changed latex tagging convention

Author: chrisjsewell

README.md

@@ -14,6 +14,7 @@ See ![notebooks/Example.ipynb](converted/Example.pdf) and ![converted/Example.pd
 - [Latex Metadata Tags](#latex-metadata-tags)
     - [Captions in a Markdown cell](#captions-in-a-markdown-cell)
 - [Citations and Bibliography](#citations-and-bibliography)
+- [Live Slideshows](#live-slideshows)
 - [Dealing with external data](#dealing-with-external-data)
 - [Miscellaneous](#miscellaneous)
 - [Acknowledgements](#acknowledgements)
@@ -152,28 +153,37 @@ c.Exporter.template_file = 'created.tplx'
 
 ## Latex Metadata Tags
 
+All information additional information, used to specify how a particular notebook/cell in latex is represented, is stored in the metadata under:
+
+```json
+{
+		"doc": {}
+}
+```
+
 ### Document Tags
 
 For **titlepage**, enter in notebook metadata:
 
 ```json
 {
-	"latex_titlepage": {
+"latex_doc": {
+  "titlepage": {
 	"author": "Authors Name",
 	"email": "[email protected]",
 	"supervisors": [
-	"First Supervisor",
-	"Second Supervisor"
+	  "First Supervisor",
+	  "Second Supervisor"
 	],
 	"title": "Main-Title",
 	"subtitle": "Sub-Title",
 	"tagline": "A tagline for the report.",
 	"institution": [
-	"Institution1",
-	"Institution2"
+	  "Institution1",
+	  "Institution2"
 	],
 	"logo": "logo_example"
-	}
+  }
 }
 ```
 
@@ -186,34 +196,40 @@ To control the output of **contents tables**:
 
 ```json
 {
-  "latex_toc": true,
-  "latex_listfigures": true,
-  "latex_listtables": true,
-  "latex_listcode": true,
+"latex_doc": {
+  "toc": true,
+  "listfigures": true,
+  "listtables": true,
+  "listcode": true,
+  }
 }
 ```
 
 ### Cell Tags
 
-To  **output ignore a markdown cell**:
+To  **ignore any cell**:
 
 ```json
 {
-	"latex_ignore" : true
+"latex_doc": {
+	"ignore" : true
+	}
 }
 ```
 
 To  **output a code block**:
 
 ```json
 {
-  "latex_code": {
+"latex_doc": {
+  "code": {
     "asfloat": true,
     "caption": "",
     "label": "code:example_sym",
     "widefigure": false,
     "placement": "H"
-  },
+    }
+  }
 }
 ```
 
@@ -227,12 +243,14 @@ For  **figures**, enter in cell metadata:
 
 ```json
 {
-	  "latex_figure": {
-	    "caption": "Figure caption.",
-	    "label": "fig:flabel",
-	    "placement": "H",
-	    "widefigure": false
-	  }
+"latex_doc": {
+  "figure": {
+    "caption": "Figure caption.",
+    "label": "fig:flabel",
+    "placement": "H",
+    "widefigure": false
+    }
+  }
 }
 ```
 
@@ -243,12 +261,14 @@ For  **tables**, enter in cell metadata:
 
 ```json
 {
-"latex_table": {
+"latex_doc": {
+     "table": {
 	    "caption": "Table caption.",
 	    "label": "tbl:tlabel",
 	    "placement": "H",
             "alternate": "gray!20"
 	  }
+   }
 }
 ```
 
@@ -260,9 +280,11 @@ For  **equations**, enter in cell metadata:
 
 ```json
 {
-	  "latex_equation": {
+  "latex_doc": {
+	  "equation": {
 	    "label": "eqn:elabel"
 	  }
+  }
 }
 ```
 
@@ -276,7 +298,9 @@ If a **markdown cell** has the metadata tag:
 
 ```json
 {
-	"latex_caption": "fig:example_mpl"
+ "latex_doc": {
+	"caption": "fig:example_mpl"
+	}
 }
 ```
 
@@ -289,10 +313,12 @@ If a subsequent **figure, table or code** cell has a label matching any stored v
 
 ```json
 {
-	"latex_figure": {
+"latex_doc": {
+	"figure": {
 	"caption": "",
 	"label": "fig:example_mpl"
 	}
+  }
 }
 ```
 
@@ -337,6 +363,12 @@ Can use:
 
 to make it look better in html, but not specifically available for drag and drop in Zotero 
 
+## Live Slideshows
+
+The [Reveal.js - Jupyter/IPython Slideshow Extension (RISE)](https://github.com/damianavila/RISE) notebook extension offers rendering as a Reveal.js-based slideshow, where you can execute code or show to the audience whatever you can show/do inside the notebook itself! Click on the image to see a demo:
+
+[![RISE Demo](https://img.youtube.com/vi/sXyFa_r1nxA/0.jpg)](https://www.youtube.com/watch?v=sXyFa_r1nxA) 
+
 ## Dealing with external data
 
 A goal for scientific publishing is automated reproducibility of analyses, which the Jupyter notebook excels at. But, more than that, it should be possible to efficiently reproduce the analysis with different data sets. This entails having **one point of access** to a data set within the notebook, rather than having copy-pasted data into variables, i.e. this:

converted/Example.pdf

@@ -452,23 +452,21 @@
 
 
 
-		
-		
-
-\begingroup
-\let\cleardoublepage\relax
-\let\clearpage\relax\tableofcontents\listoffigures\listoftables\listof{codecell}{List of Code}
-\endgroup
+		\begingroup
+    \let\cleardoublepage\relax
+    \let\clearpage\relax\tableofcontents\listoffigures\listoftables\listof{codecell}{List of Code}
+    \endgroup
 
 
 
 
 
-
 \section{Markdown}\label{markdown}
 
+
 \subsection{General}\label{general}
 
+
 Some markdown text.
 
 A list:
@@ -492,8 +490,10 @@ \subsection{General}\label{general}
   something else
 \end{enumerate}
 
+
 \subsection{References and Citations}\label{references-and-citations}
 
+
 References to \cref{fig:example}, \cref{tbl:example},
 \cref{eqn:example_sympy} and \cref{code:example_mpl}.
 
@@ -504,12 +504,15 @@ \subsection{References and Citations}\label{references-and-citations}
 
 A html citation.\cite{kirkeminde_thermodynamic_2012}
 
+
 \subsection{Todo notes}\label{todo-notes}
 
+
 \todo[inline]{an inline todo}
 
 Some text.\todo{a todo in the margins}
 
+
 \section{Images and Figures}\label{images-and-figures}
 
 
@@ -532,7 +535,6 @@ \section{Images and Figures}\label{images-and-figures}
 
 
 
-
     \begin{figure}
         \begin{center}\adjustimage{max size={0.9\linewidth}{0.4\paperheight}}{Example_files/Example_10_0.png}\end{center}
 
@@ -549,7 +551,6 @@ \section{Images and Figures}\label{images-and-figures}
 
 
 
-
     \begin{figure}
         \begin{center}\adjustimage{max size={0.9\linewidth}{0.4\paperheight}}{Example_files/Example_11_0.png}\end{center}
 
@@ -566,7 +567,6 @@ \section{Images and Figures}\label{images-and-figures}
 
 
 
-
     \begin{figure}
         \begin{center}\adjustimage{max size={0.9\linewidth}{0.4\paperheight}}{Example_files/Example_12_0.png}\end{center}
 
@@ -583,10 +583,13 @@ \section{Images and Figures}\label{images-and-figures}
 \subsection{Displaying a plot with its
 code}\label{displaying-a-plot-with-its-code}
 
+
 \newcommand{\kyfigcexampleumpl}{A matplotlib figure, with the caption set in the markdowncell above the figure.}
 
+
 \newcommand{\kycodecexampleumpl}{The plotting code for a matplotlib figure (\cref{fig:example_mpl}).}
 
+
 \begin{codecell}
         \ifdefined\kycodecexampleumpl
          \caption{\kycodecexampleumpl}
@@ -600,7 +603,6 @@ \subsection{Displaying a plot with its
 plt.legend();
 \end{lstlisting}\end{codecell}
 
-
 \begin{figure}
         \begin{center}\adjustimage{max size={0.9\linewidth}{0.4\paperheight}}{Example_files/Example_16_0.pdf}\end{center}
 
@@ -615,8 +617,10 @@ \subsection{Displaying a plot with its
 
     \section{Tables (with pandas)}\label{tables-with-pandas}
 
+
 \newcommand{\kycodecexampleupd}{The plotting code for a pandas Dataframe table (\cref{tbl:example}).}
 
+
 \begin{codecell}[H]
         \ifdefined\kycodecexampleupd
          \caption{\kycodecexampleupd}
@@ -632,19 +636,18 @@ \subsection{Displaying a plot with its
 \end{lstlisting}\end{codecell}
 
 
-
     \begin{table}[H]
 
+        
+    	\ifdefined\kytblcexample
+    	 \caption{\kytblcexample}
+    	\else
+    	 \caption{An example of a table created with pandas dataframe.}
+    	\fi
+        \label{tbl:example}
 
-	\ifdefined\kytblcexample
-	 \caption{\kytblcexample}
-	\else
-	 \caption{An example of a table created with pandas dataframe.}
-	\fi
-    \label{tbl:example}
-    
-    \centering\rowcolors{2}{gray!20}{white}
-    \begin{tabular}{lllrr}
+        \centering\rowcolors{2}{gray!20}{white}
+        \begin{tabular}{lllrr}
 \toprule
 {} &         a &  b &      c &      d \\
 \midrule
@@ -654,7 +657,7 @@ \subsection{Displaying a plot with its
 \bottomrule
 \end{tabular}
 
-    \end{table}
+        \end{table}
 
 
 
@@ -667,14 +670,15 @@ \section{Equations (with ipython or
 
 
     \begin{equation}\label{eqn:example_ipy}	
-	 a = b+c 
-    \end{equation}
+    	 a = b+c 
+        \end{equation}
 
 
 
 
 \newcommand{\kycodecexampleusym}{The plotting code for a sympy equation (\cref{eqn:example_sympy}).}
 
+
 \begin{codecell}[H]
         \ifdefined\kycodecexampleusym
          \caption{\kycodecexampleusym}
@@ -689,18 +693,14 @@ \section{Equations (with ipython or
 \end{lstlisting}\end{codecell}
 
 
-
     \begin{equation}\label{eqn:example_sympy}	
-	\left(\sqrt{5} i\right)^{\alpha} \left(\frac{1}{2} - \frac{2 i}{5} \sqrt{5}\right) + \left(- \sqrt{5} i\right)^{\alpha} \left(\frac{1}{2} + \frac{2 i}{5} \sqrt{5}\right)
-    \end{equation}
+    	\left(\sqrt{5} i\right)^{\alpha} \left(\frac{1}{2} - \frac{2 i}{5} \sqrt{5}\right) + \left(- \sqrt{5} i\right)^{\alpha} \left(\frac{1}{2} + \frac{2 i}{5} \sqrt{5}\right)
+        \end{equation}
 
 
 
 
 
-
-
-