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@Jannetty Jannetty commented Oct 20, 2025

Estimated time to review: medium, maybe medium long, its a lot of files but only because I changed the name of a class.

Summary of changes:

  • unrelated change to vector getters to make mocking easier
  • renamed PottsModuleProliferation to PottsModuleProliferationCellCycleProgression (I know that is very long I am happy to change it to something shorter but want to communicate that this proliferation module makes cells progress through the cell cycle)
  • defined new abstract class PottsModuleProliferationVolumeBasedDivision that does not make cells progress through the cell cycle. Division is entirely based on the cell's volume.
  • defined PottsModuleFlyGMCDifferentiation which extends PottsModuleProliferationVolumeBasedDivision and defines addCell so the module makes two neurons
  • broke tests from previous PottsModuleFlyGMCDifferentiation into test files for both PottsModuleFlyGMCDifferentiation and PottsModuleProliferationVolumeBasedDivision

@Jannetty Jannetty requested review from a team, allison-li-1016, cainja, daniellevahdat, jacob-evarts, jessicasyu, kristaphommatha and pohaoc2 and removed request for a team October 20, 2025 23:44
@Jannetty Jannetty self-assigned this Oct 20, 2025
@Jannetty Jannetty added type: feature Improvement or additions to the code base package: potts Related to the potts implementation category: agent Related to the agent subpackages size: medium Estimated size of issue or PR is medium labels Oct 20, 2025
@Jannetty Jannetty marked this pull request as ready for review October 20, 2025 23:45
@allison-li-1016
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allison-li-1016 commented Oct 21, 2025

Structurally it might make sense to still have a abstract PottsProliferationModule class that both the CellCycle and VolumeBased classes extends from instead of both of them extending from PottsModule directly since they're both still proliferation. The abstract class can just have step() and addCell() -- something to consider!

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category: agent Related to the agent subpackages package: potts Related to the potts implementation size: medium Estimated size of issue or PR is medium type: feature Improvement or additions to the code base

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