ballaneypranav/iGEM Wiki Starter Pack - contents.pug

## iGEM Wiki Starter Pack - contents.pug
// src/templates/contents.pug
// This is the template that all files in src/pages use.

// includes some common utility functions from templates/mixins.pug
// read more about Pug mixins at https://pugjs.org/language/mixins.html
include mixins

html(lang="en")
  // includes variables: title, tagline and requireMathJax
  // from the file that uses this template
  block headVars
  head
    meta(charset="UTF-8")
    meta(name="viewport" content="width=device-width, initial-scale=1.0")
    // this is where the title variable is plugged in
    title #{title} | iGEM [[ iGEM_team_name ]]
    // MathJax is included only if requireMathJax is true
    if requireMathJax
      script(src="https://2020.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML")
  body
    // include code for navigation menu from templates/nav.pug
    include nav.pug
    header.d-flex.justify-content-center.align-items-center
      .container
        h1= title
        p.lead.pl-1= tagline
        hr.my-4

    main
      .container
        .row
          .sidebar.col-lg-3
            .nav#contents
              h5 Contents

              ul
                //- Filled automatically from js in js/content.js
          .content.col-lg-9
            article
              // include the actual text of the article
              block article

            // include citations if any
            // citations are added in src/citations/<filename>.yml
            // and they're automatically included in the corresponding
            // Pug file in the pages directory
            // More information about this is available in the Starter Pack docs.
            block citations
            if citations
              article#references
                h1 References
                ol
                  - counter = 1
                  each citation in citations
                    if citation.type == 'article'
                      +citation_article(citation, counter)
                    if citation.type == 'webpage'
                      +citation_webpage(citation, counter)
                    if citation.type == 'book'
                      +citation_book(citation, counter)
                    - counter = counter + 1

    // include code for footer from templates/footer.pug
    include footer.pug

## iGEM Wiki Starter Pack - sample.pug
// src/pages/Sample.pug
// This is a sample page that shows how elements can be added to
// pages in the Starter Pack, and also how they look once rendered.

// extend the contents template
extends ../templates/contents.pug

// some variables that are used for metadata
// you can add your own here, and use them appropriately in contents.pug
// More information about Pug templates is available at https://pugjs.org/language/inheritance.html.
// Adding a background image is a common use case. For an example of that,
// check out our wiki at https://github.com/igembitsgoa/wiki
block headVars
    - var title = "Sample"
    - var tagline = "A sample page for the theme."
    // this variable specifies whether MathJax is required on the page
    // if false, the MathJax script is not loaded, reducing the overall loading time
    - var requireMathJax = true

// this section includes the actual content of the page
block article

    // the content is processed by a markdown filter
    // which converts Markdown to Pug
    // (html) specifies that HTML code can be written in here,
    // and will be processed as regular HTML
    :markdown-it(html)

        # Headings
        ## Level 2 Heading
        ### Level 3 Heading
        #### Level 4 Heading

        # Emphasis
        This is regular text.

        **This is bold text.**
        __This is also bold text.__

        *This is italic text.*
        _This is also italix text.*

        ***This text is bold and italic both.***
        ___This text is bold and italic both.___

        ~~Strikethrough~~

        # Lists
        1. This is item one.
        1. This is item two.
        1. It's okay to number every item as 1.
            * This is a nested list.
            * Use asterisk for an unordered list,
            * Further nesting?
            + Plus sign also works.
            - And so does minus.
        1. ~~Birds aren't real.~~

        # Links
        [Google](https://google.com)

        [Text goes in square brackets](Link-goes-in-parenthesis)

        # Blockquote

        > This is a blockquote.
        > This continues in the same paragraph.
        >
        > To change the paragraph, you have to leave a line.

        > This is another blockquote.
        >
        > **Pranav Ballaney, 2020**

        # Images

        This is a regular paragraph.
        #### This is a level 4 heading.
        [This is a link](google.com)

    // Adding images requires you to step out of the Markdown filter
    // and use the provided image mixin.
    // Arguments:
    //      figure number
    //      filename with file stored in the assets/img folder
    //      a caption and alt text for the image
    //      width as a percentage of the page width (optional, default: 80)
    +image(1, "Description--josh-withers.jpg", "Caption", 100)

    :markdown-it(html)
        Back to regular text.

        # Tables

        This is a regular paragraph, which precedes the table.
        When you want to insert a table, indent one level back and specify the plugin.
        Then indent inside again and start writing the table.


    // For adding tables, you need to use this plugin
    :markdown-it(html plugins=['markdown-it-multimd-table'])
        | This is | the table | header row |
        | ------  | --------- | ---------- |
        | 1       | 2         | 3          |
        | 4       | 5         | 6          |
        [Table 1: Caption goes here.]

    :markdown-it(html)
        And when you're done, go back to the regular markdown filter.

    :markdown-it(html)
        **Example 2:**

    :markdown-it(html plugins=['markdown-it-multimd-table'])
        | Left aligned | Center aligned | Right aligned |
        | :----------- | :------------: | ------------: |
        | 1 | 2 | 3 |
        | 4 | 5 | 6 |

    :markdown-it(html)
        **Example 3:**

    :markdown-it(html plugins=['markdown-it-multimd-table'])
        |              |          Grouping           ||
        |First Header  | Second Header | Third Header |
        | ------------ | :-----------: | -----------: |
        |Content       |          *Long Cell*        ||
        |Content       |   **Cell**    |         Cell |
        |New section   |     More      |[Data](https://google.com) |
        |And more      | With an escaped '\|'       ||

        [Table 3: Caption goes here.]

    :markdown-it(html)

        # Definitions

        <dfn>Term ~ Definition</dfn>

        This can come <dfn>anywhere in ~ the text</dfn>.

        # MathJax

        $$\int_{0}^{\infty} e^{-x^2} dx = \frac{\sqrt{\pi}}{2}$$

        $$-\frac{\hbar^2}{2m}\nabla^2\psi + V\psi = E\psi$$

        $$i\hbar\gamma^\mu\partial_\mu\psi = mc\psi$$

        $$y_k = \frac{1}{\sqrt{N}}\sum_{n=0}^{N-1}x_n\omega_N^{kn}$$

    // in-text citations are added just like links
    // but require the link to be prefixed with "#citation"
    // and contain the number corresponding to the actual
    // citation at the bottom
    :markdown-it(html)

        # Citations

        In text citation for a research article with a DOI. [Rosano et al., 2019](#citation2)

        In text citation for another research article with a DOI. [Allen & Sheridan, 2015](#citation1)

        In text citation for a book with no DOI. [Ingalls, 2013](#citation3)

        In text citation for a website with institutional author. [TNAU Agritech Portal, n.d.](#citation4)

        In text citation for a website with an author. [Author, n.d.](#citation5)

// beyond this, citations are included from src/citations/Sample.yml

//- DO NOT MODIFY THIS LINE AND ANYTHING BEYOND.

prepend citations
    - var citations = [{"authors": "Allen, M. J., & Sheridan, S. C. (2015). ", "doi": "https://doi.org/10.1007/s00484-015-1117-4", "journal": "International Journal of Biometeorology", "numbers": "62(1), 57-67. ", "title": "Mortality risks during extreme temperature events (ETEs) using a distributed lag non-linear model.", "type": "article"}, {"authors": "Rosano, A., Bella, A., Gesualdo, F., Acampora, A., Pezzotti, P., Marchetti, S., ... & Rizzo, C. (2019). ", "doi": "https://doi.org/10.1016/j.ijid.2019.08.003", "journal": "International Journal of Infectious Diseases", "numbers": "88, 127-134. ", "title": "Investigating the impact of influenza on excess mortality in all ages in Italy during recent seasons (2013/14-2016/17 seasons).", "type": "article"}, {"authors": "Allen, M. J., & Sheridan, S. C. (2015).", "journal": "International Journal of Biometeorology.", "numbers": "62(1), 57-67.", "title": "Mortality risks during extreme temperature events (ETEs) using a distributed lag non-linear model.", "type": "article", "year_published": 2015}, {"details": "(n.d.). Retrieved on June 22, 2020. from ", "title": "Agriculture: Crop production: Sugarcane. TNAU Agritech Portal.", "type": "webpage", "url": "https://google.com"}, {"details": "(March 15, 2019). Retrieved on June 22, 2020. from ", "title": "Agriculture: Crop production: Sugarcane. TNAU Agritech Portal.", "type": "webpage", "url": "https://google.com"}, {"Google_Books_URL": "https://books.google.co.in/books?id=OYr6AQAAQBAJ", "authors": "Ingalls, B. P.", "publisher": "MIT Press.", "title": "Mathematical modeling in systems biology: An introduction.", "type": "book", "year_published": "(2013)."}]
	// src/templates/contents.pug
	// This is the template that all files in src/pages use.

	// includes some common utility functions from templates/mixins.pug
	// read more about Pug mixins at https://pugjs.org/language/mixins.html
	include mixins

	html(lang="en")
	// includes variables: title, tagline and requireMathJax
	// from the file that uses this template
	block headVars
	head
	meta(charset="UTF-8")
	meta(name="viewport" content="width=device-width, initial-scale=1.0")
	// this is where the title variable is plugged in
	title #{title} \| iGEM [[ iGEM_team_name ]]
	// MathJax is included only if requireMathJax is true
	if requireMathJax
	script(src="https://2020.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML")
	body
	// include code for navigation menu from templates/nav.pug
	include nav.pug
	header.d-flex.justify-content-center.align-items-center
	.container
	h1= title
	p.lead.pl-1= tagline
	hr.my-4

	main
	.container
	.row
	.sidebar.col-lg-3
	.nav#contents
	h5 Contents

	ul
	//- Filled automatically from js in js/content.js
	.content.col-lg-9
	article
	// include the actual text of the article
	block article

	// include citations if any
	// citations are added in src/citations/<filename>.yml
	// and they're automatically included in the corresponding
	// Pug file in the pages directory
	// More information about this is available in the Starter Pack docs.
	block citations
	if citations
	article#references
	h1 References
	ol
	- counter = 1
	each citation in citations
	if citation.type == 'article'
	+citation_article(citation, counter)
	if citation.type == 'webpage'
	+citation_webpage(citation, counter)
	if citation.type == 'book'
	+citation_book(citation, counter)
	- counter = counter + 1

	// include code for footer from templates/footer.pug
	include footer.pug
	// src/pages/Sample.pug
	// This is a sample page that shows how elements can be added to
	// pages in the Starter Pack, and also how they look once rendered.

	// extend the contents template
	extends ../templates/contents.pug

	// some variables that are used for metadata
	// you can add your own here, and use them appropriately in contents.pug
	// More information about Pug templates is available at https://pugjs.org/language/inheritance.html.
	// Adding a background image is a common use case. For an example of that,
	// check out our wiki at https://github.com/igembitsgoa/wiki
	block headVars
	- var title = "Sample"
	- var tagline = "A sample page for the theme."
	// this variable specifies whether MathJax is required on the page
	// if false, the MathJax script is not loaded, reducing the overall loading time
	- var requireMathJax = true

	// this section includes the actual content of the page
	block article

	// the content is processed by a markdown filter
	// which converts Markdown to Pug
	// (html) specifies that HTML code can be written in here,
	// and will be processed as regular HTML
	:markdown-it(html)

	# Headings
	## Level 2 Heading
	### Level 3 Heading
	#### Level 4 Heading

	# Emphasis
	This is regular text.

	This is bold text.
	__This is also bold text.__

	This is italic text.
	_This is also italix text.*

	*This text is bold and italic both.*
	___This text is bold and italic both.___

	~~Strikethrough~~

	# Lists
	1. This is item one.
	1. This is item two.
	1. It's okay to number every item as 1.
	* This is a nested list.
	* Use asterisk for an unordered list,
	* Further nesting?
	+ Plus sign also works.
	- And so does minus.
	1. ~~Birds aren't real.~~

	# Links
	[Google](https://google.com)

	[Text goes in square brackets](Link-goes-in-parenthesis)

	# Blockquote

	> This is a blockquote.
	> This continues in the same paragraph.
	>
	> To change the paragraph, you have to leave a line.

	> This is another blockquote.
	>
	> Pranav Ballaney, 2020

	# Images

	This is a regular paragraph.
	#### This is a level 4 heading.
	[This is a link](google.com)

	// Adding images requires you to step out of the Markdown filter
	// and use the provided image mixin.
	// Arguments:
	// figure number
	// filename with file stored in the assets/img folder
	// a caption and alt text for the image
	// width as a percentage of the page width (optional, default: 80)
	+image(1, "Description--josh-withers.jpg", "Caption", 100)

	:markdown-it(html)
	Back to regular text.

	# Tables

	This is a regular paragraph, which precedes the table.
	When you want to insert a table, indent one level back and specify the plugin.
	Then indent inside again and start writing the table.


	// For adding tables, you need to use this plugin
	:markdown-it(html plugins=['markdown-it-multimd-table'])
	\| This is \| the table \| header row \|
	\| ------ \| --------- \| ---------- \|
	\| 1 \| 2 \| 3 \|
	\| 4 \| 5 \| 6 \|
	[Table 1: Caption goes here.]

	:markdown-it(html)
	And when you're done, go back to the regular markdown filter.

	:markdown-it(html)
	Example 2:

	:markdown-it(html plugins=['markdown-it-multimd-table'])
	\| Left aligned \| Center aligned \| Right aligned \|
	\| :----------- \| :------------: \| ------------: \|
	\| 1 \| 2 \| 3 \|
	\| 4 \| 5 \| 6 \|

	:markdown-it(html)
	Example 3:

	:markdown-it(html plugins=['markdown-it-multimd-table'])
	\| \| Grouping \|\|
	\|First Header \| Second Header \| Third Header \|
	\| ------------ \| :-----------: \| -----------: \|
	\|Content \| Long Cell \|\|
	\|Content \| Cell \| Cell \|
	\|New section \| More \|[Data](https://google.com) \|
	\|And more \| With an escaped '\\|' \|\|

	[Table 3: Caption goes here.]

	:markdown-it(html)

	# Definitions

	<dfn>Term ~ Definition</dfn>

	This can come <dfn>anywhere in ~ the text</dfn>.

	# MathJax

	$$\int_{0}^{\infty} e^{-x^2} dx = \frac{\sqrt{\pi}}{2}$$

	$$-\frac{\hbar^2}{2m}\nabla^2\psi + V\psi = E\psi$$

	$$i\hbar\gamma^\mu\partial_\mu\psi = mc\psi$$

	$$y_k = \frac{1}{\sqrt{N}}\sum_{n=0}^{N-1}x_n\omega_N^{kn}$$

	// in-text citations are added just like links
	// but require the link to be prefixed with "#citation"
	// and contain the number corresponding to the actual
	// citation at the bottom
	:markdown-it(html)

	# Citations

	In text citation for a research article with a DOI. [Rosano et al., 2019](#citation2)

	In text citation for another research article with a DOI. [Allen & Sheridan, 2015](#citation1)

	In text citation for a book with no DOI. [Ingalls, 2013](#citation3)

	In text citation for a website with institutional author. [TNAU Agritech Portal, n.d.](#citation4)

	In text citation for a website with an author. [Author, n.d.](#citation5)

	// beyond this, citations are included from src/citations/Sample.yml

	//- DO NOT MODIFY THIS LINE AND ANYTHING BEYOND.

	prepend citations
	- var citations = [{"authors": "Allen, M. J., & Sheridan, S. C. (2015). ", "doi": "https://doi.org/10.1007/s00484-015-1117-4", "journal": "International Journal of Biometeorology", "numbers": "62(1), 57-67. ", "title": "Mortality risks during extreme temperature events (ETEs) using a distributed lag non-linear model.", "type": "article"}, {"authors": "Rosano, A., Bella, A., Gesualdo, F., Acampora, A., Pezzotti, P., Marchetti, S., ... & Rizzo, C. (2019). ", "doi": "https://doi.org/10.1016/j.ijid.2019.08.003", "journal": "International Journal of Infectious Diseases", "numbers": "88, 127-134. ", "title": "Investigating the impact of influenza on excess mortality in all ages in Italy during recent seasons (2013/14-2016/17 seasons).", "type": "article"}, {"authors": "Allen, M. J., & Sheridan, S. C. (2015).", "journal": "International Journal of Biometeorology.", "numbers": "62(1), 57-67.", "title": "Mortality risks during extreme temperature events (ETEs) using a distributed lag non-linear model.", "type": "article", "year_published": 2015}, {"details": "(n.d.). Retrieved on June 22, 2020. from ", "title": "Agriculture: Crop production: Sugarcane. TNAU Agritech Portal.", "type": "webpage", "url": "https://google.com"}, {"details": "(March 15, 2019). Retrieved on June 22, 2020. from ", "title": "Agriculture: Crop production: Sugarcane. TNAU Agritech Portal.", "type": "webpage", "url": "https://google.com"}, {"Google_Books_URL": "https://books.google.co.in/books?id=OYr6AQAAQBAJ", "authors": "Ingalls, B. P.", "publisher": "MIT Press.", "title": "Mathematical modeling in systems biology: An introduction.", "type": "book", "year_published": "(2013)."}]