diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..18ace9d --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +## Ignore everything ... + + +## ...But not ignore these files + diff --git a/404.html b/404.html new file mode 100644 index 0000000..5318858 --- /dev/null +++ b/404.html @@ -0,0 +1,10 @@ +--- +layout: default +title: "404: Page not found" +permalink: 404.html +--- + +
+

404: Page not found

+

Sorry, we've misplaced that URL or it's pointing to something that doesn't exist. Head back home to try finding it again.

+
diff --git a/CNAME b/CNAME new file mode 100644 index 0000000..d2366ca --- /dev/null +++ b/CNAME @@ -0,0 +1 @@ +codeasmanuscript.org diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..85857f0 --- /dev/null +++ b/Makefile @@ -0,0 +1,21 @@ +##------------------------------------------------------------------- +# Variables +site_repo=`basename "$$PWD"` + +## List of commands to use for Makefile. +all : + @grep -E '^##' Makefile | sed -e 's/##//g' +##------------------------------------------------------------------- +## test_local : Test the site locally before building live version +test_local : + jekyll serve --watch + +## build_site : Build the GitHub pages site +build_site : + rsync -a --exclude='.git/' --exclude='.gitignore' ../workshops/ ../${site_repo}/ + ./knitpost.R + jekyll build + git clean -d -x -f + +.PHONY : build_site test_local + diff --git a/_config.yml b/_config.yml new file mode 100644 index 0000000..ea48187 --- /dev/null +++ b/_config.yml @@ -0,0 +1,30 @@ +# Dependencies +markdown: kramdown +highlighter: pygments + +# Permalinks +permalink: pretty +relative_permalinks: false + +# Setup +title: Code As Manuscript +tagline: 'Change the way you see your code.' +description: 'Writing your code and analyses as if it was the manuscript.' +url: http://codeasmanuscript.org + +author: + name: 'Code As Manuscript' + +# Custom vars +version: 2.1.0 + +github: + repo: https://github.com/codeasmanuscript + +lesson-list: [Git, Intro, Plotting, Wrangling, Rmarkdown, Macros, ODS] +category-list: [R, Git, Macros, ODS, Lessons] +tag-list: [Lessons, Git, GitHub, Macros, ODS, Assignment, Slides, Cheatsheet] + +exclude: ['lessons/template/*', gps/eventListing.md, '*.Rmd', + evals/, survey/, lessons/potentials.md, README.md] + diff --git a/_includes/head.html b/_includes/head.html new file mode 100644 index 0000000..ed6271b --- /dev/null +++ b/_includes/head.html @@ -0,0 +1,29 @@ + + + + + + + + + + {% if page.title == "Home" %} + {{ site.title }} · {{ site.tagline }} + {% else %} + {{ page.title }} · {{ site.title }} + {% endif %} + + + + + + + + + + + + + + + diff --git a/_includes/sidebar.html b/_includes/sidebar.html new file mode 100644 index 0000000..d488e71 --- /dev/null +++ b/_includes/sidebar.html @@ -0,0 +1,36 @@ +
+
+
+

+ + {{ site.title }} + +

+

{{ site.description }}

+
+ + + +

© {{ site.time | date: '%Y' }}. All rights reserved.

+
+
diff --git a/_layouts/default.html b/_layouts/default.html new file mode 100644 index 0000000..3a49ecc --- /dev/null +++ b/_layouts/default.html @@ -0,0 +1,15 @@ + + + + {% include head.html %} + + + + {% include sidebar.html %} + +
+ {{ content }} +
+ + + diff --git a/_layouts/page.html b/_layouts/page.html new file mode 100644 index 0000000..4e0d4eb --- /dev/null +++ b/_layouts/page.html @@ -0,0 +1,8 @@ +--- +layout: default +--- + +
+

{{ page.title }}

+ {{ content }} +
diff --git a/_layouts/post.html b/_layouts/post.html new file mode 100644 index 0000000..697188e --- /dev/null +++ b/_layouts/post.html @@ -0,0 +1,25 @@ +--- +layout: default +--- + +
+

{{ page.title }}

+ {{ page.date | date_to_string }} + {{ content }} +
+ +
+

Related Posts

+ +
diff --git a/atom.xml b/atom.xml new file mode 100644 index 0000000..96c9681 --- /dev/null +++ b/atom.xml @@ -0,0 +1,28 @@ +--- +layout: null +--- + + + + + {{ site.title }} + + + {{ site.time | date_to_xmlschema }} + {{ site.url }} + + {{ site.author.name }} + {{ site.author.email }} + + + {% for post in site.posts %} + + {{ post.title }} + + {{ post.date | date_to_xmlschema }} + {{ site.url }}{{ post.id }} + {{ post.content | xml_escape }} + + {% endfor %} + + diff --git a/knitpost.R b/knitpost.R new file mode 100755 index 0000000..df1f3f4 --- /dev/null +++ b/knitpost.R @@ -0,0 +1,33 @@ +#!/usr/bin/Rscript --vanilla + +# Taken and modified from +# http://varianceexplained.org/pages/workflow.html + +# compiles all .Rmd files in _R directory into .md files in the _posts +# directory, if the input file is older than the output file. + +# run ./knitpages.R to update all knitr files that need to be updated. + +KnitPost <- function(input, outfile, base.url = '/') { + # this function is a modified version of an example here: + # http://jfisher-usgs.github.com/r/2012/07/03/knitr-jekyll/ + knitr::opts_knit$set(base.url = base.url) + knitr::opts_chunk$set(fig.path = 'images/', + collapse = TRUE) + knitr::render_jekyll() + knitr::knit(input, outfile, envir = parent.frame()) + txt <- sub('^published: false', 'published: true', + readLines(outfile)) + writeLines(txt, outfile) +} + +for (infile in list.files(pattern="*.Rmd", full.names=TRUE, recursive = TRUE)) { + outfile <- paste0(sub("\\.Rmd$", ".md", infile)) + + # knit only if the input file is the last one modified + if (!file.exists(outfile) | + file.info(infile)$mtime > file.info(outfile)$mtime) { + KnitPost(infile, outfile) + } +} + diff --git a/public/css/hyde.css b/public/css/hyde.css new file mode 100644 index 0000000..bc57104 --- /dev/null +++ b/public/css/hyde.css @@ -0,0 +1,250 @@ +/* + * __ __ + * /\ \ /\ \ + * \ \ \___ __ __ \_\ \ __ + * \ \ _ `\/\ \/\ \ /'_` \ /'__`\ + * \ \ \ \ \ \ \_\ \/\ \_\ \/\ __/ + * \ \_\ \_\/`____ \ \___,_\ \____\ + * \/_/\/_/`/___/> \/__,_ /\/____/ + * /\___/ + * \/__/ + * + * Designed, built, and released under MIT license by @mdo. Learn more at + * https://github.com/poole/hyde. + */ + + +/* + * Contents + * + * Global resets + * Sidebar + * Container + * Reverse layout + * Themes + */ + + +/* + * Global resets + * + * Update the foundational and global aspects of the page. + */ + +html { + font-family: "PT Sans", Helvetica, Arial, sans-serif; +} +@media (min-width: 48em) { + html { + font-size: 12px; + } +} +@media (min-width: 58em) { + html { + font-size: 16px; + } +} + + +/* + * Sidebar + * + * Flexible banner for housing site name, intro, and "footer" content. Starts + * out above content in mobile and later moves to the side with wider viewports. + */ + +.sidebar { + text-align: center; + padding: 2rem 1rem; + color: rgba(255,255,255,.5); + background-color: #202020; +} +@media (min-width: 48em) { + .sidebar { + position: fixed; + top: 0; + left: 0; + bottom: 0; + width: 18rem; + text-align: left; + } +} + +/* Sidebar links */ +.sidebar a { + color: #fff; +} + +/* About section */ +.sidebar-about h1 { + color: #fff; + margin-top: 0; + font-family: "Abril Fatface", serif; + font-size: 3.25rem; +} + +/* Sidebar nav */ +.sidebar-nav { + margin-bottom: 1rem; +} +.sidebar-nav-item { + display: block; + line-height: 1.75; +} +a.sidebar-nav-item:hover, +a.sidebar-nav-item:focus { + text-decoration: underline; +} +.sidebar-nav-item.active { + font-weight: bold; +} + +/* Sticky sidebar + * + * Add the `sidebar-sticky` class to the sidebar's container to affix it the + * contents to the bottom of the sidebar in tablets and up. + */ + +@media (min-width: 48em) { + .sidebar-sticky { + position: absolute; + right: 1rem; + bottom: 1rem; + left: 1rem; + } +} + + +/* Container + * + * Align the contents of the site above the proper threshold with some margin-fu + * with a 25%-wide `.sidebar`. + */ + +.content { + padding-top: 4rem; + padding-bottom: 4rem; +} + +@media (min-width: 48em) { + .content { + max-width: 38rem; + margin-left: 20rem; + margin-right: 2rem; + } +} + +@media (min-width: 64em) { + .content { + margin-left: 22rem; + margin-right: 4rem; + } +} + + +/* + * Reverse layout + * + * Flip the orientation of the page by placing the `.sidebar` on the right. + */ + +@media (min-width: 48em) { + .layout-reverse .sidebar { + left: auto; + right: 0; + } + .layout-reverse .content { + margin-left: 2rem; + margin-right: 20rem; + } +} + +@media (min-width: 64em) { + .layout-reverse .content { + margin-left: 4rem; + margin-right: 22rem; + } +} + + + +/* + * Themes + * + * As of v1.1, Hyde includes optional themes to color the sidebar and links + * within blog posts. To use, add the class of your choosing to the `body`. + */ + +/* Base16 (http://chriskempson.github.io/base16/#default) */ + +/* Red */ +.theme-base-08 .sidebar { + background-color: #ac4142; +} +.theme-base-08 .content a, +.theme-base-08 .related-posts li a:hover { + color: #ac4142; +} + +/* Orange */ +.theme-base-09 .sidebar { + background-color: #d28445; +} +.theme-base-09 .content a, +.theme-base-09 .related-posts li a:hover { + color: #d28445; +} + +/* Yellow */ +.theme-base-0a .sidebar { + background-color: #f4bf75; +} +.theme-base-0a .content a, +.theme-base-0a .related-posts li a:hover { + color: #f4bf75; +} + +/* Green */ +.theme-base-0b .sidebar { + background-color: #90a959; +} +.theme-base-0b .content a, +.theme-base-0b .related-posts li a:hover { + color: #90a959; +} + +/* Cyan */ +.theme-base-0c .sidebar { + background-color: #75b5aa; +} +.theme-base-0c .content a, +.theme-base-0c .related-posts li a:hover { + color: #75b5aa; +} + +/* Blue */ +.theme-base-0d .sidebar { + background-color: #6a9fb5; +} +.theme-base-0d .content a, +.theme-base-0d .related-posts li a:hover { + color: #6a9fb5; +} + +/* Magenta */ +.theme-base-0e .sidebar { + background-color: #aa759f; +} +.theme-base-0e .content a, +.theme-base-0e .related-posts li a:hover { + color: #aa759f; +} + +/* Brown */ +.theme-base-0f .sidebar { + background-color: #8f5536; +} +.theme-base-0f .content a, +.theme-base-0f .related-posts li a:hover { + color: #8f5536; +} diff --git a/public/css/poole.css b/public/css/poole.css new file mode 100644 index 0000000..a7f147c --- /dev/null +++ b/public/css/poole.css @@ -0,0 +1,430 @@ +/* + * ___ + * /\_ \ + * _____ ___ ___\//\ \ __ + * /\ '__`\ / __`\ / __`\\ \ \ /'__`\ + * \ \ \_\ \/\ \_\ \/\ \_\ \\_\ \_/\ __/ + * \ \ ,__/\ \____/\ \____//\____\ \____\ + * \ \ \/ \/___/ \/___/ \/____/\/____/ + * \ \_\ + * \/_/ + * + * Designed, built, and released under MIT license by @mdo. Learn more at + * https://github.com/poole/poole. + */ + + +/* + * Contents + * + * Body resets + * Custom type + * Messages + * Container + * Masthead + * Posts and pages + * Pagination + * Reverse layout + * Themes + */ + + +/* + * Body resets + * + * Update the foundational and global aspects of the page. + */ + +* { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; +} + +html, +body { + margin: 0; + padding: 0; +} + +html { + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 16px; + line-height: 1.5; +} +@media (min-width: 38em) { + html { + font-size: 20px; + } +} + +body { + color: #515151; + background-color: #fff; + -webkit-text-size-adjust: 100%; + -ms-text-size-adjust: 100%; +} + +/* No `:visited` state is required by default (browsers will use `a`) */ +a { + color: #268bd2; + text-decoration: none; +} +a strong { + color: inherit; +} +/* `:focus` is linked to `:hover` for basic accessibility */ +a:hover, +a:focus { + text-decoration: underline; +} + +/* Headings */ +h1, h2, h3, h4, h5, h6 { + margin-bottom: .5rem; + font-weight: bold; + line-height: 1.25; + color: #313131; + text-rendering: optimizeLegibility; +} +h1 { + font-size: 2rem; +} +h2 { + margin-top: 1rem; + font-size: 1.5rem; +} +h3 { + margin-top: 1.5rem; + font-size: 1.25rem; +} +h4, h5, h6 { + margin-top: 1rem; + font-size: 1rem; +} + +/* Body text */ +p { + margin-top: 0; + margin-bottom: 1rem; +} + +strong { + color: #303030; +} + + +/* Lists */ +ul, ol, dl { + margin-top: 0; + margin-bottom: 1rem; +} + +dt { + font-weight: bold; +} +dd { + margin-bottom: .5rem; +} + +/* Misc */ +hr { + position: relative; + margin: 1.5rem 0; + border: 0; + border-top: 1px solid #eee; + border-bottom: 1px solid #fff; +} + +abbr { + font-size: 85%; + font-weight: bold; + color: #555; + text-transform: uppercase; +} +abbr[title] { + cursor: help; + border-bottom: 1px dotted #e5e5e5; +} + +/* Code */ +code, +pre { + font-family: Menlo, Monaco, "Courier New", monospace; +} +code { + padding: .25em .5em; + font-size: 85%; + color: #bf616a; + background-color: #f9f9f9; + border-radius: 3px; +} +pre { + display: block; + margin-top: 0; + margin-bottom: 1rem; + padding: 1rem; + font-size: .8rem; + line-height: 1.4; + white-space: pre; + white-space: pre-wrap; + word-break: break-all; + word-wrap: break-word; + background-color: #f9f9f9; +} +pre code { + padding: 0; + font-size: 100%; + color: inherit; + background-color: transparent; +} + +/* Pygments via Jekyll */ +.highlight { + margin-bottom: 1rem; + border-radius: 4px; +} +.highlight pre { + margin-bottom: 0; +} + +/* Gist via GitHub Pages */ +.gist .gist-file { + font-family: Menlo, Monaco, "Courier New", monospace !important; +} +.gist .markdown-body { + padding: 15px; +} +.gist pre { + padding: 0; + background-color: transparent; +} +.gist .gist-file .gist-data { + font-size: .8rem !important; + line-height: 1.4; +} +.gist code { + padding: 0; + color: inherit; + background-color: transparent; + border-radius: 0; +} + +/* Quotes */ +blockquote { + padding: .5rem 1rem; + margin: .8rem 0; + color: #7a7a7a; + border-left: .25rem solid #e5e5e5; +} +blockquote p:last-child { + margin-bottom: 0; +} +@media (min-width: 30em) { + blockquote { + padding-right: 5rem; + padding-left: 1.25rem; + } +} + +img { + display: block; + max-width: 100%; + margin: 0 0 1rem; + border-radius: 5px; +} + +/* Tables */ +table { + margin-bottom: 1rem; + width: 100%; + border: 1px solid #e5e5e5; + border-collapse: collapse; +} +td, +th { + padding: .25rem .5rem; + border: 1px solid #e5e5e5; +} +tbody tr:nth-child(odd) td, +tbody tr:nth-child(odd) th { + background-color: #f9f9f9; +} + + +/* + * Custom type + * + * Extend paragraphs with `.lead` for larger introductory text. + */ + +.lead { + font-size: 1.25rem; + font-weight: 300; +} + + +/* + * Messages + * + * Show alert messages to users. You may add it to single elements like a `

`, + * or to a parent if there are multiple elements to show. + */ + +.message { + margin-bottom: 1rem; + padding: 1rem; + color: #717171; + background-color: #f9f9f9; +} + + +/* + * Container + * + * Center the page content. + */ + +.container { + max-width: 48rem; + padding-left: 1rem; + padding-right: 1rem; + margin-left: auto; + margin-right: auto; +} + + +/* + * Masthead + * + * Super small header above the content for site name and short description. + */ + +.masthead { + padding-top: 1rem; + padding-bottom: 1rem; + margin-bottom: 3rem; +} +.masthead-title { + margin-top: 0; + margin-bottom: 0; + color: #505050; +} +.masthead-title a { + color: #505050; +} +.masthead-title small { + font-size: 75%; + font-weight: 400; + color: #c0c0c0; + letter-spacing: 0; +} + + +/* + * Posts and pages + * + * Each post is wrapped in `.post` and is used on default and post layouts. Each + * page is wrapped in `.page` and is only used on the page layout. + */ + +.page, +.post { + margin-bottom: 4em; +} + +/* Blog post or page title */ +.page-title, +.post-title, +.post-title a { + color: #303030; +} +.page-title, +.post-title { + margin-top: 0; +} + +/* Meta data line below post title */ +.post-date { + display: block; + margin-top: -.5rem; + margin-bottom: 1rem; + color: #9a9a9a; +} + +/* Related posts */ +.related { + padding-top: 2rem; + padding-bottom: 2rem; + border-top: 1px solid #eee; +} +.related-posts { + padding-left: 0; + list-style: none; +} +.related-posts h3 { + margin-top: 0; +} +.related-posts li small { + font-size: 75%; + color: #999; +} +.related-posts li a:hover { + color: #268bd2; + text-decoration: none; +} +.related-posts li a:hover small { + color: inherit; +} + + +/* + * Pagination + * + * Super lightweight (HTML-wise) blog pagination. `span`s are provide for when + * there are no more previous or next posts to show. + */ + +.pagination { + overflow: hidden; /* clearfix */ + margin-left: -1rem; + margin-right: -1rem; + font-family: "PT Sans", Helvetica, Arial, sans-serif; + color: #ccc; + text-align: center; +} + +/* Pagination items can be `span`s or `a`s */ +.pagination-item { + display: block; + padding: 1rem; + border: 1px solid #eee; +} +.pagination-item:first-child { + margin-bottom: -1px; +} + +/* Only provide a hover state for linked pagination items */ +a.pagination-item:hover { + background-color: #f5f5f5; +} + +@media (min-width: 30em) { + .pagination { + margin: 3rem 0; + } + .pagination-item { + float: left; + width: 50%; + } + .pagination-item:first-child { + margin-bottom: 0; + border-top-left-radius: 4px; + border-bottom-left-radius: 4px; + } + .pagination-item:last-child { + margin-left: -1px; + border-top-right-radius: 4px; + border-bottom-right-radius: 4px; + } +} diff --git a/public/css/syntax.css b/public/css/syntax.css new file mode 100644 index 0000000..15ad797 --- /dev/null +++ b/public/css/syntax.css @@ -0,0 +1,65 @@ +.highlight .hll { background-color: #ffc; } +.highlight .c { color: #999; } /* Comment */ +.highlight .err { color: #a00; background-color: #faa } /* Error */ +.highlight .k { color: #069; } /* Keyword */ +.highlight .o { color: #555 } /* Operator */ +.highlight .cm { color: #09f; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #099 } /* Comment.Preproc */ +.highlight .c1 { color: #999; } /* Comment.Single */ +.highlight .cs { color: #999; } /* Comment.Special */ +.highlight .gd { background-color: #fcc; border: 1px solid #c00 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .gr { color: #f00 } /* Generic.Error */ +.highlight .gh { color: #030; } /* Generic.Heading */ +.highlight .gi { background-color: #cfc; border: 1px solid #0c0 } /* Generic.Inserted */ +.highlight .go { color: #aaa } /* Generic.Output */ +.highlight .gp { color: #009; } /* Generic.Prompt */ +.highlight .gs { } /* Generic.Strong */ +.highlight .gu { color: #030; } /* Generic.Subheading */ +.highlight .gt { color: #9c6 } /* Generic.Traceback */ +.highlight .kc { color: #069; } /* Keyword.Constant */ +.highlight .kd { color: #069; } /* Keyword.Declaration */ +.highlight .kn { color: #069; } /* Keyword.Namespace */ +.highlight .kp { color: #069 } /* Keyword.Pseudo */ +.highlight .kr { color: #069; } /* Keyword.Reserved */ +.highlight .kt { color: #078; } /* Keyword.Type */ +.highlight .m { color: #f60 } /* Literal.Number */ +.highlight .s { color: #d44950 } /* Literal.String */ +.highlight .na { color: #4f9fcf } /* Name.Attribute */ +.highlight .nb { color: #366 } /* Name.Builtin */ +.highlight .nc { color: #0a8; } /* Name.Class */ +.highlight .no { color: #360 } /* Name.Constant */ +.highlight .nd { color: #99f } /* Name.Decorator */ +.highlight .ni { color: #999; } /* Name.Entity */ +.highlight .ne { color: #c00; } /* Name.Exception */ +.highlight .nf { color: #c0f } /* Name.Function */ +.highlight .nl { color: #99f } /* Name.Label */ +.highlight .nn { color: #0cf; } /* Name.Namespace */ +.highlight .nt { color: #2f6f9f; } /* Name.Tag */ +.highlight .nv { color: #033 } /* Name.Variable */ +.highlight .ow { color: #000; } /* Operator.Word */ +.highlight .w { color: #bbb } /* Text.Whitespace */ +.highlight .mf { color: #f60 } /* Literal.Number.Float */ +.highlight .mh { color: #f60 } /* Literal.Number.Hex */ +.highlight .mi { color: #f60 } /* Literal.Number.Integer */ +.highlight .mo { color: #f60 } /* Literal.Number.Oct */ +.highlight .sb { color: #c30 } /* Literal.String.Backtick */ +.highlight .sc { color: #c30 } /* Literal.String.Char */ +.highlight .sd { color: #c30; font-style: italic } /* Literal.String.Doc */ +.highlight .s2 { color: #c30 } /* Literal.String.Double */ +.highlight .se { color: #c30; } /* Literal.String.Escape */ +.highlight .sh { color: #c30 } /* Literal.String.Heredoc */ +.highlight .si { color: #a00 } /* Literal.String.Interpol */ +.highlight .sx { color: #c30 } /* Literal.String.Other */ +.highlight .sr { color: #3aa } /* Literal.String.Regex */ +.highlight .s1 { color: #c30 } /* Literal.String.Single */ +.highlight .ss { color: #fc3 } /* Literal.String.Symbol */ +.highlight .bp { color: #366 } /* Name.Builtin.Pseudo */ +.highlight .vc { color: #033 } /* Name.Variable.Class */ +.highlight .vg { color: #033 } /* Name.Variable.Global */ +.highlight .vi { color: #033 } /* Name.Variable.Instance */ +.highlight .il { color: #f60 } /* Literal.Number.Integer.Long */ + +.css .o, +.css .o + .nt, +.css .nt + .nt { color: #999; }