Refactor PyCIEMSS to use ChiRho and remove stale functionality #396
Conversation
This file contains 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
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
This was referenced Oct 26, 2023
* added scaffolding for ODE * tidying and linting * get modules importing and update mira * got initial state working * revise tests and lint * manually added torchdiffeq to requirements * revert debugging * remove empty interfaces * minor refactor * minor refactor * moved compile_deriv and compile_initial_state into init method for other factory methods to have access to. also removed eval_rate_law, because that might be confusing if users change it and it does nothing * typo
* progress towards TA4 interfaces * minor tidying, still incomplete * more tidying * remove attempt at pickling, and added intervention test * dynamic intervention tests working * got predictive working * added additional test * update types * update types * fix upstream time collisions in ChiRho (#400) * rename simulate to sample * add pyciemss_logging_wrapper and documentation * revise tests
* add support for regnet now that mira has been fixed * lint * uncomment other mistakenly commented tests * swap out dict access for explicit iteration * lint
* Remove package finding AND add to module exports * Clear out top-level `__init__.py` * Reinclude explicit exports * Include subpackages * Skip incorrect lint error * reorder imports for lint * revert previous commit and add missing space before noqa --------- Co-authored-by: Sam Witty <[email protected]>
* initial pass at output processing * lint * add pandas and numpy dependencies * remove outdated docstring * Remove package finding AND add to module exports (#407) (#409) * Remove package finding AND add to module exports * Clear out top-level `__init__.py` * Reinclude explicit exports * Include subpackages * Skip incorrect lint error * reorder imports for lint * revert previous commit and add missing space before noqa --------- Co-authored-by: Five Grant <[email protected]> --------- Co-authored-by: Five Grant <[email protected]>
* progress towards TA4 interfaces * minor tidying, still incomplete * more tidying * remove attempt at pickling, and added intervention test * dynamic intervention tests working * got predictive working * added additional test * update types * update types * fix upstream time collisions in ChiRho (#400) * early progress on calibration * added noise model * minor change to sampling interface * more progress * lint * lint * more merge fixes * add back petri models * temporary test fixtures while waiting on PRs to land * make * update tests and lint * lint * got calibrate working * move start_time to kwarg * added test of simulating from deterministic parameters * lint * add documentation * update fixtures to include permalink to models * remove aggregate parameters
…s models (#411) * first pass at ensemble * revision to tests * added ensemble sampling interface and tests * lint nit * register nit * added documentation? * line length * lint
* scaled noise according to size of state variable * update AMRs * add back regnet and stockflow * trivial change to trigger CI build
* add basic notebook and nbval test * nbval CI * make ensemble a module * changed imports in CI builds and added imports throughout * reran interfaces * lint
* first pass at observables * lint * fix result processing * add correction with empty observables * minor fix to name * nitpick on name * retrigger checks
* updating urls for petri and stock flow example amrs * Shortening url lengths to address linting issue * Fixing urls for linting issue * Changing AMR url in interfaces notebook * Updating model_2_path to correct url
…from API changes (#422) * bumped chirho version * pull out solver * removed IEL and pulled out solver * revised tests * reverted fixtures chagne * lint * nit * updated compiled dynamics * updated tests * lint * nit * revert changes to fixtures * updating urls for petri and stock flow example amrs (#419) (#423) * updating urls for petri and stock flow example amrs * Shortening url lengths to address linting issue * Fixing urls for linting issue * Changing AMR url in interfaces notebook * Updating model_2_path to correct url Co-authored-by: sabinala <[email protected]> * reverted changes to types * lint --------- Co-authored-by: sabinala <[email protected]>
* added separate persistent params to make bookkeeping interventions more reliable * implemented parameter intervention * added tests with annotation of important paramaters * lint * added dynamic interventions on parameters (#425) * lint and doc * Add interfaces and refactor tests (#426) * added interfaces and refactored interruptions * refactor and add to tests * scale back tests (#427) * easier tests
…ree per type (#428) * Update fixtures.py to include regnets and three examples per type * Update fixtures.py * lint --------- Co-authored-by: Sam Witty <[email protected]>
…#429) * Added parameter interventions to calibrate * refactored calibrate tests * refactor observables * fix bug in test * ignore test with underflow * made interventions a bit lighter
* bump pyciemss version * remove stale setup config
SamWitty
added
awaiting review
djinnome
reviewed
Dec 18, 2023
There was a problem hiding this comment.
I think we want to keep the functionality to calibrate CDC format data
djinnome
reviewed
Dec 18, 2023
There was a problem hiding this comment.
I think we want this functionality demonstrated in a notebook
djinnome
reviewed
Dec 18, 2023
There was a problem hiding this comment.
OUU code is coming back in after the merge to main
djinnome
reviewed
Dec 18, 2023
There was a problem hiding this comment.
Visuals coming back in after merge to main
djinnome
approved these changes
Dec 18, 2023
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.
This large refactoring PR separates out the core dynamical systems functionality (which is now supported entirely by the ChiRho dynamical systems module) from the ASKEM-specific integration. For an in-depth discussion on the motivation behind this PR, see the DARPA ASKEM slack channel.