Fix a minor bug in delay simulator #103
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…o inference-dev
…o inference-dev
…o inference-dev
…ameter inference packages
… support for least squares type parameter id. 3. Refactor inference example notebooks. 4. Added inference example notebooks.
WilliamIX
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Jun 17, 2021
ayush9pandey
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Oct 21, 2022
* Inference updates, new features, and bug fixes (#102) * add custom prior documenting notebook * gaussian prior fix * bug fixes for log uniform prior and pdf computation bound checks * option to set initial parameter seed. print convergence diagnostics * first cut at lmfit support for inference * renaming inference files and functions to be agnostic to external parameter inference packages * 1. inference.pyx bug with multiple measurements fixed. 2. Added LMFit support for least squares type parameter id. 3. Refactor inference example notebooks. 4. Added inference example notebooks. * first cut at delay support for inference * change convergence_diagnostics error to warning * fix tests * refactor inference examples * add inference test * add emcee version requirement for progress bar update * add requirement for scipy>1.6.4 and add lmfit * testing suite for inference * allow lower scipy versions * add empty line at end of test_inference * Rules and simulator upgrade (#106) * DeterministicDilutionSimulator, SafeModeSSASimulator, TimeDependentSSASimulator, and Core Lineage/Propogate Simulators deleted * Major Rule Update: ** Rules fire consistently, even when there are no reactions. ** New Rule types and firing frequencies, including specific times, every timestep, and every update. ** Tests of these new rule features * Recomputed all the frozen sim results: Why? Previously, delay reactions firing if no reactions could fire. Propensities are now recomputed ever dt, so the old results also are no longer valid. * SafeLineageCSimInterface created: this interface is analogous to the SafeModelCSimInterface and does some basic checking (and warning messages) at the expense of speed. * lineage notebooks cleanup: added turbidostat example for lineages, lineage examples split into two notebooks * Lineage fixes: Fixed an indexing bug, py_SimulateTurbidostat returns dataframes, and Turbidostat example plotting, improved py_SimulateTurbidostat wrapper Co-authored-by: William Poole <wpoole@caltech.edu> * Fix a minor bug in delay simulator (#103) * delay simulation bug fix * fix error from merge dev * Removing Bioscrape XML and adding SBML Functionality (#108) * Removed Bioscrape XML writing, bioscrape XML from the examples, and cell lineages from the advanced examples * remove propensity_annotation keyword, always write annotation to bioscrape exported SBML models * delay annotation working with propensity annotation * remove underscore shenanigans in rule writing * refactor import sbml * add rule annotation. add rule testing with annotation * fix ODE rule SBML writing and loading * remove all underscore-to-parameter code * check basic notebook - runs without problems * turn off input_printout in propensity test Co-authored-by: William Poole <wpoole@caltech.edu> Co-authored-by: ayush9pandey <ayush.9.pandey@gmail.com> * New features: Sensitivity analysis (#111) * add priors, add beta and gamma prior, and custom prior, documentation to the notebook * py_inference wrapper added * option to set initial parameter seed. print convergence diagnostics * Added LMFit support for least squares type parameter id. and added inference example notebooks. * delay support for inference * add tests for sensitivity analysis * apply rules in sensitivity analysis * minor changes * version update to 1.0.3 * Fixed some bugs involving SimulateSingleCell with length 0 or 1 timepoints arrays. * Deterministic safe mode (#113) * Fixed deterministic safemode tests * raises errors in deterministic safe mode - errors do not stop integration * less parallelization so tests don't use up all the RAM Co-authored-by: William Poole <wpoole@caltech.edu> * Slight change to how linege's SimulateSingleCell handles simulation with a single timepoint, to avoid infinite loops. * Wp inference (#118) * Add simulation control keywords rtol atol and hmax to inference and bioscrape deterministic simulation * fixed a bug which caused the CSimInterface to not update its parameters * more init_seed options, including guassian and normal priors + checking for positivity * filename option in py_inference * loguniform prior sampling initializaiton * parameters now can vary in log space * precision added to sensitivity analyss and Inference objects now save a list of params along with costs * ability to skip resetting up the cost function + optional file writing. * ability to reset PID default parameters programatically Co-authored-by: William Poole <wpoole@caltech.edu> * Delete test_printing.py * Infinite loop fix (#115) * Improved infinite loop fixes. * Delete test_printing.py Co-authored-by: Sclamons * fix docstring * Fixes issue #123 : sbml_warnings keyword error (#134) * fix sbml_warning issue with load reaction * Fix sensitivity analysis bug #126 and #125 (#136) Summary of changes: * fix sensitivity analysis bug that changed original parameter values * add docstring to py_sensitivity_analysis * delete old files and manual fix to match dev by deleting wrongly committed files * A cluster of changes to inference (#138) New features: * `parameter_conditions`: A new argument for `py_inference` that lets you set parameter conditions for data trajectories. Similar to `initial_conditions` that are on the model states, this sets conditions on parameters. * Add multiple files to write MCMC results: `mcmc_results.csv` writes the samples and `mcmc_results.txt` writes `cost_progress`. * Add stricter inference testing (optional) and add debug to stochastic pid interface Refactoring of Inference module: * remove old init_param_vals code that seemed not to be in use * update plot_mcmc_results behavior * set convergence_check default to False and modify gitignore * fix stochastic trajectories likelihood initial state set * add param condition to inference unit tests * refactor extract_data and check that parameter being estimated is not being varied through parameter_conditions * remove emcee thread argument * longer inference test, and change discard argument of emcee Co-authored-by: William Poole <wp_ix@hotmail.com> * Fix #135 by adding dtype double to inference timepoints and data (#140) * update version number to 1.1.0 Co-authored-by: William Poole <wp_ix@hotmail.com> Co-authored-by: William Poole <wpoole@caltech.edu> Co-authored-by: sclamons <sclamons@SEC-Macbook-Pro.local> Co-authored-by: Sam Clamons <sclamons@gmail.com>
ayush9pandey
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Feb 25, 2023
* delay simulation bug fix * fix error from merge dev
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has_delayfunction for Model objects.(Merge after inference-dev PR Inference updates, new features, and bug fixes #102 gets merged to see changes clearly)
Also, changes to gitignore to remove generated output files.