News

Added

• species diffusion constants to the parameters that can be fitted in parameter optimization #1092
• support for spatially varying diffusion constants #1093
• gridlines now align with pixels when zoomed in to geometry image #847

Fixed

• crash for some models with empty compartments when using DuneCopasi simulator #1089
• delay in UI responsiveness after simulation completion #1101

Removed

• macOS x86_64 (Intel) architecture binaries #1096
• Python 3.8 wheels #1093

Fixed

• crash for some models with empty compartments when using DuneCopasi simulator #1089

Added

• option to set the maximum number of CPU threads the DuneCopasi simulator can use #1082
• parameter fitting to CLI #1073
• clipping planes to 3d rendering of compartment geometry and concentrations in the GUI #972
• steady state solver in the GUI #1061

Fixed

• file dialogs not opening on macOS 15.4+ #1085

Added

• documentation for example models #1025
• linux aarch64 / arm64 binaries #1045
• NLP optimization algorithms #1053
• 3d mesh rendering of membranes between compartments #1054
• 3d visualization and 'difference' visualization in optimization #1057

Fixed

• crash on compartment re-assignment after color change #1038
• crash when meshing 3d geometries with different max cell volumes in different compartments #1055
• incorrect concentrations for 3d model simulations in python interface #1063

Added

• improved mesh visualizations #1021
• more 3d example models #1015
• more documentation #1020

Added

• Python 3.13 wheels #1002
• colors in the geometry image can now be changed #960
• voxels can be selected in the 3d rendering of the geometry image #979

Fixed

• parameter optimization error with 3d models #1007

Added

• support for using the DuneCopasi simulator with 3d models #937
• 3d volume rendering for voxel visualization #926
• visualization of 3d model geometry meshes #882
• import of geometry image files by drag and drop onto the GUI #933

Added

• support for dune-copasi 2 #908
• Python 3.12 wheels #897
• Apple Silicon wheels and binaries ssciwr/sme-osx-arm64

Added

• initial support for 3d spatial models #850
• support for anisotropic voxels #879

Changed

• disable OK button while selecting geometry image colors #878.
• image arrays in sme (Python interface) now include a z dimension #850

Fixed

• lack of geometry image could cause a crash in some cases #872

Added

• support for importing RGBA TIFF image files #862

Fixed

• incorrect function evaluations in some cases #855, #856, #857

Fixed

• incorrect initial concentrations with DUNE simulator for some models #852

Changed

• export format of Image Sampled Field from colors to indices #710 and #830.

Added

• support for importing Combine archives #828

Changed

• offer to use alternative simulator if simulation setup fails #814

Fixed

• crash caused by analytic initial species concentrations involving dividing by zero #805
• disappearing simulation progress bar dialog #752

Added

• parameter fitting functionality to GUI #757
• support for reading SBML files compressed with bzip2 #246

Changed

• GUI no longer writes logging output to console #771

Fixed

• analytic initial species concentrations were not updated when a parameter value was modified #776

Added

• support for reading compressed sampledFields #709

Changed

• TBB is now used everywhere for multithreading (previously linux Python wheels used OpenMP) #732

Fixed

• improved multi-threading performance #742
• spurious simulation times are no longer appended upon simulation #751

Added

• topology-preserving line simplification option #328
• python interface: ctrl+c now cancels a currently running simulation #665

Changed

• model reactions with invalid locations can now be seen and removed or relocated #615

Fixed

• functions with zero arguments are now fully supported #674
• python interface: setting n_threads=1 for simulate takes precedence over n_threads value in model #672
• bug where membrane reactions could disappear when geometry was changed #679
• bug where removing a compartment could result in an invalid model or a crash #685
• SBML export includes any ModifierSpecies in reactions #133

Removed

• incomplete Parametric geometry sbml export support #599

Added

• non-spatial model guided import with automatic reaction rate rescaling #607
• python interface: optional multithreading (via OpenMP) for Pixel simulations on linux #662

Fixed

• bug where loading a model with simulation data and changing model units could cause a crash #666
• show warning message before dune simulation of model with non-spatial species #664
• minimum supported version of MacOS is now 10.14 instead of 10.15 #669

Added

• python interface: access to all built-in example models #637
• python interface: view and edit uniform/analytic/image species initial concentrations #644

Changed

• compartment color assignments are now preserved when the geometry image is resized #587

Fixed

• python interface: bug where compartment geometry mask was not updated after geometry image changed #630
• slow loading of models with large geometry images #632
• avoid constructing mesh twice on model load #597
• crash when importing geometry image after importing non-spatial model #651

Added

• python interface: Model.simulation_results() provides access to existing model simulation data #622

Changed

• python interface: simulation results now provided in numpy.ndarray format #610

Fixed

• bug where opening a corrupted sme file caused a crash #618

Added

• python interface: add option to simulate without returning the results to reduce RAM usage #610
• more detailed error message when a model cannot be loaded #449

Fixed

• bug where invalid reaction rate expression caused simulation to crash #609

Added

• autocomplete when editing maths #559
• support for all L3 sbml math in reaction rates (with Pixel simulator) #569
• option to invert y-axis of images #568
• option to set size of geometry image in third dimension #582
• umol unit of amount added to built-in units #600

Changed

• simulation length/intervals only loaded from model on 'reset' click or new model load #565
• models exported as 3d SBML models (to be consistent with our 3d units for species concentrations and volumes) #588

Fixed

• bug when clicking on simulation results plot selected wrong timepoint #570
• reaction rates involving species from unrelated compartments now displays an error, instead of only giving an error on simulation #552
• simulation crash when species is changed to constant & simulation data are re-loaded #561
• inaccuracy when re-starting a simulation that was stopped early #388
• bug where compartment sizes were not updated when compartment image resolution was altered #583
• bug where invalid mesh could cause a crash #585
• bug where simulating after changing geometry image size could cause a crash #591
• incorrect units used for compartment volumes when referenced in reaction rates #584
• bug where membrane area could be incorrect on model load #595

Added

• COPASI cps file import support (if COPASI is installed and on path) #492
• shift + mouse scroll to zoom in and out of images #532
• support for spatial models with reactions whose compartment is not specified #481

Changed

• mouse scroll no longer changes species stoichiometry in reactions #549
• membrane reaction rates automatically rescaled by membrane area on non-spatial model import #557
• reactions moved between compartments and membranes rescaled by ratio of area to volume #558

Fixed

• bug loading simulation settings depending on system locale setting #535
• slow loading of simulation data #504
• bug where simulation doesn't run again after being stopped #545
• bug where selected reaction sometimes changes when reaction location is changed #548
• ensure species involved in a reaction are valid when reaction location is changed #551
• bug where loading existing simulation uses initial concentrations instead of latest simulation concentrations #541

Added

• sme file format, contains model, simulation settings and simulation results #482
• support multiple simulation lengths as comma delimited lists #464
• support for simulating models with empty compartments with the Dune-Copasi simulator #435
• option to resize the number of pixels in the geometry image #462
• option to reduce the number of colors in the geometry image #280
• support for non-integer stoichiometries in reactions #495
• optional grid and scale to geometry image #497
• python interface: DUNE simulator can now be used #276
• python interface: existing simulations can be continued #514
• zoom option to geometry image #516

Changed

• use v1.1.0 of Dune-Copasi simulator

Fixed

• python interface: revert change in default simulate() behaviour when doing a second simulation of a model #475
• multiple event related simulation bugs #484, #485, #486
• incorrect compartment name displayed in simulate display options #487
• simulation image intervals changing length of simulation #492
• bug where removing compartment could cause a crash #506
• artefacts in import of species concentrations into simulation #508
• DUNE maximum iteraction count simulation error #490

Added

• open/save as .sme filetype: contains both the model and the simulation results #461
• support for time-based events: parameters and species concentrations can be set at specified times in the simulation
• diagnostic info & image when a simulation fails #432
• zoom option for Boundary and Mesh images in the Geometry Tab
• new option in Simulation Tab to export concentrations to model as initial concentrations

Changed

• simulation is no longer reset when the Simulate tab is left in the GUI
• simulations can be continued using a different simulator
• use v1.0.0 of Dune-Copasi simulator
• GUI warns before closing a model with unsaved changes #346
• Membrane names can now be edited in the GUI and in the python interface

Fixed

• diffusion constant bug in the Pixel simulator #468
• bug in dune-copasi mesh generation that could cause a crash #434
• bug where unused diffusion constant parameter was sometimes not removed from sbml document
• data race in generating simulation concentration images #434

Removed

• incomplete Parametric geometry sbml import support #452

Added

• python library can now import a new geometry image using sme.Model.import_geometry_from_image()

Changed

• mesh generation is now done using the CGAL library

Removed

• dependence on Triangle mesh library removed due to its non-free license

Fixed

• illegal instruction crash on old CPUs #422

Added

• python library sme.Model.simulate:
  • simulation results now also contain rate of change of concentrations
  • option to return partial results instead of throwing on simulation timeout

Changed

• more accurate initial concentration interpolation for dune-copasi simulations
  • applies to both GUI simulations and exported TIFF files for stand-alone dune-copasi simulation
• improved performance of interior point determination in mesh construction

Fixed

• meshing bug where invalid 2-point boundary line could cause crash

Added

• user can edit dune-copasi Newton solver parameters
• Pixel simulator supports reactions that explicitly depend on t, x, y

Changed

• dune-copasi simulations now support membrane flux terms
  • rectangular membrane compartments no longer required
  • simpler mesh generation
  • faster and more accurate simulations
• improved boundary construction
  • use pixel edges as boundary edges instead of pixels
  • shared boundaries and their end points now unambiguously determined
• improved line simplification

Fixed

• bug in scaling of membrane reactions in Pixel simulations
  • added missing 1/a factor, where a is the width of a pixel in model units

Removed

• inconsistent RateRule support in SBML import

Added

• simulation display options are now saved

Changed

• python library API
  • lists now have name-based look-up, old name-based look-up functions removed
  • examples of old -> new change required in user code:
  • model.compartment("name") -> model.compartments["name"]
  • model.specie("name") -> model.species["name"]

Fixed

• species removal bug

Added

• python library example notebooks

Changed

• python library performance improvements

Fixed

• python library segfault / missing data issue on some linux platforms

Added

• python library documentation and example notebooks
• support for import of geometry image with alpha channel / transparency
• display compartment size and membrane length

Changed

• python library performance improvements

Fixed

• normalisation of simulation concentration images
• geometry imported from another model not saved bug
• python library segfault / missing data issue on linux
• reaction removal bug

Added

• membranes to python library
• compartment pixel mask to python library
• timeout parameter to simulate function in python library

Changelog format based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).