I am trying to run python as rmarkdwon code chunks. I was successful but rmarkdown by default uses Python2 and I want it to use Python 3. I am running it on Ubuntu with Python 2.7.6 installed and I installed anaconda with Python 3.5, which is the one I want rmarkdown use.
Here is the code and output of the python chunk in rmarkdown
import sys
print (sys.version)
and the output:
2.7.6 (default, Jun 22 2015, 17:58:13)
Any ideas?
You can add engine.path = '/path/to/python3' to override the python (2) executable. For example,
---
title: "python"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{python}
import sys
print(sys.version)
```
```{python, engine.path = '/usr/bin/python3'}
import sys
print(sys.version)
```
You can select your desired python version, as default, with an R chunk:
```{r setup, echo=FALSE}
library(knitr)
opts_chunk$set(engine.path = '/usr/bin/python3')
```
From now on your python chunks will use Python3:
```{python}
import sys
print(sys.version)
```
This way to select python version avoids to add the engine.path variable to every code chunk.
Actually, if you are running Python 3.x, which I am, I had to do the following (obviously your path to the Python3 executable might be different):
```{r Setup, echo=FALSE}
library(knitr)
opts_chunk$set('python', engine.path='/usr/local/Cellar/python3/3.6.3/bin/python3')
```
And could then create a chunk using just python and it would run in the correct version:
```{python, cache=TRUE, echo = FALSE, eval = TRUE}
import sys
print(sys.version)
```
You can use the reticulate package and insert an R chunk at the beginning:
```{r}
library(reticulate)
use_python("/usr/local/bin/python3")
```
