Root directory for python chunk in knitr?

问题

I hope this isn't as simple as it feels. I've got a basic directory set up of:

root --> Paper
     --> Code

for a paper I'm writing. I want to call a Python script in the Code directory from my knitr document in the Paper directory (something like this, but with Python instead of R). So it would be something like this:

Python script testit.py

## @knitr testit
import os
print os.getcwd()

knitr document test.Rnw saved in the Code directory:

\documentclass{article}
\begin{document}

<<setup,echo=FALSE>>=
read_chunk("testit.py")
@

<<testit,engine='python'>>=
@

\end{document}

When I compile to PDF, the answer is right:

## /Users/blah/foo/bar/Code

But document test-2.Rnw saved in the Paper directory:

\documentclass{article}
\begin{document}

<<setup,echo=FALSE>>=
opts_knit$set(root.dir="../Code/")
read_chunk("../Code/testit.py")
@

<<testit,engine='python'>>=
@

\end{document}

outputs:

## /Users/blah/foo/bar/Paper

root.dir has no obvious effect here like it would for an R chunk, and I don't know what else to try to change the directory for the Python chunk. This is a problem, because I would like the python script to operate on files in the Code directory, but of course it can't find them. I could hard code a directory change in the python script, but that seems fragile. I'd even be happy passing the root directory directly to the python interpreter as an argument to the script, were that possible (but I don't think so, because knitr uses python -c ?). Any thoughts on how to handle this? My google-fu has failed me here...

回答1:

Sorry I did not pay enough attention to the path issue for engines other than R. Now this problem has been fixed in the development version on Github.

来源：https://stackoverflow.com/questions/15512545/root-directory-for-python-chunk-in-knitr

标签

knitr