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Parse time course from actions in BNGL files #51

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jonrkarr opened this issue Jun 19, 2021 · 1 comment
Open
2 tasks done

Parse time course from actions in BNGL files #51

jonrkarr opened this issue Jun 19, 2021 · 1 comment
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enhancement New feature or request Modeling format

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jonrkarr commented Jun 19, 2021 •
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Place into biosimulators_utils.model_lang.bngl.utils

Can be done once RuleWorld/PyBioNetGen#10 is addressed.

  • Time course settings
  • Algorithm parameters e.g., seed
@jonrkarr jonrkarr added the enhancement New feature or request label Jun 19, 2021
@jonrkarr jonrkarr mentioned this issue Jun 19, 2021
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@jonrkarr jonrkarr self-assigned this Aug 4, 2021
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jonrkarr commented Aug 4, 2021

Mostly done, except several minor issues need to be corrected in PyBioNetGen. In particular, the new version fails when no action is defined. See RuleWorld/PyBioNetGen#17. When this issue is closed, the required version of PyBioNetGen should be updated and the tests for this package should be updated (expected failure should be removed from test_get_parameters_variables_for_simulation_no_actions)

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