Write / copy docs from IPython for rpy2.ipython magic

Issue #175 resolved
Dav Clark created an issue

This should include an updated version of the information in the sphynx docs on rmagic, as well as the ipython example notebook for rmagic.

Note - I'm calling lack of documentation a bug. But feel free to reassign!

Comments (13)

  1. Laurent Gautier

    Lack of documentation makes us unable to claim anything not working as a user would expect as " a (documented) feature, not a bug".

    I can understand to have this called a bug.


  2. Dav Clark reporter

    So actually, the docstrings are already there in rpy/ipython/rmagic.py, I don't know the peculiarities of sphynx (it's been a while), so if it's an easy fix to get those docs included in the rpy2 docs, that'd be good. I think we're close to where I'd be comfortable releasing - though I'd like to "fix" list conversion to use unlist() in R as opposed to np.asarray() on the python side.

    While I'm at it - would you be comfortable calling unlist on all newly created R list()'s?

  3. Dav Clark reporter

    I'm working now on getting the docs working, and it turns out the docs are hard to build / give difficult to parse error messages. So, I think it would be good to list out dependencies to build the full docs. As I understand it, that would include (beyond a working rpy2 session).

    python: pandas, numpy R: lattice, ggplot2, scales

    Anything else? Once that's there, I can tuck this into the "Installation" section in the docs.

  4. Dav Clark reporter

    Uploaded the minimal change required in interactive.rst. I'm not marking this resolved until someone else has a look and agrees that that's the right place for it... while we're at it, there's a Graphical User Interface heading with no content. What's that?

  5. Laurent Gautier

    @davclark : (Graphical User Interface) very old plans of writing how to make front-ends to R (GUI, IDE, etc..), and write a module/API along the way.

  6. Laurent Gautier

    @davclark Building the doc is not as bad as it seems, but largely undocumented. I'll had all steps to be Makefile (normally today).

  7. Laurent Gautier

    @davclark My initial reaction to unlist all created R lists is that this is not a good idea. We can make it is own issue/PR to go over options.

  8. Laurent Gautier

    I added targets to the Makefile in doc (5dd0e3d).

    To build the doc from a fresh clone, one should first make rpy2demo_graphics and only then make html or make latexpdf.

  9. Laurent Gautier

    Required R packages should be limited to:

    • ggplot2 (install it will also pull the required package reshape2)
    • hexbin
    • maps

    There is an entry in the rpy2 documentation that should contain everything needed to install R packages from Python.

  10. Dav Clark reporter

    OK - I'm building all graphics fine now. I'm seeing that at some point you checked in graphics_ggplot2withgrid.png (which is regenerated by your new make target). I'm guessing this is a mistake and I'm happy to delete it. Or, on the flipside, I can commit all the relevant graphics that are generated in that directory with it.

    Anyway, this thread is getting a bit off-topic, so I'm going to start a new thread for the unlist issue. If you're happy with the location of rpy2.ipython, please close this issue. But do let me know your answer to the question above!

  11. Laurent Gautier

    My mistake. Thanks for catching it. I think that it makes more sense to have no graphics in the repository (the exception being the logo).

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