LoLab-VU / pysb / 650
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jmuhlich 
Add BioNetGen Simulator support (#272)

* Creating new branch to implement a BNG Simulator class. Prototype, but works. Can run multiple simulations, but as of now does so with default model parameters and initial condtions. Need to setConcentration with action commands to do properly.

* Created an test for the bng simulator.

Added support for NF simulations (as well as being able to pass a "method" to the simulator to use any simulator in bng.

Adding the ability to pass param_values and initials to simulator, uses setConcentrations and setParameters (had to add to pysb/bng.py to make it work properly).

* Created a test for the bng simulator.

Added support to pass a "method" to the simulator to use any simulator in bng.

Created an NFSimulationResult

Adding the ability to pass param_values and initials to simulator, uses setConcentrations and setParameters (had to add to pysb/bng.py to make it work properly).

* Created a test for the bng simulator.

Added support to pass a "method" to the simulator to use any simulator in bng.

Created an NFSimulationResult

Adding the ability to pass param_values and initials to simulator, uses setConcentrations and setParameters (had to add to pysb/bng.py to make it work properly).

* Created an test for the bng simulator.

* Rebased to master.
Corrected example to be ssa simulation.
Removed docstring from SimulationResultNF (it was a scipyode example. Need to add nfsim download to test NF simulationresults)

* Tidy setConcentration and setParameter methods

* Don't generate network when using NFsim

* Add logging support to BNG interface

* Remove globals in bng.py and code tidying

Resolves: pysb/pysb#139

* Changing parameter and initials to g format rather than float. For EARM, there was a precision error where only 4 decimals were being printed, which resulted in rate parameters of 0.

* [WIP] Incorporate Sim class improvements

* Add network-free simulation support to Sim class

* Add NFsim support without any network generation

* Bugfixes, unit tests, more docs

* Fix load_netfile for models with synth/deg rules

* Fix tspan length in BngSimulator

* Ensure BNG simulations use resetConcentrations

* Add BngSimulator to pysb.simulator namespace

* Exact Hybrid Particle/Population simulation capability

* Use %g not %f for printing floats to BNG

* Updates to HPP simulation

* Put BNG readFile prior to actions block

* Changing from pysb.simulator.bng_ssa to pysb.simulator.bng.

* Implement changes from github PR review

* Remove code setting unused self.verbose

5810 of 7797 relevant lines covered (74.52%)

1.33 hits per line

Jobs
ID Job ID Ran Files Coverage
1 650.1 0
72.44
 Travis Job 650.1
2 650.2 0
72.2
 Travis Job 650.2
Source Files on build 650
Detailed source file information is not available for this build.