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

[Frozenlock]

I'm sorry, but I don't quite understand...

Would it be possible to send a minimum working example of your org file?



On Mon, Jan 16, 2012 at 6:21 AM, Rainer M Krug <address@hidden> wrote:
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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 <address@hidden>
>> wrote:
>>> On 12 January 2012 14:54, Frozenlock <address@hidden>
>>> 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
>>>> <address@hidden> 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
>>>>>>> <address@hidden> wrote: On 06/01/12 08:45, Eric
>>>>>>> Schulte wrote:
>>>>>>>>>> Frozenlock <address@hidden> 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:     address@hidden
>>>
>>> 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:     address@hidden
>
> Skype:      RMkrug
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