Re: Updating the Babel section of Worg

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

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On 08/02/12 15:21, Eric Schulte wrote:
> Martyn Jago <martyn.jago@btinternet.com> writes:
> 
>> Hi Thomas and Eric
>> 
>> Love it. I will try to help!
>> 
>> Worg is a great resource that is getting better and better.
>> 
>> The template looks good (Babel wise) and should be up there as a 
>> check-sheet, although maybe not as a requirement.
>> 
> 
> I agree, I've just linked to it from the languages page [1] with
> the following statement.  Please feel free to edit this directly on
> worg if it sounds too strong.

Nice - I will take a look at it.

Just to make it easier for non-regular worg contributors: I would
suggest to give an email where one can send the completed template to
to be submitted to worg.

Rainer

> 
> Note: Many languages in this table still require documentation. A 
> template is provided in the worg git repository for the addition
> of language documentation.
> 
>> 
>> Eric - perhaps mark good pages as good rather than bad pages.
>> They're not necessarily bad?
>> 
> 
> I agree, I don't think any of the pages are "bad".  Rather some
> pages simply need to be updated to use the new standard syntax.  In
> this case I would find it better to simply flag those pages which
> need to be updated, rather than litter all pages with tags.
> 
>> 
>> It would be cool to say [Tested 2 days ago] at the top of the
>> page (in a nice green) or something like that. (or validation
>> link in green / yellow / red)
>> 
> 
> I see you point, but the plan is that after this falls syntax 
> standardization we should not be making any breaking changes
> moving forward, so a page from Dec 2011 should be as valid as a
> page from Jan 2013.
> 
>> 
>> I also think that [Under development] should be removed from 
>> index.html. Worg is always under development, that's what it is?
>> 
> 
> I agree.
> 
>> 
>> For anybody that is not that familiar with Worg, you can
>> contribute to it right now - it's pure community.
>> 
> ^ well said! |
> 
> Cheers,
> 
>> 
>> Best, Martyn
>> 
>> tsd@tsdye.com (Thomas S. Dye) writes:
>> 
>>> Hi Eric,
>>> 
>>> I've attached a first draft of a template for review and
>>> revision.  It is heavily influenced by John Hendy's terrific
>>> gnuplot page.  I believe it incorporates the points in your
>>> outline.  Feel free to edit as appropriate.
>>> 
>>> All the best, Tom
>>> 
>>> 
>>> #+OPTIONS:    H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:{} -:t f:t
>>> *:t TeX:t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc #+STARTUP:
>>> align fold nodlcheck hidestars oddeven lognotestate hideblocks 
>>> #+SEQ_TODO:   TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d)
>>> CANCELED(c@) #+TAGS:       Write(w) Update(u) Fix(f) Check(c)
>>> noexport(n) #+TITLE:      Language Source Code Blocks in Org
>>> Mode #+AUTHOR:     Your name #+EMAIL:
>>> you[at]email[dot]org #+LANGUAGE:   en #+STYLE:      <style
>>> type="text/css">#outline-container-introduction{ clear:both;
>>> }</style> #+LINK_UP:    ../languages.php #+LINK_HOME:
>>> http://orgmode.org/worg/ #+EXPORT_EXCLUDE_TAGS: noexport
>>> 
>>> #+name: banner #+begin_html <div id="subtitle" style="float:
>>> center; text-align: center;"> <p> Org Mode support for <a
>>> href="http://language-site/">Language</a> </p> <p> <a
>>> href="http://language-site/"> <img
>>> src="http://language-site/graphic.file"/> </a> </p> </div> 
>>> #+end_html
>>> 
>>> * Template Checklist [0/13]
>>> :noexport: - [ ] Revise #+TITLE: - [ ] Indicate #+AUTHOR: - [ ]
>>> Add #+EMAIL: - [ ] Revise banner source block [0/3] - [ ] Add
>>> link to a useful language web site - [ ] Replace "Language"
>>> with language name - [ ] Find a suitable graphic and use it to
>>> link to the language web site - [ ] Write an [[Introduction]] -
>>> [ ] Describe [[Requirements%20and%20Setup][Requirements and
>>> Setup]] - [ ] Replace "Language" with language name in
>>> [[Org%20Mode%20Features%20for%20Language%20Source%20Code%20Blocks][Org
>>> Mode Features for Language Source Code Blocks]] - [ ] Specify
>>> [[Org%20Mode%20Configuration][Org Mode Configuration]] - [ ]
>>> Describe [[Header%20Arguments][Header Arguments]] - [ ]
>>> Describe support for [[Sessions]] - [ ] Describe
>>> [[Result%20Types][Result Types]] - [ ] Describe [[Other]]
>>> differences from supported languages - [ ] Provide brief
>>> [[Examples%20of%20Use][Examples of Use]] * Introduction - Brief
>>> description of language. - Range of typical uses within Org
>>> Mode. - Link to this Org Mode file. * Requirements and Setup -
>>> Installation and configuration of language software - Emacs
>>> configuration * Org Mode Features for Language Source Code
>>> Blocks ** Org Mode Configuration - org-babel-do-load-languages 
>>> ** Header Arguments - Language-specific default values -
>>> Language-specific header arguments ** Sessions - Support or
>>> not - Typical use for sessions ** Result Types - Which result
>>> types are supported? ** Other - Differences from other
>>> supported languages * Examples of Use - Hello World! - Common
>>> uses - Links to tutorials and other resources
>>> 
>>> 
>>> Eric Schulte <eric.schulte@gmx.com> writes:
>>> 
>>>> Hi Tom,
>>>> 
>>>> tsd@tsdye.com (Thomas S. Dye) writes:
>>>> 
>>>>> Hi Eric,
>>>>> 
>>>>> Yes, this is overdue.  I think your plan is a good one.
>>>>> 
>>>>> Perhaps a few of the individual use cases could be moved to
>>>>> FIXME, instead?  I'm thinking here of Feiming Chen's R
>>>>> setup and some of my contributions when I was experimenting
>>>>> writing LaTeX inside source code blocks.  The authors could
>>>>> resurrect these as they see fit.
>>>>> 
>>>> 
>>>> I don't know what FIXME is, but if there is a way to keep the
>>>> page in the worg git repository but remove it from the
>>>> exported HTML then that sounds ideal.
>>>> 
>>>>> 
>>>>> Hopefully, others will contribute use examples.  My sense
>>>>> from reading the list is there are many interesting ones.
>>>>> 
>>>>> I'd like it if Org mode users designed a template for the
>>>>> language specific pages.  Currently, these seem to me a
>>>>> mixed bag and it would be good to regularize them.
>>>> 
>>>> The below is a modified version of a template which can be
>>>> found in a couple of the existing language tutorials, I think
>>>> it serves as a good starting point.
>>>> 
>>>> - Install and Setup - Instillation and configuration of
>>>> software (e.g., the language itself) - Configuration of Emacs
>>>> (e.g., activate language, set command path) - Examples -
>>>> Common ways to use the language in an Org-mode document -
>>>> Special cases - are there any language-specific header
>>>> arguments - does the language support session evaluation -
>>>> does the language support all result types - is the language
>>>> different from most babel languages (e.g., C is compiled
>>>> before execution, ditaa returns files, etc...)
>>>> 
>>>>> It would also be nice to have one for each of the supported
>>>>> languages. There are 11 language specific pages now, which
>>>>> leaves quite a few languages under-documented.
>>>> 
>>>> (length org-babel-load-languages) ;; => 27
>>>> 
>>>> ls org-contrib/babel/languages/ob-doc-*|wc -l # => 11
>>>> 
>>>> It looks like we have at least 16 more to go before we hit
>>>> full language coverage.  Perhaps we should use the empty
>>>> cells in the "documentation" column in the languages table at
>>>> [1] as a sign up space for volunteers who would be willing to
>>>> write a brief tutorial demonstrating usage of Org-mode with
>>>> their favorite language.
>>>> 
>>>> Moving forward this is likely something we could request of
>>>> the contributors of new languages.
>>>> 
>>>> Also, once the template above is finalized it should be
>>>> posted on worg and linked to through the languages page.
>>>> 
>>>>> 
>>>>> I'll be happy to work on this as I can.
>>>>> 
>>>> 
>>>> Great, I don't anticipate having time to put towards this,
>>>> although I'll be happy to help troubleshoot where I can.
>>>> 
>>>> Cheers,
>>>> 
>>>>> 
>>>>> All the best, Tom
>>>>> 
>>>>> 
>>>>> Eric Schulte <eric.schulte@gmx.com> writes:
>>>>> 
>>>>>> Thanks for raising this point.  The bulk of the content
>>>>>> in the Babel portion of worg is fairly old, predating the
>>>>>> syntax standardization efforts this fall.  I've just
>>>>>> pushed some minor updates to the main babel pages, but
>>>>>> updating the language-specific tutorials and the 
>>>>>> individual use cases will be a much larger effort.
>>>>>> 
>>>>>> I'm not sure how to proceed.  One option would be to go
>>>>>> through and add a [uses deprecated syntax] tag to the top
>>>>>> of each such page, which could be removed after the page
>>>>>> has been checked and possibly updated to ensure
>>>>>> consistency with the latest syntax.
>>>>>> 
>>>>>> Given that the Babel syntax will not be changing
>>>>>> significantly moving forward now would be a good time to
>>>>>> do such a review.  Ideally this could be completed before
>>>>>> the release of Emacs 24 in a couple of months.
>>>>>> 
>>>>>> Any other ideas for update/reorganization or volunteers?
>>>>>> 
>>>>>> Cheers,
>>>>>> 
>>>>>> tsd@tsdye.com (Thomas S. Dye) writes:
>>>>>> 
>>>>>>> Hi Riccardo,
>>>>>>> 
>>>>>>> Thanks for the URL.  Org mode has evolved since this
>>>>>>> article was written.  It should probably be revised or
>>>>>>> taken off Worg.  I've copied Eric Schulte, who is
>>>>>>> better able than me to determine the correct course of
>>>>>>> action here.
>>>>>>> 
>>>>>>> In the meantime, an up-to-date description of how Org
>>>>>>> mode can be used to write literate programs has
>>>>>>> appeared in the Journal of Statistical Software.  You
>>>>>>> can find it here: http://www.jstatsoft.org/v46/i03
>>>>>>> 
>>>>>>> Perhaps you could use the examples in the JSS article
>>>>>>> to get started? If these don't work for you, or if they
>>>>>>> raise questions that are difficult to answer, please do
>>>>>>> come back to the list with your queries.
>>>>>>> 
>>>>>>> All the best, Tom
>>>>>>> 
>>>>>>> Riccardo Romoli <ric.romoli@gmail.com> writes:
>>>>>>> 
>>>>>>>> Hi, this is the URL:
>>>>>>>> 
>>>>>>>> http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html
>>>>>>>>
>>>>>>>>
>>>>>>>> 
Best
>>>>>>>> R
>>>>>>>> 
>>>>>>>> 2012/2/5 Thomas S. Dye <tsd@tsdye.com>
>>>>>>>> 
>>>>>>>>> Hi Riccardo,
>>>>>>>>> 
>>>>>>>>> This code appears to be outdated.  I don't recall
>>>>>>>>> this code on the org site.  Could you send a URL?
>>>>>>>>> 
>>>>>>>>> All the best, Tom
>>>>>>>>> 
>>>>>>>>> Riccardo Romoli <ric.romoli@gmail.com> writes:
>>>>>>>>> 
>>>>>>>>>> Hi, I'm trying to generate some figure with R,
>>>>>>>>>> into an org session.
>>>>>>>>> Firstly
>>>>>>>>>> I use the code in the org site. The problem is
>>>>>>>>>> that the code do not generate any figure.
>>>>>>>>>> 
>>>>>>>>>> This is the code:
>>>>>>>>>> 
>>>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL:
>>>>>>>>>> your-email@server.com #+BABEL: :session *R*
>>>>>>>>>> :cache yes :results output graphics :exports both
>>>>>>>>>> :tangle yes
>>>>>>>>>> 
>>>>>>>>>> * Example of Org-Babel for R Literate
>>>>>>>>>> Programming ** R text output A simple summary. 
>>>>>>>>>> #+begin_src R x <- rnorm(10) summary(x) 
>>>>>>>>>> #+end_src
>>>>>>>>>> 
>>>>>>>>>> ** R graphics output Note we use the object =x=
>>>>>>>>>> generated in previous code block, thanks to the
>>>>>>>>>> header option =:session *R*=.  The output
>>>>>>>>>> graphics file is =a.png=.
>>>>>>>>>> 
>>>>>>>>>> #+begin_src R  :file a.png y <- rnorm(10) plot(x,
>>>>>>>>>> y) #+end_src
>>>>>>>>>> 
>>>>>>>>>> Same plot with larger dimension:
>>>>>>>>>> 
>>>>>>>>>> #+begin_src R  :file b.png :width 800 :height
>>>>>>>>>> 800 plot(x, y) #+end_src
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> Where do I wrong?
>>>>>>>>>> 
>>>>>>>>>> Best Riccardo Hi, I&#39;m trying to generate some
>>>>>>>>>> figure with R, into an org session.
>>>>>>>>> Firstly I use the code in the org site. The problem
>>>>>>>>> is that the code do not generate any figure. This
>>>>>>>>> is the code:
>>>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL:
>>>>>>>>>> mailto:your-email@server.com #+BABEL: :session
>>>>>>>>>> *R* :cache yes :results output graphics :exports
>>>>>>>>>> both
>>>>>>>>> :tangle yes
>>>>>>>>>> 
>>>>>>>>>> * Example of Org-Babel for R Literate
>>>>>>>>>> Programming ** R text output A simple summary. 
>>>>>>>>>> #+begin_src R x <- rnorm(10) summary(x) 
>>>>>>>>>> #+end_src
>>>>>>>>>> 
>>>>>>>>>> ** R graphics output Note we use the object =x=
>>>>>>>>>> generated in previous code block, thanks to the
>>>>>>>>>> header option =:session *R*=.  The output
>>>>>>>>>> graphics file is =a.png=.
>>>>>>>>>> 
>>>>>>>>>> #+begin_src R  :file a.png y <- rnorm(10) plot(x,
>>>>>>>>>> y) #+end_src
>>>>>>>>>> 
>>>>>>>>>> Same plot with larger dimension:
>>>>>>>>>> 
>>>>>>>>>> #+begin_src R  :file b.png :width 800 :height
>>>>>>>>>> 800 plot(x, y) #+end_src Where do I
>>>>>>>>>> wrong?BestRiccardo
>>>>>>>>> 
>>>>>>>>> -- Thomas S. Dye http://www.tsdye.com
>>>>>>>>> 
>>>>>>>> Hi, this is the 
>>>>>>>> URL:http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.htmlBestR
>>>>>>>>
>>>>>>>> 
2012/2/5 Thomas S. Dye <span dir="ltr"><mailto:tsd@tsdye.com></span>Hi
Riccardo,
>>>>>>>> 
>>>>>>>> 
>>>>>>>> This code appears to be outdated.  I don&#39;t recall
>>>>>>>> this code on the org site.  Could you send a URL?
>>>>>>>> 
>>>>>>>> All the best, Tom
>>>>>>>> 
>>>>>>>> Riccardo Romoli <mailto:ric.romoli@gmail.com>
>>>>>>>> writes:
>>>>>>>> 
>>>>>>>>> Hi, I&#39;m trying to generate some figure with R,
>>>>>>>>> into an org session. Firstly I use the code in the
>>>>>>>>> org site. The problem is that the code do not 
>>>>>>>>> generate any figure.
>>>>>>>>> 
>>>>>>>>> This is the code:
>>>>>>>>> 
>>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL:
>>>>>>>>> mailto:your-email@server.com #+BABEL: :session *R*
>>>>>>>>> :cache yes :results output graphics :exports both
>>>>>>>>> :tangle yes
>>>>>>>>> 
>>>>>>>>> * Example of Org-Babel for R Literate Programming 
>>>>>>>>> ** R text output A simple summary. #+begin_src R x
>>>>>>>>> <- rnorm(10) summary(x) #+end_src
>>>>>>>>> 
>>>>>>>>> ** R graphics output Note we use the object =x=
>>>>>>>>> generated in previous code block, thanks to the
>>>>>>>>> header option =:session *R*=.  The output graphics
>>>>>>>>> file is =a.png=.
>>>>>>>>> 
>>>>>>>>> #+begin_src R  :file a.png y <- rnorm(10) plot(x,
>>>>>>>>> y) #+end_src
>>>>>>>>> 
>>>>>>>>> Same plot with larger dimension:
>>>>>>>>> 
>>>>>>>>> #+begin_src R  :file b.png :width 800 :height 800 
>>>>>>>>> plot(x, y) #+end_src
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> Where do I wrong?
>>>>>>>>> 
>>>>>>>>> Best Riccardo Hi, I&#39;m trying to generate some
>>>>>>>>> figure with R, into an org session. Firstly I use
>>>>>>>>> the code in the org site. The problem is that the
>>>>>>>>> code do not generate any figure. This is the code: 
>>>>>>>>> #+TITLE:Test #+AUTHOR: Your Name #+EMAIL:
>>>>>>>>> mailto:mailto:your-email@server.com #+BABEL:
>>>>>>>>> :session *R* :cache yes :results output graphics
>>>>>>>>> :exports both :tangle yes
>>>>>>>>> 
>>>>>>>>> * Example of Org-Babel for R Literate Programming 
>>>>>>>>> ** R text output A simple summary. #+begin_src R x
>>>>>>>>> <- rnorm(10) summary(x) #+end_src
>>>>>>>>> 
>>>>>>>>> ** R graphics output Note we use the object =x=
>>>>>>>>> generated in previous code block, thanks to the
>>>>>>>>> header option =:session *R*=.  The output graphics
>>>>>>>>> file is =a.png=.
>>>>>>>>> 
>>>>>>>>> #+begin_src R  :file a.png y <- rnorm(10) plot(x,
>>>>>>>>> y) #+end_src
>>>>>>>>> 
>>>>>>>>> Same plot with larger dimension:
>>>>>>>>> 
>>>>>>>>> #+begin_src R  :file b.png :width 800 :height 800 
>>>>>>>>> plot(x, y) #+end_src Where do I wrong?BestRiccardo
>>>>>>>> 
>>>>>>>> <span class="HOEnZb">-- Thomas S. Dye 
>>>>>>>> http://www.tsdye.com </span>
>>>> 
>>>> 
>>>> Footnotes: [1]
>>>> http://orgmode.org/worg/org-contrib/babel/languages.html
>> 
>> 
> 
> 
> Footnotes: [1]
> http://orgmode.org/worg/org-contrib/babel/languages.html
> 


- -- 
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
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Skype:      RMkrug
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