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Make default cell class behavior consistent between implementations #123

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jessicasyu opened this issue Nov 27, 2024 · 0 comments
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category: sim Related to the sim subpackages package: patch Related to the patch implementation 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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@jessicasyu
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If you do not define a population class in the setup file when running the patch implementation, you get an error because a default cell class is not defined. With potts, if a population class is not defined, the series instance will use a DEFAULT_CELL_CLASS instead:

public static final String DEFAULT_CELL_CLASS = "stem";

We should make the behavior consistent between the two implementations. Options:

  1. Update patch to support the DEFAULT_CELL_CLASS behavior (with the default class as tissue)
  2. Require that class is defined in the setup file and remove the DEFAULT_CELL_CLASS from potts

I think (1) would be the preferred option, but I could see (2) making setup files more clear and would work if we have the appropriate error message.

@jessicasyu jessicasyu added category: sim Related to the sim subpackages package: patch Related to the patch implementation 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 labels Nov 27, 2024
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Labels
category: sim Related to the sim subpackages package: patch Related to the patch implementation 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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