Changelog

v3.3.0 - 2024-12-16

Compare with v3.2.0

Features

• Add getString method to Parameters class by @Jannetty in #115
• Update minibox filter function to support multiple tag separators by @Jannetty in #112

Features: patch

• Implement cell cycle length tracking by @pohaoc2 in #97
• Add apoptosis age to induce change to apoptotic state by @cainja in #114

Features: potts

• Add rotateVectorAroundAxis function to Plane class with tests by @Jannetty in #117

Documentation

• Add publication abstracts to docs by @jessicasyu in #118
• Add emulation paper to publications by @cainja in #124
• Add setup file documentation by @jessicasyu in #119

Admin

• Bump action versions and update docs workflow trigger by @jessicasyu in #129

v3.2.0 - 2024-11-18

Compare with v3.1.4

Features

• Update cell make method to return container by @jessicasyu in #74
• Update cell constructors to use container by @jessicasyu in #75
• Add support for linked populations in setup file by @jessicasyu in #76
• Add support for parameter distributions by @jessicasyu in #85

Features: patch

• Add support for initialization by percentage by @jessicasyu in #53
• Add patch cell agent with random state rules by @jessicasyu in #56
• Add support for different patch initialization schemes by @jessicasyu in #81
• Pass initial glucose concentration as parameter for metabolism modules by @allison-li-1016 in #96

Features: potts

• Added class key for potts populations by @Jannetty in #11
• Make necessary PottsCell fields public, prepare for abstract setModule() function by @Jannetty in #12
• Convert PottsCell to abstract class by @Jannetty in #13
• Add support for splits with offset, direction, and split probability by @Jannetty in #16
• Add custom plane splitvoxels by @Jannetty in #46
• Refactor plane constructor to take Double3D instead of Int3D by @Jannetty in #83

Bug fixes

• Remove apoptosis checkpoint for potts cells by @jessicasyu in #18
• Replace instance of wildcard import of Module to prevent clash in Java 9 by @cainja in #65
• Fix passing in initial glucose as a parameter value by @allison-li-1016 in #99

Tests

• Remove unnecessary mocking in potts cell stem tests by @jessicasyu in #57
• Unit tests for core utilities Colors class by @cainja in #63
• Adding tests for core utilities Solver class by @cainja in #69
• Improved tests for core utilities Color class by @cainja in #73
• Adding tests for core utilities Graph class by @cainja in #64
• Adding tests for core utilities Parameter class by @cainja in #71

Admin

• Update workflows conditions for main and develop branches by @jessicasyu in #10
• Change source compatibility from 1.8 to 1.11 by @jessicasyu in #66
• Migrate to JUnit 5 by @jessicasyu in #67
• Add spotless autoformatter by @jessicasyu in #68
• Update workflows for changelog releases and Jekyll docs by @jessicasyu in #100

v3.1.4 - 2024-02-26

Compare with v3.1.3

v3.1.3 - 2024-02-05

Compare with v3.1.2

Features

• Add version to output files by @jessicasyu in #7

Bug fixes

• Swap voxel update order by @jessicasyu in #8

v3.1.2 - 2023-11-14

Compare with v3.1.1

Features

• Convert core enums to use interfaces by @jessicasyu in #3
• Update minibox to load simple fractions by @jessicasyu in #5

Bug fixes

• Update size checkpoints in potts modules by @jessicasyu in #2

Tests

• Update region adhesion unit tests by @jessicasyu in #6

Admin

• Update version handling in gradle build by @jessicasyu in #4

v3.1.1 - 2023-10-03

Compare with v3.1.0

v3.1.0 - 2023-03-01

Compare with v3.0.1

v3.0.1 - 2023-10-03

Compare with v3.0.0

v3.0.0 - 2023-01-31

Compare with v2.4