BioJulia
Announcing the BioJuliaDocs initiative! #10
Replies: 3 comments 4 replies
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This is great! I forget if we discussed this, but having a way to incorporate https://github.com/BioJulia/BioTutorials into the site as complete notebooks could be a stretch goal. |
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I was wondering if the framework for the BioJuliaDocs is already settled or whether it could be more flexible like the |
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I chose Documenter because that is what SciMLDocs uses and it's very easy to simply copy what works and add it to the website. It also includes experimental theming support via DocumenterTools.jl so it might be trivial to adapt it visually. The BioJulia website uses some elements of Hugo, and I think it would be interesting to remake it with full Hugo support or with some other framework so as to render it more aesthetically pleasing and easier to maintain. That would be a separate discussion, however. |
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Oh, I see. Yeah, Documenter is nice. I'll check the |
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We should definitely replace the BioJulia website with Franklin - I don't think we're really actively using much of the academic theme from Hugo that wouldn't be trivially replicable in Franklin |
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I just saw how the |
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I'd be open to such a thing, but probably after we've done the hard work of consolidating everything into one page. That def seems like highest priority at the moment. |
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Hello!
My name is Michael Persico (him/il), I am an undergraduate researcher that is currently undertaking a Julia Summer of Code internship. As part of the internship, I have proposed for BioJulia a common landing site for novice and experienced users alike, and today I am happy to announce that this effort is now publicly available for contributions in the form of BioJuliaDocs!
What is BioJuliaDocs exactly?
Currently, there are two common sites for users wishing to explore the BioJulia community, either the main biojulia.dev website or the official GitHub organization page . There is currently no guided, centralized approach for those wishing to dive into the ecosystem at their own pace, one that would really demonstrate the benefits BioJulia packages deliver via an overview of best features and practices.
The SciML organization has tackled this issue with their own "SciMLDocs" initiative, providing an all-encompassing view of Julia's biggest machine learning ecosystem with tutorials, package descriptions, showcases of unique code samples, and benchmarks, among other documentation. A BioJulia equivalent would thus help boost discoverability, speed up onboarding of potential contributors, highlight exciting developments, and emphasize foundational packages, good practices, and code samples proven to be invaluable in a number of biology applications.
How does this work?
Under the hood, BioJuliaDocs is essentially a large HTML document generated by Documenter.jl that can be published as a standalone site or, as hoped, an extension to the main BioJulia website. For testing purposes, A GitHub Pages site has been set up that auto-rebuilds whenever a pull request (or a new commit by maintainers) is successfully pushed. I have also set up both a project board and discussions section for the repository to more easily manage issues and new ideas or particular concerns.
Can I contribute?
NeverABSOLUTELY! 😄 This is rather massive project that will touch almost all areas of BioJulia, therefore your expertise and technical writing/programming prowess will be immensely appreciated. I am currently searching for both maintainers for the repository as well as writing contributors whom want to add to existing sections and wish to contribute their own.Remember to maintain civility between all participants as according to the BioJulia code of conduct both referenced here and in the repository. Please consult both the README and the core BioJulia guidelines before submitting issues/pull requests, and do not hesitate to ask community members over on the Slack #biology workspace or on forums. You can also reach out to me privately via my email address.
Why is there a typo here, missing documentation there, failed builds everywhere, etc.?
BioJuliaDocs is an ever-evolving project with a number of moving parts that WILL be transformed in some or many incompatible manners. The goal would be to integrate a minimum viable product into the BioJulia website sometime near the end of August, meaning complete and functional Getting Started, Overview, and Showcase pages. If you notice any issues that need correcting or have ideas for your own contributions, please do file an issue/pull request to further advance the initiative!
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