Automatically adding local variables to tangled file

Automatically adding local variables to tangled file

[Rainer M Krug]

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Hi 

I am trying to improve my workflow of literate programming of R in
org. My org file is tangled into many R files and I am using ESS to
debug.

If an error occurs, I can jump via ESS to the .R file, and in a second
step via calling org-babel-tangle-jump-to-org into the org file where
the buggy line sits.


Now this is error prone, as one (or is it only me?) is easily tempted to
edit the R file which is reverted after the next tangle.

So I was thinking: what about calling org-babel-tangle-jump-to-org
directly from ESS. Vitalie Spinu looked into this option, and came up with the
following suggestion:

If the tangled .R file contains a local variable, one could easily
identify that it is a tangled file and call org-babel-tangle-jump-to-org
and would be at the line causing the error.

Therefore my question:

Would it be possible and reasonable, to add a local variable to each
tangled file which identifies the file as an file tangled from an org
mode file?

He added the following to his config file to test the approach:

,----
|  (defvar org-babel-tangled-file nil
|      "If non-nill, current file was tangled with org-babel-tangle")
|    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
|    
|    (defun org-babel-mark-file-as-tangled ()
|      (add-file-local-variable 'org-babel-tangled-file t)
|      (basic-save-buffer))
| 
|    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
`----

and he also already added automatic redirection to the org mode file via
org-babel-tangle-jump-to-org to ESS on SVN.

To keep backwards compatibility, a variable
org-babel-tangle-add-tangled-file-variable could be introduced, which
can have the following values:

- nil :: (default) do not add anything
- t :: org-babel-tangled-file is added as t to the tangled files
- "name" :: org-babel-tangled-file is set to the org file name
- "path" :: org-babel-tangled-file is set to the path of the org file
- "all" :: org-babel-tangled-file is set to the full name including path
           of the org file

I can even imagine many more possibilities for the use of local file
variables to store meta data in the tangled file (VCS info comes to
mind, which would enable one to even go back to older revisions based on
the tangled code rather easily).

Cheers,

Rainer

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

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Re: Automatically adding local variables to tangled file

[Darlan Cavalcante Moreira]

It's a good idea to have useful information in the tangled file that can
help these functions. But since org-mode can already tangle with comments
containing useful information, isn't this enough to detect that the file
is a tangled file?

On the other hand, a local variable in the tangled files to set the buffer
to read-only could be very useful to avoid the mistake of editing the
tangled files directly.

--
Darlan

At Wed, 05 Jun 2013 16:04:59 +0200,
Rainer M Krug wrote:
> 
> Hi 
> 
> I am trying to improve my workflow of literate programming of R in
> org. My org file is tangled into many R files and I am using ESS to
> debug.
> 
> If an error occurs, I can jump via ESS to the .R file, and in a second
> step via calling org-babel-tangle-jump-to-org into the org file where
> the buggy line sits.
> 
> 
> Now this is error prone, as one (or is it only me?) is easily tempted to
> edit the R file which is reverted after the next tangle.
> 
> So I was thinking: what about calling org-babel-tangle-jump-to-org
> directly from ESS. Vitalie Spinu looked into this option, and came up with the
> following suggestion:
> 
> If the tangled .R file contains a local variable, one could easily
> identify that it is a tangled file and call org-babel-tangle-jump-to-org
> and would be at the line causing the error.
> 
> Therefore my question:
> 
> Would it be possible and reasonable, to add a local variable to each
> tangled file which identifies the file as an file tangled from an org
> mode file?
> 
> He added the following to his config file to test the approach:
> 
> ,----
> |  (defvar org-babel-tangled-file nil
> |      "If non-nill, current file was tangled with org-babel-tangle")
> |    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
> |    
> |    (defun org-babel-mark-file-as-tangled ()
> |      (add-file-local-variable 'org-babel-tangled-file t)
> |      (basic-save-buffer))
> | 
> |    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
> `----
> 
> and he also already added automatic redirection to the org mode file via
> org-babel-tangle-jump-to-org to ESS on SVN.
> 
> To keep backwards compatibility, a variable
> org-babel-tangle-add-tangled-file-variable could be introduced, which
> can have the following values:
> 
> - nil :: (default) do not add anything
> - t :: org-babel-tangled-file is added as t to the tangled files
> - "name" :: org-babel-tangled-file is set to the org file name
> - "path" :: org-babel-tangled-file is set to the path of the org file
> - "all" :: org-babel-tangled-file is set to the full name including path
>            of the org file
> 
> I can even imagine many more possibilities for the use of local file
> variables to store meta data in the tangled file (VCS info comes to
> mind, which would enable one to even go back to older revisions based on
> the tangled code rather easily).
> 
> Cheers,
> 
> Rainer
> 
> -- 
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
> 
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
> 
> Tel :       +33 - (0)9 53 10 27 44
> Cell:       +33 - (0)6 85 62 59 98
> Fax :       +33 - (0)9 58 10 27 44
> 
> Fax (D):    +49 - (0)3 21 21 25 22 44
> 
> email:      Rainer@krugs.de
> 
> Skype:      RMkrug

Re: Automatically adding local variables to tangled file

[Vitalie Spinu]

 >> Darlan Cavalcante Moreira <darcamo@gmail.com>
 >> on Wed, 05 Jun 2013 11:32:22 -0300 wrote:

 > It's a good idea to have useful information in the tangled file that can
 > help these functions. But since org-mode can already tangle with comments
 > containing useful information, isn't this enough to detect that the file
 > is a tangled file?

In principle yes, but it would be nice to avoid searching the whole
buffer for org comments on every step of the debugger. Especially given
that OP's workflow is very specific and most users won't ever need it.

Instead of local variable it might be just a simple comment at bof and a
function org-babel-tangled-file-p to quickly recognize the file.

    Vitlaie

Re: Automatically adding local variables to tangled file

[Rainer M Krug]

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On Wednesday, June 5, 2013, Darlan Cavalcante Moreira wrote:

>
> It's a good idea to have useful information in the tangled file that can
> help these functions. But since org-mode can already tangle with comments
> containing useful information, isn't this enough to detect that the file
> is a tangled file?


Yes and no. In regards to jumping to the source code, it would necessitate
a searching in the text, but it would be much easier to have it in a file
local variable. This is more standardized then a comment.


>
> On the other hand, a local variable in the tangled files to set the buffer
> to read-only could be very useful to avoid the mistake of editing the
> tangled files directly.


My reasoning - and I would make all tangled R files read only.

Cheers,

Rainer


>
> --
> Darlan
>
> At Wed, 05 Jun 2013 16:04:59 +0200,
> Rainer M Krug wrote:
> >
> > Hi
> >
> > I am trying to improve my workflow of literate programming of R in
> > org. My org file is tangled into many R files and I am using ESS to
> > debug.
> >
> > If an error occurs, I can jump via ESS to the .R file, and in a second
> > step via calling org-babel-tangle-jump-to-org into the org file where
> > the buggy line sits.
> >
> >
> > Now this is error prone, as one (or is it only me?) is easily tempted to
> > edit the R file which is reverted after the next tangle.
> >
> > So I was thinking: what about calling org-babel-tangle-jump-to-org
> > directly from ESS. Vitalie Spinu looked into this option, and came up
> with the
> > following suggestion:
> >
> > If the tangled .R file contains a local variable, one could easily
> > identify that it is a tangled file and call org-babel-tangle-jump-to-org
> > and would be at the line causing the error.
> >
> > Therefore my question:
> >
> > Would it be possible and reasonable, to add a local variable to each
> > tangled file which identifies the file as an file tangled from an org
> > mode file?
> >
> > He added the following to his config file to test the approach:
> >
> > ,----
> > |  (defvar org-babel-tangled-file nil
> > |      "If non-nill, current file was tangled with org-babel-tangle")
> > |    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
> > |
> > |    (defun org-babel-mark-file-as-tangled ()
> > |      (add-file-local-variable 'org-babel-tangled-file t)
> > |      (basic-save-buffer))
> > |
> > |    (add-hook 'org-babel-post-tangle-hook
> 'org-babel-mark-file-as-tangled)
> > `----
> >
> > and he also already added automatic redirection to the org mode file via
> > org-babel-tangle-jump-to-org to ESS on SVN.
> >
> > To keep backwards compatibility, a variable
> > org-babel-tangle-add-tangled-file-variable could be introduced, which
> > can have the following values:
> >
> > - nil :: (default) do not add anything
> > - t :: org-babel-tangled-file is added as t to the tangled files
> > - "name" :: org-babel-tangled-file is set to the org file name
> > - "path" :: org-babel-tangled-file is set to the path of the org file
> > - "all" :: org-babel-tangled-file is set to the full name including path
> >            of the org file
> >
> > I can even imagine many more possibilities for the use of local file
> > variables to store meta data in the tangled file (VCS info comes to
> > mind, which would enable one to even go back to older revisions based on
> > the tangled code rather easily).
> >
> > Cheers,
> >
> > Rainer
> >
> > --
> > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
> >
> > Centre of Excellence for Invasion Biology
> > Stellenbosch University
> > South Africa
> >
> > Tel :       +33 - (0)9 53 10 27 44
> > Cell:       +33 - (0)6 85 62 59 98
> > Fax :       +33 - (0)9 58 10 27 44
> >
> > Fax (D):    +49 - (0)3 21 21 25 22 44
> >
> > email:      Rainer@krugs.de <javascript:;>
> >
> > Skype:      RMkrug
>


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax (F):       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

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Re: Automatically adding local variables to tangled file

[Sebastien Vauban]

Hi Darlan,

Darlan Cavalcante Moreira wrote:
> On the other hand, a local variable in the tangled files to set the buffer
> to read-only could be very useful to avoid the mistake of editing the
> tangled files directly.

Waow! That makes a lot of sense, IMHO, if easily "overridable" with C-x C-q.
Because, people may want to edit the generated file and untangle it once
they've debugged their problem.

But I'd find that a good _default_ state, for trying to avoid errors.

Best regards,
  Seb

-- 
Sebastien Vauban

Re: Automatically adding local variables to tangled file

[Eric Schulte]

> It's a good idea to have useful information in the tangled file that can
> help these functions. But since org-mode can already tangle with comments
> containing useful information, isn't this enough to detect that the file
> is a tangled file?
>

I personally prefer the solution shown below of adding a file-local
variable using the post-tangle hook.  As mentioned previously this makes
the detection of tangled code much faster, simpler and less error prone
than grepping the file for comments.

>
> On the other hand, a local variable in the tangled files to set the buffer
> to read-only could be very useful to avoid the mistake of editing the
> tangled files directly.
>

We already set the permission of tangled files to be executable when
they include a shebang line.  Perhaps we could add an option (or change
the default) to set the permissions of tangled files to be read only.

Perhaps this could be done using the post-tangle hook with something
like the following.

    ;; -*- emacs-lisp -*-
    (defun org-babel-mark-tangled-as-read-only ()
      "Mark the current file read only.
    If it is executable keep it executable."
      (if (= #o755 (file-modes (buffer-file-name)))
          (set-file-modes (buffer-file-name) #o555)
          (set-file-modes (buffer-file-name) #o444)))

    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-tangled-as-read-only)

>> 
>> Therefore my question:
>> 
>> Would it be possible and reasonable, to add a local variable to each
>> tangled file which identifies the file as an file tangled from an org
>> mode file?
>> 
>> He added the following to his config file to test the approach:
>> 
>> ,----
>> |  (defvar org-babel-tangled-file nil
>> |      "If non-nill, current file was tangled with org-babel-tangle")
>> |    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
>> |    
>> |    (defun org-babel-mark-file-as-tangled ()
>> |      (add-file-local-variable 'org-babel-tangled-file t)
>> |      (basic-save-buffer))
>> | 
>> |    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
>> `----
>> 

I think the above code should be considered an implementation rather
than simply a test.  This is exactly what the post-tangle hook is
intended to support.  Is there a motivating reason for this behavior to
be "built in"?

>> 
>> and he also already added automatic redirection to the org mode file
>> via org-babel-tangle-jump-to-org to ESS on SVN.
>> 
>> To keep backwards compatibility, a variable
>> org-babel-tangle-add-tangled-file-variable could be introduced, which
>> can have the following values:
>> 
>> - nil :: (default) do not add anything
>> - t :: org-babel-tangled-file is added as t to the tangled files
>> - "name" :: org-babel-tangled-file is set to the org file name
>> - "path" :: org-babel-tangled-file is set to the path of the org file
>> - "all" :: org-babel-tangled-file is set to the full name including path
>>            of the org file
>> 
>> I can even imagine many more possibilities for the use of local file
>> variables to store meta data in the tangled file (VCS info comes to
>> mind, which would enable one to even go back to older revisions based on
>> the tangled code rather easily).
>> 

I agree that local-file variables show much promise, although I think
(at least for now) the best way to set such variables is through the
post-tangle-hook as Vitalie has already done.

Best,

>> 
>> Cheers,
>> 
>> Rainer
>> 
>> -- 
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>> 
>> Centre of Excellence for Invasion Biology
>> Stellenbosch University
>> South Africa
>> 
>> Tel :       +33 - (0)9 53 10 27 44
>> Cell:       +33 - (0)6 85 62 59 98
>> Fax :       +33 - (0)9 58 10 27 44
>> 
>> Fax (D):    +49 - (0)3 21 21 25 22 44
>> 
>> email:      Rainer@krugs.de
>> 
>> Skype:      RMkrug

-- 
Eric Schulte
http://cs.unm.edu/~eschulte

Re: Automatically adding local variables to tangled file

[Rainer M Krug]

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Eric Schulte <schulte.eric@gmail.com> writes:

[snip (4 lines)]
>>
>
> I personally prefer the solution shown below of adding a file-local
> variable using the post-tangle hook.  As mentioned previously this makes
> the detection of tangled code much faster, simpler and less error prone
> than grepping the file for comments.
>

+1

>>
>> On the other hand, a local variable in the tangled files to set the buffer
>> to read-only could be very useful to avoid the mistake of editing the
>> tangled files directly.
>>
>
> We already set the permission of tangled files to be executable when
> they include a shebang line.  Perhaps we could add an option (or change
> the default) to set the permissions of tangled files to be read only.
>
> Perhaps this could be done using the post-tangle hook with something
> like the following.
>
>     ;; -*- emacs-lisp -*-
>     (defun org-babel-mark-tangled-as-read-only ()
>       "Mark the current file read only.
>     If it is executable keep it executable."
>       (if (= #o755 (file-modes (buffer-file-name)))
>           (set-file-modes (buffer-file-name) #o555)
>           (set-file-modes (buffer-file-name) #o444)))
>
>     (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-tangled-as-read-only)
>

I think that would be a good idea to add this in a way so that it is
controled by a variable - if the variable is t, all tangled files will be set
read-only, if it is nil, none will. It might be useful to also allow
string / list of strings, which then would individual file names which
could be set as read-only.

I would leave the default as it is to guarantee backward compatibility,
although I agree that the org file is the source, and the tangled file
should not be changed.

For the time being, I will just add this code above to my emacs.org.

>>> 

[snip (7 lines)]

>>> 
>>> ,----
>>> |  (defvar org-babel-tangled-file nil
>>> |      "If non-nill, current file was tangled with org-babel-tangle")
>>> |    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
>>> |    
>>> |    (defun org-babel-mark-file-as-tangled ()
>>> |      (add-file-local-variable 'org-babel-tangled-file t)
>>> |      (basic-save-buffer))
>>> | 
>>> |    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
>>> `----
>>> 
>
> I think the above code should be considered an implementation rather
> than simply a test.  This is exactly what the post-tangle hook is
> intended to support.  Is there a motivating reason for this behavior to
> be "built in"?

As pointed out, I think the possibility to easily add local variables to
the tangled file, will be valuable. I would opt for an the buil-in
option, as this could e.g. be used to set the file read-only in emacs,
adding svn information, etc.

This could be achieved by supplying one variable containing strings,
which contains the names of the local variables to be added and their values.

For the time being, I will add the suggested code to my emacs.org.

>

[snip (19 lines)]

>>> 
>
> I agree that local-file variables show much promise, although I think
> (at least for now) the best way to set such variables is through the
> post-tangle-hook as Vitalie has already done.

Ok - I'll stick to the solutions outlined above for now.

Thanks a lot everybody,

Rainer

>
> Best,
>
>>> 
>>> Cheers,
>>> 
>>> Rainer
>>> 
>>> -- 
>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>> 
>>> Centre of Excellence for Invasion Biology
>>> Stellenbosch University
>>> South Africa
>>> 
>>> Tel :       +33 - (0)9 53 10 27 44
>>> Cell:       +33 - (0)6 85 62 59 98
>>> Fax :       +33 - (0)9 58 10 27 44
>>> 
>>> Fax (D):    +49 - (0)3 21 21 25 22 44
>>> 
>>> email:      Rainer@krugs.de
>>> 
>>> Skype:      RMkrug

-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com

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Re: Automatically adding local variables to tangled file

[Rainer M Krug]

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Rainer M Krug <Rainer@krugs.de> writes:

[snip (54 lines)]

>>>> ,----
>>>> |  (defvar org-babel-tangled-file nil
>>>> |      "If non-nill, current file was tangled with org-babel-tangle")
>>>> |    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
>>>> |    
>>>> |    (defun org-babel-mark-file-as-tangled ()
>>>> |      (add-file-local-variable 'org-babel-tangled-file t)
>>>> |      (basic-save-buffer))
>>>> | 
>>>> |    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
>>>> `----
>>>> 
>>
>> I think the above code should be considered an implementation rather
>> than simply a test.  This is exactly what the post-tangle hook is
>> intended to support.  Is there a motivating reason for this behavior to
>> be "built in"?
>
> As pointed out, I think the possibility to easily add local variables to
> the tangled file, will be valuable. I would opt for an the buil-in
> option, as this could e.g. be used to set the file read-only in emacs,
> adding svn information, etc.
>
> This could be achieved by supplying one variable containing strings,
> which contains the names of the local variables to be added and their values.
>
> For the time being, I will add the suggested code to my emacs.org.

I stumbled upon one problem, though: I want to mame the tengled file,
when nopened in emacs, to have the minor mode auto-revert-mode. So I did
the following, which obviously did not work:

,----
| (defvar org-babel-tangled-file nil
|     "If non-nill, current file was tangled with org-babel-tangle")
|   (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
|     
|   (defun org-babel-mark-file-as-tangled ()
|     (add-file-local-variable 'org-babel-tangled-file t)
|     (add-file-local-variable 'buffer-read-only t)
|     (add-file-local-variable 'eval: (auto-revert-mode))
|     (basic-save-buffer))
|   
|   (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
`----

So is tere a way, of adding the line 

,----
| eval: (auto-revert-mode)
`----

to the file local variables, so that emacs sutomatically enables
auto-revert-mode?

Thanks,

Rainer


>
>>
>
[snip (38 lines)]


-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com

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[PATCH] Don't ask "File changed on disk" in org-babel-post-tangle-hook

[Vitalie Spinu]

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The problem with org-babel-post-tangle-hook is that user is always asked
yes-or-no-p for file reversion. Calling auto revert (as Rainer tried)
will not help.

The problem is in find-file-noselect in org-babel-find-file-noselect-refresh.

The following patch fixes it by silencing find-file-noselect. Besides
reversion question, there are a couple of other warning/questions that
are silenced, but given that org-babel-find-file-noselect-refresh is
used only for reverting tangled files, this is probably not an issue.

  Vitalie


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From 2f408019b940c7e3b742dd2941f725f97645b868 Mon Sep 17 00:00:00 2001
From: Vitalie Spinu <spinuvit@gmail.com>
Date: Fri, 7 Jun 2013 12:43:55 +0200
Subject: [PATCH] avoid file warnings in org-babel-post-tangle-hook

* lisp/ob-tangle.el (org-babel-find-file-noselect-refresh): call
  find-file-noselect with 'nowarn argument to surpress yes-or-no-p
  reversion message.
---
 lisp/ob-tangle.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lisp/ob-tangle.el b/lisp/ob-tangle.el
index 95d518a..82f2c10 100644
--- a/lisp/ob-tangle.el
+++ b/lisp/ob-tangle.el
@@ -114,7 +114,7 @@ result.  The default value is `org-babel-trim'."
 (defun org-babel-find-file-noselect-refresh (file)
   "Find file ensuring that the latest changes on disk are
 represented in the file."
-  (find-file-noselect file)
+  (find-file-noselect file 'nowarn)
   (with-current-buffer (get-file-buffer file)
     (revert-buffer t t t)))
 
-- 
1.8.1.2


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 >> Rainer M Krug <Rainer@krugs.de>
 >> on Fri, 07 Jun 2013 10:32:19 +0200 wrote:

 > Rainer M Krug <Rainer@krugs.de> writes:

 > [snip (54 lines)]

 >>>>> ,----
 >>>>> |  (defvar org-babel-tangled-file nil
 >>>>> |      "If non-nill, current file was tangled with org-babel-tangle")
 >>>>> |    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
 >>>>> |    
 >>>>> |    (defun org-babel-mark-file-as-tangled ()
 >>>>> |      (add-file-local-variable 'org-babel-tangled-file t)
 >>>>> |      (basic-save-buffer))
 >>>>> | 
 >>>>> |    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
 >>>>> `----
 >>>>> 
 >>> 
 >>> I think the above code should be considered an implementation rather
 >>> than simply a test.  This is exactly what the post-tangle hook is
 >>> intended to support.  Is there a motivating reason for this behavior to
 >>> be "built in"?
 >> 
 >> As pointed out, I think the possibility to easily add local variables to
 >> the tangled file, will be valuable. I would opt for an the buil-in
 >> option, as this could e.g. be used to set the file read-only in emacs,
 >> adding svn information, etc.
 >> 
 >> This could be achieved by supplying one variable containing strings,
 >> which contains the names of the local variables to be added and their values.
 >> 
 >> For the time being, I will add the suggested code to my emacs.org.

 > I stumbled upon one problem, though: I want to mame the tengled file,
 > when nopened in emacs, to have the minor mode auto-revert-mode. So I did
 > the following, which obviously did not work:

 > ,----
 > | (defvar org-babel-tangled-file nil
 > |     "If non-nill, current file was tangled with org-babel-tangle")
 > |   (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
 > |     
 > |   (defun org-babel-mark-file-as-tangled ()
 > |     (add-file-local-variable 'org-babel-tangled-file t)
 > |     (add-file-local-variable 'buffer-read-only t)
 > |     (add-file-local-variable 'eval: (auto-revert-mode))
 > |     (basic-save-buffer))
 > |   
 > |   (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
 > `----

 > So is tere a way, of adding the line 

 > ,----
 > | eval: (auto-revert-mode)
 > `----

 > to the file local variables, so that emacs sutomatically enables
 > auto-revert-mode?

 > Thanks,

 > Rainer

 >> 
 >>> 
 >> 
 > [snip (38 lines)]

Re: [PATCH] Don't ask "File changed on disk" in org-babel-post-tangle-hook

[Eric Schulte]

Vitalie Spinu <spinuvit@gmail.com> writes:

> The problem with org-babel-post-tangle-hook is that user is always asked
> yes-or-no-p for file reversion. Calling auto revert (as Rainer tried)
> will not help.
>
> The problem is in find-file-noselect in org-babel-find-file-noselect-refresh.
>
> The following patch fixes it by silencing find-file-noselect. Besides
> reversion question, there are a couple of other warning/questions that
> are silenced, but given that org-babel-find-file-noselect-refresh is
> used only for reverting tangled files, this is probably not an issue.
>

Applied.  Thanks,

>
>   Vitalie
>
>
> From 2f408019b940c7e3b742dd2941f725f97645b868 Mon Sep 17 00:00:00 2001
> From: Vitalie Spinu <spinuvit@gmail.com>
> Date: Fri, 7 Jun 2013 12:43:55 +0200
> Subject: [PATCH] avoid file warnings in org-babel-post-tangle-hook
>
> * lisp/ob-tangle.el (org-babel-find-file-noselect-refresh): call
>   find-file-noselect with 'nowarn argument to surpress yes-or-no-p
>   reversion message.
> ---
>  lisp/ob-tangle.el | 2 +-
>  1 file changed, 1 insertion(+), 1 deletion(-)
>
> diff --git a/lisp/ob-tangle.el b/lisp/ob-tangle.el
> index 95d518a..82f2c10 100644
> --- a/lisp/ob-tangle.el
> +++ b/lisp/ob-tangle.el
> @@ -114,7 +114,7 @@ result.  The default value is `org-babel-trim'."
>  (defun org-babel-find-file-noselect-refresh (file)
>    "Find file ensuring that the latest changes on disk are
>  represented in the file."
> -  (find-file-noselect file)
> +  (find-file-noselect file 'nowarn)
>    (with-current-buffer (get-file-buffer file)
>      (revert-buffer t t t)))

-- 
Eric Schulte
http://cs.unm.edu/~eschulte

Re: [PATCH] Don't ask "File changed on disk" in org-babel-post-tangle-hook

[Rainer M Krug]

Eric Schulte <schulte.eric@gmail.com> writes:

> Vitalie Spinu <spinuvit@gmail.com> writes:
>
>> The problem with org-babel-post-tangle-hook is that user is always asked
>> yes-or-no-p for file reversion. Calling auto revert (as Rainer tried)
>> will not help.
>>
>> The problem is in find-file-noselect in org-babel-find-file-noselect-refresh.
>>
>> The following patch fixes it by silencing find-file-noselect. Besides
>> reversion question, there are a couple of other warning/questions that
>> are silenced, but given that org-babel-find-file-noselect-refresh is
>> used only for reverting tangled files, this is probably not an issue.
>>
>
> Applied.  Thanks,

Thanks a lot.

Will update then and try later.

Thanks,

Rainer

>
>>
>>   Vitalie
>>
>>
>> From 2f408019b940c7e3b742dd2941f725f97645b868 Mon Sep 17 00:00:00 2001
>> From: Vitalie Spinu <spinuvit@gmail.com>
>> Date: Fri, 7 Jun 2013 12:43:55 +0200
>> Subject: [PATCH] avoid file warnings in org-babel-post-tangle-hook
>>
>> * lisp/ob-tangle.el (org-babel-find-file-noselect-refresh): call
>>   find-file-noselect with 'nowarn argument to surpress yes-or-no-p
>>   reversion message.
>> ---
>>  lisp/ob-tangle.el | 2 +-
>>  1 file changed, 1 insertion(+), 1 deletion(-)
>>
>> diff --git a/lisp/ob-tangle.el b/lisp/ob-tangle.el
>> index 95d518a..82f2c10 100644
>> --- a/lisp/ob-tangle.el
>> +++ b/lisp/ob-tangle.el
>> @@ -114,7 +114,7 @@ result.  The default value is `org-babel-trim'."
>>  (defun org-babel-find-file-noselect-refresh (file)
>>    "Find file ensuring that the latest changes on disk are
>>  represented in the file."
>> -  (find-file-noselect file)
>> +  (find-file-noselect file 'nowarn)
>>    (with-current-buffer (get-file-buffer file)
>>      (revert-buffer t t t)))
<#secure method=pgpmime mode=sign>

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

Re: Automatically adding local variables to tangled file

[Eric Schulte]

>>
>> We already set the permission of tangled files to be executable when
>> they include a shebang line.  Perhaps we could add an option (or change
>> the default) to set the permissions of tangled files to be read only.
>>
>> Perhaps this could be done using the post-tangle hook with something
>> like the following.
>>
>>     ;; -*- emacs-lisp -*-
>>     (defun org-babel-mark-tangled-as-read-only ()
>>       "Mark the current file read only.
>>     If it is executable keep it executable."
>>       (if (= #o755 (file-modes (buffer-file-name)))
>>           (set-file-modes (buffer-file-name) #o555)
>>           (set-file-modes (buffer-file-name) #o444)))
>>
>>     (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-tangled-as-read-only)
>>
>
> I think that would be a good idea to add this in a way so that it is
> controled by a variable

I've added a :tangle-mode header argument which may be used to control
the permissions of tangled files.  See the manual for instructions on
it's usage.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte

Re: Automatically adding local variables to tangled file

[Achim Gratz]

Eric Schulte writes:
> I've added a :tangle-mode header argument which may be used to control
> the permissions of tangled files.  See the manual for instructions on
> it's usage.

The change in org-babel-read now requires that :shebang values are
quoted.  I've changed the test file accordingly as otherwise the file
couldn't be ingested.  In general I'd suggest that reading header
arguments as eLisp should at be protected against an error propagating
out of the reader function.


Regards,
Achim.
-- 
+<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+

SD adaptations for KORG EX-800 and Poly-800MkII V0.9:
http://Synth.Stromeko.net/Downloads.html#KorgSDada

Re: Automatically adding local variables to tangled file

[Eric Schulte]

Achim Gratz <Stromeko@nexgo.de> writes:

> Eric Schulte writes:
>> I've added a :tangle-mode header argument which may be used to control
>> the permissions of tangled files.  See the manual for instructions on
>> it's usage.
>
> The change in org-babel-read now requires that :shebang values are
> quoted.

Oh, I should have realized that shebang values weren't normally quoted.
I've reverted this portion of my tangle-mode patch, so the reader no
longer tries to read #-prefixed strings a elisp.  Hopefully this won't
affect too many people.

> I've changed the test file accordingly as otherwise the file couldn't
> be ingested.  In general I'd suggest that reading header arguments as
> eLisp should at be protected against an error propagating out of the
> reader function.
>

I think in most cases it would be better to know if an error has
occurred than not, and I think any sort of message output would quickly
be overwritten by the remainder of the code block execution.

Thanks for catching this quickly!

>
>
> Regards,
> Achim.

-- 
Eric Schulte
http://cs.unm.edu/~eschulte

Re: Automatically adding local variables to tangled file

[Rainer M Krug]

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Eric Schulte <schulte.eric@gmail.com> writes:

>>>
>>> We already set the permission of tangled files to be executable when
>>> they include a shebang line.  Perhaps we could add an option (or change
>>> the default) to set the permissions of tangled files to be read only.
>>>
>>> Perhaps this could be done using the post-tangle hook with something
>>> like the following.
>>>
>>>     ;; -*- emacs-lisp -*-
>>>     (defun org-babel-mark-tangled-as-read-only ()
>>>       "Mark the current file read only.
>>>     If it is executable keep it executable."
>>>       (if (= #o755 (file-modes (buffer-file-name)))
>>>           (set-file-modes (buffer-file-name) #o555)
>>>           (set-file-modes (buffer-file-name) #o444)))
>>>
>>>     (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-tangled-as-read-only)
>>>
>>
>> I think that would be a good idea to add this in a way so that it is
>> controled by a variable
>
> I've added a :tangle-mode header argument which may be used to control
> the permissions of tangled files.  See the manual for instructions on
> it's usage.


Thanks a lot. I will try it out today or tomorrow.

Cheers,

Rainer



-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com

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Problem in tangle-mode -- WAS: Automatically adding local variables to tangled file

[Rainer M Krug]

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Rainer M Krug <Rainer@krugs.de> writes:

> Eric Schulte <schulte.eric@gmail.com> writes:
>
>>>>
>>>> We already set the permission of tangled files to be executable when
>>>> they include a shebang line.  Perhaps we could add an option (or change
>>>> the default) to set the permissions of tangled files to be read only.
>>>>
>>>> Perhaps this could be done using the post-tangle hook with something
>>>> like the following.
>>>>
>>>>     ;; -*- emacs-lisp -*-
>>>>     (defun org-babel-mark-tangled-as-read-only ()
>>>>       "Mark the current file read only.
>>>>     If it is executable keep it executable."
>>>>       (if (= #o755 (file-modes (buffer-file-name)))
>>>>           (set-file-modes (buffer-file-name) #o555)
>>>>           (set-file-modes (buffer-file-name) #o444)))
>>>>
>>>>     (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-tangled-as-read-only)
>>>>
>>>
>>> I think that would be a good idea to add this in a way so that it is
>>> controled by a variable
>>
>> I've added a :tangle-mode header argument which may be used to control
>> the permissions of tangled files.  See the manual for instructions on
>> it's usage.
>
>
> Thanks a lot. I will try it out today or tomorrow.

I did, and there is a problem with tangling multiple blocks into a
single file:

The following does not work:

,----
| #+PROPERTY: tangle-mode (identity #o444)
| #+PROPERTY: tangle ./tools.R
| * Two blocks
| Block 1
| #+begin_src R
|   suitName <- function(species)
|                     {
|                       return( paste(species$layer, "suitability", sep="_") )
|                     }
| #+end_src  
| 
| Block 2
| #+begin_src R
|   statDistName <- function(species){
|       return( paste(species$layer, "disturbances_static", sep="_") )
|   }
| #+end_src  
`----

It seems that the second block can not be written, as the file is
already set to read-only.

For the moment, I exclude this setting again but will try it out as son
as it is fixed.

Cheers,

Rainer


>
> Cheers,
>
> Rainer


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

[-- Attachment #2: Type: application/pgp-signature, Size: 489 bytes --]

Re: Problem in tangle-mode -- WAS: Automatically adding local variables to tangled file

[Eric Schulte]

>>>
>>> I've added a :tangle-mode header argument which may be used to control
>>> the permissions of tangled files.  See the manual for instructions on
>>> it's usage.
>>
>>
>> Thanks a lot. I will try it out today or tomorrow.
>
> I did, and there is a problem with tangling multiple blocks into a
> single file:
>

Oh, stupid of me.  Thanks for sending this alert, I've just pushed up a
change which should fix this problem.  We now wait to set the file modes
until after all blocks are tangled and after the post-tangle-hook has
been run.

Thanks,

-- 
Eric Schulte
http://cs.unm.edu/~eschulte

BUG - Problem in tangle-mode

[Rainer M Krug]

[-- Attachment #1: Type: text/plain, Size: 1037 bytes --]


Eric Schulte <schulte.eric@gmail.com> writes:

>>>>
>>>> I've added a :tangle-mode header argument which may be used to control
>>>> the permissions of tangled files.  See the manual for instructions on
>>>> it's usage.
>>>
>>>
>>> Thanks a lot. I will try it out today or tomorrow.
>>
>> I did, and there is a problem with tangling multiple blocks into a
>> single file:
>>
>
> Oh, stupid of me.  Thanks for sending this alert, I've just pushed up a
> change which should fix this problem.  We now wait to set the file modes
> until after all blocks are tangled and after the post-tangle-hook has
> been run.
>
> Thanks,

Hi

Unfortunately, it is now worse, as even without the tangle-mode header,
I can't tangle two blocks - the second block overwrites the before
tangled blocks. It tells me that two blocks were tangled, but only the
last one is in the tangled file.

I will for revert for now to the version from yesterday.

Cheers,

Rainer

-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com

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Re: BUG - Problem in tangle-mode

[Eric Schulte]

Rainer M Krug <Rainer@krugs.de> writes:

> Eric Schulte <schulte.eric@gmail.com> writes:
>
>>>>>
>>>>> I've added a :tangle-mode header argument which may be used to control
>>>>> the permissions of tangled files.  See the manual for instructions on
>>>>> it's usage.
>>>>
>>>>
>>>> Thanks a lot. I will try it out today or tomorrow.
>>>
>>> I did, and there is a problem with tangling multiple blocks into a
>>> single file:
>>>
>>
>> Oh, stupid of me.  Thanks for sending this alert, I've just pushed up a
>> change which should fix this problem.  We now wait to set the file modes
>> until after all blocks are tangled and after the post-tangle-hook has
>> been run.
>>
>> Thanks,
>
> Hi
>
> Unfortunately, it is now worse, as even without the tangle-mode header,
> I can't tangle two blocks - the second block overwrites the before
> tangled blocks. It tells me that two blocks were tangled, but only the
> last one is in the tangled file.
>
> I will for revert for now to the version from yesterday.
>
> Cheers,
>

Just pushed up a fix.  Cheers,

-- 
Eric Schulte
http://cs.unm.edu/~eschulte

Re: BUG - Problem in tangle-mode

[Rainer M Krug]

[-- Attachment #1: Type: text/plain, Size: 1696 bytes --]

On Tuesday, June 11, 2013, Eric Schulte wrote:

> Rainer M Krug <Rainer@krugs.de <javascript:;>> writes:
>
> > Eric Schulte <schulte.eric@gmail.com <javascript:;>> writes:
> >
> >>>>>
> >>>>> I've added a :tangle-mode header argument which may be used to
> control
> >>>>> the permissions of tangled files.  See the manual for instructions on
> >>>>> it's usage.
> >>>>
> >>>>
> >>>> Thanks a lot. I will try it out today or tomorrow.
> >>>
> >>> I did, and there is a problem with tangling multiple blocks into a
> >>> single file:
> >>>
> >>
> >> Oh, stupid of me.  Thanks for sending this alert, I've just pushed up a
> >> change which should fix this problem.  We now wait to set the file modes
> >> until after all blocks are tangled and after the post-tangle-hook has
> >> been run.
> >>
> >> Thanks,
> >
> > Hi
> >
> > Unfortunately, it is now worse, as even without the tangle-mode header,
> > I can't tangle two blocks - the second block overwrites the before
> > tangled blocks. It tells me that two blocks were tangled, but only the
> > last one is in the tangled file.
> >
> > I will for revert for now to the version from yesterday.
> >
> > Cheers,
> >
>
> Just pushed up a fix.  Cheers,


Thanks. Will try it out tomorrow,

Cheers,

Rainer

>
> --
> Eric Schulte
> http://cs.unm.edu/~eschulte
>


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax (F):       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

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Re: BUG - Problem in tangle-mode

[Rainer M Krug]

[-- Attachment #1: Type: text/plain, Size: 3963 bytes --]

Rainer M Krug <r.m.krug@gmail.com> writes:

> On Tuesday, June 11, 2013, Eric Schulte wrote:
>
>> Rainer M Krug <Rainer@krugs.de <javascript:;>> writes:
>>
>> > Eric Schulte <schulte.eric@gmail.com <javascript:;>> writes:
>> >
>> >>>>>
>> >>>>> I've added a :tangle-mode header argument which may be used to
>> control
>> >>>>> the permissions of tangled files.  See the manual for instructions on
>> >>>>> it's usage.
>> >>>>
>> >>>>
>> >>>> Thanks a lot. I will try it out today or tomorrow.
>> >>>
>> >>> I did, and there is a problem with tangling multiple blocks into a
>> >>> single file:
>> >>>
>> >>
>> >> Oh, stupid of me.  Thanks for sending this alert, I've just pushed up a
>> >> change which should fix this problem.  We now wait to set the file modes
>> >> until after all blocks are tangled and after the post-tangle-hook has
>> >> been run.
>> >>
>> >> Thanks,
>> >
>> > Hi
>> >
>> > Unfortunately, it is now worse, as even without the tangle-mode header,
>> > I can't tangle two blocks - the second block overwrites the before
>> > tangled blocks. It tells me that two blocks were tangled, but only the
>> > last one is in the tangled file.
>> >
>> > I will for revert for now to the version from yesterday.
>> >
>> > Cheers,
>> >
>>
>> Just pushed up a fix.  Cheers,
>
>
> Thanks. Will try it out tomorrow,

Hi

it seems that I have no luck at the moment.

Now the post tangle hook does not seem to be called.

If I use the file below, evaluate the code to set the hook, the hook is
not executed.

,----
| #+PROPERTY: tangle ./test.R
| 
| * Internal configurations                                          :noexport:
| ** Evaluate to run post tangle script
| #+begin_src emacs-lisp :results silent :tangle no :exports none
| (add-hook 'org-babel-post-tangle-hook(
| 				      lambda () (call-process-shell-command "./postTangleScript.sh" nil 0 nil))
| 	  )
| #+end_src
| 
| ** Post tangle script
| #+begin_src sh :tangle postTangleScript.sh
| touch PostTangleScriptHasBeenExecuted
| #+end_src
| 
| #+results:
| 
| 
| * Two blocks
| Block 1
| #+begin_src R
|   suitName <- function(species)
|                     {
|                       return( paste(species$layer, "suitability", sep="_") )
|                     }
| #+end_src  
| 
| Block 2
| #+begin_src R
|   statDistName <- function(species){
|       return( paste(species$layer, "disturbances_static", sep="_") )
|   }
| #+end_src  
`----

The hook is set:
,----
| Its value is
| ((lambda nil
|    (call-process-shell-command "./postTangleScript.sh" nil 0 nil)))
| 
| Original value was nil
`----

Strangely enough, if I use

,----
| #+begin_src emacs-lisp :tangle no
| (defvar org-babel-tangled-file nil
|   "If non-nill, current file was tangled with org-babel-tangle")
| (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
| 
| (defun org-babel-mark-file-as-tangled ()
|   
|   (when  (string-match "[.]R" (buffer-file-name))
|       (add-file-local-variable 'org-babel-tangled-file t)
|     (add-file-local-variable 'buffer-read-only t)
|     ;; (add-file-local-variable 'eval: (auto-revert-mode))
|     (basic-save-buffer)))
| 
| (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
| #+end_src
`----

and evaluate this block (after resetting the post-tangle-hook), this
function is executed?

Sorry about all the hassles,

Rainer


>
> Cheers,
>
> Rainer
>
>>
>> --
>> Eric Schulte
>> http://cs.unm.edu/~eschulte
>>


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

[-- Attachment #2: Type: application/pgp-signature, Size: 489 bytes --]

Re: BUG - Problem in tangle-mode

[Eric Schulte]

[-- Attachment #1: Type: text/plain, Size: 628 bytes --]

>
> Hi
>
> it seems that I have no luck at the moment.
>
> Now the post tangle hook does not seem to be called.
>

It is called, however the shell script you are trying to execute is not
executing because it is not set as executable.  The permissions of
tangled files are set *after* the post-tangle hook is called (so that
the post-tangle hook has a chance to modify files which will eventually
be set to read only).

You example is trying to run a tangled shell script before it is set to
be executable.  This can not work.  My attached alternative of your
example does run the shell script by not assuming it is executable.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: example.org --]
[-- Type: text/x-org, Size: 890 bytes --]

#+PROPERTY: tangle ./test.R

* Internal configurations                                          :noexport:
** Evaluate to run post tangle script
#+begin_src emacs-lisp :results silent :tangle no :exports none
    (add-hook 'org-babel-post-tangle-hook
              (lambda ()
                (message "running the post-tangle shell script")
                (shell-command "bash ./postTangleScript.sh")))
#+end_src

** Post tangle script
#+begin_src sh :tangle postTangleScript.sh :results silent
touch PostTangleScriptHasBeenExecuted
#+end_src

* Two blocks
Block 1
#+begin_src R
  suitName <- function(species)
                    {
                      return( paste(species$layer, "suitability", sep="_") )
                    }
#+end_src  

Block 2
#+begin_src R
  statDistName <- function(species){
      return( paste(species$layer, "disturbances_static", sep="_") )
  }
#+end_src  

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-- 
Eric Schulte
http://cs.unm.edu/~eschulte

Re: BUG - Problem in tangle-mode

[Rainer M Krug]

Eric Schulte <schulte.eric@gmail.com> writes:

>>
>> Hi
>>
>> it seems that I have no luck at the moment.
>>
>> Now the post tangle hook does not seem to be called.
>>
>
> It is called, however the shell script you are trying to execute is not
> executing because it is not set as executable.  The permissions of
> tangled files are set *after* the post-tangle hook is called (so that
> the post-tangle hook has a chance to modify files which will eventually
> be set to read only).

That makes perfect sense - thanks.

>
> You example is trying to run a tangled shell script before it is set to
> be executable.  This can not work.  My attached alternative of your
> example does run the shell script by not assuming it is executable.

OK - I will adapt it accordingly.

Thanks a lot,

Rainer

>
> #+PROPERTY: tangle ./test.R
>
> * Internal configurations                                          :noexport:
> ** Evaluate to run post tangle script
> #+begin_src emacs-lisp :results silent :tangle no :exports none
>     (add-hook 'org-babel-post-tangle-hook
>               (lambda ()
>                 (message "running the post-tangle shell script")
>                 (shell-command "bash ./postTangleScript.sh")))
> #+end_src
>
> ** Post tangle script
> #+begin_src sh :tangle postTangleScript.sh :results silent
> touch PostTangleScriptHasBeenExecuted
> #+end_src
>
> * Two blocks
> Block 1
> #+begin_src R
>   suitName <- function(species)
>                     {
>                       return( paste(species$layer, "suitability", sep="_") )
>                     }
> #+end_src  
>
> Block 2
> #+begin_src R
>   statDistName <- function(species){
>       return( paste(species$layer, "disturbances_static", sep="_") )
>   }
> #+end_src  
<#secure method=pgpmime mode=sign>

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

SOLVED: Automatically adding local variables to tangled file

[Rainer M Krug]

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Eric Schulte <schulte.eric@gmail.com> writes:

[snip (41 lines)]

>>> He added the following to his config file to test the approach:
>>> 
>>> ,----
>>> |  (defvar org-babel-tangled-file nil
>>> |      "If non-nill, current file was tangled with org-babel-tangle")
>>> |    (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
>>> |    
>>> |    (defun org-babel-mark-file-as-tangled ()
>>> |      (add-file-local-variable 'org-babel-tangled-file t)
>>> |      (basic-save-buffer))
>>> | 
>>> |    (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
>>> `----
>>> 

[snip (5 lines)]


I tried the above approach, but I was struggling with setting up the
rules in the function definition which files should get the local
variables and which not.

I ended up with the following:

,----
| (defvar org-babel-tangled-file nil
|   "If non-nill, current file was tangled with org-babel-tangle")
| (put 'org-babel-tangled-file 'safe-local-variable 'booleanp)
| 
| (defun org-babel-mark-file-as-tangled ()
|   
|   (when  (string-match "[.]R" (buffer-file-name))
|       (add-file-local-variable 'org-babel-tangled-file t)
|     (add-file-local-variable 'buffer-read-only t)
|     ;; (add-file-local-variable 'eval: (auto-revert-mode))
|     (basic-save-buffer)))
| 
| (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled)
`----

Thanks everybody for their help,

Rainer



>

-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com

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Re: Automatically adding local variables to tangled file

[Thorsten Jolitz]

Rainer M Krug <Rainer@krugs.de> writes:

Hi,

> I am trying to improve my workflow of literate programming of R in
> org. My org file is tangled into many R files and I am using ESS to
> debug.

[...]

> Now this is error prone, as one (or is it only me?) is easily tempted to
> edit the R file which is reverted after the next tangle.

are you aware that literate programming can be done without any tangling
at all now? I had similar issues like you when using literate
programming for organizing my .emacs, and finally figured out its
actually a conceptual problem:

,------------------------------------------------------------------------
| <--- Text --- Text with Code --- | --- Code with (Comment) Text --- Code --->
`------------------------------------------------------------------------

If you write a complex text/book with source code examples, literate
programming is just perfect (see e.g. Bernt Hansens Org-mode tutorial).
But if you write code with some comment text, it becomes burdensome.
Although working with interpreted dynamic languages, your workflow with
all that tangling starts to feel similar like working with compiled
languages (with the frequent tangling step replacing the frequent
compilation step).

So, looking at the line above, right from the '|' you really might want
to work in a source code buffer to enjoy all the advantages of Lisps (or
R's) dynamic. Its about programming with some text then, not vice versa.

You can do this with outshine.el and outorg.el (and optionally
navi-mode.el and poporg.el), see the tutorial on Worg
(http://orgmode.org/worg/org-tutorials/org-outside-org.html).

Short example:

Structure your R file like an Org-mode file:

,-----------------------------------------------------------------------------
| ## * my-sources.R --- my R Source file
| ##   :PROPERTIES:
| ##   :copyright: my_name
| ##   :copyright-years: 2013
| ##   :version:  0.9
| ##   :created:  21-01-2013
| ##   :licence:  GPL 2 or later (free software)
| ##   :licence-url: http://www.gnu.org/licenses/
| ##   :author:   my_name
| ##   :author_email: my_email AT gamil DOT com
| ##   :inspiration: foo bar
| ##   :keywords: foo bar
| ##   :END:
|
| ## ** Commentary
|
| ## Geometry Object Model from "OGC OpenGIS Simple Features Specification for
| ## SQL" Revision. 1.1 [...]
|
| ## ** Changes
|
| ## | author  | version | date            |
| ## |---------+---------+-----------------|
| ## | my_name |     0.9 | <2013-06-05 Mi> |
|
| ## * code
| ## ** My first R Function
|
| ## simple example function from the manual
| twosam <- function(y1, y2) {
|          n1  <- length(y1); n2  <- length(y2)
|          yb1 <- mean(y1);   yb2 <- mean(y2)
|          s1  <- var(y1);    s2  <- var(y2)
|          s <- ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
|          tst <- (yb1 - yb2)/sqrt(s*(1/n1 + 1/n2))
|          tst
|        }
|
| ## ** My second R Function
|
| ## another simple example function from the manual
| bslash <- function(X, y) {
|        X <- qr(X)
|        qr.coef(X, y)
|      }
|
| ## my-sources.R ends here
`-----------------------------------------------------------------------------

With outline-minor-mode and outshine.el activated, you will have all the
structure-editing and outline-navigation commands you are used to from
Org-mode. But you can program in this buffer directly without any
intermediate steps, and send your functions or whatever via ESS to the R
process-buffer.

The literate programming part comes from outorg.el then. With 

,------
| C-c ’
`------

on or inside any header in this file, the subtree at point is offered
for editing in a temporary Org buffer, with all source code enclosed in
source blocks and all comment text uncommented, e.g. 

,--------------------------------------------------
| ** My first R Function
| 
| simple example function from the manual
| #+begin_src ess
| twosam <- function(y1, y2) {
|          n1  <- length(y1); n2  <- length(y2)
|          yb1 <- mean(y1);   yb2 <- mean(y2)
|          s1  <- var(y1);    s2  <- var(y2)
|          s <- ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
|          tst <- (yb1 - yb2)/sqrt(s*(1/n1 + 1/n2))
|          tst
|        }
| #+end_src
`--------------------------------------------------

With 

,----------
| C-u C-c '
`----------

the whole buffer is converted to Org. 

You can then do your (comment) text editing will full Org-mode
functionality, and since the headlines are converted too, you can export
to any backend or use other Org functions that act on headlines. 

When you are done, just type 

,----
| M-#
`----

and the temporary Org-mode buffer is killed and all the changes are
applied to the original source code buffer. 

So you really have the look&feel of Org-mode in your source code
buffers, but without the annoying and error prone tangling. It works
for all kinds of major modes (emacs-lisp, picolisp, ess, and, at least in
theory, all others).

This way the line between Org-mode and source code buffers is blurring
and literate programming becomes more efficient and enjoyable. 

--
cheers,
Thorsten