Lineage beta #71
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Lineage beta #71
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added 6 commits
June 11, 2020 13:51
wasn't checking cell death correctly
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.
ayush9pandey
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Oct 2, 2020
WilliamIX
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Nov 3, 2020
* Ode safe mode (#67) via Deterministic Safe Interface * Interface Safemode unit tests * 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. * Lineage beta (#71): Fixed global volume distribution problem wasn't checking cell death correctly * Added new lineage examples * update readme travis tag (#75) Co-authored-by: William Poole <wp_ix@hotmail.com> Co-authored-by: William Poole <wpoole@caltech.edu>
ayush9pandey
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Nov 3, 2020
* 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>
ayush9pandey
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Aug 22, 2022
Safe mode (#67) changes: * Deterministic Safe Interface Code written * Creating some tests * Interface Safemode unit tests complete * Updated py_simulate_model to allow Safe Deterministic simulations * Added checks to safemode, timestep control to py_simulate_model, code reuse in massaction propensities * 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 SBML read/write changes: * Bioscrape annotations fix (#65) * renamed local parameters extended to bioscrape propensity annotations * Added Unit Tests for SBML reading and writing with and without annotations * Fix for SBML kinetic law formula when importing and writing SBML #89 (#93) * add checks to rate law math ast * Testing and other packaging related changes: * Model comparison removed from test_utils * Adds a test to make sure running initialize twice isn't a problem. * changing paths to work across platforms * added pandas to requirements * Added tests to compare general propensities to bioscrape propensities * update readme travis tag (#75) * Switch to Github Actions (#84): 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 * Making Bioscrape pip Installable (#86): This PR creates a single setup.py file which automatically compiles Bioscrape's cython code. * Manifest is ignored * Mid-debug version, trying to figure out why simulations produce NaNs in serialization testing * Fixes some bugs in serialization testing Bug fixes: * C vector bug fix (#69): Clears c_vectors in model._create_vectors * Remove underscore from parameter definition (#68) * Fixed Bioscrape XML loading and added deprecated warning for bioscrape XML Lineage changes: * 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 * Makes Models and LineageModels picklable; Refactors test_propensities_via_annotations.py test. * Adds turbidostat capability to Lineages, along with unit tests for the priority queue used by turbidostat * Removes a few unused files * index bounds checking for Lineage.py_get_schnitz * Fixed perfect partitioning rounding error * Fixes np.object-related warning. * Fixes a warning in serialization tests * Fixed some bugs involving SimulateSingleCell with length 0 or 1 timepoints arrays. Inference changes: * add priors, and custom prior * py_inference wrapper added * add beta and gamma prior * 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 * 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 * Slight change to how linege's SimulateSingleCell handles simulation with 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 analysis 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 Other core bioscrape changes: * Expands serialization tests to check deterministic simulations as well as stochastic ones. * minor fix to sympy_species_and_parameters * merged turbidostat and serialization * Merges serialization and turbidostat into dev, with minor fixes. * Cython Statistics for SSA Trajectories (#101): 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 * 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. * version update to 1.0.3 Bioscrape XML deprecated now with the following commits: * 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 New features: Sensitivity analysis (#111) * add tests for sensitivity analysis * apply rules in sensitivity analysis Co-authored-by: William Poole <wpoole@caltech.edu> Co-authored-by: Ayush Pandey <ayush.9.pandey@gmail.com> Co-authored-by: Sam Clamons <sclamons@gmail.com>
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Merging Lineage Beta into Master - this will let people use Lineage simulations (which are still in beta) without having to switch branches.
Note that Non-interacting lineages via the functions "py_simulate_lineage" and "py_propogate_cells" are quite stable. The interacting versions of these "py_simulate_interacting_lineage" and "py_propogate_interacting_cells" are still buggy.