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moved active parts of rorg.org to top, and added bugs section

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Dan Davison 2009-03-31 10:24:15 -04:00
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@ -3,6 +3,261 @@
#+SEQ_TODO: TODO PROPOSED | DONE DROPPED MAYBE #+SEQ_TODO: TODO PROPOSED | DONE DROPPED MAYBE
#+STARTUP: oddeven #+STARTUP: oddeven
* Tasks
** TODO evaluation of shell code as background process? [DED]
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]
** 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)
* Bugs
** 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
* 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=
#+begin_src sh :replace t
date
#+end_src
#+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 :replace t
hist(rgamma(20,3,3))
a <- 9
b <- 17
a + b
#+end_src
: 26
** 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
---
- 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 :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
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,
but if you do you might find this [[file:block][block-snippet]] org-mode snippet
useful (I use it all the time).
* Overview * Overview
This project is basically about putting source code into org This project is basically about putting source code into org
files. This isn't just code to look pretty as a source code example, files. This isn't just code to look pretty as a source code example,
@ -648,233 +903,5 @@ existing independently of any tables or source code blocks is novel
and probably has some advantages (and probably shortfalls). and probably has some advantages (and probably shortfalls).
* 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=
#+begin_src sh :replace t
date
#+end_src
#+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 :replace t
hist(rgamma(20,3,3))
a <- 9
b <- 17
a + b
#+end_src
: 26
** 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
---
- 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 :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
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,
but if you do you might find this [[file:block][block-snippet]] org-mode snippet
useful (I use it all the time).
* Buffer Dictionary * Buffer Dictionary
LocalWords: DBlocks dblocks litorgy el eric LocalWords: DBlocks dblocks litorgy el eric