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@Jannetty Jannetty commented Oct 17, 2025

Estimated time to review: small

Brief justification of changes
We do not have good experimental data to inform the parameters defining time spent in each phase of the cell cycle for the fly cell agents. We therefore want to remove the phases of the cell cycle from the "proliferation" (in this case differentiation) modules of the fly cells. This pull request removes progression through the cell cycle from the GMC differentiation module.

Summary of changes

  • unrelated change to vector getters to make mocking vector getter behavior easier in tests
  • Changed PottsModuleGMCDifferentiation to extend PottsModule instead of PottsModuleProliferationSimple
  • added necessary fields to PottsModuleGMCDifferentiation that used to be taken care of by the PottsModuleProliferationSimple constructor (cellGrowthRate and sizeTarget)
  • added PottsModuleGMCDifferentiation tests to make sure addCell is called correctly in step

@Jannetty Jannetty self-assigned this Oct 17, 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: small Estimated size of issue or PR is small labels Oct 17, 2025
@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 17, 2025 19:16
@Jannetty Jannetty marked this pull request as ready for review October 17, 2025 19:23
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@cainja I actually think I'm going to change the way I have done this. Because both the GMCs and the Stem cells will need to have "proliferation" modules that do not step through the cell cycle, I think I want to make a different proliferation abstract class that mimics the patch proliferation module in that it does not have explicit progression through each phase of the cell cycle. Then both the GMCs and Stem cells can implement that abstract class.

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Closing because #199 addresses this issue in a different more scalable way

@Jannetty Jannetty closed this Oct 20, 2025
@Jannetty Jannetty deleted the jannetty/update-flygmc-module branch October 21, 2025 00:18
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category: agent Related to the agent subpackages package: potts Related to the potts implementation size: small Estimated size of issue or PR is small type: feature Improvement or additions to the code base

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