juliahealth/juliahealth.github.io

Website for the JuliaHealth organization (powered by Franklin.jl).

juliahealth.github.io's Issues

[FEATURE] Compare JuliaHealth Capabilities To Other Ecosystems

@Jay-sanjay and I were chatting about methods for benchmarking the JuliaHealth ecosystem against other ecosystems. I mentioned that benchmarking in terms of speed/performance would most likely not be possible but in terms of functionalities covered, I think this could be useful. Therefore, creating a table to host on the JuliaHealth website that aims to showcase the capabilities of JuliaHealth in relation to other available frameworks in Python and R would be great to add to the JuliaHealth website.

This would encompass looking for the following aspects of other ecosystems:

1. Identify key functionalities provided by prominent health frameworks in Python and R.
2. Evaluate and demonstrate how these functionalities can be achieved or approximated within JuliaHealth.
3. Create a comprehensive table comparing functionalities across ecosystems, detailing their availability and implementation in JuliaHealth.

A potential table could look something like this:

Functionality	Julia	R	Python
Building OMOP CDM Patient Cohorts	OHDSICohortExpressions.jl†	CirceR
Cofactor OMOP CDM Patients	OMOPCDMCohortCreator.jl	Characterization‡

† Not an official JuliaHealth package
‡ Limited support

[DOCS] Migrating from Documenter.jl to DocumenterVitepress.jl

Issue Description

Difficulty: Beginner

Time: 2 - 4 hours

Description: The aim of this issue is to support the major refactor beginning across all of JuliaHealth to improve discoverability and unity of the JuliaHealth ecosystem as it pertains to documentation. This issue's purpose is to provide guidance on how one will migrate the JuliaHealth website built on Documenter.jl to DocumenterVitepress.jl to support a more winsome entry point to new Julians curious about health research within the Julia community. It builds upon the completion of #126.

Note: The decision to migrate to DocumenterVitepress was decided in the March 2024 JuliaHealth monthly meeting.

Requirements

• Add DocumenterVitepress.jl dependency
• Migrate the Documenter.jl make.jl file to a compatible DocumenterVitepress.jl make.jl file
• Make sure each page renders correctly

Expected Outcomes

After this transition is completed, the website should go from looking like this:

To something more like this:

Additional Notes

For how to approach this issue, I would suggest the following steps:

First, if you have never worked with Documenter.jl before, I would highly recommend these videos and resources:

• Documenter.jl Deep Dive
• Documenter.jl Official Documentation
• How To Locally Preview Documenter.jl Documentation

Next, I would recommend creating a practice folder (repository) on your computer to download Documenter to. From there, I would follow the above tutorials and guides to create a documentation website on your own computer from scratch. Once you know how to create a documentation website, how to add pages, and how to write documentation for the website, you are ready for the next step!

Second, I would then create a fork of the JuliaHealth website. Within this fork, I would add Documenter.jl to this fork and remove Franklin.jl. You can do this from within the Julia REPL.

Third, you will now need to begin migrating the make.jl file to DocumenterVitepress. This will take some time and the way to preview the documentation locally can be a bit challenging. In case there are any problems, please see the resources section for help.

Third, once you are done with this, go ahead and open a Pull Request with all your changes saved to your fork. At this point, myself or someone from within JuliaHealth will review this PR to suggest changes or help with fixes.

Then, you should be done with this PR!

Other Resources

Julia Slack:

• documentation channel - you should post here first
• helpdesk channel - this would be to get more attention to your issue but maybe not as precise as you need.
• health-and-medicine channel - this is where most of JuliaHealth is located these days.

Julia Discourse - I would advise posting here if you have an issue that you feel is long or requires a lot of time to explain as you might lose it within Julia Slack. Consider cross-posting your forum post to the Julia Slack in helpdesk and/or documentation.

[FEATURE] Enumerating Subecosystems within Juliahealth

As we've continued to build JuliaHealth, it is becoming more and more apparent to me that there exist multiple smaller ecosystems within JuliaHealth (I call them "sub-ecosystems" or "subecosystems" as they are a subset of the greater JuliaHealth ecosystem). What would be great is to have a webpage on the JuliaHealth website that enumerates these subecosystems and perhaps categorizes some of the packages. This categorizing doesn't have to be intensely strict as one package could have multiple use cases across the subecosystem.

But I think this could be useful to list out functionalities that JuliaHealth has and who is the contact person or "owner" for those suite of packages belonging to that subecosystem. So far, I have seen the following subecosystems emerge with their associated subecosystem owners:

• Observational Health Subecosystem - @TheCedarPrince
• Medical Imaging Subecosystem - @jakubMitura14
• Standards and Interoperability Subecosystem - @Tokazama

I am not sure if there are others off the top of my head, but that is what I have seen so far. Having this webpage I think would be great and perhaps a pleasant orienting force to new members of the JuliaHealth ecosystem as a whole.

[DOCS] Transitioning JuliaHealth Website to Documenter.jl

Issue Description

Difficulty: Beginner

Time: 10 - 15 hours

Description: The aim of this issue is to support the major refactor beginning across all of JuliaHealth to improve discoverability and unity of the JuliaHealth ecosystem as it pertains to documentation. This issue's purpose is to provide guidance on how one will migrate the JuliaHealth website to Documenter.jl to support a more robust documentation ecosystem. It is part of the JuliaHealth Documentation Overhaul organization project.

Requirements

• Remove Franklin.jl dependency
• Migrate Franklin.jl syntax in pages to Documenter.jl syntax
• Add Documenter.jl dependency
• Make each page compatible with Documenter.jl
• Make sure the documentation page is deployed live on github pages
  • NOTE: JuliaHealth reviewers can help with this set-up
• Check links within website to make sure they are accurate

Expected Outcomes

After this transition is completed, the website should go from looking like this:

To a layout that looks more like this:

NOTE: Each main page of the JuliaHealth website should be on the left hand side of the Documenter.jl "drawer" as shown in the second photo.

Additional Notes

For how to approach this issue, I would suggest the following steps:

First, if you have never worked with Documenter.jl before, I would highly recommend these videos and resources:

• Documenter.jl Deep Dive
• Documenter.jl Official Documentation
• How To Locally Preview Documenter.jl Documentation

Next, I would recommend creating a practice folder (repository) on your computer to download Documenter to. From there, I would follow the above tutorials and guides to create a documentation website on your own computer from scratch. Once you know how to create a documentation website, how to add pages, and how to write documentation for the website, you are ready for the next step!

Second, I would then create a fork of the JuliaHealth website. Within this fork, I would add Documenter.jl to this fork and remove Franklin.jl. You can do this from within the Julia REPL. Then, the major work begins by slowly migrating each page and entry from the JuliaHealth website to the Documenter.jl layout. This will take some time here!

Third, once you are done with this, go ahead and open a Pull Request with all your changes saved to your fork. At this point, myself or someone from within JuliaHealth (maybe @Jay-sanjay or @DilumAluthge) will review this PR to suggest changes or help with fixes. There will need to be some additional tweaks to make the documentation live by the JuliaHealth administrators so at that point, we will help to make sure it is live.

Then, you should be done with this PR!

Other Resources

Julia Slack:

• documentation channel - you should post here first
• helpdesk channel - this would be to get more attention to your issue but maybe not as precise as you need.
• health-and-medicine channel - this is where most of JuliaHealth is located these days.

Julia Discourse - I would advise posting here if you have an issue that you feel is long or requires a lot of time to explain as you might lose it within Julia Slack. Consider cross-posting your forum post to the Julia Slack in helpdesk and/or documentation.

[DOCS] Add JuliaHealth Tutorials Section for Discoverability

One of the biggest conclusions that @Farreeda helped me realize (as well as some additional discussions with @DilumAluthge and @gdalle) is that the biggest problem facing JuliaHealth isn't so much the development of novel packages (although, granted, there are features that still need to be implemented in Julia) but rather novel compositions of how packages that already exist within the Julia ecosystem can be composed together to address problems within the context of Julia-based health research.

To kick off the JuliaHealth tutorials section, @Farreeda has been doing great work in developing a small pipeline showing how pre-existing tools within Julia can be used to address patient-level prediction questions. We need to add a new page for tutorials as well as the prediction tutorial.

[Bug] page doesn't open on the browser directly

This error appears
julia> serve() ┌ Franklin Warning: in <config.md> │ No 'config.md' file found. It is recommended to keep one. │ │ Relevant pointers: │ - workflow and folder structure: https://franklinjl.org/workflow/ └ ERROR: ArgumentError: The current directory doesn't have a _layoutor_cssfolder; change directory to a valid Franklin folder.
Each time it only works when changing the commit by those steps written by @TheCedarPrince

1. Move to the dev branch of the website
2. Run git log to make sure I am on commit "Remove Franklin compat entry"
3. If not, add the remote by doing "git remote add juliahealth https://github.com/JuliaHealth/juliahealth.github.io"
4. Then, pull from the remote by doing "git fetch juliahealth"
5. Then, merge the local dev branch with juliahealth/dev by doing "git merge juliahealth/dev" from your local dev branch
6. Open Julia then activate the environment
7. Instantiate or update the environment at this point
8. Run "using Franklin" and then "serve()"

[BUG] Arbitrary Failure of Generating Package List

Hi @DilumAluthge ,

I was just rebuilding the JuliaHealth website and all of a sudden, the package list functionality seems to be failing: https://github.com/JuliaHealth/juliahealth.github.io/actions/runs/5941161601/job/16111528130

Do you have any idea what be going wrong with this code? It might be a quick fix as I haven't changed a single thing in the code there that you have written. Sadly, this is blocking me from publishing public meeting notes at the moment. 😞

If you don't have time to fix/take a look, I can try my hand at making a fix here and there.

Thanks!

~ tcp 🌳

[Bug] The JuliaHealth logo issue

I found that the juliahealth logo seems to be deformed on Android interface, image attached

@TheCedarPrince could you please look over it once . Thanks !!

adding medical segmentation

Hello I created some tools for medical image 3D segmentation
https://github.com/jakubMitura14/MedPipe3D.jl

I had Julia Con workshops
https://www.youtube.com/watch?v=BlEV10Shbb8

I thought that maybe to increase reach of those tools they could be added to the page?

[DOCS] Describing the Medical Imaging Subecosystem

@jakubMitura14 @cncastillo and I were chatting about the need to describe the Medical Imaging Subecosystem within JuliaHealth. I think what we need is a new section on the JuliaHealth website that discusses the following about this subecosystem:

• What is medical imaging?
• What part of medical imaging does JuliaHealth focus on?
• What tools does JuliaHealth provide for medical imaging?
• What are goals of the medical imaging subecosystem
• Where can I learn more about doing medical imaging work within JuliaHealth?
• Who should I reach out to about medical imagining within JuliaHealth?

Do you think anything else should be added here folks? Any other ideas at the moment?

Accept donations

I would be happy to setup a recurring donation, like I did with the BioJulia, but they stopped the donations.
It would be awesome if JuliaHealth will provide a way to help the project financially.

Remove the iguana

Same small issue as the first point of JuliaSymbolics/SymbolicUtils.jl#43 basically either remove the favicon line in _layout/head.html or replace the _assets/favicon.png

I should remove that iguana in the templates, I had it there for fun in the beginning but now I think I probably should make it a big red question mark or something 😱

[DOCS] Add Section for Google Summer of Code Fellows

This new section should highlight the work done by past Google Summer of Code fellows! This is to both recognize their valiant efforts as part of the growing JuliaHealth ecosystem as well as to document what did and did not work well throughout their respective fellowships to help us improve as fellows and mentors. Excited we are getting to add this page in! 🎉

[FEATURE] Unify JuliaHealth Documentation Like SciML's Documentation

I absolutely adore the attempt at unified documentation like in the SciML ecosystem. The source code is here: https://docs.sciml.ai/Overview/stable/

I have no idea how they really did it, but I think it is a fantastic idea and wish that we could start something similar within JuliaHealth. I think the first step might be to start with MultiDocumenter.jl. Although I am not fully certain myself.

Test issue, please ignore