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sep:software:softtex:faq [2008/07/22 17:53]
altheyab created
sep:software:softtex:faq [2015/05/27 02:06] (current)
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 +====== Tex F.A.Q. ======
 +
This page is for SEP users. It reflects an actual e-mail correspondence. This page is for SEP users. It reflects an actual e-mail correspondence.
-  - [[#sideplot|Activesideplot does not work as before]] +  - [[#Activesideplot does not work as before]] 
-  - [[#prog|What macro should I use to include a program in the paper?]] +  - [[#What macro should I use to include a program in the paper?]] 
-  - [[#xtex|I tried to read a dvi file with xtex, but couldn't see any figures]] +  - [[#I tried to read a dvi file with xtex, but couldn't see any figures]] 
-  - [[#xdvi|I tried to read a dvi file with xdvi ("make read"), but couldn't see any figures]] +  - [[#I tried to read a dvi file with xdvi ("make read"), but couldn't see any figures]] 
-  - [[#book|How do I create (maintain) a book (a report, etc.)?]] +  - [[#How do I create (maintain) a book (a report, etc.)?]] 
-  - [[#ps2gif|"make html" fails to create a GIF figure from my postscript]] +  - [[#"make html" fails to create a GIF figure from my postscript]] 
-  - [[#input|My LaTeX file (paper.tex) is an assembly file of several text files. Do I need to do something special?]] +  - [[#My LaTeX file (paper.tex) is an assembly file of several text files. Do I need to do something special?]] 
-  - [[#old|What if I want to use the old SEP macros?]] +  - [[#What if I want to use the old SEP macros?]] 
-  - [[#self|I noticed a bug in the general macros (scripts, makerules.) How do I fix it myself?]] +  - [[#I noticed a bug in the general macros (scripts, makerules.) How do I fix it myself?]] 
-  - [[#home|How do I install the tex system on my home computer?]] +  - [[#How do I install the tex system on my home computer?]] 
-  - [[#netscape|What do I put in my netscape options to make all the .sepsh's work?]] +  - [[#What do I put in my netscape options to make all the .sepsh's work?]] 
-  - [[#nomake|How do I process a LaTeX file without "make"?]] +  - [[#How do I process a LaTeX file without "make"?]] 
-  - [[#bio|How do I add (change) my biography in an SEP report?]] +  - [[#How do I add (change) my biography in an SEP report?]] 
-  - [[#seg97|How do I create an SEG abstract?]] +  - [[#How do I create an SEG abstract?]] 
-  - [[#doublespace|How do I introduce double line spacing in my document?]] +  - [[#How do I introduce double line spacing in my document?]] 
-  - [[#syscall|What happened with syscall buttons?]] +  - [[#What happened with syscall buttons?]] 
-  - [[#thesis|Is there a thesis macro?]] +  - [[#Is there a thesis macro?]] 
-  - [[#geophysics|How do I typeset a paper for //Geophysics//?]] +  - [[#How do I typeset a paper for //Geophysics//?]] 
-  - [[#gp|How do I typeset a paper for //Geophysical Prospecting//?]] +  - [[#How do I typeset a paper for //Geophysical Prospecting//?]] 
-  - [[#links|How do I include hyperlinks in an HTML file produced by LaTeX2HTML?]] +  - [[#How do I include hyperlinks in an HTML file produced by LaTeX2HTML?]] 
-  - [[#resume|How do I typeset a resume?]] +  - [[#How do I typeset a resume?]] 
-  - [[#index|How do I index my pages for the full-text search on the web?]] +  - [[#How do I index my pages for the full-text search on the web?]] 
-  - [[#bibtex|What bibtex databases are available?]]+  - [[#What bibtex databases are available?]]
---- ----
-==== [[|Activesideplot does not work as before]] ====+==== Activesideplot does not work as before ====
This is a little backward compatibility problem. Previously, you could use something like **\activesideplot{plot}{2in}{}{Caption}**, where **2in** was taken as the plot height. Now you have to say **\activesideplot{plot}{height=2in}{Caption}** explicitly. You can use either one or both or none of width and height. If you use only one of them, the aspect ratio should be preserved by default. Some other possible keys in the argument to activeplot (supplied by the graphicx package) are: This is a little backward compatibility problem. Previously, you could use something like **\activesideplot{plot}{2in}{}{Caption}**, where **2in** was taken as the plot height. Now you have to say **\activesideplot{plot}{height=2in}{Caption}** explicitly. You can use either one or both or none of width and height. If you use only one of them, the aspect ratio should be preserved by default. Some other possible keys in the argument to activeplot (supplied by the graphicx package) are:
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-==== [[|What macro should I use to include a program in the paper?]] ====+==== What macro should I use to include a program in the paper? ====
-If you have a file called **file.f90**, **\listing{file.f90}** will do. If you want to reference it in a different place, try **\progblock{label}{file.f90}** and reference it with **\ref{prog:label}**. For cross-referencing among different chapters in a book there is also **\gprogblock{label}{file.f90}**. These are referenced with **\ref{/prog:label}**. You can find more information in the [[index.html#SEP2e|standard documentation]] on SEP2e.+If you have a file called **file.f90**, **\listing{file.f90}** will do. If you want to reference it in a different place, try **\progblock{label}{file.f90}** and reference it with **\ref{prog:label}**. For cross-referencing among different chapters in a book there is also **\gprogblock{label}{file.f90}**. These are referenced with **\ref{/prog:label}**. You can find more information in the [[sep:software:softtex#SEP2e (with THESIS options)|standard documentation]] on SEP2e.
---- ----
-==== [[|I tried to read a dvi file with xtex, but couldn't see any figures]] ====+==== I tried to read a dvi file with xtex, but couldn't see any figures ====
If you create a dvi file with SEP2e, **xtex** will not display figures in it. This is also true for non-SEP latex files that don't use xtex macro. If you really want to use xtex, try **make xtex**. It will creates a dvi file using the old macros. Xtex has been declared obsolete, and we expect it to move slowly out of usage... If you create a dvi file with SEP2e, **xtex** will not display figures in it. This is also true for non-SEP latex files that don't use xtex macro. If you really want to use xtex, try **make xtex**. It will creates a dvi file using the old macros. Xtex has been declared obsolete, and we expect it to move slowly out of usage...
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---- ----
-==== [[|I tried to read a dvi file with xdvi ("make read"), but couldn't see any figures]] ====+==== I tried to read a dvi file with xdvi ("make read"), but couldn't see any figures ====
By the makerule default, **xdvi** starts with **-nopostscript ** option. To activate a display of encapsulated postscript figures, press the **View PS** button on the right menu bar. If you see a file name in a box instead of a figure, check if this figure is listed in your makefile's **RESULTSER**, **RESULTSCR**, or **RESULTSNR** list. By the makerule default, **xdvi** starts with **-nopostscript ** option. To activate a display of encapsulated postscript figures, press the **View PS** button on the right menu bar. If you see a file name in a box instead of a figure, check if this figure is listed in your makefile's **RESULTSER**, **RESULTSCR**, or **RESULTSNR** list.
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---- ----
-==== [[|How do I create (maintain) a book (a report, etc.)?]] ====+==== How do I create (maintain) a book (a report, etc.)? ====
It has never been easier (though it probably should be). The system of book maintenance, described below, has been tested on SEP reports (from SEP-92 to SEP-94), SEPHELP document, Jon's books (from FGDP to TDF), and Biondo's lecture notes. It has never been easier (though it probably should be). The system of book maintenance, described below, has been tested on SEP reports (from SEP-92 to SEP-94), SEPHELP document, Jon's books (from FGDP to TDF), and Biondo's lecture notes.
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---- ----
-==== [[|"make html" fails to create a GIF figure from my postscript]] ====+==== "make html" fails to create a GIF figure from my postscript ====
The **pstogif ** script does break sometimes, especially with non-vplot figures. I haven't seen enough examples to notice the pattern, but, for example, none of my Mathematica figures could convert to GIF. I hope we will find a way around it after getting more experience. You may try converting postscript to GIF with **xv**. The **pstogif ** script does break sometimes, especially with non-vplot figures. I haven't seen enough examples to notice the pattern, but, for example, none of my Mathematica figures could convert to GIF. I hope we will find a way around it after getting more experience. You may try converting postscript to GIF with **xv**.
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---- ----
-==== [[|My LaTeX file (paper.tex) is an assembly file of several text files. Do I need to do something special?]] ====+==== My LaTeX file (paper.tex) is an assembly file of several text files. Do I need to do something special? ====
Include files like file1.tex, file2.tex in your paper with \input{file1}, \input{file2}. Additionally, put **paper.tex: file1.tex file2.tex ...** in your makefile to let **make** touch paper.tex for you each time one of those files changes. Include files like file1.tex, file2.tex in your paper with \input{file1}, \input{file2}. Additionally, put **paper.tex: file1.tex file2.tex ...** in your makefile to let **make** touch paper.tex for you each time one of those files changes.
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---- ----
-==== [[|What if I want to use the old SEP macros?]] ====+==== What if I want to use the old SEP macros? ====
The old macros still exist on our system. If you really want to use them, put **LATOPTS = class=old** in your makefile or simply run **gmake xtex**. The old macros still exist on our system. If you really want to use them, put **LATOPTS = class=old** in your makefile or simply run **gmake xtex**.
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---- ----
-==== [[|I noticed a bug in the general macros (scripts, makerules.) How do I fix it myself?]] ====+==== I noticed a bug in the general macros (scripts, makerules.) How do I fix it myself? ====
Feel free to do that. The makerules are in **$SEPINC**, the tex macros are in **$TEXMF/tex/latex/sep2e**, the tex-related perl scripts are in **/usr/local/share/TEX/bin**. Please use RCS if you make any changes. Feel free to do that. The makerules are in **$SEPINC**, the tex macros are in **$TEXMF/tex/latex/sep2e**, the tex-related perl scripts are in **/usr/local/share/TEX/bin**. Please use RCS if you make any changes.
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---- ----
-==== [[|How do I install the tex system on my home computer?]] ====+==== How do I install the tex system on my home computer? ====
To get the most current version of the tex macros, scripts, and makerules, run **~sergey/tarit** and ftp the **sep2e.tar.gz** file. This file contains everything you need for tex processing. Unpack it from the root directory with **tar xvzf sep2e.tar.gz**. You may need to run **rehash** and **texconfig rehash** to update the system. This distribution doesn't contain yet the scripts and extra programs required by **gmake html**. To get the most current version of the tex macros, scripts, and makerules, run **~sergey/tarit** and ftp the **sep2e.tar.gz** file. This file contains everything you need for tex processing. Unpack it from the root directory with **tar xvzf sep2e.tar.gz**. You may need to run **rehash** and **texconfig rehash** to update the system. This distribution doesn't contain yet the scripts and extra programs required by **gmake html**.
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---- ----
-==== [[|What do I put in my netscape options to make all the buttons (.sepsh scripts) work?]] ====+==== What do I put in my netscape options to make all the buttons (.sepsh scripts) work? ====
Check your **~/.netscape/preferences** file. It should say something like Check your **~/.netscape/preferences** file. It should say something like
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---- ----
-==== [[|How do I process a LaTeX file without "make"?]] ====+==== How do I process a LaTeX file without "make"? ====
If for some reason you don't want to use make, run **Latify paper.tex > paper.ltx** to create a valid latex file and **latex2dvi paper.ltx** to process it with LaTeX. For figures to show up in the DVI file, you need to use \plot (\sideplot) instead of \activeplot (\activesideplot). If for some reason you don't want to use make, run **Latify paper.tex > paper.ltx** to create a valid latex file and **latex2dvi paper.ltx** to process it with LaTeX. For figures to show up in the DVI file, you need to use \plot (\sideplot) instead of \activeplot (\activesideplot).
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---- ----
-==== [[|How do I add (change) my biography in an SEP report?]] ====+==== How do I add (change) my biography in an SEP report? ====
To add or update your biography and/or picture in the report, follow the following procedure: To add or update your biography and/or picture in the report, follow the following procedure:
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---- ----
-==== [[|How do I create an SEG abstract?]] ====+==== How do I create an SEG abstract? ====
-Simply put **LATOPTS = class=seg97** into your makefile (or run **gmake LATOPTS=class=seg97 paper.ps**). After you create a postscript file, you need to take it to Adobe Distiller. The result will be a PDF file, ready for electronic submission. \\ \\  Several people pointed out to me that the font size in SEG abstracts turns out smaller than usual. You shouldn't worry about it, because this size complies precisely with the sample abstract, distributed by SEG. \\  The seg97 class is designed to fit the SEP style. That is, it knows about all the macros we use in our papers and translates them accordingly. There is a smaller export version, called [[index.html#SEG|seg-99]].+Simply put **LATOPTS = class=seg97** into your makefile (or run **gmake LATOPTS=class=seg97 paper.ps**). After you create a postscript file, you need to take it to Adobe Distiller. The result will be a PDF file, ready for electronic submission. \\ \\  Several people pointed out to me that the font size in SEG abstracts turns out smaller than usual. You shouldn't worry about it, because this size complies precisely with the sample abstract, distributed by SEG. \\  The seg97 class is designed to fit the SEP style. That is, it knows about all the macros we use in our papers and translates them accordingly. There is a smaller export version, called seg-99.
---- ----
-==== [[|How do I introduce double line spacing in my document?]] ====+==== How do I introduce double line spacing in my document? ====
A simple command for doublespace is A simple command for doublespace is
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---- ----
-==== [[|What happened with syscall buttons?]] ====+==== What happened with syscall buttons? ====
They are back! In the "old days", we used those buttons with **xtex** (now obsolete). Now **\syscall{comm}** will translate into a link to **comm.sepsh** and allow you to execute virtually any make command from the HTML version of your document. To create the **sepshell** files automatically, put a list of the buttons in your makefile under **SYSCALLS** variable. This is mostly useful for TAs, preparing interactive exercises. They are back! In the "old days", we used those buttons with **xtex** (now obsolete). Now **\syscall{comm}** will translate into a link to **comm.sepsh** and allow you to execute virtually any make command from the HTML version of your document. To create the **sepshell** files automatically, put a list of the buttons in your makefile under **SYSCALLS** variable. This is mostly useful for TAs, preparing interactive exercises.
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---- ----
-==== [[|Is there a thesis macro?]] ====+==== Is there a thesis macro? ====
-Yes! The [[index.html#SEP2e|sep2e class]] has now a thesis option, connected with the standard LaTeX2e package for Stanford University theses. \\  February 2007, Brad Artman made some updates, to include the latest [[http://help-csli.stanford.edu/tex/suthesis/|suthesis2e.sty]] style file. Check out an entire [[Thesis|Thesis/Adm]] directory of files that will build (in Make) your thesis in 3 formats.+Yes! The [[sep:software:softtex#SEP2e (with THESIS options)|sep2e class]] has now a thesis option, connected with the standard LaTeX2e package for Stanford University theses. \\  February 2007, Brad Artman made some updates, to include the latest [[http://help-csli.stanford.edu/tex/suthesis/|suthesis2e.sty]] style file. Check out an entire [[http://sepwww.stanford.edu/software/softtex/Thesis/|Thesis/Adm]] directory of files that will build (in Make) your thesis in 3 formats.
-**BE CAREFUL!!** The book definitions contain a rule to make a paper.tex file in your Adm directory. Get the [[Thesis|whole directory]] to make things go smoothly (/net/sepwww/sepwww/pub/software/softtex/Thesis).+**BE CAREFUL!!** The book definitions contain a rule to make a paper.tex file in your Adm directory. Get the [[http://sepwww.stanford.edu/software/softtex/Thesis/|whole directory]] to make things go smoothly (/net/sepwww/sepwww/pub/software/softtex/Thesis).
-Basically, follow the instructions on [[#book|book maintainence]]. with these additional definitions:+Basically, follow the instructions on [[#How do I create (maintain) a book (a report, etc.)?|book maintainence]]. with these additional definitions:
  - Change **LATOPTS** in your "administration" makefile to **LATOPTS = option=thesis**   - Change **LATOPTS** in your "administration" makefile to **LATOPTS = option=thesis**
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---- ----
-==== [[|How do I typeset a paper for //Geophysics//?]] ====+==== How do I typeset a paper for //Geophysics//? ====
-Use **geophysics**, a LaTeX2e class. Check out the RSF [[http://rsf.sourceforge.net/wiki/index.php/SEGTeX| SEGtex]] website for the latest. **\old{}** and **\new{}** commands are great for sending in marked revisions. Makeing the pdf with and without the **LATOPTS option=revised** statement will either include only the things in **\new{}**, or both with strike-out and color changes. \\  Put **LATOPTS = class=geophysics** in your makefile, run the usual make commands (**make read**, **make print**, etc), and your SEP report paper will appear in the form ready for submission to //Geophysics//. \\  Also new are form-fillable pdf's that //Geophysics// wants filled out for your submission. [[2sentsum_form.pdf|2 sentance summary. ]] [[auaddres.form.pdf|Address. ]] [[auchklst-form.pdf|Checklist. ]] [[pagechg_form.pdf|Pagecharge. ]]\\+Use **geophysics**, a LaTeX2e class. Check out the RSF [[http://rsf.sourceforge.net/wiki/index.php/SEGTeX| SEGtex]] website for the latest. **\old{}** and **\new{}** commands are great for sending in marked revisions. Makeing the pdf with and without the **LATOPTS option=revised** statement will either include only the things in **\new{}**, or both with strike-out and color changes. \\  Put **LATOPTS = class=geophysics** in your makefile, run the usual make commands (**make read**, **make print**, etc), and your SEP report paper will appear in the form ready for submission to //Geophysics//.
---- ----
-==== [[|How do I typeset a paper for //Geophysical Prospecting//?]] ====+==== How do I typeset a paper for //Geophysical Prospecting//? ====
Use can also use the **geophysics** class supplimented with some changes in the style of bibliography references. Put the following in your makefile: \\ **LATOPTS = class=geophysics include='\bibpunct{(}{)}{;}{a}{}{\,}' bibstyle=eage**\\  The usual make commands (**make read**, **make print**, etc) will prepare your SEP report paper for submission to //Geophysical Prospecting//. Use can also use the **geophysics** class supplimented with some changes in the style of bibliography references. Put the following in your makefile: \\ **LATOPTS = class=geophysics include='\bibpunct{(}{)}{;}{a}{}{\,}' bibstyle=eage**\\  The usual make commands (**make read**, **make print**, etc) will prepare your SEP report paper for submission to //Geophysical Prospecting//.
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---- ----
-==== [[|How do I include hyperlinks in an HTML file produced by LaTeX2HTML?]] ====+==== How do I include hyperlinks in an HTML file produced by LaTeX2HTML? ====
Use the **html** LaTeX2e package, provided together with LaTeX2HTML. \\  To do that, put **LATOPTS = style=html** in your makefile. The commands to use in your LaTeX file are Use the **html** LaTeX2e package, provided together with LaTeX2HTML. \\  To do that, put **LATOPTS = style=html** in your makefile. The commands to use in your LaTeX file are
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---- ----
-==== [[|How do I typeset a resume?]] ====+==== How do I typeset a resume? ====
Look under Look under
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---- ----
-==== [[|How do I index my pages for the full-text search on the web?]] ====+==== How do I index my pages for the full-text search on the web? ====
Run **swish-e -c congiffile** on the web server. Here **configfile** is a configuration file. The configuration file for SEP reports is in Run **swish-e -c congiffile** on the web server. Here **configfile** is a configuration file. The configuration file for SEP reports is in
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  /public/docs/toc_html/docs-config   /public/docs/toc_html/docs-config
-. The configuration file for Jon's books is in+  * The configuration file for Jon's books is in
  /sepwww/pub/sep/prof/prof-config   /sepwww/pub/sep/prof/prof-config
-.+
---- ----
-==== [[|What bibtex databases are available?]] ====+==== What bibtex databases are available? ====
The SEP bibtex databases are located in The SEP bibtex databases are located in
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or use [[http://sepwww.stanford.edu/search.html|the web search]] or use [[http://sepwww.stanford.edu/search.html|the web search]]
-{{page>sep:footer}}+{{page>share:footer&nofooter&noeditbtn}}
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