Replicate infrastructure from Day 1

.gitignore

@@ -0,0 +1,15 @@
+*.pyc
+*~
+.DS_Store
+.ipynb
+.ipynb_checkpoints
+.sass-cache
+.jekyll-cache/
+__pycache__
+_site
+.Rproj.user
+.Rhistory
+.RData
+.idea/
+_site/
+venv/

Makefile

@@ -7,6 +7,10 @@ JEKYLL=jekyll
 JEKYLL_VERSION=3.8.5
 PARSER=bin/markdown_ast.rb
 DST=_site
+SLIDES_DIR=slides
+SLIDES_MD=$(wildcard $(SLIDES_DIR)/[0-9][0-9]-*.md)
+SLIDES_HTML=$(patsubst %.md, %.html, $(SLIDES_MD))
+SLIDES_THEME=white
 
 # Controls
 .PHONY : commands clean files
@@ -22,11 +26,11 @@ docker-serve :
 	docker run --rm -it -v ${PWD}:/srv/jekyll -p 127.0.0.1:4000:4000 jekyll/jekyll:${JEKYLL_VERSION} make serve
 
 ## serve            : run a local server.
-serve : lesson-md
+serve : lesson-md slides
 	${JEKYLL} serve
 
 ## site             : build files but do not run a server.
-site : lesson-md
+site : lesson-md slides
 	${JEKYLL} build
 
 # repo-check        : check repository settings.
@@ -38,6 +42,8 @@ clean :
 	@rm -rf ${DST}
 	@rm -rf .sass-cache
 	@rm -rf bin/__pycache__
+	@rm -f ${SLIDES_HTML}
+	@rm -f ${SLIDES_DIR}/index.html
 	@find . -name .DS_Store -exec rm {} \;
 	@find . -name '*~' -exec rm {} \;
 	@find . -name '*.pyc' -exec rm {} \;
@@ -119,3 +125,23 @@ lesson-fixme :
 #-------------------------------------------------------------------------------
 
 -include commands.mk
+
+.PHONY: slides
+slides: $(SLIDES_HTML) $(SLIDES_DIR)/index.html
+
+$(SLIDES_DIR)/index.html: $(SLIDES_DIR)/index.md
+	@cd $(SLIDES_DIR)
+	pandoc $< -o $@ -s
+	@cd ..
+
+$(SLIDES_DIR)/%.html: $(SLIDES_DIR)/%.md
+	@cd $(SLIDES_DIR)
+	pandoc -t revealjs -s -o $@ $< -V theme=$(SLIDES_THEME)
+	@cd ..
+
+.PHONY: variables
+variables:
+	@echo SLDIES_MD: $(SLIDES_MD)
+	@echo SLIDES_HTML: $(SLIDES_HTML)
+	@echo THEME: $(THEME)
+

_config.yml

@@ -29,7 +29,7 @@ kind: "lesson"
 repository: <USERNAME>/<PROJECT>
 
 # Email address, no mailto:
-email: "[email protected]"
+email: "[email protected]"
 
 # Sites.
 amy_site: "https://amy.software-carpentry.org/workshops"
@@ -62,7 +62,7 @@ instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post
 
 
 # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
-start_time: 0
+start_time: 570
 
 # Specify that things in the episodes collection should be output.
 collections:
@@ -96,6 +96,7 @@ exclude:
   - Makefile
   - bin/
   - .Rproj.user/
+  - venv/
 
 # Turn on built-in syntax highlighting.
 highlighter: rouge

_includes/carpentries.html

@@ -27,7 +27,7 @@
 </div>
 <div class="row">
   <div class="col-md-2" align="center">
-    <a href="{{ site.swc_site }}"><img src="{{ relative_root_path }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" /></a>
+    <a href="{{ site.swc_site }}"><img src="{{ relative_root_path }}/assets/img/sabs-logo.png" alt="Software Carpentry logo" /></a>
   </div>
   <div class="col-md-8">
      <p>Since 1998, <a href="{{ site.swc_site }}">Software Carpentry</a> has

_includes/lesson_footer.html

@@ -7,39 +7,17 @@
 <footer>
   <div class="row">
     <div class="col-md-6 copyright" align="left">
+<!--
 	{% if site.carpentry == "swc" %}
 	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
 	by <a href="{{ site.carpentries_site }}">The Carpentries</a>
         <br>
         Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
 	by <a href="{{ site.swc_site }}">Software Carpentry Foundation</a>
-	{% elsif site.carpentry == "dc" %}
-	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
-	by <a href="{{ site.carpentries_site }}">The Carpentries</a>
-        <br>
-        Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
-	by <a href="{{ site.dc_site }}">Data Carpentry</a>
-	{% elsif site.carpentry == "lc" %}
-	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–{{ 'now' | date: "%Y" }}
-	by <a href="{{ site.lc_site }}">Library Carpentry</a>
-	{% elsif site.carpentry == "cp" %}
-	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
-	by <a href="{{ site.carpentries_site }}">The Carpentries</a>
 	{% endif %}
+-->
     </div>
     <div class="col-md-6 help-links" align="right">
-	{% if page.source %}
-	{% if page.source == "Rmd" %}
-	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Edit on GitHub</a>
-	{% endif %}
-	{% else %}
-	<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit on GitHub</a>
-	{% endif %}
-	/
-	<a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md" data-checker-ignore>Contributing</a>
-	/
-	<a href="{{ repo_url }}/">Source</a>
-	/
 	<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a>
 	/
 	<a href="mailto:{{ site.email }}">Contact</a>

_includes/navbar.html

@@ -17,7 +17,7 @@
       {% comment %} Select what logo to display. {% endcomment %}
       {% if site.carpentry == "swc" %}
       <a href="{{ site.swc_site }}" class="pull-left">
-        <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/swc-icon-blue.svg %}" alt="Software Carpentry logo" />
+        <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/sabs-logo.png %}" alt="Software Carpentry logo" />
       </a>
       {% elsif site.carpentry == "dc" %}
       <a href="{{ site.dc_site }}" class="pull-left">
@@ -75,13 +75,6 @@
 
 	{% comment %} Always show license. {% endcomment %}
         <li><a href="{{ relative_root_path }}{% link LICENSE.md %}">License</a></li>
-	{% if page.source %}
-	{% if page.source == "Rmd" %}
-	<li><a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
-	{% endif %}
-	{% else %}
-	<li><a href="{{repo_url}}/edit/{{ default_branch}}/{{page.path}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
-	{% endif %}
       </ul>
       <form class="navbar-form navbar-right" role="search" id="search" onsubmit="google_search(); return false;">
         <div class="form-group">

assets/css/lesson.scss

@@ -205,8 +205,8 @@ footer .help-links
 }
 
 img.navbar-logo {
-  height: 40px; // synchronize with height of navbar
-  padding-top: 5px;
+  height: 50px; // synchronize with height of navbar
+  padding-top: 2px;
   padding-right: 10px;
 }
 

index.md

@@ -14,4 +14,7 @@ FIXME: home page introduction
 > FIXME
 {: .prereq}
 
+# Slides
+Slides are accessible [here](/slides/index.html).
+
 {% include links.md %}

slides/01-introduction.html

@@ -0,0 +1,67 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <meta charset="utf-8">
+  <meta name="generator" content="pandoc">
+  <meta name="author" content="SSI">
+  <title>SABS</title>
+  <meta name="apple-mobile-web-app-capable" content="yes">
+  <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
+  <link rel="stylesheet" href="reveal.js/css/reveal.css">
+  <style type="text/css">
+      code{white-space: pre-wrap;}
+      span.smallcaps{font-variant: small-caps;}
+      span.underline{text-decoration: underline;}
+      div.column{display: inline-block; vertical-align: top; width: 50%;}
+  </style>
+  <link rel="stylesheet" href="reveal.js/css/theme/white.css" id="theme">
+  <!-- Printing and PDF exports -->
+  <script>
+    var link = document.createElement( 'link' );
+    link.rel = 'stylesheet';
+    link.type = 'text/css';
+    link.href = window.location.search.match( /print-pdf/gi ) ? 'reveal.js/css/print/pdf.css' : 'reveal.js/css/print/paper.css';
+    document.getElementsByTagName( 'head' )[0].appendChild( link );
+  </script>
+  <!--[if lt IE 9]>
+  <script src="reveal.js/lib/js/html5shiv.js"></script>
+  <![endif]-->
+</head>
+<body>
+  <div class="reveal">
+    <div class="slides">
+
+<section id="title-slide">
+  <h1 class="title">SABS</h1>
+  <p class="author">SSI</p>
+</section>
+
+<section id="day-2-intro" class="slide level1">
+<h1>Day 2 intro</h1>
+<p>Introduction</p>
+</section>
+    </div>
+  </div>
+
+  <script src="reveal.js/lib/js/head.min.js"></script>
+  <script src="reveal.js/js/reveal.js"></script>
+
+  <script>
+
+      // Full list of configuration options available at:
+      // https://github.com/hakimel/reveal.js#configuration
+      Reveal.initialize({
+        // Push each slide change to the browser history
+        history: true,
+
+        // Optional reveal.js plugins
+        dependencies: [
+          { src: 'reveal.js/lib/js/classList.js', condition: function() { return !document.body.classList; } },
+          { src: 'reveal.js/plugin/zoom-js/zoom.js', async: true },
+          { src: 'reveal.js/plugin/notes/notes.js', async: true }
+        ]
+      });
+    </script>
+    </body>
+</html>

slides/01-introduction.md

@@ -0,0 +1,5 @@
+% SABS
+% SSI
+
+# Day 2 intro
+Introduction

slides/index.html

@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
+<head>
+  <meta charset="utf-8" />
+  <meta name="generator" content="pandoc" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+  <title>Slides</title>
+  <style type="text/css">
+      code{white-space: pre-wrap;}
+      span.smallcaps{font-variant: small-caps;}
+      span.underline{text-decoration: underline;}
+      div.column{display: inline-block; vertical-align: top; width: 50%;}
+  </style>
+  <!--[if lt IE 9]>
+    <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
+  <![endif]-->
+</head>
+<body>
+<header>
+<h1 class="title">Slides</h1>
+</header>
+<ul>
+<li><a href="01-introduction.html">01 Introduction</a></li>
+</ul>
+</body>
+</html>

slides/index.md

@@ -0,0 +1,3 @@
+% Slides
+
+- [01 Introduction](01-introduction.html)

slides/reveal.js/.gitignore

@@ -0,0 +1,13 @@
+.idea/
+*.iml
+*.iws
+*.eml
+out/
+.DS_Store
+.svn
+log/*.log
+tmp/**
+node_modules/
+.sass-cache
+css/reveal.min.css
+js/reveal.min.js

slides/reveal.js/.travis.yml

@@ -0,0 +1,5 @@
+language: node_js
+node_js:
+  - 11
+after_script:
+  - npm run build -- retire

slides/reveal.js/CONTRIBUTING.md

@@ -0,0 +1,23 @@
+## Contributing
+
+Please keep the [issue tracker](http://github.com/hakimel/reveal.js/issues) limited to **bug reports**, **feature requests** and **pull requests**.
+
+
+### Personal Support
+If you have personal support or setup questions the best place to ask those are [StackOverflow](http://stackoverflow.com/questions/tagged/reveal.js).
+
+
+### Bug Reports
+When reporting a bug make sure to include information about which browser and operating system you are on as well as the necessary steps to reproduce the issue. If possible please include a link to a sample presentation where the bug can be tested.
+
+
+### Pull Requests
+- Should follow the coding style of the file you work in, most importantly:
+  - Tabs to indent
+  - Single-quoted strings
+- Should be made towards the **dev branch**
+- Should be submitted from a feature/topic branch (not your master)
+
+
+### Plugins
+Please do not submit plugins as pull requests. They should be maintained in their own separate repository. More information here: https://github.com/hakimel/reveal.js/wiki/Plugin-Guidelines

slides/reveal.js/LICENSE

@@ -0,0 +1,19 @@
+Copyright (C) 2019 Hakim El Hattab, http://hakim.se, and reveal.js contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.