GSoC Week 13

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Getting into the last phase of Google Summer of Code 2020, I mainly worked last week on updating the stochastic simulations support to make use of the present SBSCL classes and refactored different things. The summary of the work done with the meeting updates are:


  • Mentors suggested merging the refactor-interpreter branch to the fern branch as reviewing PR takes more time, and there is not enough time left and also, after this two more PRs (with formatting and documenting updates) needs to be made. This is now done and also the PR is quite ready to merge now with many updates made this week.
  • BiGG models tests were completely ignored before from the Travis build which has now been fixed with some minor fixes also in FluxBalanceAnalysis that now simulates all the BiGG models successfully.
  • Also, I added the reference results from cobrapy and compared the SBSCL results with them, and all the tests passed successfully that confirmed that SBSCL works excellent with the SBML models with fbc extension.
  • SedMLExecutorTest has also been updated to run some of the ignored tests and with this only 2 tests are now ignored which seems to be for some reason now.
  • SedML files URNs have been updated now which made the Travis pass again successfully.
  • The tons of processViolation logs for constraints in the Travis build are now fixed to just show when the violation has started and ended instead of at every instant.
  • SBMLTestSuiteTest and StochasticTestSuiteTest are now refactored completely with completely organized into different methods doing specific tasks.
  • Also, all the requested changes by mentors in the PR are now updated with the PR almost ready to get merged. You can see the PR here.
  • The main task done this week was to remove the complete SBMLNetwork dependency from most of the classes of FERN now and are updated now to work using the SBMLinterpreter which now makes stochastic simulations to run better with the SBSCL classes.
  • Also, an issue #55 is created for discussion of making FERN free from the SBMLNetwork and other classes and instead start using the current SBSCL classes.


These were the main updates with many minor updates which can be seen through the commits from the PR #54. The completely updated work can be found at the fern branch at my forked repository.


Regards!

Location: Deesa, Gujarat, India

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