Converting all docs and tutorials to Quarto

[shravanngoswamii]

No description provided.

[yebai]

@shravanngoswamii It might be better to split this into several smaller PRs so we can review it. I suggest that we first convert jmd to qmd without changing any other files (e.g. do not change building scripts, or reorganise folder structure). This allows us to see the edits in the docs and tutorial texts. Then, we can have another PR update the building workflow, etc.

[shravanngoswamii]

Ok, so you want to just replace jmd files with qmd without touching any other files!

One thing I would like to mention that each file will be renamed to index.qmd!

[yebai]

One thing I would like to mention that each file will be renamed to index.qmd!

If you add a commit to rename all files and then add all the changes, Git will correctly track them.

[shravanngoswamii]

For now, they all will execute without any error because I put "eval=false" on the code blocks where I was getting errors and these are only a few documents from only tutorials section!

[shravanngoswamii]

Warnings in Using Turing section:

1. • Using Turing: External Samplers - Preview and Code Block
2. • I do not know if this progress log is meant to be visible or not - Preview and Code Block

Warnings in the Tutorials section:

1. • 01-gaussian-mixture-model: Warning - Preview and Code Block, cc @JasonPekos
2. • 02-logistic-regression: Warning - Preview and Code Block
3. • 03-bayesian-neural-network: Almost all code blocks are giving warning - Preview and Code floating point precision warning.
4. • 07-poisson-regression
     • Link in Line 1 is not valid
     • Warning - Preview and Code Block
5. • 08-multinomial-logistic-regression: Warning - Preview and Code Block
6. • 11-probabilistic-pca: Warning - Preview and Code Block
7. • 15-gaussian-processes: Warning - Preview (Scroll to last 2nd code block) and Code Block

Errors in Tutorials section:

1. • 00-introduction: this code block is giving error - Code Block, it was echoed false so there is not preview for it!
2. • 05-linear-regression: These Code Blocks from line 65 are failing to execute.
3. • 08-multinomial-logistic-regression: These Code Blocks are not executing successfully: Code Blocks
     • Reason: in the current .jmd version, there is a parameter - fig_ext=".png" passed along with code block but there no feature like this in Quarto as far as I know!
     • MCMCChains related error.
4. • 09-variational-inference: This Code Block failing to execute! for now, I put the eval: false on it!
     • VI inference result assertation fails.
5. • 10-bayesian-differential-equations: I do not know if this is an issue or not because here after this Code Block, its like never-ending execution, I waited for more than an hour but the execution is not ending after this code block, for now, I put an eval: false on all code blocks after this!
     • lots of warning in the SDE part -- planed to separate the SDE part into a separate tutorial.

[yebai]

08-multinomial-logistic-regression: These Code Blocks are not executing successfully: Code Blocks
Reason: in the current .jmd version, there is a parameter - fig_ext=".png" passed along with code block but there no feature like this in Quarto as far as I know!

Can you find an alternative way to visualise the result?

[shravanngoswamii]

Can you find an alternative way to visualise the result?

Ok, I will search for it!

[yebai]

10-bayesian-differential-equations: I do not know if this is an issue or not because here after this Code Block, its like never-ending execution, I waited for more than an hour but the execution is not ending after this code block, for now, I put an eval: false on all code blocks after this!

@devmotion, is this a known issue?

[shravanngoswamii]

10-bayesian-differential-equations: I do not know if this is an issue or not because here after this Code Block, its like never-ending execution, I waited for more than an hour but the execution is not ending after this code block, for now, I put an eval: false on all code blocks after this!

@devmotion, is this a known issue?

I checked again, there is no error in that notebook because it did run fine in github actions, and in my laptop its like never ending!

it still have many warnings!

[JasonPekos]

@yebai can you please have a look at

• https://turinglang.org/turing-test-website/docs/tutorials/10-bayesian-differential-equations/#inference-of-a-stochastic-differential-equation
• (scroll a bit) https://turinglang.org/turing-test-website/docs/tutorials/08-multinomial-logistic-regression/#model-declaration

Ok, for Bayesian differential equations, I think this may not be a super simple fix. Here is an unresolved issue with the same problem: TuringLang/Turing.jl#1722 (actually this same broken tutorial is mentioned here). I think the first thing I'd try would be to swap out some of the truncated Normals to LogNormals, and maybe we won't get the same issues.

I don't actually know the logic behind the pretty tight truncation because I haven't done much SDEs — surely this isn't ideal? It's not surprising to me that there's weird gradient stuff happening here.

I will try fiddling around with the model to see if I can get something working 🧐 .