Carpentries style

.gitignore

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

.gitlab-ci.yml

@@ -1,25 +1,24 @@
 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

@@ -0,0 +1 @@
+FIXME: list authors' names and email addresses.

CITATION

@@ -0,0 +1 @@
+FIXME: describe how to cite this lesson.

CODE_OF_CONDUCT.md

@@ -0,0 +1,11 @@
+---
+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 %}

Makefile

@@ -0,0 +1,121 @@
+## ========================================
+## 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

@@ -1,5 +1,5 @@
-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

@@ -0,0 +1,5 @@
+---
+title: About
+---
+{% include carpentries.html %}
+{% include links.md %}

_extras/discuss.md

@@ -0,0 +1,6 @@
+---
+title: Discussion
+---
+FIXME
+
+{% include links.md %}

_extras/figures.md

@@ -0,0 +1,68 @@
+---
+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

@@ -0,0 +1,6 @@
+---
+title: "Instructor Notes"
+---
+FIXME
+
+{% include links.md %}

_includes/aio-script.md

@@ -0,0 +1,38 @@
+{% 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 %}