moved active parts of rorg.org to top, and added bugs section
This commit is contained in:
Dan Davison
parent
d8f8161be5
commit
1896489b6a
483
rorg.org
483
rorg.org
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@ -3,6 +3,261 @@
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#+SEQ_TODO: TODO PROPOSED | DONE DROPPED MAYBE
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#+STARTUP: oddeven
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* Tasks
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** TODO evaluation of shell code as background process? [DED]
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After C-c C-c on an R code block, the process may appear to block,
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but C-g can be used to reclaim control of the .org buffer, without
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interrupting the R evalution. However I believe this is not true
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of bash/sh evaluation. [Haven't tried other languages]
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** litorgy-R
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*** TODO ability to select which of multiple R sessions is being used
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(like ess-switch-process in .R buffers)
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*** TODO a header argument specifying silent evaluation (no output)
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* Bugs
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** Args out of range error
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The following block resulted in the error below [DED]. It ran without
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error directly in the shell.
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#+begin_src sh
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cd ~/work/genopca
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for platf in ill aff ; do
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for pop in CEU YRI ASI ; do
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rm -f $platf/hapmap-genos-$pop-all $platf/hapmap-rs-all
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cat $platf/hapmap-genos-$pop-* > $platf/hapmap-genos-$pop-all
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cat $platf/hapmap-rs-* > $platf/hapmap-rs-all
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done
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done
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#+end_src
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executing source block with sh...
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finished executing source block
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string-equal: Args out of range: "", -1, 0
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* Sandbox
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This is a place for code examples
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** litorgy.el beginning functionality
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After evaluating litorgy.el and litorgy-script.el, you should be able
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to evaluate the following blocks of code by pressing =\C-c\C-c= on the
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header lines. *Note*: your version of org-mode must be at least 6.23
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or later.
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To run these examples open both [[file:litorgy/litorgy.el][litorgy.el]], [[file:litorgy/litorgy-script.el][litorgy-script.el]] and
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evaluate them with =M-x eval-buffer=
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#+begin_src sh :replace t
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date
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#+end_src
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#+begin_src ruby
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puts Time.now
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#+end_src
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#+begin_src python
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print "Hello world!"
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#+end_src
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** litorgy-R
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To run these examples open both [[file:litorgy/litorgy.el][litorgy.el]], [[file:litorgy/litorgy-R.el][litorgy-R.el]] and evaluate
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them with =M-x eval-buffer=
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#+begin_src R :replace t
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hist(rgamma(20,3,3))
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a <- 9
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b <- 17
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a + b
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#+end_src
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: 26
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** free variables
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First assign the variable with some sort of interpreted line
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- this is independent of any particular type of source code
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- this could use references to table ranges
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** resource reference example
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This block holds an array of information written in [[http://www.yaml.org][YAML]]
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#name: yaml-array
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#+begin_src yaml
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---
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- 1
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- 2
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- 3
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- 4
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- 5
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#+end_src
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This next block saves the information in the YAML array into the ruby
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variable =ya= and then in ruby it multiplies each variable in the =ya=
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by 2.
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#name: ruby-array
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#assign: ya = yaml-array
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#+begin_src ruby
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ya.map{ |e| e * 2 }
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#+end_src
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This final block takes the output of the ruby block, and writes it to
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cell =0,0= through =0,3= of the table
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#name: example-table
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#assign: self[0, (1..3)] = ruby-array
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| example results |
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|-----------------|
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| |
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| |
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| |
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** litorgy plays with tables
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Alright, this should demonstrate both the ability of litorgy to read
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tables into a lisp source code block, and to then convert the results
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of the source code block into an org table. It's using the classic
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"lisp is elegant" demonstration transpose function. To try this
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out...
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|
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1. evaluate [[file:litorgy/init.el]] to load litorgy and friends
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2. evaluate the transpose definition =\C-u \C-c\C-c= on the beginning of
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the source block (prefix arg to inhibit output)
|
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3. evaluate the next source code block, this should read in the table
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because of the =:var table=previous=, then transpose the table, and
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finally it should insert the transposed table into the buffer
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immediately following the block
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*** Emacs lisp
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#+begin_src emacs-lisp
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(defun transpose (table)
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(apply #'mapcar* #'list table))
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#+end_src
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#+TBLNAME: sandbox
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| 1 | 2 | 3 |
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| 4 | schulte | 6 |
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#+begin_src emacs-lisp :var table=previous :replace t
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(transpose table)
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#+end_src
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#+begin_src emacs-lisp :var table=sandbox :replace t
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(transpose table)
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#+end_src
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*** Ruby and Python
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#+begin_src ruby :var table=sandbox :replace t
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table.first.join(" - ")
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#+end_src
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: "1 - 2 - 3"
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#+begin_src python :var table=sandbox :replace t
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table[0]
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#+end_src
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| 1 | 2 | 3 |
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#+begin_src ruby :var table=sandbox :replace t
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table
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#+end_src
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| 1 | 2 | 3 |
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| 4 | "schulte" | 6 |
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#+begin_src python :var table=sandbox :replace t
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table
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#+end_src
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| 1 | 2 | 3 |
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| 4 | "schulte" | 6 |
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*** R
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#+begin_src R :replace t
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a <- 9
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b <- 8
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#+end_src
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#+begin_src R :replace t
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x <- c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1))
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x
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#+end_src
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: -2.059712 -1.299807 -2.518628 -4.319525 -1.944779 -5.345708 -3.921314
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: -2.841109 -0.963475 -2.465979 4.092037 1.299202 1.476687 2.128594
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: 3.200629 1.990952 1.888890 3.561541 3.818319 1.969161
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* COMMENT Commentary
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I'm seeing this as like commit notes, and a place for less formal
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communication of the goals of our changes.
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** Eric <2009-02-06 Fri 15:41>
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I think we're getting close to a comprehensive set of objectives
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(although since you two are the real R user's I leave that decision up
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to you). Once we've agreed on a set of objectives and agreed on at
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least to broad strokes of implementation, I think we should start
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listing out and assigning tasks.
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** Eric <2009-02-09 Mon 14:25>
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I've done a fairly destructive edit of this file. The main goal was
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to enforce a structure on the document that we can use moving forward,
|
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so that any future objective changes are all made to the main
|
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objective list.
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|
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I apologize for removing sections written by other people. I did this
|
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when they were redundant or it was not clear how to fit them into this
|
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structure. Rest assured if the previous text wasn't persisted in git
|
||||
I would have been much more cautious about removing it.
|
||||
|
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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.
|
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** Dan <2009-02-12 Thu 10:23>
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Good job Eric with major works on this file.
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** Eric <2009-02-22 Sun 13:17>
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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.
|
||||
|
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See the [[* litorgy.el beginning functionality][Sandbox]] for evaluable examples.
|
||||
|
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** Eric <2009-02-23 Mon 15:12>
|
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While thinking about how to implement the transfer of data between
|
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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]])
|
||||
|
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** Eric <2009-02-23 Mon 17:53>
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So as I start populating this file with source code blocks I figure I
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should share this... I don't know if you guys use [[http://code.google.com/p/smart-snippet/][yasnippet]] at all,
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but if you do you might find this [[file:block][block-snippet]] org-mode snippet
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useful (I use it all the time).
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* Overview
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This project is basically about putting source code into org
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files. This isn't just code to look pretty as a source code example,
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@ -648,233 +903,5 @@ existing independently of any tables or source code blocks is novel
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and probably has some advantages (and probably shortfalls).
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|
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|
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* Tasks
|
||||
** TODO evaluation as background process? [DED]
|
||||
** litorgy-R
|
||||
*** TODO ability to select which of multiple R sessions is being used (like ess-switch-process in .R buffers)
|
||||
*** TODO a header argument specifying silent evaluation (no output)
|
||||
|
||||
* Sandbox
|
||||
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=
|
||||
|
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#+begin_src sh :replace t
|
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date
|
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#+end_src
|
||||
|
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#+begin_src ruby
|
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puts Time.now
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#+end_src
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|
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#+begin_src python
|
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print "Hello world!"
|
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#+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=
|
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|
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#+begin_src R :replace t
|
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hist(rgamma(20,3,3))
|
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a <- 9
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b <- 17
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a + b
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#+end_src
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|
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: 26
|
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|
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|
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** 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
|
||||
|
||||
This block holds an array of information written in [[http://www.yaml.org][YAML]]
|
||||
|
||||
#name: yaml-array
|
||||
#+begin_src yaml
|
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---
|
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- 1
|
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- 2
|
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- 3
|
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- 4
|
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- 5
|
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#+end_src
|
||||
|
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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
|
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ya.map{ |e| e * 2 }
|
||||
#+end_src
|
||||
|
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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
|
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| 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
|
||||
|
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#+TBLNAME: sandbox
|
||||
| 1 | 2 | 3 |
|
||||
| 4 | schulte | 6 |
|
||||
|
||||
#+begin_src emacs-lisp :var table=previous :replace t
|
||||
(transpose table)
|
||||
#+end_src
|
||||
|
||||
#+begin_src emacs-lisp :var table=sandbox :replace t
|
||||
(transpose table)
|
||||
#+end_src
|
||||
|
||||
*** Ruby and Python
|
||||
|
||||
#+begin_src ruby :var table=sandbox :replace t
|
||||
table.first.join(" - ")
|
||||
#+end_src
|
||||
|
||||
: "1 - 2 - 3"
|
||||
|
||||
#+begin_src python :var table=sandbox :replace t
|
||||
table[0]
|
||||
#+end_src
|
||||
|
||||
| 1 | 2 | 3 |
|
||||
|
||||
#+begin_src ruby :var table=sandbox :replace t
|
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table
|
||||
#+end_src
|
||||
|
||||
| 1 | 2 | 3 |
|
||||
| 4 | "schulte" | 6 |
|
||||
|
||||
#+begin_src python :var table=sandbox :replace t
|
||||
table
|
||||
#+end_src
|
||||
|
||||
| 1 | 2 | 3 |
|
||||
| 4 | "schulte" | 6 |
|
||||
|
||||
*** R
|
||||
|
||||
#+begin_src R :replace t
|
||||
a <- 9
|
||||
b <- 8
|
||||
|
||||
#+end_src
|
||||
|
||||
#+begin_src R :replace t
|
||||
x <- c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1))
|
||||
x
|
||||
#+end_src
|
||||
|
||||
: -2.059712 -1.299807 -2.518628 -4.319525 -1.944779 -5.345708 -3.921314
|
||||
: -2.841109 -0.963475 -2.465979 4.092037 1.299202 1.476687 2.128594
|
||||
: 3.200629 1.990952 1.888890 3.561541 3.818319 1.969161
|
||||
|
||||
|
||||
|
||||
* 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,
|
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but if you do you might find this [[file:block][block-snippet]] org-mode snippet
|
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useful (I use it all the time).
|
||||
|
||||
|
||||
* Buffer Dictionary
|
||||
LocalWords: DBlocks dblocks litorgy el eric
|
||||
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|
|
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Reference in New Issue