Research in the Gweon Group
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| #format inline_latex #pragma latex_preamble latexPreamble = MoinMoin in Griffin = |
#pragma footnote-style plain # default; to use superscript use "sup" ## page was renamed from MoinMoin in Griffin |
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| <<TableOfContents>> | == Slide show is cool == I find it cool, anyway. For this reason, the "SS" link is provided at top of every page. If you click it, a slide show version of the page will be displayed. Use arrow keys to navigate. Or space bar, which is equivalent to the down arrow. Use the escape key to get out of the slide show mode. Or, if you move your mouse to the top of the window, a menu will appear. In order to make a page slide show friendly, you will need to divide contents in small chunks using ''level 1'' headings as in {{{ = <title> = }}} Note also that anything before the first level 1 heaving will not show up in the slide show mode. |
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| As of June 7, 2011, !MathJax has been installed in Griffin and it seems to work fine. !MathJax is an HTML processor that recognizes LaTeX markups. ~-Accordingly, the format 'inline_latex' is no longer the default format applied to wiki pages in Griffin. (See the striked out line below, in the next section.) This means that the inline_latex format needs to be declared explicitly, if the latex format ever needs to be used. For a historical reason, ''this'' page continues to use the inline_latex format as the default format (see the first line of the source code). However, all !MathJax markups used in this page are applicable in other pages without modification.-~ As the latex parser has some issues related to many small cache images that it creates and the subsequent surge protection problem, it should be replaced by !MathJax for most uses. |
As of June 7, 2011, !MathJax has been installed in Griffin and it seems to work fine. !MathJax is an HTML processor that recognizes LaTeX markups. |
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{{{#!wiki |
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| Notice that, in the second and the third methods, no line breakage is allowed. This is due to the insertion of line number IDs by !MoinMoin, for one. To avoid this ugliness and the lack of readability, the parser must be called more formally, as shown in the following example. By the way, note that !MathJax is just a HTML (post-)processor, and !MoinMoin is told to simply pass the raw text marked as mathjax format (using any of these methods described here) to !MathJax, and so, an interesting side effect is that, ''any'' HTML can be included with the mathjax text. | Notice that, in the second and the third methods, no line breakage is allowed within the math environment. To avoid this ugliness and the lack of readability, the parser must be called more formally, as shown in the following example. (~-By the way, note that !MathJax is just a HTML post-processor, and !MoinMoin is told to simply pass the raw text marked as mathjax format (using any of these methods described here) to !MathJax, and so, an interesting side effect is that, ''any'' HTML markup can be included in the mathjax parser environment. The example below includes such a markup.-~) |
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| }}} | |
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| ----- == LaTeX Parser in Griffin (Deprecated) == |
== LaTeX == |
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| {{{#!wiki warning | Check out <<ln(http://en.wikibooks.org/wiki/LaTeX, this wonderful book on the web)>> if you are not familiar with LaTeX, or even if. |
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| While the latex parser is kept around ''for a while,'' it ''is being phased out.'' | == LaTeX parser in Griffin (deprecated) == |
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| Now, !MathJax is given a higher priority. The main advantages of !MathJax are the full scalability, and the lack of proliferation of small attachment files. This stands in contrast to the disadvantages of the latex parser: the triggering of ''surge protection'' when there are many latex expressions in a single page as each in-line math expression begets a parser instance. (The latex parser does seem to have the advantage of the speed of display, ... perhaps ..., as images are cached.) | It is also possible to use a latex parser, instead of a !MathJax parser. However, this is not recommended. The latex parser is kept for some special page like [[MoinMoin in Griffin (Old)|this one]], where you can read more about the deprecated latex parser, if you insist. |
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| Keeping both !MathJax and latex means that there are conflicts. For instance, in-line math objects marked by a pair of \$'s or a pair of \$\$'s are now passed to !MathJax, not to latex, ''no matter what the declared parser is.'' To force them to be interpreted by latex, the following solution has been devised: immediately after the opening token (\$ or \$\$), if there is a ':', then the expression is passed to latex (sans that ':' of course). | == Custom macros in Griffin == |
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| Some information in this section is outdated, for this reason. Some strange errors can occur if the latex parser is used. This document is an example of how sometimes the dollar sign must be represented in order for it to show up correctly. '''All in all, the latex parser is discouraged, unless it is absolutely necessary to use it.''' }}} A customized parser is installed in Griffin to make it easy to use LaTeX expressions. The LaTeX parser is used whenever there is a LaTeX instruction in the body of the document. The LaTeX parser is used automatically in Griffin. The parser was downloaded from <<ln(http://johannes.sipsolutions.net/Projects/new-moinmoin-latex,here)>>, and customized and updated locally. [Outdated paragraph] --(The default format of any wiki page is inline_latex.)-- This is equivalent to having, at top of the document, the following declaration. {{{ #format inline_latex }}} [Outdated paragraph] --(This is the default format in Griffin.)-- If you do not use any latex formatting at all in a page, this is fine, of course. That page will act just like a normal wiki page. See one [[#Caveats|caveat]] about the GUI editor below. The following declaration must be at top of the document in order to change the parser to the default plain vanilla one. {{{ #format wiki }}} === Customizing the LaTeX environment === The default preamble of the LaTeX in Griffin is the following. {{{#!highlight latex numbers=off \documentclass[12pt]{article} \pagestyle{empty} \usepackage[utf8]{inputenc} \usepackage{amsmath} }}} This preamble is not changeable, but other stuff can be added to this preamble in several ways. ==== Using a preamble page ==== This is probably the most reasonable way. For this method to work, first a page needs to be created within a Wiki that contains texts to be used as LaTeX preamble. For instance, suppose the following text is saved in the page named latexPreambleGHG. {{{ \usepackage{dsfont} % This is just a test. }}} Now, suppose you have the following in another page. {{{ #format inline_latex # This line is not necessary in Griffin. #pragma latex_preamble latexPreambleGHG ... other texts ... $:\mathds{C}$ }}} That code {{{\$:\mathds{C}\$}}} should give you this output: $:\mathds{C}$. Note the new symbol ':' that is now required after the first \$ due to conflict with !MathJax. ==== Other methods ==== The preamble can be included in the latex macro itself. === Caveats === * If there are two many latex elements in a page, then you might trigger a "surge protection" mechanism. If this mechanism becomes a hindrance, let me know. Possibly, the surge protection setting is something that has not found the optimal setting yet. * The GUI editor does not work in !MoinMoin for formats other than the plain "wiki" format. Only if you give a certain page this format, by including a line "#format wiki" at the top, you will be able to see the "Edit (GUI)" button. A GUI editor is not necessary normally, in my opinion, but often a less used feature can be discovered in GUI menus. ----- == Macros in Griffin == |
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| === Linking URLs === | == Linking URLs == |
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| === Linking DOIs === | == Linking DOIs == |
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| === Linking Attachments === la, lia (to do -- need to document) |
== Linking attachments == |
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| === Citing References (Bibtex etc.) === | Image files and other files are stored as attachments in Moin. They can then be included in the page by using macros such as {{{lia}}} or {{{la}}}. Note that these are custom macros at griffin. 1. First, upload your file by using the {{{AttachFile}}} action. This action can be activated by clicking on the {{{A}}} link above, or by the keystroke {{{a}}} anywhere in a page. 1. Once you have an attachment file, you can link to it by something like {{{<<lia(test.png, clickable = True, scale = 0.5)>>}}} or {{{<<la(test.pdf, "My cool pdf file")>>}}}. In the first case, we are using the {{{lia}}} macro (link image attachment), and in the second case, we are using the {{{la}}} macro (link attachment). * ~-Note the lack of space between {{{la}}}/{{{lia}}} and {{{(}}}. That ''is'' significant! That is, there should not be any space between the macro name and the parenthesis.-~ * ~-For {{{lia}}}, the argument {{{clickable}}} is true by default. So, in the above example, it is not necessary.-~ 1. To align an image at the center of the line is a bit tricky. You can accomplish this by {{{ <<c>> <<lia(test.png, scale = 0.8, align = "center")>> <<c(1)>> }}} Here, {{{c}}} is a simple macro for center-aligning, and its optional argument, specified in the last line here, indicates whether it is ending the center-aligning or not (as opposed to beginning it). == Citing references (Bibtex etc.) == |
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| ----- == Odds and Ends == |
== Raw html markups == h<<fn(Hey, here is a simple name!)>> == Signing the document == If you like to leave a signature, after you edit a file, or, more frequently, after you make a comment to an existing page, you can write @``SIG@. This will expand to your user name and a time stamp. == Odds and ends == |
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| Do you want to write '\$'? Well, then you have to remember the number 36! Or, you can also escape \$ (this behavior is provided by !MathJax, an HTML (post-)processor). | Do you want to write '\$'? Well, then all you have to remember is the number 36! Or, you can also escape \$ (this behavior is due to the use of !MathJax, an HTML post-processor, in Griffin). |
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| ----- | ---- |
Slide show is cool
I find it cool, anyway. For this reason, the "SS" link is provided at top of every page. If you click it, a slide show version of the page will be displayed. Use arrow keys to navigate. Or space bar, which is equivalent to the down arrow. Use the escape key to get out of the slide show mode. Or, if you move your mouse to the top of the window, a menu will appear.
In order to make a page slide show friendly, you will need to divide contents in small chunks using level 1 headings as in
= <title> =
Note also that anything before the first level 1 heaving will not show up in the slide show mode.
MathJax in Griffin
As of June 7, 2011, MathJax has been installed in Griffin and it seems to work fine. MathJax is an HTML processor that recognizes LaTeX markups.
To use MathJax, inline expressions can be enclosed by a pair of \$'s (the expression \( ... \) is not allowed, as it seems to conflict with MoinMoin). Displayed math formulas can come in a pair of $$'s, or \[ ... \]. However, this method restricts only a single line input (the output can be multiple lines) due to the MoinMoin inserting HTML tags before MathJax can go interpret formulas. The solution for more complex expressions is to call the mathjax parser explicitly. Here are some examples.
Here is an in-line math: $y = 20$.
- Lorentz equation!
$$\begin{align} \dot{x} & = \sigma(y-x) \\ \dot{y} & = \rho x - y - xz \\ \dot{z} & = -\beta z + xy \end{align}$$
- Lorentz equation, again!
\[\begin{align} \dot{x} & = \sigma(y-x) \\ \dot{y} & = \rho x - y - xz \\ \dot{z} & = -\beta z + xy \end{align}\]
Notice that, in the second and the third methods, no line breakage is allowed within the math environment. To avoid this ugliness and the lack of readability, the parser must be called more formally, as shown in the following example. (By the way, note that MathJax is just a HTML post-processor, and MoinMoin is told to simply pass the raw text marked as mathjax format (using any of these methods described here) to MathJax, and so, an interesting side effect is that, any HTML markup can be included in the mathjax parser environment. The example below includes such a markup.)
Lorentz equation — "correctly" done!
Lorentz Equation
\[ \begin{align} \dot{x} & = \sigma(y-x) \\ \dot{y} & = \rho x - y - xz \\ \dot{z} & = -\beta z + xy \end{align} \]
LaTeX
Check out this wonderful book on the web if you are not familiar with LaTeX, or even if.
LaTeX parser in Griffin (deprecated)
It is also possible to use a latex parser, instead of a MathJax parser. However, this is not recommended. The latex parser is kept for some special page like this one, where you can read more about the deprecated latex parser, if you insist.
Custom macros in Griffin
New macros have been added to Griffin to make it quick to include URL links, DOI links, and attachments, etc.
Linking URLs
A URL can be linked like this.
<<ln(http://www.jstor.org/stable/1734697,"A must read by PWA.")>> This lovely article is both deep and popular <<lnfn(http://www.jstor.org/stable/1734697,"A must read by PWA.")>>. This lovely article is both deep and popular <<lnfn(http://www.jstor.org/stable/1734697,"Science 4 August 1972: Vol. 177 no. 4047, pp. 393-396. 'More is Different'.")>>.
This results in the following.
This lovely article is both deep and popular [1].
This lovely article is both deep and popular [2].
Linking DOIs
A DOI can be linked like this.
<<doi(10.1126/science.177.4047.393,"A must read by PWA.")>> This lovely article is both deep and popular <<doifn(10.1126/science.177.4047.393,"A must read by PWA.")>>. This lovely article is both deep and popular <<doifn(10.1126/science.177.4047.393,"Science 4 August 1972: Vol. 177 no. 4047, pp. 393-396. 'More is Different'.")>>.
This results in the following.
This lovely article is both deep and popular [3].
This lovely article is both deep and popular [4].
As an aside, this article is NOT accessible through OCA if I use the Science link (the DOI link), but it IS accessible through OCA if I use JSTOR.org link. This is a useful thing to know as far as papers published in Science are concerned.
Linking attachments
Image files and other files are stored as attachments in Moin. They can then be included in the page by using macros such as lia or la. Note that these are custom macros at griffin.
First, upload your file by using the AttachFile action. This action can be activated by clicking on the A link above, or by the keystroke a anywhere in a page.
Once you have an attachment file, you can link to it by something like <<lia(test.png, clickable = True, scale = 0.5)>> or <<la(test.pdf, "My cool pdf file")>>. In the first case, we are using the lia macro (link image attachment), and in the second case, we are using the la macro (link attachment).
Note the lack of space between la/lia and (. That is significant! That is, there should not be any space between the macro name and the parenthesis.
For lia, the argument clickable is true by default. So, in the above example, it is not necessary.
- To align an image at the center of the line is a bit tricky. You can accomplish this by
<<c>> <<lia(test.png, scale = 0.8, align = "center")>> <<c(1)>>Here, c is a simple macro for center-aligning, and its optional argument, specified in the last line here, indicates whether it is ending the center-aligning or not (as opposed to beginning it).
Citing references (Bibtex etc.)
cite (to do -- need to document)
Raw html markups
h [5]
Signing the document
If you like to leave a signature, after you edit a file, or, more frequently, after you make a comment to an existing page, you can write @SIG@. This will expand to your user name and a time stamp.
Odds and ends
Do you want to write '&' but the parser refuses to do so? Then, try
&
Do you want to write '\$'? Well, then all you have to remember is the number 36! Or, you can also escape \$ (this behavior is due to the use of MathJax, an HTML post-processor, in Griffin).
$