Dev to master #74
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Dev to master #74
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* 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>
* 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>
* 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>
* 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>
ayush9pandey
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Oct 13, 2020
ayush9pandey
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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>
WilliamIX
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* 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>
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@ayush9pandey thanks for pointing out that dev was not fully merged into master. We should absolutely make sure these are merged [I thought I did this two weeks ago, but apparently it didn't go through completely somehow...]
Let me know if you have any comments on this PR - it should probably be merged before the Inference one.