Display python stdout when using knitr

[dfalbel]

Fixes #1387 and fix #331

The approach used in this PR is to register a knitr hook that runs at the begining and end of each document chunk. In the begining of each chunk we remap Python's std streams to the same as R's (so knitr can capture them), at the end of the chunk we reset the streams to the default reticulate behavior (which is configurable with the RETICULATE_REMAP_OUTPUT_STREAMS env var).

Another approach would be to always set a output remap class in Python that would check at runtime if knitting is in progress by checking getOption('knitr.in.progress')), but this felt problematic because of possible concurrent calls, and the need to call R from the main thread.

This PR changes the default behavior of reticulate when rendering RMarkdown files, but users can easily go back to the previous behavior by setting include=FALSE in the chunk options. We also honor the RETICULATE_REMAP_OUTPUT_STREAMS if it's set:

• if it's set to "0" we never set-up the hook and there's no output redirection.
• If it's set to "1" we also don't set the hook as redirections are already in place.

[t-kalinowski]

This is great @dfalbel. I left some comments in line.
Thank you!

[t-kalinowski]

I might be misunderstand the order of events here. Does knitr call the knitr::knit_hooks with before = TRUE before it has resolved the chunk engines (meaning, before the reticulate namespace is loaded)?

My understanding is this code is either executing before knitr is loaded, or after, but never before reticulate has initialized python, and always before knitr has asked reticulate to process the chunk.

[dfalbel]

It's possible that a code in an R engine tries to print to stdout from python (eg using reticulate), in such case the hook is called with before = TRUE and at this point reticulate might have not loaded python yet - or even reticulate might not yet been namespace attached yet.

[t-kalinowski]

I see, so it's possible this call to set_output_streams() will initialize python, yes?

[t-kalinowski]

Look great, thank you!
Would you like to add a NEWS entry?

[t-kalinowski]

@dfalbel Can you please take a look at this failing test? I think it's related to this PR:
https://github.com/tidymodels/parsnip/actions/runs/5601457969/jobs/10253128187#step:8:581