Add basic output formatting #405
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* 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]>
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Squashed and merged myself, as @fivegrant approved. |
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* remove all files except interfaces and integration demo * remove tests * minor refactor of dependencies and added lint * added back in github workflows * add quote around 3.10 * added makefile for offline lint testing * ran make format * removed Ensemble * added types for interfaces, and deleted ODE implementations * lint * fixed makefile for tests * get test_modules_import working * lint * remove src from directory * remove stale notebooks * remove src from lint scripts * modify setup.cfg * added pytest cov * remove .gitignore in notebook * remove stale INSTALL.md * remove pytest-cov * rename test to tests * update scripts with new tests filepath * fix Makefile to point to correct tests * AMR and MIRA integration with Chirho (#398) * 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 * `simulate` TA4 interface (#399) * 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 * remove placeholder parameters (#403) * Support for regulatory networks (#404) * 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 (#407) * 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]> * Add basic output formatting (#405) * 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]> * `calibrate` TA4 interface (#401) * 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 * Basic functionality for sampling from an ensemble of dynamical systems models (#411) * first pass at ensemble * revision to tests * added ensemble sampling interface and tests * lint nit * register nit * added documentation? * line length * lint * Update test fixtures to include new gold-standard AMRs (#415) * scaled noise according to size of state variable * update AMRs * add back regnet and stockflow * trivial change to trigger CI build * Add basic integration notebook and CI for testing notebooks (#416) * add basic notebook and nbval test * nbval CI * make ensemble a module * changed imports in CI builds and added imports throughout * reran interfaces * lint * Add observables to sample output (#412) * 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 (#419) * 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 * Bump ChiRho version in dependencies and update any changes resulting 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]> * scale back tests (#427) * Parameter Intervention (#424) * 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 * Adding regnet urls to fixtures, and limiting number of examples to three 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]> * Add parameter interventions to calibrate and refactor interface tests (#429) * Added parameter interventions to calibrate * refactored calibrate tests * refactor observables * fix bug in test * ignore test with underflow * made interventions a bit lighter * Add datafile input for `calibrate` (#432) * add data loading utilities * added data loading utilities to calibrate interface * updated tests with new data loading utilities * lint * bump pyciemss version (#433) * bump pyciemss version * remove stale setup config --------- Co-authored-by: Five Grant <[email protected]> Co-authored-by: sabinala <[email protected]>
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This PR adds basic output formatting to match the previous interface for TA4 integration.