Community Bonding Period - Last Meeting and Work Update

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Hi,


We had our last meeting of the community bonding period last week on 26th May. As always, it was again great meeting the mentors. We discussed further on the issues of running the SBMLTestSuite tests and some other points with this. And, now the community bonding period has ended, and many new changes have been added to SBSCL. Here’s the summary of the work done in a week with the meeting:


  • Continuing the discussion about the SBMLTestSuite tests from my last blog, we decided to compare the plots of the SBSCL simulator results with the pre-defined results and check the distances between them. For this, we decided to use the SBML Test Runner, a standalone desktop application with a GUI for controlling SBML-compatible applications and making them run test cases from the SBML Test Suite.

  • I worked on this and made a wrapper for SBML Test Runner to run the tests using the SBSCL simulator. The documentation for how to work with SBML Test Runner has also been added to the INSTALL.md file (currently, present in the forked repository).

  • One of my mentors, Shalin Shah, suggested making GitHub projects for each of the milestones stated in the proposal for proper management of the work. I created these projects in my forked repository, which can be viewed here.

  • Then, it was discussed to make tests for the two newly added classes: MaxAbsDistance and MaxRelDistance. I added the tests to the forked repository, which confirmed the successful working of both the classes.

  • We also decided that I should make PRs on completion of phases or after completing a major milestone of the project.

  • The mentors also suggested adding the updated tests from the SBML Test Suite repository present at the develop branch [Link]. I updated the script to get the new tests from the SBML Test Suite.

  • We discussed publishing SBSCL to the maven central. This needs some account creation for the long term maintenance, which will be done by my mentor Andreas Dräger.

  • We even discussed adding code coverage feature to the SBSCL. But covering all the classes in the tests becomes a hectic task, especially in Java, as suggested by Mykola Zakharchuk.

  • With this, in this week, I also moved all the script files under a single folder scripts present under /src/tests/ folder.

  • We also discussed with the SBML Test Runner team how they were comparing the simulator’s solution with the pre-defined results. We got the new metric to compare that even was consistent and compliant to the community standards and decided to add that for SBMLTestSuite tests in SBSCL. The distance metric is as follows:



  • This metric was added to SBSCL, but after this, 223 tests failed out of 1809 tests. On analyzing, I found out that many were comp tests that failed due to the JSBML issues, while some of them were FBC tests, and other tests were SBML that deviated from the results by some significant value. We discussed this with some FBC issues in the next meeting, about which I will be soon posting.


All the updated changes are present at the develop branch in my forked repository present at this link.

Till next time,

Regards!

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