* convert rmarkdown (rmd) files to orgmode?
@ 2016-07-20 4:28 Xebar Saram
[not found] ` <CAJ1MqVF4Cq3ogH34P6AtSf0-ZX7ic=tApuX-ad=+14pLF7p1Aw@mail.gmail.com>
0 siblings, 1 reply; 8+ messages in thread
From: Xebar Saram @ 2016-07-20 4:28 UTC (permalink / raw)
To: org mode
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Hi all
anyone know of a way to convert rmarkdown (rmd) files to orgmode?
im preparing a R course and lots of cool examples in R are in rmd format so
it could be very useful to me
best
Z
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^ permalink raw reply [flat|nested] 8+ messages in thread[parent not found: <CAJ1MqVF4Cq3ogH34P6AtSf0-ZX7ic=tApuX-ad=+14pLF7p1Aw@mail.gmail.com>]
* Re: convert rmarkdown (rmd) files to orgmode? [not found] ` <CAJ1MqVF4Cq3ogH34P6AtSf0-ZX7ic=tApuX-ad=+14pLF7p1Aw@mail.gmail.com> @ 2016-07-20 11:15 ` Xebar Saram 2016-07-20 17:20 ` Charles C. Berry 0 siblings, 1 reply; 8+ messages in thread From: Xebar Saram @ 2016-07-20 11:15 UTC (permalink / raw) To: Philip Hudson, org mode [-- Attachment #1: Type: text/plain, Size: 1036 bytes --] thx phil the Rmd format is actually quite different than md so that conversion didnt go well i ended up doing a 2 step conversion: in R (via the GUI or through R -e command line), first convert the Rmd files to md files: require(knitr) # required for knitting from rmd to md require(markdown) # required for md to html knit('test.rmd', 'test.md') # creates md file then use pandoc to convert the md files to org: pandoc -o test.org test.md this gives an almost 1:1 org file thx Z On Wed, Jul 20, 2016 at 1:08 PM, Philip Hudson <phil.hudson@iname.com> wrote: > pandoc -f markdown -t org myfile.rmd > > On 20 July 2016 at 05:28, Xebar Saram <zeltakc@gmail.com> wrote: > > Hi all > > > > anyone know of a way to convert rmarkdown (rmd) files to orgmode? > > > > im preparing a R course and lots of cool examples in R are in rmd format > so > > it could be very useful to me > > > > best > > > > Z > > > > -- > Phil Hudson http://hudson-it.ddns.net > @UWascalWabbit PGP/GnuPG ID: 0x887DCA63 > [-- Attachment #2: Type: text/html, Size: 2034 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: convert rmarkdown (rmd) files to orgmode? 2016-07-20 11:15 ` Xebar Saram @ 2016-07-20 17:20 ` Charles C. Berry 2016-07-20 17:29 ` Xebar Saram 0 siblings, 1 reply; 8+ messages in thread From: Charles C. Berry @ 2016-07-20 17:20 UTC (permalink / raw) To: Xebar Saram; +Cc: org mode, Philip Hudson On Wed, 20 Jul 2016, Xebar Saram wrote: > thx phil > > the Rmd format is actually quite different than md so that conversion didnt > go well > I tried this pandoc -f markdown -t org input-file.Rmd -o output-file.org then I opened `output-file.org' and put this src block at the very top: #+BEGIN_SRC emacs-lisp :results silent (replace-regexp "^=[{]r \\([^}]*\\)[}]\\(.*\\)=$" "#+name: \\1 ,#+begin_src R \\2 ,#+end_src") #+END_SRC When I execute that code block, all the converted code chunks become src blocks. This isn't perfect as chunk options are appended to the `#+NAME:...' line, but if you want to play with the regexp's you can probably get it to pick those out and put them on a separate line. Or just write another src block with another `replace-regexp' to fix those lines. With a little effort you can write a command file for `sed' to do what the code block above does and then pipe the pandoc output to that command like this: : pandoc -f markdown -t org input-file.Rmd | \ : sed -f convert-chunks > output-file.org and you have an org document ready (or almost ready) to go. HTH, Chuck ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: convert rmarkdown (rmd) files to orgmode? 2016-07-20 17:20 ` Charles C. Berry @ 2016-07-20 17:29 ` Xebar Saram 2016-07-20 17:42 ` Charles C. Berry 0 siblings, 1 reply; 8+ messages in thread From: Xebar Saram @ 2016-07-20 17:29 UTC (permalink / raw) To: Charles C. Berry; +Cc: org mode, Philip Hudson [-- Attachment #1: Type: text/plain, Size: 1599 bytes --] thx for the tips! when i try to run the source block : #+BEGIN_SRC emacs-lisp :results silent (replace-regexp "^=[{]r \\([^}]*\\)[}]\\(.*\\)=$" "#+name: \\1 ,#+begin_src R \\2 ,#+end_src") #+END_SRC i just get a nil in the message area. what am i missing? thx Z On Wed, Jul 20, 2016 at 8:20 PM, Charles C. Berry <ccberry@ucsd.edu> wrote: > On Wed, 20 Jul 2016, Xebar Saram wrote: > > thx phil >> >> the Rmd format is actually quite different than md so that conversion >> didnt >> go well >> >> > I tried this > > pandoc -f markdown -t org input-file.Rmd -o output-file.org > > then I opened `output-file.org' and put this src block at the very top: > > #+BEGIN_SRC emacs-lisp :results silent > (replace-regexp "^=[{]r \\([^}]*\\)[}]\\(.*\\)=$" > "#+name: \\1 > ,#+begin_src R > \\2 > ,#+end_src") > > #+END_SRC > > When I execute that code block, all the converted code chunks become src > blocks. > > This isn't perfect as chunk options are appended to the `#+NAME:...' line, > but if you want to play with the regexp's you can probably get it to pick > those out and put them on a separate line. Or just write another src block > with another `replace-regexp' to fix those lines. > > With a little effort you can write a command file for `sed' to do what the > code block above does and then pipe the pandoc output to that command like > this: > > : pandoc -f markdown -t org input-file.Rmd | \ > : sed -f convert-chunks > output-file.org > > and you have an org document ready (or almost ready) to go. > > > HTH, > > Chuck > > [-- Attachment #2: Type: text/html, Size: 2655 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: convert rmarkdown (rmd) files to orgmode? 2016-07-20 17:29 ` Xebar Saram @ 2016-07-20 17:42 ` Charles C. Berry 2016-07-20 18:00 ` Xebar Saram 0 siblings, 1 reply; 8+ messages in thread From: Charles C. Berry @ 2016-07-20 17:42 UTC (permalink / raw) To: Xebar Saram; +Cc: org mode, Philip Hudson On Wed, 20 Jul 2016, Xebar Saram wrote: > thx for the tips! > > when i try to run the source block : > > #+BEGIN_SRC emacs-lisp :results silent > (replace-regexp "^=[{]r \\([^}]*\\)[}]\\(.*\\)=$" > "#+name: \\1 > ,#+begin_src R > \\2 > ,#+end_src") > > #+END_SRC > > i just get a nil in the message area. what am i missing? > Nothing! The `:results silent' should suppress any output. Anyway, what you should see is that the code chunks that pandoc placed inside equal signs like : ={r my-name} code = are now in src blocks. I think you need to put the src block at the top or add a : (goto-char (point-min)) as its first line to be sure it converts all the code chunks. Chuck ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: convert rmarkdown (rmd) files to orgmode? 2016-07-20 17:42 ` Charles C. Berry @ 2016-07-20 18:00 ` Xebar Saram 2016-07-21 6:48 ` Xebar Saram 0 siblings, 1 reply; 8+ messages in thread From: Xebar Saram @ 2016-07-20 18:00 UTC (permalink / raw) To: Charles C. Berry; +Cc: org mode, Philip Hudson [-- Attachment #1: Type: text/plain, Size: 1153 bytes --] ahh i see what you mean. thats a cool tip yet i find i have to find/replace also for images, find/replace to change example blocks to R code blocks etc which is quite tedious since i have about 50 of these converted Rmd to org files :) ill keep investigating this and report back thx so much for the tips! :) Z On Wed, Jul 20, 2016 at 8:42 PM, Charles C. Berry <ccberry@ucsd.edu> wrote: > On Wed, 20 Jul 2016, Xebar Saram wrote: > > thx for the tips! >> >> when i try to run the source block : >> >> #+BEGIN_SRC emacs-lisp :results silent >> (replace-regexp "^=[{]r \\([^}]*\\)[}]\\(.*\\)=$" >> "#+name: \\1 >> ,#+begin_src R >> \\2 >> ,#+end_src") >> >> #+END_SRC >> >> i just get a nil in the message area. what am i missing? >> >> > > Nothing! > > The `:results silent' should suppress any output. > > Anyway, what you should see is that the code chunks that pandoc placed > inside equal signs like > > : ={r my-name} code = > > are now in src blocks. > > I think you need to put the src block at the top or add a > > : (goto-char (point-min)) > > as its first line to be sure it converts all the code chunks. > > > Chuck > [-- Attachment #2: Type: text/html, Size: 1835 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: convert rmarkdown (rmd) files to orgmode? 2016-07-20 18:00 ` Xebar Saram @ 2016-07-21 6:48 ` Xebar Saram 2016-07-21 16:27 ` Charles C. Berry 0 siblings, 1 reply; 8+ messages in thread From: Xebar Saram @ 2016-07-21 6:48 UTC (permalink / raw) To: Charles C. Berry; +Cc: org mode, Philip Hudson [-- Attachment #1: Type: text/plain, Size: 1685 bytes --] Hi again Chuck: is there a way to modify you nice code regex code snippet to simultaneously change all example blocks to R blocks in a converted rmd>org file? so when executing the block all example blocks: #+BEGIN_EXAMPLE help.search("rnorm") #+END_EXAMPLE will turn into R blocks #+BEGIN_SRC R :session Rorg :results none help.search("rnorm") #+END_SRC thx! Z On Wed, Jul 20, 2016 at 9:00 PM, Xebar Saram <zeltakc@gmail.com> wrote: > ahh i see what you mean. > > thats a cool tip yet i find i have to find/replace also for images, > find/replace to change example blocks to R code blocks etc which is quite > tedious since i have about 50 of these converted Rmd to org files :) > ill keep investigating this and report back > > thx so much for the tips! :) > > Z > > On Wed, Jul 20, 2016 at 8:42 PM, Charles C. Berry <ccberry@ucsd.edu> > wrote: > >> On Wed, 20 Jul 2016, Xebar Saram wrote: >> >> thx for the tips! >>> >>> when i try to run the source block : >>> >>> #+BEGIN_SRC emacs-lisp :results silent >>> (replace-regexp "^=[{]r \\([^}]*\\)[}]\\(.*\\)=$" >>> "#+name: \\1 >>> ,#+begin_src R >>> \\2 >>> ,#+end_src") >>> >>> #+END_SRC >>> >>> i just get a nil in the message area. what am i missing? >>> >>> >> >> Nothing! >> >> The `:results silent' should suppress any output. >> >> Anyway, what you should see is that the code chunks that pandoc placed >> inside equal signs like >> >> : ={r my-name} code = >> >> are now in src blocks. >> >> I think you need to put the src block at the top or add a >> >> : (goto-char (point-min)) >> >> as its first line to be sure it converts all the code chunks. >> >> >> Chuck >> > > [-- Attachment #2: Type: text/html, Size: 3032 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: convert rmarkdown (rmd) files to orgmode? 2016-07-21 6:48 ` Xebar Saram @ 2016-07-21 16:27 ` Charles C. Berry 0 siblings, 0 replies; 8+ messages in thread From: Charles C. Berry @ 2016-07-21 16:27 UTC (permalink / raw) To: Xebar Saram; +Cc: org mode, Philip Hudson On Wed, 20 Jul 2016, Xebar Saram wrote: > Hi again > > Chuck: > > is there a way to modify you nice code regex code snippet to simultaneously > change all example blocks to R blocks in a converted rmd>org file? > so when executing the block all example blocks: > > > #+BEGIN_EXAMPLE > help.search("rnorm") > #+END_EXAMPLE > > will turn into R blocks > > #+BEGIN_SRC R :session Rorg :results none > help.search("rnorm") > #+END_SRC > The obvious thing is to do this with two additional `replace' operations. Interactively, you can use `replace-string' to do this, since those are fixed strings and there are no backreferences to worry about. I think there is a dired-mode incantation that would allow you to do this on all files in a directory if you wanted. But see the docstring for 'replace-string' which shows a better incantation for programmatically doing the changes. IMO, you would be better served by doiing this in a scripting language like bash or python, but even R could do it. One reason for using a scripting language is that unless you are a wiz at elisp, it is easier to report back the changes that are made in context; if you convert something that truly *is* an example block, you want to know about it so you can back out that change. Also, it is possible that the R code in the file you are converting will contain characters that will foil the regexp matching and you really need to catch those. I'd be tempted to do it in R - at least in part - so I could parse() the result to check that it is valid code. The ESS suite has some parsing capabilities, but if you do not already know them using R will be a lot easier. An example block that does not produce valid code might be something you should leave as an example block. Write a script that does all the conversion including the pandoc bit. Then run that at the command line. Chuck ^ permalink raw reply [flat|nested] 8+ messages in thread
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2016-07-20 4:28 convert rmarkdown (rmd) files to orgmode? Xebar Saram
[not found] ` <CAJ1MqVF4Cq3ogH34P6AtSf0-ZX7ic=tApuX-ad=+14pLF7p1Aw@mail.gmail.com>
2016-07-20 11:15 ` Xebar Saram
2016-07-20 17:20 ` Charles C. Berry
2016-07-20 17:29 ` Xebar Saram
2016-07-20 17:42 ` Charles C. Berry
2016-07-20 18:00 ` Xebar Saram
2016-07-21 6:48 ` Xebar Saram
2016-07-21 16:27 ` Charles C. Berry
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