convert_ipynb silently drops raw cells with no format in metadata

[katrinabrock]

Description

Because of this line, if a python notebook has a raw type cell that does not have format specified in the metadata, that cell is completely omitted when convert_ipynb transforms the notebook to rmd. IMO this is inconsistent with how raw cells are described in jupyter docs as well as how jupyterhub handles them. Testing with jupyterhub (I tested with server version 6.5.4), content in raw cells that are not specified as latex or html get transferred verbatim into both formats. Example below.

Suggested Resolutions

• If this is the expected behavior, it would be nice for it to be documented in help text of convert_ipynb function. Currently, raw cells are not mentioned at all.
• Otherwise, it would be nice to give users a way to pass these cells through in some way. IMO ideal would be for the user to be able to chose whether to put raw cells directly into the Rmd as though they were Rmd or to put them in in code not running code blocks.

MRE

Python Notebook

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "17e25b19",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "regular code cell\n"
     ]
    }
   ],
   "source": [
    "print('regular code cell')"
   ]
  },
  {
   "cell_type": "raw",
   "id": "bea4ed8a",
   "metadata": {},
   "source": [
    "print('raw cell')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4545441e",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.15"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}

RMarkdown actual result

---
title: An R Markdown document converted from "mre.ipynb" 
output: html_document
---

```{python}
print('regular code cell')
```

Backslashes added so it will show up properly on github.

Rmarkdown expected result

---
title: An R Markdown document converted from "mre.ipynb" 
output: html_document
---

```{python}
print('regular code cell')
```
print('raw cell')

jupyterhub html result

jupyterhub latex result

Checklist

When filing a bug report, please check the boxes below to confirm that you have provided us with the information we need. Have you:

• formatted your issue so it is easier for us to read?

• included a minimal, self-contained, and reproducible example?

• pasted the output from xfun::session_info('rmarkdown') in your issue?

• upgraded all your packages to their latest versions (including your versions of R, the RStudio IDE, and relevant R packages)?

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Session Info

``` xfun::session_info('rmarkdown') R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS, RStudio 0

Locale:
LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8
LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

Package version:
base64enc_0.1.3 bslib_0.8.0 cachem_1.1.0 cli_3.6.3
digest_0.6.37 evaluate_1.0.1 fastmap_1.2.0 fontawesome_0.5.3
fs_1.6.5 glue_1.8.0 graphics_4.3.2 grDevices_4.3.2
highr_0.11 htmltools_0.5.8.1 jquerylib_0.1.4 jsonlite_1.8.9
knitr_1.49 lifecycle_1.0.4 memoise_2.0.1 methods_4.3.2
mime_0.12 R6_2.5.1 rappdirs_0.3.3 rlang_1.1.4
rmarkdown_2.29 sass_0.4.9 stats_4.3.2 tinytex_0.54
tools_4.3.2 utils_4.3.2 xfun_0.49 yaml_2.3.10

Pandoc version: 3.6

</details>

[yihui]

Sounds like the fix should be simple enough. Do you mean that we return(x) instead of return() here?

rmarkdown/R/jupyter.R

Line 107 in 204879f

if (length(fmt) != 1) return()

[katrinabrock]

Yes, and maybe line 109 as well. I can make a PR if you agree this is a bug.

[yihui]

Sure. Please do. Thank you very much!