From: Rainer M Krug <r.m.krug@gmail.com>
To: Eric Schulte <eric.schulte@gmx.com>
Cc: Martyn Jago <martyn.jago@btinternet.com>, emacs-orgmode@gnu.org
Subject: Re: Updating the Babel section of Worg
Date: Wed, 08 Feb 2012 15:44:06 +0100 [thread overview]
Message-ID: <4F328A36.9010501@gmail.com> (raw)
In-Reply-To: <87zkctcsma.fsf@gmx.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'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'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'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'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
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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next prev parent reply other threads:[~2012-02-08 14:44 UTC|newest]
Thread overview: 17+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-02-04 22:52 Generating plot with org-babel-R Riccardo Romoli
2012-02-04 23:37 ` Thomas S. Dye
2012-02-05 11:08 ` Riccardo Romoli
2012-02-05 16:45 ` Thomas S. Dye
2012-02-05 19:29 ` Updating the Babel section of Worg Was: " Eric Schulte
2012-02-06 5:43 ` Thomas S. Dye
2012-02-06 21:20 ` Updating the Babel section of Worg Eric Schulte
2012-02-08 0:01 ` Thomas S. Dye
2012-02-08 1:04 ` Martyn Jago
2012-02-08 14:21 ` Eric Schulte
2012-02-08 14:44 ` Rainer M Krug [this message]
2012-02-08 15:27 ` Eric Schulte
2012-02-08 14:14 ` Eric Schulte
2012-02-09 17:20 ` Thomas S. Dye
2012-02-18 21:53 ` Eric Schulte
2012-02-08 15:41 ` John Hendy
2012-02-06 21:12 ` Generating plot with org-babel-R Riccardo Romoli
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