Dev to Master for v1.2 #148
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* Dev (#70) * Ode safe mode (#67) * Deterministic Safe Interface Code written * Creating some tests * Interface Safemode unit tests complete * Updated py_simulate_model to allow Safe Deterministic simulations * Bioscrape annotations fix (#65) * renamed local parameters extended to bioscrape propensity annotations * Added Unit Tests for SBML reading and writing with and without annotations * Model comparison removed from test_utils * changing paths to work across platforms * added pandas to requirements * Remove underscore from parameter definition (#68) * Fixed Bioscrape XML loading and added depricated warning for bioscrape XML * Added tests to compare general propensities to bioscrape propensities * C vector bug fix (#69): Clears c_vectors in model._create_vectors * Adds a test to make sure running initialize twice isn't a problem. Co-authored-by: William Poole <wpoole@caltech.edu> * Lineage beta (#71) * Fixed global volume distribution problem wasn't checking cell death correctly * Minor changes to lineages Fixed a bug where arrays of length 0 were being made. Tried to find other places to debug this seg-fault problem. I believe it might now be an issue when running bioscrape inside jupyter notebooks??? When running on the prompt I can run tons of simulations no problem. * Added new lineage examples * forgot the sbml file! Co-authored-by: William Poole <wpoole@caltech.edu> * Dev to master (#74) * Ode safe mode (#67) * Deterministic Safe Interface Code written * Creating some tests * Interface Safemode unit tests complete * Updated py_simulate_model to allow Safe Deterministic simulations Co-authored-by: William Poole <wpoole@caltech.edu> * Bioscrape annotations fix (#65) * renamed local parameters extended to bioscrape propensity annotations * Added Unit Tests for SBML reading and writing with and without annotations * Model comparison removed from test_utils * changing paths to work across platforms * added pandas to requirements Co-authored-by: William Poole <wpoole@caltech.edu> * Remove underscore from parameter definition (#68) * Fixed Bioscrape XML loading and added depricated warning for bioscrape XML * Added tests to compare general propensities to bioscrape propensities Co-authored-by: William Poole <wpoole@caltech.edu> * C vector bug fix (#69) * Clears c_vectors in model._create_vectors * Adds a test to make sure running initialize twice isn't a problem. Co-authored-by: William Poole <wpoole@caltech.edu> Co-authored-by: William Poole <wpoole@caltech.edu> * update readme travis tag (#75) Co-authored-by: William Poole <wp_ix@hotmail.com> Co-authored-by: William Poole <wpoole@caltech.edu>
Switching from Travis CI to Github actions. Now tests on Mac OS, Linux, and Windows with python versions 3.6, 3.7, and 3.8 Co-authored-by: William Poole <wpoole@caltech.edu>
This PR creates a single setup.py file which automatically compiles Bioscrape's cython code.
… reuse in massaction propensities
…_via_annotations.py test.
…93) * add priors, and custom prior * py_inference wrapper added * merge master * add beta and gamma prior * add custom prior documenting notebook * all notebooks work * typo bug fix * minor update to inference notebooks * gaussian prior fix * bug fixes for log uniform prior and pdf computation bound checks * add checks to rate law math ast
…e priority queue used by turbidostat
…l as stochastic ones.
…in serialization testing
SSResult.emperical_distribution and py_empirical_distribution cythonize distribution and marginal distribution calculations. SSAresult.first_moment, second_moment, correlation, and standard_deviation cython methods now all exist. As well as python wrappers. * added max_counts_list to allow truncation of the empirical distribution * add doc strings * Fast statistics for SSA trajectories examples Co-authored-by: William Poole <wpoole@caltech.edu>
* index bounds checking for Lineage.py_get_schnitz * Fixed perfect partitioning rounding error Co-authored-by: William Poole <wpoole@caltech.edu>
* 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
* delay simulation bug fix * fix error from merge dev
* 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>
* 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
* 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>
…ith a single timepoint, to avoid infinite loops.
* 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>
* Improved infinite loop fixes. * Delete test_printing.py Co-authored-by: Sclamons
* fix sbml_warning issue with load reaction
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>
Changes summary: * update badge * set hmax default to zero * add corner dependency * update version
* Bioscrape v1.2.0 (#141) * remove 3.6 testing in favor of 3.10 testing * add quotes around 3.10 for CI * remove old trash files: temp.pck, simbio.m etc * fix compatibility spelling * fix python capitalization * try branch specific actions CI * rename CIs to test_bioscrape and deploy_bioscrape * add joss badge, update CI badge
* InferenceSetup pickles * added __getstate__ and __setstate__ methods with tests * Allow keyword 'pool' to be used with emcee Note: this is actually not faster in cases where numpy is automatically threading on multiple cores (which is the default behavior on MacOS and Linux). Co-authored-by: Ayush Pandey <ayush.9.pandey@gmail.com> Co-authored-by: William Poole <wpoole@caltech.edu>
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* Dev to Master for v1.2 (#148)
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