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Fixes for BNGL importer #470

Merged
merged 4 commits into from Oct 28, 2019
Merged

Fixes for BNGL importer #470

merged 4 commits into from Oct 28, 2019

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@alubbock
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alubbock commented Oct 21, 2019

Fixes for importing BNGL models containing the following:

  • Expressions referencing observables (ScipyOdeSimulator failure;
    observables don't get expanded by expand_expr())
  • Parameters containing ^ (exponentation) (model fails to import)

This PR adds unit tests which round-trips BNGL export for PySB
example models, runs network generation, and single-steps an
integrator. These tests caught the above issues.

Fixes for importing BNGL models containing the following:

* Expressions referencing observables (ScipyOdeSimulator failure;
  observables don't get expanded by `expand_expr()`)
* Parameters containing ^ (exponentation) (model fails to import)

This PR adds unit tests which round-trips BNGL export for PySB
example models, runs network generation, and single-steps an
integrator. These tests caught the above issues.
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codecov-io commented Oct 22, 2019

Codecov Report

Merging #470 into master will increase coverage by 0.04%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #470      +/-   ##
==========================================
+ Coverage   79.84%   79.88%   +0.04%     
==========================================
  Files          99       99              
  Lines       10113    10134      +21     
==========================================
+ Hits         8075     8096      +21     
  Misses       2038     2038
Impacted Files Coverage Δ
pysb/generator/bng.py 96.77% <100%> (ø) ⬆️
pysb/importers/bngl.py 92.98% <100%> (+0.15%) ⬆️
pysb/core.py 88.39% <100%> (+0.02%) ⬆️
pysb/tests/test_exporters.py 89.47% <100%> (+2.17%) ⬆️

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@alubbock alubbock merged commit cf08a76 into pysb:master Oct 28, 2019
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@alubbock alubbock deleted the alubbock:bngl_import_fixes branch Oct 28, 2019
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