From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: Updating the Babel section of Worg Date: Wed, 08 Feb 2012 15:44:06 +0100 Message-ID: <4F328A36.9010501@gmail.com> References: <87mx8xyt7q.fsf_-_@gmx.com> <87pqdrlkuw.fsf_-_@gmx.com> <87zkctcsma.fsf@gmx.com> Reply-To: R.M.Krug@gmail.com Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([140.186.70.92]:40390) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv8ks-0008OM-CE for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:44:25 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Rv8kl-00083k-Cn for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:44:18 -0500 Received: from mail-we0-f169.google.com ([74.125.82.169]:34966) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Rv8kl-00083U-1d for emacs-orgmode@gnu.org; Wed, 08 Feb 2012 09:44:11 -0500 Received: by wera13 with SMTP id a13so551190wer.0 for ; Wed, 08 Feb 2012 06:44:10 -0800 (PST) In-Reply-To: <87zkctcsma.fsf@gmx.com> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Eric Schulte Cc: Martyn Jago , emacs-orgmode@gnu.org -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 08/02/12 15:21, Eric Schulte wrote: > Martyn Jago 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: #+LINK_UP: ../languages.php #+LINK_HOME: >>> http://orgmode.org/worg/ #+EXPORT_EXCLUDE_TAGS: noexport >>> >>> #+name: banner #+begin_html >>> #+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 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 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 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 >>>>>>>> >>>>>>>>> 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 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 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 >>>>>>>> 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 >>>>>>>> >>>>>>>> -- Thomas S. Dye >>>>>>>> http://www.tsdye.com >>>> >>>> >>>> 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk8yijYACgkQoYgNqgF2egrYOgCePUalLt/aey4qysCIwfXsJC3i Z7oAni4fmMDJbQpnEiHcu7KwQ3/eo14I =hls7 -----END PGP SIGNATURE-----