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nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
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GitHub Action to support WikiPathways curation #212

Closed egonw closed 1 year ago

egonw commented 2 years ago

Background

WikiPathways has started putting GPML files on GitHub. With an GitHub action, the GPML is converted into other formats, including SVG. This approach is also used to run curation tests, to support the curators in improving the pathways. Tests can be simple, like testing for missing Xref identifiers or finding unconnected lines, but also more complex, like finding metabolites that get converted to gene, which is a rare process (DNA synthesis).

Goal

The goal of this project is to develop a GitHub action that reacts on Pull Requests (PRs), generates an SVG and a curation report, and reports this as a comment to the PR.

The idea is similar how many tools have "bots" running to provide feedback on pull requests. For example, codecov is a bot that runs a code coverage test and reports the output as a comment: https://github.com/egonw/bacting/pull/79#issuecomment-1004352994

Difficulty Level: Medium

The tools can be run on a default Ubuntu image and WikiPathways already has a GitHub Action to reply to GPML changes. Yet, the right integration has yet to be done.

Size and Length of Project

The project commitment is medium: 175 hours with a timeline of 12 and 22 weeks.

Skills

You need to have used GitHub, Linux GNU/Linux (like Ubuntu), be familiar with Java software development, and have some experience with Java build environments like Ant or Maven.

Essential skills: Java, GitHub

Public Repository

None yet.

Potential Mentors

Egon Willighagen - @egonw Anders Riutta - @ariutta

Ritwick01 commented 2 years ago

Hello,@egonw I am Ritwick Pal, a second-year student at IIIT-Delhi. I have used been using Java for developmental work and even used it to develop projects including a game. I am really interested in contributing to this project. I am new to open-source, so can you please guide me as to how to get started.

egonw commented 2 years ago

@Ritwick01, please email me (egon.willighagen AT gmail) with more information about the Java projects you worked on and how they are build and, if applicable, how you currently use GitHub Actions.

khanspers commented 2 years ago

A reminder that the application period opens on Monday April 4. Proposals to NRNB must be submitted on the official GSoC Site (https://summerofcode.withgoogle.com/) before April 19, 18:00 UTC to be considered, and contributors are encouraged to submit proposals in draft format early, so that mentors can give feedback directly at the GSoC site.

AkMo3 commented 2 years ago

Hi @egonw, I am interested in contributing to this project. I had sent a mail containing all the required details. Please have a look.

AlexanderPico commented 2 years ago

IMPORTANT REMINDER: GSoC 2022 is for new “beginners” to open source.

Applicants are expected to review eligibility requirements prior to applying. We can not accept applications from contributors with prior open source development experience. From the GSoC FAQ https://developers.google.com/open-source/gsoc/faq:

Can someone already participating in open source be a GSoC Contributor?

The goal of GSoC is to bring new contributors into open source organizations. GSoC can also help beginner contributors learn the ins and outs of open source while being mentored by experienced community members. GSoC is for new and beginner contributors to open source, it is not for experienced contributors to open source.

egonw commented 2 years ago

@AkMo3, thank you for applying to this position and working out the idea. And good luck with your selected project!

Gairick52 commented 1 year ago

@egonw Hey i am beginner in this project can you suggest me beginner friendly issues to contribute to

egonw commented 1 year ago

@egonw Hey i am beginner in this project can you suggest me beginner friendly issues to contribute to

Hi, I don't know you and you have not introduced yourself. I cannot suggest anything like this, I'm sorry.

egonw commented 1 year ago

BTW, this issue is not actually this relevant. It's mostly implemented by now.

Gairick52 commented 1 year ago

@egonw apologies,i am gairick dam currently doing my masters in computer applications in mumbai,india i am new in open source world,please suggest me some beginner friendly issues

egonw commented 1 year ago

@egonw apologies,i am gairick dam currently doing my masters in computer applications in mumbai,india i am new in open source world,please suggest me some beginner friendly issues

If you are new to open source, working on issues is not the way to start. Instead, please consider instead:

Gairick52 commented 1 year ago

@egonw apologies,i am gairick dam currently doing my masters in computer applications in mumbai,india i am new in open source world,please suggest me some beginner friendly issues

If you are new to open source, working on issues is not the way to start. Instead, please consider instead:

  • pick an open source tool you find interesting
  • make sure to compile it locally and that you can run the tests
  • think about what functionality you like to add
  • implement that functionality
  • submit your code as a patch

Thanks for your guidance i will follow this