-
Notifications
You must be signed in to change notification settings - Fork 110
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
drbergman
wants to merge
30
commits into
MathCancer:development
Choose a base branch
from
drbergman:rules-upgrade
base: development
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
There was a problem hiding this 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
See README.md
Waiting on reviews before rebase and resolve merge conflicts.