
- src/kernel/browser-interface.lisp
  src/kernel/mdl.lisp
  src/kernel/utilities.lisp
  src/graphics/browser.lisp
  src/graphics/editor.lisp
  src/graphics/mdl-command-viewer.lisp
  src/graphics/mdl-command-emacs.lisp:
  MDL commands are formatted in a pretty way for output to command viewer,
  EMACS or file
- src/kernel/mdl.lisp: interprete
  Mixins of FDL part slot are now sorted alphabetically to avoid
  circular class precedence lists
- src/kernel/optimize.lisp: NEW
  - Substitute variables rather than generating coupling equations
  - Substitution of state variables in mexpressions of help variables does
    not work in general, because of wrong pattern initialization.
    e.g., pattern is out of bounds in ba-process.cg

-------------------------------------------------------------------
 0.5.3
-------------------------------------------------------------------
- src/kernel/cg.lisp:
  bug fixed in format-cg-cmd-obj for process-values

-------------------------------------------------------------------
 0.5.4, 1998-09-25
-------------------------------------------------------------------
- Version as of SFB-412 evaluation - report for funding period 1996-1998
- Presentation of kb/hafke/obertopp and kb/distillation (tmm-process, ba-process)
- src/kernel/utilities.lisp:
  print-class-tree writes class tree to stdout
- src/kernel/editor-interface.lisp:
  set-diva-file-names modifies the keywords
  :diva-cg-file-name, :diva-fortran-files-subname, :diva-data-file-name
  and :diva-latex-file-name of a module;
  write-diva-files writes CG files and calls the CG
- src/kernel/mdl.lisp:
  The keywords :diva-cg-file-name, :diva-fortran-files-subname,
  :diva-data-file-name and :diva-latex-file-name have been added to
  define-module
- src/kernel/roots-mixins.lisp:
  The slots for :diva-cg-file-name, :diva-fortran-files-subname,
  :diva-data-file-name and :diva-latex-file-name have been added to
  promot-class-mixin;
  modified method cg-filename to determine the default CG filename of a module
- src/graphics/*.lisp:
  Model output to DIVA added  

-------------------------------------------------------------------
 0.5.5, 1998-11-03
-------------------------------------------------------------------
- src/graphics/editor.lisp, model-editor.lisp: added output to EPS file
- Help variables are no longer written as indexed CG-help variables in the
  case of indexed modules. They are rather multiply assigned in equation
  loops.
- Support of ACL 5.0 added
  src/kernel/error.lisp and src/kernel/mdl.lisp: without-package-locks
  added because of use of symbols class and type
- Bug fixed in src/kernel/roots-mixins.lisp: path-indices
  Do not generate indices in model name if
  a variable (strong part of a module)
  has been propagated to an indexed terminal. 
  
-------------------------------------------------------------------
 0.5.5.0
-------------------------------------------------------------------
- Inserted a branch into CVS to keep a clean working version
  This should be a mostly bugfree release, without new errors from
  the new GUI development.


-------------------------------------------------------------------
 0.5.6, 1999-01-07
-------------------------------------------------------------------
- Development release
- src/kernel/mdl2diva reports errors correctly
- src/kernel/optimize.lisp does the job of optimizing linked 
  state-variables to help-variables in most cases. For safety reasons 
  it is optional to do this
- The project for the GUI in Java/JFC with connection via ILU has 
  been started

-------------------------------------------------------------------
 0.6.0, 2000-06-20
-------------------------------------------------------------------
- The optimizer is broken due to new structures in the kernel
- errors.lisp has been renamed into conditions.lisp because
  we use conditions now for error reporting
- The principle of using FDL has changed. ProMoT implements now it's 
  own superclasses. this should be extended for the interactive
  editing of classes without using MDL.
- The Java GUI has now almost the same functionality as the Clim one
- Clim is still possible but I will stop the development on it
- Images and scripting is now written to run almost automatical

-------------------------------------------------------------------
 0.6.0.0
-------------------------------------------------------------------
- New stable version instead of version 0.5.5
- Optimizer is ok now
- Emacs and Java should work together through the old interface
- Still some bugs in the GUI

-------------------------------------------------------------------
 0.7.0, 2004-11-09
-------------------------------------------------------------------
- No detailed information

-------------------------------------------------------------------
 0.7.1, 2005-05-12
-------------------------------------------------------------------
- No detailed information

-------------------------------------------------------------------
 0.7.2, 2006-08-16
-------------------------------------------------------------------
- Stable version with new features
- SBML support matures
- Diana output is fully functional
- Support for structural models
- Visual exploration of models
- Graphical editing of variable values

-------------------------------------------------------------------
 0.8.0, 2008-02-22
-------------------------------------------------------------------
- Many extensions in the GUI
- Undo for many commands
- Automated layout and model documentation
- Automated consistency checking

-------------------------------------------------------------------
 0.8.1, 2008-08-15
------------------------------------------------------------------- 
- Import of CNA (CellNetAnalyzer) models
- Bug fixes in generation of HTML documentation
- (Partial) bug fix for renaming of connected slots 
  (see BUGS.txt for limitations)
- Modularization support in visual editing
- Bug fixes in the variable editor
- Support for import and export of layout information in the 
  Visual Explorer
- Windows version (since September 2008)

-------------------------------------------------------------------
 0.8.2, 2009-08-17, r8738
------------------------------------------------------------------- 
- Priorities on check results of checker
- Distinguishing between errors and warnings in checker
- Some on-the-fly-checks for dynamic modeling
- Copy/paste support in editor
- De-modularization support (elevation of a modules content to current level)
  variables and equations (math), places and transitions (events) not elevated
- Flipping of nodes in editor for logical models
- Refresh-action in editor
- Status bar in editor showing status of the editor and checker
- Initial support for synthetic biology by scripts generating mdl
- Property to mark exportable models
- Setting modules to be ignored in export (logical modeling)
- Variable for map-number and monotony in logical library and editable in the GUI
- Check of corresponding equation-system for a module, visualization of 
  under- and/or overdetermined parts in incidence matrix or visual editor
- Improved visual scenario editor in explorer
- Improved support for workflow CellNetAnalyzer
- Warning for unsaved changes on exit
- Command for creation of new models
- Reduced clutter in menus and toolbars
- Dialogs and control panels reworked for clarity and utility
- New ProMoT logo
- Documentation updates 

-------------------------------------------------------------------
 0.8.3, 2010-08-31, linux: r9285, win: r9303 
------------------------------------------------------------------- 
New Features
- Option for direct loading of libraries for logical and dynamic modeling
- Start simulation with Diana from ProMoT GUI
- Parametrize model with Diana
- Comparison of models and visualization of comparison results
- Layout algorithm to visually flatten the model in Visual Explorer
- Logical model of EGF receptor signaling added to knowledge base

Improvements
- Update libraries for logical and dynamic modeling (directions, SBO terms) 
- Scripts for conversion of models to updated libraries
- Refactoring of rename of terminals in Visual Editor 
- Recalculation of terminal positions after changing canvas size in Visual Editor
- Create links of submodules automatically by names in Visual Editor
- Set the map number to a selection of nodes (only logical modeling)
- Warning of redefinition of classes 
- Import/export of node/edge attribute files in Visual Explorer
- Hierarchy Zoom for edges, Zoom along edge
- FishEye Zoom considers edge handle points
- Flexible handling of visibility of node/edge labels in Visual Explorer
- Extend node size to label text in Visual Explorer 
- Improved scenario 'Logical Network' 
- Visualization of submodules with/without terminals 
- Export network to yEd format 
- Improved exception handling in ProMoT
- Documentation updates

Bugfixes
- SBML import/export (import events, reversible flag, compartment handling)
- Stability issues of Visual Explorer
- Correct rendering of edge arrows in Visual Explorer 
- Update view after attribute file is imported in Visual Explorer

-------------------------------------------------------------------
 0.8.4, 2011-08-21, r9456
-------------------------------------------------------------------
New Features
- Support of ACL 8.2 added
- New global scenario 'Hierarchical Level' for visualization

Improvements
- New build procedure and ProMoT is now installed under \usr\local\promot 
  instead of \usr\local\diana\promot
- Update Piccolo2d to version 1.3.1
- Documentation updates
- Extend model statistics report in explorer: 
  Edges with TimeScale > 1, Edges with LogicalExcluded = 1
- reduced-library.mdl: special concentration module with 
  additional variable (conc-sink-var) 

Bugfixes
- Corrected paths of some mdl files in the knowledge base
- Corrected 'Create link' dialog 
  (automatic connection of terminals on submodules)

-------------------------------------------------------------------
 0.8.5, 2012-09-21, r9659
-------------------------------------------------------------------
New Features
- Support of ACL 9.0 added
- Support of the Process-Interaction-Model concept 
  by the Process-Interaction-Library and model specialized model
  converters (export of rule-based models in BNGL from a PIM, 
  conversion of PIMs to site-specific logical models)
  documented in a new tutorial
- Extended Visual Scenarios: add options for handling layout and
  exploration schemes 
- Visual Explorer: new option for exporting the complete network map
  when only a small portion is displayed 

Improvements
- Menu item, tooltips and shortcuts are added and more consistent

Bugfixes
- Option 'Edit Scripts...' now runs also on Windows without errors