org-mode/rorg.org

#+OPTIONS:    H:3 num:nil toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t TeX:t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc
#+TITLE: rorg --- Code evaluation in org-mode, with an emphasis on R
#+SEQ_TODO:  TODO OPEN PROPOSED | DONE RESOLVED REJECTED
#+STARTUP: oddeven

* Tasks [7/14]

** TODO test for litorgy
since we are accumulating this nice collection of source-code blocks
in the sandbox section we should make use of them as unit tests.
What's more, we should be able to actually use litorgy to run these
tests.

We would just need to cycle over every source code block under the
sandbox, run it, and assert that the return value is equal to what we
expect.

I have the feeling that this should be possible using only litorgical
functions with minimal or no additional elisp.  It would be very cool
for litorgy to be able to test itself.

** TODO source blocks as functions

Allow source code blocks to be called like functions, with arguments
specified.  We are already able to call a source-code block and assign
it's return result to a variable.  This would just add the ability to
specify the values of the arguments to the source code block assuming
any exist.  For an example see 

When a variable appears in a header argument, how do we differentiate
between it's value being a reference or a literal value?  I guess this
could work just like a programming language.  If it's escaped or in
quotes, then we count it as a literal, otherwise we try to look it up
and evaluate it.

** TODO figure out how to handle graphic output
This is listed under [[* graphical output][graphical output]] in out objectives.

How should this work for R?  For example how are files included with
Sweave?  Would/Should we just mimic the behavior of Sweave with the
addition of support for poping up graphics during live evaluation of a
source code block.

I think the best way to approach this would be to start with an
example R source-code block and then work up from there.

** TODO ability to select which of multiple sessions is being used
   Increasingly it is looking like we're going to want to run all
   source code blocks in comint buffer (sessions).  Which will have
   the benefits of
   1) allowing background execution
   2) maintaining state between source-blocks
      - allowing inline blocks w/o header arguments 

*** R sessions
    (like ess-switch-process in .R buffers)
    
    Maybe this could be packaged into a header argument, something
    like =:R_session= which could accept either the name of the
    session to use, or the string =prompt=, in which case we could use
    the =ess-switch-process= command to select a new process.
    
** TODO evaluation of shell code as background process? 
   After C-c C-c on an R code block, the process may appear to
   block, but C-g can be used to reclaim control of the .org buffer,
   without interrupting the R evalution. However I believe this is not
   true of bash/sh evaluation. [Haven't tried other languages] Perhaps
   a solution is just to background the individual shell commands.

   The other languages (aside from emacs lisp) are run through the
   shell, so if we find a shell solution it should work for them as
   well.
   
   Adding an ampersand seems to be a supported way to run commands in
   the background (see [[http://www.emacswiki.org/emacs/ExecuteExternalCommand#toc4][external-commands]]).  Although a more extensible
   solution may involve the use of the [[elisp:(progn (describe-function 'call-process-region) nil)][call-process-region]] function.
   
   Going to try this out in a new file [[file:litorgy/litorgy-proc.el][litorgy-proc.el]].  This should
   contain functions for asynchronously running generic shell commands
   in the background, and then returning their input.

*** partial update of org-mode buffer
   The sleekest solution to this may be using a comint buffer, and
   then defining a filter function which would incrementally interpret
   the results as they are returned, including insertion into the
   org-mode buffer.  This may actually cause more problems than it is
   worth, what with the complexities of identifying the types of
   incrementally returned results, and the need for maintenance of a
   process marker in the org buffer.

*** 'working' spinner
    It may be nice and not too difficult to place a spinner on/near the
    evaluating source code block

** TODO conversion of output from interactive shell, R (and python) sessions to litorgy buffers
   [DED] This would be a nice feature I think. Although a litorgy purist
   would say that it's working the wrong way round... After some
   interactive work in a *R* buffer, you save the buffer, maybe edit
   out some lines, and then convert it to litorgy format for
   posterity. Same for a shell session either in a *shell* buffer, or
   pasted from another terminal emulator. And python of course.

** PROPOSED re-implement helper functions from org-R
Much of the power of org-R seems to be in it's helper functions for
the quick graphing of tables.  Should we try to re-implement these
functions on top of litorgy?

I'm thinking this may be useful both to add features to litorgy-R and
also to potentially suggest extensions of the framework.  For example
one that comes to mind is the ability to treat a source-code block
like a function which accepts arguments and returns results. Actually
this can be it's own TODO (see [[* source blocks as functions][source blocks as functions]]).

** DONE folding of code blocks? [2/2]
   [DED] In similar way to using outline-minor-mode for folding function
   bodies, can we fold code blocks?  #+begin whatever statements are
   pretty ugly, and in any case when you're thinking about the overall
   game plan you don't necessarily want to see the code for each Step.

*** DONE folding of source code block
    Sounds good, and wasn't too hard to implement.  Code blocks should
    now be fold-able in the same manner as headlines (by pressing TAB
    on the first line).

*** REJECTED folding of results
    So, lets do a three-stage tab cycle... First fold the src block,
    then fold the results, then unfold.
    
    There's no way to tell if the results are a table or not w/o
    actually executing the block which would be too expensive of an
    operation.

** DONE inline source code blocks [2/2]
   Like the =\R{ code }= blocks

   not sure what the format should be, maybe just something simple
   like =src_lang{}= where lang is the name of the source code
   language to be evaluated.

   The biggest problem I see with these is that their main use would
   be to show the value of a variable, but the variable would need to
   be assigned through a header argument (aside from in languages like
   R in which all execution takes place in a session).  Requiring a
   header argument for a inline blocks defeats the purpose of a small,
   concise inline-able block.

   Maybe this makes a good case for all source code having the option
   of specifying a session.  I'll add that to the [[ability to select which of multiple sessions is being used][session TODO]].

*** DONE evaluation with \C-c\C-c
Putting aside the header argument issue for now we can just run these
with the following default header arguments
- =:results= :: silent
- =:exports= :: results

*** DONE inline exportation
Need to add an interblock hook (or some such) through org-exp-blocks
** DONE selective export of text, code, figures
   [DED] The litorgy buffer contains everything (code, headings and
   notes/prose describing what you're up to, textual/numeric/graphical
   code output, etc). However on export to html / LaTeX one might want
   to include only a subset of that content. For example you might
   want to create a presentation of what you've done which omits the
   code.

   [EMS] So I think this should be implemented as a property which can
   be set globally or on the outline header level (I need to review
   the mechanics of org-mode properties).  And then as a source block
   header argument which will apply only to a specific source code
   block.  A header argument of =:export= with values of
   
   - =code= :: just show the code in the source code block
   - =none= :: don't show the code or the results of the evaluation
   - =results= :: just show the results of the code evaluation (don't
                  show the actual code)
   - =both= :: show both the source code, and the results

this will be done in [[* (sandbox) selective export][(sandbox) selective export]].

** DONE a header argument specifying silent evaluation (no output)
This would be useful across all types of source block.  Currently
there is a =:replace t= option to control output, this could be
generalized to an =:output= option which could take the following
options (maybe more)

- =t= :: this would be the default, and would simply insert the
         results after the source block
- =replace= :: to replace any results which may already be there
- =silent= :: this would inhibit any insertion of the results

This is now implemented see the example in the [[* silent evaluation][sandbox]]

** DONE assign variables from tables in R
This is now working (see [[* (sandbox table) R][(sandbox-table)-R]]).  Although it's not that
impressive until we are able to print table results from R.

** DONE insert 2-D R results as tables
everything is working but R and shell

*** DONE shells

*** DONE R

This has already been tackled by Dan in [[file:existing_tools/org-R.el::defconst%20org%20R%20write%20org%20table%20def][org-R:check-dimensions]].  The
functions there should be useful in combination with [[http://cran.r-project.org/doc/manuals/R-data.html#Export-to-text-files][R-export-to-csv]]
as a means of converting multidimensional R objects to emacs lisp.

It may be as simple as first checking if the data is multidimensional,
and then, if so using =write= to write the data out to a temporary
file from which emacs can read the data in using =org-table-import=.

Looking into this further, is seems that there is no such thing as a
scalar in R [[http://tolstoy.newcastle.edu.au/R/help/03a/3733.html][R-scalar-vs-vector]].  In that light I am not sure how to
deal with trivial vectors (scalars) in R.  I'm tempted to just treat
them as vectors, but then that would lead to a proliferation of
trivial 1-cell tables...

** DONE allow variable initialization from source blocks
Currently it is possible to initialize a variable from an org-mode
table with a block argument like =table=sandbox= (note that the
variable doesn't have to named =table=) as in the following example

#+TBLNAME: sandbox
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+begin_src emacs-lisp :var table=sandbox :results replace
(message (format "table = %S" table))
#+end_src

: "table = ((1 2 3) (4 \"schulte\" 6))"

It would be good to allow initialization of variables from the results
of other source blocks in the same manner.  This would probably
require the addition of =#+SRCNAME: example= lines for the naming of
source blocks, also the =table=sandbox= syntax may have to be expanded
to specify whether the target is a source code block or a table
(alternately we could just match the first one with the given name
whether it's a table or a source code block).

At least initially I'll try to implement this so that there is no need
to specify whether the reference is to a table or a source-code block.
That seems to be simpler both in terms of use and implementation.

This is now working for emacs-lisp, ruby and python (and mixtures of
the three) source blocks.  See the examples in the [[* (sandbox) referencing other source blocks][sandbox]].

This is currently working only with emacs lisp as in the following
example in the [[* emacs lisp source reference][emacs lisp source reference]].


* Bugs [2/2]
** RESOLVED Args out of range error
   
The following block resulted in the error below [DED]. It ran without
error directly in the shell.
#+begin_src sh
cd ~/work/genopca
for platf in ill aff ; do
    for pop in CEU YRI ASI ; do
	rm -f $platf/hapmap-genos-$pop-all $platf/hapmap-rs-all
	cat $platf/hapmap-genos-$pop-* > $platf/hapmap-genos-$pop-all
	cat $platf/hapmap-rs-* > $platf/hapmap-rs-all
    done
done
#+end_src
  
 executing source block with sh...
finished executing source block
string-equal: Args out of range: "", -1, 0

the error =string-equal: Args out of range: "", -1, 0= looks like what
used to be output when the block returned an empty results string.
This should be fixed in the current version, you should now see the
following message =no result returned by source block=.

** RESOLVED ruby arrays not recognized as such

Something is wrong in [[file:litorgy/litorgy-script.el]] related to the
recognition of ruby arrays as such.

#+begin_src ruby :results replace
[1, 2, 3, 4]
#+end_src

| 1 | 2 | 3 | 4 |

#+begin_src python :results replace
[1, 2, 3, 4]
#+end_src

| 1 | 2 | 3 | 4 |


* Sandbox
  :PROPERTIES:
  :CUSTOM_ID: sandbox
  :END:
This is a place for code examples

** litorgy.el beginning functionality
After evaluating litorgy.el and litorgy-script.el, you should be able
to evaluate the following blocks of code by pressing =\C-c\C-c= on the
header lines. *Note*: your version of org-mode must be at least 6.23
or later.

To run these examples open both [[file:litorgy/litorgy.el][litorgy.el]], [[file:litorgy/litorgy-script.el][litorgy-script.el]] and
evaluate them with =M-x eval-buffer=

#+begin_src sh  :results replace
date
#+end_src

: Sun Apr  5 10:10:05 PDT 2009

#+begin_src ruby
puts Time.now
#+end_src

#+begin_src python
print "Hello world!"
#+end_src


** litorgy-R
To run these examples open both [[file:litorgy/litorgy.el][litorgy.el]], [[file:litorgy/litorgy-R.el][litorgy-R.el]] and evaluate
them with =M-x eval-buffer=

#+begin_src R :results replace
a <- 9
b <- 17
a + b
#+end_src

| 26 |


#+begin_src R
hist(rgamma(20,3,3))
#+end_src


** free variables

First assign the variable with some sort of interpreted line
- this is independent of any particular type of source code
- this could use references to table ranges



** resource reference example
*Note*: this example is largely *defunct*, see the
[[* litorgy plays with tables][litorgy-plays-with-tables]] section below.

This block holds an array of information written in [[http://www.yaml.org][YAML]]

#name: yaml-array
#+begin_src yaml
--- 
- 1
- 2
- 3
- 4
- 5
#+end_src

This next block saves the information in the YAML array into the ruby
variable =ya= and then in ruby it multiplies each variable in the =ya=
by 2.

#name: ruby-array
#assign: ya = yaml-array
#+begin_src ruby
ya.map{ |e| e * 2 }
#+end_src

This final block takes the output of the ruby block, and writes it to
cell =0,0= through =0,3= of the table

#name: example-table
#assign: self[0, (1..3)] = ruby-array
| example results |
|-----------------|
|                 |
|                 |
|                 |


** litorgy plays with tables
Alright, this should demonstrate both the ability of litorgy to read
tables into a lisp source code block, and to then convert the results
of the source code block into an org table.  It's using the classic
"lisp is elegant" demonstration transpose function.  To try this
out...

1. evaluate [[file:litorgy/init.el]] to load litorgy and friends
2. evaluate the transpose definition =\C-u \C-c\C-c= on the beginning of
   the source block (prefix arg to inhibit output)
3. evaluate the next source code block, this should read in the table
   because of the =:var table=previous=, then transpose the table, and
   finally it should insert the transposed table into the buffer
   immediately following the block

*** Emacs lisp

#+begin_src emacs-lisp
(defun transpose (table)
  (apply #'mapcar* #'list table))
#+end_src

#+TBLNAME: sandbox
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+begin_src emacs-lisp :var table=previous :results replace
(transpose table)
#+end_src

#+begin_src emacs-lisp :var table=sandbox :results replace
(transpose table)
#+end_src

#+begin_src emacs-lisp
'(1 2 3 4 5)
#+end_src

| 1 | 2 | 3 | 4 | 5 |


*** Ruby and Python

#+begin_src ruby :var table=sandbox :results replace
table.first.join(" - ")
#+end_src

: "1 - 2 - 3"

#+begin_src python :var table=sandbox :results replace
table[0]
#+end_src

| 1 | 2 | 3 |

#+begin_src ruby :var table=sandbox :results replace
table
#+end_src

| 1 |         2 | 3 |
| 4 | "schulte" | 6 |

#+begin_src python :var table=sandbox :results replace
table
#+end_src

| 1 |         2 | 3 |
| 4 | "schulte" | 6 |

*** (sandbox table) R

#+TBLNAME: sandbox_r
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+begin_src R :results replace
x <- c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1))
x
#+end_src

#+begin_src R var tabel=sandbox_r :results replace
tabel
#+end_src

| 1 |         2 | 3 |
| 4 | "schulte" | 6 |



*** shell
Now shell commands are converted to tables using =org-table-import=
and if these tables are non-trivial (i.e. have multiple elements) then
they are imported as org-mode tables...

#+begin_src sh
ls -l
#+end_src

| "total"      | 96 | ""         | ""         |    "" |   "" | "" | ""                |
| "-rw-r--r--" |  1 | "eschulte" | "eschulte" |    57 | 2009 |  7 | "block"           |
| "-rw-r--r--" |  1 | "eschulte" | "eschulte" | 35147 | 2009 |  7 | "COPYING"         |
| "drwxr-xr-x" |  4 | "eschulte" | "eschulte" |  4096 | 2009 | 16 | "existing_tools"  |
| "drwxr-xr-x" |  2 | "eschulte" | "eschulte" |  4096 | 2009 | 10 | "litorgy"         |
| "-rw-r--r--" |  1 | "eschulte" | "eschulte" |   277 | 2009 | 15 | "README.markdown" |
| "-rw-r--r--" |  1 | "eschulte" | "eschulte" | 41385 | 2009 | 10 | "rorg.org"        |



** silent evaluation

#+begin_src ruby
:im_the_results
#+end_src

#+begin_src ruby :results silent
:im_the_results
#+end_src

#+begin_src ruby :results replace
:im_the_results
#+end_src


** (sandbox) referencing other source blocks
Doing this in emacs-lisp first because it's trivial to convert
emacs-lisp results to and from emacs-lisp.

*** emacs lisp source reference
This first example performs a calculation in the first source block
named =top=, the results of this calculation are then saved into the
variable =first= by the header argument =:var first=top=, and it is
used in the calculations of the second source block.

#+SRCNAME: top
#+begin_src emacs-lisp
(+ 4 2)
#+end_src

#+begin_src emacs-lisp :var first=top :results replace
(* first 3)
#+end_src

This example is the same as the previous only the variable being
passed through is a table rather than a number.

#+begin_src emacs-lisp :results silent
(defun transpose (table)
  (apply #'mapcar* #'list table))
#+end_src

#+TBLNAME: top_table
| 1 |       2 | 3 |
| 4 | schulte | 6 |

#+SRCNAME: second_src_example
#+begin_src emacs-lisp :var table=top_table
(transpose table)
#+end_src

#+begin_src emacs-lisp :var table=second_src_example :results replace
(transpose table)
#+end_src

*** ruby python
Now working for ruby

#+srcname: start
#+begin_src ruby
89
#+end_src

#+begin_src ruby :var other=start :results replace
2 * other
#+end_src

: 178

and for python

#+SRCNAME: start_two
#+begin_src python
98
#+end_src

#+begin_src python :var another=start_two :results replace
another*3
#+end_src

: 294


*** mixed languages
Since all variables are converted into Emacs Lisp it is no problem to
reference variables specified in another language.

#+SRCNAME: ruby-block
#+begin_src ruby
2
#+end_src

#+SRCNAME: lisp_block
#+begin_src emacs-lisp :var ruby-variable=ruby-block
(* ruby-variable 8)
#+end_src

#+begin_src python :var lisp_var=lisp_block
lisp_var + 4
#+end_src

*** R
not yet implemented

#+srcname: first_r
#+begin_src R :results replace
a <- 9
a
#+end_src

: 9

#+begin_src R :var other=first_r :results replace
other + 2
#+end_src

: 11



** (sandbox) selective export

For exportation tests and examples see (including exportation of
inline source code blocks) [[file:test-export.org]]


** (sandbox) source blocks as functions

#+srcname: default
#+begin_src emacs-lisp
5
#+end_src

#+srcname: triple
#+begin_src emacs-lisp :var n=default :results replace
(* 3 n)
#+end_src

: 15

#+begin_src emacs-lisp :var result=triple(n=8)
result
#+end_src

#+begin_src ruby :var num="eric"
num+" schulte"
#+end_src

: "eric schulte"


* COMMENT Commentary
I'm seeing this as like commit notes, and a place for less formal
communication of the goals of our changes.

** Eric <2009-02-06 Fri 15:41>
I think we're getting close to a comprehensive set of objectives
(although since you two are the real R user's I leave that decision up
to you).  Once we've agreed on a set of objectives and agreed on at
least to broad strokes of implementation, I think we should start
listing out and assigning tasks.

** Eric <2009-02-09 Mon 14:25>
I've done a fairly destructive edit of this file.  The main goal was
to enforce a structure on the document that we can use moving forward,
so that any future objective changes are all made to the main
objective list.

I apologize for removing sections written by other people.  I did this
when they were redundant or it was not clear how to fit them into this
structure.  Rest assured if the previous text wasn't persisted in git
I would have been much more cautious about removing it.

I hope that this outline structure should be able to remain stable
through the process of fleshing out objectives, and cashing those
objectives out into tasks.  That said, please feel free to make any
changes that you see fit.

** Dan <2009-02-12 Thu 10:23>
   Good job Eric with major works on this file.

** Eric <2009-02-22 Sun 13:17>
So I skipped ahead and got started on the fun part.  Namely stubbing
out some of the basic functionality.  Please don't take any of the
decisions I've made so far (on things like names, functionality,
design etc...) as final decisions, I'm of course open to and hoping
for improvement.

So far [[file:litorgy/litorgy.el][litorgy.el]] and [[file:litorgy/litorgy-script.el][litorgy-script.el]] can be used to evaluate source
code blocks of simple scripting languages.  It shouldn't be too hard
(any takers) to write a litorgy-R.el modeled after litorgy-script.el
to use for evaluating R code files.

See the [[* litorgy.el beginning functionality][Sandbox]] for evaluable examples.

** Eric <2009-02-23 Mon 15:12>
While thinking about how to implement the transfer of data between
source blocks and the containing org-mode file, I decided it *might*
be useful to explicitly support the existence of variables which exist
independent of source blocks or tables.  I'd appreciate any
feedback... (see [[free explicit variables][free explicit variables]])

** Eric <2009-02-23 Mon 17:53>
So as I start populating this file with source code blocks I figure I
should share this... I don't know if you guys use [[http://code.google.com/p/smart-snippet/][yasnippet]] at all,
but if you do you might find this [[file:block][block-snippet]] org-mode snippet
useful (I use it all the time).


* Overview
This project is basically about putting source code into org
files. This isn't just code to look pretty as a source code example,
but code to be evaluated. Org files have 3 main export targets: org,
html and latex. Once we have implemented a smooth bi-directional flow
of data between org-mode formats (including tables, and maybe lists
and property values) and source-code blocks, we will be able to use
org-mode's built in export to publish the results of evaluated source
code in any org-supported format using org-mode as an intermediate
format.  We have a current focus on R code, but we are regarding that
more as a working example than as a defining feature of the project.

The main objectives of this project are...

# Lets start with this list and make changes as appropriate.  Please
# try to make changes to this list, rather than starting any new
# lists.

- [[* evaluation of embedded source code][evaluation of embedded source code]]
  - [[* execution on demand and on export][execution on demand and on export]]
  - [[* source blocks][source blocks]]
  - [[* header arguments][header arguments]]
  - [[* inline source evaluation][inline source evaluation]]
  - [[* included source file evaluation][included source file evaluation]] ?? maybe
  - [[* caching of evaluation][caching of evaluation]]
- [[* interaction with the source-code's process][interaction with the source-code's process]]
- [[* output of code evaluation][output of code evaluation]]
  - [[* textual/numeric output][textual/numeric output]]
  - [[* graphical output][graphical output]]
  - [[* file creation][non-graphics file creation]]
  - [[* side effects][side effects]]
- [[* reference to data and evaluation results][reference to data and evaluation results]]
  - [[* reference format][reference format]]
  - [[* source-target pairs][source-target pairs]]
    - [[* source block output from org tables][source block output from org tables]]
    - [[* source block outpt from other source block][source block outpt from other source block]]
    - [[* source block output from org list][source block output from org list]] ?? maybe
    - [[* org table from source block][org table from source block]]
    - [[* org table from org table][org table from org table]]
    - [[* org properties from source block][org properties from source block]]
    - [[* org properties from org table][org properties from org table]]
- [[* export][export]]


* Objectives and Specs

** evaluation of embedded source code

*** execution on demand and on export
    Let's use an asterisk to indicate content which includes the *result* of code evaluation, rather than the code itself. Clearly
    we have a requirement for the following transformation:

    org \to org*

    Let's say this transformation is effected by a function
    `org-eval-buffer'. This transformation is necessary when the
    target format is org (say you want to update the values in an org
    table, or generate a plot and create an org link to it), and it
    can also be used as the first step by which to reach html and
    latex:
    
    org \to org* \to html

    org \to org* \to latex

    Thus in principle we can reach our 3 target formats with
    `org-eval-buffer', `org-export-as-latex' and `org-export-as-html'.
    
    An extra transformation that we might want is
    
    org \to latex

    I.e. export to latex without evaluation of code, in such a way that R
    code can subsequently be evaluated using
    =Sweave(driver=RweaveLatex)=, which is what the R community is
    used to. This would provide a `bail out' avenue where users can
    escape org mode and enter a workflow in which the latex/noweb file
    is treated as source.

**** How do we implement `org-eval-buffer'?
    
     AIUI The following can all be viewed as implementations of
     org-eval-buffer for R code:

     (see this question again posed in [[file:litorgy/litorgy-R.el::Maybe%20the%20following%20be%20replaced%20with%20a%20method%20using%20ess%20execute][litorgy-R.el]])
    
***** org-eval-light
      This is the beginnings of a general evaluation mechanism, that
      could evaluate python, ruby, shell, perl, in addition to R.
      The header says it's based on org-eval

      what is org-eval??
      
      org-eval was written by Carsten.  It lives in the
      org/contrib/lisp directory because it is too dangerous to
      include in the base.  Unlike org-eval-light org-eval evaluates
      all source blocks in an org-file when the file is first opened,
      which could be a security nightmare for example if someone
      emailed you a pernicious file.
      
***** org-R
      This accomplishes org \to org* in elisp by visiting code blocks
      and evaluating code using ESS.

***** RweaveOrg
      This accomplishes org \to org* using R via
      
: Sweave("file-with-unevaluated-code.org", driver=RweaveOrg, syntax=SweaveSyntaxOrg)

***** org-exp-blocks.el
      Like org-R, this achieves org \to org* in elisp by visiting code
      blocks and using ESS to evaluate R code.

*** source blocks
(see [[* Special editing and evaluation of source code][Special editing and evaluation of source code]])

*** header arguments
(see [[* block headers/parameters][block headers/parameters]])

There are going to be many cases where we want to use header arguments
to change the evaluation options of source code, to pass external
information to a block of source code and control the inclusion of
evaluation results.

*** inline source evaluation
*** included source file evaluation
It may be nice to be able to include an entire external file of source
code, and then evaluate and export that code as if it were in the
file.  The format for such a file inclusion could optionally look like
the following

: #+include_src filename header_arguments

*** caching of evaluation

Any kind of code that can have a block evaluated could optionally define
a function to write the output to a file, or to serialize the output of
the function.  If a document or block is configured to cache input,
write all cached blocks to their own files and either a) hash them, or
b) let git and org-attach track them.  Before a block gets eval'd, we
check to see if it has changed.  If a document or block is configured to
cache output and a print/serialize function is available, write the
output of each cached block to its own file.  When the file is eval'd
and some sort of display is called for, only update the display if the
output has changed.  Each of these would have an override, presumably
something like (... & force) that could be triggered with a prefix arg
to the eval or export function.

For R, I would say

#+begin_src emacs-lisp
;; fake code that only pretends to work
(add-hook 'rorg-store-output-hook 
    '("r" lambda (block-environment block-label)
        (ess-exec (concat "save.image("
                          block-environment
                          ", file = " block-label
                          ".Rdata, compress=TRUE)"))))
#+end_src

The idea being that for r blocks that get eval'd, if output needs to be
stored, you should write the entire environment that was created in that
block to an Rdata file.

(see [[* block scoping][block scoping]])

** interaction with the source-code's process
We should settle on a uniform API for sending code and receiving
output from a source process.  Then to add a new language all we need
to do is implement this API.

for related notes see ([[* Interaction with the R process][Interaction with the R process]])

** output of code evaluation
*** textual/numeric output
    We (optionally) incorporate the text output as text in the target
    document
*** graphical output
    We either link to the graphics or (html/latex) include them
    inline.
    
    I would say, if the block is being evaluated interactively then
    lets pop up the image in a new window, and if it is being exported
    then we can just include a link to the file which will be exported
    appropriately by org-mode.
    
*** non-graphics files
    ? We link to other file output
*** side effects
If we are using a continuous process in (for example an R process
handled by ESS) then any side effects of the process (for example
setting values of R variables) will be handled automatically

Are there side-effects which need to be considered aside from those
internal to the source-code evaluation process?

** reference to data and evaluation results
   I think this will be very important.  I would suggest that since we
   are using lisp we use lists as our medium of exchange.  Then all we
   need are functions going converting all of our target formats to and
   from lists.  These functions are already provided by for org tables.

   It would be a boon both to org users and R users to allow org tables
   to be manipulated with the R programming language.  Org tables give R
   users an easy way to enter and display data; R gives org users a
   powerful way to perform vector operations, statistical tests, and
   visualization on their tables.

   This means that we will need to consider unique id's for source
   blocks, as well as for org tables, and for any other data source or
   target.

*** Implementations
**** naive
     Naive implementation would be to use =(org-export-table "tmp.csv")=
     and =(ess-execute "read.csv('tmp.csv')")=.  
**** org-R
     org-R passes data to R from two sources: org tables, or csv
     files. Org tables are first exported to a temporary csv file
     using [[file:existing_tools/org-R.el::defun%20org%20R%20export%20to%20csv%20csv%20file%20options][org-R-export-to-csv]].
**** org-exp-blocks
     org-exp-blocks uses [[org-interblock-R-command-to-string]] to send
     commands to an R process running in a comint buffer through ESS.
     org-exp-blocks has no support for dumping table data to R process, or
     vice versa.

**** RweaveOrg
     NA

*** reference format
    This will be tricky, Dan has already come up with a solution for R, I
    need to look more closely at that and we should try to come up with a
    formats for referencing data from source-code in such a way that it
    will be as source-code-language independent as possible.
    
    Org tables already have a sophisticated reference system in place
    that allows referencing table ranges in other files, as well as
    specifying constants in the header arguments of a table.  This is
    described in [[info:org:References]].

**** Dan: thinking aloud re: referencing data from R
     Suppose in some R code, we want to reference data in an org
     table. I think that requires the use of 'header arguments', since
     otherwise, under pure evaluation of a code block without header
     args, R has no way to locate the data in the org buffer. So that
     suggests a mechanism like that used by org-R whereby table names
     or unique entry IDs are used to reference org tables (and indeed
     potentially row/column ranges within org tables, although that
     subsetting could also be done in R).

     Specifically what org-R does is write the table to a temp csv
     file, and tell R the name of that file. However:

     1. We are not limited to a single source of input; the same sort
        of thing could be done for several sources of input

     2. I don't think we even have to use temp files. An alternative
        would be to have org pass the table contents as a csv-format
        string to textConnection() in R, thus creating an arbitrary
        number of input objects in the appropriate R environment
        (scope) from which the R code can read data when necessary.

	That suggests a header option syntax something like
    
#+begin_src emacs-lisp
'(:R-obj-name-1 tbl-name-or-id-1 :R-obj-name-2 tbl-name-or-id-2)
#+end_src emacs-lisp

As a result of passing that option, the code would be able to access
the data referenced by table-name-or-id-2 via read.table(R-obj-name-1).

An extension of that idea would be to allow remote files to be used as
data sources. In this case one might need just the remote file (if
it's a csv file), or if it's an org file then the name of the file
plus a table reference within that org file. Thus maybe something like

#+begin_src emacs-lisp
'((R-obj-name-1 . (:tblref tbl-name-or-id-1 :file file-1))
  (R-obj-name-2 . (:tblref tbl-name-or-id-2 :file file-2)))
#+end_src emacs-lisp

**** Eric: referencing data in general
So here's some thoughts for referencing data (henceforth referred to
as *resources*).  I think this is the next thing we need to tackle for
implementation to move forward.  We don't need to implement everything
below right off the bat, but I'd like to get these lists as full as
possible so we don't make any implementation assumptions which
preclude real needs.

We need to reference resources of the following types...

- table (list)
- output from a source code block (list or hash)
- property values of an outline header (hash)
- list (list)
- description list (hash)
- more?...

All of these resources will live in org files which could be

- the current file (default)
- another file on the same system (path)
- another file on the web (url)
- another file in a git repo (file and commit hash)

What information should each of these resources be able to supply?
I'm thinking (again not that we'll implement all of these but just to
think of them)...

- ranges or points of vector data
- key/value pairs from a hash
- when the object was last modified
- commit info (author, date, message, sha, etc...)
- pointers to the resources upon which the resource relies

So we need a referencing syntax powerful enough to handle all of these
alternatives.  Maybe something like =path:sha:name:range= where

- path :: is empty for the current file, is a path for files on the
          same system, and is a url otherwise
- sha :: is an option git commit indicator
- name :: is the table/header/source-block name or id for location
          inside of the org file (this would not be optional)
- range :: would indicate which information is requested from the
           resource, so it could be a range to access parts of a
           table, or the names of properties to be referenced from an
           outline header

Once we agree on how this should work, I'll try to stub out some code,
so that we can get some simple subset of this functionality working,
hopefully something complex enough to do the following...
- [[* resource reference example][resource-reference-example]]

***** questions
****** multiple outputs
Do we want things like a source code block to leave multiple outputs,
or do we only want them to be able to output one vector or hash?

****** environment (state and side-effects)
This design assumes that any changes will explicitly pass data in a
functional programming style.  This makes no assumptions about things
like source code blocks changing state (in general state changes lead
to more difficult debugging).

- Do we want to take steps so ensure we do things like execute
  consecutive R blocks in different environment, or do we want to
  allow state changes?
- Does this matter?

****** passing arguments to resources
So I(eric) may be getting ahead of myself here, but what do you think
about the ability to pass arguments to resources.  I'm having visions
of google map-reduce, processes spread out across multiple machines.

Maybe we could do this by allowing the arguments to be specified?

*** source-target pairs

    The following can be used for special considerations based on
    source-target pairs

    Dan: I don't quite understand this subtree; Eric -- could you give
    a little more explanation of this and of your comment above
    regarding using [[lists as our medium of exchange]]?
    
**** source block output from org tables
**** source block outpt from other source block
**** source block output from org list
**** org table from source block
**** org table from org table
**** org properties from source block
**** org properties from org table
     
** export
   once the previous objectives are met export should be fairly simple.
   Basically it will consist of triggering the evaluation of source code
   blocks with the org-export-preprocess-hook.

   This block export evaluation will be aware of the target format
   through the htmlp and latexp variables, and can then create quoted
   =#+begin_html= and =#+begin_latex= blocks appropriately.
   
   There will also need to be a set of header arguments related to
   code export.  These would be similar to the results header
   arguments but would apply to how to handle execution and results
   during export.


* Notes
** Block Formats
   Unfortunately org-mode how two different block types, both useful.
   In developing RweaveOrg, a third was introduced.

   Eric is leaning towards using the =#+begin_src= blocks, as that is
   really what these blocks contain: source code.  Austin believes
   that specifying export options at the beginning of a block is
   useful functionality, to be preserved if possible.

   Note that upper and lower case are not relevant in block headings.

*** PROPOSED block format
I (Eric) propose that we use the syntax of source code blocks as they
currently exist in org-mode with the addition of *evaluation*,
*header-arguments*, *exportation*, *single-line-blocks*, and
*references-to-table-data*.

1) *evaluation*: These blocks can be evaluated through =\C-c\C-c= with
   a slight addition to the code already present and working in
   [[file:existing_tools/org-eval-light.el][org-eval-light.el]].  All we should need to add for R support would
   be an appropriate entry in [[org-eval-light-interpreters]] with a
   corresponding evaluation function.  For an example usinga
   org-eval-light see [[* src block evaluation w/org-eval-light]].

2) *header-arguments*: These can be implemented along the lines of
   Austin's header arguments in [[file:existing_tools/RweaveOrg/org-sweave.el][org-sweave.el]].

3) *exportation*: Should be as similar as possible to that done by
   Sweave, and hopefully can re-use some of the code currently present
   in [[file:existing_tools/exp-blocks/org-exp-blocks.el ][org-exp-blocks.el]].

4) *single-line-blocks*: It seems that it is useful to be able to
   place a single line of R code on a line by itself.  Should we add
   syntax for this similar to Dan's =#+RR:= lines?  I would lean
   towards something here that can be re-used for any type of source
   code in the same manner as the =#+begin_src R= blocks, maybe
   =#+src_R=? Dan: I'm fine with this, but don't think single-line
   blocks are a priority. My =#+R= lines were something totally
   different: an attempt to have users specify R code implicitly,
   using org-mode option syntax.

5) *references-to-table-data*: I get this impression that this is
   vital to the efficient use of R code in an org file, so we should
   come up with a way to reference table data from a single-line-block
   or from an R source-code block.  It looks like Dan has already done
   this in [[file:existing_tools/org-R.el][org-R.el]].

Syntax

Multi-line Block
: #+begin_src lang header-arguments
:  body
: #+end
- lang :: the language of the block (R, shell, elisp, etc...)
- header-arguments :: a list of optional arguments which control how
     the block is evaluated and exported, and how the results are handled
- body :: the actual body of the block

Single-line Block
: #+begin_src lang body
- It's not clear how/if we would include header-arguments into a
  single line block.  Suggestions? Can we just leave them out?  Dan:
  I'm not too worried about single line blocks to start off
  with. Their main advantage seems to be that they save 2 lines.
  Eric: Fair enough, lets not worry about this now, also I would guess
  that any code simple enough to fit on one line wouldn't need header
  arguments anyways.

Include Block
: #+include_src lang filename header-arguments
- I think this would be useful, and should be much more work (Dan:
  didn't get the meaning of that last clause!?).  Eric: scratch that,
  I meant "*shouldn't* be too much work" :) That way whole external
  files of source code could be evaluated as if they were an inline
  block. Dan: again I'd say not a massive priority, as I think all the
  languages we have in mind have facilities for doing this natively,
  thus I think the desired effect can often be achieved from within a
  #+begin_src block.  Eric: Agreed, while this would be a nice thing
  to include we shouldn't wast too much effort on it in the beginning.

What do you think?  Does this accomplish everything we want to be able
to do with embedded R source code blocks?

***** src block evaluation w/org-eval-light
here's an example using org-eval-light.el

first load the org-eval-light.el file

[[elisp:(load (expand-file-name "org-eval-light.el" (expand-file-name "existing_tools" (file-name-directory buffer-file-name))))]]

then press =\C-c\C-c= inside of the following src code snippet.  The
results should appear in a comment immediately following the source
code block.  It shouldn't be too hard to add R support to this
function through the `org-eval-light-interpreters' variable.

(Dan: The following causes error on export to HTML hence spaces inserted at bol)

 #+begin_src shell
date
 #+end_src

*** existing formats
**** Source code blocks 
    Org has an extremely useful method of editing source code and
    examples in their native modes.  In the case of R code, we want to
    be able to use the full functionality of ESS mode, including
    interactive evaluation of code.

    Source code blocks look like the following and allow for the
    special editing of code inside of the block through
    `org-edit-special'.

#+BEGIN_SRC r

,## hit C-c ' within this block to enter a temporary buffer in r-mode.

,## while in the temporary buffer, hit C-c C-c on this comment to
,## evaluate this block
a <- 3
a

,## hit C-c ' to exit the temporary buffer
#+END_SRC     

**** dblocks
    dblocks are useful because org-mode will automatically call
    `org-dblock-write:dblock-type' where dblock-type is the string
    following the =#+BEGIN:= portion of the line.

    dblocks look like the following and allow for evaluation of the
    code inside of the block by calling =\C-c\C-c= on the header of
    the block.  

#+BEGIN: dblock-type
#+END:

**** R blocks
     In developing RweaveOrg, Austin created [[file:existing_tools/RweaveOrg/org-sweave.el][org-sweave.el]].  This
     allows for the kind of blocks shown in [[file:existing_tools/RweaveOrg/testing.Rorg][testing.Rorg]].  These blocks
     have the advantage of accepting options to the Sweave preprocessor
     following the #+BEGIN_R declaration.

*** block headers/parameters
Regardless of the syntax/format chosen for the source blocks, we will
need to be able to pass a list of parameters to these blocks.  These
should include (but should certainly not be limited to)
- label or id :: Label of the block, should we provide facilities for
                 automatically generating a unique one of these?
- file :: names of file to which graphical/textual/numerical/tabular output
  should be written.  Do we need this, or should this be controlled
  through the source code itself?
- results :: indication of where the results should be placed, maybe
             the following values...
  - append :: *default* meaning just append to the current buffer
              immediately following the current source block
  - replace :: like append, but replace any results currently there
  - file :: save the results in a new file, and place a link to the
            file into the current buffer immediately following the
            source code block
  - table :: save the results into a table, maybe use a table id:range
             to identify which table and where therein
  - nil :: meaning just discard the results
- not sure of a good name here :: flags for when/if the block should
     be evaluated (on export etc...)
- again can't thing of a concise name :: flags for how the results of
     the export should be displayed/included
- scope :: flag indicating whether the block should have a local or
           global scope
- flags specific to the language of the source block
- etc...

I think fleshing out this list is an important next step.

** Interaction with the R process

We should take care to implement this in such a way that all of the
different components which have to interactive with R including:
- evaluation of source code blocks
- automatic evaluation on export
- evaluation of \R{} snippets
- evaluation of single source code lines
- evaluation of included source code files
- sending/receiving vector data

I think we currently have two implementations of interaction with R
processes; [[file:existing_tools/org-R.el][org-R.el]] and [[file:existing_tools/exp-blocks/org-exp-blocks.el ][org-exp-blocks.el]].  We should be sure to take
the best of each of these approaches.

More on the exchange of data at between org-mode and source code
blocks at [[* reference to data and evaluation results][reference to data and evaluation results]].

** block scoping
(see [[* caching of evaluation][caching of evaluation]])

This inadvertently raises the issue of scoping.  The pretend function
pretends that we will create a block-local scope, and that we can save
just the things in that scope.  Sweave takes the make-everything-global
approach.  I can see advantages either way.  If we make block-local
scopes, we can save each one independently, and generally speaking it
seems like more granularity==more control.  If we make everything
global, we can refer to entities declared in earlier blocks without
having to explicitly import those entities into the current block.  I
think this counts in the "need to think about it early on" category.

If we did want block-local scopes, in R we can start every eval with
something like

;; fake code that pretends to create a new, empty environment
(ess-exec (concat block-env " <- new.env()"))
(ess-exec (concat "eval(" block-contents ", envir=" block-env ")"))

If we decide we want block-scoping, I'm sure Dan and I can figure out
the right way to do this in R, if he hasn't already.  I haven't thought
at all about how these scope issues generalize to, say, bash blocks.

Maybe this is something that should be controlled by a header
argument?

** =\C-c\C-c= evaluation

With org-mode version at least 6.23, see the documentation for
[[info:org:Context-sensitive%20commands][info:org:Context-sensitive commands]].

** free explicit variables
Maybe we should have some idea of variables independent of any
particular type of source code or source block.  These could be
variables that have a value inside of the scope of the org-mode file,
and they could be used as a transport mechanism for information
transfer between org-tables, org-lists, and different source-blocks.

Each type of source code (and org-mode types like tables, lists,
etc...) would need to implement functions for converting different
types of data to and from these variables (which would be elisp
variables).

So for example say we want to read the values from a table into an R
block, perform some calculations, and then write the results back into
the table.  We could
1) assign the table to a variable
   - the table would be converted into a lisp vector (list of lists)
   - the vector would be saved in the variable
2) an R source block would reference the variable
   - the variable would be instantiated into an R variable (through
     mechanisms mentioned [[* Dan: thinking aloud re: referencing data from R][elsewhere]])
   - the R code is executed, and the value of the variable *inside of
     R* is updated
   - when the R block finished the value of the variable *globally in
     the org buffer* would be updated
3) optionally the global value of the variable would be converted back
   into an org-mode table and would be used to overwrite the existing
   table.

What do you think?

This might not be too different from what we were already talking
about, but I think the introduction of the idea of having variables
existing independently of any tables or source code blocks is novel
and probably has some advantages (and probably shortfalls).


* Buffer Dictionary
 LocalWords:  DBlocks dblocks litorgy el eric