Skip to content

Rules upgrade and extensions #370

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 30 commits into
base: development
Choose a base branch
from

Conversation

drbergman
Copy link
Collaborator

See README.md

Waiting on reviews before rebase and resolve merge conflicts.

drbergman added 29 commits April 1, 2024 14:52
Can use an xml to specify rules, improving on the previous csv format.
set names as attributes to make elements searchable without needing to step into them
As upregulation is applied first, it makes absolutely no sense to allow rules to have a max value equal to the base value (it's just wasting our time).
However, downregulation being applied second could make sense for it to equal the base value, having the effect of pulling back down an upregulation event.

This could mean that min values can be omitted and replaced with the base value. But for simplicity, I will keep requiring min values be explicitly supplied when decreasing signals are present.
- about midway between 1.14.0 and 1.14.1
- need to go back and decide how to handle the "old" rules
- right now, just ignoring them (and breaking old projects in the process)
- also some cleaning
- make sure to look at previous commit for notes
- only need a signal reference for AbstractHill signals
- make these fall into new class RelativeSignals
- others fall into AbsoluteSignals
- example showing off many of these new rules
- these allow for memory-ful behaviors where signals lead to either accumulation or attenuation of the behavior over time
- basically, if a behavior is ruled, then they it can either be set, accumulated, or attenuated
- set is the default behavior and what has happened before
- accumulation and attenuation will move away from the base behavior if they process a positive signal
- otherwise they relax to the base
- the top-level signal for these behaviors are still mediators
- but now the mediator sets the rate of accumulation or attenuation
- a positive rate means the behavior is moving away from the base
- a negative rate means the behavior is relaxing to the base
- users will likely want the base behavior to be negative so that in the absence of increasing signals the behavior will relax to the base
@drbergman drbergman requested a review from Copilot April 16, 2025 16:34
Copy link

@Copilot Copilot AI left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Copilot reviewed 57 out of 66 changed files in this pull request and generated 3 comments.

Files not reviewed (9)
  • Makefile: Language not supported
  • sample_projects/Makefile-default: Language not supported
  • sample_projects/asymmetric_division/Makefile: Language not supported
  • sample_projects/biorobots/Makefile: Language not supported
  • sample_projects/cancer_biorobots/Makefile: Language not supported
  • sample_projects/cancer_immune/Makefile: Language not supported
  • sample_projects/celltypes3/Makefile: Language not supported
  • sample_projects/custom_division/Makefile: Language not supported
  • sample_projects/heterogeneity/Makefile: Language not supported

- more informative error on bad mediator vals
- readme udpate
@drbergman drbergman self-assigned this May 22, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant