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Author SHA1 Message Date
Dan Davison b3afff4392 Merge branch 'session' into library-of-babel 2009-06-13 18:57:34 -04:00
Dan Davison b300b62b9c OK, I'm getting confused in magit and committing only a single hunk 
when I intended several. Hence, the commit note for this commit is the
commit note filed with the previous commit: da82dae939
 2009-06-13 18:51:23 -04:00
Dan Davison da82dae939 Implementing library functions as a new (pseudo) interpreter called 
'babel'. Added a speculative function which creates a hash table
containing parsed versions of all source blocks in a buffer -- I was
wondering whether we should 'load' the library-of-babel into memory in
this fashion, rather than searching for code blocks in buffers /
files.
 2009-06-13 18:49:24 -04:00
Dan Davison 317a062a9a New variable org-babel-named-src-block-regexp to match src block with 
srcname, and function org-babel-named-src-block-regexp-for-name
returning regexp matching a block with a particular
name. org-babel-named-src-block-regexp is set by
org-babel-set-interpreters.
 2009-06-13 18:46:26 -04:00
Dan Davison e0909d8458 New variable org-babel-named-src-block-regexp, to match a block with its srcname, and simple version of function org-babel-find-named-block. 2009-06-13 18:43:24 -04:00
Eric Schulte 3b026b806e shell source blocks no longer hang 2009-06-13 14:49:57 -07:00
Dan Davison 90094f9b7c Started again with lob implementation. 
I'm now proposing to implement it, at least temporarily, as a
degenerate source block (has no body), with interpreter name
'babel'. These 'babel' blocks will use a :srcname header arg to refer
to the source code block that they will use for their body. This
source code block might be in the 'library of babel'. If so it will
use a conventional variable name for its 'main data argument' such as
__data__. Then the babel block (not to be confused with a code block
in the lob) would use :var __data__=ref, where ref is a resource
reference resolved as usual.
 2009-06-12 23:45:14 -04:00
Dan Davison f5684b7deb Still getting started with lob. 
I plan to get rid of much of this and just implement it as a new
language with a degenerate source block for now (i.e. no body).
 2009-06-12 23:02:19 -04:00
Dan Davison 68c3fb2b52 Starting to create `library of babel' branch. 
This is intended to provide off-the-shelf data plotting and analysis
functions. Current idea is to introduce a new line, perhaps something
like #+babel or #+babel_lib, which will reference (a) some data
and (b) a source block to apply to the data. Code being stolen from
org-babel.el (conceivably some abstraction of some of those functions
could be done to avoid code duplication).
 2009-06-12 20:26:28 -04:00
Eric Schulte b56e6b0285 removing Austin F. Frank from copyright and author lines 2009-06-12 16:55:42 -07:00
Eric Schulte d261e178e9 passing all but one test 2009-06-12 16:50:53 -07:00
Eric Schulte e0fe83c8d2 moving org-babel-lisp into the langs directory 2009-06-12 16:44:06 -07:00
Eric Schulte b7c32fc5d8 passing almost all tests 2009-06-12 16:34:06 -07:00
Eric Schulte d41466e5bc now really passing all basic tests 2009-06-12 16:23:28 -07:00
Eric Schulte 8f9ae7314a now passing basic-ruby test 2009-06-12 16:08:51 -07:00
Eric Schulte 5675e56585 sessions are now working in R 2009-06-12 15:31:52 -07:00
Eric Schulte 9623b16914 fixed some weird long-prompt issues with shell comint buffer 2009-06-12 15:20:23 -07:00
Eric Schulte 2dea1ea367 shell is now handling multiple sessions 2009-06-12 14:56:30 -07:00
Eric Schulte f4798d3e83 python can now handle multiple sessions 2009-06-12 14:49:11 -07:00
Eric Schulte 39a4a85ba1 protecting against spurious spaces in header arguments 2009-06-12 13:46:40 -07:00
Eric Schulte 431715e6db shell support is pretty much working 2009-06-12 13:09:20 -07:00
Eric Schulte 8ab8bf6ed4 quoting "%"s in messages 2009-06-12 13:07:56 -07:00
Eric Schulte fe8393bf71 small documentation tweaks 2009-06-12 09:24:03 -07:00
Eric Schulte b64be81363 moving language-specific files into their own directory 2009-06-12 08:59:38 -07:00
Eric Schulte 1be99d1b35 python is basically up to snuff (needs more work on sessions) 2009-06-12 08:46:00 -07:00
Eric Schulte 018a8fcb98 removed spurious "\t" in ruby variable assignation 2009-06-12 08:45:43 -07:00
Eric Schulte 190a66c6af ruby now respects the scalar/vector :results header arguments 2009-06-12 08:33:51 -07:00
Eric Schulte 82e7c86ea3 R evaluation is pretty much up to snuff 2009-06-12 08:29:21 -07:00
Eric Schulte 86e4597a7a R results now obey the scalar/vector :results header arguments 2009-06-12 08:10:54 -07:00
Eric Schulte e0dcbce75e evaluation is working in R capturing both outputs and values 2009-06-12 07:55:33 -07:00
Eric Schulte 005e682948 making progress bringing org-babel-R.el into the new evaluation schema 2009-06-11 17:04:42 -07:00
Eric Schulte 0e8ae41dfc tweak variable name in org-babel-ruby 2009-06-11 16:28:21 -07:00
Eric Schulte 2c1b04eecb ruby is now working with sessions, output-based-results, and value(functional)-based-results 2009-06-11 15:34:34 -07:00
Eric Schulte 6698edbe83 finally think I'm on the right track for output vs. values, mostly working w/ruby 
- moved ruby functions into their own buffer
  - removed org-babel-sessions.el
  - drastically scaled down org-babel-comint.el (may grow later if we
    find duplication between language buffers)
  - removed org-babel-script.el
  - adjusted org-babel-init.el to reflect new file layout

For the big breakthrough see `org-babel-ruby-evaluate' in
org-babel-ruby.el.  This will be the model upon which all future
language evaluations will be built.
 2009-06-11 15:15:59 -07:00
Eric Schulte 8620cc414c generalizing command to read results from a file into elisp 2009-06-11 15:04:10 -07:00
Eric Schulte 9040ad657b adding string manipulation functions to org-babel.el 2009-06-11 14:31:37 -07:00
Eric Schulte 2081b95410 Revert "org-babel-comint-with-output is now fully self-contained and side-effect free" 
This seems to be causing problems...

This reverts commit 0573fc4d9c.
 2009-06-11 12:55:39 -07:00
Eric Schulte dc551fab04 beefed up org-babel-comint-wait-for-output but it still sometimes misses multiple outputs 2009-06-11 12:44:14 -07:00
Eric Schulte f5481ab666 looks like out comint waiting function needs some work... 2009-06-11 12:35:48 -07:00
Eric Schulte 0573fc4d9c org-babel-comint-with-output is now fully self-contained and side-effect free 2009-06-11 12:16:37 -07:00
Eric Schulte eacce7b29d `org-babel-comint-in-buffer' now declares it's indentation 2009-06-11 07:32:31 -07:00
Eric Schulte aa410df722 added nice little macro to capture output 2009-06-10 22:18:59 -07:00
Eric Schulte 8d0fd18933 working on org-babel-comint for automatically keeping a ring 2009-06-10 17:27:06 -07:00
Eric Schulte 23c61abf90 more robust org-babel-chomp 2009-06-10 16:17:04 -07:00
Eric Schulte 9c70974391 started working on ruby 'script' execution 2009-06-09 16:33:36 -07:00
Eric Schulte f3da4d0321 functional results now working with org-babel-comint and org-babel-script 2009-06-09 16:10:43 -07:00
Eric Schulte 39d1674f30 org-babel-R is now able to assign variables 2009-06-09 15:28:59 -07:00
Eric Schulte d3f1d07066 org-babel-R can now run in 'script' mode 2009-06-09 15:02:01 -07:00
Eric Schulte 4da3ddc623 Merge branch 'session' of git@github.com:eschulte/org-babel into session 2009-06-08 15:05:08 -07:00
Eric Schulte cdb41f5106 working on org-babel-script.el (winnowing, and using org-babel-comint.el) 2009-06-08 15:03:04 -07:00
Dan Davison 1e4c3389b6 As was just done for branch master, removing all support for hlines/colnames -- they persist in branch rowcolnames. Also removing comments. These should never have been present in this branch. 2009-06-06 18:12:42 -04:00
Eric Schulte b533d9d446 cleaned up org-babel-comint and removed helper functions 2009-06-03 20:52:01 -07:00
Eric Schulte fe75562a64 org-babel-comint is basically working 2009-06-03 20:51:36 -07:00
Eric Schulte e1aeec8ab1 begun implementing org-babel-comint 
a collection of functions to simplify interaction with comint-mode
  buffers
 2009-06-03 20:18:18 -07:00
Eric Schulte c175d3ce0d playing with org-babel-script and comint buffers/functions 2009-06-03 17:37:50 -07:00
Eric Schulte 2a663b9e09 R is now using last output (with default session) and passing all tests 2009-06-03 15:59:27 -07:00
Eric Schulte 49db1e523c Merge branch 'master' into session 
Conflicts:
	org-babel.org
 2009-06-03 15:30:10 -07:00
Eric Schulte 39f7174884 Revert "Revert "Make org table result have header row and hline when appropriate..."" 
This reverts commit dff01091dc.

Yes, this is a reversion of a reversion, as the original commit has
been reverted in the master branch, I'm now just going to revert the
reversion and then merge with master to maintain inter-branch
cohesion.

oh, did I mention... "revert"
 2009-06-03 15:26:32 -07:00
Dan Davison 02b265b2e3 Reverted tentative and hackish support for hline in R output. I have left a commented line and an unused function while I am thinking about this, and pending me learning git better. However I haven't yet reverted the ability of R to recognise hlines in var references, so the grades example still works. All sbe tests are passed. 2009-06-03 12:09:52 -04:00
Eric Schulte dff01091dc Revert "Make org table result have header row and hline when appropriate..." 
This reverts commit e4263daf76.

I'm reverting this commit in the sesion branch because it is breaking
the tests for R, as it no longer allows R source code blocks to return
scalar values.  Hopefully this issue will be fixed in the master
branch before I merge the session branch back in.
 2009-06-02 16:29:30 -07:00
Eric Schulte bba80bb837 working on sessions 2009-06-02 16:26:57 -07:00
Eric Schulte c38294d21f DONE Remove protective commas from # comments before evaluating 2009-06-01 16:56:59 -07:00
Dan Davison e4263daf76 Make org table result have header row and hline when appropriate. (This should have been included with commit a39d68640e). The approach I've taken is to make R always write the column names into the tsv file. If the result does not have user-supplied column-names, then R writes default column names of the form V1,V2,...,V$numcols. After reading the tsv back into lisp, we check whether it has "real" column names or the R defaults. If it has real column names, then I give the org table an hline. 
I expect this will conflict with Eric's work on sessions, but we can deal with that.

There is a remaining quoting issue that needs to be dealt
with. E.g. with an unquoted string in the input, it comes out as
quoted in the result. This seems bad, since if you use the output as
new input you get something different (with extra
quoting). (non-idempotence if that's the right term).

| col1 | col2    | col3 |
|------+---------+------|
|    1 | 2       |    3 |
|    4 | schulte |    6 |

tabel

| "col1" | "col2"    | "col3" |
|--------+-----------+--------|
|      1 | 2         |      3 |
|      4 | "schulte" |      6 |
 2009-05-30 16:45:26 -04:00
Dan Davison eb29bef93f Made org-babel-remove-result interactive. Eric if you agree do you want to decide on a binding? 2009-05-30 15:59:46 -04:00
Dan Davison a39d68640e Allowing org-tables with hline to be referred to and passed into R. If hline is present, the first row of the table becomes the column names in R. This allows the grades example to run for me which was not true before. Eric: any commits I make should be viewed as tentative -- feel free to reject or recode them. 2009-05-30 15:00:06 -04:00
Dan Davison 2ca59eaa0f Preventing end of buffer error when no newline after #+end_src 2009-05-29 23:34:50 -04:00
Eric Schulte d49084b73d small additions to org-babel-comint.el 2009-05-29 17:45:40 -07:00
Eric Schulte c5a58ad6aa moving generalized comint functions to new file org-babel-comint.el 2009-05-27 19:00:13 -07:00
Eric Schulte 2c3c91ed12 removed org-babel-ui (tabbing blocks) as the functionality will be included in org-mode core 2009-05-27 16:34:48 -07:00
Eric Schulte 9aa713be8c updated tag line 2009-05-24 14:10:03 -07:00
Eric Schulte 6614df037f now passing all tests with new name "org-babel" 2009-05-24 14:08:02 -07:00
Eric Schulte 9247200bb0 renaming the org-babel/ directory to the lisp/ directory 2009-05-24 13:56:20 -07:00