Changing Python executable to Ananconda

[rouseguy]

I use Anaconda as my Python distribution.

How do I set the notebook so that it picks the Anaconda's Python and not the system default ?

[rouseguy]

Figured this out. Need to use engine.path

```{python, engine.path="/anaconda/bin/python"}
import pandas as pd
print(pd.__version__)
data = pd.read_csv("~/Documents/data/train.csv")
print(train.head())

[MGallow]

This is a minor issue but is there a way to set Rstudio to default to the correct engine.path?

[kevinushey]

Good question -- I think this could be accomplished with a knitr hook, e.g. in a setup chunk (pseudocode):

```{r setup}
knit_hooks$set(engine = function(before, options, envir) {
    # detect python, set engine.path
})
```

@yihui, does this sound like a solution?

[yihui]

@kevinushey It is a solution, but perhaps it feels a little weird. I just added a more straightforward approach to knitr, and you can install the development version via

devtools::install_github('yihui/knitr')

Then you can set up the path of python in a code chunk like this:

```{setup, include=FALSE}
knitr::opts_chunk$set(engine.path = list(python = '/anaconda/bin/python'))
```

And the rest of python code chunks will use /anaconda/bin/python.

[kevinushey]

@yihui that's awesome, thanks!

[MichaelChirico]

for the record this should be documented here: http://rmarkdown.rstudio.com/authoring_knitr_engines.html

[aedobbyn]

Unfortunately, neither setting my opts_chunk like this nor editing my .Rprofile to add Sys.setenv(PATH = paste("<path_to_python3>", Sys.getenv("PATH"), sep=":")) has set the default python correctly. I have no trouble setting an individual chunk to run python3 by setting the engine.path for that chunk, but setting all chunks to default to python3 hasn't worked; it still defaults to python2 (the Apple default in /usr/bin/python). I'm on version 1.1.423 of RStudio for Mac and R version 3.3.3. @yihui I'd love to hear any suggestions about what I might be doing wrong.

Edit
The inline chunk does say the version is Python 2.7.10 but when it's knit it says the same chunk is Python 3.6.3 😕

[mjbeyeler]

I'm having the same issue. I can't get RStudio to recognize my Anaconda 2 python.

What WOULD work, is adding Anaconda to %PATH%, but I don't want to do that because that causes all sorts of other troubles in Windows.

[github-actions]

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