[BUG?][babel] Re: Including source when exporting in PDF

[Rainer M Krug <r.m.krug@gmail.com>]

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On 15/01/12 06:29, Frozenlock wrote:
> This babel block should do the following:
> 
> - When exporting, automatically tangle the babel blocks. - Then
> take the resulting files and add them to a zip file, along with the
> original .org file. - Add the necessary \usepackage and latex
> commands to insert the zipfile.
> 
> Let me know if something isn't like you want.
> 
> Here is the babel block to add to your source (org) file:
> 
> ======================================== #+BEGIN_SRC emacs-lisp
> :results org :exports results :var 
> buffer-file-name=(buffer-file-name) (let ((filename
> (file-name-nondirectory (file-name-sans-extension 
> buffer-file-name)))) (shell-command (concat "zip -j " filename
> ".zip " filename".org " (mapconcat '(lambda (arg) 
> (convert-standard-filename (expand-file-name arg))) 
> (org-babel-tangle) " "))) (concat
> "#+LATEX_HEADER:\\usepackage{attachfile2}\n" "#+LATEX: \\vfill
> \\textattachfile[print=false,color=0.5 0.5
> 0.5]{"filename".zip}{Source (.org) \\& other files...}\n")) 
> #+END_SRC ==============================

Thanks for this code - it looks good, but there is a serious problem:

src_emacs_lisp{} expressions are evaluated and replaced with the
result in the org file, which does not happen when tangling from the
buffer itself.
Example:

################################################
* name src_emacs-lisp{(buffer-file-name)}
#+BEGIN_SRC emacs-lisp :results org :exports results :var
buffer-file-name=(buffer-file-name)
  (org-babel-tangle)
#+END_SRC
################################################

If I export the file above, the file get changed to:

################################################
* name

#+BEGIN_SRC emacs-lisp :results org :exports results :var
buffer-file-name=(buffer-file-name)
  (org-babel-tangle)
#+END_SRC
################################################

Is there something wrong with the code?

Rainer


> 
> 
> On a related note, I've added some improvements to my own way to 
> export in multiple format and add the files along with the source.
> The latex commands and usepackage are included, so no need to add
> them elswhere in the org file:
> 
> ============================== # Make sure this babel block is the
> last one in the buffer; # block after this one won't be evaluated
> before the txt and html export. #+BEGIN_SRC emacs-lisp :results org
> :exports results :var buffer-file-name=(buffer-file-name) (let
> ((org-export-babel-evaluate nil)); don't evaluate in 'recursive'
> exports (save-window-excursion ;; avoid leakage when more than one
> org export in block (org-export-as-ascii
> org-export-headline-levels)) (save-window-excursion
> (org-export-as-html org-export-headline-levels)) (let ((filename
> (file-name-nondirectory (file-name-sans-extension 
> buffer-file-name))) (to-include-files (directory-files
> (file-name-directory buffer-file-name)))) (shell-command (concat
> "zip -j " filename  ".zip " (mapconcat '(lambda (arg) arg) 
> (remove-if '(lambda (file) (string-match
> "\\.$\\|\\.pdf$\\|\\.atfi$\\|\\.tex$\\|#" file)) ;; don't include
> useless files to-include-files) " "))) (concat
> "#+LATEX_HEADER:\\usepackage{attachfile2}\n" "#+LATEX: \\vfill
> \\textattachfile[print=false,color=0.5 0.5 
> 0.5]{"filename".zip}{Source (.org) & html, txt...}\n"))) #+END_SRC 
> ==============================
> 
> 
> Enjoy!
> 
> 
> 
> On Thu, Jan 12, 2012 at 8:59 AM, Rainer M Krug <r.m.krug@gmail.com>
> wrote:
>> On 12 January 2012 14:54, Frozenlock <frozenlock@gmail.com>
>> wrote:
>>> The code block I previously sent only require you to specify
>>> which _extension_ you want or don't want. No need to include
>>> any specific filename (other than the .zip file in the latex
>>> "include" command).
>>> 
>>> Am I to understand you want something to include *all and only*
>>> tangled files?
>> 
>> Yes - and the files do have different extensions (e.g. .R, .sh,
>> .sub, none) and are not tangled necessarily in a specific
>> directory.
>> 
>> and the original org file, but that is not a problem.
>> 
>> Rainer
>> 
>>> 
>>> --
>>> 
>>> I tried ":exports result" with no success. I'll try to send a
>>> minimum working example shortly.
>>> 
>>> On Thu, Jan 12, 2012 at 4:11 AM, Rainer M Krug
>>> <r.m.krug@gmail.com> wrote:
> On 12/01/12 03:06, Frozenlock wrote:
>>>>>> To include multiple files, I export all of the required
>>>>>> files before the PDF creation and zip them. This way, I
>>>>>> only need to include a single zip file.
> 
> Good idea.
> 
>>>>>> 
>>>>>> #+BEGIN_SRC emacs-lisp :exports none ;; various exports 
>>>>>> (save-window-excursion (org-export-as-ascii 
>>>>>> org-export-headline-levels)) (save-window-excursion 
>>>>>> (org-export-as-html org-export-headline-levels))
>>>>>> 
>>>>>> ;;zip the required files (let ((filename
>>>>>> (file-name-sans-extension (file-name-nondirectory
>>>>>> (buffer-file-name))))) (shell-command (concat "zip "
>>>>>> filename ".zip " (mapconcat '(lambda (arg) arg) 
>>>>>> (remove-if '(lambda (filename) (string-match 
>>>>>> "\\.$\\|\\.pdf$\\|\\.atfi$\\|#" filename))
>>>>>> (directory-files (file-name-directory
>>>>>> (buffer-file-name)))) " ")))) #+END_SRC
>>>>>> 
>>>>>> (I've added this code in a babel block to evaluate just
>>>>>> before the PDF export.)
> 
> I actually did not want to fiddle with the file names, as it is to 
> easy to forget some: this concerns in my case literate programming
> of a simulation model in R, resul;ting in several files of
> different extensions - it is to easy to forget one.
> 
> If I tangle, I get all the names of the tangled files, but I do
> not know how I can feed them into the zip file.
> 
>>>>>> 
>>>>>> As you can see, I make sure I don't include a previous
>>>>>> PDF, or any other useless file.
> 
> True.
> 
>>>>>> 
>>>>>> If you wish to add only a single type of file, simply
>>>>>> replace "remove-if" by "remove-if-not" and change the
>>>>>> value in the string-match function. For example, 
>>>>>> "\\.$\\|\\.pdf$\\|\\.atfi$\\|#" would become "\\.lisp$"
>>>>>> to include all your exported lisp files.
>>>>>> 
>>>>>> Hope this helps!
>>>>>> 
>>>>>> 
>>>>>> By the way, I can't get the code block to be evaluated 
>>>>>> automatically when I export to PDF, any clue on how to do
>>>>>> that?
> 
> I assume, it is caused by the :exports none - so no evaluation is
> done on export. Try changing it to :exports result and then
> generate an empty result, or a list of files included in the zip
> file.
> 
> Cheers,
> 
> Rainer
> 
> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Wed, Jan 11, 2012 at 10:28 AM, Rainer M Krug 
>>>>>> <r.m.krug@gmail.com> wrote: On 06/01/12 08:45, Eric
>>>>>> Schulte wrote:
>>>>>>>>> Frozenlock <frozenlock@gmail.com> writes:
>>>>>>>>> 
>>>>>>>>>> I am a strong advocate in keeping the source of 
>>>>>>>>>> everything.
>>>>>>>>>> 
>>>>>>>>>> However, Â a source can easily be lost if it
>>>>>>>>>> doesn't follow the document. In LaTeX, there's a
>>>>>>>>>> package to attach a file to a PDF (like when you
>>>>>>>>>> attach a file to an email). By doing so, the
>>>>>>>>>> source will follow the PDF even if the common 
>>>>>>>>>> reader have no clue what it's for, or even how to
>>>>>>>>>> use it.
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> This sounds like a great Reproducible Research
>>>>>>>>> practice.
>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> Here is how I attach my org source to every
>>>>>>>>>> document I export to PDF:
>>>>>>>>>> 
>>>>>>>>>> ;; Include the source file for every exported
>>>>>>>>>> PDF (org-mode) (eval-after-load "org-exp"
>>>>>>>>>> '(defadvice org-export-as-latex (around
>>>>>>>>>> org-export-add-source-pdf activate) "Add the
>>>>>>>>>> source (org file) to the resulting pdf file" (let
>>>>>>>>>> ((filename (buffer-name))) ad-do-it ;do the 
>>>>>>>>>> function (let ((latex-buffer ad-return-value))
>>>>>>>>>> (set-buffer latex-buffer) (while
>>>>>>>>>> (re-search-forward "\\\\usepackage{.+}" nil t));
>>>>>>>>>> go to the end of packages (insert
>>>>>>>>>> "\n\\usepackage{attachfile2}"); the package
>>>>>>>>>> needed to attach files (when (re-search-forward 
>>>>>>>>>> "\\\\end{document}" nil t) (forward-line -1)
>>>>>>>>>> (insert (concat "\\vfill\n" "\\footnotesize\n"
>>>>>>>>>> "The source of this document is an Org-Mode file
>>>>>>>>>> attached here:" "\n\\attachfile" "{" filename
>>>>>>>>>> "}"))) (save-buffer)))))
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> This is by no mean a patch, but rather a quick
>>>>>>>>>> hack. Perhaps someone with a working knowledge of
>>>>>>>>>> the org-export could find a way to add a source
>>>>>>>>>> option?
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> I think this practice may not actually require any
>>>>>>>>> changes to the Org-mode core. Â The attached small
>>>>>>>>> Org-mode file will attach itself to pdf exports
>>>>>>>>> using only features already present in Org-mode.
>>>>>> 
>>>>>> Following this idea - how can I easily attach all files
>>>>>> created by tangling? Is there a programmatic way, without
>>>>>> having to specify them manually?
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Rainer
>>>>>> 
>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> Thanks for sharing this idea!
>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> Cheers!
>>>>>>>>>> 
>>>>>>>>> 
>>>>>> 
>>>>>> 
> 
>> 
>> 
>> 
>> -- 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

- -- 
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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