Release Notes – Magnolia

Bug Fixes and Improvements

Complete redesign of code editor: editor now supports find/replace, code folding, and code completion
Many improvements to plotting from Python scripts
Inclusion of additional probability distributions in MCMC engine
Fixed: Application performance problems on Windows
Fixed: Examples not correctly installed on Windows
Fixed: An error should be reported when ODE solver fails
Fixed: MCMC plots fail is start row > actual sample count
Fixed: Negative values not supported in args to distributions in MCMC file
Fixed: When the CSL file for a model is closed, it’s entry should be removed from list ini model inspector
Fixed: Parser fails if comment follows line continuation character
Fixed: The “save” menu/toolbar option should do nothing when a plot is the active document
Fixed: “Find” function in code editor fails sporadically
Fixed: Using sliders, it’s possible to start another simulation before previous one has finished
Fixed: Inclusion of an integer variable in model causes the variable to be plotted at end of run
Fixed: Sorting on parameter slider panel causes problems
Fixed: Numeric literals are assumed to be floating point, even when they shouldn’t

Known Bugs/Limitations

Documentation for features newly added as of this release is incomplete.
MCMC sampler is not fully optimized for hierarchical models; this will be fixed in the release version.
IMPLC operator not supported
DELAY operator not supported
Submodel variables/constants not usable from interactive plots; workaround: mirror submodes variables/constant in main MODEL section (see Control Loop example)
Submodel variables/constants not usable from CMD scripts
TABLEs with dimension higher than one are not supported
Extra entries in file history are created every time a Python script is executed

Bug Fixes and Improvements

Added capability for interactive debugging of models: step by time or derivative calculation, break on variable values, monitor evolution of model variables.
Local file version histories are now maintained. Press the “clock” icon on a code editor toolbar to view the local history of the associated file. Review file changes at each save, revert to previous versions.
Initial experimental implementation of MCMC sampling. A specialized language has been developed for the specification of statistical models; see the butadiene example in the Language/Parameter Estimation folder for an example. Plots have been added to quickly view sample chains and histograms of posterior marginal distributions.
Last active folder in the file browser panel and any open documents are remembered and preserved between sessions in Magnolia.

Known Bugs/Limitations

Documentation for features newly added as of this release is incomplete.
MCMC only provides uniform, normal and lognormal distributions in this version; additional distributions will be provided in the release version. MCMC sampler is not fully optimized for hierarchical models; this will be fixed in the release version.
IMPLC operator not supported
DELAY operator not supported
Submodel variables/constants not usable from interactive plots; workaround: mirror submodes variables/constant in main MODEL section (see Control Loop example)
Submodel variables/constants not usable from CMD scripts
TABLEs with dimension higher than one are not supported
“Replace” option not available in code editors
“Comment” and “indent” selected section operators don’t work in Python and CMD code

Bug Fixes and Improvements

Initial version of documentation completed
Context menus added to code editors, command output window and command input prompt
prepare @all no longer attempts to prepare non-numeric fields
Fixed: print command was generating incorrect results
Fixed: lower limit on y axis was not being honored with log axis scaling
Setting of logical and string values in model from CMD file code now working
Warning added if dataset name starts with numeric; dataset names which don’t adhere to CSL variable naming conventions can be wrapped in single-quotes
Various additions and improvements to example models
Reliability of main menu stop button improved

Known Bugs/Limitations

IMPLC operator not supported
DELAY operator not supported
Submodel variables/constants not usable from interactive plots; workaround: mirror submodes variables/constant in main MODEL section (see Control Loop example)
Submodel variables/constants not usable from CMD scripts
TABLEs with dimension higher than one are not supported
“Replace” option not available in code editors
“Comment” and “indent” selected section operators don’t work in Python and CMD code

Bug Fixes and Improvements

Fixed: was unable to save example models on Windows, depending on installation folder
Plot export (data, image) is now working
Plot settings are now immediately saved when the plot settings dialog “apply” button is pressed
“About” menu option now displays an “About Magnolia” screen
Fixed: plot settings could become corrupted if variables/constants were removed from model
Plot settings dialog now issues error when min axis range value is greater than max axis range
Initial limits on slider are now correct when default value of parameter is less than zero
Plot axis autoscale settings were not persisted with other pot settings
Magnolia logo is now used for application icon on Windows

Known Bugs/Limitations

Incomplete documentation
IMPLC operator not supported
DELAY operator not supported
Submodel variables/constants not usable from interactive plots; workaround: mirror submodes variables/constant in main MODEL section (see Control Loop example)
Submodel variables/constants not usable from CMD scripts
TABLEs with dimension higher than one are not supported
“Stop” toolbar button not working reliably

Bug Fixes and Improvements

Known Bugs/Limitations

“About” menu option on main menu does nothing
Incomplete documentation
IMPLC operator not supported
DELAY operator not supported
Submodel variables/constants not usable from interactive plots; workaround: mirror submodes variables/constant in main MODEL section (see Control Loop example)
TABLEs with dimension higher than one are not supported
Export of plot data not supported
“Stop” toolbar button not working reliably

Note: this is the first version for which Release Notes have been provided.

Known Bugs/Limitations

Incomplete documentation
IMPLC operator not supported
DELAY operator not supported
Occasional crashes during translation of models with SUBMODEL sections
Submodel variables/constants not usable from interactive plots; workaround: mirror submodes variables/constant in main MODEL section (see Control Loop example)
TABLEs with dimension higher than one are not supported
Export of plot data not supported
“Save as…” not working for all file types
“Stop” toolbar button not working reliably