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# ChangeLog

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## Unreleased

### GUI
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  * Introduced an Interactive Configurable Model Graph
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  * Support Tagging, Filtering and Sorting of Model Components
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  * Switched to Qt5
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  * Support reading and writing (gz) compressed models
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### MorpheusML
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  * The space symbol (Space/SpaceSymbol) now always provides the location in orthogonal coordinates, also on hexagonal lattices.
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  * AddCell accepts Count instead of Condition as the number of cells to be placed.
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  * ClusterTracker can cluster cells of multiple cell types.
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  * Logger
    * gained support for conditional logging using Logger/Restrictions/@condition
    * learned to use discrete colors for integer data
  * Gnuplotter
    * allows to set a z-slice per Plot and also Arrows and Labels follow the z-slize filter.
    * cell opacity moved to Plot/Cells/@opacity
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  * Added Populations InitVectorProperty with optional spherical notation
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  * Lattice size now can also be specified through expressions
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  * Contact energies now support expressions with access to symbols of involved cells
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  * Rework of XSD specifcation
    * XSD parser supports extension of complexTypes
    * Plugins are extension of base types
    * Registration of plugins as members of <xs:all> groups
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  * Added **@tags** and **Annotation** nodes to all model components
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### Simulator
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  * Performance improvements for Mappers and Reporters using OpenMP parallelization
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  * Support reading (gz) compressed models
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  * Added Test system for full XML models
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  * Restructured CMake build to make use of targets and boosted requrements to cmake>=3.3.0
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### Bug Fixes
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  * Fix cell property initialization override priority (InitProperty takes highest priority)
  * Fixed diffusion scaling on hexagonal lattices (was raised by factor 0.5)
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## Release 2.1.1

### Bug fixes
  * Fix a rare crash upon ChangeCellType 
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  * Fix reading numeric html encoded utf8 characters
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## Release 2.1

### GUI
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  * Reworked DelayProperty/Variable that allows varying delay times and history initialisation from expression
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  * Largely improve SBML import
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     * Provide more import target options
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     * Add support for multiple compartments and variable size compartments
     * Support delays by via DelayProperties
     * Support Events with delays
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     * Support HMC (comp)
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  * Fix MacOS crash on double-clicking symbol list
  * Fix Windows SBML support (suitible library build)
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  * Fix Windows Job removal to also remove all related files
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### MorpheusML
  * Expose local symbols to the input of the Neighborhood(Vector)Reporter
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  * Allow constant expressions in time-step specifications
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  * MorpheusML version bump 4.0

### Simulator
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  * Add adaptive step size ODE solvers: adaptive45 (Dormand-Prince), adaptive45_ck (Cash-Karp), adaptive_23 (Bogacki-Shampine)
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  * Renewed implementation of Poissonian Disc Population Initializer
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  * Command line option for setting the output directory added
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  * Fix rare misplacement in box object initializer
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  * Reduce memory footprint
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## Patch 2.0.1
  * Fixed VectorRules not working
  * Fixed broken image table for parameter sweeps

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## Release 2.0
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### MorpheusML
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  * The generalized **Mapper** now takes care to map information between spatial contexts, replaces the CellReporter
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  * The **Function** plugin now supports parametric functions and function overloading.
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  * The new **External** plugin allows to run external code during analysis steps
  * The new **ContactLogger** tracks cell contacts over time
  * The value of a **Constant** can be provided via expression
  * The new **VectorField** can represent spatial vector data
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  * Multiple **Population** per CellType are now supported
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  * **GnuPlotter** layout adjustments to efficiently support large lattices
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  * Binary **VTK** export (performance)
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  * Full support for **snapshotting** simulation states
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  * Removed any remains of time / space units

### GUI
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  * Largely improved inApp documentation
  * Adaptive multiline editor panel for expressions in attributes
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  * Reenabled SBML import
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  * Allow Copy/Paste & Drag/Drop of external XML model snippets 
  * Optionally preset random seeds for parameter sweeps
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### Simulator
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  * Many fixes to cell population initializers
  * **Symbolic Linking** infrastructure rewritten to enable extensibility
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  * Scheduling fixes for **DelayProperties**
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  * **Gnuplotter** and **Logger** now deal better with sub and superscript in symbol names or descriptions
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  * **Field boundaries** can be expressions
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  * Added **GoogleTest** as testing framework
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  * Performance improvements, i.e.
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    * Added dynamic EdgeTracker defragmentation
    * Parallelized diffusion in domain Fields
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    * Precalculating constant expressions at initialisation
    * ...
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### others
  * Tons of compiler compatibility fixes
  * Doxygen issue workarounds
  
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## 1.9.3 
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  * Initial import