Sourcing a python virtualenv inside R markdown?

[tere...@ucdavis.edu]

Hello All,

Does anyone have experience sourcing a python virtualenv inside of R markdown? I tried what I thought was the intuitive thing:

```{r}

getwd()

```

```{bash}

source eteEnv/bin/activate

```

```{python}

from ete3 import NCBITaxa

ncbi = NCBITaxa()

ncbi.update_taxonomy_database()

```

But this was not successful. I also tried calling the virtualenv with the package reticulate using `use_virtualenv(virtualenv, required = TRUE)`, and this was not successful either.

Does anyone have experience with this?

Best,

Taylor

[Ryan Peek]

A question along these exact lines came up today, see https://twitter.com/noamross/status/890923806608457729 for discussion. Short answer is system/reticulate seems only option.

Alternatively, Nick Santos recently shared a great tool (Windows only at the moment) going from the other direction, using R calls from python. Check it out:

https://github.com/ucd-cws/launchR

Thanks

R

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Center for Watershed Sciences, UC Davis

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[C. Titus Brown]

Hi Taylor,

the bash and python namespaces are almost certainly quite separate -
RMarkdown is presumably choosing a specific Python interpreter to
run.

Some googling

'python2 python3 rmarkdown'

and

'which python interpreter rmarkdown'

suggests that the answer is to specify the interpreter you want to use
via engine.path - see

http://rmarkdown.rstudio.com/authoring_knitr_engines.html

Here you would specify engine.path to be 'eteEnv/bin/python'.

Let me know if that works!

cheers,
--titus

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C. Titus Brown, ctb...@ucdavis.edu

[Alex Mandel]

What about using a Jupyter notebook with a mix of R and Python in
different chunks?

Alex Mandel, PhD

Center for Spatial Sciences
http://spatial.ucdavis.edu
Geospatial and Farming Systems Research Consortium
http://gfc.ucdavis.edu
University of California, Davis

[Taylor Reiter]

Thank you all for the suggestions!

Alex, I have used jupyter before and mixed kernels and like that solution quite a bit, however here I specifically wanted an .Rmd file that would render to an html...and wanted to know if I could use Rmarkdown for this sort of thing in the future :)

Titus, before you responded, tried: 

```

source eteEnv/bin/activate

Rscript -e "library(knitr); knit('oil_species_taxonomy.Rmd')" 

```

from the command line andthe document found the right python and rendered, however as an .md document, and not as a .html.

I tried your fix and it worked like a charm...thank you!!!

My python code blocks now read:

```{python, , engine.path = "./eteEnv/bin/python"}

from ete3 import NCBITaxa

...

```

Best,

Taylor

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