Carpentries style

.gitignore

@@ -2,3 +2,4 @@
 .sass-cache*
 Gemfile.lock
 _site*
+.travis.yml

.gitlab-ci.yml

 image: ruby:2.5
+
 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
+  - apt-get -y update
+  - apt-get install -y python3
+  - apt-get install -y python3-pip
+  - gem install json kramdown jekyll
+  - pip3 install pyyaml
 
 pages:
   stage: deploy
   script:
-    - bundle exec jekyll build -d public
+    - make --always-make site
   artifacts:
     paths:
     - public
   only:
     - master
+    - carpentries-style
+    - theme

AUTHORS

+FIXME: list authors' names and email addresses.
\ No newline at end of file

CITATION

+FIXME: describe how to cite this lesson.
\ No newline at end of file

CODE_OF_CONDUCT.md

+---
+layout: page
+title: "Contributor Code of Conduct"
+---
+As contributors and maintainers of this project,
+we pledge to follow the [Carpentry Code of Conduct][coc].
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by following our [reporting guidelines][coc-reporting].
+
+{% include links.md %}

Gemfile

-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]
-
-# install GH-flavoured MD plugin
-group :jekyll_plugins do
-  gem 'jekyll-commonmark-ghpages'
-end

Makefile

+## ========================================
+## Commands for both workshop and lesson websites.
+
+# Settings
+MAKEFILES=Makefile $(wildcard *.mk)
+JEKYLL=jekyll
+JEKYLL_VERSION=3.8.5
+PARSER=bin/markdown_ast.rb
+DST=public
+
+# Controls
+.PHONY : commands clean files
+.NOTPARALLEL:
+all : commands
+
+## commands         : show all commands.
+commands :
+	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
+
+## docker-serve     : use docker to build the site
+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
+	${JEKYLL} serve
+
+## site             : build files but do not run a server.
+site : lesson-md
+	${JEKYLL} build -d ${DST}
+
+# repo-check        : check repository settings.
+repo-check :
+	@bin/repo_check.py -s .
+
+## clean            : clean up junk files.
+clean :
+	@rm -rf ${DST}
+	@rm -rf .sass-cache
+	@rm -rf bin/__pycache__
+	@find . -name .DS_Store -exec rm {} \;
+	@find . -name '*~' -exec rm {} \;
+	@find . -name '*.pyc' -exec rm {} \;
+
+## clean-rmd        : clean intermediate R files (that need to be committed to the repo).
+clean-rmd :
+	@rm -rf ${RMD_DST}
+	@rm -rf fig/rmd-*
+
+## ----------------------------------------
+## Commands specific to workshop websites.
+
+.PHONY : workshop-check
+
+## workshop-check   : check workshop homepage.
+workshop-check :
+	@bin/workshop_check.py .
+
+## ----------------------------------------
+## Commands specific to lesson websites.
+
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+
+# RMarkdown files
+RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
+RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
+
+# Lesson source files in the order they appear in the navigation menu.
+MARKDOWN_SRC = \
+  index.md \
+  CODE_OF_CONDUCT.md \
+  setup.md \
+  $(sort $(wildcard _episodes/*.md)) \
+  reference.md \
+  $(sort $(wildcard _extras/*.md)) \
+  LICENSE.md
+
+# Generated lesson files in the order they appear in the navigation menu.
+HTML_DST = \
+  ${DST}/index.html \
+  ${DST}/conduct/index.html \
+  ${DST}/setup/index.html \
+  $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
+  ${DST}/reference/index.html \
+  $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
+  ${DST}/license/index.html
+
+## lesson-md        : convert Rmarkdown files to markdown
+lesson-md : ${RMD_DST}
+
+_episodes/%.md: _episodes_rmd/%.Rmd
+	@bin/knit_lessons.sh $< $@
+
+## lesson-check     : validate lesson Markdown.
+lesson-check : lesson-fixme
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
+
+## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
+lesson-check-all :
+	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
+
+## unittest         : run unit tests on checking tools.
+unittest :
+	@bin/test_lesson_check.py
+
+## lesson-files     : show expected names of generated files for debugging.
+lesson-files :
+	@echo 'RMD_SRC:' ${RMD_SRC}
+	@echo 'RMD_DST:' ${RMD_DST}
+	@echo 'MARKDOWN_SRC:' ${MARKDOWN_SRC}
+	@echo 'HTML_DST:' ${HTML_DST}
+
+## lesson-fixme     : show FIXME markers embedded in source files.
+lesson-fixme :
+	@fgrep -i -n FIXME ${MARKDOWN_SRC} || true
+
+#-------------------------------------------------------------------------------
+# Include extra commands if available.
+#-------------------------------------------------------------------------------
+
+-include commands.mk

_config.yml

-title: Image Analysis Training
-email: image-analysis-support@embl.de
+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
@@ -8,11 +8,49 @@ url: "https://grp-bio-it.embl-community.io/" # the base hostname & protocol for
 contributing: CONTRIBUTING
 
 # Build settings
-markdown: CommonMarkGhPages
-commonmark:
-  options: ["SMART"]
+# Turn on built-in syntax highlighting.
 highlighter: rouge
 exclude: ["README.md", "TEACHING.md"]
 
 # options are: "NONE", "ImageJ GUI", "ImageJ Macro", "Jython", "MATLAB"
 default-platform: "NONE"
+
+life_cycle: "pre-alpha"
+kind: "lesson"
+
+# Sites
+repo_url: "https://git.embl.de/grp-bio-it/image-analysis-training-resources"
+cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
+
+# Specify that things in the episodes collection should be output.
+collections:
+  modules:
+    output: true
+    permalink: /:path/index.html
+  extras:
+    output: true
+    permalink: /:path/index.html
+
+# Set the default layout for things in the modules collection.
+defaults:
+  - values:
+      root: .
+      layout: page
+  - scope:
+      path: ""
+      type: modules
+    values:
+      root: ..
+      layout: module
+  - scope:
+      path: ""
+      type: extras
+    values:
+      root: ..
+      layout: page
+
+# Files and directories that are not to be copied.
+exclude:
+  - Makefile
+  - bin/
+  - .Rproj.user/

_extras/about.md

+---
+title: About
+---
+{% include carpentries.html %}
+{% include links.md %}

_extras/discuss.md

+---
+title: Discussion
+---
+FIXME
+
+{% include links.md %}

_extras/figures.md

+---
+title: Figures
+---
+
+{% include base_path.html %}
+
+<script>
+  window.onload = function() {
+    var lesson_episodes = [
+    {% for episode in site.episodes %}
+    "{{ episode.url }}"{% unless forloop.last %},{% endunless %}
+    {% endfor %}
+    ];
+
+    var xmlHttp = [];  /* Required since we are going to query every episode. */
+    for (i=0; i < lesson_episodes.length; i++) {
+
+      xmlHttp[i] = new XMLHttpRequest();
+      xmlHttp[i].episode = lesson_episodes[i];  /* To enable use this later. */
+      xmlHttp[i].onreadystatechange = function() {
+
+        if (this.readyState == 4 && this.status == 200) {
+          var parser = new DOMParser();
+          var htmlDoc = parser.parseFromString(this.responseText,"text/html");
+          var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
+
+          var article_here = document.getElementById(this.episode);
+          var images = htmlDocArticle.getElementsByTagName("img");
+
+          if (images.length > 0) {
+            var h1text = htmlDocArticle.getElementsByTagName("h1")[0].innerHTML;
+
+            var htitle = document.createElement('h2');
+            htitle.innerHTML = h1text;
+            article_here.appendChild(htitle);
+
+            var image_num = 0;
+            for (let image of images) {
+              image_num++;
+
+              var title = document.createElement('p');
+              title.innerHTML = "<strong>Figure " + image_num + ".</strong> " + image.alt;
+              article_here.appendChild(title);
+
+              article_here.appendChild(image.cloneNode(false));
+
+              if (image_num < images.length) {
+                var hr = document.createElement('hr');
+                article_here.appendChild(hr);
+              }
+            }
+          }
+        }
+      }
+      episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
+      xmlHttp[i].open("GET", episode_url);
+      xmlHttp[i].send(null);
+    }
+  }
+</script>
+{% comment %}
+Create anchor for each one of the episodes.
+{% endcomment %}
+{% for episode in site.episodes %}
+<article id="{{ episode.url }}" class="figures"></article>
+{% endfor %}
+
+{% include links.md %}

_extras/guide.md

+---
+title: "Instructor Notes"
+---
+FIXME
+
+{% include links.md %}

_includes/aio-script.md

+{% comment %}
+As a maintainer, you don't need to edit this file.
+If you notice that something doesn't work, please 
+open an issue: https://github.com/carpentries/styles/issues/new
+{% endcomment %}
+
+<script>
+  window.onload = function() {
+    var lesson_episodes = [
+    {% for episode in site.episodes %}
+    "{{ episode.url}}"{% unless forloop.last %},{% endunless %}
+    {% endfor %}
+    ];
+    var xmlHttp = [];  /* Required since we are going to query every episode. */
+    for (i=0; i < lesson_episodes.length; i++) {
+      xmlHttp[i] = new XMLHttpRequest();
+      xmlHttp[i].episode = lesson_episodes[i];  /* To enable use this later. */
+      xmlHttp[i].onreadystatechange = function() {
+        if (this.readyState == 4 && this.status == 200) {
+          var article_here = document.getElementById(this.episode);
+          var parser = new DOMParser();
+          var htmlDoc = parser.parseFromString(this.responseText,"text/html");
+          var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
+          article_here.innerHTML = htmlDocArticle.innerHTML;
+        }
+      }
+      var episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
+      xmlHttp[i].open("GET", episode_url);
+      xmlHttp[i].send(null);
+    }
+  }
+</script>
+{% comment %}
+Create an anchor for every episode.
+{% endcomment %}
+{% for episode in site.episodes %}
+<article id="{{ episode.url }}"></article>
+{% endfor %}

_includes/all_keypoints.html

+{% comment %}
+  Display key points of all episodes for reference.
+{% endcomment %}
+
+{% include base_path.html %}
+
+<h2>Key Points</h2>
+<table class="table table-striped">
+{% for episode in site.episodes %}
+  {% unless episode.break %}
+    <tr>
+      <td class="col-md-3">
+        <a href="{{ relative_root_path }}{{ episode.url }}">{{ episode.title }}</a>
+      </td>
+      <td class="col-md-9">
+        <ul>
+        {% for keypoint in episode.keypoints %}
+        <li>{{ keypoint|markdownify }}</li>
+        {% endfor %}
+        </ul>
+      </td>
+    </tr>
+  {% endunless %}
+{% endfor %}
+</table>

_includes/base_path.html

+{% comment %}
+This is adapted from: https://ricostacruz.com/til/relative-paths-in-jekyll
+
+`page.url` gives the URL of the current page with a leading /:
+
+- when the URL ends with the extension (e.g., /foo/bar.html) then we can get
+  the depth by counting the number of / and remove - 1
+- when the URL ends with a / (e.g. /foo/bar/) then the number / gives the depth
+  directly
+{% endcomment %}
+
+{% assign relative_root_path = '' %}
+
+{% assign last_char = page.url | slice: -1 %}
+
+{% if last_char == "/"}
+{% assign offset = 0 %}
+{% else %}
+{% assign offset = 1 %}
+{% endif %}
+
+{% assign depth = page.url | split: '/' | size | minus: offset %}
+{% if    depth <= 1 %}{% assign relative_root_path = '.' %}
+{% elsif depth == 2 %}{% assign relative_root_path = '..' %}
+{% elsif depth == 3 %}{% assign relative_root_path = '../..' %}
+{% elsif depth == 4 %}{% assign relative_root_path = '../../..' %}
+{% endif %}

_includes/binarization/exercises/binarization_jython.md

@@ -4,18 +4,16 @@ This file should contain language-specific exercises, *written* in **Markdown**
 
 #### Exercise 1
 
-What is the solution to the first exercise? 
+What is the solution to the first exercise?
 
-<details>
-<summary>Solution</summary>
-This is the solution to the first exercise.
-</details>
+> ## Solution
+> This is the solution to the first exercise.
+{: .solution}
 
 #### Exercise 2
 
 What is the solution to the second exercise?
 
-<details>
-<summary>Solution</summary>
-This is the solution to the second exercise.
-</details>
+> ## Solution
+> This is the solution to the second exercise.
+{: .solution}

_includes/carpentries.html

+{% comment %}
+  General description of Software, Data, and Library Carpentry.
+{% endcomment %}
+
+{% include base_path.html %}
+
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.carpentries_site }}"><img src="{{ relative_root_path }}/assets/img/cp-logo-blue.svg" alt="The Carpentries logo" /></a>
+  </div>
+  <div class="col-md-8">
+    <p><a href="{{ site.carpentries_site }}">The Carpentries</a> comprises
+    Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers,
+    Maintainers, helpers, and supporters who share a mission to teach
+    foundational coding and data science skills to researchers and people 
+    working in library- and information-related roles. In January,
+    2018, The Carpentries was formed by the merger of Software Carpentry and
+    Data Carpentry. Library Carpentry became an official Carpentries Lesson Program in November 2018.</p>
+
+    <p>While individual lessons and workshops continue to be run under each
+    lesson project, The Carpentries provide overall staffing and governance, as
+    well as support for assessment, instructor training and mentoring.
+    Memberships are joint, and the Carpentries project maintains a shared Code
+    of Conduct. The Carpentries is a fiscally sponsored project of Community
+    Initiatives, a registered 501(c)3 non-profit based in California, USA.</p>
+  </div>
+</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>
+  </div>
+  <div class="col-md-8">
+     <p>Since 1998, <a href="{{ site.swc_site }}">Software Carpentry</a> has
+    been teaching researchers across all disciplines the foundational coding
+    skills they need to get more done in less time and with less pain. Its
+    volunteer instructors have run hundreds of events for thousands of learners
+    around the world. Now that all research involves some degree of
+    computational work, whether with big data, cloud computing, or simple task
+    automation, these skills are needed more than ever.</p>
+  </div>
+</div>
+<br/>
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.dc_site }}"><img src="{{ relative_root_path }}/assets/img/dc-icon-black.svg" alt="Data Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    <p><a href="{{ site.dc_site }}">Data Carpentry</a> develops and teaches
+    workshops on the fundamental data skills needed to conduct research. Its
+    target audience is researchers who have little to no prior computational
+    experience, and its lessons are domain specific, building on learners'
+    existing knowledge to enable them to quickly apply skills learned to their
+    own research. Data Carpentry workshops take researchers through the entire
+    data life cycle.</p>
+  </div>
+</div>
+<br/>
+<div class="row">
+  <div class="col-md-2" align="center">
+    <a href="{{ site.lc_site }}"><img src="{{ relative_root_path }}/assets/img/lc-icon-black.png" alt="Library Carpentry logo" /></a>
+  </div>
+  <div class="col-md-8">
+    <p><a href="{{ site.lc_site }}">Library Carpentry</a> develops lessons and
+    teaches workshops for and with people working in library- and
+    information-related roles. Its goal is to create an on-ramp to empower this
+    community to use software and data in their own work, as well as be
+    advocates for and train others in efficient, effective and reproducible data
+    and software practices.</p>
+  </div>
+</div>

_includes/dc/intro.html

+<p>
+  <a href="{{site.dc_site}}">Data Carpentry</a>
+  aims to help researchers get their work done
+  in less time and with less pain
+  by teaching them basic research computing skills.
+  This hands-on workshop will cover basic concepts and tools,
+  including program design, version control, data management,
+  and task automation.
+  Participants will be encouraged to help one another
+  and to apply what they have learned to their own research problems.
+</p>
+<p align="center">
+  <em>
+    For more information on what we teach and why,
+    please see our paper
+    "<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">Best Practices for Scientific Computing</a>".
+  </em>
+</p>

_includes/dc/schedule.html

+<div class="row">
+  <div class="col-md-6">
+    <h3>Day 1</h3>
+    <table class="table table-striped">
+      <tr> <td>09:00</td>  <td>Automating tasks with the Unix shell</td> </tr>
+      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
+      <tr> <td>13:00</td>  <td>Building programs with Python</td> </tr>
+      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
+    </table>
+  </div>
+  <div class="col-md-6">
+    <h3>Day 2</h3>
+    <table class="table table-striped">
+      <tr> <td>09:00</td>  <td>Version control with Git</td> </tr>
+      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
+      <tr> <td>13:00</td>  <td>Managing data with SQL</td> </tr>
+      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
+      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
+    </table>
+  </div>
+</div>

_includes/dc/syllabus.html

+<div class="row">
+  <div class="col-md-6">
+    <h3 id="syllabus-shell">The Unix Shell</h3>
+    <ul>
+      <li>Files and directories</li>
+      <li>History and tab completion</li>
+      <li>Pipes and redirection</li>
+      <li>Looping over files</li>
+      <li>Creating and running shell scripts</li>
+      <li>Finding things</li>
+      <li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
+    </ul>
+  </div>
+  <div class="col-md-6">
+    <h3 id="syllabus-python">Programming in Python</h3>
+    <ul>
+      <li>Using libraries</li>
+      <li>Working with arrays</li>
+      <li>Reading and plotting data</li>
+      <li>Creating and using functions</li>
+      <li>Loops and conditionals</li>
+      <li>Defensive programming</li>
+      <li>Using Python from the command line</li>