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master: 79%

Ran 03 May 2017 01:49AM UTC

Files 86

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Committed 03 May 2017 01:40AM UTC coverage: 71.668% (+0.1%) from 71.544%

Job # 562.2

Build Type

push

travis-ci

Committed by

jmuhlich

Commit Message

Read Expression values from BNG .gdat files (#250)

* Modified pysb.bng.BngBaseInterface.read_simulation_results() to read in
header names from the .gdat file rather than set the names equal to the
names of model.observables. This is necessary because BNG can be
instructed to print function (Expression) values to the .gdat file with
the 'print_functions=1' argument. This also required changing the 'if'
statement from a check on whether model.observables exists to whether
the .gdat file exists (since, in principle, the .gdat file could contain
only functions).

* Add NFsim simulation result support

NFsim generates a .gdat (groups, i.e. observables/expressions) but not a
.cdat (species concentrations) file. I've updated read_simulation_results in
the BioNetGen interface to take into account simulation results may create
.cdat, .gdat, or both.

I've also made the .gdat file reader only open the file once for efficiency,
and added an NFsim unit test (Simulator class support coming soon).

Coverage Stats

4652 of 6491 relevant lines covered (71.67%)

0.72 hits per line

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master: 79%

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