I'm trying the earlier attachments again from the message that didn't make it into the archive, minus the binary .pdf file.

- Thomas On Sat, Mar 31, 2012 at 12:53 PM, Thomas Coffee <thomasmcof...@gmail.com> wrote: > Hi Xu, > > I notice your email shows up in the archive thread but mine does not, > and thus neither do the attachments. Any idea how to change this? > > Here is a modified preferences file that preserves a pdflatex-only > update pathway, allowing the user to update the LaTeX only without > updating the Sage computations. > > I will try emailing lyx-devel. > > Thanks, > Thomas > > > On Sat, Mar 31, 2012 at 4:48 AM, Xu Wang <xuwang...@gmail.com> wrote: >> 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

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example.lyx**

*Description:* application/lyx

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sage.module**

*Description:* Binary data

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preferences**

*Description:* Binary data

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setup.sh**

*Description:* Bourne shell script

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compile-pdf-sage.sh**

*Description:* Bourne shell script