How to make a python variable persist between chunk in a markdown notebook?

Variable are not retained from one chunk to the next in notebook mode, but they are retained when knitting the markdown document to html.

I made a sample document available as a gist called pythonvariables.Rmd, the content of this file is:

---
title: "R Notebook"
output:
html_document:
df_print: paged
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(reticulate)
```

```{python}
x = 1
```

```{python}
print(x)
```

```{r}
print(py$x)
```


In Rstudio version 1.1.453, in notebook mode, when running one chunk after the other, the output of the print(x) python chunk is:

print(x)

Traceback (most recent call last):
File "C:UsersrougipaAppDataLocalTemp2RtmpQFW3Rjchunk-code-1d44920f50.txt", line 1, in <module>
print(x)
NameError: name 'x' is not defined


However the issue doesn't appear when the Rmd is compiled to html. The output of the print(x) python chunk is 1 as expected.

print(x)

It's related to the third comment by pjcrosbie in this knitr bug request: Python environment persistance across chunks #1440.
– Paul Rougieux
Jun 27 at 14:11

Gists can disappear or change over time, could you include the (current) source of the Rmarkdown document to keep this question self-sufficient?
– r2evans
Jun 27 at 14:34

If a question is related to RStudio, please state its version. Without that information, a blind guess is that the latest (preview) version might have fixed your problem: rstudio.com/products/rstudio/download/preview
– Yihui Xie
Jun 28 at 15:00

1 Answer
1

This functionality works in Rstudio preview 1.2.747. Question kept for historical purposes.

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