663
79%

Ran 24 Jul 2017 09:35PM UTC

Jobs 2

Files 95

Run time 31s

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Build # 663

Build Type

push

travis-ci

Committed by

jmuhlich

Commit Message

Fix StochKitSimulator for models w/ expressions (#277)

* Fix StochKitSimulator for models w/ expressions

* Speed up StochKit export with loop optimisation

* More StochKit speedy speedy

* Fix error with StochKit error message (!)

* Add expand_obs for symbolic Observable expansion

* Fix tspan length for StochKit

* Fix StochKit doctest

* Use mass-action rates in StochKit where possible

Non mass-action rates in StochKit require compilation as C code before
simulation can take place. For large models this takes a long time.

I've added a check to see if a reaction is mass-action, and to export it
as such in StochKit XML if so. This should speed up compilation time.

I've also added an EXTENDED_DEBUG support to StochKitSimulator, which logs
the resultant StochKit XML within PySB.

* Allow models with 'vol' param with StochKit

* Improve formatting of dict comprehension

Coverage Stats

5825 of 7826 relevant lines covered (74.43%)

1.32 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	663.1	24 Jul 2017 09:35PM UTC	0	72.35	Travis Job 663.1
2	663.2	24 Jul 2017 09:35PM UTC	0	72.11	Travis Job 663.2

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