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Ran 05 Feb 2019 05:51PM UTC

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Committed 25 Jan 2019 07:12PM UTC coverage: 78.557% (+0.1%) from 78.417%

Job # PYVER=3.6

Build Type

push

travis-ci

Committed by

alubbock

Commit Message

Small modifications to support BNG's 'stop_if' method (#407)

* Some small modifications to support the 'stop_if' method in BNG, which
allows one to define a logical function that if True will terminate a
simulation. First problem is that BNG creates a new internal function
called '_stop_if' that gets output to the .gdat file. This was causing
problems in PySB since the number of defined Expressions wasn't matching
the number of functions in the .gdat file. Fixed this by explicitly
using the length of 'model.expressions' when reading in the .gdat file.
Second problem is that if 'stop_if' is satisfied at the outset BNG will
immediately quit, only outputting the initial state to the .cdat and
.gdat files. This meant that PySB was reading this in as a single numpy
array, rather than an array of arrays, which was causing a downstream
error. Fixed this by requiring the number of dimensions 'ndmin=2' in the
'numpy.loadtxt' calls. Also added a small test model to the validation
test suite called 'test_stop_if'.

* Fix BNG gdat parsing when constant expressions in model

* Fix test so works consistently across platforms

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