Skip to content

Latest commit

 

History

History
143 lines (109 loc) · 4.97 KB

release_notes_pre_2_9_5.md

File metadata and controls

143 lines (109 loc) · 4.97 KB

Release 2.9.4

  • reposition New,Copy,Delete buttons on Microenv and Cell Types tabs
  • better About info in Studio menu
  • this release doc; cleanup README
  • cleanup dirs to be less nanoHUB-template

Release 2.9.3

  • remove Rules for now
  • add voxel and mechanics grid toggles to 2D View
  • remove rules subtab code in Cell Types module

Release 2.9.2

  • logging for debugging (not just errors)
  • sanity checks for vis3D with existing output
  • fix crazy Config checkbox for csv (move to non-zeroth column)

Release 2.9.1

  • fix bugs related to not having ICs tab created in cell_def_tab.py (thanks Grant Maxey)
  • switch to pcolormesh instead of contourf for 2D substrates
  • View menu: allow Gouraud shading for pcolormesh
  • logging for debugging
  • full config path in title
  • plot legend if already exists in output dir
  • improved Rules tab: Load, Save, etc.

Release 2.9.0

  • fix bugs related to allowing for empty <custom_data> (thanks Issy Cowlishaw)
  • fix show voxels (for 3D)
  • vtk 3D viewer cmds
  • fix cmap and min,max (3D)
  • detect incomplete final .svg

Release 2.8.6

  • more cutting planes for 3D vis
  • option to plot all voxels in 3D vis
  • fix logic of Dirichlet boundaries toggles

Release 2.8.5

  • gracefully handle deprecated cycle "transition_rates" in config file
  • fix bug related to specified output dir in 3D vis
  • add some ABM benchmark data files

Release 2.8.4

  • awareness of where it's being run from and behaving appropriately
  • use latest pyMCDS.py
  • try to properly Cancel a Run (studio mode) on Windows
  • check for bogus colormap ranges
  • add couple checks for "old" config file syntax: missing virtual walls, missing death params

Release 2.8.3

  • fix undefined exec_file bug
  • add nuclei checkbox/plotting for 2D
  • various improvements to 3D plotting
  • have ICs tab plot reset to match config_tab domain
  • fix ICs bug for cells.csv for disk hex
  • populate_tree_cell_defs now updates various widget combobox entries
  • add a few config files and cells.csv for ABM benchmarks

Release 2.8.2

  • added command line arguments (see --help)
  • several improvements for 3D plotting (using VTK); still missing color-by-celltype
  • added some 3D models in /data

Release 2.8.1

  • ICs: Compute radius from celltype volume. Improve widgets layout.

Release 2.8.0

  • Provide a tab to create common setup_tissue patterns (cells.csv)

Release 2.7.9

  • bug fix for toggling Chemotaxis vs. Advanced Chemotaxis (Thanks Daniel Bergman!)

Release 2.7.8

  • update VERSION.txt

Release 2.7.7

  • Disable keyboard navigation through items in the QTreeWidget

Release 2.7.6

  • When we load a new model, part of the reset needs to reset cell_adhesion_affinity_celltype to None (thanks to Joel Eliason for catching and reporting this!)

Release 2.7.5

  • Fix bug on maintaining cell def state of mechanics cell adhesion affinity

Release 2.7.4

  • Provide at least minimal validation of the config file being loaded. It cannot use the legacy hierarchical syntax; it needs to provide explicit parameters for each <cell_definition>.

Release 2.7.3

  • When a cell type is deleted, also delete it in the dicts associated with mechanics:cell adhesion affinities and interactions:*

Release 2.7.2

  • Allow starting the PMB from anywhere

Release 2.7.1

  • fixes for the PhysiBoSS cell lines sample

Release 2.7.0

  • operate directly on a .xml file instead of a copy
  • provide a /data/backup to keep copies of original sample models

Release 2.6.0

Update of the PhysiBoSS intracellular interface.

Update of the XML structure:

  • Added dropdowns for signals, behaviours, and nodes in mapping
  • Automatic update of signals, behaviours according to
  • Automatic update of maboss model nodes according to BND file

Release 2.5.0

  • handle conserved attribute on custom data (if true, daughter cells split quantity evenly)
  • allow CSV vector of values for custom data; drop validation (of numeric value)
  • resolve headache of default dark-mode on macOS/arm64 (from conda install -c anaconda pyqt)

Release 2.4.1

  • check for 3D model: (zmax-zmin)>dz ; set <use_2D> accordingly
  • bug fixes for Studio modules

Release 2.4

  • mostly improvements related to the Studio version, e.g.
  • allow for Plotting from different output folders (rf. Config Basics)
  • Warn user if SVG and full output intervals do not match
  • Disable Run Simulation button when one starts
  • Stop a running simulation if a new model is selected from File menu
  • Provide a Legend tab to display the cell types' colors legend

Release 2.3.1

  • prevent Cell Types subtabs from scrolling away
  • update VERSION and README :/

Release 2.2.0

  • provide get_pgms.sh bash script to get sample executables
  • update pmb.py and run_tab.py to provide mostly-working Studio

Release 2.1.0

  • update data/interactions.xml to match PhysiCell v1.10
  • provide normalize_each_gradient in motility | advanced_chemotaxis

Release 2.0.0

This release captures most of the functionality provided in PhysiCell 1.10.0