Commit cd90fd19 authored by Julius Hossain's avatar Julius Hossain

Merge branch 'master' of...

Merge branch 'master' of git.embl.de:grp-bio-it/image-analysis-training-resources into binarization_julius
parents d935c771 b2f48e34
Pipeline #9756 passed with stage
in 31 seconds
File deleted
*.DS_Store
image: ruby:2.3
variables:
JEKYLL_ENV: production
LC_ALL: C.UTF-8
before_script:
- bundle install
test:
stage: test
script:
- bundle exec jekyll build -d test
artifacts:
paths:
- test
pages:
stage: deploy
script:
- bundle exec jekyll build -d public
artifacts:
paths:
- public
only:
- jekyll
- master
source "https://rubygems.org"
ruby RUBY_VERSION
# This will help ensure the proper Jekyll version is running.
gem "jekyll", "3.4.0"
# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
title: Image Analysis Training
email: image-analysis-support@embl.de
description: > # this means to ignore newlines until "baseurl:"
A collection of material for teaching image analysis.
Includes concept maps, exercises, example data
baseurl: "/image-analysis-training-resources" # the subpath of your site, e.g. /blog
url: "https://grp-bio-it.embl-community.io/" # the base hostname & protocol for your site
# Build settings
markdown: kramdown
exclude: ["README.md", "CONTRIBUTING.md", "TEACHING.md"]
<footer class="site-footer">
<div class="wrapper">
<h2 class="footer-heading">{{ site.title }}</h2>
<div class="footer-col-wrapper">
<div class="footer-col footer-col-1">
<ul class="contact-list">
<li>{{ site.title }}</li>
<li><a href="mailto:{{ site.email }}">{{ site.email }}</a></li>
</ul>
</div>
<div class="footer-col footer-col-2">
<ul class="social-media-list">
{% if site.github_username %}
<li>
{% include icon-github.html username=site.github_username %}
</li>
{% endif %}
{% if site.twitter_username %}
<li>
{% include icon-twitter.html username=site.twitter_username %}
</li>
{% endif %}
</ul>
</div>
<div class="footer-col footer-col-3">
<p>{{ site.description }}</p>
<p>Use of this site falls under <a href="https://www.embl.de/aboutus/privacy_policy/index.html">EMBL's Privacy Policy</a>.</p>
</div>
</div>
</div>
</footer>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>{% if page.title %}{{ page.title | escape }}{% else %}{{ site.title | escape }}{% endif %}</title>
<meta name="description" content="{% if page.excerpt %}{{ page.excerpt | strip_html | strip_newlines | truncate: 160 }}{% else %}{{ site.description }}{% endif %}">
<link rel="stylesheet" href="{{ "/css/main.css" | prepend: site.baseurl }}">
<link rel="canonical" href="{{ page.url | replace:'index.html','' | prepend: site.baseurl | prepend: site.url }}">
<link rel="alternate" type="application/rss+xml" title="{{ site.title }}" href="{{ "/feed.xml" | prepend: site.baseurl | prepend: site.url }}">
</head>
<header class="site-header">
<div class="wrapper">
<a class="site-title" href="{{ site.baseurl }}/">{{ site.title }}</a>
<nav class="site-nav">
<a href="#" class="menu-icon">
<svg viewBox="0 0 18 15">
<path fill="#424242" d="M18,1.484c0,0.82-0.665,1.484-1.484,1.484H1.484C0.665,2.969,0,2.304,0,1.484l0,0C0,0.665,0.665,0,1.484,0 h15.031C17.335,0,18,0.665,18,1.484L18,1.484z"/>
<path fill="#424242" d="M18,7.516C18,8.335,17.335,9,16.516,9H1.484C0.665,9,0,8.335,0,7.516l0,0c0-0.82,0.665-1.484,1.484-1.484 h15.031C17.335,6.031,18,6.696,18,7.516L18,7.516z"/>
<path fill="#424242" d="M18,13.516C18,14.335,17.335,15,16.516,15H1.484C0.665,15,0,14.335,0,13.516l0,0 c0-0.82,0.665-1.484,1.484-1.484h15.031C17.335,12.031,18,12.696,18,13.516L18,13.516z"/>
</svg>
</a>
<div class="trigger">
{% for my_page in site.pages %}
{% if my_page.title %}
<a class="page-link" href="{{ my_page.url | prepend: site.baseurl }}">{{ my_page.title }}</a>
{% endif %}
{% endfor %}
</div>
</nav>
</div>
</header>
<a href="https://github.com/{{ include.username }}"><span class="icon icon--github">{% include icon-github.svg %}</span><span class="username">{{ include.username }}</span></a>
<svg viewBox="0 0 16 16"><path fill="#828282" d="M7.999,0.431c-4.285,0-7.76,3.474-7.76,7.761 c0,3.428,2.223,6.337,5.307,7.363c0.388,0.071,0.53-0.168,0.53-0.374c0-0.184-0.007-0.672-0.01-1.32 c-2.159,0.469-2.614-1.04-2.614-1.04c-0.353-0.896-0.862-1.135-0.862-1.135c-0.705-0.481,0.053-0.472,0.053-0.472 c0.779,0.055,1.189,0.8,1.189,0.8c0.692,1.186,1.816,0.843,2.258,0.645c0.071-0.502,0.271-0.843,0.493-1.037 C4.86,11.425,3.049,10.76,3.049,7.786c0-0.847,0.302-1.54,0.799-2.082C3.768,5.507,3.501,4.718,3.924,3.65 c0,0,0.652-0.209,2.134,0.796C6.677,4.273,7.34,4.187,8,4.184c0.659,0.003,1.323,0.089,1.943,0.261 c1.482-1.004,2.132-0.796,2.132-0.796c0.423,1.068,0.157,1.857,0.077,2.054c0.497,0.542,0.798,1.235,0.798,2.082 c0,2.981-1.814,3.637-3.543,3.829c0.279,0.24,0.527,0.713,0.527,1.437c0,1.037-0.01,1.874-0.01,2.129 c0,0.208,0.14,0.449,0.534,0.373c3.081-1.028,5.302-3.935,5.302-7.362C15.76,3.906,12.285,0.431,7.999,0.431z"/></svg>
<a href="https://twitter.com/{{ include.username }}"><span class="icon icon--twitter">{% include icon-twitter.svg %}</span><span class="username">{{ include.username }}</span></a>
<svg viewBox="0 0 16 16"><path fill="#828282" d="M15.969,3.058c-0.586,0.26-1.217,0.436-1.878,0.515c0.675-0.405,1.194-1.045,1.438-1.809c-0.632,0.375-1.332,0.647-2.076,0.793c-0.596-0.636-1.446-1.033-2.387-1.033c-1.806,0-3.27,1.464-3.27,3.27 c0,0.256,0.029,0.506,0.085,0.745C5.163,5.404,2.753,4.102,1.14,2.124C0.859,2.607,0.698,3.168,0.698,3.767 c0,1.134,0.577,2.135,1.455,2.722C1.616,6.472,1.112,6.325,0.671,6.08c0,0.014,0,0.027,0,0.041c0,1.584,1.127,2.906,2.623,3.206 C3.02,9.402,2.731,9.442,2.433,9.442c-0.211,0-0.416-0.021-0.615-0.059c0.416,1.299,1.624,2.245,3.055,2.271 c-1.119,0.877-2.529,1.4-4.061,1.4c-0.264,0-0.524-0.015-0.78-0.046c1.447,0.928,3.166,1.469,5.013,1.469 c6.015,0,9.304-4.983,9.304-9.304c0-0.142-0.003-0.283-0.009-0.423C14.976,4.29,15.531,3.714,15.969,3.058z"/></svg>
<!DOCTYPE html>
<html>
{% include head.html %}
<body>
{% include header.html %}
<div class="page-content">
<div class="wrapper">
{{ content }}
</div>
</div>
{% include footer.html %}
</body>
</html>
---
layout: default
---
<article class="post">
<header class="post-header">
<h1 class="post-title">{{ page.title }}</h1>
</header>
<div class="post-content">
{{ content }}
</div>
</article>
/**
* Reset some basic elements
*/
body, h1, h2, h3, h4, h5, h6,
p, blockquote, pre, hr,
dl, dd, ol, ul, figure {
margin: 0;
padding: 0;
}
/**
* Basic styling
*/
body {
font: $base-font-weight #{$base-font-size}/#{$base-line-height} $base-font-family;
color: $text-color;
background-color: $background-color;
-webkit-text-size-adjust: 100%;
-webkit-font-feature-settings: "kern" 1;
-moz-font-feature-settings: "kern" 1;
-o-font-feature-settings: "kern" 1;
font-feature-settings: "kern" 1;
font-kerning: normal;
}
/**
* Set `margin-bottom` to maintain vertical rhythm
*/
h1, h2, h3, h4, h5, h6,
p, blockquote, pre,
ul, ol, dl, figure,
%vertical-rhythm {
margin-bottom: $spacing-unit / 2;
}
/**
* Images
*/
img {
max-width: 100%;
vertical-align: middle;
}
/**
* Figures
*/
figure > img {
display: block;
}
figcaption {
font-size: $small-font-size;
}
/**
* Lists
*/
ul, ol {
margin-left: $spacing-unit;
}
li {
> ul,
> ol {
margin-bottom: 0;
}
}
/**
* Headings
*/
h1, h2, h3, h4, h5, h6 {
font-weight: $base-font-weight;
}
/**
* Links
*/
a {
color: $brand-color;
text-decoration: none;
&:visited {
color: darken($brand-color, 15%);
}
&:hover {
color: $text-color;
text-decoration: underline;
}
}
/**
* Blockquotes
*/
blockquote {
color: $grey-color;
border-left: 4px solid $grey-color-light;
padding-left: $spacing-unit / 2;
font-size: 18px;
letter-spacing: -1px;
font-style: italic;
> :last-child {
margin-bottom: 0;
}
}
/**
* Code formatting
*/
pre,
code {
font-size: 15px;
border: 1px solid $grey-color-light;
border-radius: 3px;
background-color: #eef;
}
code {
padding: 1px 5px;
}
pre {
padding: 8px 12px;
overflow-x: auto;
> code {
border: 0;
padding-right: 0;
padding-left: 0;
}
}
/**
* Wrapper
*/
.wrapper {
max-width: -webkit-calc(#{$content-width} - (#{$spacing-unit} * 2));
max-width: calc(#{$content-width} - (#{$spacing-unit} * 2));
margin-right: auto;
margin-left: auto;
padding-right: $spacing-unit;
padding-left: $spacing-unit;
@extend %clearfix;
@include media-query($on-laptop) {
max-width: -webkit-calc(#{$content-width} - (#{$spacing-unit}));
max-width: calc(#{$content-width} - (#{$spacing-unit}));
padding-right: $spacing-unit / 2;
padding-left: $spacing-unit / 2;
}
}
/**
* Clearfix
*/
%clearfix {
&:after {
content: "";
display: table;
clear: both;
}
}
/**
* Icons
*/
.icon {
> svg {
display: inline-block;
width: 16px;
height: 16px;
vertical-align: middle;
path {
fill: $grey-color;
}
}
}
/**
* Site header
*/
.site-header {
border-top: 5px solid $grey-color-dark;
border-bottom: 1px solid $grey-color-light;
min-height: 56px;
// Positioning context for the mobile navigation icon
position: relative;
}
.site-title {
font-size: 26px;
font-weight: 300;
line-height: 56px;
letter-spacing: -1px;
margin-bottom: 0;
float: left;
&,
&:visited {
color: $grey-color-dark;
}
}
.site-nav {
float: right;
line-height: 56px;
.menu-icon {
display: none;
}
.page-link {
color: $text-color;
line-height: $base-line-height;
// Gaps between nav items, but not on the last one
&:not(:last-child) {
margin-right: 20px;
}
}
@include media-query($on-palm) {
position: absolute;
top: 9px;
right: $spacing-unit / 2;
background-color: $background-color;
border: 1px solid $grey-color-light;
border-radius: 5px;
text-align: right;
.menu-icon {
display: block;
float: right;
width: 36px;
height: 26px;
line-height: 0;
padding-top: 10px;
text-align: center;
> svg {
width: 18px;
height: 15px;
path {
fill: $grey-color-dark;
}
}
}
.trigger {
clear: both;
display: none;
}
&:hover .trigger {
display: block;
padding-bottom: 5px;
}
.page-link {
display: block;
padding: 5px 10px;
&:not(:last-child) {
margin-right: 0;
}
margin-left: 20px;
}
}
}
/**
* Site footer
*/
.site-footer {
border-top: 1px solid $grey-color-light;
padding: $spacing-unit 0;
}
.footer-heading {
font-size: 18px;
margin-bottom: $spacing-unit / 2;
}
.contact-list,
.social-media-list {
list-style: none;
margin-left: 0;
}
.footer-col-wrapper {
font-size: 15px;
color: $grey-color;
margin-left: -$spacing-unit / 2;
@extend %clearfix;
}
.footer-col {
float: left;
margin-bottom: $spacing-unit / 2;
padding-left: $spacing-unit / 2;
}
.footer-col-1 {
width: -webkit-calc(35% - (#{$spacing-unit} / 2));
width: calc(35% - (#{$spacing-unit} / 2));
}
.footer-col-2 {
width: -webkit-calc(20% - (#{$spacing-unit} / 2));
width: calc(20% - (#{$spacing-unit} / 2));
}
.footer-col-3 {
width: -webkit-calc(45% - (#{$spacing-unit} / 2));
width: calc(45% - (#{$spacing-unit} / 2));
}
@include media-query($on-laptop) {
.footer-col-1,
.footer-col-2 {
width: -webkit-calc(50% - (#{$spacing-unit} / 2));
width: calc(50% - (#{$spacing-unit} / 2));
}
.footer-col-3 {
width: -webkit-calc(100% - (#{$spacing-unit} / 2));
width: calc(100% - (#{$spacing-unit} / 2));
}
}
@include media-query($on-palm) {
.footer-col {
float: none;
width: -webkit-calc(100% - (#{$spacing-unit} / 2));
width: calc(100% - (#{$spacing-unit} / 2));
}
}
/**
* Page content
*/
.page-content {
padding: $spacing-unit 0;
}
.page-heading {
font-size: 20px;
}
.post-list {
margin-left: 0;
list-style: none;
> li {
margin-bottom: $spacing-unit;
}
}
.post-meta {
font-size: $small-font-size;
color: $grey-color;
}
.post-link {
display: block;
font-size: 24px;
}
/**
* Posts
*/
.post-header {
margin-bottom: $spacing-unit;
}
.post-title {
font-size: 42px;
letter-spacing: -1px;
line-height: 1;
@include media-query($on-laptop) {
font-size: 36px;
}
}
.post-content {
margin-bottom: $spacing-unit;
h2 {
font-size: 32px;
@include media-query($on-laptop) {
font-size: 28px;
}
}
h3 {
font-size: 26px;
@include media-query($on-laptop) {
font-size: 22px;
}
}
h4 {
font-size: 20px;
@include media-query($on-laptop) {
font-size: 18px;
}
}
}
/**
* Syntax highlighting styles
*/
.highlight {
background: #fff;
@extend %vertical-rhythm;
.highlighter-rouge & {
background: #eef;
}
.c { color: #998; font-style: italic } // Comment
.err { color: #a61717; background-color: #e3d2d2 } // Error
.k { font-weight: bold } // Keyword
.o { font-weight: bold } // Operator
.cm { color: #998; font-style: italic } // Comment.Multiline
.cp { color: #999; font-weight: bold } // Comment.Preproc
.c1 { color: #998; font-style: italic } // Comment.Single
.cs { color: #999; font-weight: bold; font-style: italic } // Comment.Special
.gd { color: #000; background-color: #fdd } // Generic.Deleted
.gd .x { color: #000; background-color: #faa } // Generic.Deleted.Specific
.ge { font-style: italic } // Generic.Emph
.gr { color: #a00 } // Generic.Error
.gh { color: #999 } // Generic.Heading
.gi { color: #000; background-color: #dfd } // Generic.Inserted
.gi .x { color: #000; background-color: #afa } // Generic.Inserted.Specific
.go { color: #888 } // Generic.Output
.gp { color: #555 } // Generic.Prompt
.gs { font-weight: bold } // Generic.Strong
.gu { color: #aaa } // Generic.Subheading
.gt { color: #a00 } // Generic.Traceback
.kc { font-weight: bold } // Keyword.Constant
.kd { font-weight: bold } // Keyword.Declaration
.kp { font-weight: bold } // Keyword.Pseudo
.kr { font-weight: bold } // Keyword.Reserved
.kt { color: #458; font-weight: bold } // Keyword.Type
.m { color: #099 } // Literal.Number
.s { color: #d14 } // Literal.String
.na { color: #008080 } // Name.Attribute
.nb { color: #0086B3 } // Name.Builtin
.nc { color: #458; font-weight: bold } // Name.Class
.no { color: #008080 } // Name.Constant
.ni { color: #800080 } // Name.Entity
.ne { color: #900; font-weight: bold } // Name.Exception
.nf { color: #900; font-weight: bold } // Name.Function
.nn { color: #555 } // Name.Namespace
.nt { color: #000080 } // Name.Tag
.nv { color: #008080 } // Name.Variable
.ow { font-weight: bold } // Operator.Word
.w { color: #bbb } // Text.Whitespace
.mf { color: #099 } // Literal.Number.Float
.mh { color: #099 } // Literal.Number.Hex
.mi { color: #099 } // Literal.Number.Integer
.mo { color: #099 } // Literal.Number.Oct
.sb { color: #d14 } // Literal.String.Backtick
.sc { color: #d14 } // Literal.String.Char
.sd { color: #d14 } // Literal.String.Doc
.s2 { color: #d14 } // Literal.String.Double
.se { color: #d14 } // Literal.String.Escape
.sh { color: #d14 } // Literal.String.Heredoc
.si { color: #d14 } // Literal.String.Interpol
.sx { color: #d14 } // Literal.String.Other
.sr { color: #009926 } // Literal.String.Regex
.s1 { color: #d14 } // Literal.String.Single
.ss { color: #990073 } // Literal.String.Symbol
.bp { color: #999 } // Name.Builtin.Pseudo
.vc { color: #008080 } // Name.Variable.Class
.vg { color: #008080 } // Name.Variable.Global
.vi { color: #008080 } // Name.Variable.Instance
.il { color: #099 } // Literal.Number.Integer.Long
}
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