Thanks for continuing to support the module. I'm not sure if you have the time, but it would be great if some the useful tips were posted on a wiki page, which many users find easier to read than going through an email conversation. You could make a page and then link to it from the module description: http://wiki.lyx.org/Layouts/Modules#toc7
Thanks, Scott On Fri, Feb 15, 2013 at 3:42 PM, Thomas Coffee <thomasmcof...@gmail.com> wrote: > In case it is helpful to anyone, I am posting below a recent > conversation working out some issues with an installation of the > SageTeX module previously discussed on this thread: > > > Dear mr McCoffee, > > I was very excited when I discovered your module for integrating Sage > with LyX. But I'm afraid I need a little bit more help to make it > work. > > I managed to setup the one-step conversion in LyX, however, when I > apply it to your file example.lyx all sage-blocks display as double > questionmarks in the .pdf file. Can you point me to a more detailed > tutorial on how to use this LyX module? > > Here is what I did: > > downloaded example.lyx, setup.sh, compile-pdf-sage.sh, sage.module > and preferences to the desktop > edited setup.sh to reflect non-standard paths on my system > (~/.lyx2 and /opt/sage-5.2) > ran setup.sh (sudo bash setup.sh) > > I checked that compile-pdf-sage.sh is copied to the sage directory, > the preferences file to ~/lyx2 and sage.module to the layouts folder > in ~/lyx2. > > I also copied sagetex.sty to /home/dd/texmf, my user texmf folder. > > I noticed the following error in the console from which I started LyX2: > > insets/InsetLayout.cpp (191): Flex insets must have names of the form > `Flex:<name>'. > This one has the name `sagecommand' > > I hope you can help me out, > yours sincerely > > Dirk Danckaert > > > > Hi Dirk, > > I'm currently running LyX 2.0.0 with Sage 4.8 on Ubuntu 11.10. Since > my Sage version is old (for complicated reasons), it's possible > something has changed in SageTeX, but let's try some other things > before I install another Sage. > > I get the same message you do about the insets, along with some other > LyX complaints, and they are not causing me problems (yet), so that > may not be something to worry about. > > Since you're on Ubuntu, one possible source of trouble (which happened > to me when I changed machines) is that, if you're using TeXLive, the > potentially mis-matched version of SageTeX that it includes can stick > around and pre-empt the correct one (even if you've followed the > instructions --- http://www.sagemath.org/doc/installation/sagetex.html > --- to install the one from your Sage distribution into LaTeX. Try > making sure it's gone by doing something like > > sudo rm -r /usr/share/texmf-texlive/tex/latex/sagetex > sudo texhash > > - Thomas > > > > Hi Thomas, > > I have corrected at least one error while checking things out again. > Seems the copying of sagetex.sty had not been done as it should. > However, still no joy. I did the two sudo-commands, with no > error-messages. I loaded example.lyx and tried a .pdf-export (I chose > /File/Export/PDF (pdflatex+sagetex). As a result I got the error > message > > An error occurred while running: > > compile-pdf-sage.sh "example.sagetex.sage" > > > I tried to make sense of that but I couldn't: > > compile-pdf-sage.sh must be located in the SAGE-directory, isn't it? > So how does it find the .sagetex.sage-file? > > I tried to locate example.sagetex.sage (I thought this is an > intermediate file produced by LyX) in the directory that contained > example.lyx (a folder on my desktop) but it wasn't there. > > Is there perhaps a simpler test that I could perform, e.g. just > calculate 1+1 in LyX? > > Dirk > > > > Hi Dirk, > > In order to figure out what's going on, please try running LyX from a > terminal window and running the export again --- then the error > messages from the call to compile-pdf-sage.sh will be visible in the > terminal. > > I believe you edited the setup.sh script included with the module to > point to your Sage installation at /opt/sage-5.2. The script normally > puts compile-pdf-sage.sh in this same directory and adds that > directory to the execution path. However, it doesn't make that change > to the execution path permanent --- when you start a new shell, it > won't be there --- so in retrospect, it's probably a better idea to > move or link compile-pdf-sage.sh to somewhere like /usr/local/bin > where it can always be found. You can always do `echo $PATH' to make > sure it's somewhere findable. (The reason I did it this way was that, > in the Sage installations I had used before, it was normally necessary > to permanently add the Sage directory to the execution path anyway, so > it didn't occur to me this would be a problem.) > > In the LyX that I'm running, it does all its LaTeX file operations in > an auto-generated temporary directory with a name like > `/tmp/lyx_tmpdir.J23736/lyx_tmpbuf2' (to avoid cluttering your file > system). This is where I would expect `example.sagetex.sage' to > appear. It might be helpful to see the files it generates in this > directory to make sure things are working right --- but whenever we > make any changes, clear out the old files so we know what's new. > > If you want, you can replace the Sage insets in example.lyx with a > single simpler one, but I doubt it will help much --- once we get Sage > doing its job, the whole thing should run very fast. > > > - Thomas > > > > Hi Thomas, > > First I have to thank you for your time and patience. But I think I'm > making progress. As you assumed, the system couldn't find > compile-pdf-sage.sh, and I learned a lesson in using the terminal. > (I'm an ex-windows user, and hence I acquired some bad habits I > guess.) > > I then moved compile-pdf-sage.sh to /usr/local/bin and - on second try > - had a complaint about permissions. I then change-modded the > permissions on compile-pdf-sage.sh to 777, and this time the script > was executed. > > However, now it is TeX which is complaining. This is the message on > which the script hangs (I stop it with some <Ctrl-C>'s, or just by > waiting long enough).dd@Dokux:~$ lyx2 > > insets/InsetLayout.cpp (191): Flex insets must have names of the > form `Flex:<name>'. > This one has the name `sagecommand' > Ignoring LyXType declaration. > LyX: Unknown InsetLayout tag [around line 2 of file current > token: 'custom' context: ''] > LyX: Unknown InsetLayout tag [around line 12 of file current > token: 'OptionalArgs' context: ''] > LyX: Unknown InsetLayout tag [around line 13 of file current > token: '0' context: ''] > LyX: Unknown InsetLayout tag [around line 13 of file > /tmp/lyx_tmpdir.TJ2300/convert_layout.kn2300 current token: > 'OptionalArgs' context: ''] > LyX: Unknown InsetLayout tag [around line 14 of file > /tmp/lyx_tmpdir.TJ2300/convert_layout.kn2300 current token: '0' > context: ''] > > Running: pdflatex "example.tex" > /dev/null > This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) > entering extended mode > (./example.tex > LaTeX2e <2009/09/24> > Babel <v3.8l> and hyphenation patterns for english, usenglishmax, > dumylang, noh > yphenation, farsi, arabic, croatian, bulgarian, ukrainian, > russian, czech, slov > ak, danish, dutch, finnish, french, basque, ngerman, german, > german-x-2009-06-1 > 9, ngerman-x-2009-06-19, ibycus, monogreek, greek, ancientgreek, > hungarian, san > skrit, italian, latin, latvian, lithuanian, mongolian2a, > mongolian, bokmal, nyn > orsk, romanian, irish, coptic, serbian, turkish, welsh, esperanto, > uppersorbian > , estonian, indonesian, interlingua, icelandic, kurmanji, > slovenian, polish, po > rtuguese, spanish, galician, catalan, swedish, ukenglish, pinyin, loaded. > > Running: pdflatex "example.tex" > /dev/null > This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) > entering extended mode > (./example.tex > LaTeX2e <2009/09/24> > Babel <v3.8l> and hyphenation patterns for english, usenglishmax, > dumylang, noh > yphenation, farsi, arabic, croatian, bulgarian, ukrainian, > russian, czech, slov > ak, danish, dutch, finnish, french, basque, ngerman, german, > german-x-2009-06-1 > 9, ngerman-x-2009-06-19, ibycus, monogreek, greek, ancientgreek, > hungarian, san > skrit, italian, latin, latvian, lithuanian, mongolian2a, > mongolian, bokmal, nyn > orsk, romanian, irish, coptic, serbian, turkish, welsh, esperanto, > uppersorbian > , estonian, indonesian, interlingua, icelandic, kurmanji, > slovenian, polish, po > rtuguese, spanish, galician, catalan, swedish, ukenglish, pinyin, loaded. > > Running: compile-pdf-sage.sh "example.sagetex.sage" > This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) > entering extended mode > (./example.sagetex.sage > LaTeX2e <2009/09/24> > Babel <v3.8l> and hyphenation patterns for english, usenglishmax, > dumylang, noh > yphenation, farsi, arabic, croatian, bulgarian, ukrainian, > russian, czech, slov > ak, danish, dutch, finnish, french, basque, ngerman, german, > german-x-2009-06-1 > 9, ngerman-x-2009-06-19, ibycus, monogreek, greek, ancientgreek, > hungarian, san > skrit, italian, latin, latvian, lithuanian, mongolian2a, > mongolian, bokmal, nyn > orsk, romanian, irish, coptic, serbian, turkish, welsh, esperanto, > uppersorbian > , estonian, indonesian, interlingua, icelandic, kurmanji, > slovenian, polish, po > rtuguese, spanish, galician, catalan, swedish, ukenglish, pinyin, loaded. > ! You can't use `macro parameter character #' in vertical mode. > l.1 # > # -*- encoding: utf-8 -*- > > It seems a bit strange that pdfTeX should process the file three > times. Maybe I should have left the comment lines in the script? > Here's the compile-pdf-sage.sh script that I am running: > > #!/bin/bash > > sagefile=$1 > texfile=${sagefile%.sagetex.sage}.tex > > # for one-step conversion, uncomment lines below and corresponding > line in ~/.lyx/preferences > > texfile=$1 > sagefile=${texfile%.tex}.sagetex.sage > pdflatex $texfile > > sage $sagefile > pdflatex $texfile > > exit 0 > > I found the lyx temporary directory too. I see now that TeX is trying > to tex example.sagetex.sage, which is meant to be processed by sage of > course. If you should need them I can send you the tex-logs too, or I > can try to analyse them myself if you can tell what to look for. > > > Dirk > > > > Hi Dirk, > > Yes, for now you should leave the three lines commented out in > compile-pdf-sage.sh as they were originally. > > The module was designed to support two different modes of doing the > conversion: (a) a two-step mode, the default; and (b) a one-step mode. > If you uncomment the lines in compile-pdf-sage.sh, it tries to use the > one-step mode, but in order for this to work at all, you also need to > uncomment the corresponding LyX preferences line included in the > `preferences' file. > > Looking at the `preferences' file, you'll see that in the two-step > mode, we tell LyX that it can convert "sagetex" to "sage" using > pdflatex, and can convert "sage" to "pdf10" using compile-pdf-sage.sh. > LyX figures out that in order to convert "sagetex" to "pdf10", it > should do both of these in order. In this mode, it will run > compile-pdf-sage.sh on a Sage file, so the original lines in > compile-pdf-sage.sh must remain commented out for this to work. The > advantage of the two-step mode is that any errors generated on the > first run of pdflatex will show up in LyX, so you can easily see if > there's a LaTeX problem in your document. > > In the one-step mode, the preferences file tells LyX that to convert > "sagetex" to "pdf10", it can just use compile-pdf-sage.sh directly. So > LyX runs compile-pdf-sage.sh on a TeX file, and those lines need to be > uncommented. The compile-pdf-sage.sh script then does all three steps > itself: (1) run pdflatex on the TeX file, (2) run sage on the Sage > file, and (3) run pdflatex on the TeX file again to incorporate the > results from Sage. > > Leave the original stuff commented out for now so we can use the > default two-step mode. > > > Thomas > > > > Hi Thomas, > > It works! Works like a charm! Thank you very much: it don't think I > would have managed to get it working on my own. The possibility to > define a graph from within LyX will be very useful to me. > > I see that LyX generates a .pdf, in the same directory as the .lyx > source file. That's perfectly workable, but can I set things up so > that I have the .pdf automatically opened, as when using normal LyX? > > I thought the 2-step mode would require two actions from the user, > each time you wanted to process a LyX-file. I understand now that it > is only the software that does two steps. So what are the advantages > of using the one-step process? > > Dirk > > > > Hi Dirk, > > That's great! I hope it's useful to you --- if you make or think of > any improvements, do let me know so we can make them available. I am > not actively using it myself at the moment, so I have not made any > updates since the initial version. > > It's odd that your PDF file doesn't open automatically, which it does > for me. When I select View >> View (Other Formats) >> PDF > (pdflatex+sagetex) from the LyX menu on my system, the PDF opens > automatically in evince. The lines of the LyX preferences file > included with the module contain the following: > > \Format pdf10 pdf "PDF (pdflatex+sagetex)" g xdg-open "" > "document,vector,menu=export" > > \viewer_alternatives pdf10 xdg-open > \viewer_alternatives pdf10 okular > \viewer_alternatives pdf10 evince > \viewer_alternatives pdf10 xpdf > > The first line gives the name "pdf10" to the output format we get from > choosing that option from the View menu (LyX uses the other > "\converter" lines in file to work out a conversion path to yield that > format). The other lines above tell it what commands to try for > opening the resulting file (xdg-open just keeps track of default > applications for opening various file types, like you have probably > experienced on Windows). If for some reason you don't have any of > these PDF viewers, or your xdg-open doesn't point to any suitable > viewer, your file might not open. Otherwise, I'm not sure ... but I > think you could always hack it by adding something like the following > at the end of comple-pdf-sage.sh before the exit code: > > pdffile=${texfile%.tex}.pdf > evince $pdffile > > (By the way, the current shell script doesn't play nice with file > names containing spaces ... you can fix this by putting quotation > marks around anything beginning with `$'.) > > I can't think of a good reason to use the one-step mode instead of the > two-step mode, but I seem to recall I kept it because it was > implemented by the person who started work on this module (Murat > Yildizoglu). It's conceivable it could be marginally faster since LyX > wouldn't pay attention to any LaTeX messages, but I doubt that's > significant. The main way to gain speed is to only run pdflatex (and > not Sage) if the Sage computations have not changed, by using the > regular pdflatex option from the View menu in LyX --- this is why the > module leaves that option as the default view method. > > Until I get around to writing a better README file, would you mind if > I append the transcript of our exchange to the lyx-users thread about > the module? In case others run into any similar problems ... > > Cheers, > Thomas > > > > Hi Thomas, > > one improvement I can suggest right away: just eliminate that one-step > process. If its performance gain is indeed minimal, I see no reason to > keep it. I for one was confused as to its purpose. > > The reason the PDF did not open automatically was because I used the > File >> Export menu, in stead of the View menu. When I choose View >> > etc., the PDF does open automatically. I'm a bit puzzled why the new > format 'PDF (pdflatex + sagetex)' doesn't show up under the toolbar > button 'View other formats'. I always used this toolbar in stead of > the View menu, and I just didn't think of it (I mean: the menu). > > Of course you can post our exchange to the lyx-forum. I think the > combination of LyX - hands down the best text processor I ever worked > with - and Sage opens vast possibilities. It really should get more > publicity. > > It seems like a good idea to learn a bit more about the workings of > LyX. Perhaps you can point me to a good source of information about, > e.g., the format and purpose of the various entries in the lyx options > file? Is it dangerous to edit it by hand? (there's a warning not to do > so) Could I e.g. just clear it and build it anew from inside LyX? > > Thanks again, Thomas, you have been most helpful. > > > > Hi Dirk, > > one improvement I can suggest right away: just eliminate that > one-step process. If its performance gain is indeed minimal, I see no > reason to keep it. I for one was confused as to its purpose. > > > I agree the annotations about it were confusing ... when I get a > chance to update, I will change this. > > > The reason the PDF did not open automatically was because I used > the File >> Export menu, in stead of the View menu. When I choose View >>> etc., the PDF does open automatically. I'm a bit puzzled why the > new format 'PDF (pdflatex + sagetex)' doesn't show up under the > toolbar button 'View other formats'. I always used this toolbar in > stead of the View menu, and I just didn't think of it (I mean: the > menu). > > > Never noticed that before ... I've filed it as a bug: > http://www.lyx.org/trac/ticket/8550 > > > Of course you can post our exchange to the lyx-forum. I think the > combination of LyX - hands down the best text processor I ever worked > with - and Sage opens vast possibilities. It really should get more > publicity. > > > In the past I have made extensive use of Mathematica, whose "notebook" > documents provide a tightly integrated literate programming > environment. However, since my main interest in literate programming > has been for reproducible research, this platform had some severe > limitations (openness, availability to everyone, sophisticated > document features for paper-writing, and extensibility of the > underlying computation system). I am currently using LyX and Sage for > my Ph.D. thesis, and feel like I've finally found the right set of > tools (though of course there's always more to do). > > > It seems like a good idea to learn a bit more about the workings > of LyX. Perhaps you can point me to a good source of information > about, e.g., the format and purpose of the various entries in the lyx > options file? Is it dangerous to edit it by hand? (there's a warning > not to do so) Could I e.g. just clear it and build it anew from inside > LyX? > > > I never found a good guide to all of this, though just now I came > across this page that might be a good place to start: > http://www.oak-tree.us/2010/07/13/custom-lyx-modules/ . There's some > information in the Customization manual (Section 5: Installing New > Document Classes, Layouts, and Templates), but not enough to explain > the whole module system. I started from a version of this module > already built by Murat (you can see our discussion here: > http://www.mail-archive.com/lyx-users@lists.lyx.org/msg91798.html ), > so I gradually just figured out how to tweak things to get them to > work. > > Everything that we added to the LyX preferences file for purposes of > this module can be changed from within LyX under Tools >> Preferences. > If you go there, you'll see the changes we made already appear in the > GUI. > > > Thanks again, Thomas, you have been most helpful. > > > My pleasure --- thanks for trying it out! > > > > On Mon, Apr 2, 2012 at 12:31 PM, Thomas Coffee <thomasmcof...@gmail.com> > wrote: >> The attachments on this thread have been posted to the wiki (thanks >> Christian): >> >> http://wiki.lyx.org/Layouts/Modules/#toc7 >> http://wiki.lyx.org/uploads/Modules/Sage >> >> Note that if you customize the sage.module file, you can load the >> changes immediately by entering "layout-reload" in the minibuffer. >> >> As Murat has done: I hereby grant permission to license my >> contributions to the sage module for LyX under the GNU General Public >> License, version 2 or later. >> >> - Thomas >> >> >> On Sun, Apr 1, 2012 at 12:03 PM, Murat Yildizoglu <myi...@gmail.com> wrote: >>> Good idea, thanks a lot for the suggestion Xu. Here is my statement (I put >>> the devel list as CC) : >>> >>> I hereby grant permission to license my contributions to the SAGE module for >>> LyX under the GNU >>> General Public Licence, version 2 or later. >>> >>> Murat Yildizoglu >>> >>> >>> 2012/3/31 Xu Wang <xuwang...@gmail.com> >>>> >>>> Dear Thomas >>>> >>>> Excellent news! Thank you for your continued work. I have not taken a fine >>>> look at this yet, but I also use Ubuntu so it looks like it might be >>>> useful. >>>> >>>> I'm not sure but I think for your contributions to be used you have to >>>> give permission explicitly. Look at this email: >>>> >>>> http://www.mail-archive.com/lyx-devel@lists.lyx.org/msg161963.html >>>> You can send something like that to the development list, lyx-devel >>>> >>>> And it could be a good idea for Murat to do the same. >>>> >>>> I'm not sure though. >>>> >>>> In any case, thank you for your continued work. I am appreciative. Xu >>>> >>>> >>>> >>>> On Sat, Mar 31, 2012 at 3:08 AM, Thomas Coffee <thomasmcof...@gmail.com> >>>> wrote: >>>>> >>>>> Hi Murat and Xu, >>>>> >>>>> I found your thread in the archives and did some further work on the >>>>> LyX-SageTeX module that Murat posted previously. >>>>> >>>>> I fixed a few things that did not work for me in the version described >>>>> earlier, and expanded the module specification to provide some >>>>> additional conveniences for including literate Sage code in LyX >>>>> documents. There's still much room for development and customization. >>>>> >>>>> The attachments comprise a set of files and a shell script "setup.sh" >>>>> that should largely automate the configuration process on GNU/Linux >>>>> systems. >>>>> >>>>> *** Help needed: >>>>> >>>>> For other interested users, I'd like to upload this to >>>>> http://wiki.lyx.org/Layouts/Modules, but I get browser errors for >>>>> links anywhere under the upload path wiki.lyx.org/ipfm. The page >>>>> http://wiki.lyx.org/Site/AboutUploading also tells me I will need >>>>> someone to tell me the upload password. Can anyone assist? >>>>> >>>>> Thanks, >>>>> Thomas >>>>> >>>>> >>>>> > Hi Xu, >>>>> > >>>>> > Thank you for your appreciation. I cannot advance anymore without any >>>>> > help >>>>> > from Lyx gurus. >>>>> > I think I have extracted all the information I can from the help docs. >>>>> > If I >>>>> > get any answer to my questions, I can construct a little bit smarter >>>>> > module >>>>> > but the one we have now is already usable. With some supplementary >>>>> > tricks >>>>> > from the sagetex documentation and through manual executions of the >>>>> > latex-sage-latex chain, it is possible to make a lot of computations. >>>>> > >>>>> > I was also very agreeably surprised that this module can be used for >>>>> > conversion to HTML from LyX, with figures and all. >>>>> > >>>>> > I attach to this message the module in its actual stage and some >>>>> > instruction for making the conversion chain functional. I hope this >>>>> > would >>>>> > already help some of you. >>>>> > >>>>> > As soon as I have more information, I will try to complete the module >>>>> > file. >>>>> > >>>>> > Best regards, >>>>> > >>>>> > Murat >>>>> > >>>>> > 2011/10/31 Xu Wang <xuwang...@gmail.com> >>>>> > >>>>> > > Dear Murat, >>>>> > > >>>>> > > This is great! I have been waiting for something like this for a long >>>>> > > time. I also like the Sweave-like philosophy of this. It's more >>>>> > > transparent >>>>> > > and reproducible. >>>>> > > >>>>> > > I am looking forward to the final release with much excitement. >>>>> > > >>>>> > > Thank you for your work! >>>>> > > >>>>> > > Best, >>>>> > > >>>>> > > Xu >>>>> > > >>>>> > > >>>>> > > On Mon, Oct 31, 2011 at 12:54 PM, Murat Yildizoglu >>>>> > > <myi...@gmail.com>wrote: >>>>> > > >>>>> > >> Just another mail to correct a problem with the preceding Lyx file >>>>> > >> (see >>>>> > >> the new file attached, and the $ signs in ERT boxes, this is >>>>> > >> connected with >>>>> > >> the problem I describe below) and ask a question about insets again: >>>>> > >> >>>>> > >> What kind of Flex insets can be included in a math mode text? Is >>>>> > >> this >>>>> > >> possible at all? Especially in displayed equation where one would >>>>> > >> like to >>>>> > >> include results from SAge computations? >>>>> > >> I cannot write the following in math mode in Lyx, putting the left >>>>> > >> member >>>>> > >> in a displayed equation and the right member in a sagecode inset >>>>> > >> that would >>>>> > >> be converted to the expression I give >>>>> > >> (\sage{integral(x/(x^2+1),x,0,1)) >>>>> > >> \dfrac{\partial^{4}y}{\partial >>>>> > >> x^{4}}=\sage{integral(x/(x^2+1),x,0,1)} >>>>> > >> >>>>> > >> I meet two problems: >>>>> > >> 1/ I cannot insert a Flex:sagecommand inset in a displayed equation, >>>>> > >> Lyx >>>>> > >> just goes to the next line before inserting it... >>>>> > >> 2/ I cannot type the sagetex instruction (*sage{} ) by hand, >>>>> > >> because >>>>> > >> "x^2" in the right member must not be interpreted by LyX, since >>>>> > >> Sage will >>>>> > >> need it for its computation. >>>>> > >> >>>>> > >> I can of course type everything in an ERT, but this cannot be called >>>>> > >> "integration" can it? ;-) >>>>> > >> >>>>> > >> I have reread again the help document on layouts and insets, and I >>>>> > >> have >>>>> > >> checked the files that come in the layout folder of LyX, but cannot >>>>> > >> find >>>>> > >> any answer to my question. >>>>> > >> >>>>> > >> Sorry for bothering you again with my problems... I hope that Sage >>>>> > >> integration will interest other people... >>>>> > >> >>>>> > >> Murat >>>>> > >> >>>>> > >> I definitely need the help of a Lyx wizard who understands well the >>>>> > >> insets and their integration in Lyx/Latex... >>>>> > >> >>>>> > >> >>>>> > >> >>>>> > >> 2011/10/31 Murat Yildizoglu <myi...@gmail.com> >>>>> > >> >>>>> > >>> Just to show you the kind of niceties that such an integration can >>>>> > >>> bring, I send you two files. One is the Lyx source and the other >>>>> > >>> one is the >>>>> > >>> final PDF. >>>>> > >>> In Lyx, I just click on the Preview button and wait a little bit >>>>> > >>> to get >>>>> > >>> the final PDF that I show here, with results of the computations >>>>> > >>> done by >>>>> > >>> Sage and converted back to Latex. >>>>> > >>> >>>>> > >>> The module isfar from perfect yet (this is the first module I am >>>>> > >>> creating), a better integration between the Latex output by Sage, >>>>> > >>> and the >>>>> > >>> math mode in LyX would be implemented to have nice equations >>>>> > >>> typeset with >>>>> > >>> equation numbers and what not. You can also see that the output of >>>>> > >>> the >>>>> > >>> integral by Sage is not very beautiful... >>>>> > >>> >>>>> > >>> I will continue to work on this module, but it is already useful >>>>> > >>> for me >>>>> > >>> and eliminates some regrets I feel ;-), since I have dropped >>>>> > >>> Scientific >>>>> > >>> Workplace in favor of LyX. >>>>> > >>> >>>>> > >>> I hope that you will like this new possibilities. >>>>> > >>> >>>>> > >>> Best regards, >>>>> > >>> >>>>> > >>> Murat >>>>> > >>> >>>>> > >>> PS. Sage lives in: http://www.sagemath.org >>>>> > >>> >>>>> > >>> >>>>> > >>> -- >>>>> > >>> Prof. Murat Yildizoglu >>>>> > >>> >>>>> > >>> Université Montesquieu Bordeaux IV >>>>> > >>> GREThA (UMR CNRS 5113) >>>>> > >>> Avenue Léon Duguit >>>>> > >>> 33608 Pessac cedex >>>>> > >>> France >>>>> > >>> >>>>> > >>> yi...@u-bordeaux4.fr >>>>> > >>> >>>>> > >>> http://yildizoglu.info >>>>> > >>> >>>>> > >>> http://www.twitter.com/yildizoglu >>>>> > >>> >>>>> > >>> >>>>> > >> >>>>> > >> >>>>> > >> -- >>>>> > >> Prof. Murat Yildizoglu >>>>> > >> >>>>> > >> Université Montesquieu Bordeaux IV >>>>> > >> GREThA (UMR CNRS 5113) >>>>> > >> Avenue Léon Duguit >>>>> > >> 33608 Pessac cedex >>>>> > >> France >>>>> > >> >>>>> > >> yi...@u-bordeaux4.fr >>>>> > >> >>>>> > >> http://yildizoglu.info >>>>> > >> >>>>> > >> http://www.twitter.com/yildizoglu >>>>> > >> >>>>> > >> >>>>> > > >>>>> > >>>>> > >>>>> > -- >>>>> > Prof. Murat Yildizoglu >>>>> > >>>>> > Université Montesquieu Bordeaux IV >>>>> > GREThA (UMR CNRS 5113) >>>>> > Avenue Léon Duguit >>>>> > 33608 Pessac cedex >>>>> > France >>>>> > >>>>> > yi...@u-bordeaux4.fr >>>>> > >>>>> > h <http://myildi.e-jemed.org/>ttp://yildizoglu.info >>>>> > >>>>> > http://www.twitter.com/yildizoglu >>>>> > >>>>> > The Sage module allows the use of the open source Sage mathematical >>>>> > platform >>>>> > for computations in Lyx (with results inserted in the final PDF file), >>>>> > in a >>>>> > somewhat similar way for R-project with the Sweave module. >>>>> > >>>>> > To be able to use it, you must have Sage installed on your computer and >>>>> > the >>>>> > "sage" command must be in the path. >>>>> > See : http://www.sagemath.org/ >>>>> > >>>>> > Sage speaks Latex and can interact with it through the sagetex.sty >>>>> > package. >>>>> > >>>>> > See: http://www.sagemath.org/doc/tutorial/sagetex.html#sec-sagetex >>>>> > >>>>> > INSTALLATION >>>>> > >>>>> > 0/ You must have a working Sage system on your computer and the sage >>>>> > command >>>>> > must be on the PATH (open a console and type sage and RETURN key to >>>>> > check it >>>>> > this is the case). >>>>> > >>>>> > 1/Add the sage.module in the layouts folder of your local LyX >>>>> > configuration >>>>> > (depends on the system). Start LyX and reconfigure it. >>>>> > You can now add the Sage module to a new document. This module provides >>>>> > - the environments: sageblock and sagesilent >>>>> > - the commands: \sage (to be used in-line) and \sageplot (as an >>>>> > environment, >>>>> > can be included in a Figure float) >>>>> > and it needs the sagetex.sty package to be available in your local Tex >>>>> > installation. >>>>> > Justfollow the instructions given in the documentation of this package, >>>>> > for >>>>> > example >>>>> > >>>>> > >>>>> > >>>>> > 2/ Add the following sections elements in the preferences file that >>>>> > lives in >>>>> > your personal lyx config folder (depends on the system) >>>>> > >>>>> > # FORMATS SECTION ########################## >>>>> > # >>>>> > >>>>> > \format "pdf10" "pdf" "PDF" "" >>>>> > "\"/Applications/_Editiontextes/Skim.app/Contents/MacOS/Skim\"" "" >>>>> > "document,vector,menu=export" >>>>> > \format "sage" "sage" "Sage" "" "" "" "document" >>>>> > \default_view_format pdf10 >>>>> > >>>>> > # >>>>> > # CONVERTERS SECTION ########################## >>>>> > # >>>>> > >>>>> > >>>>> > \converter "latex" "sage" "latex" "latex" >>>>> > \converter "sage" "pdf10" "compile-pdf-sage.sh $$b" "" >>>>> > >>>>> > 3/ You need a bash file for automatically running the .sage file and >>>>> > get the >>>>> > results in the final pdf file >>>>> > >>>>> > This compile-pdf-sage.sh should be on your path, with the following >>>>> > content: >>>>> > #!/bin/sh >>>>> > >>>>> > /Applications/_Recherche/Sage-4.7-OSX-64bit-10.6.app/Contents/Resources/sage/sage >>>>> > $1.sage >>>>> > pdflatex $1.tex >>>>> > exit 0 >>>>> > >>>>> > Otherwise, >>>>> > You can just convert your Lyx document to Sage and then go to the >>>>> > temporary >>>>> > folder and execute manually >>>>> > >>>>> > (pdf)latex mysagedoc.tex -> generates mysagedoc.sage >>>>> > sage mysagedoc.sage >>>>> > (pdf)latex mysagedoc.tex >>>>> > >>>>> > Remaining problems and questions: >>>>> > 1/ How to setup options for environments? Example: >>>>> > \sageplot[width=12cm]{plot(sin(x), 0, pi), axes=True} -> Bug fix by >>>>> > Richard >>>>> > 2/ How to insert Flex insets in math mode, in displayed equations? >>>>> > $\dfrac{\partial^{4}y}{\partial >>>>> > x^{4}}=\sage{integral(x/(x^2+1),x,0,1)}$ >>>>> > x^2 must not be interpreted by LyX in the second part of the equality, >>>>> > since >>>>> > Sage will need it for its computation. >>>>> > 3/ \sage{} does not automatically switch to the math mode. These insets >>>>> > must be >>>>> > inserted between two $ sign put in ERT boxes. Then, the problem remains >>>>> > for the >>>>> > displayed equations where one would like to include Sage results. >>>> >>>> >>> >>> >>> >>> -- >>> Prof. Murat Yildizoglu >>> >>> Université Montesquieu Bordeaux IV >>> GREThA (UMR CNRS 5113) >>> Avenue Léon Duguit >>> 33608 Pessac cedex >>> France >>> >>> Bureau : F-331 >>> >>> yi...@u-bordeaux4.fr >>> >>> http://yildizoglu.info >>> >>> http://www.twitter.com/yildizoglu >>>
