Community Bonding Period - First Meeting and Weekly work update

-

Hi,


Last week on the 12th of May, I had my first online meeting with my mentors on Google Hangouts. It was a fantastic experience meeting them. We discussed how to start with the project. Here’s the summary of the meeting and the weekly work done:


  • There was a discussion for understanding the overall structure of the project.
  • The most important suggestion from mentors was to write tests for any of the new features added. It confirms the results of the code and also makes it easy for the reviewers.
  • We decided to start working on the small issues currently present in the codebase.
  • The first issue discussed to solve was the Travis CI failing issue (#34) for SBSCL. It was just upgrading Travis to OpenJDK11 and OracleJDK11 from the OracleJDK8 (which requires a license and all). I resolved the issue, but again, Travis failed with some issues due to a class from JSBML (#36), which will be solved once JSBML updates it (currently, those specific tests are skipped from Travis).
  • Also, I updated SBSCL to JSBML 1.5 while working on the Travis CI fails.
  • Then, a small issue to be solved was changing the Link for the Travis build icon in the README, which currently directed to some other link (#33).
  • All three issues are resolved, and the PR is made for the same (PR #37).
  • Also, there was a suggestion that once the coding period starts, I should document the significant changes in the SBSCL to the GitHub pages.
  • I will be working on the project by forking the original repository [Link] and making changes in this forked repository [Link] and will make pull requests from time to time as I make significant changes in the SBSCL.
  • We decided to make a slack channel for quick discussions related to the project.
  • We decided to meet at 13:00 UTC (evening, according to IST) every Tuesday for the weekly discussions of the project.


Regards!

Location: Ahmedabad, Gujarat, India

Comments

  1. Shalin ShahMay 23, 2020 at 4:04 AM

    Looks like you are making good progress already. :)

    One suggestion though: Instead of sending multiple PRs, just keep pushing all your work in your own fork. Eventually towards the end of summer, you can great one giant pull request. This will ensure there is one place with all the summary of your contributions and also avoid us approving your PRs several times. See this for reference - https://github.com/draeger-lab/SBSCL/pull/2

    ReplyDelete

Post a Comment

Popular posts from this blog

Starting Google Summer of Code 2020

-
Image
Hi, I am Hemil Panchiwala, 2nd year CSE student at the Indian Institute of Technology, Roorkee, India. I am incredibly excited to share that I was selected in the Google Summer of Code (GSoC) this year with the National Resource for Network Biology (NRNB) as a mentoring organization. I will be working on the project " Simulation of system biology models in Java: support for new features " in this program. I am incredibly thankful to the wonderful mentors, namely Dr. Andreas Dräger , Dr. Matthias König , Mykola Zakharchuk, and Shalin Shah , who helped me to get selected and will guide me throughout this project. This blog series is dedicated mainly to share my progress for the project. The official coding period starts from 1st June, and the community bonding period has currently begun. In this period, I will be exploring the codebase with solving some small issues and will discuss the implementation details with the mentors and finalize them. What is NRNB? The aim of the
Read more

GSoC Week 10

-
Image
This week I mainly worked on adding the support of the stochastic simulation to SBSCL. And, it is excellent that the simulation is giving great results with most tests passing. This addition of stochastic simulation has improved SBSCL supporting most of the simulation types now, which makes it a fully-featured simulation library. Now, here’s the summary of the work done this week with the topics discussed in the meeting: Mentors suggested writing the work done overview of the week before some hours of the meeting so that they can go through and provide their views in the meeting properly. We then mainly discussed the stochastic simulation implementation (using FERN) and the runtime due to simulating many times to get the mean and standard deviation. We decided to test all the models from the stochastic test suite and update the result format according to the test suite results. I worked on this mainly, and now the output format of the result is updated. The new test file StochasticTest
Read more

GSoC Week 11

-
Last week, I mainly worked on passing the current failing stochastic tests and ran Travis CI successfully. With this, we also started working on refactoring the SBMLinterpreter class, which has become quite a big class doing many things. Here is the quick summary of the updates from the weekly meeting with the work updates: In the meeting, we mainly discussed the failing stochastic tests. We decided to work on them and check whether the results were converging towards the pre-defined results on increasing the number of simulations or not. If they don't, then it was for sure that there is some issue in the implementation. So, I started working on that, and the small issue I found was that while comparing with the pre-defined results, the wrong column was considered from the pre-defined results, which made some tests fail. It is fixed now through this commit . After this, on further checking, we saw that some of the tests were like failing all the time regardless of the number of sim
Read more