{% include base_path %} {% for post in site.awards reversed %} {% include archive-single-award.html %}

---

{% endfor %}

{% include base_path %} {% include group-by-array collection=site.posts field="categories" %} {% for category in group_names %} {% assign posts = group_items[forloop.index0] %}

{{ category }}

{% for post in posts %} {% include archive-single.html %} {% endfor %} {% endfor %}

{% include base_path %} {% capture written_label %}'None'{% endcapture %} {% for collection in site.collections %} {% unless collection.output == false or collection.label == "posts" %} {% capture label %}{{ collection.label }}{% endcapture %} {% if label != written_label %}

{{ label }}

{% capture written_label %}{{ label }}{% endcapture %} {% endif %} {% endunless %} {% for post in collection.docs %} {% unless collection.output == false or collection.label == "posts" %} {% include archive-single.html %} {% endunless %} {% endfor %} {% endfor %}

{% include base_path %} {% include cv-template.html %}

{% include base_path %} Education ====== * Ph.D in Version Control Theory, GitHub University, 2018 (expected) * M.S. in Jekyll, GitHub University, 2014 * B.S. in GitHub, GitHub University, 2012 Work experience ====== * Spring 2024: Academic Pages Collaborator * GitHub University * Duties includes: Updates and improvements to template * Supervisor: The Users * Fall 2015: Research Assistant * GitHub University * Duties included: Merging pull requests * Supervisor: Professor Hub * Summer 2015: Research Assistant * GitHub University * Duties included: Tagging issues * Supervisor: Professor Git Skills ====== * Skill 1 * Skill 2 * Sub-skill 2.1 * Sub-skill 2.2 * Sub-skill 2.3 * Skill 3 Publications ======

{% for post in site.publications reversed %} {% include archive-single-cv.html %} {% endfor %}

Talks ======

{% for post in site.talks reversed %} {% include archive-single-talk-cv.html %} {% endfor %}

Teaching ======

{% for post in site.teaching reversed %} {% include archive-single-cv.html %} {% endfor %}

Service and leadership ====== * Currently signed in to 43 different slack teams

/* * This file controls what is imported from /_sass * * Note that the files are processed in the order they are imported, so they are partly sorted by the dependencies. Also, the first two lines of the file are required by Jekyll. */ @import "vendor/breakpoint/breakpoint", "themes", "theme/{{ site.site_theme | default: 'default' | append: '_light' }}", "theme/{{ site.site_theme | default: 'default' | append: '_dark' }}", "include/mixins", "vendor/susy/susy", "layout/reset", "layout/base", "include/utilities", "layout/tables", "layout/buttons", "layout/notices", "layout/masthead", "layout/navigation", "layout/footer", "syntax", "layout/forms", "layout/page", "layout/archive", "layout/sidebar", "layout/json_cv", "vendor/font-awesome/fontawesome", "vendor/font-awesome/solid", "vendor/font-awesome/brands" ;

{ "name": {{ site.title | jsonify }}, "short_name": {{ site.name | jsonify }}, "description": {{ site.description | jsonify }}, "start_url": "{{ site.baseurl | default: '/' }}", "lang": {{ site.locale | default: "en" | jsonify }}, "icons": [ { "src": "/images/favicon-192x192.png", "sizes": "192x192", "type": "image/png" }, { "src": "/images/favicon-512x512.png", "sizes": "512x512", "type": "image/png" } ] }

{% include toc %} ## Locations of key files/directories * Basic config options: _config.yml * Top navigation bar config: _data/navigation.yml * Single pages: _pages/ * Collections of pages are .md or .html files in: * _publications/ * _portfolio/ * _posts/ * _teaching/ * _talks/ * Footer: _includes/footer.html * Static files (like PDFs): /files/ * Profile image (can set in _config.yml): images/profile.png ## Tips and hints * Name a file ".md" to have it render in markdown, name it ".html" to render in HTML. * Go to the [commit list](https://github.com/academicpages/academicpages.github.io/commits/master) (on your repo) to find the last version GitHub built with Jekyll. * Green check: successful build * Orange circle: building * Red X: error * No icon: not built * Academic Pages uses [Jekyll Kramdown](https://jekyllrb.com/docs/configuration/markdown/), GitHub Flavored Markdown (GFM) parser, which is similar to the version of Markdown used on GitHub, but may have some minor differences. * Some of emoji supported on GitHub should be supposed via the [Jemoji](https://github.com/jekyll/jemoji) plugin :computer:. * The best list of the supported emoji can be found in the [Emojis for Jekyll via Jemoji](https://www.fabriziomusacchio.com/blog/2021-08-16-emojis_for_Jekyll/#computer) blog post. * While GitHub Pages prevents server side code from running, client-side scripts are supported. * This means that Google Analytics is supported, and [the wiki](https://github.com/academicpages/academicpages.github.io/wiki/Adding-Google-Analytics) should contain the most up-to-date information on getting it working. * Your CV can be written using either Markdown ([preview](https://academicpages.github.io/cv/)) or generated via JSON ([preview](https://academicpages.github.io/cv-json/)) and the layouts are slightly different. You can update the path to the one being used in `_data/navigation.yml` with the JSON formatted CV being hidden by default. * The [Liquid syntax guide](https://shopify.github.io/liquid/tags/control-flow/) is a useful guide for those that want to add functionality to the template or to become contributors to the [template on GitHub](https://github.com/academicpages/academicpages.github.io). ## MathJax Support for MathJax (version 3.* via [jsDelivr](https://www.jsdelivr.com/), [documentation](https://docs.mathjax.org/en/latest/)) is included in the template: $$ \displaylines{ \nabla \cdot E= \frac{\rho}{\epsilon_0} \\\ \nabla \cdot B=0 \\\ \nabla \times E= -\partial_tB \\\ \nabla \times B = \mu_0 \left(J + \varepsilon_0 \partial_t E \right) } $$ The default delimiters of `$$...$$` and `\\[...\\]` are supported for displayed mathematics, while `\\(...\\)` should be used for in-line mathematics (ex., \\(a^2 + b^2 = c^2\\)) **Note** that since Academic Pages uses Markdown which cases some interference with MathJax and LaTeX for escaping characters and new lines, although [some workarounds exist](https://math.codidact.com/posts/278763/278772#answer-278772). In some cases, such as when you are including MathJax in a `citation` field for publications, it may be necessary to use `\(...\)` for inline delineation. ## Mermaid diagrams Academic Pages includes support for [Mermaid diagrams](https://mermaid.js.org/) (version 11.* via [jsDelivr](https://www.jsdelivr.com/)) and in addition to their [tutorials](https://mermaid.js.org/ecosystem/tutorials.html) and [GitHub documentation](https://github.com/mermaid-js/mermaid) the basic syntax is as follows: ```markdown ```mermaid graph LR A-->B ``` ``` Which produces the following plot with the [default theme](https://mermaid.js.org/config/theming.html) applied: ```mermaid graph LR A-->B ``` While a more advanced plot with the `forest` theme applied looks like the following: ```mermaid --- config: theme: 'forest' --- graph TD; A-->B; A-->C; B-->D; C-->D; ``` ## Plotly Academic Pages includes support for Plotly diagrams via a hook in the Markdown code elements, although those that are comfortable with HTML and JavaScript can also access it [via those routes](https://plotly.com/javascript/getting-started/). Plotly is included via an `npm` [package](https://www.npmjs.com/package/plotly.js?activeTab=readme) and is distributed as part of the minimized JavaScript that is part of the template. In order to render a Plotly plot via Markdown the relevant plot data need to be added as follows: ```markdown ```plotly { "data": [ { "x": [1, 2, 3, 4], "y": [10, 15, 13, 17], "type": "scatter" }, { "x": [1, 2, 3, 4], "y": [16, 5, 11, 9], "type": "scatter" } ] } ``` ``` **Important!** Since the data is parsed as JSON *all* of the keys will need to be quoted for the plot to render. The use of a tool like [JSONLint](https://jsonlint.com/) to check syntax is highly recommended. {: .notice} Which produces the following: ```plotly { "data": [ { "x": [1, 2, 3, 4], "y": [10, 15, 13, 17], "type": "scatter" }, { "x": [1, 2, 3, 4], "y": [16, 5, 11, 9], "type": "scatter" } ] } ``` Essentially what is taking place is that the [Plotly attributes](https://plotly.com/javascript/reference/index/) are being taken from the code block as JSON data, parsed, and passed to Plotly along with a theme that matches the current site theme (i.e., a light theme, or a dark theme). This allows all plots that can be described via the `data` attribute to rendered with some limitations for the theme of the plot. ```plotly { "data": [ { "x": [1, 2, 3, 4, 5], "y": [1, 6, 3, 6, 1], "mode": "markers", "type": "scatter", "name": "Team A", "text": ["A-1", "A-2", "A-3", "A-4", "A-5"], "marker": { "size": 12 } }, { "x": [1.5, 2.5, 3.5, 4.5, 5.5], "y": [4, 1, 7, 1, 4], "mode": "markers", "type": "scatter", "name": "Team B", "text": ["B-a", "B-b", "B-c", "B-d", "B-e"], "marker": { "size": 12 } } ], "layout": { "xaxis": { "range": [ 0.75, 5.25 ] }, "yaxis": { "range": [0, 8] }, "title": {"text": "Data Labels Hover"} } } ``` ```plotly { "data": [{ "x": [1, 2, 3], "y": [4, 5, 6], "type": "scatter" }, { "x": [20, 30, 40], "y": [50, 60, 70], "xaxis": "x2", "yaxis": "y2", "type": "scatter" }], "layout": { "grid": { "rows": 1, "columns": 2, "pattern": "independent" }, "title": { "text": "Simple Subplot" } } } ``` ```plotly { "data": [{ "z": [[10, 10.625, 12.5, 15.625, 20], [5.625, 6.25, 8.125, 11.25, 15.625], [2.5, 3.125, 5.0, 8.125, 12.5], [0.625, 1.25, 3.125, 6.25, 10.625], [0, 0.625, 2.5, 5.625, 10]], "type": "contour" }], "layout": { "title": { "text": "Basic Contour Plot" } } } ``` ## Markdown guide Academic Pages uses [kramdown](https://kramdown.gettalong.org/index.html) for Markdown rendering, which has some differences from other Markdown implementations such as GitHub's. In addition to this guide, please see the [kramdown Syntax page](https://kramdown.gettalong.org/syntax.html) for full documentation. ### Header three #### Header four ##### Header five ###### Header six ## Blockquotes Single line blockquote: > Quotes are cool. ## Tables ### Table 1 | Entry | Item | | | -------- | ------ | ------------------------------------------------------------ | | [John Doe](#) | 2016 | Description of the item in the list | | [Jane Doe](#) | 2019 | Description of the item in the list | | [Doe Doe](#) | 2022 | Description of the item in the list | ### Table 2 | Header1 | Header2 | Header3 | |:--------|:-------:|--------:| | cell1 | cell2 | cell3 | | cell4 | ce ll5 | cell6 | |-----------------------------| | cell1 | cell2 | cell3 | | cell4 | cell5 | cell6 | |=============================| | Foot1 | Foot2 | Foot3 | ## Definition Lists Definition List Title : Definition list division. Startup : A startup company or startup is a company or temporary organization designed to search for a repeatable and scalable business model. #dowork : Coined by Rob Dyrdek and his personal body guard Christopher "Big Black" Boykins, "Do Work" works as a self motivator, to motivating your friends. Do It Live : I'll let Bill O'Reilly [explain](https://www.youtube.com/watch?v=O_HyZ5aW76c "We'll Do It Live") this one. ## Unordered Lists (Nested) * List item one * List item one * List item one * List item two * List item three * List item four * List item two * List item three * List item four * List item two * List item three * List item four ## Ordered List (Nested) 1. List item one 1. List item one 1. List item one 2. List item two 3. List item three 4. List item four 2. List item two 3. List item three 4. List item four 2. List item two 3. List item three 4. List item four ## Buttons Make any link standout more when applying the `.btn` class. ## Notices Basic notices or call-outs are supported using the following syntax: ```markdown **Watch out!** You can also add notices by appending `{: .notice}` to the line following paragraph. {: .notice} ``` which wil render as: **Watch out!** You can also add notices by appending `{: .notice}` to the line following paragraph. {: .notice} ### Footnotes Footnotes can be useful for clarifying points in the text, or citing information.[^1] Markdown support numeric footnotes, as well as text as long as the values are unique.[^note] ```markdown This is the regular text.[^1] This is more regular text.[^note] [^1]: This is the footnote itself. [^note]: This is another footnote. ``` [^1]: Such as this footnote. [^note]: When using text for footnotes markers, no spaces are permitted in the name. ## HTML Tags ### Address Tag

1 Infinite Loop
Cupertino, CA 95014
United States

### Anchor Tag (aka. Link) This is an example of a [link](https://github.com "GitHub"). ### Abbreviation Tag The abbreviation CSS stands for "Cascading Style Sheets". *[CSS]: Cascading Style Sheets ### Cite Tag "Code is poetry." ---Automattic ### Code Tag You will learn later on in these tests that `word-wrap: break-word;` will be your best friend. You can also write larger blocks of code with syntax highlighting supported for some languages, such as Python: ```python print('Hello World!') ``` or R: ```R print("Hello World!", quote = FALSE) ``` ### Details Tag (collapsible sections) The HTML `

` tag works well with Markdown and allows you to include collapsible sections, see [W3Schools](https://www.w3schools.com/tags/tag_details.asp) for more information on how to use the tag.

Collapsed by default

This section was collapsed by default!

The source code: ```HTML

Collapsed by default

This section was collapsed by default!

``` Or, you can leave a section open by default by including the `open` attribute in the tag:

Open by default

This section is open by default thanks to open in the <details open> tag!

### Emphasize Tag The emphasize tag should _italicize_ text. ### Insert Tag This tag should denote inserted text. ### Keyboard Tag This scarcely known tag emulates keyboard text, which is usually styled like the `` tag. ### Preformatted Tag This tag styles large blocks of code.

.post-title {
  margin: 0 0 5px;
  font-weight: bold;
  font-size: 38px;
  line-height: 1.2;
  and here's a line of some really, really, really, really long text, just to see how the PRE tag handles it and to find out how it overflows;
}

### Quote Tag Developers, developers, developers… –Steve Ballmer ### Strike Tag This tag will let you strikeout text. ### Strong Tag This tag shows **bold text**. ### Subscript Tag Getting our science styling on with H₂O, which should push the "2" down. ### Superscript Tag Still sticking with science and Isaac Newton's E = MC², which should lift the 2 up. ### Variable Tag This allows you to denote variables. *** **Footnotes** The footnotes in the page will be returned following this line, return to the section on Markdown Footnotes. </div> </article> </div>

Page not in menu

This is a page not in the menu. You can use markdown in this page. Heading 1 ====== Heading 2 ======

Page Archive

{% include base_path %} {% for post in site.pages %} {% include archive-single.html %} {% endfor %}

Portfolio

{% include base_path %} {% for post in site.portfolio %} {% include archive-single.html %} {% endfor %}

Publications

{% if site.author.googlescholar %}

You can also find my articles on my Google Scholar profile.

{% endif %} {% include base_path %} {% if site.publication_category %} {% for category in site.publication_category %} {% assign title_shown = false %} {% for post in site.publications reversed %} {% if post.category != category[0] %} {% continue %} {% endif %} {% unless title_shown %}

{{ category[1].title }}

---

{% assign title_shown = true %} {% endunless %} {% include archive-single-pub.html %} {% endfor %} {% endfor %} {% else %} {% for post in site.publications reversed %} {% include archive-single-pub.html %} {% endfor %} {% endif %}

Sitemap

{% include base_path %} A list of all the posts and pages found on the site. For you robots out there, there is an [XML version]({{ base_path }}/sitemap.xml) available for digesting as well.

Pages

{% for post in site.pages %} {% include archive-single.html %} {% endfor %}

Posts

{% for post in site.posts %} {% include archive-single.html %} {% endfor %} {% capture written_label %}'None'{% endcapture %} {% for collection in site.collections %} {% unless collection.output == false or collection.label == "posts" %} {% capture label %}{{ collection.label }}{% endcapture %} {% if label != written_label %}

{{ label }}

{% capture written_label %}{{ label }}{% endcapture %} {% endif %} {% endunless %} {% for post in collection.docs %} {% unless collection.output == false or collection.label == "posts" %} {% include archive-single.html %} {% endunless %} {% endfor %} {% endfor %}

Posts by Tags

{% include base_path %} {% include group-by-array collection=site.posts field="tags" %} {% for tag in group_names %} {% assign posts = group_items[forloop.index0] %}

{{ tag }}

{% for post in posts %} {% include archive-single.html %} {% endfor %} {% endfor %}

Talk map

This map is generated from a Jupyter Notebook file in talkmap.ipynb, which mines the location fields in the .md files in _talks/.

Teaching

{% include base_path %} {% for post in site.teaching reversed %} {% include archive-single.html %} {% endfor %}

Terms and Privacy Policy

{% include base_path %} {% include toc %} ## Privacy Policy The privacy of my visitors is extremely important. This Privacy Policy outlines the types of personal information that is received and collected and how it is used. First and foremost, I will never share your email address or any other personal information to anyone without your direct consent. ### Log Files Like many other websites, this site uses log files to help learn about when, from where, and how often traffic flows to this site. The information in these log files include: * Internet Protocol addresses (IP) * Types of browser * Internet Service Provider (ISP) * Date and time stamp * Referring and exit pages * Number of clicks All of this information is not linked to anything that is personally identifiable. ### Cookies and Web Beacons When you visit this site "convenience" cookies are stored on your computer when you submit a comment to help you log in faster to [Disqus](https://disqus.com) the next time you leave a comment. Third-party advertisers may also place and read cookies on your browser and/or use web beacons to collect information. This site has no access or control over these cookies. You should review the respective privacy policies on any and all third-party ad servers for more information regarding their practices and how to opt-out. If you wish to disable cookies, you may do so through your web browser options. Instructions for doing so can be found on the specific web browsers' websites. #### Google Analytics Google Analytics is a web analytics tool I use to help understand how visitors engage with this website. It reports website trends using cookies and web beacons without identifying individual visitors. You can read [Google Analytics Privacy Policy](https://www.google.com/analytics/learn/privacy.html).

Blog posts

{% include base_path %} {% capture written_year %}'None'{% endcapture %} {% for post in site.posts %} {% capture year %}{{ post.date | date: '%Y' }}{% endcapture %} {% if year != written_year %}

{{ year }}

{% capture written_year %}{{ year }}{% endcapture %} {% endif %} {% include archive-single.html %} {% endfor %}

@import "jekyll-theme-primer";

{"/about/":"https://ammaryacoub.github.io/","/about.html":"https://ammaryacoub.github.io/","/resume-json":"https://ammaryacoub.github.io/cv-json/","/resume":"https://ammaryacoub.github.io/cv/","/md/":"https://ammaryacoub.github.io/markdown/","/markdown.html":"https://ammaryacoub.github.io/markdown/","/nmp/":"https://ammaryacoub.github.io/non-menu-page/","/nmp.html":"https://ammaryacoub.github.io/non-menu-page/","/wordpress/blog-posts/":"https://ammaryacoub.github.io/year-archive/"}

Markdown Generator

# Markdown Generator This directory contains various ways of creating Markdown for your site. In general, filenames that end with `.ipynb` or `.py` are similar, but may contain different documentation or are intended to be run from with GitHub when deploying your site. ## Python Scripts The .py files are Python scripts that that can be run from the command line (ex., `python3 publications.py publications.csv`) with the objective of also ensuring that they have reduced requirements for packages, which may allow them to run when deploying your site from within GitHub. ## Jupyter Notebooks These .ipynb files are Jupyter notebook files that convert a TSV containing structured data about talks (`talks.tsv`) or presentations (`presentations.tsv`) into individual markdown files that will be properly formatted for the academicpages template. The notebooks contain a lot of documentation about the process.

{% if page.xsl %}{% endif %}<feed xmlns="http://www.w3.org/2005/Atom" {% if site.lang %}xml:lang="{{ site.lang }}"{% endif %}>Jekyll<link href="{{ '/' | absolute_url }}" rel="alternate" type="text/html" {% if site.lang %}hreflang="{{ site.lang }}" {% endif %}/>{{ site.time | date_to_xmlschema }}{{ page.url | absolute_url | xml_escape }}{% assign title = site.title | default: site.name %}{% if page.collection != "posts" %}{% assign collection = page.collection | capitalize %}{% assign title = title | append: " | " | append: collection %}{% endif %}{% if page.category %}{% assign category = page.category | capitalize %}{% assign title = title | append: " | " | append: category %}{% endif %}{% if title %}{% endif %}{% if site.description %}{{ site.description | xml_escape }}{% endif %}{% if site.author %}{{ site.author.name | default: site.author | xml_escape }}{% if site.author.email %}{{ site.author.email | xml_escape }}{% endif %}{% if site.author.uri %}{{ site.author.uri | xml_escape }}{% endif %}{% endif %}{% if page.tags %}{% assign posts = site.tags[page.tags] %}{% else %}{% assign posts = site[page.collection] %}{% endif %}{% if page.category %}{% assign posts = posts | where: "categories", page.category %}{% endif %}{% unless site.show_drafts %}{% assign posts = posts | where_exp: "post", "post.draft != true" %}{% endunless %}{% assign posts = posts | sort: "date" | reverse %}{% assign posts_limit = site.feed.posts_limit | default: 10 %}{% for post in posts limit: posts_limit %}<entry{% if post.lang %}{{" "}}xml:lang="{{ post.lang }}"{% endif %}>{% assign post_title = post.title | smartify | strip_html | normalize_whitespace | xml_escape %} {{ post.date | date_to_xmlschema }}{{ post.last_modified_at | default: post.date | date_to_xmlschema }}{{ post.id | absolute_url | xml_escape }}{% assign excerpt_only = post.feed.excerpt_only | default: site.feed.excerpt_only %}{% unless excerpt_only %}<![CDATA[{{ post.content | strip }}]]>{% endunless %}{% assign post_author = post.author | default: post.authors[0] | default: site.author %}{% assign post_author = site.data.authors[post_author] | default: post_author %}{% assign post_author_email = post_author.email | default: nil %}{% assign post_author_uri = post_author.uri | default: nil %}{% assign post_author_name = post_author.name | default: post_author %}{{ post_author_name | default: "" | xml_escape }}{% if post_author_email %}{{ post_author_email | xml_escape }}{% endif %}{% if post_author_uri %}{{ post_author_uri | xml_escape }}{% endif %}{% if post.category %}{% elsif post.categories %}{% for category in post.categories %}{% endfor %}{% endif %}{% for tag in post.tags %}{% endfor %}{% assign post_summary = post.description | default: post.excerpt %}{% if post_summary and post_summary != empty %}

<![CDATA[{{ post_summary | strip_html | normalize_whitespace }}]]>

{% endif %}{% assign post_image = post.image.path | default: post.image %}{% if post_image %}{% unless post_image contains "://" %}{% assign post_image = post_image | absolute_url %}{% endunless %}{% endif %}</entry>{% endfor %}</feed>

{% if page.xsl %} {% endif %} {% assign collections = site.collections | where_exp:'collection','collection.output != false' %}{% for collection in collections %}{% assign docs = collection.docs | where_exp:'doc','doc.sitemap != false' %}{% for doc in docs %} {{ doc.url | replace:'/index.html','/' | absolute_url | xml_escape }} {% if doc.last_modified_at or doc.date %}{{ doc.last_modified_at | default: doc.date | date_to_xmlschema }} {% endif %} {% endfor %}{% endfor %}{% assign pages = site.html_pages | where_exp:'doc','doc.sitemap != false' | where_exp:'doc','doc.url != "/404.html"' %}{% for page in pages %} {{ page.url | replace:'/index.html','/' | absolute_url | xml_escape }} {% if page.last_modified_at %}{{ page.last_modified_at | date_to_xmlschema }} {% endif %} {% endfor %}{% assign static_files = page.static_files | where_exp:'page','page.sitemap != false' | where_exp:'page','page.name != "404.html"' %}{% for file in static_files %} {{ file.path | replace:'/index.html','/' | absolute_url | xml_escape }} {{ file.modified_time | date_to_xmlschema }} {% endfor %}

Sitemap: {{ "sitemap.xml" | absolute_url }}