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LoLab-VU / pysb / 663
79%

Build:
DEFAULT BRANCH: master
Ran 24 Jul 2017 09:35PM UTC
Jobs 2
Files 95
Run time 31s
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jmuhlich
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

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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